Merge branch 'hotfix-2.0.x' into 'master'

Hotfix 2.0.1

See merge request openflexure/openflexure-microscope-server!49

openflexure_microscope/api/app.py

@@ -1,10 +1,6 @@
 #!/usr/bin/env python
 from gevent import monkey
-
-# Patch most system modules. Leave threads untouched so we can still use them normally if needed.
-print("Monkey patching with Gevenet")
 monkey.patch_all()
-print("Monkey patching successful")
 
 import time
 import atexit

openflexure_microscope/api/default_extensions/scan.py

@@ -198,6 +198,7 @@ def tile(
                 else:
                     # Run slow autofocus. Client should provide dz ~ 50
                     autofocus_extension.autofocus(
+                        microscope,
                         range(-3 * autofocus_dz, 4 * autofocus_dz, autofocus_dz)
                     )
                     logging.debug("Finished autofocus")

poetry.lock

@@ -277,7 +277,7 @@ description = "Python implementation of LabThings, based on the Flask microframe
 name = "labthings"
 optional = false
 python-versions = ">=3.6,<4.0"
-version = "0.3.0"
+version = "0.4.0"
 
 [package.dependencies]
 Flask = ">=1.1.1,<2.0.0"
@@ -358,12 +358,13 @@ version = "1.13.2b0"
 [package.extras]
 array = ["numpy"]
 doc = ["sphinx"]
-test = ["coverage", "pytest", "mock", "pillow", "numpy"]
+test = ["pillow", "coverage", "mock", "numpy", "pytest"]
 
 [package.source]
 reference = "79177fa7f28d6d5c6eab5ba814b420b1785b6b24"
 type = "git"
 url = "https://github.com/rwb27/picamera.git"
+
 [[package]]
 category = "main"
 description = "Python Imaging Library (Fork)"
@@ -716,7 +717,7 @@ ifaddr = "*"
 rpi = ["picamera", "RPi.GPIO"]
 
 [metadata]
-content-hash = "71b15705721aa7447357d24e79c6ff77f6844b4191eceb5e90a14942c5375b91"
+content-hash = "f7bb806f267f9f38aedfe6bb4ef6d23deef9df991c7117bd58f8c0e83c64b2b4"
 python-versions = "^3.6"
 
 [metadata.files]
@@ -883,8 +884,8 @@ jinja2 = [
     {file = "Jinja2-2.11.1.tar.gz", hash = "sha256:93187ffbc7808079673ef52771baa950426fd664d3aad1d0fa3e95644360e250"},
 ]
 labthings = [
-    {file = "labthings-0.3.0-py3-none-any.whl", hash = "sha256:605999a8fe09a52ad32a4763020b81e5d1b7b786478b47e1f45594aa10bcdd2d"},
-    {file = "labthings-0.3.0.tar.gz", hash = "sha256:cc93ee4510fc1304a450346e11d0069541142e8867cfcf8e4381a872abf16a6c"},
+    {file = "labthings-0.4.0-py3-none-any.whl", hash = "sha256:75fe8f65b89783bb852ad4d1463b2f721ea42f03ae06fbe3df76b85d8c65eac1"},
+    {file = "labthings-0.4.0.tar.gz", hash = "sha256:e6b5c6c322915808f8833ec9aa81c7ede08282a0946a28562b5ca77549099ef4"},
 ]
 lazy-object-proxy = [
     {file = "lazy-object-proxy-1.4.3.tar.gz", hash = "sha256:f3900e8a5de27447acbf900b4750b0ddfd7ec1ea7fbaf11dfa911141bc522af0"},
@@ -937,6 +938,11 @@ markupsafe = [
     {file = "MarkupSafe-1.1.1-cp37-cp37m-manylinux1_x86_64.whl", hash = "sha256:ba59edeaa2fc6114428f1637ffff42da1e311e29382d81b339c1817d37ec93c6"},
     {file = "MarkupSafe-1.1.1-cp37-cp37m-win32.whl", hash = "sha256:b00c1de48212e4cc9603895652c5c410df699856a2853135b3967591e4beebc2"},
     {file = "MarkupSafe-1.1.1-cp37-cp37m-win_amd64.whl", hash = "sha256:9bf40443012702a1d2070043cb6291650a0841ece432556f784f004937f0f32c"},
+    {file = "MarkupSafe-1.1.1-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:6788b695d50a51edb699cb55e35487e430fa21f1ed838122d722e0ff0ac5ba15"},
+    {file = "MarkupSafe-1.1.1-cp38-cp38-manylinux1_i686.whl", hash = "sha256:cdb132fc825c38e1aeec2c8aa9338310d29d337bebbd7baa06889d09a60a1fa2"},
+    {file = "MarkupSafe-1.1.1-cp38-cp38-manylinux1_x86_64.whl", hash = "sha256:13d3144e1e340870b25e7b10b98d779608c02016d5184cfb9927a9f10c689f42"},
+    {file = "MarkupSafe-1.1.1-cp38-cp38-win32.whl", hash = "sha256:596510de112c685489095da617b5bcbbac7dd6384aeebeda4df6025d0256a81b"},
+    {file = "MarkupSafe-1.1.1-cp38-cp38-win_amd64.whl", hash = "sha256:e8313f01ba26fbbe36c7be1966a7b7424942f670f38e666995b88d012765b9be"},
     {file = "MarkupSafe-1.1.1.tar.gz", hash = "sha256:29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b"},
 ]
 marshmallow = [

pyproject.toml

@@ -35,7 +35,7 @@ pyserial = "^3.4" # Used for sangaboard (basic_serial_instrument) until we move
 
 python-dateutil = "^2.8"
 psutil = "^5.6.7" # Autostorage extension
-labthings = "0.3.0"
+labthings = "0.4.0"
 
 [tool.poetry.extras]
 rpi = ["picamera", "RPi.GPIO"]