From ed6e22d0201f99342488150b7e593de9a3b053a6 Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Thu, 4 Aug 2022 17:08:34 +0100
Subject: [PATCH 01/25] Bump version and add sangaboard v4 dependency

---
 setup.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/setup.py b/setup.py
index 80f1096e..4da4f1f1 100644
--- a/setup.py
+++ b/setup.py
@@ -22,7 +22,7 @@ with open(path.join(here, "README.md"), encoding="utf-8") as f:
 
 setup(
     name="openflexure-microscope-server",
-    version="2.10.1",
+    version="2.11.0",
     description="Python module, and Flask-based web API, to run the OpenFlexure Microscope.",
     long_description=long_description,
     long_description_content_type="text/markdown",
@@ -52,7 +52,7 @@ setup(
         "python-dateutil ~= 2.8",
         "psutil ~= 5.6.7",  # Autostorage extension
         "opencv-python-headless ~= 4.5.1",
-        "sangaboard ~= 0.2",
+        "sangaboard ~= 0.3.0",
         "expiringdict ~= 1.2.1",
         "camera-stage-mapping == 0.1.4",
         "picamerax ~= 20.9.1",

From d98cc3ff34c4d6e67cc090af3fa7a11a3505adce Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Mon, 8 Aug 2022 21:56:43 +0100
Subject: [PATCH 02/25] Update sangaboard dependency and re-lock

Dependencies could use some revision - in particular could we use
Flask 2?  That's a LabThings issue really...

I have updated a few dependencies (mostly dev ones), as ever Black is
an issue - have reverted to the previous pinned prerelease because the
full release is incompatible with flask 2.
---
 Pipfile.lock | 1799 +++++++++++++++++++++++++++++---------------------
 setup.py     |   22 +-
 2 files changed, 1061 insertions(+), 760 deletions(-)

diff --git a/Pipfile.lock b/Pipfile.lock
index 04c8a27a..451728eb 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -41,13 +41,22 @@
             "markers": "python_version >= '3.6'",
             "version": "==0.5.2"
         },
+        "atomicwrites": {
+            "hashes": [
+                "sha256:03513b104b7c627ac3ff75b85b54843e5710b5fa400231eb419b441c9d1ef9a7",
+                "sha256:81b2c9071a49367a7f770170e5eec8cb66567cfbbc8c73d20ce5ca4a8d71cf11"
+            ],
+            "markers": "sys_platform == 'win32'",
+            "version": "==1.4.1"
+        },
         "attrs": {
             "hashes": [
-                "sha256:149e90d6d8ac20db7a955ad60cf0e6881a3f20d37096140088356da6c716b0b1",
-                "sha256:ef6aaac3ca6cd92904cdd0d83f629a15f18053ec84e6432106f7a4d04ae4f5fb"
+                "sha256:29adc2665447e5191d0e7c568fde78b21f9672d344281d0c6e1ab085429b22b6",
+                "sha256:6d9391612040005651f4f45d6bfc257484a8f93f15ffdcf3f8dbd21f9e20ce39",
+                "sha256:86efa402f67bf2df34f51a335487cf46b1ec130d02b8d39fd248abfd30da551c"
             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
-            "version": "==21.2.0"
+            "markers": "python_version >= '3.5'",
+            "version": "==22.1.0"
         },
         "camera-stage-mapping": {
             "hashes": [
@@ -59,10 +68,12 @@
         },
         "certifi": {
             "hashes": [
-                "sha256:2bbf76fd432960138b3ef6dda3dde0544f27cbf8546c458e60baf371917ba9ee",
-                "sha256:50b1e4f8446b06f41be7dd6338db18e0990601dce795c2b1686458aa7e8fa7d8"
+                "sha256:84c85a9078b11105f04f3036a9482ae10e4621616db313fe045dd24743a0820d",
+                "sha256:cbd4c168c00e6c24b3fdf4e9f34c7c459810173b3a3cb9ab14a219f7549d4263",
+                "sha256:fe86415d55e84719d75f8b69414f6438ac3547d2078ab91b67e779ef69378412"
             ],
-            "version": "==2021.5.30"
+            "markers": "python_version >= '3.6'",
+            "version": "==2022.6.15"
         },
         "chardet": {
             "hashes": [
@@ -74,11 +85,12 @@
         },
         "charset-normalizer": {
             "hashes": [
-                "sha256:88fce3fa5b1a84fdcb3f603d889f723d1dd89b26059d0123ca435570e848d5e1",
-                "sha256:c46c3ace2d744cfbdebceaa3c19ae691f53ae621b39fd7570f59d14fb7f2fd12"
+                "sha256:1698523254cfe01135e7e863524c1fcfebb007d0512d4815d9699f3e38dfaab4",
+                "sha256:5189b6f22b01957427f35b6a08d9a0bc45b46d3788ef5a92e978433c7a35f8a5",
+                "sha256:575e708016ff3a5e3681541cb9d79312c416835686d054a23accb873b254f413"
             ],
-            "markers": "python_version >= '3'",
-            "version": "==2.0.3"
+            "markers": "python_version >= '3.6'",
+            "version": "==2.1.0"
         },
         "click": {
             "hashes": [
@@ -89,6 +101,15 @@
             "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
             "version": "==7.1.2"
         },
+        "colorama": {
+            "hashes": [
+                "sha256:2e3098fdcfc0107a135ba8bae5ddb6224bbb7fb7026db2d1b066d5af8bcca063",
+                "sha256:854bf444933e37f5824ae7bfc1e98d5bce2ebe4160d46b5edf346a89358e99da",
+                "sha256:e6c6b4334fc50988a639d9b98aa429a0b57da6e17b9a44f0451f930b6967b7a4"
+            ],
+            "markers": "sys_platform == 'win32'",
+            "version": "==0.4.5"
+        },
         "colorzero": {
             "hashes": [
                 "sha256:0e60d743a6b8071498a56465f7719c96a5e92928f858bab1be2a0d606c9aa0f8",
@@ -98,68 +119,60 @@
         },
         "coverage": {
             "hashes": [
-                "sha256:004d1880bed2d97151facef49f08e255a20ceb6f9432df75f4eef018fdd5a78c",
-                "sha256:01d84219b5cdbfc8122223b39a954820929497a1cb1422824bb86b07b74594b6",
-                "sha256:040af6c32813fa3eae5305d53f18875bedd079960822ef8ec067a66dd8afcd45",
-                "sha256:06191eb60f8d8a5bc046f3799f8a07a2d7aefb9504b0209aff0b47298333302a",
-                "sha256:13034c4409db851670bc9acd836243aeee299949bd5673e11844befcb0149f03",
-                "sha256:13c4ee887eca0f4c5a247b75398d4114c37882658300e153113dafb1d76de529",
-                "sha256:184a47bbe0aa6400ed2d41d8e9ed868b8205046518c52464fde713ea06e3a74a",
-                "sha256:18ba8bbede96a2c3dde7b868de9dcbd55670690af0988713f0603f037848418a",
-                "sha256:1aa846f56c3d49205c952d8318e76ccc2ae23303351d9270ab220004c580cfe2",
-                "sha256:217658ec7187497e3f3ebd901afdca1af062b42cfe3e0dafea4cced3983739f6",
-                "sha256:24d4a7de75446be83244eabbff746d66b9240ae020ced65d060815fac3423759",
-                "sha256:2910f4d36a6a9b4214bb7038d537f015346f413a975d57ca6b43bf23d6563b53",
-                "sha256:2949cad1c5208b8298d5686d5a85b66aae46d73eec2c3e08c817dd3513e5848a",
-                "sha256:2a3859cb82dcbda1cfd3e6f71c27081d18aa251d20a17d87d26d4cd216fb0af4",
-                "sha256:2cafbbb3af0733db200c9b5f798d18953b1a304d3f86a938367de1567f4b5bff",
-                "sha256:2e0d881ad471768bf6e6c2bf905d183543f10098e3b3640fc029509530091502",
-                "sha256:30c77c1dc9f253283e34c27935fded5015f7d1abe83bc7821680ac444eaf7793",
-                "sha256:3487286bc29a5aa4b93a072e9592f22254291ce96a9fbc5251f566b6b7343cdb",
-                "sha256:372da284cfd642d8e08ef606917846fa2ee350f64994bebfbd3afb0040436905",
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-                "sha256:c0891a6a97b09c1f3e073a890514d5012eb256845c451bd48f7968ef939bf4ae",
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-                "sha256:f11642dddbb0253cc8853254301b51390ba0081750a8ac03f20ea8103f0c56b6"
+                "sha256:03d9f920ef695ae5a46f131708343cbb8c44e92c764f1a763f7540674c9df555",
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+                "sha256:52f8b9fcf3c5e427d51bbab1fb92b575a9a9235d516f175b24712bcd4b5be917",
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+                "sha256:ab9ef0187d6c62b09dec83a84a3b94f71f9690784c84fd762fb3cf2d2b44c914",
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+                "sha256:b104b6b1827d6a22483c469e3983a204bcf9c6bf7544bf90362c4654ebc2edf3",
+                "sha256:bc698580216050b5f4a34d2cdd2838b429c53314f1c4835fab7338200a8396f2",
+                "sha256:cdf7b83f04a313a21afb1f8730fe4dd09577fefc53bbdfececf78b2006f4268e",
+                "sha256:d5191d53afbe5b6059895fa7f58223d3751c42b8101fb3ce767e1a0b1a1d8f87",
+                "sha256:d75314b00825d70e1e34b07396e23f47ed1d4feedc0122748f9f6bd31a544840",
+                "sha256:e4d64304acf79766e650f7acb81d263a3ea6e2d0d04c5172b7189180ff2c023c",
+                "sha256:ec2ae1f398e5aca655b7084392d23e80efb31f7a660d2eecf569fb9f79b3fb94",
+                "sha256:eff095a5aac7011fdb51a2c82a8fae9ec5211577f4b764e1e59cfa27ceeb1b59",
+                "sha256:f1eda5cae434282712e40b42aaf590b773382afc3642786ac3ed39053973f61f",
+                "sha256:f217850ac0e046ede611312703423767ca032a7b952b5257efac963942c055de",
+                "sha256:f50d3a822947572496ea922ee7825becd8e3ae6fbd2400cd8236b7d64b17f285",
+                "sha256:fc294de50941d3da66a09dca06e206297709332050973eca17040278cb0918ff",
+                "sha256:ff9832434a9193fbd716fbe05f9276484e18d26cc4cf850853594bb322807ac3"
             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_version < '4'",
-            "version": "==5.5"
+            "markers": "python_version >= '3.7'",
+            "version": "==6.4.3"
         },
         "expiringdict": {
             "hashes": [
-                "sha256:3eb293ca7ff15ed283d8e3ae9bbc5b1cbd2d60c906b08b38c7437380e8a2f697",
-                "sha256:fe2ba427220425c3c8a3d29f6d2e2985bcee323f8bcd4021e68ebefbd90d8250"
+                "sha256:09a5d20bc361163e6432a874edd3179676e935eb81b925eccef48d409a8a45e8",
+                "sha256:300fb92a7e98f15b05cf9a856c1415b3bc4f2e132be07daa326da6414c23ee09",
+                "sha256:5ced493f465d46cb39014399f0be41329056629f019226c02accfb4f990b3dea"
             ],
-            "version": "==1.2.1"
+            "version": "==1.2.2"
         },
         "flask": {
             "hashes": [
@@ -186,26 +199,38 @@
         },
         "idna": {
             "hashes": [
-                "sha256:14475042e284991034cb48e06f6851428fb14c4dc953acd9be9a5e95c7b6dd7a",
-                "sha256:467fbad99067910785144ce333826c71fb0e63a425657295239737f7ecd125f3"
+                "sha256:84d9dd047ffa80596e0f246e2eab0b391788b0503584e8945f2368256d2735ff",
+                "sha256:9d643ff0a55b762d5cdb124b8eaa99c66322e2157b69160bc32796e824360e6d",
+                "sha256:a8c56282ad8491e5d10c5d44e9e4ce38e37a16bc03ebb54fdcaf9d05b8e0c309"
             ],
-            "markers": "python_version >= '3'",
-            "version": "==3.2"
+            "markers": "python_version >= '3.5'",
+            "version": "==3.3"
         },
         "ifaddr": {
             "hashes": [
-                "sha256:1f9e8a6ca6f16db5a37d3356f07b6e52344f6f9f7e806d618537731669eb1a94",
-                "sha256:d1f603952f0a71c9ab4e705754511e4e03b02565bc4cec7188ad6415ff534cd3"
+                "sha256:085e0305cfe6f16ab12d72e2024030f5d52674afad6911bb1eee207177b8a748",
+                "sha256:0998123149175f29de1271c4088edff8ee9274873debac057a1b40149568be87",
+                "sha256:cc0cbfcaabf765d44595825fb96a99bb12c79716b73b44330ea38ee2b0c4aed4"
             ],
-            "version": "==0.1.7"
+            "version": "==0.2.0"
         },
         "importlib-metadata": {
             "hashes": [
-                "sha256:079ada16b7fc30dfbb5d13399a5113110dab1aa7c2bc62f66af75f0b717c8cac",
-                "sha256:9f55f560e116f8643ecf2922d9cd3e1c7e8d52e683178fecd9d08f6aa357e11e"
+                "sha256:637245b8bab2b6502fcbc752cc4b7a6f6243bb02b31c5c26156ad103d3d45670",
+                "sha256:7401a975809ea1fdc658c3aa4f78cc2195a0e019c5cbc4c06122884e9ae80c23",
+                "sha256:e7ecbb71f096b849877646bd54174277459d95c9ae2be3d59ab2b56c456b2e0b"
             ],
             "markers": "python_version < '3.8'",
-            "version": "==4.6.1"
+            "version": "==4.12.0"
+        },
+        "importlib-resources": {
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             "hashes": [
@@ -215,13 +240,6 @@
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@@ -240,151 +258,144 @@
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-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
-            "version": "==0.1.5"
+            "markers": "python_version >= '3.7' and python_version < '4'",
+            "version": "==0.2.3"
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         "openapi-spec-validator": {
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-            "version": "==0.3.1"
+            "version": "==0.4.0"
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         "opencv-python-headless": {
             "hashes": [
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-                "sha256:fd0f0629e27d97eec2f51500afbe0845876fdcd89d412035f4d7beb618c51066",
-                "sha256:ff4de00d4f19d622561dee58a5121045ca265df3665751d14433149bbd748f55"
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+                "sha256:4bdf982574bf2fefc5f82c86df7cb42e56ad627874c7c0f4d94ecf4ae8885304",
+                "sha256:567a54c1919bcf5b3d20a9830e3c511e57134de8def286ce137c3544a892f98c",
+                "sha256:62e31878641a8f96e773118d1eea9f34bdda87c9990a0faab04ebaafb5ae015c",
+                "sha256:672b5657a36a642d7b38b8ae94a266c7abaedfa3bb31276d0b889d2a96615f22",
+                "sha256:a60e9ff48854ec37be391e19dd634883cc26c2f0f814e5325b3deca33420912c",
+                "sha256:c3c2dda44d601757a508b07d628537c49f31223ad4edd0f747a70d4c852a7b98",
+                "sha256:ca4f013fa958f60fb2327fe87e6127c1ac0ab536890b1d4b00847f417b7af1ba",
+                "sha256:dcf472cf3b31c4e3f7135378aac6f4c5da5b49a07145c825e38bc23af17ce43f"
             ],
             "markers": "python_version >= '3.6'",
-            "version": "==4.5.3.56"
+            "version": "==4.5.5.64"
         },
         "openflexure-microscope-server": {
             "editable": true,
@@ -392,11 +403,12 @@
         },
         "packaging": {
             "hashes": [
-                "sha256:7dc96269f53a4ccec5c0670940a4281106dd0bb343f47b7471f779df49c2fbe7",
-                "sha256:c86254f9220d55e31cc94d69bade760f0847da8000def4dfe1c6b872fd14ff14"
+                "sha256:36bb3108f8e33f88e52e7985b4068e2585b67e5b7b3a0fa2817f9852bc39d2ef",
+                "sha256:dd47c42927d89ab911e606518907cc2d3a1f38bbd026385970643f9c5b8ecfeb",
+                "sha256:ef103e05f519cdc783ae24ea4e2e0f508a9c99b2d4969652eed6a2e1ea5bd522"
             ],
             "markers": "python_version >= '3.6'",
-            "version": "==21.0"
+            "version": "==21.3"
         },
         "picamerax": {
             "hashes": [
@@ -450,23 +462,34 @@
             "markers": "python_version >= '3.5'",
             "version": "==7.2.0"
         },
+        "pkgutil-resolve-name": {
+            "hashes": [
+                "sha256:23dcc36937a564cabe07363c490c1b5acc4019fe299788a7ad3e28f1be5fc506",
+                "sha256:357d6c9e6a755653cfd78893817c0853af365dd51ec97f3d358a819373bbd174",
+                "sha256:ca27cc078d25c5ad71a9de0a7a330146c4e014c2462d9af19c6b828280649c5e"
+            ],
+            "markers": "python_version < '3.9'",
+            "version": "==1.3.10"
+        },
         "pluggy": {
             "hashes": [
-                "sha256:15b2acde666561e1298d71b523007ed7364de07029219b604cf808bfa1c765b0",
-                "sha256:966c145cd83c96502c3c3868f50408687b38434af77734af1e9ca461a4081d2d"
+                "sha256:4224373bacce55f955a878bf9cfa763c1e360858e330072059e10bad68531159",
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             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
-            "version": "==0.13.1"
+            "markers": "python_version >= '3.6'",
+            "version": "==1.0.0"
         },
         "prance": {
             "extras": [
                 "osv"
             ],
             "hashes": [
-                "sha256:03374b020a4f643c71fc941bb7d1e4852331732714b4b6ebbbd53dd5f75adacf",
-                "sha256:43ebe3a5b38f0c65c428427004c4d8ce8d7155ddad50610276c89c192680f138"
+                "sha256:1686e6a2f3fe2d8e7084ca3f6b32fbe0489bc633c433d2071a09967e6360cd1f",
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-            "version": "==0.21.2"
+            "version": "==0.21.8.0"
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         "psutil": {
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@@ -490,47 +513,50 @@
         },
         "py": {
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-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
-            "version": "==1.10.0"
+            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
+            "version": "==1.11.0"
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         "pyparsing": {
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-                "sha256:ef9d7589ef3c200abe66653d3f1ab1033c3c419ae9b9bdb1240a85b024efc88b"
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-            "markers": "python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'",
-            "version": "==2.4.7"
+            "markers": "python_full_version >= '3.6.8'",
+            "version": "==3.0.9"
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         "pyrsistent": {
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-            "markers": "python_version >= '3.6'",
-            "version": "==0.18.0"
+            "markers": "python_version >= '3.7'",
+            "version": "==0.18.1"
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         "pyserial": {
             "hashes": [
@@ -541,11 +567,12 @@
         },
         "pytest": {
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-                "sha256:50bcad0a0b9c5a72c8e4e7c9855a3ad496ca6a881a3641b4260605450772c54b",
-                "sha256:91ef2131a9bd6be8f76f1f08eac5c5317221d6ad1e143ae03894b862e8976890"
+                "sha256:13d0e3ccfc2b6e26be000cb6568c832ba67ba32e719443bfe725814d3c42433c",
+                "sha256:3a953992342eac0f5593ec15173bbc2a836bb32ac782dad85d2fa4b329d4b7d8",
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-            "markers": "python_version >= '3.6'",
-            "version": "==6.2.4"
+            "markers": "python_version >= '3.7'",
+            "version": "==7.1.2"
         },
         "pytest-cov": {
             "hashes": [
@@ -578,6 +605,7 @@
                 "sha256:607774cbba28732bfa802b54baa7484215f530991055bb562efbed5b2f20a45e",
                 "sha256:6c78645d400265a062508ae399b60b8c167bf003db364ecb26dcab2bda048253",
                 "sha256:72a01f726a9c7851ca9bfad6fd09ca4e090a023c00945ea05ba1638c09dc3347",
+                "sha256:7318f36ecd539646767465d194cbbe9c248f243ba0117c3d043c660d69cfeceb",
                 "sha256:74c1485f7707cf707a7aef42ef6322b8f97921bd89be2ab6317fd782c2d53183",
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                 "sha256:8c1be557ee92a20f184922c7b6424e8ab6691788e6d86137c5d93c1a6ec1b8fb",
@@ -601,18 +629,63 @@
         },
         "requests": {
             "hashes": [
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-                "sha256:b8aa58f8cf793ffd8782d3d8cb19e66ef36f7aba4353eec859e74678b01b07a7"
+                "sha256:7c5599b102feddaa661c826c56ab4fee28bfd17f5abca1ebbe3e7f19d7c97983",
+                "sha256:8fefa2a1a1365bf5520aac41836fbee479da67864514bdb821f31ce07ce65349",
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-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'",
-            "version": "==2.26.0"
+            "markers": "python_version >= '3.7' and python_version < '4'",
+            "version": "==2.28.1"
+        },
+        "ruamel.yaml": {
+            "hashes": [
+                "sha256:5a81d994d11f98c7e7288636ea5bef647359641353411cebf8d2cce3a4a12385",
+                "sha256:742b35d3d665023981bd6d16b3d24248ce5df75fdb4e2924e93a05c1f8b61ca7",
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+            ],
+            "markers": "python_version >= '3'",
+            "version": "==0.17.21"
+        },
+        "ruamel.yaml.clib": {
+            "hashes": [
+                "sha256:0847201b767447fc33b9c235780d3aa90357d20dd6108b92be544427bea197dd",
+                "sha256:09c589bc916ac7bbabfe92c4cba2a0fe57c0f33a8b3a23a2baa2750a89709876",
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+            "version": "==0.2.6"
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         "sangaboard": {
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@@ -632,6 +705,7 @@
                 "sha256:ad7269254de06743fb4768f658753de47d8b54e4672c5ebe8612a007a088bd48",
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                 "sha256:b79104878003487e2b4639a20b9092b02e1bad07fc4cf924b495cf413748a777",
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@@ -640,6 +714,15 @@
             "markers": "python_version < '3.10' and python_version >= '3.7'",
             "version": "==1.6.3"
         },
+        "semantic-version": {
+            "hashes": [
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+                "sha256:dc5baeac289ab6817f916c9cb73cef9448e973aa6f7b6c42c27ef39d0ba03ac9",
+                "sha256:de78a3b8e0feda74cabc54aab2da702113e33ac9d9eb9d2389bcf1f58b7d9177"
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+            "version": "==2.10.0"
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@@ -656,38 +739,40 @@
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             "version": "==1.16.0"
         },
-        "toml": {
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-            "version": "==0.10.2"
+            "markers": "python_version >= '3.7'",
+            "version": "==2.0.1"
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             "markers": "python_version < '3.8'",
-            "version": "==3.7.4.3"
+            "version": "==4.3.0"
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-            "version": "==1.26.6"
+            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5' and python_version < '4'",
+            "version": "==1.26.11"
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         "webargs": {
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-            "markers": "python_version >= '3.6'",
-            "version": "==8.0.0"
+            "markers": "python_full_version >= '3.7.2'",
+            "version": "==8.2.0"
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         "werkzeug": {
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@@ -699,19 +784,20 @@
         },
         "zeroconf": {
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-                "sha256:de14268be7a449691f74463cce5ecbeeb7e5f572878a28285b11236b0171d407"
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-            "version": "==0.33.1"
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-                "sha256:f5812b1e007e48cff63449a5e9f4e7ebea716b4111f9c4f9a645f91d579bf0c4"
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+                "sha256:47c40d7fe183a6f21403a199b3e4192cca5774656965b0a4988ad2f8feb5f009",
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-            "markers": "python_version >= '3.6'",
-            "version": "==3.5.0"
+            "markers": "python_version < '3.10'",
+            "version": "==3.8.1"
         }
     },
     "develop": {
@@ -751,34 +837,45 @@
         },
         "astroid": {
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-                "sha256:8a398dfce302c13f14bab13e2b14fe385d32b73f4e4853b9bdfb64598baa1975"
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+                "sha256:bb24615c77f4837c707669d16907331374ae8a964650a66999da3f5ca68dc946"
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-            "markers": "python_version ~= '3.6'",
-            "version": "==2.5.6"
+            "markers": "python_full_version >= '3.6.2'",
+            "version": "==2.11.7"
+        },
+        "atomicwrites": {
+            "hashes": [
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+                "sha256:81b2c9071a49367a7f770170e5eec8cb66567cfbbc8c73d20ce5ca4a8d71cf11"
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+            "markers": "sys_platform == 'win32'",
+            "version": "==1.4.1"
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-                "sha256:ef6aaac3ca6cd92904cdd0d83f629a15f18053ec84e6432106f7a4d04ae4f5fb"
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-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
-            "version": "==21.2.0"
+            "markers": "python_version >= '3.5'",
+            "version": "==22.1.0"
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         "babel": {
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-                "sha256:bc0c176f9f6a994582230df350aa6e05ba2ebe4b3ac317eab29d9be5d2768da0"
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-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
-            "version": "==2.9.1"
+            "markers": "python_full_version >= '3.6.0'",
+            "version": "==2.10.3"
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-            "markers": "python_version >= '3.6'",
+            "markers": "python_full_version >= '3.6.0'",
             "version": "==18.9b0"
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@@ -791,10 +888,12 @@
         },
         "certifi": {
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-                "sha256:50b1e4f8446b06f41be7dd6338db18e0990601dce795c2b1686458aa7e8fa7d8"
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-            "version": "==2021.5.30"
+            "markers": "python_version >= '3.6'",
+            "version": "==2022.6.15"
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         "chardet": {
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@@ -806,11 +905,12 @@
         },
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-            "markers": "python_version >= '3'",
-            "version": "==2.0.3"
+            "markers": "python_version >= '3.6'",
+            "version": "==2.1.0"
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         "click": {
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@@ -821,6 +921,15 @@
             "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
             "version": "==7.1.2"
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+        "colorama": {
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+            "markers": "sys_platform == 'win32'",
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@@ -830,61 +939,61 @@
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@@ -896,10 +1005,11 @@
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@@ -918,11 +1028,12 @@
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@@ -934,34 +1045,47 @@
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-            "markers": "python_version >= '3'",
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@@ -971,20 +1095,14 @@
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@@ -1004,101 +1122,143 @@
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-            "version": "==4.5.3.56"
+            "version": "==4.5.5.64"
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         "openflexure-microscope-server": {
             "editable": true,
@@ -1296,11 +1451,12 @@
         },
         "packaging": {
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-            "version": "==21.0"
+            "version": "==21.3"
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             "hashes": [
@@ -1362,31 +1518,50 @@
             "markers": "python_version >= '3.5'",
             "version": "==7.2.0"
         },
+        "pkgutil-resolve-name": {
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-            "version": "==0.13.1"
+            "markers": "python_version >= '3.6'",
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-            "version": "==0.10.0"
+            "markers": "python_version >= '3.7'",
+            "version": "==0.16.0"
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@@ -1410,63 +1585,68 @@
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@@ -1477,11 +1657,12 @@
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@@ -1501,10 +1682,11 @@
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@@ -1521,6 +1703,7 @@
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@@ -1544,26 +1727,63 @@
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@@ -1583,6 +1803,7 @@
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@@ -1591,6 +1812,15 @@
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             "version": "==1.6.3"
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@@ -1609,10 +1839,11 @@
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@@ -1650,15 +1881,17 @@
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@@ -1673,7 +1906,7 @@
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@@ -1700,89 +1933,97 @@
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-                "sha256:f328adcfebed9f11301eaedfa48e15bdece9b519fb27e6a8c01aa52a17ec31b3",
-                "sha256:f8afcf15cc511ada719a88e013cec87c11aff7b91f019295eb4530f96fe5ef2f",
-                "sha256:fb1bbeac803adea29cedd70781399c99138358c26d05fcbd23c13016b7f5ec65"
+                "sha256:0261195c2062caf107831e92a76764c81227dae162c4f75192c0d489faf751a2",
+                "sha256:0fdbcf2fef0ca421a3f5912555804296f0b0960f0418c440f5d6d3abb549f3e1",
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+                "sha256:211260621ab1cd7324e0798d6be953d00b74e0428382991adfddb352252f1d62",
+                "sha256:267e3f78697a6c00c689c03db4876dd1efdfea2f251a5ad6555e82a26847b4ac",
+                "sha256:2efae9db7a8c05ad5547d522e7dbe62c83d838d3906a3716d1478b6c1d61388d",
+                "sha256:370788a63915e82fd6f212865a596a0fefcbb7d408bbbb13dea723d971ed8bdc",
+                "sha256:39e21ceb7388e4bb37f4c679d72707ed46c2fbf2a5609b8b8ebc4b067d977df2",
+                "sha256:3e123d878ba170397916557d31c8f589951e353cc95fb7f24f6bb69adc1a8a97",
+                "sha256:4879da6c9b73443f97e731b617184a596ac1235fe91f98d279a7af36c796da35",
+                "sha256:4e964b4ff86550a7a7d56345c7864b18f403f5bd7380edf44a3c1fb4ee7ac6c6",
+                "sha256:5a824176c0beca4492bcb9f1b0f0602723cb582872844d86108cc56898fef4f4",
+                "sha256:5c2af3ab3ade2e1e6de497ba632264104f2f591c7fdd8a17ae107a0b56126278",
+                "sha256:639c5f0b21776605dd6c9dbe592d5228f021404dafd377e2b7ac046b0349b1a1",
+                "sha256:669dd0c4167f6f2cd9f57041e03c3c2ebf9063d0757dc89f79ba1daa2bfca9d4",
+                "sha256:6778e1b2f81dfc7bc58e4b259363b83d2e509a65198e85d5700dfae4c6c8ff1c",
+                "sha256:683407d92dc953c8a7347119596f0b0e6c55eb98ebebd9b23437501b28dcbb8e",
+                "sha256:79b1e0869db7c830ba6a981d58711c88b6677506e648496b1f64ac7d15633aec",
+                "sha256:7d5d014b7daa8b0bf2eaef684295acae12b036d79f54178b92a2b6a56f92278f",
+                "sha256:98f80dee3c03455e92796b58b98ff6ca0b2a6f652120c263efdba4d6c5e58f72",
+                "sha256:a94d55d142c9265f4ea46fab70977a1944ecae359ae867397757d836ea5a3f47",
+                "sha256:a9916d2bb8865f973824fb47436fa45e1ebf2efd920f2b9f99342cb7fab93f72",
+                "sha256:c542eeda69212fa10a7ada75e668876fdec5f856cd3d06829e6aa64ad17c8dfe",
+                "sha256:cf4afcfac006ece570e32d6fa90ab74a17245b83dfd6655a6f68568098345ff6",
+                "sha256:ebd9d7f80ccf7a82ac5f88c521115cc55d84e35bf8b446fcd7836eb6b98929a3",
+                "sha256:ed855bbe3eb3715fca349c80174cfcfd699c2f9de574d40527b8429acae23a66"
             ],
             "markers": "python_version < '3.8' and implementation_name == 'cpython'",
-            "version": "==1.4.3"
+            "version": "==1.5.4"
         },
         "types-python-dateutil": {
             "hashes": [
-                "sha256:39bfe0bde61fc673b8fa28167bd78622d976210f791971b9f3e10877cbf119a4",
-                "sha256:e6486ca27b6dde73e0ec079a9e1b03e208766e6bc7f1e08964a7e9104a5c7d7a"
+                "sha256:6284df1e4783d8fc6e587f0317a81333856b872a6669a282f8a325342bce7fa8",
+                "sha256:bfd3eb39c7253aea4ba23b10f69b017d30b013662bb4be4ab48b20bbd763f309",
+                "sha256:e01c1fd83012ef522d99e26e2c6a24a97bf519e148e45f526eb35bd3fbddb285"
             ],
-            "version": "==0.1.4"
+            "version": "==2.8.19"
         },
         "types-setuptools": {
             "hashes": [
-                "sha256:71ed0f4c71d8fb5f3026a90ae82d163c13749b110e157d82126725ac8f714360",
-                "sha256:b3ada82b21dcb8e0cafd7658d8a16018a000e55bdb7f6f3cec033223360563ce"
+                "sha256:c8c9ebee23f2b0480ba0dd6c0be77a91413f2bb183e7dfe8b397c38a8839b07e",
+                "sha256:f568830d82b48783a0df00646bc84effeddb4886bf0f19708fbbadeb552b6ece",
+                "sha256:f954044034066cd3d8ceccc87e2d5cebe7a96c9f87996f61c3c6a92cd56cc8a4"
             ],
-            "version": "==57.0.0"
+            "version": "==63.4.0"
         },
         "typing-extensions": {
             "hashes": [
-                "sha256:7cb407020f00f7bfc3cb3e7881628838e69d8f3fcab2f64742a5e76b2f841918",
-                "sha256:99d4073b617d30288f569d3f13d2bd7548c3a7e4c8de87db09a9d29bb3a4a60c",
-                "sha256:dafc7639cde7f1b6e1acc0f457842a83e722ccca8eef5270af2d74792619a89f"
+                "sha256:25642c956049920a5aa49edcdd6ab1e06d7e5d467fc00e0506c44ac86fbfca02",
+                "sha256:4e110e067718fa35420fa8739d968edfacd2bb6b4988923875ba9406ad40d7c2",
+                "sha256:e6d2677a32f47fc7eb2795db1dd15c1f34eff616bcaf2cfb5e997f854fa1c4a6"
             ],
             "markers": "python_version < '3.8'",
-            "version": "==3.7.4.3"
+            "version": "==4.3.0"
         },
         "urllib3": {
             "hashes": [
-                "sha256:39fb8672126159acb139a7718dd10806104dec1e2f0f6c88aab05d17df10c8d4",
-                "sha256:f57b4c16c62fa2760b7e3d97c35b255512fb6b59a259730f36ba32ce9f8e342f"
+                "sha256:07265ad30322b1319de9d7980cbad8024eee4b4f9cd3ebf7a5736bae8540583a",
+                "sha256:c33ccba33c819596124764c23a97d25f32b28433ba0dedeb77d873a38722c9bc",
+                "sha256:ea6e8fb210b19d950fab93b60c9009226c63a28808bc8386e05301e25883ac0a"
             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_version < '4'",
-            "version": "==1.26.6"
+            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5' and python_version < '4'",
+            "version": "==1.26.11"
         },
         "webargs": {
             "hashes": [
-                "sha256:565666bafd08dd375fae995a9d4187604741efc27b8ec7c5b5bcb0ae90b2c677",
-                "sha256:7b06eebf23d05ebec1aa97e9c373deadaa8194866fae79c56e0453804db7a756"
+                "sha256:30af59b4cc9d0f8c766fe0eb2789cf3be95621c0590a899f8262074367d7a140",
+                "sha256:6746327faf549533bf30be7333f99541b6c60a85f23acf1bb0bea68498e3bcd7",
+                "sha256:99d68940c452e07726485a15fef43f12f8ae6c0c5b391bcba76065d4527fb85d"
             ],
-            "markers": "python_version >= '3.6'",
-            "version": "==8.0.0"
+            "markers": "python_full_version >= '3.7.2'",
+            "version": "==8.2.0"
         },
         "werkzeug": {
             "hashes": [
@@ -1794,29 +2035,93 @@
         },
         "wrapt": {
             "hashes": [
-                "sha256:1ba3a6bcb5014ed4d9c98afe8aa47b5ed320f84292b4f1b9f6afa0f4b2b91351",
-                "sha256:548a5381002654b72c8b8d1e167722e2a11169535d017d79d9cdee76502c1bc6",
-                "sha256:b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7",
-                "sha256:c16fd7cad3d27a5db392ae0e6215533a912a7d3d83a40b8cf275744276989780",
-                "sha256:d3294c918c5529e50b5454d39b589648d9baf6152e380067606d5566d71369a0"
+                "sha256:00b6d4ea20a906c0ca56d84f93065b398ab74b927a7a3dbd470f6fc503f95dc3",
+                "sha256:01c205616a89d09827986bc4e859bcabd64f5a0662a7fe95e0d359424e0e071b",
+                "sha256:02b41b633c6261feff8ddd8d11c711df6842aba629fdd3da10249a53211a72c4",
+                "sha256:07f7a7d0f388028b2df1d916e94bbb40624c59b48ecc6cbc232546706fac74c2",
+                "sha256:11871514607b15cfeb87c547a49bca19fde402f32e2b1c24a632506c0a756656",
+                "sha256:1b376b3f4896e7930f1f772ac4b064ac12598d1c38d04907e696cc4d794b43d3",
+                "sha256:21ac0156c4b089b330b7666db40feee30a5d52634cc4560e1905d6529a3897ff",
+                "sha256:257fd78c513e0fb5cdbe058c27a0624c9884e735bbd131935fd49e9fe719d310",
+                "sha256:2b39d38039a1fdad98c87279b48bc5dce2c0ca0d73483b12cb72aa9609278e8a",
+                "sha256:2cf71233a0ed05ccdabe209c606fe0bac7379fdcf687f39b944420d2a09fdb57",
+                "sha256:2fe803deacd09a233e4762a1adcea5db5d31e6be577a43352936179d14d90069",
+                "sha256:3232822c7d98d23895ccc443bbdf57c7412c5a65996c30442ebe6ed3df335383",
+                "sha256:34aa51c45f28ba7f12accd624225e2b1e5a3a45206aa191f6f9aac931d9d56fe",
+                "sha256:36f582d0c6bc99d5f39cd3ac2a9062e57f3cf606ade29a0a0d6b323462f4dd87",
+                "sha256:380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d",
+                "sha256:3c8c1d977f924144020c6a35e0c6dcf32174269f7608284cfff266739e5ebea3",
+                "sha256:40e7bc81c9e2b2734ea4bc1aceb8a8f0ceaac7c5299bc5d69e37c44d9081d43b",
+                "sha256:43ca3bbbe97af00f49efb06e352eae40434ca9d915906f77def219b88e85d907",
+                "sha256:4fcc4649dc762cddacd193e6b55bc02edca674067f5f98166d7713b193932b7f",
+                "sha256:5a0f54ce2c092aaf439813735584b9537cad479575a09892b8352fea5e988dc0",
+                "sha256:5a9a0d155deafd9448baff28c08e150d9b24ff010e899311ddd63c45c2445e28",
+                "sha256:5b02d65b9ccf0ef6c34cba6cf5bf2aab1bb2f49c6090bafeecc9cd81ad4ea1c1",
+                "sha256:60db23fa423575eeb65ea430cee741acb7c26a1365d103f7b0f6ec412b893853",
+                "sha256:642c2e7a804fcf18c222e1060df25fc210b9c58db7c91416fb055897fc27e8cc",
+                "sha256:6a9a25751acb379b466ff6be78a315e2b439d4c94c1e99cb7266d40a537995d3",
+                "sha256:6b1a564e6cb69922c7fe3a678b9f9a3c54e72b469875aa8018f18b4d1dd1adf3",
+                "sha256:6d323e1554b3d22cfc03cd3243b5bb815a51f5249fdcbb86fda4bf62bab9e164",
+                "sha256:6e743de5e9c3d1b7185870f480587b75b1cb604832e380d64f9504a0535912d1",
+                "sha256:709fe01086a55cf79d20f741f39325018f4df051ef39fe921b1ebe780a66184c",
+                "sha256:7b7c050ae976e286906dd3f26009e117eb000fb2cf3533398c5ad9ccc86867b1",
+                "sha256:7d2872609603cb35ca513d7404a94d6d608fc13211563571117046c9d2bcc3d7",
+                "sha256:7ef58fb89674095bfc57c4069e95d7a31cfdc0939e2a579882ac7d55aadfd2a1",
+                "sha256:80bb5c256f1415f747011dc3604b59bc1f91c6e7150bd7db03b19170ee06b320",
+                "sha256:81b19725065dcb43df02b37e03278c011a09e49757287dca60c5aecdd5a0b8ed",
+                "sha256:833b58d5d0b7e5b9832869f039203389ac7cbf01765639c7309fd50ef619e0b1",
+                "sha256:88bd7b6bd70a5b6803c1abf6bca012f7ed963e58c68d76ee20b9d751c74a3248",
+                "sha256:8ad85f7f4e20964db4daadcab70b47ab05c7c1cf2a7c1e51087bfaa83831854c",
+                "sha256:8c0ce1e99116d5ab21355d8ebe53d9460366704ea38ae4d9f6933188f327b456",
+                "sha256:8d649d616e5c6a678b26d15ece345354f7c2286acd6db868e65fcc5ff7c24a77",
+                "sha256:903500616422a40a98a5a3c4ff4ed9d0066f3b4c951fa286018ecdf0750194ef",
+                "sha256:9736af4641846491aedb3c3f56b9bc5568d92b0692303b5a305301a95dfd38b1",
+                "sha256:988635d122aaf2bdcef9e795435662bcd65b02f4f4c1ae37fbee7401c440b3a7",
+                "sha256:9cca3c2cdadb362116235fdbd411735de4328c61425b0aa9f872fd76d02c4e86",
+                "sha256:9e0fd32e0148dd5dea6af5fee42beb949098564cc23211a88d799e434255a1f4",
+                "sha256:9f3e6f9e05148ff90002b884fbc2a86bd303ae847e472f44ecc06c2cd2fcdb2d",
+                "sha256:a85d2b46be66a71bedde836d9e41859879cc54a2a04fad1191eb50c2066f6e9d",
+                "sha256:a9a52172be0b5aae932bef82a79ec0a0ce87288c7d132946d645eba03f0ad8a8",
+                "sha256:aa31fdcc33fef9eb2552cbcbfee7773d5a6792c137b359e82879c101e98584c5",
+                "sha256:b014c23646a467558be7da3d6b9fa409b2c567d2110599b7cf9a0c5992b3b471",
+                "sha256:b21bb4c09ffabfa0e85e3a6b623e19b80e7acd709b9f91452b8297ace2a8ab00",
+                "sha256:b5901a312f4d14c59918c221323068fad0540e34324925c8475263841dbdfe68",
+                "sha256:b9b7a708dd92306328117d8c4b62e2194d00c365f18eff11a9b53c6f923b01e3",
+                "sha256:c672b8d8e5d5c28b4234f2467b4332360a5e80722135b40708848ebdcc00abe6",
+                "sha256:d1967f46ea8f2db647c786e78d8cc7e4313dbd1b0aca360592d8027b8508e24d",
+                "sha256:d52a25136894c63de15a35bc0bdc5adb4b0e173b9c0d07a2be9d3ca64a332735",
+                "sha256:d77c85fedff92cf788face9bfa3ebaa364448ebb1d765302e9af11bf449ca36d",
+                "sha256:d79d7d5dc8a32b7093e81e97dad755127ff77bcc899e845f41bf71747af0c569",
+                "sha256:dbc895796d981952ea242c3ce8b49eff452f2238c46d6170c1e70894e6364d95",
+                "sha256:dbcda74c67263139358f4d188ae5faae95c30929281bc6866d00573783c422b7",
+                "sha256:ddaea91abf8b0d13443f6dac52e89051a5063c7d014710dcb4d4abb2ff811a59",
+                "sha256:dee0ce50c6a2dd9056c20db781e9c1cfd33e77d2d569f5d1d9321c641bb903d5",
+                "sha256:dee60e1de1898bde3b238f18340eec6148986da0455d8ba7848d50470a7a32fb",
+                "sha256:e2f83e18fe2f4c9e7db597e988f72712c0c3676d337d8b101f6758107c42425b",
+                "sha256:e3fb1677c720409d5f671e39bac6c9e0e422584e5f518bfd50aa4cbbea02433f",
+                "sha256:ee2b1b1769f6707a8a445162ea16dddf74285c3964f605877a20e38545c3c462",
+                "sha256:ee6acae74a2b91865910eef5e7de37dc6895ad96fa23603d1d27ea69df545015",
+                "sha256:ef3f72c9666bba2bab70d2a8b79f2c6d2c1a42a7f7e2b0ec83bb2f9e383950af"
             ],
-            "version": "==1.12.1"
+            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
+            "version": "==1.14.1"
         },
         "zeroconf": {
             "hashes": [
-                "sha256:46992d0786129c769c652c875221d394a63bdbef12832d443ac9e521005d46e1",
-                "sha256:ac88738639669f924859a4e01d9742f3783e619e710103f4a0d321a47f260fd2",
-                "sha256:de14268be7a449691f74463cce5ecbeeb7e5f572878a28285b11236b0171d407"
+                "sha256:055355de58edb58708471f76e6ad486f4796ec6d2c7cb97c16b295a00856e789",
+                "sha256:71ebebbc35d4703d72a3635127626d511d5ee7da4b3946430eac2cdadca81b12",
+                "sha256:95b4fd11e0498ec8e38d0a0ff50e3bd7250be2b02d131ef8501b12cd3a499d66"
             ],
-            "version": "==0.33.1"
+            "version": "==0.33.4"
         },
         "zipp": {
             "hashes": [
-                "sha256:957cfda87797e389580cb8b9e3870841ca991e2125350677b2ca83a0e99390a3",
-                "sha256:f5812b1e007e48cff63449a5e9f4e7ebea716b4111f9c4f9a645f91d579bf0c4"
+                "sha256:05b45f1ee8f807d0cc928485ca40a07cb491cf092ff587c0df9cb1fd154848d2",
+                "sha256:47c40d7fe183a6f21403a199b3e4192cca5774656965b0a4988ad2f8feb5f009",
+                "sha256:bdc5a7bbededd545d1accdf26304ba4add03dd8dc3f9dac4f0e9ee7d89ac7121"
             ],
-            "markers": "python_version >= '3.6'",
-            "version": "==3.5.0"
+            "markers": "python_version < '3.10'",
+            "version": "==3.8.1"
         }
     }
 }
diff --git a/setup.py b/setup.py
index 4da4f1f1..ea01d24f 100644
--- a/setup.py
+++ b/setup.py
@@ -52,7 +52,7 @@ setup(
         "python-dateutil ~= 2.8",
         "psutil ~= 5.6.7",  # Autostorage extension
         "opencv-python-headless ~= 4.5.1",
-        "sangaboard ~= 0.3.0",
+        "sangaboard ~= 0.3.2",
         "expiringdict ~= 1.2.1",
         "camera-stage-mapping == 0.1.4",
         "picamerax ~= 20.9.1",
@@ -60,7 +60,7 @@ setup(
         "pytest-cov ~= 2.10.1",
         "piexif ~= 1.1.3",
         "labthings ~= 1.3.0",
-        "typing-extensions ~= 3.7.4",  # Needed for some type-hints in Python < 3.8 (e.g. Literal)
+        "typing-extensions ~= 4.3.0",  # Needed for some type-hints in Python < 3.8 (e.g. Literal)
         "RPi.GPIO ~= 0.7.0; platform_machine == 'armv7l'",
     ],
     # "dev" specifies extra packages used for development (linting, testing, etc.)
@@ -71,19 +71,15 @@ setup(
             "sphinx < 4.0",  # Currently httpdomain isn't ready for 4.0
             "sphinxcontrib-openapi ~= 0.7",
             "sphinx_rtd_theme ~=0.5.2",
-            "rope ~= 0.14.0",
-            "pylint ~= 2.8.0",  # 2.9.2 crashes and I've not yet figured out why.
-            "pytest ~= 6.1.2",
-            "mypy ~= 0.790",
+            "pylint ~= 2.14.0",  # 2.9.2 crashes and I've not yet figured out why.
+            "pytest ~= 7.1.2",
+            "mypy ~= 0.971",
             "types-python-dateutil",
             "types-setuptools",
-            "poethepoet ~= 0.10.0",
-            "freezegun ~= 1.0.0",
-            "lxml ~= 4.6",
-            "black == 18.9b0",  # Because black is in prerelease, giving a flexible version
-            # specifier causes all manner of problems.  A fixed version
-            # avoids issues with prereleases (which are normally not
-            # allowed by pipenv) but can be a bit of a pain sometimes!
+            "poethepoet ~= 0.16.0",
+            "freezegun ~= 1.2.1",
+            "lxml ~= 4.9",
+            "black == 18.9b0",
         ]
     },
     dependency_links=[],

From 3aa2721d28eb308403037398ea4b47de763f3593 Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Mon, 8 Aug 2022 22:19:30 +0100
Subject: [PATCH 03/25] Update changelog (version is already 2.11.0)

---
 CHANGELOG.md | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 72d184b2..2a1b877c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,8 @@
+# [v2.11.0](https://gitlab.com/openflexure/openflexure-microscope-server/compare/v2.10.1...v2.11.0) (2022-08-08)
+## New features
+* Background detection can now be used in scans, if you have the background-detect extension. ([!153](https://gitlab.com/openflexure/openflexure-microscope-server/-/merge_requests/153))
+* Support for Sangaboard firmware v1, via updated `sangaboard` dependency ([!154](https://gitlab.com/openflexure/openflexure-microscope-server/-/merge_requests/154))
+
 # [v2.10.1](https://gitlab.com/openflexure/openflexure-microscope-server/compare/v2.10.0...v2.10.1) (2022-01-17)
 ## Bug fixes
 * Fixed a typo in the serialisation of numpy arrays (#243) ([!148](https://gitlab.com/openflexure/openflexure-microscope-server/-/merge_requests/148))

From 9b7fba55b611169770f13e394b111c3e47d28cba Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Mon, 8 Aug 2022 22:22:55 +0100
Subject: [PATCH 04/25] Update CI script to new syntax

---
 .gitlab-ci.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 076758a9..f380d303 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -58,7 +58,9 @@ mypy:
 
   artifacts:
     reports:
-      cobertura: openflexure_microscope/cobertura.xml
+      coverage_report: 
+        coverage_format: cobertura
+        path: openflexure_microscope/cobertura.xml
 
   only:
     - branches

From a9fff24848f2c41a4c48bf083be257047740deee Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Tue, 9 Aug 2022 07:16:44 +0100
Subject: [PATCH 05/25] Explicitly specify encoding

The update to pylint means we were failing because open()
doesn't specify the encoding everywhere.  I have now specified utf-8
everywhere.  This was patchy before, and is default behaviour on the
Pi.  There's a slim chance it will cause some issues on Windows, but
that shouldn't affect anyone outside the developers.

I've also ignored a couple of new spurious warnings, and explicitly
ignored some unused variables.
---
 openflexure_microscope/api/app.py                           | 4 ++--
 openflexure_microscope/api/default_extensions/autofocus.py  | 2 +-
 .../api/default_extensions/camera_stage_mapping.py          | 2 +-
 openflexure_microscope/api/utilities/__init__.py            | 2 +-
 openflexure_microscope/camera/base.py                       | 2 +-
 openflexure_microscope/captures/capture.py                  | 3 ++-
 openflexure_microscope/config.py                            | 6 +++---
 openflexure_microscope/rescue/check_picamera.py             | 2 +-
 openflexure_microscope/rescue/check_sangaboard.py           | 2 +-
 scripts/zenodo/upload_to_zenodo.py                          | 4 ++--
 tests/test_app.py                                           | 2 +-
 11 files changed, 16 insertions(+), 15 deletions(-)

diff --git a/openflexure_microscope/api/app.py b/openflexure_microscope/api/app.py
index 95908a51..ccd302bc 100644
--- a/openflexure_microscope/api/app.py
+++ b/openflexure_microscope/api/app.py
@@ -261,10 +261,10 @@ def generate_openapi():
     if fname.endswith(".json"):
         import json
 
-        with open(fname, "w") as fd:
+        with open(fname, "w", encoding="utf-8") as fd:
             json.dump(labthing.spec.to_dict(), fd)
     else:
-        with open(fname, "w") as fd:
+        with open(fname, "w", encoding="utf-8") as fd:
             fd.write(labthing.spec.to_yaml())
 
 
diff --git a/openflexure_microscope/api/default_extensions/autofocus.py b/openflexure_microscope/api/default_extensions/autofocus.py
index 04d98d3b..fa482dee 100644
--- a/openflexure_microscope/api/default_extensions/autofocus.py
+++ b/openflexure_microscope/api/default_extensions/autofocus.py
@@ -245,7 +245,7 @@ def extension_action(args=None):
                 # Run the action
                 return func(self.extension, **arguments)
 
-            def get(self, *args, **kwargs):  # pylint: disable=useless-super-delegation
+            def get(self, *args, **kwargs):  # pylint: disable=useless-super-delegation,arguments-differ
                 # Explicitly wrap the `get` method to allow us to add a docstring
                 return super().get(*args, **kwargs)
 
diff --git a/openflexure_microscope/api/default_extensions/camera_stage_mapping.py b/openflexure_microscope/api/default_extensions/camera_stage_mapping.py
index 032660ba..d87aad45 100644
--- a/openflexure_microscope/api/default_extensions/camera_stage_mapping.py
+++ b/openflexure_microscope/api/default_extensions/camera_stage_mapping.py
@@ -200,7 +200,7 @@ class CSMExtension(BaseExtension):
             "linear_calibration_y": cal_y,
         }
 
-        with open(CSM_DATAFILE_PATH, "w") as f:
+        with open(CSM_DATAFILE_PATH, "w", encoding="utf-8") as f:
             json.dump(data, f, cls=JSONEncoder)
 
         return data
diff --git a/openflexure_microscope/api/utilities/__init__.py b/openflexure_microscope/api/utilities/__init__.py
index 5460580a..c94c73f9 100644
--- a/openflexure_microscope/api/utilities/__init__.py
+++ b/openflexure_microscope/api/utilities/__init__.py
@@ -81,7 +81,7 @@ def init_default_extensions(extension_dir: str):
         create_file(default_ext_path)
 
         logging.info("Populating %s...", (default_ext_path))
-        with open(default_ext_path, "w") as outfile:
+        with open(default_ext_path, "w", encoding="utf-8") as outfile:
             outfile.write(_DEFAULT_EXTENSION_INIT)
 
 
diff --git a/openflexure_microscope/camera/base.py b/openflexure_microscope/camera/base.py
index c7835b63..12f51946 100644
--- a/openflexure_microscope/camera/base.py
+++ b/openflexure_microscope/camera/base.py
@@ -54,7 +54,7 @@ class FrameStream(io.BytesIO):
         t: Optional[Type[BaseException]],
         value: Optional[BaseException],
         traceback: Optional[TracebackType],
-    ) -> Optional[bool]:
+    ) -> None:
         self.stop_tracking()
         return super().__exit__(t, value, traceback)
 
diff --git a/openflexure_microscope/captures/capture.py b/openflexure_microscope/captures/capture.py
index e4a5df68..1cd08a8f 100644
--- a/openflexure_microscope/captures/capture.py
+++ b/openflexure_microscope/captures/capture.py
@@ -120,7 +120,8 @@ class CaptureObject(object):
         logging.debug("Finished writing to disk %s", self.file)
 
     def open(self, mode):
-        return open(self.file, mode)
+        # We don't specify an encoding because this will be a binary file.
+        return open(self.file, mode) # pylint: disable=unspecified-encoding
 
     def split_file_path(self, filepath: str):
         """
diff --git a/openflexure_microscope/config.py b/openflexure_microscope/config.py
index 5788a385..f7b9552f 100644
--- a/openflexure_microscope/config.py
+++ b/openflexure_microscope/config.py
@@ -88,7 +88,7 @@ def load_json_file(config_path) -> dict:
 
     logging.info("Loading %s...", config_path)
 
-    with open(config_path) as config_file:
+    with open(config_path, encoding="utf-8") as config_file:
         try:
             config_data = json.load(config_file)
         except json.decoder.JSONDecodeError as e:
@@ -112,7 +112,7 @@ def save_json_file(config_path: str, config_dict: dict):
     logging.info("Saving %s...", config_path)
     logging.debug(config_dict)
 
-    with open(config_path, "w") as outfile:
+    with open(config_path, "w", encoding="utf-8") as outfile:
         json.dump(config_dict, outfile, cls=JSONEncoder, indent=2, sort_keys=True)
 
 
@@ -150,7 +150,7 @@ def initialise_file(config_path, populate: str = "{}\n"):
         create_file(config_path)
 
         logging.info("Populating %s...", (config_path))
-        with open(config_path, "w") as outfile:
+        with open(config_path, "w", encoding="utf-8") as outfile:
             outfile.write(populate)
 
 
diff --git a/openflexure_microscope/rescue/check_picamera.py b/openflexure_microscope/rescue/check_picamera.py
index 5490e13e..e8a5a113 100644
--- a/openflexure_microscope/rescue/check_picamera.py
+++ b/openflexure_microscope/rescue/check_picamera.py
@@ -26,7 +26,7 @@ def main():
 
     try:
         import picamerax
-    except Exception as e:  # pylint: disable=W0703
+    except Exception as _:  # pylint: disable=W0703
         error_sources.append(PICAMERA_IMPORT_ERROR)
     else:
         try:
diff --git a/openflexure_microscope/rescue/check_sangaboard.py b/openflexure_microscope/rescue/check_sangaboard.py
index 13b154b1..e7b23b6b 100644
--- a/openflexure_microscope/rescue/check_sangaboard.py
+++ b/openflexure_microscope/rescue/check_sangaboard.py
@@ -20,7 +20,7 @@ def main():
             # Try connecting on the specified port
             try:
                 stage = Sangaboard(stage_port)
-            except FileNotFoundError as e:
+            except FileNotFoundError as _:
                 if stage_port:
                     error_sources.append(
                         ErrorSource(
diff --git a/scripts/zenodo/upload_to_zenodo.py b/scripts/zenodo/upload_to_zenodo.py
index 244e63ce..aa30ce18 100644
--- a/scripts/zenodo/upload_to_zenodo.py
+++ b/scripts/zenodo/upload_to_zenodo.py
@@ -31,7 +31,7 @@ def script_directory(path):
 
 
 def get_meta():
-    with open(script_directory("metadata.yaml")) as f:
+    with open(script_directory("metadata.yaml"), encoding="utf-8") as f:
         metadata = f.read()
 
     return yaml.safe_load(metadata)
@@ -51,7 +51,7 @@ def main():
         zenodo.upload_file(deposit["id"], path)
 
     link = deposit["links"]["latest_draft_html"]
-    with open("zenodo-link.html", "w") as f:
+    with open("zenodo-link.html", "w", encoding="utf-8") as f:
         f.write(f'<a href="{link}">{link}</a>')
 
 
diff --git a/tests/test_app.py b/tests/test_app.py
index 0e16c58b..17c6076b 100644
--- a/tests/test_app.py
+++ b/tests/test_app.py
@@ -28,7 +28,7 @@ def test_thing_description_valid():
     # TODO: it would be nice to put this into LabThings
     # First load the schema from file and check it validates
     schema_fname = os.path.join(os.path.dirname(__file__), "w3c_td_schema.json")
-    schema = json.load(open(schema_fname, "r"))
+    schema = json.load(open(schema_fname, "r"), encoding="utf-8")
     jsonschema.Draft7Validator.check_schema(schema)
 
     # Build a TD dictionary

From 54045214586838128300a1f3aa78c5e516f9de24 Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Tue, 9 Aug 2022 09:36:25 +0100
Subject: [PATCH 06/25] Use different names for unused variables

mypy flagged too many assignments to `_` which this commit fixes.
---
 openflexure_microscope/rescue/check_picamera.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/openflexure_microscope/rescue/check_picamera.py b/openflexure_microscope/rescue/check_picamera.py
index e8a5a113..c9618f91 100644
--- a/openflexure_microscope/rescue/check_picamera.py
+++ b/openflexure_microscope/rescue/check_picamera.py
@@ -26,11 +26,11 @@ def main():
 
     try:
         import picamerax
-    except Exception as _:  # pylint: disable=W0703
+    except Exception as _e:  # pylint: disable=W0703
         error_sources.append(PICAMERA_IMPORT_ERROR)
     else:
         try:
-            _ = picamerax.PiCamera()
+            _cam = picamerax.PiCamera()
         except picamerax.PiCameraError as e:
             msg = e.args[0]
             if msg in PICAMERA_ERROR_MAP:

From 78ef9c531ba3cc016886e66319a11c4c1634954b Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Tue, 9 Aug 2022 09:37:03 +0100
Subject: [PATCH 07/25] Format fixes from black

---
 openflexure_microscope/api/default_extensions/autofocus.py | 4 +++-
 openflexure_microscope/captures/capture.py                 | 2 +-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/openflexure_microscope/api/default_extensions/autofocus.py b/openflexure_microscope/api/default_extensions/autofocus.py
index fa482dee..f6fc5aaf 100644
--- a/openflexure_microscope/api/default_extensions/autofocus.py
+++ b/openflexure_microscope/api/default_extensions/autofocus.py
@@ -245,7 +245,9 @@ def extension_action(args=None):
                 # Run the action
                 return func(self.extension, **arguments)
 
-            def get(self, *args, **kwargs):  # pylint: disable=useless-super-delegation,arguments-differ
+            def get(
+                self, *args, **kwargs
+            ):  # pylint: disable=useless-super-delegation,arguments-differ
                 # Explicitly wrap the `get` method to allow us to add a docstring
                 return super().get(*args, **kwargs)
 
diff --git a/openflexure_microscope/captures/capture.py b/openflexure_microscope/captures/capture.py
index 1cd08a8f..1cc6f05c 100644
--- a/openflexure_microscope/captures/capture.py
+++ b/openflexure_microscope/captures/capture.py
@@ -121,7 +121,7 @@ class CaptureObject(object):
 
     def open(self, mode):
         # We don't specify an encoding because this will be a binary file.
-        return open(self.file, mode) # pylint: disable=unspecified-encoding
+        return open(self.file, mode)  # pylint: disable=unspecified-encoding
 
     def split_file_path(self, filepath: str):
         """

From e22f36b308b5ae5ce335cb962ceece00c988e30b Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Tue, 9 Aug 2022 12:52:57 +0100
Subject: [PATCH 08/25] Start explicit metadata argument for marshmallow

A side effect of re-locking dependencies is having a newer marshmallow.
This deprecates having `description=` as a keyword, and puts it in a
separate metadata arg instead.

This commit is the start of my search-and-replaceing to update to the new
format.
---
 docs/source/extensions/actions.rst            |  2 +-
 .../example_extension/05_actions.py           |  2 +-
 .../example_extension/06_tasks_locks.py       |  2 +-
 .../extensions/example_extension/07_ev_gui.py |  2 +-
 docs/source/extensions/marshaling.rst         |  8 ++---
 .../api/default_extensions/autofocus.py       | 32 +++++++++----------
 .../camera_stage_mapping.py                   | 14 ++++----
 .../picamera_autocalibrate/extension.py       | 12 +++----
 .../api/default_extensions/scan.py            | 14 ++++----
 .../api/dev_extensions/tools.py               |  2 +-
 .../api/v2/views/actions/camera.py            | 12 +++----
 .../api/v2/views/actions/stage.py             |  8 ++---
 .../api/v2/views/captures.py                  |  2 +-
 openflexure_microscope/api/v2/views/stage.py  |  4 +--
 14 files changed, 58 insertions(+), 58 deletions(-)

diff --git a/docs/source/extensions/actions.rst b/docs/source/extensions/actions.rst
index 1a9fb2ac..481c66ed 100644
--- a/docs/source/extensions/actions.rst
+++ b/docs/source/extensions/actions.rst
@@ -18,7 +18,7 @@ Like properties, we use a special view class to identify a view as an action: ``
         Take an image capture and return it without saving
         """
         # Expect a "use_video_port" boolean, which defaults to True if none is given
-        args = {"use_video_port": fields.Boolean(missing=True)}
+        args = {"use_video_port": fields.Boolean(load_default=True)}
 
         # Our success response (200) returns an image (image/jpeg mimetype)
         responses = {
diff --git a/docs/source/extensions/example_extension/05_actions.py b/docs/source/extensions/example_extension/05_actions.py
index ca2578db..b260b92c 100644
--- a/docs/source/extensions/example_extension/05_actions.py
+++ b/docs/source/extensions/example_extension/05_actions.py
@@ -91,7 +91,7 @@ class QuickCaptureAPI(ActionView):
     """
 
     # Expect a "use_video_port" boolean, which defaults to True if none is given
-    args = {"use_video_port": fields.Boolean(missing=True)}
+    args = {"use_video_port": fields.Boolean(load_default=True)}
 
     # Our success response (200) returns an image (image/jpeg mimetype)
     responses = {200: {"content": {"image/jpeg": {}}}}
diff --git a/docs/source/extensions/example_extension/06_tasks_locks.py b/docs/source/extensions/example_extension/06_tasks_locks.py
index 79f9b1ef..8412ad65 100644
--- a/docs/source/extensions/example_extension/06_tasks_locks.py
+++ b/docs/source/extensions/example_extension/06_tasks_locks.py
@@ -69,7 +69,7 @@ class TimelapseAPIView(ActionView):
             required=True, example=5, description="Number of images"
         ),
         "t_between": fields.Number(
-            missing=1, example=1, description="Time (seconds) between images"
+            load_default=1, example=1, description="Time (seconds) between images"
         ),
     }
 
diff --git a/docs/source/extensions/example_extension/07_ev_gui.py b/docs/source/extensions/example_extension/07_ev_gui.py
index 42b40751..0541a533 100644
--- a/docs/source/extensions/example_extension/07_ev_gui.py
+++ b/docs/source/extensions/example_extension/07_ev_gui.py
@@ -102,7 +102,7 @@ class TimelapseAPIView(ActionView):
             required=True, example=5, description="Number of images"
         ),
         "t_between": fields.Number(
-            missing=1, example=1, description="Time (seconds) between images"
+            load_default=1, example=1, description="Time (seconds) between images"
         ),
     }
 
diff --git a/docs/source/extensions/marshaling.rst b/docs/source/extensions/marshaling.rst
index f56ae20b..54310486 100644
--- a/docs/source/extensions/marshaling.rst
+++ b/docs/source/extensions/marshaling.rst
@@ -23,7 +23,7 @@ A **field** describes the data type of a single parameter, as well as any other
 
 .. code-block:: python
 
-    fields.String(required=False, missing="Default value", example="Example value")
+    fields.String(required=False, load_default="Default value", example="Example value")
 
 A **schema** is a collection of keys and fields describing how an object should be serialized/deserialized. Schemas can be created in several ways, either by creating a ``Schema`` class, or by passing a dictionary of key-field pairs. Both methods will be discussed in the following examples.
 
@@ -43,7 +43,7 @@ For example, if you are creating an API route, in which you expect parameters ``
     class UserSchema(Schema):
         name = fields.String(required=True)
         age = fields.Integer(required=True)
-        job = fields.String(required=False, missing="Unknown")
+        job = fields.String(required=False, load_default="Unknown")
 
 To inform your POST method to expect these arguments, use the ``args`` class attribute:
 
@@ -63,7 +63,7 @@ Alternatively, if your schema is only used in a single location, it may be simpl
         args = {
             "name": fields.String(required=True),
             "age": fields.Integer(required=True),
-            "job": fields.String(required=False, missing="Unknown")
+            "job": fields.String(required=False, load_default="Unknown")
         }
 
         def post(self, args):
@@ -88,7 +88,7 @@ This JSON data is the parsed, converted into a Python dictionary, and passed as
         args = {
             "name": fields.String(required=True),
             "age": fields.Integer(required=True),
-            "job": fields.String(required=False, missing="Unknown")
+            "job": fields.String(required=False, load_default="Unknown")
         }
 
         def post(self, args):
diff --git a/openflexure_microscope/api/default_extensions/autofocus.py b/openflexure_microscope/api/default_extensions/autofocus.py
index f6fc5aaf..c3ad4baf 100644
--- a/openflexure_microscope/api/default_extensions/autofocus.py
+++ b/openflexure_microscope/api/default_extensions/autofocus.py
@@ -349,7 +349,7 @@ class AutofocusExtension(BaseExtension):
         args={
             "dz": fields.List(
                 fields.Int(),
-                description="An ascending list of relative z positions",
+                metadata={"description": "An ascending list of relative z positions"},
                 example=[int(x) for x in np.linspace(-300, 300, 7)],
             )
         }
@@ -410,7 +410,7 @@ class AutofocusExtension(BaseExtension):
 
     @extension_action(
         args={
-            "dz": fields.Int(required=True, description="The relative Z move to make")
+            "dz": fields.Int(required=True, metadata={"description": "The relative Z move to make"})
         }
     )
     def move_and_measure(
@@ -432,9 +432,9 @@ class AutofocusExtension(BaseExtension):
     @extension_action(
         args={
             "dz": fields.Int(
-                missing=2000,
+                load_default=2000,
                 example=2000,
-                description="Total Z range to search over (in stage steps)",
+                metadata={"description": "Total Z range to search over (in stage steps)"},
             )
         }
     )
@@ -528,14 +528,14 @@ class AutofocusExtension(BaseExtension):
     @extension_action(
         args={
             "dz": fields.Int(
-                missing=500,
+                load_default=500,
                 example=500,
-                description="Total Z range to move down, then up (in stage steps)",
+                metadata={"description": "Total Z range to move down, then up (in stage steps)"},
             ),
             "delay": fields.Int(
-                missing=5,
+                load_default=5,
                 example=5,
-                description="How long to measure sharpness for after the move",
+                metadata={"description": "How long to measure sharpness for after the move"},
             ),
         }
     )
@@ -556,23 +556,23 @@ class AutofocusExtension(BaseExtension):
     @extension_action(
         args={
             "dz": fields.Int(
-                missing=2000,
+                load_default=2000,
                 example=2000,
-                description="Total Z range to search over (in stage steps)",
+                metadata={"description": "Total Z range to search over (in stage steps)"},
             ),
             "target_z": fields.Int(
-                missing=0,
+                load_default=0,
                 example=-100,
-                description="Target finishing position, relative to the focus.",
+                metadata={"description": "Target finishing position, relative to the focus."},
             ),
             "initial_move_up": fields.Bool(
-                missing=True,
-                description="Set to Flase to disable the initial move upwards",
+                load_default=True,
+                metadata={"description": "Set to Flase to disable the initial move upwards"},
             ),
             "backlash": fields.Int(
-                missing=25,
+                load_default=25,
                 minimum=0,
-                description="Distance to undershoot, before correction move.",
+                metadata={"description": "Distance to undershoot, before correction move."},
             ),
         }
     )
diff --git a/openflexure_microscope/api/default_extensions/camera_stage_mapping.py b/openflexure_microscope/api/default_extensions/camera_stage_mapping.py
index d87aad45..398069c8 100644
--- a/openflexure_microscope/api/default_extensions/camera_stage_mapping.py
+++ b/openflexure_microscope/api/default_extensions/camera_stage_mapping.py
@@ -298,10 +298,10 @@ class CalibrateXYView(ActionView):
 class MoveInImageCoordinatesView(ActionView):
     args = {
         "x": fields.Float(
-            description="The number of pixels to move in X", required=True, example=100
+            metadata={"description": "The number of pixels to move in X"}, required=True, example=100
         ),
         "y": fields.Float(
-            description="The number of pixels to move in Y", required=True, example=100
+            metadata={"description": "The number of pixels to move in Y"}, required=True, example=100
         ),
     }
 
@@ -316,10 +316,10 @@ class MoveInImageCoordinatesView(ActionView):
 class ClosedLoopMoveInImageCoordinatesView(ActionView):
     args = {
         "x": fields.Float(
-            description="The number of pixels to move in X", required=True, example=100
+            metadata={"description": "The number of pixels to move in X"}, required=True, example=100
         ),
         "y": fields.Float(
-            description="The number of pixels to move in Y", required=True, example=100
+            metadata={"description": "The number of pixels to move in Y"}, required=True, example=100
         ),
     }
 
@@ -336,13 +336,13 @@ class ClosedLoopMoveInImageCoordinatesView(ActionView):
 class TestClosedLoopSpiralScanView(ActionView):
     args = {
         "x_step": fields.Float(
-            description="The number of pixels to move in X", required=True, example=100
+            metadata={"description": "The number of pixels to move in X"}, required=True, example=100
         ),
         "y_step": fields.Float(
-            description="The number of pixels to move in Y", required=True, example=100
+            metadata={"description": "The number of pixels to move in Y"}, required=True, example=100
         ),
         "N": fields.Int(
-            description="The number of rings in the spiral scan",
+            metadata={"description": "The number of rings in the spiral scan"},
             required=True,
             example=3,
         ),
diff --git a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
index 1a0bf539..7c2f3cba 100644
--- a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
+++ b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
@@ -172,20 +172,20 @@ class DeleteLSTView(ActionView):
 class AutoExposureFromRawView(ActionView):
     args = {
         "target_white_level": fields.Int(
-            missing=700,
+            load_default=700,
             example=700,
             description=(
                 "The pixel value (10-bit format) that we aim for when adjusting shutter/gain."
             ),
         ),
         "max_iterations": fields.Int(
-            missing=20,
+            load_default=20,
             description=(
                 "The number of adjustments to the camera's settings to make before giving up."
             ),
         ),
         "tolerance": fields.Float(
-            missing=0.05,
+            load_default=0.05,
             example=0.05,
             description=(
                 "We stop adjusting when we get within this fraction of the target "
@@ -193,7 +193,7 @@ class AutoExposureFromRawView(ActionView):
             ),
         ),
         "percentile": fields.Float(
-            missing=99.9,
+            load_default=99.9,
             example=99.9,
             description=(
                 "A float between 0 and 100 setting the centile to use "
@@ -212,7 +212,7 @@ class AutoExposureFromRawView(ActionView):
 class AutoWhiteBalanceFromRawView(ActionView):
     args = {
         "percentile": fields.Float(
-            missing=99.9,
+            load_default=99.9,
             example=99.9,
             description=(
                 "A float between 0 and 100 setting the centile to use "
@@ -232,7 +232,7 @@ class GetRawChannelPercentilesView(ActionView):
     args = {
         "percentile": fields.Float(
             example=99.9,
-            description="A float between 0 and 100 setting the centile to calculate",
+            metadata={"description": "A float between 0 and 100 setting the centile to calculate"},
         )
     }
     schema = fields.List(fields.Integer)
diff --git a/openflexure_microscope/api/default_extensions/scan.py b/openflexure_microscope/api/default_extensions/scan.py
index a9a765f3..8f2ff80a 100644
--- a/openflexure_microscope/api/default_extensions/scan.py
+++ b/openflexure_microscope/api/default_extensions/scan.py
@@ -578,19 +578,19 @@ class ScanExtension(BaseExtension):
 
 
 class TileScanArgs(FullCaptureArgs):
-    namemode = fields.String(missing="coordinates", example="coordinates")
+    namemode = fields.String(load_default="coordinates", example="coordinates")
     grid = fields.List(
         fields.Integer(validate=marshmallow.validate.Range(min=1)),
-        missing=[3, 3, 3],
+        load_default=[3, 3, 3],
         example=[3, 3, 3],
     )
-    style = fields.String(missing="raster")
-    autofocus_dz = fields.Integer(missing=50)
-    fast_autofocus = fields.Boolean(missing=False)
+    style = fields.String(load_default="raster")
+    autofocus_dz = fields.Integer(load_default=50)
+    fast_autofocus = fields.Boolean(load_default=False)
     stride_size = fields.List(
-        fields.Integer, missing=[2000, 1500, 100], example=[2000, 1500, 100]
+        fields.Integer, load_default=[2000, 1500, 100], example=[2000, 1500, 100]
     )
-    detect_empty_fields_and_skip_autofocus = fields.Boolean(missing=False)
+    detect_empty_fields_and_skip_autofocus = fields.Boolean(load_default=False)
 
 
 class TileScanAPI(ActionView):
diff --git a/openflexure_microscope/api/dev_extensions/tools.py b/openflexure_microscope/api/dev_extensions/tools.py
index f8da0a03..b7959d2b 100644
--- a/openflexure_microscope/api/dev_extensions/tools.py
+++ b/openflexure_microscope/api/dev_extensions/tools.py
@@ -24,7 +24,7 @@ class RaiseException(ActionView):
 
 class SleepFor(ActionView):
     schema = {"TimeAsleep": fields.Float()}
-    args = {"time": fields.Float(description="Time to sleep, in seconds", example=0.5)}
+    args = {"time": fields.Float(metadata={"description": "Time to sleep, in seconds"}, example=0.5)}
 
     def post(self, args):
         sleep_time: int = args.get("time", 0)
diff --git a/openflexure_microscope/api/v2/views/actions/camera.py b/openflexure_microscope/api/v2/views/actions/camera.py
index a6ef3b12..10f1286d 100644
--- a/openflexure_microscope/api/v2/views/actions/camera.py
+++ b/openflexure_microscope/api/v2/views/actions/camera.py
@@ -15,18 +15,18 @@ class CaptureResizeSchema(Schema):
 
 
 class BasicCaptureArgs(Schema):
-    use_video_port = fields.Boolean(missing=False)
+    use_video_port = fields.Boolean(load_default=False)
     bayer = fields.Boolean(
-        missing=False, description="Include raw bayer data in capture"
+        load_default=False, metadata={"description": "Include raw bayer data in capture"}
     )
     resize = fields.Nested(CaptureResizeSchema(), required=False)
 
 
 class FullCaptureArgs(BasicCaptureArgs):
     filename = fields.String(example="MyFileName")
-    temporary = fields.Boolean(missing=False, description="Delete capture on shutdown")
-    annotations = fields.Dict(missing={}, example={"Client": "SwaggerUI"})
-    tags = fields.List(fields.String, missing=[], example=["docs"])
+    temporary = fields.Boolean(load_default=False, metadata={"description": "Delete capture on shutdown"})
+    annotations = fields.Dict(load_default={}, example={"Client": "SwaggerUI"})
+    tags = fields.List(fields.String, load_default=[], example=["docs"])
 
 
 class CaptureAPI(ActionView):
@@ -113,7 +113,7 @@ class GPUPreviewStartAPI(ActionView):
     in the format ``[x, y, width, height]``.
     """
 
-    args = {"window": fields.List(fields.Integer, missing=[], example=[0, 0, 640, 480])}
+    args = {"window": fields.List(fields.Integer, load_default=[], example=[0, 0, 640, 480])}
 
     def post(self, args):
         """
diff --git a/openflexure_microscope/api/v2/views/actions/stage.py b/openflexure_microscope/api/v2/views/actions/stage.py
index dd87e7e0..1488ea2e 100644
--- a/openflexure_microscope/api/v2/views/actions/stage.py
+++ b/openflexure_microscope/api/v2/views/actions/stage.py
@@ -7,11 +7,11 @@ from labthings.views import ActionView
 class MoveStageAPI(ActionView):
     args = {
         "absolute": fields.Boolean(
-            missing=False, example=False, description="Move to an absolute position"
+            load_default=False, example=False, metadata={"description": "Move to an absolute position"}
         ),
-        "x": fields.Int(missing=None, example=100, allow_none=False),
-        "y": fields.Int(missing=None, example=100, allow_none=False),
-        "z": fields.Int(missing=None, example=20, allow_none=False),
+        "x": fields.Int(load_default=None, example=100, allow_none=False),
+        "y": fields.Int(load_default=None, example=100, allow_none=False),
+        "z": fields.Int(load_default=None, example=20, allow_none=False),
     }
 
     def post(self, args):
diff --git a/openflexure_microscope/api/v2/views/captures.py b/openflexure_microscope/api/v2/views/captures.py
index 44f056ca..4935bb46 100644
--- a/openflexure_microscope/api/v2/views/captures.py
+++ b/openflexure_microscope/api/v2/views/captures.py
@@ -59,7 +59,7 @@ class CaptureSchema(ImageSchema):
     # without the server having to do a tonne of file IO
     dataset = fields.Nested(BasicDatasetSchema())
     file = fields.String(
-        data_key="path", description="Path of file on microscope device"
+        data_key="path", metadata={"description": "Path of file on microscope device"}
     )
     # No need to make a schema for links as we only ever
     # create the dictionary right here in `generate_links`
diff --git a/openflexure_microscope/api/v2/views/stage.py b/openflexure_microscope/api/v2/views/stage.py
index 21d19e94..9db97aed 100644
--- a/openflexure_microscope/api/v2/views/stage.py
+++ b/openflexure_microscope/api/v2/views/stage.py
@@ -7,10 +7,10 @@ class StageTypeProperty(PropertyView):
     """The type of the stage"""
 
     schema = fields.String(
-        missing=None,
+        load_default=None,
         example="SangaStage",
         validate=validate.OneOf(["SangaStage", "SangaDeltaStage"]),
-        description="The translation stage geometry",
+        metadata={"description": "The translation stage geometry"},
         allow_none=False,
     )
 

From 9dbb083ee7603d7eb149d7070e08887e0988cd7d Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Tue, 9 Aug 2022 13:16:10 +0100
Subject: [PATCH 09/25] More Marshmallow argument updates

---
 .../example_extension/02_adding_views.py      |  2 +-
 .../example_extension/03_marshaling_data.py   |  2 +-
 .../example_extension/04_properties.py        |  2 +-
 .../example_extension/05_actions.py           |  2 +-
 .../example_extension/06_tasks_locks.py       |  4 +-
 .../extensions/example_extension/07_ev_gui.py |  4 +-
 docs/source/extensions/marshaling.rst         |  4 +-
 docs/source/extensions/properties.rst         |  2 +-
 .../api/default_extensions/autofocus.py       | 42 +++++++----
 .../api/default_extensions/autostorage.py     |  2 +-
 .../camera_stage_mapping.py                   | 17 ++---
 .../picamera_autocalibrate/extension.py       | 73 ++++++++++---------
 .../api/default_extensions/scan.py            |  6 +-
 .../api/dev_extensions/tools.py               |  2 +-
 .../api/v2/views/actions/camera.py            | 12 +--
 .../api/v2/views/actions/stage.py             |  8 +-
 .../api/v2/views/captures.py                  |  2 +-
 openflexure_microscope/api/v2/views/stage.py  |  3 +-
 18 files changed, 102 insertions(+), 87 deletions(-)

diff --git a/docs/source/extensions/example_extension/02_adding_views.py b/docs/source/extensions/example_extension/02_adding_views.py
index be2bb820..77b49aee 100644
--- a/docs/source/extensions/example_extension/02_adding_views.py
+++ b/docs/source/extensions/example_extension/02_adding_views.py
@@ -46,7 +46,7 @@ class ExampleIdentifyView(View):
 class ExampleRenameView(View):
     # Expect a request parameter called "name", which is a string.
     # Passed to the argument "args".
-    args = fields.String(required=True, example="My Example Microscope")
+    args = fields.String(required=True, metadata={"example": "My Example Microscope"})
 
     def post(self, args):
         # Look for our new name in the request body
diff --git a/docs/source/extensions/example_extension/03_marshaling_data.py b/docs/source/extensions/example_extension/03_marshaling_data.py
index 2bf270fe..cca86fd6 100644
--- a/docs/source/extensions/example_extension/03_marshaling_data.py
+++ b/docs/source/extensions/example_extension/03_marshaling_data.py
@@ -49,7 +49,7 @@ class ExampleRenameView(View):
     # Format our returned object using MicroscopeIdentifySchema
     schema = MicroscopeIdentifySchema()
     # Expect a request parameter called "name", which is a string. Pass to argument "args".
-    args = {"name": fields.String(required=True, example="My Example Microscope")}
+    args = {"name": fields.String(required=True, metadata={"example": "My Example Microscope"})}
 
     def post(self, args):
         # Look for our "name" parameter in the request arguments
diff --git a/docs/source/extensions/example_extension/04_properties.py b/docs/source/extensions/example_extension/04_properties.py
index 6df7069d..7d7a4cc9 100644
--- a/docs/source/extensions/example_extension/04_properties.py
+++ b/docs/source/extensions/example_extension/04_properties.py
@@ -53,7 +53,7 @@ class ExampleIdentifyView(PropertyView):
 # We can use a single schema as the input and output will be formatted identically
 # Eg. We always expect a "name" string argument, and always return a "name" string attribute
 class ExampleRenameView(PropertyView):
-    schema = {"name": fields.String(required=True, example="My Example Microscope")}
+    schema = {"name": fields.String(required=True, metadata={"example": "My Example Microscope"})}
 
     def get(self):
         """
diff --git a/docs/source/extensions/example_extension/05_actions.py b/docs/source/extensions/example_extension/05_actions.py
index b260b92c..ca5d6980 100644
--- a/docs/source/extensions/example_extension/05_actions.py
+++ b/docs/source/extensions/example_extension/05_actions.py
@@ -56,7 +56,7 @@ class ExampleIdentifyView(PropertyView):
 # We can use a single schema as the input and output will be formatted identically
 # Eg. We always expect a "name" string argument, and always return a "name" string attribute
 class ExampleRenameView(PropertyView):
-    schema = {"name": fields.String(required=True, example="My Example Microscope")}
+    schema = {"name": fields.String(required=True, metadata={"example": "My Example Microscope"})}
 
     def get(self):
         """
diff --git a/docs/source/extensions/example_extension/06_tasks_locks.py b/docs/source/extensions/example_extension/06_tasks_locks.py
index 8412ad65..6c23e8ab 100644
--- a/docs/source/extensions/example_extension/06_tasks_locks.py
+++ b/docs/source/extensions/example_extension/06_tasks_locks.py
@@ -66,10 +66,10 @@ class TimelapseAPIView(ActionView):
 
     args = {
         "n_images": fields.Integer(
-            required=True, example=5, description="Number of images"
+            required=True, metadata={"example": 5, "description": "Number of images"}
         ),
         "t_between": fields.Number(
-            load_default=1, example=1, description="Time (seconds) between images"
+            load_default=1, metadata={"example": 1, "description": "Time (seconds) between images"}
         ),
     }
 
diff --git a/docs/source/extensions/example_extension/07_ev_gui.py b/docs/source/extensions/example_extension/07_ev_gui.py
index 0541a533..12b2ce09 100644
--- a/docs/source/extensions/example_extension/07_ev_gui.py
+++ b/docs/source/extensions/example_extension/07_ev_gui.py
@@ -99,10 +99,10 @@ class TimelapseAPIView(ActionView):
 
     args = {
         "n_images": fields.Integer(
-            required=True, example=5, description="Number of images"
+            required=True, metadata={"example": 5, "description": "Number of images"}
         ),
         "t_between": fields.Number(
-            load_default=1, example=1, description="Time (seconds) between images"
+            load_default=1, metadata={"example": 1, "description": "Time (seconds) between images"}
         ),
     }
 
diff --git a/docs/source/extensions/marshaling.rst b/docs/source/extensions/marshaling.rst
index 54310486..2ed5e93a 100644
--- a/docs/source/extensions/marshaling.rst
+++ b/docs/source/extensions/marshaling.rst
@@ -23,7 +23,7 @@ A **field** describes the data type of a single parameter, as well as any other
 
 .. code-block:: python
 
-    fields.String(required=False, load_default="Default value", example="Example value")
+    fields.String(required=False, load_default="Default value", metadata={"example: "Example value"})
 
 A **schema** is a collection of keys and fields describing how an object should be serialized/deserialized. Schemas can be created in several ways, either by creating a ``Schema`` class, or by passing a dictionary of key-field pairs. Both methods will be discussed in the following examples.
 
@@ -146,7 +146,7 @@ Our ``rename`` view class may now look like:
         # Format our returned object using MicroscopeIdentifySchema
         schema = MicroscopeIdentifySchema()
         # Expect a request parameter called "name", which is a string. Pass to argument "args".
-        args = {"name": fields.String(required=True, example="My Example Microscope")}
+        args = {"name": fields.String(required=True, metadata={"example": "My Example Microscope"})}
 
         def post(self, args):
             # Look for our "name" parameter in the request arguments
diff --git a/docs/source/extensions/properties.rst b/docs/source/extensions/properties.rst
index 3a86e2d5..fedc5055 100644
--- a/docs/source/extensions/properties.rst
+++ b/docs/source/extensions/properties.rst
@@ -78,7 +78,7 @@ We will implement the ``schema`` attribute in our ``ExampleRenameView`` view fro
     # We can use a single schema as the input and output will be formatted identically
     # Eg. We always expect a "name" string argument, and always return a "name" string attribute
     class ExampleRenameView(PropertyView):
-        schema = {"name": fields.String(required=True, example="My Example Microscope")}
+        schema = {"name": fields.String(required=True, metadata={"example": "My Example Microscope"})}
     
         def get(self):
             """
diff --git a/openflexure_microscope/api/default_extensions/autofocus.py b/openflexure_microscope/api/default_extensions/autofocus.py
index c3ad4baf..f7eeb394 100644
--- a/openflexure_microscope/api/default_extensions/autofocus.py
+++ b/openflexure_microscope/api/default_extensions/autofocus.py
@@ -349,8 +349,10 @@ class AutofocusExtension(BaseExtension):
         args={
             "dz": fields.List(
                 fields.Int(),
-                metadata={"description": "An ascending list of relative z positions"},
-                example=[int(x) for x in np.linspace(-300, 300, 7)],
+                metadata={
+                    "description": "An ascending list of relative z positions",
+                    "example": [int(x) for x in np.linspace(-300, 300, 7)],
+                }
             )
         }
     )
@@ -433,8 +435,10 @@ class AutofocusExtension(BaseExtension):
         args={
             "dz": fields.Int(
                 load_default=2000,
-                example=2000,
-                metadata={"description": "Total Z range to search over (in stage steps)"},
+                metadata={
+                    "description": "Total Z range to search over (in stage steps)",
+                    "example": 2000,
+                },
             )
         }
     )
@@ -529,13 +533,17 @@ class AutofocusExtension(BaseExtension):
         args={
             "dz": fields.Int(
                 load_default=500,
-                example=500,
-                metadata={"description": "Total Z range to move down, then up (in stage steps)"},
+                metadata={
+                    "description": "Total Z range to move down, then up (in stage steps)",
+                    "example": 500,
+                },
             ),
             "delay": fields.Int(
                 load_default=5,
-                example=5,
-                metadata={"description": "How long to measure sharpness for after the move"},
+                metadata={
+                    "description": "How long to measure sharpness for after the move",
+                    "example": 5,
+                },
             ),
         }
     )
@@ -557,13 +565,17 @@ class AutofocusExtension(BaseExtension):
         args={
             "dz": fields.Int(
                 load_default=2000,
-                example=2000,
-                metadata={"description": "Total Z range to search over (in stage steps)"},
+                metadata={
+                    "description": "Total Z range to search over (in stage steps)",
+                    "example": 2000,
+                },
             ),
             "target_z": fields.Int(
                 load_default=0,
-                example=-100,
-                metadata={"description": "Target finishing position, relative to the focus."},
+                metadata={
+                    "description": "Target finishing position, relative to the focus.",
+                    "example": -100,
+                },
             ),
             "initial_move_up": fields.Bool(
                 load_default=True,
@@ -571,8 +583,10 @@ class AutofocusExtension(BaseExtension):
             ),
             "backlash": fields.Int(
                 load_default=25,
-                minimum=0,
-                metadata={"description": "Distance to undershoot, before correction move."},
+                metadata={
+                    "description": "Distance to undershoot, before correction move.",
+                    "minimum": 0,
+                },
             ),
         }
     )
diff --git a/openflexure_microscope/api/default_extensions/autostorage.py b/openflexure_microscope/api/default_extensions/autostorage.py
index ab32bf44..aa67875d 100644
--- a/openflexure_microscope/api/default_extensions/autostorage.py
+++ b/openflexure_microscope/api/default_extensions/autostorage.py
@@ -242,7 +242,7 @@ class GetLocationsView(PropertyView):
 
 
 class PreferredLocationView(PropertyView):
-    schema = fields.String(required=True, example="Default")
+    schema = fields.String(required=True, metadata={"example": "Default"})
 
     def get(self):
         self.extension.check_location()
diff --git a/openflexure_microscope/api/default_extensions/camera_stage_mapping.py b/openflexure_microscope/api/default_extensions/camera_stage_mapping.py
index 398069c8..53b3789d 100644
--- a/openflexure_microscope/api/default_extensions/camera_stage_mapping.py
+++ b/openflexure_microscope/api/default_extensions/camera_stage_mapping.py
@@ -279,7 +279,7 @@ class CSMExtension(BaseExtension):
 
 
 class Calibrate1DView(ActionView):
-    args = {"direction": fields.List(fields.Float(), required=True, example=[1, 0, 0])}
+    args = {"direction": fields.List(fields.Float(), required=True, metadata={"example": [1, 0, 0]})}
 
     def post(self, args):
         """Calibrate one axis of the microscope stage against the camera."""
@@ -298,10 +298,10 @@ class CalibrateXYView(ActionView):
 class MoveInImageCoordinatesView(ActionView):
     args = {
         "x": fields.Float(
-            metadata={"description": "The number of pixels to move in X"}, required=True, example=100
+            metadata={"description": "The number of pixels to move in X", "example": 100,}, required=True,
         ),
         "y": fields.Float(
-            metadata={"description": "The number of pixels to move in Y"}, required=True, example=100
+            metadata={"description": "The number of pixels to move in Y", "example": 100,}, required=True,
         ),
     }
 
@@ -316,10 +316,10 @@ class MoveInImageCoordinatesView(ActionView):
 class ClosedLoopMoveInImageCoordinatesView(ActionView):
     args = {
         "x": fields.Float(
-            metadata={"description": "The number of pixels to move in X"}, required=True, example=100
+            metadata={"description": "The number of pixels to move in X", "example": 100,}, required=True,
         ),
         "y": fields.Float(
-            metadata={"description": "The number of pixels to move in Y"}, required=True, example=100
+            metadata={"description": "The number of pixels to move in Y", "example": 100,}, required=True,
         ),
     }
 
@@ -336,15 +336,14 @@ class ClosedLoopMoveInImageCoordinatesView(ActionView):
 class TestClosedLoopSpiralScanView(ActionView):
     args = {
         "x_step": fields.Float(
-            metadata={"description": "The number of pixels to move in X"}, required=True, example=100
+            metadata={"description": "The number of pixels to move in X", "example": 100,}, required=True,
         ),
         "y_step": fields.Float(
-            metadata={"description": "The number of pixels to move in Y"}, required=True, example=100
+            metadata={"description": "The number of pixels to move in Y", "example": 100,}, required=True,
         ),
         "N": fields.Int(
-            metadata={"description": "The number of rings in the spiral scan"},
+            metadata={"description": "The number of rings in the spiral scan", "example": 100,},
             required=True,
-            example=3,
         ),
     }
 
diff --git a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
index 7c2f3cba..642c5a60 100644
--- a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
+++ b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
@@ -169,39 +169,49 @@ class DeleteLSTView(ActionView):
             microscope.save_settings()
 
 
+percentile_field = fields.Float(
+    load_default=99.9,
+    metadata={
+        "example": 99.9,
+        "description": (
+            "A float between 0 and 100 setting the centile to use "
+            "to measure the white point of the image.  A value "
+            "of 99.9 allows 0.1% of the pixels to be erroneously "
+            "bright - this helps stability in low light."
+        ),
+    },
+)
+
+
 class AutoExposureFromRawView(ActionView):
     args = {
         "target_white_level": fields.Int(
             load_default=700,
-            example=700,
-            description=(
-                "The pixel value (10-bit format) that we aim for when adjusting shutter/gain."
-            ),
+            metadata={
+                "example": 700,
+                "description": (
+                    "The pixel value (10-bit format) that we aim for when adjusting shutter/gain."
+                ),
+            },
         ),
         "max_iterations": fields.Int(
-            load_default=20,
-            description=(
-                "The number of adjustments to the camera's settings to make before giving up."
-            ),
+            load_default=20,metadata={
+                "description": (
+                    "The number of adjustments to the camera's settings to make before giving up."
+                ),
+            },
         ),
         "tolerance": fields.Float(
             load_default=0.05,
-            example=0.05,
-            description=(
-                "We stop adjusting when we get within this fraction of the target "
-                "value.  It is a number between 0 and 1, usually 0.01--0.1."
-            ),
-        ),
-        "percentile": fields.Float(
-            load_default=99.9,
-            example=99.9,
-            description=(
-                "A float between 0 and 100 setting the centile to use "
-                "to measure the white point of the image.  A value "
-                "of 99.9 allows 0.1% of the pixels to be erroneously "
-                "bright - this helps stability in low light."
-            ),
+            metadata={
+                "example": 0.05,
+                "description": (
+                    "We stop adjusting when we get within this fraction of the target "
+                    "value.  It is a number between 0 and 1, usually 0.01--0.1."
+                ),
+            },
         ),
+        "percentile": percentile_field,
     }
 
     def post(self, args):
@@ -211,16 +221,7 @@ class AutoExposureFromRawView(ActionView):
 
 class AutoWhiteBalanceFromRawView(ActionView):
     args = {
-        "percentile": fields.Float(
-            load_default=99.9,
-            example=99.9,
-            description=(
-                "A float between 0 and 100 setting the centile to use "
-                "to measure the white point of the image.  A value "
-                "of 99.9 allows 0.1% of the pixels to be erroneously "
-                "bright - this helps stability in low light."
-            ),
-        )
+        "percentile": percentile_field,
     }
 
     def post(self, args):
@@ -231,8 +232,10 @@ class AutoWhiteBalanceFromRawView(ActionView):
 class GetRawChannelPercentilesView(ActionView):
     args = {
         "percentile": fields.Float(
-            example=99.9,
-            metadata={"description": "A float between 0 and 100 setting the centile to calculate"},
+            metadata={
+                "description": "A float between 0 and 100 setting the centile to calculate",
+                "example": 99.9,
+            },
         )
     }
     schema = fields.List(fields.Integer)
diff --git a/openflexure_microscope/api/default_extensions/scan.py b/openflexure_microscope/api/default_extensions/scan.py
index 8f2ff80a..794230ac 100644
--- a/openflexure_microscope/api/default_extensions/scan.py
+++ b/openflexure_microscope/api/default_extensions/scan.py
@@ -578,17 +578,17 @@ class ScanExtension(BaseExtension):
 
 
 class TileScanArgs(FullCaptureArgs):
-    namemode = fields.String(load_default="coordinates", example="coordinates")
+    namemode = fields.String(load_default="coordinates", metadata={"example": "coordinates"})
     grid = fields.List(
         fields.Integer(validate=marshmallow.validate.Range(min=1)),
         load_default=[3, 3, 3],
-        example=[3, 3, 3],
+        metadata={"example": [3, 3, 3]},
     )
     style = fields.String(load_default="raster")
     autofocus_dz = fields.Integer(load_default=50)
     fast_autofocus = fields.Boolean(load_default=False)
     stride_size = fields.List(
-        fields.Integer, load_default=[2000, 1500, 100], example=[2000, 1500, 100]
+        fields.Integer, load_default=[2000, 1500, 100], metadata={"example":[2000, 1500, 100]}
     )
     detect_empty_fields_and_skip_autofocus = fields.Boolean(load_default=False)
 
diff --git a/openflexure_microscope/api/dev_extensions/tools.py b/openflexure_microscope/api/dev_extensions/tools.py
index b7959d2b..a19cdc71 100644
--- a/openflexure_microscope/api/dev_extensions/tools.py
+++ b/openflexure_microscope/api/dev_extensions/tools.py
@@ -24,7 +24,7 @@ class RaiseException(ActionView):
 
 class SleepFor(ActionView):
     schema = {"TimeAsleep": fields.Float()}
-    args = {"time": fields.Float(metadata={"description": "Time to sleep, in seconds"}, example=0.5)}
+    args = {"time": fields.Float(metadata={"description": "Time to sleep, in seconds", "example": 0.5})}
 
     def post(self, args):
         sleep_time: int = args.get("time", 0)
diff --git a/openflexure_microscope/api/v2/views/actions/camera.py b/openflexure_microscope/api/v2/views/actions/camera.py
index 10f1286d..c73cbac1 100644
--- a/openflexure_microscope/api/v2/views/actions/camera.py
+++ b/openflexure_microscope/api/v2/views/actions/camera.py
@@ -10,8 +10,8 @@ from openflexure_microscope.api.v2.views.captures import CaptureSchema
 
 
 class CaptureResizeSchema(Schema):
-    width = fields.Integer(example=640, required=True)
-    height = fields.Integer(example=480, required=True)
+    width = fields.Integer(metadata={"example":640}, required=True)
+    height = fields.Integer(metadata={"example": 480}, required=True)
 
 
 class BasicCaptureArgs(Schema):
@@ -23,10 +23,10 @@ class BasicCaptureArgs(Schema):
 
 
 class FullCaptureArgs(BasicCaptureArgs):
-    filename = fields.String(example="MyFileName")
+    filename = fields.String(metadata={"example": "MyFileName"})
     temporary = fields.Boolean(load_default=False, metadata={"description": "Delete capture on shutdown"})
-    annotations = fields.Dict(load_default={}, example={"Client": "SwaggerUI"})
-    tags = fields.List(fields.String, load_default=[], example=["docs"])
+    annotations = fields.Dict(load_default={}, metadata={"example": {"Client": "SwaggerUI"}})
+    tags = fields.List(fields.String, load_default=[], metadata={"example": ["docs"]})
 
 
 class CaptureAPI(ActionView):
@@ -113,7 +113,7 @@ class GPUPreviewStartAPI(ActionView):
     in the format ``[x, y, width, height]``.
     """
 
-    args = {"window": fields.List(fields.Integer, load_default=[], example=[0, 0, 640, 480])}
+    args = {"window": fields.List(fields.Integer, load_default=[], metadata={"example": [0, 0, 640, 480]})}
 
     def post(self, args):
         """
diff --git a/openflexure_microscope/api/v2/views/actions/stage.py b/openflexure_microscope/api/v2/views/actions/stage.py
index 1488ea2e..d5e79ba1 100644
--- a/openflexure_microscope/api/v2/views/actions/stage.py
+++ b/openflexure_microscope/api/v2/views/actions/stage.py
@@ -7,11 +7,11 @@ from labthings.views import ActionView
 class MoveStageAPI(ActionView):
     args = {
         "absolute": fields.Boolean(
-            load_default=False, example=False, metadata={"description": "Move to an absolute position"}
+            load_default=False, metadata={"description": "Move to an absolute position", "example": False}
         ),
-        "x": fields.Int(load_default=None, example=100, allow_none=False),
-        "y": fields.Int(load_default=None, example=100, allow_none=False),
-        "z": fields.Int(load_default=None, example=20, allow_none=False),
+        "x": fields.Int(load_default=None, metadata={"example": 100}, allow_none=False),
+        "y": fields.Int(load_default=None, metadata={"example": 100}, allow_none=False),
+        "z": fields.Int(load_default=None, metadata={"example": 20}, allow_none=False),
     }
 
     def post(self, args):
diff --git a/openflexure_microscope/api/v2/views/captures.py b/openflexure_microscope/api/v2/views/captures.py
index 4935bb46..64fe536b 100644
--- a/openflexure_microscope/api/v2/views/captures.py
+++ b/openflexure_microscope/api/v2/views/captures.py
@@ -24,7 +24,7 @@ class InstrumentSchema(Schema):
 
 class ImageSchema(Schema):
     id = fields.UUID()
-    time = fields.String(format="date")
+    time = fields.String(metadata={"format": "date"})
     format = fields.String()
     name = fields.String()
     tags = fields.List(fields.String())
diff --git a/openflexure_microscope/api/v2/views/stage.py b/openflexure_microscope/api/v2/views/stage.py
index 9db97aed..66bd8f4f 100644
--- a/openflexure_microscope/api/v2/views/stage.py
+++ b/openflexure_microscope/api/v2/views/stage.py
@@ -8,9 +8,8 @@ class StageTypeProperty(PropertyView):
 
     schema = fields.String(
         load_default=None,
-        example="SangaStage",
         validate=validate.OneOf(["SangaStage", "SangaDeltaStage"]),
-        metadata={"description": "The translation stage geometry"},
+        metadata={"description": "The translation stage geometry", "example": "SangaStage",},
         allow_none=False,
     )
 

From 106b50d333f969197056c92b100544ab66c6109c Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Tue, 9 Aug 2022 13:17:45 +0100
Subject: [PATCH 10/25] Format fixes from black

---
 .../example_extension/03_marshaling_data.py   |  6 ++-
 .../example_extension/04_properties.py        |  6 ++-
 .../example_extension/05_actions.py           |  6 ++-
 .../example_extension/06_tasks_locks.py       |  3 +-
 .../extensions/example_extension/07_ev_gui.py |  3 +-
 .../api/default_extensions/autofocus.py       | 10 ++--
 .../camera_stage_mapping.py                   | 47 +++++++++++++++----
 .../picamera_autocalibrate/extension.py       | 11 ++---
 .../api/default_extensions/scan.py            |  8 +++-
 .../api/dev_extensions/tools.py               |  6 ++-
 .../api/v2/views/actions/camera.py            | 19 ++++++--
 .../api/v2/views/actions/stage.py             |  3 +-
 openflexure_microscope/api/v2/views/stage.py  |  5 +-
 13 files changed, 101 insertions(+), 32 deletions(-)

diff --git a/docs/source/extensions/example_extension/03_marshaling_data.py b/docs/source/extensions/example_extension/03_marshaling_data.py
index cca86fd6..6769874f 100644
--- a/docs/source/extensions/example_extension/03_marshaling_data.py
+++ b/docs/source/extensions/example_extension/03_marshaling_data.py
@@ -49,7 +49,11 @@ class ExampleRenameView(View):
     # Format our returned object using MicroscopeIdentifySchema
     schema = MicroscopeIdentifySchema()
     # Expect a request parameter called "name", which is a string. Pass to argument "args".
-    args = {"name": fields.String(required=True, metadata={"example": "My Example Microscope"})}
+    args = {
+        "name": fields.String(
+            required=True, metadata={"example": "My Example Microscope"}
+        )
+    }
 
     def post(self, args):
         # Look for our "name" parameter in the request arguments
diff --git a/docs/source/extensions/example_extension/04_properties.py b/docs/source/extensions/example_extension/04_properties.py
index 7d7a4cc9..1250b084 100644
--- a/docs/source/extensions/example_extension/04_properties.py
+++ b/docs/source/extensions/example_extension/04_properties.py
@@ -53,7 +53,11 @@ class ExampleIdentifyView(PropertyView):
 # We can use a single schema as the input and output will be formatted identically
 # Eg. We always expect a "name" string argument, and always return a "name" string attribute
 class ExampleRenameView(PropertyView):
-    schema = {"name": fields.String(required=True, metadata={"example": "My Example Microscope"})}
+    schema = {
+        "name": fields.String(
+            required=True, metadata={"example": "My Example Microscope"}
+        )
+    }
 
     def get(self):
         """
diff --git a/docs/source/extensions/example_extension/05_actions.py b/docs/source/extensions/example_extension/05_actions.py
index ca5d6980..e1551efd 100644
--- a/docs/source/extensions/example_extension/05_actions.py
+++ b/docs/source/extensions/example_extension/05_actions.py
@@ -56,7 +56,11 @@ class ExampleIdentifyView(PropertyView):
 # We can use a single schema as the input and output will be formatted identically
 # Eg. We always expect a "name" string argument, and always return a "name" string attribute
 class ExampleRenameView(PropertyView):
-    schema = {"name": fields.String(required=True, metadata={"example": "My Example Microscope"})}
+    schema = {
+        "name": fields.String(
+            required=True, metadata={"example": "My Example Microscope"}
+        )
+    }
 
     def get(self):
         """
diff --git a/docs/source/extensions/example_extension/06_tasks_locks.py b/docs/source/extensions/example_extension/06_tasks_locks.py
index 6c23e8ab..25fb803f 100644
--- a/docs/source/extensions/example_extension/06_tasks_locks.py
+++ b/docs/source/extensions/example_extension/06_tasks_locks.py
@@ -69,7 +69,8 @@ class TimelapseAPIView(ActionView):
             required=True, metadata={"example": 5, "description": "Number of images"}
         ),
         "t_between": fields.Number(
-            load_default=1, metadata={"example": 1, "description": "Time (seconds) between images"}
+            load_default=1,
+            metadata={"example": 1, "description": "Time (seconds) between images"},
         ),
     }
 
diff --git a/docs/source/extensions/example_extension/07_ev_gui.py b/docs/source/extensions/example_extension/07_ev_gui.py
index 12b2ce09..3f5f3196 100644
--- a/docs/source/extensions/example_extension/07_ev_gui.py
+++ b/docs/source/extensions/example_extension/07_ev_gui.py
@@ -102,7 +102,8 @@ class TimelapseAPIView(ActionView):
             required=True, metadata={"example": 5, "description": "Number of images"}
         ),
         "t_between": fields.Number(
-            load_default=1, metadata={"example": 1, "description": "Time (seconds) between images"}
+            load_default=1,
+            metadata={"example": 1, "description": "Time (seconds) between images"},
         ),
     }
 
diff --git a/openflexure_microscope/api/default_extensions/autofocus.py b/openflexure_microscope/api/default_extensions/autofocus.py
index f7eeb394..045a7878 100644
--- a/openflexure_microscope/api/default_extensions/autofocus.py
+++ b/openflexure_microscope/api/default_extensions/autofocus.py
@@ -352,7 +352,7 @@ class AutofocusExtension(BaseExtension):
                 metadata={
                     "description": "An ascending list of relative z positions",
                     "example": [int(x) for x in np.linspace(-300, 300, 7)],
-                }
+                },
             )
         }
     )
@@ -412,7 +412,9 @@ class AutofocusExtension(BaseExtension):
 
     @extension_action(
         args={
-            "dz": fields.Int(required=True, metadata={"description": "The relative Z move to make"})
+            "dz": fields.Int(
+                required=True, metadata={"description": "The relative Z move to make"}
+            )
         }
     )
     def move_and_measure(
@@ -579,7 +581,9 @@ class AutofocusExtension(BaseExtension):
             ),
             "initial_move_up": fields.Bool(
                 load_default=True,
-                metadata={"description": "Set to Flase to disable the initial move upwards"},
+                metadata={
+                    "description": "Set to Flase to disable the initial move upwards"
+                },
             ),
             "backlash": fields.Int(
                 load_default=25,
diff --git a/openflexure_microscope/api/default_extensions/camera_stage_mapping.py b/openflexure_microscope/api/default_extensions/camera_stage_mapping.py
index 53b3789d..532b431f 100644
--- a/openflexure_microscope/api/default_extensions/camera_stage_mapping.py
+++ b/openflexure_microscope/api/default_extensions/camera_stage_mapping.py
@@ -279,7 +279,11 @@ class CSMExtension(BaseExtension):
 
 
 class Calibrate1DView(ActionView):
-    args = {"direction": fields.List(fields.Float(), required=True, metadata={"example": [1, 0, 0]})}
+    args = {
+        "direction": fields.List(
+            fields.Float(), required=True, metadata={"example": [1, 0, 0]}
+        )
+    }
 
     def post(self, args):
         """Calibrate one axis of the microscope stage against the camera."""
@@ -298,10 +302,18 @@ class CalibrateXYView(ActionView):
 class MoveInImageCoordinatesView(ActionView):
     args = {
         "x": fields.Float(
-            metadata={"description": "The number of pixels to move in X", "example": 100,}, required=True,
+            metadata={
+                "description": "The number of pixels to move in X",
+                "example": 100,
+            },
+            required=True,
         ),
         "y": fields.Float(
-            metadata={"description": "The number of pixels to move in Y", "example": 100,}, required=True,
+            metadata={
+                "description": "The number of pixels to move in Y",
+                "example": 100,
+            },
+            required=True,
         ),
     }
 
@@ -316,10 +328,18 @@ class MoveInImageCoordinatesView(ActionView):
 class ClosedLoopMoveInImageCoordinatesView(ActionView):
     args = {
         "x": fields.Float(
-            metadata={"description": "The number of pixels to move in X", "example": 100,}, required=True,
+            metadata={
+                "description": "The number of pixels to move in X",
+                "example": 100,
+            },
+            required=True,
         ),
         "y": fields.Float(
-            metadata={"description": "The number of pixels to move in Y", "example": 100,}, required=True,
+            metadata={
+                "description": "The number of pixels to move in Y",
+                "example": 100,
+            },
+            required=True,
         ),
     }
 
@@ -336,13 +356,24 @@ class ClosedLoopMoveInImageCoordinatesView(ActionView):
 class TestClosedLoopSpiralScanView(ActionView):
     args = {
         "x_step": fields.Float(
-            metadata={"description": "The number of pixels to move in X", "example": 100,}, required=True,
+            metadata={
+                "description": "The number of pixels to move in X",
+                "example": 100,
+            },
+            required=True,
         ),
         "y_step": fields.Float(
-            metadata={"description": "The number of pixels to move in Y", "example": 100,}, required=True,
+            metadata={
+                "description": "The number of pixels to move in Y",
+                "example": 100,
+            },
+            required=True,
         ),
         "N": fields.Int(
-            metadata={"description": "The number of rings in the spiral scan", "example": 100,},
+            metadata={
+                "description": "The number of rings in the spiral scan",
+                "example": 100,
+            },
             required=True,
         ),
     }
diff --git a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
index 642c5a60..0049a83d 100644
--- a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
+++ b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
@@ -195,10 +195,11 @@ class AutoExposureFromRawView(ActionView):
             },
         ),
         "max_iterations": fields.Int(
-            load_default=20,metadata={
+            load_default=20,
+            metadata={
                 "description": (
                     "The number of adjustments to the camera's settings to make before giving up."
-                ),
+                )
             },
         ),
         "tolerance": fields.Float(
@@ -220,9 +221,7 @@ class AutoExposureFromRawView(ActionView):
 
 
 class AutoWhiteBalanceFromRawView(ActionView):
-    args = {
-        "percentile": percentile_field,
-    }
+    args = {"percentile": percentile_field}
 
     def post(self, args):
         with find_picamera() as (picamera, _, _):
@@ -235,7 +234,7 @@ class GetRawChannelPercentilesView(ActionView):
             metadata={
                 "description": "A float between 0 and 100 setting the centile to calculate",
                 "example": 99.9,
-            },
+            }
         )
     }
     schema = fields.List(fields.Integer)
diff --git a/openflexure_microscope/api/default_extensions/scan.py b/openflexure_microscope/api/default_extensions/scan.py
index 794230ac..d3f83a50 100644
--- a/openflexure_microscope/api/default_extensions/scan.py
+++ b/openflexure_microscope/api/default_extensions/scan.py
@@ -578,7 +578,9 @@ class ScanExtension(BaseExtension):
 
 
 class TileScanArgs(FullCaptureArgs):
-    namemode = fields.String(load_default="coordinates", metadata={"example": "coordinates"})
+    namemode = fields.String(
+        load_default="coordinates", metadata={"example": "coordinates"}
+    )
     grid = fields.List(
         fields.Integer(validate=marshmallow.validate.Range(min=1)),
         load_default=[3, 3, 3],
@@ -588,7 +590,9 @@ class TileScanArgs(FullCaptureArgs):
     autofocus_dz = fields.Integer(load_default=50)
     fast_autofocus = fields.Boolean(load_default=False)
     stride_size = fields.List(
-        fields.Integer, load_default=[2000, 1500, 100], metadata={"example":[2000, 1500, 100]}
+        fields.Integer,
+        load_default=[2000, 1500, 100],
+        metadata={"example": [2000, 1500, 100]},
     )
     detect_empty_fields_and_skip_autofocus = fields.Boolean(load_default=False)
 
diff --git a/openflexure_microscope/api/dev_extensions/tools.py b/openflexure_microscope/api/dev_extensions/tools.py
index a19cdc71..954b67e1 100644
--- a/openflexure_microscope/api/dev_extensions/tools.py
+++ b/openflexure_microscope/api/dev_extensions/tools.py
@@ -24,7 +24,11 @@ class RaiseException(ActionView):
 
 class SleepFor(ActionView):
     schema = {"TimeAsleep": fields.Float()}
-    args = {"time": fields.Float(metadata={"description": "Time to sleep, in seconds", "example": 0.5})}
+    args = {
+        "time": fields.Float(
+            metadata={"description": "Time to sleep, in seconds", "example": 0.5}
+        )
+    }
 
     def post(self, args):
         sleep_time: int = args.get("time", 0)
diff --git a/openflexure_microscope/api/v2/views/actions/camera.py b/openflexure_microscope/api/v2/views/actions/camera.py
index c73cbac1..c649d601 100644
--- a/openflexure_microscope/api/v2/views/actions/camera.py
+++ b/openflexure_microscope/api/v2/views/actions/camera.py
@@ -10,22 +10,27 @@ from openflexure_microscope.api.v2.views.captures import CaptureSchema
 
 
 class CaptureResizeSchema(Schema):
-    width = fields.Integer(metadata={"example":640}, required=True)
+    width = fields.Integer(metadata={"example": 640}, required=True)
     height = fields.Integer(metadata={"example": 480}, required=True)
 
 
 class BasicCaptureArgs(Schema):
     use_video_port = fields.Boolean(load_default=False)
     bayer = fields.Boolean(
-        load_default=False, metadata={"description": "Include raw bayer data in capture"}
+        load_default=False,
+        metadata={"description": "Include raw bayer data in capture"},
     )
     resize = fields.Nested(CaptureResizeSchema(), required=False)
 
 
 class FullCaptureArgs(BasicCaptureArgs):
     filename = fields.String(metadata={"example": "MyFileName"})
-    temporary = fields.Boolean(load_default=False, metadata={"description": "Delete capture on shutdown"})
-    annotations = fields.Dict(load_default={}, metadata={"example": {"Client": "SwaggerUI"}})
+    temporary = fields.Boolean(
+        load_default=False, metadata={"description": "Delete capture on shutdown"}
+    )
+    annotations = fields.Dict(
+        load_default={}, metadata={"example": {"Client": "SwaggerUI"}}
+    )
     tags = fields.List(fields.String, load_default=[], metadata={"example": ["docs"]})
 
 
@@ -113,7 +118,11 @@ class GPUPreviewStartAPI(ActionView):
     in the format ``[x, y, width, height]``.
     """
 
-    args = {"window": fields.List(fields.Integer, load_default=[], metadata={"example": [0, 0, 640, 480]})}
+    args = {
+        "window": fields.List(
+            fields.Integer, load_default=[], metadata={"example": [0, 0, 640, 480]}
+        )
+    }
 
     def post(self, args):
         """
diff --git a/openflexure_microscope/api/v2/views/actions/stage.py b/openflexure_microscope/api/v2/views/actions/stage.py
index d5e79ba1..d13774ab 100644
--- a/openflexure_microscope/api/v2/views/actions/stage.py
+++ b/openflexure_microscope/api/v2/views/actions/stage.py
@@ -7,7 +7,8 @@ from labthings.views import ActionView
 class MoveStageAPI(ActionView):
     args = {
         "absolute": fields.Boolean(
-            load_default=False, metadata={"description": "Move to an absolute position", "example": False}
+            load_default=False,
+            metadata={"description": "Move to an absolute position", "example": False},
         ),
         "x": fields.Int(load_default=None, metadata={"example": 100}, allow_none=False),
         "y": fields.Int(load_default=None, metadata={"example": 100}, allow_none=False),
diff --git a/openflexure_microscope/api/v2/views/stage.py b/openflexure_microscope/api/v2/views/stage.py
index 66bd8f4f..bcfec3a9 100644
--- a/openflexure_microscope/api/v2/views/stage.py
+++ b/openflexure_microscope/api/v2/views/stage.py
@@ -9,7 +9,10 @@ class StageTypeProperty(PropertyView):
     schema = fields.String(
         load_default=None,
         validate=validate.OneOf(["SangaStage", "SangaDeltaStage"]),
-        metadata={"description": "The translation stage geometry", "example": "SangaStage",},
+        metadata={
+            "description": "The translation stage geometry",
+            "example": "SangaStage",
+        },
         allow_none=False,
     )
 

From 80d026d7788e9efa4e59f582de264380ca651fd6 Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Tue, 9 Aug 2022 13:18:07 +0100
Subject: [PATCH 11/25] Downgrade markupsafe so jinja2 still works

---
 Pipfile.lock | 294 +++++++++++++++++++++++++++++++--------------------
 setup.py     |   1 +
 2 files changed, 178 insertions(+), 117 deletions(-)

diff --git a/Pipfile.lock b/Pipfile.lock
index 451728eb..3dd42ee3 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -30,7 +30,7 @@
                 "sha256:6613dbc39f41cd58942a697f11c8762ba18422bd173fe0bdfc1535b83d3f84f0",
                 "sha256:79029486d36a0d7f3c659dbf6ae50a91fbed0c22dcd5376f592e076c130bc7f9"
             ],
-            "markers": "python_version >= '3.6'",
+            "markers": "python_full_version >= '3.6.0'",
             "version": "==4.7.1"
         },
         "apispec-webframeworks": {
@@ -38,7 +38,7 @@
                 "sha256:0db35b267914b3f8c562aca0261957dbcb4176f255eacc22520277010818dcf3",
                 "sha256:482c563abbcc2a261439476cb3f1a7c7284cc997c322c574d48c111643e9c04e"
             ],
-            "markers": "python_version >= '3.6'",
+            "markers": "python_full_version >= '3.6.0'",
             "version": "==0.5.2"
         },
         "atomicwrites": {
@@ -63,7 +63,7 @@
                 "sha256:02a409bd2cb193b20d9eb015ca31400bd3e1721ec5d702e1b96de54608ff5a8f",
                 "sha256:d39c3afebb59ec865fb1247dfd951d7090c159ab0cf3e4291e0869d3be33776c"
             ],
-            "markers": "python_version >= '3.6' and python_version < '4'",
+            "markers": "python_version < '4' and python_full_version >= '3.6.0'",
             "version": "==0.1.4"
         },
         "certifi": {
@@ -72,7 +72,7 @@
                 "sha256:cbd4c168c00e6c24b3fdf4e9f34c7c459810173b3a3cb9ab14a219f7549d4263",
                 "sha256:fe86415d55e84719d75f8b69414f6438ac3547d2078ab91b67e779ef69378412"
             ],
-            "markers": "python_version >= '3.6'",
+            "markers": "python_full_version >= '3.6.0'",
             "version": "==2022.6.15"
         },
         "chardet": {
@@ -89,7 +89,7 @@
                 "sha256:5189b6f22b01957427f35b6a08d9a0bc45b46d3788ef5a92e978433c7a35f8a5",
                 "sha256:575e708016ff3a5e3681541cb9d79312c416835686d054a23accb873b254f413"
             ],
-            "markers": "python_version >= '3.6'",
+            "markers": "python_full_version >= '3.6.0'",
             "version": "==2.1.0"
         },
         "click": {
@@ -270,56 +270,85 @@
                 "sha256:83e5a8849d556b8e6c3138b1284148095f4e3ed983dad15096262c7b31c5947e",
                 "sha256:e01842fc6e38594c3ea787911d30ebbc70bc67ed6f58544b38ab4572d46eb60e"
             ],
-            "markers": "python_version >= '3.6' and python_version < '4'",
+            "markers": "python_version < '4' and python_full_version >= '3.6.0'",
             "version": "==1.3.2"
         },
         "markupsafe": {
             "hashes": [
-                "sha256:0212a68688482dc52b2d45013df70d169f542b7394fc744c02a57374a4207003",
-                "sha256:04ecce2077c9c531334c847b604835e8e909f73d1fe596ceae30c8046ca90686",
-                "sha256:089cf3dbf0cd6c100f02945abeb18484bd1ee57a079aefd52cffd17fba910b88",
-                "sha256:10c1bfff05d95783da83491be968e8fe789263689c02724e0c691933c52994f5",
-                "sha256:33b74d289bd2f5e527beadcaa3f401e0df0a89927c1559c8566c066fa4248ab7",
-                "sha256:3799351e2336dc91ea70b034983ee71cf2f9533cdff7c14c90ea126bfd95d65a",
-                "sha256:3ce11ee3f23f79dbd06fb3d63e2f6af7b12db1d46932fe7bd8afa259a5996603",
-                "sha256:421be9fbf0ffe9ffd7a378aafebbf6f4602d564d34be190fc19a193232fd12b1",
-                "sha256:43093fb83d8343aac0b1baa75516da6092f58f41200907ef92448ecab8825135",
-                "sha256:46d00d6cfecdde84d40e572d63735ef81423ad31184100411e6e3388d405e247",
-                "sha256:4a33dea2b688b3190ee12bd7cfa29d39c9ed176bda40bfa11099a3ce5d3a7ac6",
-                "sha256:4b9fe39a2ccc108a4accc2676e77da025ce383c108593d65cc909add5c3bd601",
-                "sha256:56442863ed2b06d19c37f94d999035e15ee982988920e12a5b4ba29b62ad1f77",
-                "sha256:635983650c67c69118fe07c52f799b789d17edb9051777476b646278602d47dd",
-                "sha256:671cd1187ed5e62818414afe79ed29da836dde67166a9fac6d435873c44fdd02",
-                "sha256:694deca8d702d5db21ec83983ce0bb4b26a578e71fbdbd4fdcd387daa90e4d5e",
-                "sha256:6a074d34ee7a5ce3effbc526b7083ec9731bb3cbf921bbe1d3005d4d2bdb3a63",
-                "sha256:6d0072fea50feec76a4c418096652f2c3238eaa014b2f94aeb1d56a66b41403f",
-                "sha256:6fbf47b5d3728c6aea2abb0589b5d30459e369baa772e0f37a0320185e87c980",
-                "sha256:7f91197cc9e48f989d12e4e6fbc46495c446636dfc81b9ccf50bb0ec74b91d4b",
-                "sha256:86b1f75c4e7c2ac2ccdaec2b9022845dbb81880ca318bb7a0a01fbf7813e3812",
-                "sha256:8dc1c72a69aa7e082593c4a203dcf94ddb74bb5c8a731e4e1eb68d031e8498ff",
-                "sha256:8e3dcf21f367459434c18e71b2a9532d96547aef8a871872a5bd69a715c15f96",
-                "sha256:8e576a51ad59e4bfaac456023a78f6b5e6e7651dcd383bcc3e18d06f9b55d6d1",
-                "sha256:96e37a3dc86e80bf81758c152fe66dbf60ed5eca3d26305edf01892257049925",
-                "sha256:97a68e6ada378df82bc9f16b800ab77cbf4b2fada0081794318520138c088e4a",
-                "sha256:99a2a507ed3ac881b975a2976d59f38c19386d128e7a9a18b7df6fff1fd4c1d6",
-                "sha256:a49907dd8420c5685cfa064a1335b6754b74541bbb3706c259c02ed65b644b3e",
-                "sha256:b09bf97215625a311f669476f44b8b318b075847b49316d3e28c08e41a7a573f",
-                "sha256:b7bd98b796e2b6553da7225aeb61f447f80a1ca64f41d83612e6139ca5213aa4",
-                "sha256:b87db4360013327109564f0e591bd2a3b318547bcef31b468a92ee504d07ae4f",
-                "sha256:bcb3ed405ed3222f9904899563d6fc492ff75cce56cba05e32eff40e6acbeaa3",
-                "sha256:d4306c36ca495956b6d568d276ac11fdd9c30a36f1b6eb928070dc5360b22e1c",
-                "sha256:d5ee4f386140395a2c818d149221149c54849dfcfcb9f1debfe07a8b8bd63f9a",
-                "sha256:dda30ba7e87fbbb7eab1ec9f58678558fd9a6b8b853530e176eabd064da81417",
-                "sha256:e04e26803c9c3851c931eac40c695602c6295b8d432cbe78609649ad9bd2da8a",
-                "sha256:e1c0b87e09fa55a220f058d1d49d3fb8df88fbfab58558f1198e08c1e1de842a",
-                "sha256:e72591e9ecd94d7feb70c1cbd7be7b3ebea3f548870aa91e2732960fa4d57a37",
-                "sha256:e8c843bbcda3a2f1e3c2ab25913c80a3c5376cd00c6e8c4a86a89a28c8dc5452",
-                "sha256:efc1913fd2ca4f334418481c7e595c00aad186563bbc1ec76067848c7ca0a933",
-                "sha256:f121a1420d4e173a5d96e47e9a0c0dcff965afdf1626d28de1460815f7c4ee7a",
-                "sha256:fc7b548b17d238737688817ab67deebb30e8073c95749d55538ed473130ec0c7"
+                "sha256:01a9b8ea66f1658938f65b93a85ebe8bc016e6769611be228d797c9d998dd298",
+                "sha256:023cb26ec21ece8dc3907c0e8320058b2e0cb3c55cf9564da612bc325bed5e64",
+                "sha256:0446679737af14f45767963a1a9ef7620189912317d095f2d9ffa183a4d25d2b",
+                "sha256:04635854b943835a6ea959e948d19dcd311762c5c0c6e1f0e16ee57022669194",
+                "sha256:060b790af48b3d1cb6776a1e8956fb41106c6befaca717181c41a1728147dc73",
+                "sha256:0717a7390a68be14b8c793ba258e075c6f4ca819f15edfc2a3a027c823718567",
+                "sha256:0955295dd5eec6cb6cc2fe1698f4c6d84af2e92de33fbcac4111913cd100a6ff",
+                "sha256:0d4b31cc67ab36e3392bbf3862cfbadac3db12bdd8b02a2731f509ed5b829724",
+                "sha256:10f82115e21dc0dfec9ab5c0223652f7197feb168c940f3ef61563fc2d6beb74",
+                "sha256:168cd0a3642de83558a5153c8bd34f175a9a6e7f6dc6384b9655d2697312a646",
+                "sha256:1d609f577dc6e1aa17d746f8bd3c31aa4d258f4070d61b2aa5c4166c1539de35",
+                "sha256:1f2ade76b9903f39aa442b4aadd2177decb66525062db244b35d71d0ee8599b6",
+                "sha256:20dca64a3ef2d6e4d5d615a3fd418ad3bde77a47ec8a23d984a12b5b4c74491a",
+                "sha256:2a7d351cbd8cfeb19ca00de495e224dea7e7d919659c2841bbb7f420ad03e2d6",
+                "sha256:2d7d807855b419fc2ed3e631034685db6079889a1f01d5d9dac950f764da3dad",
+                "sha256:2ef54abee730b502252bcdf31b10dacb0a416229b72c18b19e24a4509f273d26",
+                "sha256:36bc903cbb393720fad60fc28c10de6acf10dc6cc883f3e24ee4012371399a38",
+                "sha256:37205cac2a79194e3750b0af2a5720d95f786a55ce7df90c3af697bfa100eaac",
+                "sha256:3c112550557578c26af18a1ccc9e090bfe03832ae994343cfdacd287db6a6ae7",
+                "sha256:3dd007d54ee88b46be476e293f48c85048603f5f516008bee124ddd891398ed6",
+                "sha256:4296f2b1ce8c86a6aea78613c34bb1a672ea0e3de9c6ba08a960efe0b0a09047",
+                "sha256:47ab1e7b91c098ab893b828deafa1203de86d0bc6ab587b160f78fe6c4011f75",
+                "sha256:49e3ceeabbfb9d66c3aef5af3a60cc43b85c33df25ce03d0031a608b0a8b2e3f",
+                "sha256:4dc8f9fb58f7364b63fd9f85013b780ef83c11857ae79f2feda41e270468dd9b",
+                "sha256:4efca8f86c54b22348a5467704e3fec767b2db12fc39c6d963168ab1d3fc9135",
+                "sha256:53edb4da6925ad13c07b6d26c2a852bd81e364f95301c66e930ab2aef5b5ddd8",
+                "sha256:5855f8438a7d1d458206a2466bf82b0f104a3724bf96a1c781ab731e4201731a",
+                "sha256:594c67807fb16238b30c44bdf74f36c02cdf22d1c8cda91ef8a0ed8dabf5620a",
+                "sha256:5b6d930f030f8ed98e3e6c98ffa0652bdb82601e7a016ec2ab5d7ff23baa78d1",
+                "sha256:5bb28c636d87e840583ee3adeb78172efc47c8b26127267f54a9c0ec251d41a9",
+                "sha256:60bf42e36abfaf9aff1f50f52644b336d4f0a3fd6d8a60ca0d054ac9f713a864",
+                "sha256:611d1ad9a4288cf3e3c16014564df047fe08410e628f89805e475368bd304914",
+                "sha256:6300b8454aa6930a24b9618fbb54b5a68135092bc666f7b06901f897fa5c2fee",
+                "sha256:63f3268ba69ace99cab4e3e3b5840b03340efed0948ab8f78d2fd87ee5442a4f",
+                "sha256:6557b31b5e2c9ddf0de32a691f2312a32f77cd7681d8af66c2692efdbef84c18",
+                "sha256:693ce3f9e70a6cf7d2fb9e6c9d8b204b6b39897a2c4a1aa65728d5ac97dcc1d8",
+                "sha256:6a7fae0dd14cf60ad5ff42baa2e95727c3d81ded453457771d02b7d2b3f9c0c2",
+                "sha256:6c4ca60fa24e85fe25b912b01e62cb969d69a23a5d5867682dd3e80b5b02581d",
+                "sha256:6fcf051089389abe060c9cd7caa212c707e58153afa2c649f00346ce6d260f1b",
+                "sha256:7d91275b0245b1da4d4cfa07e0faedd5b0812efc15b702576d103293e252af1b",
+                "sha256:89c687013cb1cd489a0f0ac24febe8c7a666e6e221b783e53ac50ebf68e45d86",
+                "sha256:8d206346619592c6200148b01a2142798c989edcb9c896f9ac9722a99d4e77e6",
+                "sha256:905fec760bd2fa1388bb5b489ee8ee5f7291d692638ea5f67982d968366bef9f",
+                "sha256:97383d78eb34da7e1fa37dd273c20ad4320929af65d156e35a5e2d89566d9dfb",
+                "sha256:984d76483eb32f1bcb536dc27e4ad56bba4baa70be32fa87152832cdd9db0833",
+                "sha256:99df47edb6bda1249d3e80fdabb1dab8c08ef3975f69aed437cb69d0a5de1e28",
+                "sha256:9f02365d4e99430a12647f09b6cc8bab61a6564363f313126f775eb4f6ef798e",
+                "sha256:a30e67a65b53ea0a5e62fe23682cfe22712e01f453b95233b25502f7c61cb415",
+                "sha256:ab3ef638ace319fa26553db0624c4699e31a28bb2a835c5faca8f8acf6a5a902",
+                "sha256:aca6377c0cb8a8253e493c6b451565ac77e98c2951c45f913e0b52facdcff83f",
+                "sha256:add36cb2dbb8b736611303cd3bfcee00afd96471b09cda130da3581cbdc56a6d",
+                "sha256:b2b16984860d962a9f7f42c8f84ecdb74993b803a705309bb0acea7f032e37e7",
+                "sha256:b2f4bf27480f5e5e8ce285a8c8fd176c0b03e93dcc6646477d4630e83440c6a9",
+                "sha256:b7f2d075102dc8c794cbde1947378051c4e5180d52d276987b8d28a3bd58c17d",
+                "sha256:baa1a4e8f868845af802979fcdbf0bb11f94f1cb7ced4c4b8a351bb60d108145",
+                "sha256:be98f628055368795d818ebf93da628541e10b75b41c559fdf36d104c5787066",
+                "sha256:bf5d821ffabf0ef3533c39c518f3357b171a1651c1ff6827325e4489b0e46c3c",
+                "sha256:c47adbc92fc1bb2b3274c4b3a43ae0e4573d9fbff4f54cd484555edbf030baf1",
+                "sha256:cdfba22ea2f0029c9261a4bd07e830a8da012291fbe44dc794e488b6c9bb353a",
+                "sha256:d6c7ebd4e944c85e2c3421e612a7057a2f48d478d79e61800d81468a8d842207",
+                "sha256:d7f9850398e85aba693bb640262d3611788b1f29a79f0c93c565694658f4071f",
+                "sha256:d8446c54dc28c01e5a2dbac5a25f071f6653e6e40f3a8818e8b45d790fe6ef53",
+                "sha256:deb993cacb280823246a026e3b2d81c493c53de6acfd5e6bfe31ab3402bb37dd",
+                "sha256:e0f138900af21926a02425cf736db95be9f4af72ba1bb21453432a07f6082134",
+                "sha256:e9936f0b261d4df76ad22f8fee3ae83b60d7c3e871292cd42f40b81b70afae85",
+                "sha256:f0567c4dc99f264f49fe27da5f735f414c4e7e7dd850cfd8e69f0862d7c74ea9",
+                "sha256:f5653a225f31e113b152e56f154ccbe59eeb1c7487b39b9d9f9cdb58e6c79dc5",
+                "sha256:f826e31d18b516f653fe296d967d700fddad5901ae07c622bb3705955e1faa94",
+                "sha256:f8ba0e8349a38d3001fae7eadded3f6606f0da5d748ee53cc1dab1d6527b9509",
+                "sha256:f9081981fe268bd86831e5c75f7de206ef275defcb82bc70740ae6dc507aee51",
+                "sha256:fa130dd50c57d53368c9d59395cb5526eda596d3ffe36666cd81a44d56e48872"
             ],
-            "markers": "python_version >= '3.7'",
-            "version": "==2.1.1"
+            "markers": "python_full_version >= '3.6.0'",
+            "version": "==2.0.1"
         },
         "marshmallow": {
             "hashes": [
@@ -394,11 +423,12 @@
                 "sha256:ca4f013fa958f60fb2327fe87e6127c1ac0ab536890b1d4b00847f417b7af1ba",
                 "sha256:dcf472cf3b31c4e3f7135378aac6f4c5da5b49a07145c825e38bc23af17ce43f"
             ],
-            "markers": "python_version >= '3.6'",
+            "markers": "python_full_version >= '3.6.0'",
             "version": "==4.5.5.64"
         },
         "openflexure-microscope-server": {
             "editable": true,
+            "extras": [],
             "path": "."
         },
         "packaging": {
@@ -407,7 +437,7 @@
                 "sha256:dd47c42927d89ab911e606518907cc2d3a1f38bbd026385970643f9c5b8ecfeb",
                 "sha256:ef103e05f519cdc783ae24ea4e2e0f508a9c99b2d4969652eed6a2e1ea5bd522"
             ],
-            "markers": "python_version >= '3.6'",
+            "markers": "python_full_version >= '3.6.0'",
             "version": "==21.3"
         },
         "picamerax": {
@@ -477,7 +507,7 @@
                 "sha256:74134bbf457f031a36d68416e1509f34bd5ccc019f0bcc952c7b909d06b37bd3",
                 "sha256:f2d9abbfd1465ce5d1e261e51cc15afc87ede2ae079c7c7c8d894b1cc37ba123"
             ],
-            "markers": "python_version >= '3.6'",
+            "markers": "python_full_version >= '3.6.0'",
             "version": "==1.0.0"
         },
         "prance": {
@@ -817,7 +847,7 @@
                 "sha256:6613dbc39f41cd58942a697f11c8762ba18422bd173fe0bdfc1535b83d3f84f0",
                 "sha256:79029486d36a0d7f3c659dbf6ae50a91fbed0c22dcd5376f592e076c130bc7f9"
             ],
-            "markers": "python_version >= '3.6'",
+            "markers": "python_full_version >= '3.6.0'",
             "version": "==4.7.1"
         },
         "apispec-webframeworks": {
@@ -825,7 +855,7 @@
                 "sha256:0db35b267914b3f8c562aca0261957dbcb4176f255eacc22520277010818dcf3",
                 "sha256:482c563abbcc2a261439476cb3f1a7c7284cc997c322c574d48c111643e9c04e"
             ],
-            "markers": "python_version >= '3.6'",
+            "markers": "python_full_version >= '3.6.0'",
             "version": "==0.5.2"
         },
         "appdirs": {
@@ -867,7 +897,7 @@
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@@ -875,7 +905,7 @@
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@@ -1598,7 +1658,7 @@
                 "sha256:5eb116118f9612ff1ee89ac96437bb6b49e8f04d8a13b514ba26f620208e26eb",
                 "sha256:dc9c10fb40944260f6ed4c688ece0cd2048414940f1cea51b8b226318411c519"
             ],
-            "markers": "python_full_version >= '3.6.0'",
+            "markers": "python_version >= '3.6'",
             "version": "==2.12.0"
         },
         "pylint": {
@@ -1881,7 +1941,7 @@
                 "sha256:d412243dfb797ae3ec2b59eca0e52dac12e75a241bf0e4eb861e450d06c6ed07",
                 "sha256:f5f8bb2d0d629f398bf47d0d69c07bc13b65f75a81ad9e2f71a63d4b7a2f6db2"
             ],
-            "markers": "python_full_version >= '3.6.0'",
+            "markers": "python_version >= '3.6'",
             "version": "==2.0.0"
         },
         "sphinxcontrib-httpdomain": {
@@ -1906,7 +1966,7 @@
                 "sha256:1c1bd10d7653912c59a42f727c62cbb7b75f7905ddd9ccc477ebfd1bc69f0cf3",
                 "sha256:3c2a33c1d24733e6f22a0091b8172d08c723a7f192699f0dbfac99bb380dcb31"
             ],
-            "markers": "python_full_version >= '3.6.0'",
+            "markers": "python_version >= '3.6'",
             "version": "==0.7.0"
         },
         "sphinxcontrib-qthelp": {
@@ -1947,7 +2007,7 @@
                 "sha256:69e0675671a2eed1c08a53f342c955c4ead5d373a10f756219bf39f3d4f0018a",
                 "sha256:d1b49c3e460f5910b22d799b13513504acb4f5fcaee01660ee66f07bd45a271c"
             ],
-            "markers": "python_version < '4.0' and python_full_version >= '3.6.0'",
+            "markers": "python_version >= '3.6' and python_version < '4'",
             "version": "==0.11.2"
         },
         "typed-ast": {
diff --git a/setup.py b/setup.py
index ea01d24f..84ca4179 100644
--- a/setup.py
+++ b/setup.py
@@ -51,6 +51,7 @@ setup(
         "scipy ~= 1.6.1",
         "python-dateutil ~= 2.8",
         "psutil ~= 5.6.7",  # Autostorage extension
+        "markupsafe ~= 2.0.0",  # 2.1.x breaks jinja2
         "opencv-python-headless ~= 4.5.1",
         "sangaboard ~= 0.3.2",
         "expiringdict ~= 1.2.1",

From f2f00b0d11feb6bd2a3d43f0046d935e3026aa92 Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Tue, 9 Aug 2022 13:33:10 +0100
Subject: [PATCH 12/25] Update w3c schema to 2020 format

The `thing-context` definition used a 2019 draft of how to specify a
tuple (where `items` set the mandatory items and `additionalItems`
set the rest).  These have been renamed to `prefixItems` and `items`
respectively, and I have applied this change.  Schema now validates
again :)
---
 tests/w3c_td_schema.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/w3c_td_schema.json b/tests/w3c_td_schema.json
index 62194083..e15f1bbf 100644
--- a/tests/w3c_td_schema.json
+++ b/tests/w3c_td_schema.json
@@ -66,10 +66,10 @@
         "thing-context": {
             "oneOf": [{
                     "type": "array",
-                    "items": [{
+                    "prefixItems": [{
                         "$ref": "#/definitions/thing-context-w3c-uri"
                     }],
-                    "additionalItems": {
+                    "items": {
                         "anyOf": [{
                                 "$ref": "#/definitions/anyUri"
                             },

From ba62bdf86799629377584423b1de96ee7badef92 Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Tue, 21 Mar 2023 12:51:03 +0000
Subject: [PATCH 13/25] Update pysangaboard to 0.3.3

---
 Pipfile.lock | 1622 +++++++++++++++++++++++++++++---------------------
 setup.py     |    2 +-
 2 files changed, 946 insertions(+), 678 deletions(-)

diff --git a/Pipfile.lock b/Pipfile.lock
index 3dd42ee3..620fd3f2 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -30,7 +30,7 @@
                 "sha256:6613dbc39f41cd58942a697f11c8762ba18422bd173fe0bdfc1535b83d3f84f0",
                 "sha256:79029486d36a0d7f3c659dbf6ae50a91fbed0c22dcd5376f592e076c130bc7f9"
             ],
-            "markers": "python_full_version >= '3.6.0'",
+            "markers": "python_version >= '3.6'",
             "version": "==4.7.1"
         },
         "apispec-webframeworks": {
@@ -38,42 +38,32 @@
                 "sha256:0db35b267914b3f8c562aca0261957dbcb4176f255eacc22520277010818dcf3",
                 "sha256:482c563abbcc2a261439476cb3f1a7c7284cc997c322c574d48c111643e9c04e"
             ],
-            "markers": "python_full_version >= '3.6.0'",
+            "markers": "python_version >= '3.6'",
             "version": "==0.5.2"
         },
-        "atomicwrites": {
-            "hashes": [
-                "sha256:03513b104b7c627ac3ff75b85b54843e5710b5fa400231eb419b441c9d1ef9a7",
-                "sha256:81b2c9071a49367a7f770170e5eec8cb66567cfbbc8c73d20ce5ca4a8d71cf11"
-            ],
-            "markers": "sys_platform == 'win32'",
-            "version": "==1.4.1"
-        },
         "attrs": {
             "hashes": [
-                "sha256:29adc2665447e5191d0e7c568fde78b21f9672d344281d0c6e1ab085429b22b6",
-                "sha256:6d9391612040005651f4f45d6bfc257484a8f93f15ffdcf3f8dbd21f9e20ce39",
-                "sha256:86efa402f67bf2df34f51a335487cf46b1ec130d02b8d39fd248abfd30da551c"
+                "sha256:29e95c7f6778868dbd49170f98f8818f78f3dc5e0e37c0b1f474e3561b240836",
+                "sha256:c9227bfc2f01993c03f68db37d1d15c9690188323c067c641f1a35ca58185f99"
             ],
-            "markers": "python_version >= '3.5'",
-            "version": "==22.1.0"
+            "markers": "python_version >= '3.6'",
+            "version": "==22.2.0"
         },
         "camera-stage-mapping": {
             "hashes": [
                 "sha256:02a409bd2cb193b20d9eb015ca31400bd3e1721ec5d702e1b96de54608ff5a8f",
                 "sha256:d39c3afebb59ec865fb1247dfd951d7090c159ab0cf3e4291e0869d3be33776c"
             ],
-            "markers": "python_version < '4' and python_full_version >= '3.6.0'",
+            "markers": "python_version >= '3.6' and python_version < '4.0'",
             "version": "==0.1.4"
         },
         "certifi": {
             "hashes": [
-                "sha256:84c85a9078b11105f04f3036a9482ae10e4621616db313fe045dd24743a0820d",
-                "sha256:cbd4c168c00e6c24b3fdf4e9f34c7c459810173b3a3cb9ab14a219f7549d4263",
-                "sha256:fe86415d55e84719d75f8b69414f6438ac3547d2078ab91b67e779ef69378412"
+                "sha256:35824b4c3a97115964b408844d64aa14db1cc518f6562e8d7261699d1350a9e3",
+                "sha256:4ad3232f5e926d6718ec31cfc1fcadfde020920e278684144551c91769c7bc18"
             ],
-            "markers": "python_full_version >= '3.6.0'",
-            "version": "==2022.6.15"
+            "markers": "python_version >= '3.6'",
+            "version": "==2022.12.7"
         },
         "chardet": {
             "hashes": [
@@ -85,12 +75,84 @@
         },
         "charset-normalizer": {
             "hashes": [
-                "sha256:1698523254cfe01135e7e863524c1fcfebb007d0512d4815d9699f3e38dfaab4",
-                "sha256:5189b6f22b01957427f35b6a08d9a0bc45b46d3788ef5a92e978433c7a35f8a5",
-                "sha256:575e708016ff3a5e3681541cb9d79312c416835686d054a23accb873b254f413"
+                "sha256:04afa6387e2b282cf78ff3dbce20f0cc071c12dc8f685bd40960cc68644cfea6",
+                "sha256:04eefcee095f58eaabe6dc3cc2262f3bcd776d2c67005880894f447b3f2cb9c1",
+                "sha256:0be65ccf618c1e7ac9b849c315cc2e8a8751d9cfdaa43027d4f6624bd587ab7e",
+                "sha256:0c95f12b74681e9ae127728f7e5409cbbef9cd914d5896ef238cc779b8152373",
+                "sha256:0ca564606d2caafb0abe6d1b5311c2649e8071eb241b2d64e75a0d0065107e62",
+                "sha256:10c93628d7497c81686e8e5e557aafa78f230cd9e77dd0c40032ef90c18f2230",
+                "sha256:11d117e6c63e8f495412d37e7dc2e2fff09c34b2d09dbe2bee3c6229577818be",
+                "sha256:11d3bcb7be35e7b1bba2c23beedac81ee893ac9871d0ba79effc7fc01167db6c",
+                "sha256:12a2b561af122e3d94cdb97fe6fb2bb2b82cef0cdca131646fdb940a1eda04f0",
+                "sha256:12d1a39aa6b8c6f6248bb54550efcc1c38ce0d8096a146638fd4738e42284448",
+                "sha256:1435ae15108b1cb6fffbcea2af3d468683b7afed0169ad718451f8db5d1aff6f",
+                "sha256:1c60b9c202d00052183c9be85e5eaf18a4ada0a47d188a83c8f5c5b23252f649",
+                "sha256:1e8fcdd8f672a1c4fc8d0bd3a2b576b152d2a349782d1eb0f6b8e52e9954731d",
+                "sha256:20064ead0717cf9a73a6d1e779b23d149b53daf971169289ed2ed43a71e8d3b0",
+                "sha256:21fa558996782fc226b529fdd2ed7866c2c6ec91cee82735c98a197fae39f706",
+                "sha256:22908891a380d50738e1f978667536f6c6b526a2064156203d418f4856d6e86a",
+                "sha256:3160a0fd9754aab7d47f95a6b63ab355388d890163eb03b2d2b87ab0a30cfa59",
+                "sha256:322102cdf1ab682ecc7d9b1c5eed4ec59657a65e1c146a0da342b78f4112db23",
+                "sha256:34e0a2f9c370eb95597aae63bf85eb5e96826d81e3dcf88b8886012906f509b5",
+                "sha256:3573d376454d956553c356df45bb824262c397c6e26ce43e8203c4c540ee0acb",
+                "sha256:3747443b6a904001473370d7810aa19c3a180ccd52a7157aacc264a5ac79265e",
+                "sha256:38e812a197bf8e71a59fe55b757a84c1f946d0ac114acafaafaf21667a7e169e",
+                "sha256:3a06f32c9634a8705f4ca9946d667609f52cf130d5548881401f1eb2c39b1e2c",
+                "sha256:3a5fc78f9e3f501a1614a98f7c54d3969f3ad9bba8ba3d9b438c3bc5d047dd28",
+                "sha256:3d9098b479e78c85080c98e1e35ff40b4a31d8953102bb0fd7d1b6f8a2111a3d",
+                "sha256:3dc5b6a8ecfdc5748a7e429782598e4f17ef378e3e272eeb1340ea57c9109f41",
+                "sha256:4155b51ae05ed47199dc5b2a4e62abccb274cee6b01da5b895099b61b1982974",
+                "sha256:49919f8400b5e49e961f320c735388ee686a62327e773fa5b3ce6721f7e785ce",
+                "sha256:53d0a3fa5f8af98a1e261de6a3943ca631c526635eb5817a87a59d9a57ebf48f",
+                "sha256:5f008525e02908b20e04707a4f704cd286d94718f48bb33edddc7d7b584dddc1",
+                "sha256:628c985afb2c7d27a4800bfb609e03985aaecb42f955049957814e0491d4006d",
+                "sha256:65ed923f84a6844de5fd29726b888e58c62820e0769b76565480e1fdc3d062f8",
+                "sha256:6734e606355834f13445b6adc38b53c0fd45f1a56a9ba06c2058f86893ae8017",
+                "sha256:6baf0baf0d5d265fa7944feb9f7451cc316bfe30e8df1a61b1bb08577c554f31",
+                "sha256:6f4f4668e1831850ebcc2fd0b1cd11721947b6dc7c00bf1c6bd3c929ae14f2c7",
+                "sha256:6f5c2e7bc8a4bf7c426599765b1bd33217ec84023033672c1e9a8b35eaeaaaf8",
+                "sha256:6f6c7a8a57e9405cad7485f4c9d3172ae486cfef1344b5ddd8e5239582d7355e",
+                "sha256:7381c66e0561c5757ffe616af869b916c8b4e42b367ab29fedc98481d1e74e14",
+                "sha256:73dc03a6a7e30b7edc5b01b601e53e7fc924b04e1835e8e407c12c037e81adbd",
+                "sha256:74db0052d985cf37fa111828d0dd230776ac99c740e1a758ad99094be4f1803d",
+                "sha256:75f2568b4189dda1c567339b48cba4ac7384accb9c2a7ed655cd86b04055c795",
+                "sha256:78cacd03e79d009d95635e7d6ff12c21eb89b894c354bd2b2ed0b4763373693b",
+                "sha256:80d1543d58bd3d6c271b66abf454d437a438dff01c3e62fdbcd68f2a11310d4b",
+                "sha256:830d2948a5ec37c386d3170c483063798d7879037492540f10a475e3fd6f244b",
+                "sha256:891cf9b48776b5c61c700b55a598621fdb7b1e301a550365571e9624f270c203",
+                "sha256:8f25e17ab3039b05f762b0a55ae0b3632b2e073d9c8fc88e89aca31a6198e88f",
+                "sha256:9a3267620866c9d17b959a84dd0bd2d45719b817245e49371ead79ed4f710d19",
+                "sha256:a04f86f41a8916fe45ac5024ec477f41f886b3c435da2d4e3d2709b22ab02af1",
+                "sha256:aaf53a6cebad0eae578f062c7d462155eada9c172bd8c4d250b8c1d8eb7f916a",
+                "sha256:abc1185d79f47c0a7aaf7e2412a0eb2c03b724581139193d2d82b3ad8cbb00ac",
+                "sha256:ac0aa6cd53ab9a31d397f8303f92c42f534693528fafbdb997c82bae6e477ad9",
+                "sha256:ac3775e3311661d4adace3697a52ac0bab17edd166087d493b52d4f4f553f9f0",
+                "sha256:b06f0d3bf045158d2fb8837c5785fe9ff9b8c93358be64461a1089f5da983137",
+                "sha256:b116502087ce8a6b7a5f1814568ccbd0e9f6cfd99948aa59b0e241dc57cf739f",
+                "sha256:b82fab78e0b1329e183a65260581de4375f619167478dddab510c6c6fb04d9b6",
+                "sha256:bd7163182133c0c7701b25e604cf1611c0d87712e56e88e7ee5d72deab3e76b5",
+                "sha256:c36bcbc0d5174a80d6cccf43a0ecaca44e81d25be4b7f90f0ed7bcfbb5a00909",
+                "sha256:c3af8e0f07399d3176b179f2e2634c3ce9c1301379a6b8c9c9aeecd481da494f",
+                "sha256:c84132a54c750fda57729d1e2599bb598f5fa0344085dbde5003ba429a4798c0",
+                "sha256:cb7b2ab0188829593b9de646545175547a70d9a6e2b63bf2cd87a0a391599324",
+                "sha256:cca4def576f47a09a943666b8f829606bcb17e2bc2d5911a46c8f8da45f56755",
+                "sha256:cf6511efa4801b9b38dc5546d7547d5b5c6ef4b081c60b23e4d941d0eba9cbeb",
+                "sha256:d16fd5252f883eb074ca55cb622bc0bee49b979ae4e8639fff6ca3ff44f9f854",
+                "sha256:d2686f91611f9e17f4548dbf050e75b079bbc2a82be565832bc8ea9047b61c8c",
+                "sha256:d7fc3fca01da18fbabe4625d64bb612b533533ed10045a2ac3dd194bfa656b60",
+                "sha256:dd5653e67b149503c68c4018bf07e42eeed6b4e956b24c00ccdf93ac79cdff84",
+                "sha256:de5695a6f1d8340b12a5d6d4484290ee74d61e467c39ff03b39e30df62cf83a0",
+                "sha256:e0ac8959c929593fee38da1c2b64ee9778733cdf03c482c9ff1d508b6b593b2b",
+                "sha256:e1b25e3ad6c909f398df8921780d6a3d120d8c09466720226fc621605b6f92b1",
+                "sha256:e633940f28c1e913615fd624fcdd72fdba807bf53ea6925d6a588e84e1151531",
+                "sha256:e89df2958e5159b811af9ff0f92614dabf4ff617c03a4c1c6ff53bf1c399e0e1",
+                "sha256:ea9f9c6034ea2d93d9147818f17c2a0860d41b71c38b9ce4d55f21b6f9165a11",
+                "sha256:f645caaf0008bacf349875a974220f1f1da349c5dbe7c4ec93048cdc785a3326",
+                "sha256:f8303414c7b03f794347ad062c0516cee0e15f7a612abd0ce1e25caf6ceb47df",
+                "sha256:fca62a8301b605b954ad2e9c3666f9d97f63872aa4efcae5492baca2056b74ab"
             ],
-            "markers": "python_full_version >= '3.6.0'",
-            "version": "==2.1.0"
+            "markers": "python_full_version >= '3.7.0'",
+            "version": "==3.1.0"
         },
         "click": {
             "hashes": [
@@ -103,12 +165,11 @@
         },
         "colorama": {
             "hashes": [
-                "sha256:2e3098fdcfc0107a135ba8bae5ddb6224bbb7fb7026db2d1b066d5af8bcca063",
-                "sha256:854bf444933e37f5824ae7bfc1e98d5bce2ebe4160d46b5edf346a89358e99da",
-                "sha256:e6c6b4334fc50988a639d9b98aa429a0b57da6e17b9a44f0451f930b6967b7a4"
+                "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44",
+                "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6"
             ],
             "markers": "sys_platform == 'win32'",
-            "version": "==0.4.5"
+            "version": "==0.4.6"
         },
         "colorzero": {
             "hashes": [
@@ -119,52 +180,68 @@
         },
         "coverage": {
             "hashes": [
-                "sha256:03d9f920ef695ae5a46f131708343cbb8c44e92c764f1a763f7540674c9df555",
-                "sha256:04010af3c06ce2bfeb3b1e4e05d136f88d88c25f76cd4faff5d1fd84d11581ea",
-                "sha256:05de0762c1caed4a162b3e305f36cf20a548ff4da0be6766ad5c870704be3660",
-                "sha256:068d6f2a893af838291b8809c876973d885543411ea460f3e6886ac0ee941732",
-                "sha256:0a84376e4fd13cebce2c0ef8c2f037929c8307fb94af1e5dbe50272a1c651b5d",
-                "sha256:0e34247274bde982bbc613894d33f9e36358179db2ed231dd101c48dd298e7b0",
-                "sha256:0e3a41aad5919613483aad9ebd53336905cab1bd6788afd3995c2a972d89d795",
-                "sha256:306788fd019bb90e9cbb83d3f3c6becad1c048dd432af24f8320cf38ac085684",
-                "sha256:39ebd8e120cb77a06ee3d5fc26f9732670d1c397d7cd3acf02f6f62693b89b80",
-                "sha256:411fdd9f4203afd93b056c0868c8f9e5e16813e765de962f27e4e5798356a052",
-                "sha256:4822327b35cb032ff16af3bec27f73985448f08e874146b5b101e0e558b613dd",
-                "sha256:52f8b9fcf3c5e427d51bbab1fb92b575a9a9235d516f175b24712bcd4b5be917",
-                "sha256:53c8edd3b83a4ddba3d8c506f1359401e7770b30f2188f15c17a338adf5a14db",
-                "sha256:555a498999c44f5287cc95500486cd0d4f021af9162982cbe504d4cb388f73b5",
-                "sha256:59fc88bc13e30f25167e807b8cad3c41b7218ef4473a20c86fd98a7968733083",
-                "sha256:5a559aab40c716de80c7212295d0dc96bc1b6c719371c20dd18c5187c3155518",
-                "sha256:5de1e9335e2569974e20df0ce31493d315a830d7987e71a24a2a335a8d8459d3",
-                "sha256:6630d8d943644ea62132789940ca97d05fac83f73186eaf0930ffa715fbdab6b",
-                "sha256:73a10939dc345460ca0655356a470dd3de9759919186a82383c87b6eb315faf2",
-                "sha256:7856ea39059d75f822ff0df3a51ea6d76307c897048bdec3aad1377e4e9dca20",
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-            "version": "==6.4.3"
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@@ -191,20 +268,18 @@
         },
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-            "version": "==0.18.2"
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@@ -216,29 +291,27 @@
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@@ -258,11 +331,19 @@
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@@ -270,9 +351,51 @@
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@@ -347,16 +470,16 @@
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-            "version": "==3.17.0"
+            "version": "==3.19.0"
         },
         "numpy": {
             "hashes": [
@@ -393,23 +516,23 @@
                 "sha256:f17e562de9edf691a42ddb1eb4a5541c20dd3f9e65b09ded2beb0799c0cf29bb",
                 "sha256:fdffbfb6832cd0b300995a2b08b8f6fa9f6e856d562800fea9182316d99c4e8e"
             ],
-            "markers": "python_version >= '3.7'",
+            "markers": "python_version < '3.11' and python_version >= '3.7'",
             "version": "==1.21.6"
         },
         "openapi-schema-validator": {
             "hashes": [
-                "sha256:2c64907728c3ef78e23711c8840a423f0b241588c9ed929855e4b2d1bb0cf5f2",
-                "sha256:9bae709212a19222892cabcc60cafd903cbf4b220223f48583afa3c0e3cc6fc4"
+                "sha256:79f37f38ef9fd5206b924ed7a6f382cea7b649b3b56383c47f1906082b7b9015",
+                "sha256:c573e2be2c783abae56c5a1486ab716ca96e09d1c3eab56020d1dc680aa57bf8"
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-            "markers": "python_version >= '3.7' and python_version < '4'",
-            "version": "==0.2.3"
+            "markers": "python_full_version >= '3.7.0' and python_full_version < '4.0.0'",
+            "version": "==0.4.4"
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         "openapi-spec-validator": {
             "hashes": [
-                "sha256:06900ac4d546a1df3642a779da0055be58869c598e3042a2fef067cfd99d04d0",
-                "sha256:97f258850afc97b048f7c2653855e0f88fa66ac103c2be5077c7960aca2ad49a"
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+                "sha256:4145478f26df16059c147406eaaa59b77ff60e3461ba6edb9aa84d481ed89aaf"
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-            "version": "==0.4.0"
+            "version": "==0.5.6"
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         "opencv-python-headless": {
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@@ -423,12 +546,11 @@
                 "sha256:ca4f013fa958f60fb2327fe87e6127c1ac0ab536890b1d4b00847f417b7af1ba",
                 "sha256:dcf472cf3b31c4e3f7135378aac6f4c5da5b49a07145c825e38bc23af17ce43f"
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-            "markers": "python_full_version >= '3.6.0'",
+            "markers": "python_version >= '3.6'",
             "version": "==4.5.5.64"
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         "openflexure-microscope-server": {
             "editable": true,
-            "extras": [],
             "path": "."
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         "packaging": {
@@ -437,9 +559,17 @@
                 "sha256:dd47c42927d89ab911e606518907cc2d3a1f38bbd026385970643f9c5b8ecfeb",
                 "sha256:ef103e05f519cdc783ae24ea4e2e0f508a9c99b2d4969652eed6a2e1ea5bd522"
             ],
-            "markers": "python_full_version >= '3.6.0'",
+            "markers": "python_version >= '3.6'",
             "version": "==21.3"
         },
+        "pathable": {
+            "hashes": [
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+                "sha256:cdd7b1f9d7d5c8b8d3315dbf5a86b2596053ae845f056f57d97c0eefff84da14"
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+            "version": "==0.4.3"
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                 "sha256:8dc45542644ed9c67e3b331e90bcffa04098e8b056a42d0fedb25769b0b1f17e",
@@ -507,7 +637,7 @@
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                 "sha256:f2d9abbfd1465ce5d1e261e51cc15afc87ede2ae079c7c7c8d894b1cc37ba123"
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-            "markers": "python_full_version >= '3.6.0'",
+            "markers": "python_version >= '3.6'",
             "version": "==1.0.0"
         },
         "prance": {
@@ -515,11 +645,10 @@
                 "osv"
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-            "version": "==0.21.8.0"
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@@ -541,15 +670,6 @@
             "markers": "python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'",
             "version": "==5.6.7"
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-            "version": "==1.11.0"
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@@ -561,32 +681,36 @@
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@@ -597,12 +721,11 @@
         },
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         "pytest-cov": {
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@@ -659,12 +782,19 @@
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             "markers": "python_version >= '3.7' and python_version < '4'",
-            "version": "==2.28.1"
+            "version": "==2.28.2"
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+        "rfc3339-validator": {
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         "ruamel.yaml": {
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@@ -677,45 +807,52 @@
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@@ -761,6 +898,14 @@
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             "version": "==2.13.0"
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@@ -774,7 +919,7 @@
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@@ -783,17 +928,16 @@
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@@ -822,21 +966,21 @@
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-            "version": "==3.8.1"
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@@ -847,7 +991,7 @@
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@@ -874,31 +1018,21 @@
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@@ -953,12 +1158,11 @@
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@@ -1058,29 +1276,26 @@
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@@ -1101,38 +1316,35 @@
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@@ -1152,11 +1364,19 @@
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@@ -1371,16 +1586,16 @@
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@@ -1393,48 +1608,54 @@
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@@ -1471,23 +1692,23 @@
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@@ -1501,12 +1722,11 @@
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@@ -1515,7 +1735,7 @@
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@@ -1526,6 +1746,14 @@
             "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
             "version": "==0.2.1"
         },
+        "pathable": {
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+                "sha256:cdd7b1f9d7d5c8b8d3315dbf5a86b2596053ae845f056f57d97c0eefff84da14"
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+            "version": "==0.4.3"
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                 "sha256:8dc45542644ed9c67e3b331e90bcffa04098e8b056a42d0fedb25769b0b1f17e",
@@ -1533,6 +1761,13 @@
             ],
             "version": "==20.9.1"
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+        "picobox": {
+            "hashes": [
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@@ -1589,11 +1824,11 @@
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@@ -1601,27 +1836,26 @@
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+            "markers": "python_version >= '3.6'",
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@@ -1654,12 +1888,11 @@
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@@ -1681,32 +1914,36 @@
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@@ -1717,12 +1954,11 @@
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@@ -1742,11 +1978,11 @@
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@@ -1787,12 +2023,19 @@
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@@ -1913,6 +2171,14 @@
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@@ -1998,17 +2263,16 @@
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@@ -2039,24 +2303,22 @@
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+                "sha256:40737a081d7497efea35ab9304b829b857f21558acfc7b3272f908d33b0d9d4c",
+                "sha256:41d07d029dd4157ae27beab04d22b8e261eddfc6ecd64ff7000b10dc8b3a5727",
+                "sha256:46ed616d5fb42f98630ed70c3529541408166c22cdfd4540b88d5f21006b0eff",
+                "sha256:493d389a2b63c88ad56cdc35d0fa5752daac56ca755805b1b0c530f785767d5e",
+                "sha256:4ff0d20f2e670800d3ed2b220d40984162089a6e2c9646fdb09b85e6f9a8fc29",
+                "sha256:54accd4b8bc202966bafafd16e69da9d5640ff92389d33d28555c5fd4f25ccb7",
+                "sha256:56374914b132c702aa9aa9959c550004b8847148f95e1b824772d453ac204a72",
+                "sha256:578383d740457fa790fdf85e6d346fda1416a40549fe8db08e5e9bd281c6a475",
+                "sha256:58d7a75d731e8c63614222bcb21dd992b4ab01a399f1f09dd82af17bbfc2368a",
+                "sha256:5c5aa28df055697d7c37d2099a7bc09f559d5053c3349b1ad0c39000e611d317",
+                "sha256:5fc8e02f5984a55d2c653f5fea93531e9836abbd84342c1d1e17abc4a15084c2",
+                "sha256:63424c681923b9f3bfbc5e3205aafe790904053d42ddcc08542181a30a7a51bd",
+                "sha256:64b1df0f83706b4ef4cfb4fb0e4c2669100fd7ecacfb59e091fad300d4e04640",
+                "sha256:74934ebd71950e3db69960a7da29204f89624dde411afbfb3b4858c1409b1e98",
+                "sha256:75669d77bb2c071333417617a235324a1618dba66f82a750362eccbe5b61d248",
+                "sha256:75760a47c06b5974aa5e01949bf7e66d2af4d08cb8c1d6516af5e39595397f5e",
+                "sha256:76407ab327158c510f44ded207e2f76b657303e17cb7a572ffe2f5a8a48aa04d",
+                "sha256:76e9c727a874b4856d11a32fb0b389afc61ce8aaf281ada613713ddeadd1cfec",
+                "sha256:77d4c1b881076c3ba173484dfa53d3582c1c8ff1f914c6461ab70c8428b796c1",
+                "sha256:780c82a41dc493b62fc5884fb1d3a3b81106642c5c5c78d6a0d4cbe96d62ba7e",
+                "sha256:7dc0713bf81287a00516ef43137273b23ee414fe41a3c14be10dd95ed98a2df9",
+                "sha256:7eebcdbe3677e58dd4c0e03b4f2cfa346ed4049687d839adad68cc38bb559c92",
+                "sha256:896689fddba4f23ef7c718279e42f8834041a21342d95e56922e1c10c0cc7afb",
+                "sha256:96177eb5645b1c6985f5c11d03fc2dbda9ad24ec0f3a46dcce91445747e15094",
+                "sha256:96e25c8603a155559231c19c0349245eeb4ac0096fe3c1d0be5c47e075bd4f46",
+                "sha256:9d37ac69edc5614b90516807de32d08cb8e7b12260a285ee330955604ed9dd29",
+                "sha256:9ed6aa0726b9b60911f4aed8ec5b8dd7bf3491476015819f56473ffaef8959bd",
+                "sha256:a487f72a25904e2b4bbc0817ce7a8de94363bd7e79890510174da9d901c38705",
+                "sha256:a4cbb9ff5795cd66f0066bdf5947f170f5d63a9274f99bdbca02fd973adcf2a8",
+                "sha256:a74d56552ddbde46c246b5b89199cb3fd182f9c346c784e1a93e4dc3f5ec9975",
+                "sha256:a89ce3fd220ff144bd9d54da333ec0de0399b52c9ac3d2ce34b569cf1a5748fb",
+                "sha256:abd52a09d03adf9c763d706df707c343293d5d106aea53483e0ec8d9e310ad5e",
+                "sha256:abd8f36c99512755b8456047b7be10372fca271bf1467a1caa88db991e7c421b",
+                "sha256:af5bd9ccb188f6a5fdda9f1f09d9f4c86cc8a539bd48a0bfdc97723970348418",
+                "sha256:b02f21c1e2074943312d03d243ac4388319f2456576b2c6023041c4d57cd7019",
+                "sha256:b06fa97478a5f478fb05e1980980a7cdf2712015493b44d0c87606c1513ed5b1",
+                "sha256:b0724f05c396b0a4c36a3226c31648385deb6a65d8992644c12a4963c70326ba",
+                "sha256:b130fe77361d6771ecf5a219d8e0817d61b236b7d8b37cc045172e574ed219e6",
+                "sha256:b56d5519e470d3f2fe4aa7585f0632b060d532d0696c5bdfb5e8319e1d0f69a2",
+                "sha256:b67b819628e3b748fd3c2192c15fb951f549d0f47c0449af0764d7647302fda3",
+                "sha256:ba1711cda2d30634a7e452fc79eabcadaffedf241ff206db2ee93dd2c89a60e7",
+                "sha256:bbeccb1aa40ab88cd29e6c7d8585582c99548f55f9b2581dfc5ba68c59a85752",
+                "sha256:bd84395aab8e4d36263cd1b9308cd504f6cf713b7d6d3ce25ea55670baec5416",
+                "sha256:c99f4309f5145b93eca6e35ac1a988f0dc0a7ccf9ccdcd78d3c0adf57224e62f",
+                "sha256:ca1cccf838cd28d5a0883b342474c630ac48cac5df0ee6eacc9c7290f76b11c1",
+                "sha256:cd525e0e52a5ff16653a3fc9e3dd827981917d34996600bbc34c05d048ca35cc",
+                "sha256:cdb4f085756c96a3af04e6eca7f08b1345e94b53af8921b25c72f096e704e145",
+                "sha256:ce42618f67741d4697684e501ef02f29e758a123aa2d669e2d964ff734ee00ee",
+                "sha256:d06730c6aed78cee4126234cf2d071e01b44b915e725a6cb439a879ec9754a3a",
+                "sha256:d5fe3e099cf07d0fb5a1e23d399e5d4d1ca3e6dfcbe5c8570ccff3e9208274f7",
+                "sha256:d6bcbfc99f55655c3d93feb7ef3800bd5bbe963a755687cbf1f490a71fb7794b",
+                "sha256:d787272ed958a05b2c86311d3a4135d3c2aeea4fc655705f074130aa57d71653",
+                "sha256:e169e957c33576f47e21864cf3fc9ff47c223a4ebca8960079b8bd36cb014fd0",
+                "sha256:e20076a211cd6f9b44a6be58f7eeafa7ab5720eb796975d0c03f05b47d89eb90",
+                "sha256:e826aadda3cae59295b95343db8f3d965fb31059da7de01ee8d1c40a60398b29",
+                "sha256:eef4d64c650f33347c1f9266fa5ae001440b232ad9b98f1f43dfe7a79435c0a6",
+                "sha256:f2e69b3ed24544b0d3dbe2c5c0ba5153ce50dcebb576fdc4696d52aa22db6034",
+                "sha256:f87ec75864c37c4c6cb908d282e1969e79763e0d9becdfe9fe5473b7bb1e5f09",
+                "sha256:fbec11614dba0424ca72f4e8ba3c420dba07b4a7c206c8c8e4e73f2e98f4c559",
+                "sha256:fd69666217b62fa5d7c6aa88e507493a34dec4fa20c5bd925e4bc12fce586639"
             ],
             "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
-            "version": "==1.14.1"
+            "version": "==1.15.0"
         },
         "zeroconf": {
             "hashes": [
@@ -2176,12 +2445,11 @@
         },
         "zipp": {
             "hashes": [
-                "sha256:05b45f1ee8f807d0cc928485ca40a07cb491cf092ff587c0df9cb1fd154848d2",
-                "sha256:47c40d7fe183a6f21403a199b3e4192cca5774656965b0a4988ad2f8feb5f009",
-                "sha256:bdc5a7bbededd545d1accdf26304ba4add03dd8dc3f9dac4f0e9ee7d89ac7121"
+                "sha256:112929ad649da941c23de50f356a2b5570c954b65150642bccdd66bf194d224b",
+                "sha256:48904fc76a60e542af151aded95726c1a5c34ed43ab4134b597665c86d7ad556"
             ],
-            "markers": "python_version < '3.10'",
-            "version": "==3.8.1"
+            "markers": "python_version >= '3.7'",
+            "version": "==3.15.0"
         }
     }
 }
diff --git a/setup.py b/setup.py
index 84ca4179..d1ec7659 100644
--- a/setup.py
+++ b/setup.py
@@ -53,7 +53,7 @@ setup(
         "psutil ~= 5.6.7",  # Autostorage extension
         "markupsafe ~= 2.0.0",  # 2.1.x breaks jinja2
         "opencv-python-headless ~= 4.5.1",
-        "sangaboard ~= 0.3.2",
+        "sangaboard ~= 0.3.3",
         "expiringdict ~= 1.2.1",
         "camera-stage-mapping == 0.1.4",
         "picamerax ~= 20.9.1",

From 8e50a90fb2b5875a9889555c8e23fc9107b212f0 Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Tue, 21 Mar 2023 15:04:49 +0000
Subject: [PATCH 14/25] Explicitly mark arguments as optional

mypy now considers implicitly Optional arguments
to be errors - I have made them now explicitly
Optional, which passes.
---
 openflexure_microscope/camera/pi.py  | 8 ++++----
 openflexure_microscope/config.py     | 4 +++-
 openflexure_microscope/microscope.py | 2 +-
 3 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/openflexure_microscope/camera/pi.py b/openflexure_microscope/camera/pi.py
index 4f892734..6052363b 100644
--- a/openflexure_microscope/camera/pi.py
+++ b/openflexure_microscope/camera/pi.py
@@ -30,7 +30,7 @@ import logging
 import time
 
 # Type hinting
-from typing import BinaryIO, Tuple, Union
+from typing import BinaryIO, Tuple, Union, Optional
 
 import numpy as np
 
@@ -307,7 +307,7 @@ class PiCameraStreamer(BaseCamera):
             self.picamera.zoom = new_fov
 
     def start_preview(
-        self, fullscreen: bool = True, window: Tuple[int, int, int, int] = None
+        self, fullscreen: bool = True, window: Optional[Tuple[int, int, int, int]] = None
     ):
         """Start the on board GPU camera preview."""
         with self.lock(timeout=1):
@@ -462,9 +462,9 @@ class PiCameraStreamer(BaseCamera):
         output: Union[str, BinaryIO],
         fmt: str = "jpeg",
         use_video_port: bool = False,
-        resize: Tuple[int, int] = None,
+        resize: Optional[Tuple[int, int]] = None,
         bayer: bool = True,
-        thumbnail: Tuple[int, int, int] = None,
+        thumbnail: Optional[Tuple[int, int, int]] = None,
     ):
         """
         Capture a still image to a StreamObject.
diff --git a/openflexure_microscope/config.py b/openflexure_microscope/config.py
index f7b9552f..8ceed138 100644
--- a/openflexure_microscope/config.py
+++ b/openflexure_microscope/config.py
@@ -3,6 +3,8 @@ import json
 import logging
 import os
 import shutil
+from typing import Optional
+
 
 from .json import JSONEncoder
 from .paths import CONFIGURATION_FILE_PATH, SETTINGS_FILE_PATH
@@ -17,7 +19,7 @@ class OpenflexureSettingsFile:
         expand (bool): Expand paths to valid auxillary config files.
     """
 
-    def __init__(self, path: str, defaults: dict = None):
+    def __init__(self, path: str, defaults: Optional[dict] = None):
         defaults = defaults or {}
 
         # Set arguments
diff --git a/openflexure_microscope/microscope.py b/openflexure_microscope/microscope.py
index f97d3dc6..83f8d591 100644
--- a/openflexure_microscope/microscope.py
+++ b/openflexure_microscope/microscope.py
@@ -370,7 +370,7 @@ class Microscope:
         folder: str = "",
         temporary: bool = False,
         use_video_port: bool = False,
-        resize: Tuple[int, int] = None,
+        resize: Optional[Tuple[int, int]] = None,
         bayer: bool = True,
         fmt: str = "jpeg",
         annotations: Optional[Dict[str, str]] = None,

From f6691cbc11acff04a76ce8c32f947e7ab9c0a75c Mon Sep 17 00:00:00 2001
From: Joe Knapper <jak44@bath.ac.uk>
Date: Tue, 21 Mar 2023 15:05:21 +0000
Subject: [PATCH 15/25] Update openapi.py with live links to WoT documentation

---
 openflexure_microscope/api/openapi.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/openflexure_microscope/api/openapi.py b/openflexure_microscope/api/openapi.py
index f0605954..77677740 100644
--- a/openflexure_microscope/api/openapi.py
+++ b/openflexure_microscope/api/openapi.py
@@ -8,8 +8,8 @@ API_TAGS = [
             "embedded in the JSON action description."
         ),
         "externalDocs": {
-            "url": "https://iot.mozilla.org/wot/#action-resource",
-            "description": "Mozilla's description of Web of Things 'Action' resources.",
+            "url": "https://www.w3.org/TR/wot-thing-description/#actionaffordance",
+            "description": "w3's description of Web of Things 'Action' resources.",
         },
     },
     {
@@ -19,8 +19,8 @@ API_TAGS = [
             "state of the microscope."
         ),
         "externalDocs": {
-            "url": "https://iot.mozilla.org/wot/#property-resource",
-            "description": "Mozilla's description of Web of Things 'Property' resources.",
+            "url": "https://www.w3.org/TR/wot-thing-description/#propertyaffordance",
+            "description": "w3's description of Web of Things 'Property' resources.",
         },
     },
     {"name": "captures", "description": ""},

From 824248583d60f7103a0b87031a58c31d8d501708 Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Tue, 21 Mar 2023 15:05:22 +0000
Subject: [PATCH 16/25] Add !154 to changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2a1b877c..b87bff32 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,7 @@
 ## New features
 * Background detection can now be used in scans, if you have the background-detect extension. ([!153](https://gitlab.com/openflexure/openflexure-microscope-server/-/merge_requests/153))
 * Support for Sangaboard firmware v1, via updated `sangaboard` dependency ([!154](https://gitlab.com/openflexure/openflexure-microscope-server/-/merge_requests/154))
+* Fixed links in the OpenAPI documentation describing actions etc. ([!155](https://gitlab.com/openflexure/openflexure-microscope-server/-/merge_requests/154))
 
 # [v2.10.1](https://gitlab.com/openflexure/openflexure-microscope-server/compare/v2.10.0...v2.10.1) (2022-01-17)
 ## Bug fixes

From 4b73fd82f6e66f80da3bc63e2b792b6b9fca717e Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Tue, 21 Mar 2023 15:11:24 +0000
Subject: [PATCH 17/25] Format fix

---
 openflexure_microscope/camera/pi.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/openflexure_microscope/camera/pi.py b/openflexure_microscope/camera/pi.py
index 6052363b..f3a1db16 100644
--- a/openflexure_microscope/camera/pi.py
+++ b/openflexure_microscope/camera/pi.py
@@ -307,7 +307,9 @@ class PiCameraStreamer(BaseCamera):
             self.picamera.zoom = new_fov
 
     def start_preview(
-        self, fullscreen: bool = True, window: Optional[Tuple[int, int, int, int]] = None
+        self,
+        fullscreen: bool = True,
+        window: Optional[Tuple[int, int, int, int]] = None,
     ):
         """Start the on board GPU camera preview."""
         with self.lock(timeout=1):

From 1f558bbeb7096c2b6b859a5a28a59342d594463e Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Wed, 22 Mar 2023 08:58:04 +0000
Subject: [PATCH 18/25] OpenAPI Validation Fixes

OpenAPI validation seems to have become stricter about checking for None defaults
in parameters that don't allow None. I have
modified two things as a result:

1. StageTypeProperty (used to pick between SangaStage and SangaDeltaStage)
now defaults to SangaStage (which is the
original behaviour anyway)
2. It is now allowed to pass x,y,z=None when making a move - this is the same as
not passing the respective argument, so the
function already correctly handled this case.
---
 openflexure_microscope/api/v2/views/actions/stage.py | 6 +++---
 openflexure_microscope/api/v2/views/stage.py         | 2 +-
 openflexure_microscope/camera/pi.py                  | 2 +-
 openflexure_microscope/config.py                     | 1 -
 4 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/openflexure_microscope/api/v2/views/actions/stage.py b/openflexure_microscope/api/v2/views/actions/stage.py
index d13774ab..20412a6f 100644
--- a/openflexure_microscope/api/v2/views/actions/stage.py
+++ b/openflexure_microscope/api/v2/views/actions/stage.py
@@ -10,9 +10,9 @@ class MoveStageAPI(ActionView):
             load_default=False,
             metadata={"description": "Move to an absolute position", "example": False},
         ),
-        "x": fields.Int(load_default=None, metadata={"example": 100}, allow_none=False),
-        "y": fields.Int(load_default=None, metadata={"example": 100}, allow_none=False),
-        "z": fields.Int(load_default=None, metadata={"example": 20}, allow_none=False),
+        "x": fields.Int(load_default=None, metadata={"example": 100}, allow_none=True),
+        "y": fields.Int(load_default=None, metadata={"example": 100}, allow_none=True),
+        "z": fields.Int(load_default=None, metadata={"example": 20}, allow_none=True),
     }
 
     def post(self, args):
diff --git a/openflexure_microscope/api/v2/views/stage.py b/openflexure_microscope/api/v2/views/stage.py
index bcfec3a9..c6437a24 100644
--- a/openflexure_microscope/api/v2/views/stage.py
+++ b/openflexure_microscope/api/v2/views/stage.py
@@ -7,7 +7,7 @@ class StageTypeProperty(PropertyView):
     """The type of the stage"""
 
     schema = fields.String(
-        load_default=None,
+        load_default="SangaStage",
         validate=validate.OneOf(["SangaStage", "SangaDeltaStage"]),
         metadata={
             "description": "The translation stage geometry",
diff --git a/openflexure_microscope/camera/pi.py b/openflexure_microscope/camera/pi.py
index f3a1db16..e46360fa 100644
--- a/openflexure_microscope/camera/pi.py
+++ b/openflexure_microscope/camera/pi.py
@@ -30,7 +30,7 @@ import logging
 import time
 
 # Type hinting
-from typing import BinaryIO, Tuple, Union, Optional
+from typing import BinaryIO, Optional, Tuple, Union
 
 import numpy as np
 
diff --git a/openflexure_microscope/config.py b/openflexure_microscope/config.py
index 8ceed138..b2db8546 100644
--- a/openflexure_microscope/config.py
+++ b/openflexure_microscope/config.py
@@ -5,7 +5,6 @@ import os
 import shutil
 from typing import Optional
 
-
 from .json import JSONEncoder
 from .paths import CONFIGURATION_FILE_PATH, SETTINGS_FILE_PATH
 

From 3f9c3447de7ccdcb2d5c1f53aa22b78d4ac73663 Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Thu, 23 Mar 2023 13:31:25 +0000
Subject: [PATCH 19/25] Fixed typos in comments spotted in code review

---
 openflexure_microscope/api/default_extensions/autofocus.py | 4 ++--
 openflexure_microscope/api/openapi.py                      | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/openflexure_microscope/api/default_extensions/autofocus.py b/openflexure_microscope/api/default_extensions/autofocus.py
index 045a7878..0f953c11 100644
--- a/openflexure_microscope/api/default_extensions/autofocus.py
+++ b/openflexure_microscope/api/default_extensions/autofocus.py
@@ -543,7 +543,7 @@ class AutofocusExtension(BaseExtension):
             "delay": fields.Int(
                 load_default=5,
                 metadata={
-                    "description": "How long to measure sharpness for after the move",
+                    "description": "How long to measure sharpness for after the move, in seconds",
                     "example": 5,
                 },
             ),
@@ -582,7 +582,7 @@ class AutofocusExtension(BaseExtension):
             "initial_move_up": fields.Bool(
                 load_default=True,
                 metadata={
-                    "description": "Set to Flase to disable the initial move upwards"
+                    "description": "Set to False to disable the initial move upwards"
                 },
             ),
             "backlash": fields.Int(
diff --git a/openflexure_microscope/api/openapi.py b/openflexure_microscope/api/openapi.py
index 77677740..006b518c 100644
--- a/openflexure_microscope/api/openapi.py
+++ b/openflexure_microscope/api/openapi.py
@@ -9,7 +9,7 @@ API_TAGS = [
         ),
         "externalDocs": {
             "url": "https://www.w3.org/TR/wot-thing-description/#actionaffordance",
-            "description": "w3's description of Web of Things 'Action' resources.",
+            "description": "W3C's description of Web of Things 'Action' resources.",
         },
     },
     {
@@ -20,7 +20,7 @@ API_TAGS = [
         ),
         "externalDocs": {
             "url": "https://www.w3.org/TR/wot-thing-description/#propertyaffordance",
-            "description": "w3's description of Web of Things 'Property' resources.",
+            "description": "W3C's description of Web of Things 'Property' resources.",
         },
     },
     {"name": "captures", "description": ""},

From 62eef8f8e1b2fd460f1e5204362e1d409b7998ac Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Mon, 3 Apr 2023 20:32:52 +0100
Subject: [PATCH 20/25] Re-lock dependencies on a Raspberry Pi

I couldn't install this on a Pi, because it incorrectly chose
versions of e.g. numpy that did not exist in binary form for the
pi. I re-locked dependencies with:

`PIP_ONLY_BINARY=":all:" pipenv lock --dev`

This forced the use of wheels, and not only completed but did so
in ~10 minutes.
---
 Pipfile.lock | 215 ++++++++++++++++++++++++++-------------------------
 1 file changed, 111 insertions(+), 104 deletions(-)

diff --git a/Pipfile.lock b/Pipfile.lock
index 620fd3f2..ecb75ddd 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -163,14 +163,6 @@
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@@ -483,41 +475,39 @@
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@@ -796,6 +786,19 @@
             "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
             "version": "==0.1.4"
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@@ -900,11 +903,11 @@
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@@ -1156,14 +1159,6 @@
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@@ -1659,41 +1654,39 @@
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@@ -1763,10 +1756,11 @@
         },
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@@ -1978,11 +1972,11 @@
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             "hashes": [
@@ -2037,6 +2031,19 @@
             "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
             "version": "==0.1.4"
         },
+        "rpi.gpio": {
+            "hashes": [
+                "sha256:15311d3b063b71dee738cd26570effc9985a952454d162937c34e08c0fc99902",
+                "sha256:26b2ade4bb353bbe5417a64e40b45cdf00a82f27c2d320c0dd46c59751959d77",
+                "sha256:29226823da8b5ccb9001d795a944f2e00924eeae583490f0bc7317581172c624",
+                "sha256:57b6c044ef5375a78c8dda27cdfadf329e76aa6943cd6cffbbbd345a9adf9ca5",
+                "sha256:77afb817b81331ce3049a4b8f94a85e41b7c404d8e56b61ac0f1eb75c3120868",
+                "sha256:96ea7e5bf6bf592828487bfa7d3d1d0e432d5d1682e9e33b4dab398914628fcd",
+                "sha256:b86b66dc02faa5461b443a1e1f0c1d209d64ab5229696f32fb3b0215e0600c8c",
+                "sha256:cd61c4b03c37b62bba4a5acfea9862749c33c618e0295e7e90aa4713fb373b70"
+            ],
+            "version": "==0.7.1"
+        },
         "ruamel.yaml": {
             "hashes": [
                 "sha256:5a81d994d11f98c7e7288636ea5bef647359641353411cebf8d2cce3a4a12385",
@@ -2141,11 +2148,11 @@
         },
         "setuptools": {
             "hashes": [
-                "sha256:2ee892cd5f29f3373097f5a814697e397cf3ce313616df0af11231e2ad118077",
-                "sha256:b78aaa36f6b90a074c1fa651168723acbf45d14cb1196b6f02c0fd07f17623b2"
+                "sha256:257de92a9d50a60b8e22abfcbb771571fde0dbf3ec234463212027a4eeecbe9a",
+                "sha256:e728ca814a823bf7bf60162daf9db95b93d532948c4c0bea762ce62f60189078"
             ],
             "markers": "python_version >= '3.7'",
-            "version": "==67.6.0"
+            "version": "==67.6.1"
         },
         "six": {
             "hashes": [
@@ -2268,11 +2275,11 @@
         },
         "tomlkit": {
             "hashes": [
-                "sha256:07de26b0d8cfc18f871aec595fda24d95b08fef89d147caa861939f37230bf4b",
-                "sha256:71b952e5721688937fb02cf9d354dbcf0785066149d2855e44531ebdd2b65d73"
+                "sha256:5325463a7da2ef0c6bbfefb62a3dc883aebe679984709aee32a317907d0a8d3c",
+                "sha256:f392ef70ad87a672f02519f99967d28a4d3047133e2d1df936511465fbb3791d"
             ],
-            "markers": "python_version >= '3.6'",
-            "version": "==0.11.6"
+            "markers": "python_version >= '3.7'",
+            "version": "==0.11.7"
         },
         "typed-ast": {
             "hashes": [
@@ -2308,17 +2315,17 @@
         },
         "types-python-dateutil": {
             "hashes": [
-                "sha256:c640f2eb71b4b94a9d3bfda4c04250d29a24e51b8bad6e12fddec0cf6e96f7a3",
-                "sha256:fbecd02c19cac383bf4a16248d45ffcff17c93a04c0794be5f95d42c6aa5de39"
+                "sha256:357553f8056cfbb8ce8ea0ca4a6a3480268596748360df73a94c2b8c113a5b06",
+                "sha256:de66222c54318c2e05ceb4956976d16696240a45fc2c98e54bfe9a56ce5e1eff"
             ],
-            "version": "==2.8.19.10"
+            "version": "==2.8.19.11"
         },
         "types-setuptools": {
             "hashes": [
-                "sha256:3a708e66c7bdc620e4d0439f344c750c57a4340c895a4c3ed2d0fc4ae8eb9962",
-                "sha256:dae5a4a659dbb6dba57773440f6e2dbdd8ef282dc136a174a8a59bd33d949945"
+                "sha256:a5efd019b53c5793a112e0112b91bb402df749f75ee7abe681b6240841650ce4",
+                "sha256:fb46e651c6b5880ec8932a8876aa832071d612b2954fc5156b09cd263927d85b"
             ],
-            "version": "==67.6.0.5"
+            "version": "==67.6.0.6"
         },
         "typing-extensions": {
             "hashes": [

From 12fd9a5f4a32ec189d92678a03f4ccb7e664001e Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Mon, 3 Apr 2023 20:38:57 +0100
Subject: [PATCH 21/25] Mention dependencies in readme

---
 README.md | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 6f080169..9fc174db 100644
--- a/README.md
+++ b/README.md
@@ -69,7 +69,7 @@ To set up a development version of the software (most likely using emulated came
 * Create a virtual environment and activate it:
   * `python -m venv .venv`
   * `source .venv/bin/activate` (on Linux) or `.venv/Scripts/activate` (on Windows)
-  * `pip install pipenv`
+  * `pip install --upgrade pip wheel pipenv`
   * `pipenv install --dev` (This will install development dependencies.  If you don't need these, `pipenv install` will get you just the dependencies needed to run the server, which takes about half the time.)
 * Finally, run the server:
   * You can use `ofm serve` or `ofm restart` on the Raspberry Pi to manage the server.
@@ -146,6 +146,9 @@ As of `2.10.0b0` we have switched to using `pipenv` for managing dependencies, a
 * `pyproject.toml` is retained, but *no longer includes package metadata or dependencies* and does not have a `[tool.poetry]` table.  It does define the build system as per PEP517, which is `setuptools`, and it also contains settings for `black`, `poe` and `isort`.
 * `Pipfile` is very minimal, and only declares dependencies on the current module, i.e. the dependencies declared in `setup.py`.  It also specifies the Python version.  This allows us to single-source dependency information from `setup.py` but use the dependency resolution/locking functionality of `pipenv`
 * `Pipfile.lock` locks the dependency versions in the same way as `poetry.lock` used to, i.e. it specifies exact versions of everything, derived from the looser specifications in `setup.py`.
+* Dependency resolution is a pain, in part because compiling packages like scipy and numpy from source on a Pi is slow and unreliable. To avoid this, we usually lock the dependencies on a Raspberry Pi, using:
+  `PIP_ONLY_BINARY=":all:" pipenv lock --dev`
+  This forces the use of wheels only, and thus restricts us to things that built OK on Piwheels.  The resulting Pipfile.lock should then work nicely on other Raspberry Pis (as well as other platforms).
 
 ## Creating releases
 

From fdafeca4465de42a683d7a0b06649251edda7e2b Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Mon, 3 Apr 2023 22:03:57 +0100
Subject: [PATCH 22/25] Only consider piwheels in Pipfile

Including both piwheels and pypi in Pipfile caused hash mismatches,
which caused installation to fail. I've removed pypi, but this may
break installation on other platforms.

I may need to duplicate Pipfile and Pipfile.lock, one for Pi and
one for non-Pi platforms.

I can confim this commit installed successfully on a Pi.
---
 Pipfile      |   5 -
 Pipfile.lock | 305 +++++++++++++++++++--------------------------------
 2 files changed, 115 insertions(+), 195 deletions(-)

diff --git a/Pipfile b/Pipfile
index 41154045..5e1b4315 100644
--- a/Pipfile
+++ b/Pipfile
@@ -1,8 +1,3 @@
-[[source]]
-url = "https://pypi.python.org/simple"
-verify_ssl = true
-name = "pypi"
-
 [[source]]
 url = "https://www.piwheels.org/simple"
 verify_ssl = true
diff --git a/Pipfile.lock b/Pipfile.lock
index ecb75ddd..7ded8cd7 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -1,18 +1,13 @@
 {
     "_meta": {
         "hash": {
-            "sha256": "d9e26ffd8878bb646a19ad3fbbd184b817225750a442ce5e858889415f011a41"
+            "sha256": "742e956ae3ee7147a09b3b6b6c32efbc74e7ff3e6e392f85b851441840ac55a6"
         },
         "pipfile-spec": 6,
         "requires": {
             "python_version": "3.7"
         },
         "sources": [
-            {
-                "name": "pypi",
-                "url": "https://pypi.python.org/simple",
-                "verify_ssl": true
-            },
             {
                 "name": "piwheels",
                 "url": "https://www.piwheels.org/simple",
@@ -44,6 +39,7 @@
         "attrs": {
             "hashes": [
                 "sha256:29e95c7f6778868dbd49170f98f8818f78f3dc5e0e37c0b1f474e3561b240836",
+                "sha256:52dd1548aaa4d65af91f99015a21718f8bbd3a45577e565cdd28b8a891da97a5",
                 "sha256:c9227bfc2f01993c03f68db37d1d15c9690188323c067c641f1a35ca58185f99"
             ],
             "markers": "python_version >= '3.6'",
@@ -60,7 +56,8 @@
         "certifi": {
             "hashes": [
                 "sha256:35824b4c3a97115964b408844d64aa14db1cc518f6562e8d7261699d1350a9e3",
-                "sha256:4ad3232f5e926d6718ec31cfc1fcadfde020920e278684144551c91769c7bc18"
+                "sha256:4ad3232f5e926d6718ec31cfc1fcadfde020920e278684144551c91769c7bc18",
+                "sha256:cb52c7519140a4c2b84314220b3f08768882bb58176f3acc039ccac101d51870"
             ],
             "markers": "python_version >= '3.6'",
             "version": "==2022.12.7"
@@ -75,84 +72,10 @@
         },
         "charset-normalizer": {
             "hashes": [
-                "sha256:04afa6387e2b282cf78ff3dbce20f0cc071c12dc8f685bd40960cc68644cfea6",
-                "sha256:04eefcee095f58eaabe6dc3cc2262f3bcd776d2c67005880894f447b3f2cb9c1",
-                "sha256:0be65ccf618c1e7ac9b849c315cc2e8a8751d9cfdaa43027d4f6624bd587ab7e",
-                "sha256:0c95f12b74681e9ae127728f7e5409cbbef9cd914d5896ef238cc779b8152373",
-                "sha256:0ca564606d2caafb0abe6d1b5311c2649e8071eb241b2d64e75a0d0065107e62",
-                "sha256:10c93628d7497c81686e8e5e557aafa78f230cd9e77dd0c40032ef90c18f2230",
-                "sha256:11d117e6c63e8f495412d37e7dc2e2fff09c34b2d09dbe2bee3c6229577818be",
-                "sha256:11d3bcb7be35e7b1bba2c23beedac81ee893ac9871d0ba79effc7fc01167db6c",
-                "sha256:12a2b561af122e3d94cdb97fe6fb2bb2b82cef0cdca131646fdb940a1eda04f0",
-                "sha256:12d1a39aa6b8c6f6248bb54550efcc1c38ce0d8096a146638fd4738e42284448",
-                "sha256:1435ae15108b1cb6fffbcea2af3d468683b7afed0169ad718451f8db5d1aff6f",
-                "sha256:1c60b9c202d00052183c9be85e5eaf18a4ada0a47d188a83c8f5c5b23252f649",
-                "sha256:1e8fcdd8f672a1c4fc8d0bd3a2b576b152d2a349782d1eb0f6b8e52e9954731d",
-                "sha256:20064ead0717cf9a73a6d1e779b23d149b53daf971169289ed2ed43a71e8d3b0",
-                "sha256:21fa558996782fc226b529fdd2ed7866c2c6ec91cee82735c98a197fae39f706",
-                "sha256:22908891a380d50738e1f978667536f6c6b526a2064156203d418f4856d6e86a",
-                "sha256:3160a0fd9754aab7d47f95a6b63ab355388d890163eb03b2d2b87ab0a30cfa59",
-                "sha256:322102cdf1ab682ecc7d9b1c5eed4ec59657a65e1c146a0da342b78f4112db23",
-                "sha256:34e0a2f9c370eb95597aae63bf85eb5e96826d81e3dcf88b8886012906f509b5",
-                "sha256:3573d376454d956553c356df45bb824262c397c6e26ce43e8203c4c540ee0acb",
-                "sha256:3747443b6a904001473370d7810aa19c3a180ccd52a7157aacc264a5ac79265e",
-                "sha256:38e812a197bf8e71a59fe55b757a84c1f946d0ac114acafaafaf21667a7e169e",
-                "sha256:3a06f32c9634a8705f4ca9946d667609f52cf130d5548881401f1eb2c39b1e2c",
-                "sha256:3a5fc78f9e3f501a1614a98f7c54d3969f3ad9bba8ba3d9b438c3bc5d047dd28",
-                "sha256:3d9098b479e78c85080c98e1e35ff40b4a31d8953102bb0fd7d1b6f8a2111a3d",
-                "sha256:3dc5b6a8ecfdc5748a7e429782598e4f17ef378e3e272eeb1340ea57c9109f41",
-                "sha256:4155b51ae05ed47199dc5b2a4e62abccb274cee6b01da5b895099b61b1982974",
-                "sha256:49919f8400b5e49e961f320c735388ee686a62327e773fa5b3ce6721f7e785ce",
-                "sha256:53d0a3fa5f8af98a1e261de6a3943ca631c526635eb5817a87a59d9a57ebf48f",
-                "sha256:5f008525e02908b20e04707a4f704cd286d94718f48bb33edddc7d7b584dddc1",
-                "sha256:628c985afb2c7d27a4800bfb609e03985aaecb42f955049957814e0491d4006d",
-                "sha256:65ed923f84a6844de5fd29726b888e58c62820e0769b76565480e1fdc3d062f8",
-                "sha256:6734e606355834f13445b6adc38b53c0fd45f1a56a9ba06c2058f86893ae8017",
-                "sha256:6baf0baf0d5d265fa7944feb9f7451cc316bfe30e8df1a61b1bb08577c554f31",
-                "sha256:6f4f4668e1831850ebcc2fd0b1cd11721947b6dc7c00bf1c6bd3c929ae14f2c7",
-                "sha256:6f5c2e7bc8a4bf7c426599765b1bd33217ec84023033672c1e9a8b35eaeaaaf8",
-                "sha256:6f6c7a8a57e9405cad7485f4c9d3172ae486cfef1344b5ddd8e5239582d7355e",
-                "sha256:7381c66e0561c5757ffe616af869b916c8b4e42b367ab29fedc98481d1e74e14",
-                "sha256:73dc03a6a7e30b7edc5b01b601e53e7fc924b04e1835e8e407c12c037e81adbd",
-                "sha256:74db0052d985cf37fa111828d0dd230776ac99c740e1a758ad99094be4f1803d",
-                "sha256:75f2568b4189dda1c567339b48cba4ac7384accb9c2a7ed655cd86b04055c795",
-                "sha256:78cacd03e79d009d95635e7d6ff12c21eb89b894c354bd2b2ed0b4763373693b",
-                "sha256:80d1543d58bd3d6c271b66abf454d437a438dff01c3e62fdbcd68f2a11310d4b",
-                "sha256:830d2948a5ec37c386d3170c483063798d7879037492540f10a475e3fd6f244b",
-                "sha256:891cf9b48776b5c61c700b55a598621fdb7b1e301a550365571e9624f270c203",
-                "sha256:8f25e17ab3039b05f762b0a55ae0b3632b2e073d9c8fc88e89aca31a6198e88f",
-                "sha256:9a3267620866c9d17b959a84dd0bd2d45719b817245e49371ead79ed4f710d19",
-                "sha256:a04f86f41a8916fe45ac5024ec477f41f886b3c435da2d4e3d2709b22ab02af1",
-                "sha256:aaf53a6cebad0eae578f062c7d462155eada9c172bd8c4d250b8c1d8eb7f916a",
-                "sha256:abc1185d79f47c0a7aaf7e2412a0eb2c03b724581139193d2d82b3ad8cbb00ac",
-                "sha256:ac0aa6cd53ab9a31d397f8303f92c42f534693528fafbdb997c82bae6e477ad9",
-                "sha256:ac3775e3311661d4adace3697a52ac0bab17edd166087d493b52d4f4f553f9f0",
-                "sha256:b06f0d3bf045158d2fb8837c5785fe9ff9b8c93358be64461a1089f5da983137",
-                "sha256:b116502087ce8a6b7a5f1814568ccbd0e9f6cfd99948aa59b0e241dc57cf739f",
-                "sha256:b82fab78e0b1329e183a65260581de4375f619167478dddab510c6c6fb04d9b6",
-                "sha256:bd7163182133c0c7701b25e604cf1611c0d87712e56e88e7ee5d72deab3e76b5",
-                "sha256:c36bcbc0d5174a80d6cccf43a0ecaca44e81d25be4b7f90f0ed7bcfbb5a00909",
-                "sha256:c3af8e0f07399d3176b179f2e2634c3ce9c1301379a6b8c9c9aeecd481da494f",
-                "sha256:c84132a54c750fda57729d1e2599bb598f5fa0344085dbde5003ba429a4798c0",
-                "sha256:cb7b2ab0188829593b9de646545175547a70d9a6e2b63bf2cd87a0a391599324",
-                "sha256:cca4def576f47a09a943666b8f829606bcb17e2bc2d5911a46c8f8da45f56755",
-                "sha256:cf6511efa4801b9b38dc5546d7547d5b5c6ef4b081c60b23e4d941d0eba9cbeb",
-                "sha256:d16fd5252f883eb074ca55cb622bc0bee49b979ae4e8639fff6ca3ff44f9f854",
-                "sha256:d2686f91611f9e17f4548dbf050e75b079bbc2a82be565832bc8ea9047b61c8c",
-                "sha256:d7fc3fca01da18fbabe4625d64bb612b533533ed10045a2ac3dd194bfa656b60",
-                "sha256:dd5653e67b149503c68c4018bf07e42eeed6b4e956b24c00ccdf93ac79cdff84",
-                "sha256:de5695a6f1d8340b12a5d6d4484290ee74d61e467c39ff03b39e30df62cf83a0",
-                "sha256:e0ac8959c929593fee38da1c2b64ee9778733cdf03c482c9ff1d508b6b593b2b",
-                "sha256:e1b25e3ad6c909f398df8921780d6a3d120d8c09466720226fc621605b6f92b1",
-                "sha256:e633940f28c1e913615fd624fcdd72fdba807bf53ea6925d6a588e84e1151531",
-                "sha256:e89df2958e5159b811af9ff0f92614dabf4ff617c03a4c1c6ff53bf1c399e0e1",
-                "sha256:ea9f9c6034ea2d93d9147818f17c2a0860d41b71c38b9ce4d55f21b6f9165a11",
-                "sha256:f645caaf0008bacf349875a974220f1f1da349c5dbe7c4ec93048cdc785a3326",
-                "sha256:f8303414c7b03f794347ad062c0516cee0e15f7a612abd0ce1e25caf6ceb47df",
-                "sha256:fca62a8301b605b954ad2e9c3666f9d97f63872aa4efcae5492baca2056b74ab"
+                "sha256:1799ad8111efa28db62e1b9773eba32dcc9fd0cd9d7c631bd4858eb15a30f858"
             ],
             "markers": "python_full_version >= '3.7.0'",
-            "version": "==3.1.0"
+            "version": "==3.0.1"
         },
         "click": {
             "hashes": [
@@ -187,6 +110,7 @@
                 "sha256:420f94a35e3e00a2b43ad5740f935358e24478354ce41c99407cddd283be00d2",
                 "sha256:4ac0f522c3b6109c4b764ffec71bf04ebc0523e926ca7cbe6c5ac88f84faced0",
                 "sha256:4c752d5264053a7cf2fe81c9e14f8a4fb261370a7bb344c2a011836a96fb3f57",
+                "sha256:4eef796938e3759c6b6814dbd615b1d3597a376b3174d05aed9f75f6fc6a1650",
                 "sha256:4f01911c010122f49a3e9bdc730eccc66f9b72bd410a3a9d3cb8448bb50d65d3",
                 "sha256:4f68ee32d7c4164f1e2c8797535a6d0a3733355f5861e0f667e37df2d4b07140",
                 "sha256:4fa54fb483decc45f94011898727802309a109d89446a3c76387d016057d2c84",
@@ -222,7 +146,8 @@
                 "sha256:db8c2c5ace167fd25ab5dd732714c51d4633f58bac21fb0ff63b0349f62755a8",
                 "sha256:e2926b8abedf750c2ecf5035c07515770944acf02e1c46ab08f6348d24c5f94d",
                 "sha256:e627dee428a176ffb13697a2c4318d3f60b2ccdde3acdc9b3f304206ec130ccd",
-                "sha256:efe1c0adad110bf0ad7fb59f833880e489a61e39d699d37249bdf42f80590169"
+                "sha256:efe1c0adad110bf0ad7fb59f833880e489a61e39d699d37249bdf42f80590169",
+                "sha256:f47e4fd792793c19b66a09a7c79390490d7707dfc9c8c1a42cbd55110c73468b"
             ],
             "markers": "python_version >= '3.7'",
             "version": "==7.2.2"
@@ -230,6 +155,7 @@
         "exceptiongroup": {
             "hashes": [
                 "sha256:232c37c63e4f682982c8b6459f33a8981039e5fb8756b2074364e5055c498c9e",
+                "sha256:64c69a1565ab9821c7aaca26c5457827f8b899595b9a1e9ab78abbf10e8b17a5",
                 "sha256:d484c3090ba2889ae2928419117447a14daf3c1231d5e30d0aae34f354f01785"
             ],
             "markers": "python_version < '3.11'",
@@ -260,6 +186,7 @@
         },
         "future": {
             "hashes": [
+                "sha256:06cf12592a81bdba6c2f05be3be47da76c8beedce11c5539e5edea9de9b9eac6",
                 "sha256:34a17436ed1e96697a86f9de3d15a3b0be01d8bc8de9c1dffd59fb8234ed5307"
             ],
             "markers": "python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'",
@@ -268,7 +195,8 @@
         "idna": {
             "hashes": [
                 "sha256:814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4",
-                "sha256:90b77e79eaa3eba6de819a0c442c0b4ceefc341a7a2ab77d7562bf49f425c5c2"
+                "sha256:90b77e79eaa3eba6de819a0c442c0b4ceefc341a7a2ab77d7562bf49f425c5c2",
+                "sha256:bcac1132a4eadea8321490704e2349b752e29c6ec2f1c27d372010e76ebd3fa1"
             ],
             "markers": "python_version >= '3.5'",
             "version": "==3.4"
@@ -284,6 +212,7 @@
         "importlib-metadata": {
             "hashes": [
                 "sha256:43ce9281e097583d758c2c708c4376371261a02c34682491a8e98352365aad20",
+                "sha256:ab197eeef247b9bfe3d3d91334921e09626181362991c0479b1340aabc00532f",
                 "sha256:ff80f3b5394912eb1b108fcfd444dc78b7f1f3e16b16188054bd01cb9cb86f09"
             ],
             "markers": "python_version < '3.8'",
@@ -292,7 +221,8 @@
         "importlib-resources": {
             "hashes": [
                 "sha256:4be82589bf5c1d7999aedf2a45159d10cb3ca4f19b2271f8792bc8e6da7b22f6",
-                "sha256:7b1deeebbf351c7578e09bf2f63fa2ce8b5ffec296e0d349139d43cca061a81a"
+                "sha256:7b1deeebbf351c7578e09bf2f63fa2ce8b5ffec296e0d349139d43cca061a81a",
+                "sha256:f36205b58b84e2f35777817eb7ac6506a21982ad9954a72ab0833abf36c44183"
             ],
             "markers": "python_version < '3.9'",
             "version": "==5.12.0"
@@ -332,7 +262,8 @@
         "jsonschema-spec": {
             "hashes": [
                 "sha256:34471d8b60e1f06d174236c4d3cf9590fbf3cff1cc733b28d15cd83672bcd062",
-                "sha256:824c743197bbe2104fcc6dce114a4082bf7f7efdebf16683510cb0ec6d8d53d0"
+                "sha256:824c743197bbe2104fcc6dce114a4082bf7f7efdebf16683510cb0ec6d8d53d0",
+                "sha256:8a9534ec1165fd4e5727c758e848a1e0129e704dc87010bf739c592b0b1f4d55"
             ],
             "markers": "python_full_version >= '3.7.0' and python_full_version < '4.0.0'",
             "version": "==0.1.4"
@@ -350,6 +281,7 @@
             "hashes": [
                 "sha256:09763491ce220c0299688940f8dc2c5d05fd1f45af1e42e636b2e8b2303e4382",
                 "sha256:0a891e4e41b54fd5b8313b96399f8b0e173bbbfc03c7631f01efbe29bb0bcf82",
+                "sha256:0e988a556683ec90e9f3284c650746cfadc122effd9073d3db065e145403f7c7",
                 "sha256:189bbd5d41ae7a498397287c408617fe5c48633e7755287b21d741f7db2706a9",
                 "sha256:18b78ec83edbbeb69efdc0e9c1cb41a3b1b1ed11ddd8ded602464c3fc6020494",
                 "sha256:1aa3de4088c89a1b69f8ec0dcc169aa725b0ff017899ac568fe44ddc1396df46",
@@ -373,6 +305,7 @@
                 "sha256:b40387277b0ed2d0602b8293b94d7257e17d1479e257b4de114ea11a8cb7f2d7",
                 "sha256:bfb38f9ffb53b942f2b5954e0f610f1e721ccebe9cce9025a38c8ccf4a5183a4",
                 "sha256:cbf9b082426036e19c6924a9ce90c740a9861e2bdc27a4834fd0a910742ac1e8",
+                "sha256:cd6184026be98242806204c8dc2398d5bbd19ea105ec93826af5f6176b7913e3",
                 "sha256:d9e25ef10a39e8afe59a5c348a4dbf29b4868ab76269f81ce1674494e2565a6e",
                 "sha256:db1c1722726f47e10e0b5fdbf15ac3b8adb58c091d12b3ab713965795036985f",
                 "sha256:e7c21c95cae3c05c14aafffe2865bbd5e377cfc1348c4f7751d9dc9a48ca4bda",
@@ -467,11 +400,10 @@
         },
         "marshmallow": {
             "hashes": [
-                "sha256:90032c0fd650ce94b6ec6dc8dfeb0e3ff50c144586462c389b81a07205bedb78",
-                "sha256:93f0958568da045b0021ec6aeb7ac37c81bfcccbb9a0e7ed8559885070b3a19b"
+                "sha256:d41d690f5e799ebd9a97e761be71524ca3a728442e01c029dd029654778e0797"
             ],
             "markers": "python_version >= '3.7'",
-            "version": "==3.19.0"
+            "version": "==3.18.0"
         },
         "numpy": {
             "hashes": [
@@ -488,6 +420,8 @@
                 "sha256:69077388c5a4b997442b843dbdc3a85b420fb693ec8e33020bb24d647c164fa5",
                 "sha256:74b85a17528ca60cf98381a5e779fc0264b4a88b46025e6bcbe9621f46bb3e63",
                 "sha256:81225e58ef5fce7f1d80399575576fc5febec79a8a2742e8ef86d7b03beef49f",
+                "sha256:826319c22f05d7b50c3637af5563234edbb02f5634a08d314d21ef00271a32fe",
+                "sha256:8731b4e638adcdefe10ecad3d8c3ae60eec7311cdfd34ecdb72a41df56071be8",
                 "sha256:8890b3360f345e8360133bc078d2dacc2843b6ee6059b568781b15b97acbe39f",
                 "sha256:92aafa03da8658609f59f18722b88f0a73a249101169e28415b4fa148caf7e41",
                 "sha256:9864424631775b0c052f3bd98bc2712d131b3e2cd95d1c0c68b91709170890b0",
@@ -511,6 +445,7 @@
         },
         "openapi-schema-validator": {
             "hashes": [
+                "sha256:33661cd8a06d5112dec52d758dda55e543e4a7c9f0efc2901dcf83ebd5604055",
                 "sha256:79f37f38ef9fd5206b924ed7a6f382cea7b649b3b56383c47f1906082b7b9015",
                 "sha256:c573e2be2c783abae56c5a1486ab716ca96e09d1c3eab56020d1dc680aa57bf8"
             ],
@@ -520,7 +455,8 @@
         "openapi-spec-validator": {
             "hashes": [
                 "sha256:1189d0618ae0678ccf6c883cc1266d381454eece6f21fcf330cc7caea5fc25eb",
-                "sha256:4145478f26df16059c147406eaaa59b77ff60e3461ba6edb9aa84d481ed89aaf"
+                "sha256:4145478f26df16059c147406eaaa59b77ff60e3461ba6edb9aa84d481ed89aaf",
+                "sha256:92721d4a905a1e47a574d67f38dad32b64f7146b3f63d18edf0f3aa97afad207"
             ],
             "version": "==0.5.6"
         },
@@ -636,6 +572,7 @@
             ],
             "hashes": [
                 "sha256:814a523bc1ff18383c12cb523ce44c90fe8792bf5f48d8cc33c9f658276658ed",
+                "sha256:a9d0389da9919cf266a6668aeb1dec294f844f99c256ee6c2e36a9451b69a57b",
                 "sha256:c15e9ca889b56262e4c2aee354f52918ba5e54f46bb3da42b806d8bbd8255ee9"
             ],
             "version": "==0.22.11.4.0"
@@ -672,6 +609,7 @@
         "pyrsistent": {
             "hashes": [
                 "sha256:016ad1afadf318eb7911baa24b049909f7f3bb2c5b1ed7b6a8f21db21ea3faa8",
+                "sha256:0a76a451d782433be74a500c6a072d1c6669481bfcbcdd985d12f0965fa6b87e",
                 "sha256:1a2994773706bbb4995c31a97bc94f1418314923bd1048c6d964837040376440",
                 "sha256:20460ac0ea439a3e79caa1dbd560344b64ed75e85d8703943e0b66c2a6150e4a",
                 "sha256:3311cb4237a341aa52ab8448c27e3a9931e2ee09561ad150ba94e4cfd3fc888c",
@@ -681,6 +619,7 @@
                 "sha256:49c32f216c17148695ca0e02a5c521e28a4ee6c5089f97e34fe24163113722da",
                 "sha256:4b774f9288dda8d425adb6544e5903f1fb6c273ab3128a355c6b972b7df39dcf",
                 "sha256:4c18264cb84b5e68e7085a43723f9e4c1fd1d935ab240ce02c0324a8e01ccb64",
+                "sha256:55ff9ca4735904a3897f5d03170c56122b724bf2ead32def8999fbb6949c7bb5",
                 "sha256:5a474fb80f5e0d6c9394d8db0fc19e90fa540b82ee52dba7d246a7791712f74a",
                 "sha256:64220c429e42a7150f4bfd280f6f4bb2850f95956bde93c6fda1b70507af6ef3",
                 "sha256:878433581fc23e906d947a6814336eee031a00e6defba224234169ae3d3d6a98",
@@ -712,6 +651,7 @@
         "pytest": {
             "hashes": [
                 "sha256:130328f552dcfac0b1cec75c12e3f005619dc5f874f0a06e8ff7263f0ee6225e",
+                "sha256:a6377f55b06d85889e6db60ee185b02e0aa87af517ec2eec93075d1a9bc22648",
                 "sha256:c99ab0c73aceb050f68929bc93af19ab6db0558791c6a0715723abe9d0ade9d4"
             ],
             "markers": "python_version >= '3.7'",
@@ -773,7 +713,8 @@
         "requests": {
             "hashes": [
                 "sha256:64299f4909223da747622c030b781c0d7811e359c37124b4bd368fb8c6518baa",
-                "sha256:98b1b2782e3c6c4904938b84c0eb932721069dfdb9134313beff7c83c2df24bf"
+                "sha256:98b1b2782e3c6c4904938b84c0eb932721069dfdb9134313beff7c83c2df24bf",
+                "sha256:e77536e318369f207754c018f33a97b68adec830f33bee3507d296683ba1d416"
             ],
             "markers": "python_version >= '3.7' and python_version < '4'",
             "version": "==2.28.2"
@@ -789,13 +730,16 @@
         "rpi.gpio": {
             "hashes": [
                 "sha256:15311d3b063b71dee738cd26570effc9985a952454d162937c34e08c0fc99902",
+                "sha256:231f6142c25975a7e39b96faf4905f05f97dba6809e8c5f0d58f284b35b4b821",
                 "sha256:26b2ade4bb353bbe5417a64e40b45cdf00a82f27c2d320c0dd46c59751959d77",
                 "sha256:29226823da8b5ccb9001d795a944f2e00924eeae583490f0bc7317581172c624",
+                "sha256:5073d1972727cfad38a1a42f02da91dc41f137679290aa804ab6c410168347ac",
                 "sha256:57b6c044ef5375a78c8dda27cdfadf329e76aa6943cd6cffbbbd345a9adf9ca5",
                 "sha256:77afb817b81331ce3049a4b8f94a85e41b7c404d8e56b61ac0f1eb75c3120868",
                 "sha256:96ea7e5bf6bf592828487bfa7d3d1d0e432d5d1682e9e33b4dab398914628fcd",
                 "sha256:b86b66dc02faa5461b443a1e1f0c1d209d64ab5229696f32fb3b0215e0600c8c",
-                "sha256:cd61c4b03c37b62bba4a5acfea9862749c33c618e0295e7e90aa4713fb373b70"
+                "sha256:cd61c4b03c37b62bba4a5acfea9862749c33c618e0295e7e90aa4713fb373b70",
+                "sha256:e5dfec2c4ccb7dbe9eef3dfc76a3b04121fc62d77fd8fbe1a8e841468a1b0c4c"
             ],
             "version": "==0.7.1"
         },
@@ -827,9 +771,11 @@
                 "sha256:763d65baa3b952479c4e972669f679fe490eee058d5aa85da483ebae2009d231",
                 "sha256:7bdb4c06b063f6fd55e472e201317a3bb6cdeeee5d5a38512ea5c01e1acbdd93",
                 "sha256:8831a2cedcd0f0927f788c5bdf6567d9dc9cc235646a434986a852af1cb54b4b",
+                "sha256:8f73b665f03f70986e4b5c4708b9e553b931d34b815032452327fa7c2a9099bf",
                 "sha256:91a789b4aa0097b78c93e3dc4b40040ba55bef518f84a40d4442f713b4094acb",
                 "sha256:92460ce908546ab69770b2e576e4f99fbb4ce6ab4b245345a3869a0a0410488f",
                 "sha256:99e77daab5d13a48a4054803d052ff40780278240a902b880dd37a51ba01a307",
+                "sha256:9c361022618feec80a1d5e874970d8dae234815097638ed104a40593b602eb5c",
                 "sha256:a234a20ae07e8469da311e182e70ef6b199d0fbeb6c6cc2901204dd87fb867e8",
                 "sha256:a7b301ff08055d73223058b5c46c55638917f04d21577c95e00e0c4d79201a6b",
                 "sha256:be2a7ad8fd8f7442b24323d24ba0b56c51219513cfa45b9ada3b87b76c374d4b",
@@ -852,6 +798,7 @@
         },
         "sangaboard": {
             "hashes": [
+                "sha256:4b678ad7a814aa4f3ccccfc8790bb941222e6ee2c93586baf488220165dae304",
                 "sha256:4bfc58f1b7493c858b6b314d8b57a26b019ea2724737050000fa559251d3e050",
                 "sha256:4e945e876a094be9fb62f5a7282a06be4a3eb386d2032c615bff4f42dbb74bc8"
             ],
@@ -904,6 +851,7 @@
         "setuptools": {
             "hashes": [
                 "sha256:257de92a9d50a60b8e22abfcbb771571fde0dbf3ec234463212027a4eeecbe9a",
+                "sha256:ae060e31efa47ebd031bdf444908164a9c54dbfe734c97afd5d8e52afbad723a",
                 "sha256:e728ca814a823bf7bf60162daf9db95b93d532948c4c0bea762ce62f60189078"
             ],
             "markers": "python_version >= '3.7'",
@@ -937,7 +885,8 @@
         "urllib3": {
             "hashes": [
                 "sha256:8a388717b9476f934a21484e8c8e61875ab60644d29b9b39e11e4b9dc1c6b305",
-                "sha256:aa751d169e23c7479ce47a0cb0da579e3ede798f994f5816a74e4f4500dcea42"
+                "sha256:aa751d169e23c7479ce47a0cb0da579e3ede798f994f5816a74e4f4500dcea42",
+                "sha256:c3909b2a8d21bf543d661269ff27ff0d3feefc600d8a2e09cea4c0f46e45301a"
             ],
             "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'",
             "version": "==1.26.15"
@@ -970,6 +919,7 @@
         "zipp": {
             "hashes": [
                 "sha256:112929ad649da941c23de50f356a2b5570c954b65150642bccdd66bf194d224b",
+                "sha256:3ee3c5a49d3e276dcf8e83f5f11e93dab67f20b843e7ab2dee428c857d11b3b3",
                 "sha256:48904fc76a60e542af151aded95726c1a5c34ed43ab4134b597665c86d7ad556"
             ],
             "markers": "python_version >= '3.7'",
@@ -980,7 +930,8 @@
         "alabaster": {
             "hashes": [
                 "sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3",
-                "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"
+                "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2",
+                "sha256:be75d1de040fc86cb9b6fea8ade4016d5f21714678f5fb209bb71d4752eaa211"
             ],
             "markers": "python_version >= '3.6'",
             "version": "==0.7.13"
@@ -1024,6 +975,7 @@
         "attrs": {
             "hashes": [
                 "sha256:29e95c7f6778868dbd49170f98f8818f78f3dc5e0e37c0b1f474e3561b240836",
+                "sha256:52dd1548aaa4d65af91f99015a21718f8bbd3a45577e565cdd28b8a891da97a5",
                 "sha256:c9227bfc2f01993c03f68db37d1d15c9690188323c067c641f1a35ca58185f99"
             ],
             "markers": "python_version >= '3.6'",
@@ -1031,6 +983,7 @@
         },
         "babel": {
             "hashes": [
+                "sha256:7d4b39b8f00d62b71bf643d554db2e99e2845fbdb69da9577dd7cb512e1da053",
                 "sha256:b4246fb7677d3b98f501a39d43396d3cafdc8eadb045f4a31be01863f655c610",
                 "sha256:cc2d99999cd01d44420ae725a21c9e3711b3aadc7976d6147f622d8581963455"
             ],
@@ -1056,7 +1009,8 @@
         "certifi": {
             "hashes": [
                 "sha256:35824b4c3a97115964b408844d64aa14db1cc518f6562e8d7261699d1350a9e3",
-                "sha256:4ad3232f5e926d6718ec31cfc1fcadfde020920e278684144551c91769c7bc18"
+                "sha256:4ad3232f5e926d6718ec31cfc1fcadfde020920e278684144551c91769c7bc18",
+                "sha256:cb52c7519140a4c2b84314220b3f08768882bb58176f3acc039ccac101d51870"
             ],
             "markers": "python_version >= '3.6'",
             "version": "==2022.12.7"
@@ -1071,84 +1025,10 @@
         },
         "charset-normalizer": {
             "hashes": [
-                "sha256:04afa6387e2b282cf78ff3dbce20f0cc071c12dc8f685bd40960cc68644cfea6",
-                "sha256:04eefcee095f58eaabe6dc3cc2262f3bcd776d2c67005880894f447b3f2cb9c1",
-                "sha256:0be65ccf618c1e7ac9b849c315cc2e8a8751d9cfdaa43027d4f6624bd587ab7e",
-                "sha256:0c95f12b74681e9ae127728f7e5409cbbef9cd914d5896ef238cc779b8152373",
-                "sha256:0ca564606d2caafb0abe6d1b5311c2649e8071eb241b2d64e75a0d0065107e62",
-                "sha256:10c93628d7497c81686e8e5e557aafa78f230cd9e77dd0c40032ef90c18f2230",
-                "sha256:11d117e6c63e8f495412d37e7dc2e2fff09c34b2d09dbe2bee3c6229577818be",
-                "sha256:11d3bcb7be35e7b1bba2c23beedac81ee893ac9871d0ba79effc7fc01167db6c",
-                "sha256:12a2b561af122e3d94cdb97fe6fb2bb2b82cef0cdca131646fdb940a1eda04f0",
-                "sha256:12d1a39aa6b8c6f6248bb54550efcc1c38ce0d8096a146638fd4738e42284448",
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-                "sha256:1c60b9c202d00052183c9be85e5eaf18a4ada0a47d188a83c8f5c5b23252f649",
-                "sha256:1e8fcdd8f672a1c4fc8d0bd3a2b576b152d2a349782d1eb0f6b8e52e9954731d",
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-                "sha256:21fa558996782fc226b529fdd2ed7866c2c6ec91cee82735c98a197fae39f706",
-                "sha256:22908891a380d50738e1f978667536f6c6b526a2064156203d418f4856d6e86a",
-                "sha256:3160a0fd9754aab7d47f95a6b63ab355388d890163eb03b2d2b87ab0a30cfa59",
-                "sha256:322102cdf1ab682ecc7d9b1c5eed4ec59657a65e1c146a0da342b78f4112db23",
-                "sha256:34e0a2f9c370eb95597aae63bf85eb5e96826d81e3dcf88b8886012906f509b5",
-                "sha256:3573d376454d956553c356df45bb824262c397c6e26ce43e8203c4c540ee0acb",
-                "sha256:3747443b6a904001473370d7810aa19c3a180ccd52a7157aacc264a5ac79265e",
-                "sha256:38e812a197bf8e71a59fe55b757a84c1f946d0ac114acafaafaf21667a7e169e",
-                "sha256:3a06f32c9634a8705f4ca9946d667609f52cf130d5548881401f1eb2c39b1e2c",
-                "sha256:3a5fc78f9e3f501a1614a98f7c54d3969f3ad9bba8ba3d9b438c3bc5d047dd28",
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-                "sha256:fca62a8301b605b954ad2e9c3666f9d97f63872aa4efcae5492baca2056b74ab"
+                "sha256:1799ad8111efa28db62e1b9773eba32dcc9fd0cd9d7c631bd4858eb15a30f858"
             ],
             "markers": "python_full_version >= '3.7.0'",
-            "version": "==3.1.0"
+            "version": "==3.0.1"
         },
         "click": {
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@@ -1183,6 +1063,7 @@
                 "sha256:420f94a35e3e00a2b43ad5740f935358e24478354ce41c99407cddd283be00d2",
                 "sha256:4ac0f522c3b6109c4b764ffec71bf04ebc0523e926ca7cbe6c5ac88f84faced0",
                 "sha256:4c752d5264053a7cf2fe81c9e14f8a4fb261370a7bb344c2a011836a96fb3f57",
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@@ -1218,13 +1099,15 @@
                 "sha256:db8c2c5ace167fd25ab5dd732714c51d4633f58bac21fb0ff63b0349f62755a8",
                 "sha256:e2926b8abedf750c2ecf5035c07515770944acf02e1c46ab08f6348d24c5f94d",
                 "sha256:e627dee428a176ffb13697a2c4318d3f60b2ccdde3acdc9b3f304206ec130ccd",
-                "sha256:efe1c0adad110bf0ad7fb59f833880e489a61e39d699d37249bdf42f80590169"
+                "sha256:efe1c0adad110bf0ad7fb59f833880e489a61e39d699d37249bdf42f80590169",
+                "sha256:f47e4fd792793c19b66a09a7c79390490d7707dfc9c8c1a42cbd55110c73468b"
             ],
             "markers": "python_version >= '3.7'",
             "version": "==7.2.2"
         },
         "deepmerge": {
             "hashes": [
+                "sha256:331d8c8421dee318d7cae881c752f82a72573ab3740ef1b1f0d258f39ee1b41c",
                 "sha256:4c27a0db5de285e1a7ceac7dbc1531deaa556b627dea4900c8244581ecdfea2d",
                 "sha256:59e6ef80b77dc52af3882a1ea78da22bcfc91ae9cdabc0c80729049fe295ff8b"
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@@ -1232,6 +1115,7 @@
         },
         "dill": {
             "hashes": [
+                "sha256:918795da4042490399dd7b3f5bdee9d7ae11cfdb3a9fc5e460b82142543fd3ba",
                 "sha256:a07ffd2351b8c678dfc4a856a3005f8067aea51d6ba6c700796a4d9e280f39f0",
                 "sha256:e5db55f3687856d8fbdab002ed78544e1c4559a130302693d839dfe8f93f2373"
             ],
@@ -1271,6 +1155,7 @@
         },
         "freezegun": {
             "hashes": [
+                "sha256:6684d606f2bba9f2032404a3be04fd691a9ee00ca241c3fa638da0d160b59856",
                 "sha256:cd22d1ba06941384410cd967d8a99d5ae2442f57dfafeff2fda5de8dc5c05446",
                 "sha256:ea1b963b993cb9ea195adbd893a48d573fda951b0da64f60883d7e988b606c9f"
             ],
@@ -1279,6 +1164,7 @@
         },
         "future": {
             "hashes": [
+                "sha256:06cf12592a81bdba6c2f05be3be47da76c8beedce11c5539e5edea9de9b9eac6",
                 "sha256:34a17436ed1e96697a86f9de3d15a3b0be01d8bc8de9c1dffd59fb8234ed5307"
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             "markers": "python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'",
@@ -1287,7 +1173,8 @@
         "idna": {
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                 "sha256:814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4",
-                "sha256:90b77e79eaa3eba6de819a0c442c0b4ceefc341a7a2ab77d7562bf49f425c5c2"
+                "sha256:90b77e79eaa3eba6de819a0c442c0b4ceefc341a7a2ab77d7562bf49f425c5c2",
+                "sha256:bcac1132a4eadea8321490704e2349b752e29c6ec2f1c27d372010e76ebd3fa1"
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             "version": "==3.4"
@@ -1312,6 +1199,7 @@
         "importlib-metadata": {
             "hashes": [
                 "sha256:43ce9281e097583d758c2c708c4376371261a02c34682491a8e98352365aad20",
+                "sha256:ab197eeef247b9bfe3d3d91334921e09626181362991c0479b1340aabc00532f",
                 "sha256:ff80f3b5394912eb1b108fcfd444dc78b7f1f3e16b16188054bd01cb9cb86f09"
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@@ -1320,7 +1208,8 @@
         "importlib-resources": {
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                 "sha256:4be82589bf5c1d7999aedf2a45159d10cb3ca4f19b2271f8792bc8e6da7b22f6",
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+                "sha256:7b1deeebbf351c7578e09bf2f63fa2ce8b5ffec296e0d349139d43cca061a81a",
+                "sha256:f36205b58b84e2f35777817eb7ac6506a21982ad9954a72ab0833abf36c44183"
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             "markers": "python_version < '3.9'",
             "version": "==5.12.0"
@@ -1335,6 +1224,7 @@
         },
         "isort": {
             "hashes": [
+                "sha256:01ad8ce890fe8743f0011655d1e538e8495ba0a0fd2f0801a99f0126cc6160f8",
                 "sha256:6be1f76a507cb2ecf16c7cf14a37e41609ca082330be4e3436a18ef74add55db",
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@@ -1368,7 +1258,8 @@
         "jsonschema-spec": {
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             "version": "==0.1.4"
@@ -1386,6 +1277,7 @@
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@@ -1409,6 +1301,7 @@
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                 "sha256:cbf9b082426036e19c6924a9ce90c740a9861e2bdc27a4834fd0a910742ac1e8",
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@@ -1456,6 +1349,7 @@
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@@ -1471,6 +1365,7 @@
                 "sha256:925073b2fe14ab9b87e73f9a5fde6ce6392da430f3004d8b72cc86f746f5163b",
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                 "sha256:9b22c5c66f67ae00c0199f6055705bc3eb3fcb08d03d2ec4059a2b1b25ed48d7",
+                "sha256:9e3e6e15b0ab6e5c47d1170be3978b50b3d2bf61dd01fc1922f803c94bd52d98",
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@@ -1586,11 +1481,10 @@
         },
         "marshmallow": {
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-            "version": "==3.19.0"
+            "version": "==3.18.0"
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@@ -1604,6 +1498,7 @@
         "mistune": {
             "hashes": [
                 "sha256:0246113cb2492db875c6be56974a7c893333bf26cd92891c85f63151cee09d34",
+                "sha256:34d10acf296d022df53f686d2792a24447b440bc35ee7a124c334297e14661d3",
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@@ -1623,6 +1518,7 @@
                 "sha256:3d80e36b7d7a9259b740be6d8d906221789b0d836201af4234093cae89ced0cd",
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                 "sha256:4307270436fd7694b41f913eb09210faff27ea4979ecbcd849e57d2da2f65305",
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@@ -1647,7 +1543,8 @@
         "mypy-extensions": {
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                 "sha256:4392f6c0eb8a5668a69e23d168ffa70f0be9ccfd32b5cc2d26a34ae5b844552d",
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             "version": "==1.0.0"
@@ -1667,6 +1564,8 @@
                 "sha256:69077388c5a4b997442b843dbdc3a85b420fb693ec8e33020bb24d647c164fa5",
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                 "sha256:81225e58ef5fce7f1d80399575576fc5febec79a8a2742e8ef86d7b03beef49f",
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                 "sha256:9864424631775b0c052f3bd98bc2712d131b3e2cd95d1c0c68b91709170890b0",
@@ -1690,6 +1589,7 @@
         },
         "openapi-schema-validator": {
             "hashes": [
+                "sha256:33661cd8a06d5112dec52d758dda55e543e4a7c9f0efc2901dcf83ebd5604055",
                 "sha256:79f37f38ef9fd5206b924ed7a6f382cea7b649b3b56383c47f1906082b7b9015",
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@@ -1699,7 +1599,8 @@
         "openapi-spec-validator": {
             "hashes": [
                 "sha256:1189d0618ae0678ccf6c883cc1266d381454eece6f21fcf330cc7caea5fc25eb",
-                "sha256:4145478f26df16059c147406eaaa59b77ff60e3461ba6edb9aa84d481ed89aaf"
+                "sha256:4145478f26df16059c147406eaaa59b77ff60e3461ba6edb9aa84d481ed89aaf",
+                "sha256:92721d4a905a1e47a574d67f38dad32b64f7146b3f63d18edf0f3aa97afad207"
             ],
             "version": "==0.5.6"
         },
@@ -1836,7 +1737,8 @@
         "poethepoet": {
             "hashes": [
                 "sha256:3c958792ce488661ba09df67ba832a1b3141aa640236505ee60c23f4b1db4dbc",
-                "sha256:493d5d47b4cb0894dde6a69d14129ba39ef3f124fabda1f83ebb39bbf737a40e"
+                "sha256:493d5d47b4cb0894dde6a69d14129ba39ef3f124fabda1f83ebb39bbf737a40e",
+                "sha256:737d91d16e21258d47d8e4121fc5ca1cebf4ac702f37efb05c370d2c08f218f5"
             ],
             "markers": "python_version >= '3.7'",
             "version": "==0.16.5"
@@ -1847,6 +1749,7 @@
             ],
             "hashes": [
                 "sha256:814a523bc1ff18383c12cb523ce44c90fe8792bf5f48d8cc33c9f658276658ed",
+                "sha256:a9d0389da9919cf266a6668aeb1dec294f844f99c256ee6c2e36a9451b69a57b",
                 "sha256:c15e9ca889b56262e4c2aee354f52918ba5e54f46bb3da42b806d8bbd8255ee9"
             ],
             "version": "==0.22.11.4.0"
@@ -1883,6 +1786,7 @@
         "pygments": {
             "hashes": [
                 "sha256:b3ed06a9e8ac9a9aae5a6f5dbe78a8a58655d17b43b93c078f094ddc476ae297",
+                "sha256:c2fe87a7618b6f4ebdde31913d4e6c1bccf1caf7f0651f659f3acd37a75cba68",
                 "sha256:fa7bd7bd2771287c0de303af8bfdfc731f51bd2c6a47ab69d117138893b82717"
             ],
             "markers": "python_version >= '3.6'",
@@ -1909,6 +1813,7 @@
         "pyrsistent": {
             "hashes": [
                 "sha256:016ad1afadf318eb7911baa24b049909f7f3bb2c5b1ed7b6a8f21db21ea3faa8",
+                "sha256:0a76a451d782433be74a500c6a072d1c6669481bfcbcdd985d12f0965fa6b87e",
                 "sha256:1a2994773706bbb4995c31a97bc94f1418314923bd1048c6d964837040376440",
                 "sha256:20460ac0ea439a3e79caa1dbd560344b64ed75e85d8703943e0b66c2a6150e4a",
                 "sha256:3311cb4237a341aa52ab8448c27e3a9931e2ee09561ad150ba94e4cfd3fc888c",
@@ -1918,6 +1823,7 @@
                 "sha256:49c32f216c17148695ca0e02a5c521e28a4ee6c5089f97e34fe24163113722da",
                 "sha256:4b774f9288dda8d425adb6544e5903f1fb6c273ab3128a355c6b972b7df39dcf",
                 "sha256:4c18264cb84b5e68e7085a43723f9e4c1fd1d935ab240ce02c0324a8e01ccb64",
+                "sha256:55ff9ca4735904a3897f5d03170c56122b724bf2ead32def8999fbb6949c7bb5",
                 "sha256:5a474fb80f5e0d6c9394d8db0fc19e90fa540b82ee52dba7d246a7791712f74a",
                 "sha256:64220c429e42a7150f4bfd280f6f4bb2850f95956bde93c6fda1b70507af6ef3",
                 "sha256:878433581fc23e906d947a6814336eee031a00e6defba224234169ae3d3d6a98",
@@ -1949,6 +1855,7 @@
         "pytest": {
             "hashes": [
                 "sha256:130328f552dcfac0b1cec75c12e3f005619dc5f874f0a06e8ff7263f0ee6225e",
+                "sha256:a6377f55b06d85889e6db60ee185b02e0aa87af517ec2eec93075d1a9bc22648",
                 "sha256:c99ab0c73aceb050f68929bc93af19ab6db0558791c6a0715723abe9d0ade9d4"
             ],
             "markers": "python_version >= '3.7'",
@@ -1973,7 +1880,8 @@
         "pytz": {
             "hashes": [
                 "sha256:1d8ce29db189191fb55338ee6d0387d82ab59f3d00eac103412d64e0ebd0c588",
-                "sha256:a151b3abb88eda1d4e34a9814df37de2a80e301e68ba0fd856fb9b46bfbbbffb"
+                "sha256:a151b3abb88eda1d4e34a9814df37de2a80e301e68ba0fd856fb9b46bfbbbffb",
+                "sha256:dcb23b3d3f96b1c61a06ccc55e8b19dbb430b7571dc8a112432909a14dd64063"
             ],
             "markers": "python_version < '3.9'",
             "version": "==2023.3"
@@ -2018,7 +1926,8 @@
         "requests": {
             "hashes": [
                 "sha256:64299f4909223da747622c030b781c0d7811e359c37124b4bd368fb8c6518baa",
-                "sha256:98b1b2782e3c6c4904938b84c0eb932721069dfdb9134313beff7c83c2df24bf"
+                "sha256:98b1b2782e3c6c4904938b84c0eb932721069dfdb9134313beff7c83c2df24bf",
+                "sha256:e77536e318369f207754c018f33a97b68adec830f33bee3507d296683ba1d416"
             ],
             "markers": "python_version >= '3.7' and python_version < '4'",
             "version": "==2.28.2"
@@ -2034,13 +1943,16 @@
         "rpi.gpio": {
             "hashes": [
                 "sha256:15311d3b063b71dee738cd26570effc9985a952454d162937c34e08c0fc99902",
+                "sha256:231f6142c25975a7e39b96faf4905f05f97dba6809e8c5f0d58f284b35b4b821",
                 "sha256:26b2ade4bb353bbe5417a64e40b45cdf00a82f27c2d320c0dd46c59751959d77",
                 "sha256:29226823da8b5ccb9001d795a944f2e00924eeae583490f0bc7317581172c624",
+                "sha256:5073d1972727cfad38a1a42f02da91dc41f137679290aa804ab6c410168347ac",
                 "sha256:57b6c044ef5375a78c8dda27cdfadf329e76aa6943cd6cffbbbd345a9adf9ca5",
                 "sha256:77afb817b81331ce3049a4b8f94a85e41b7c404d8e56b61ac0f1eb75c3120868",
                 "sha256:96ea7e5bf6bf592828487bfa7d3d1d0e432d5d1682e9e33b4dab398914628fcd",
                 "sha256:b86b66dc02faa5461b443a1e1f0c1d209d64ab5229696f32fb3b0215e0600c8c",
-                "sha256:cd61c4b03c37b62bba4a5acfea9862749c33c618e0295e7e90aa4713fb373b70"
+                "sha256:cd61c4b03c37b62bba4a5acfea9862749c33c618e0295e7e90aa4713fb373b70",
+                "sha256:e5dfec2c4ccb7dbe9eef3dfc76a3b04121fc62d77fd8fbe1a8e841468a1b0c4c"
             ],
             "version": "==0.7.1"
         },
@@ -2072,9 +1984,11 @@
                 "sha256:763d65baa3b952479c4e972669f679fe490eee058d5aa85da483ebae2009d231",
                 "sha256:7bdb4c06b063f6fd55e472e201317a3bb6cdeeee5d5a38512ea5c01e1acbdd93",
                 "sha256:8831a2cedcd0f0927f788c5bdf6567d9dc9cc235646a434986a852af1cb54b4b",
+                "sha256:8f73b665f03f70986e4b5c4708b9e553b931d34b815032452327fa7c2a9099bf",
                 "sha256:91a789b4aa0097b78c93e3dc4b40040ba55bef518f84a40d4442f713b4094acb",
                 "sha256:92460ce908546ab69770b2e576e4f99fbb4ce6ab4b245345a3869a0a0410488f",
                 "sha256:99e77daab5d13a48a4054803d052ff40780278240a902b880dd37a51ba01a307",
+                "sha256:9c361022618feec80a1d5e874970d8dae234815097638ed104a40593b602eb5c",
                 "sha256:a234a20ae07e8469da311e182e70ef6b199d0fbeb6c6cc2901204dd87fb867e8",
                 "sha256:a7b301ff08055d73223058b5c46c55638917f04d21577c95e00e0c4d79201a6b",
                 "sha256:be2a7ad8fd8f7442b24323d24ba0b56c51219513cfa45b9ada3b87b76c374d4b",
@@ -2097,6 +2011,7 @@
         },
         "sangaboard": {
             "hashes": [
+                "sha256:4b678ad7a814aa4f3ccccfc8790bb941222e6ee2c93586baf488220165dae304",
                 "sha256:4bfc58f1b7493c858b6b314d8b57a26b019ea2724737050000fa559251d3e050",
                 "sha256:4e945e876a094be9fb62f5a7282a06be4a3eb386d2032c615bff4f42dbb74bc8"
             ],
@@ -2149,6 +2064,7 @@
         "setuptools": {
             "hashes": [
                 "sha256:257de92a9d50a60b8e22abfcbb771571fde0dbf3ec234463212027a4eeecbe9a",
+                "sha256:ae060e31efa47ebd031bdf444908164a9c54dbfe734c97afd5d8e52afbad723a",
                 "sha256:e728ca814a823bf7bf60162daf9db95b93d532948c4c0bea762ce62f60189078"
             ],
             "markers": "python_version >= '3.7'",
@@ -2181,7 +2097,8 @@
         "sphinx-mdinclude": {
             "hashes": [
                 "sha256:02afadf4597aecf8255a702956eff5b8c5cb9658ea995c3d361722d2ed78cca9",
-                "sha256:2998e3d18b3022c9983d1b72191fe37e25ffccd54165cbe3acb22cceedd91af4"
+                "sha256:2998e3d18b3022c9983d1b72191fe37e25ffccd54165cbe3acb22cceedd91af4",
+                "sha256:bdd78064b93df1ddea00b0778bf9c0fc3f83a805c66c79fdd08e7f48fb3d8537"
             ],
             "markers": "python_version >= '3.6'",
             "version": "==0.5.3"
@@ -2220,7 +2137,8 @@
         "sphinxcontrib-httpdomain": {
             "hashes": [
                 "sha256:21eefe1270e4d9de8d717cc89ee92cc4871b8736774393bafc5e38a6bb77b1d5",
-                "sha256:6c2dfe6ca282d75f66df333869bb0ce7331c01b475db6809ff9d107b7cdfe04b"
+                "sha256:6c2dfe6ca282d75f66df333869bb0ce7331c01b475db6809ff9d107b7cdfe04b",
+                "sha256:bb0c47784bde6354c4f5c3be20f94dcfc5dd4f595a0b0b3dcba96ec725472049"
             ],
             "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
             "version": "==1.8.1"
@@ -2236,7 +2154,8 @@
         "sphinxcontrib-openapi": {
             "hashes": [
                 "sha256:04fcf87c259345162a504ce3dfee0f71389f507c3797798dc531c7748995b4eb",
-                "sha256:45ecad2a98e304d3665c133ea08a7083a2b5d86e75c6b64c60389240b3927ad5"
+                "sha256:45ecad2a98e304d3665c133ea08a7083a2b5d86e75c6b64c60389240b3927ad5",
+                "sha256:84c1df31a1e66e0a362d5d8cd74363f36cbea9e6ee6d0fcb4dcee778470b1819"
             ],
             "markers": "python_version >= '3.7'",
             "version": "==0.8.1"
@@ -2316,12 +2235,14 @@
         "types-python-dateutil": {
             "hashes": [
                 "sha256:357553f8056cfbb8ce8ea0ca4a6a3480268596748360df73a94c2b8c113a5b06",
-                "sha256:de66222c54318c2e05ceb4956976d16696240a45fc2c98e54bfe9a56ce5e1eff"
+                "sha256:de66222c54318c2e05ceb4956976d16696240a45fc2c98e54bfe9a56ce5e1eff",
+                "sha256:f37eada27a398e2dc2a64e171af7820c6db83faa07fd0cf8612a0f0b4060c70f"
             ],
             "version": "==2.8.19.11"
         },
         "types-setuptools": {
             "hashes": [
+                "sha256:5bff4b5d6d774717a05b35d00cb5a2b8c481b7759a357d8db2837d7f0c607e00",
                 "sha256:a5efd019b53c5793a112e0112b91bb402df749f75ee7abe681b6240841650ce4",
                 "sha256:fb46e651c6b5880ec8932a8876aa832071d612b2954fc5156b09cd263927d85b"
             ],
@@ -2339,7 +2260,8 @@
         "urllib3": {
             "hashes": [
                 "sha256:8a388717b9476f934a21484e8c8e61875ab60644d29b9b39e11e4b9dc1c6b305",
-                "sha256:aa751d169e23c7479ce47a0cb0da579e3ede798f994f5816a74e4f4500dcea42"
+                "sha256:aa751d169e23c7479ce47a0cb0da579e3ede798f994f5816a74e4f4500dcea42",
+                "sha256:c3909b2a8d21bf543d661269ff27ff0d3feefc600d8a2e09cea4c0f46e45301a"
             ],
             "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'",
             "version": "==1.26.15"
@@ -2373,6 +2295,7 @@
                 "sha256:26458da5653aa5b3d8dc8b24192f574a58984c749401f98fff994d41d3f08da1",
                 "sha256:2cf56d0e237280baed46f0b5316661da892565ff58309d4d2ed7dba763d984b8",
                 "sha256:2e51de54d4fb8fb50d6ee8327f9828306a959ae394d3e01a1ba8b2f937747d86",
+                "sha256:2e95b9f272a61060f36f044c0cd44d37a7c096426e781a0c4eef05b72f4d9d80",
                 "sha256:2fbfbca668dd15b744418265a9607baa970c347eefd0db6a518aaf0cfbd153c0",
                 "sha256:38adf7198f8f154502883242f9fe7333ab05a5b02de7d83aa2d88ea621f13364",
                 "sha256:3a8564f283394634a7a7054b7983e47dbf39c07712d7b177b37e03f2467a024e",
@@ -2409,6 +2332,7 @@
                 "sha256:a4cbb9ff5795cd66f0066bdf5947f170f5d63a9274f99bdbca02fd973adcf2a8",
                 "sha256:a74d56552ddbde46c246b5b89199cb3fd182f9c346c784e1a93e4dc3f5ec9975",
                 "sha256:a89ce3fd220ff144bd9d54da333ec0de0399b52c9ac3d2ce34b569cf1a5748fb",
+                "sha256:aa98b980245a21a8bd6cd507e6dac545245ec1773058f4707d6619b242293f67",
                 "sha256:abd52a09d03adf9c763d706df707c343293d5d106aea53483e0ec8d9e310ad5e",
                 "sha256:abd8f36c99512755b8456047b7be10372fca271bf1467a1caa88db991e7c421b",
                 "sha256:af5bd9ccb188f6a5fdda9f1f09d9f4c86cc8a539bd48a0bfdc97723970348418",
@@ -2453,6 +2377,7 @@
         "zipp": {
             "hashes": [
                 "sha256:112929ad649da941c23de50f356a2b5570c954b65150642bccdd66bf194d224b",
+                "sha256:3ee3c5a49d3e276dcf8e83f5f11e93dab67f20b843e7ab2dee428c857d11b3b3",
                 "sha256:48904fc76a60e542af151aded95726c1a5c34ed43ab4134b597665c86d7ad556"
             ],
             "markers": "python_version >= '3.7'",

From d0aad6633c46392f266f65a1a2767e0567c52b0c Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Thu, 6 Apr 2023 15:20:48 +0100
Subject: [PATCH 23/25] Redo CI to run on armv6

I've refactored the CI substantially, using the
new `extends` keyword to tidy it up a lot.
I have also changed from running the Python
tests on Python:3.7 to using a Raspberry Pi
OS from the Balena project.

This means we are now ONLY locking
dependencies for the Pi, and we are no longer
expecting the Pipfile to work on non-arm
systems.
---
 .gitlab-ci.yml | 109 ++++++++++++-------------------------------------
 1 file changed, 26 insertions(+), 83 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index f380d303..62e557ab 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -6,8 +6,12 @@ stages:
   - deploy
 
 # Re-usable block to install (and cache) Poetry and openflexure-microscope-server
-.python-install-template: &python-install
+.python:
+  image: balenalib/raspberry-pi:buster
+  retry: 1
   before_script:
+    - apt-get update
+    - apt-get install python3 python3-pip python3-venv
     - python3 -m venv .venv        # NB this does not overwrite an existing cached venv
     - source .venv/bin/activate
     - pip install pipenv           # Should be cached after first run
@@ -17,9 +21,14 @@ stages:
     paths:
       - .cache/pip
       - .venv
+  only:
+    - branches
+    - merge_requests
+    - tags
+    - web
 
-# Re-usable block to install (and cache) openflexure-microscope-server static app
-.node-install-template: &node-install
+.javascript:
+  image: node:15
   before_script:
     - cd webapp
     - npm install
@@ -27,95 +36,54 @@ stages:
     key: "${CI_COMMIT_REF_SLUG}"
     paths:
       - webapp/node_modules
-
-# Python static analysis with PyLint
-pylint:
-  stage: analysis
-  image: python:3.7
-  retry: 1
-
-  <<: *python-install
-
-  script:
-    - poe pylint
-
   only:
     - branches
     - merge_requests
     - tags
     - web
 
+# Python static analysis with PyLint
+pylint:
+  stage: analysis
+  extends: .python
+  script:
+    - poe pylint
+
 # Python type checking with Mypy
 mypy:
   stage: analysis
-  image: python:3.7
-  retry: 1
-
-  <<: *python-install
-
+  extends: .python
   script:
     - poe mypy
-
   artifacts:
     reports:
       coverage_report: 
         coverage_format: cobertura
         path: openflexure_microscope/cobertura.xml
 
-  only:
-    - branches
-    - merge_requests
-    - tags
-    - web
-
 # Python style analysis with Black
 black:
   stage: analysis
-  image: python:3.7
-  retry: 1
   allow_failure: true
-
-  <<: *python-install
-
+  extends: .python
   script:
-    # Run static build script
     - poe black_check
 
-  only:
-    - branches
-    - merge_requests
-    - tags
-    - web
-
 # Python unit tests with PyTest
 pytest:
   stage: testing
-  image: python:3.7
-  retry: 1
-
-  <<: *python-install
-
+  extends: .python
   script:
     - poe test
-
-  only:
-    - branches
-    - merge_requests
-    - tags
-    - web
-
   artifacts:
     when: always
     reports:
       junit: pytest_report.xml
 
+# Generate and validate OpenAPI description
 openapi:
   stage: testing
-  image: python:3.7
-  retry: 1
-
-  <<: *python-install
-
+  extends: .python
   script:
     - mkdir -p docs/build/
     - ofm-generate-openapi -o docs/build/swagger.yaml --validate
@@ -125,53 +93,28 @@ openapi:
     expire_in: 1 week
     paths:
       - "./docs/build/swagger.yaml"
-  
-  only:
-    - branches
-    - merge_requests
-    - tags
-    - web
 
 # JavaScript linting with ESLint (via Vue CLI)
 eslint:
   stage: analysis
-  image: node:15
-
-  <<: *node-install
-
+  extends: .javascript
   script:
     # Build JS application for production
     - npm run lint
 
-  only:
-    - branches
-    - merge_requests
-    - tags
-    - web
-
 # Build JS app
 build:
   stage: build
-  image: node:15
-
-  <<: *node-install
-
+  extends: .javascript
   script:
     # Build JS application for production
     - npm run build
-
   artifacts:
     name: "dist"
     expire_in: 1 week
     paths:
       - "openflexure_microscope/api/static/dist/"
 
-  only:
-    - master
-    - merge_requests
-    - tags
-    - web
-
 # Package application into distribution tarball
 package:
   stage: package

From a95baee25f64dfa9e5fc052a8718697859e53e7e Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Thu, 6 Apr 2023 16:03:20 +0100
Subject: [PATCH 24/25] Fix lxml and update README

lxml requires an apt-installed package to work.
I've also mentioned in README that Pipfile
is now pi-specific.
---
 .gitlab-ci.yml | 2 +-
 README.md      | 8 ++++++--
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 62e557ab..2eca4a4c 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -11,7 +11,7 @@ stages:
   retry: 1
   before_script:
     - apt-get update
-    - apt-get install python3 python3-pip python3-venv
+    - apt-get install python3 python3-pip python3-venv libxslt1.1
     - python3 -m venv .venv        # NB this does not overwrite an existing cached venv
     - source .venv/bin/activate
     - pip install pipenv           # Should be cached after first run
diff --git a/README.md b/README.md
index 9fc174db..78777586 100644
--- a/README.md
+++ b/README.md
@@ -147,8 +147,9 @@ As of `2.10.0b0` we have switched to using `pipenv` for managing dependencies, a
 * `Pipfile` is very minimal, and only declares dependencies on the current module, i.e. the dependencies declared in `setup.py`.  It also specifies the Python version.  This allows us to single-source dependency information from `setup.py` but use the dependency resolution/locking functionality of `pipenv`
 * `Pipfile.lock` locks the dependency versions in the same way as `poetry.lock` used to, i.e. it specifies exact versions of everything, derived from the looser specifications in `setup.py`.
 * Dependency resolution is a pain, in part because compiling packages like scipy and numpy from source on a Pi is slow and unreliable. To avoid this, we usually lock the dependencies on a Raspberry Pi, using:
-  `PIP_ONLY_BINARY=":all:" pipenv lock --dev`
-  This forces the use of wheels only, and thus restricts us to things that built OK on Piwheels.  The resulting Pipfile.lock should then work nicely on other Raspberry Pis (as well as other platforms).
+  `PIP_ONLY_BINARY="numpy, scipy, matplotlib" pipenv lock --dev`
+  This forces the use of wheels only, and thus restricts us to things that built OK on Piwheels.  The resulting Pipfile.lock should then work nicely on other Raspberry Pis.
+* **The Pipfile we use is now Raspberry Pi-specific** so if you attempt to use it on other platforms it will probably fail. This is because we've removed `pypi` to avoid hash conflicts. The CI now runs on a Raspberry Pi image, so that the tests use a similar environment to our deployment.  Currently, changing the `[source]` entry back to PyPi will allow you to re-lock the dependencies on other platforms. In the future we may need to maintain two Pipfiles and two Pipfile.lock files.
 
 ## Creating releases
 
@@ -169,3 +170,6 @@ As of `2.10.0b0` we have switched to using `pipenv` for managing dependencies, a
 
 The Microscope module, and Flask app, both support plugins for extending lower-level functionality not well suited to web API calls. The current documentation can be found [here](https://openflexure-microscope-software.readthedocs.io/en/latest/plugins.html).
 If you want to add functions to the microscope software, this is probably the best mechanism to use if it works for you.
+
+
+```

From 7abdbdde4a8c034565c751890bf45c9eb2e819d7 Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Thu, 6 Apr 2023 21:27:51 +0100
Subject: [PATCH 25/25] Add full list of server prerequisites

The server needs various packages installed on
the system. This list is lifted from the SD card
builder repository.
---
 .gitlab-ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 2eca4a4c..570113ae 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -11,7 +11,7 @@ stages:
   retry: 1
   before_script:
     - apt-get update
-    - apt-get install python3 python3-pip python3-venv libxslt1.1
+    - apt-get install apt-utils curl wget python3 python3-pip python3-venv raspi-gpio libgfortran3 libatlas3-base libffi-dev vim git-lfs libtiff5 libpango-1.0-0 libavcodec58 libgdk-pixbuf2.0-0 libjasper1 libswscale5 libpangocairo-1.0-0 libilmbase23 libatk1.0-0 libgtk-3-0 libwebp6 libcairo2 libavutil56 libcairo-gobject2 libopenexr23 libavformat58 libxslt1.1
     - python3 -m venv .venv        # NB this does not overwrite an existing cached venv
     - source .venv/bin/activate
     - pip install pipenv           # Should be cached after first run