Merge branch 'frame' into 'master'

eV submodule & new distribution system

See merge request openflexure/openflexure-microscope-server!59

.gitattributes

@@ -1 +0,0 @@
-openflexure_microscope/api/static/** filter=lfs diff=lfs merge=lfs -text

.gitlab-ci.yml

@@ -0,0 +1,73 @@
+stages:
+  - build
+  - deploy
+
+
+# Cache modules in between jobs
+cache:
+  key: ${CI_COMMIT_REF_SLUG}
+  paths:
+  - node_modules/
+
+
+# Electron app build
+build:
+  stage: build
+  image: nikolaik/python-nodejs:python3.7-nodejs14
+
+  variables:
+    GIT_SUBMODULE_STRATEGY: recursive
+
+  before_script:
+    - git submodule sync --recursive
+    - git submodule update --init --recursive
+    - curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py | python
+
+  script:
+    # Install server
+    - $HOME/.poetry/bin/poetry install
+    # Run static build script
+    - $HOME/.poetry/bin/poetry run build_static
+    # Build distribution archive
+    - mkdir -p dist
+    - tar -c --exclude-vcs --exclude-from .tarignore -vzf dist/openflexure-microscope-server-${CI_COMMIT_REF_NAME}.tar.gz .
+
+  artifacts:
+    name: "dist"
+    expire_in: 1 week
+    paths:
+      - "./dist/*"
+
+  only:
+    - merge_requests
+    - tags
+    - web
+
+
+# Deploy to builds.openflexure.org
+deploy:
+  stage: deploy
+  dependencies:
+    - build
+  image: ubuntu:latest
+  
+  before_script:
+    - 'which ssh-agent || ( apt-get update -y && apt-get install openssh-client -y )'
+    - eval $(ssh-agent -s)
+    - ssh-add <(echo "$SSH_PRIVATE_KEY_BATH_OPENFLEXURE_BASE64" | base64 --decode)
+    - mkdir -p ~/.ssh
+    - echo -e "Host *\n\tStrictHostKeyChecking no\n\n" > ~/.ssh/config
+    
+  script:
+    # Install rsync if not already installed
+    - 'which rsync || ( apt-get update -y && apt-get install rsync -y )'
+    
+    # Upload the builds folder to openflexure-microscope builds 
+    - rsync -hrvz -e ssh dist/ ci-user@openflexure.bath.ac.uk:/var/www/build/openflexure-microscope-server
+    
+    # Run update-latest.py on the build server
+    - ssh -t ci-user@openflexure.bath.ac.uk "/var/www/build/update-latest.py"
+    
+  only:
+    - tags
+    - web

.gitmodules

@@ -0,0 +1,4 @@
+[submodule "openflexure_microscope/api/static"]
+	path = openflexure_microscope/api/static
+	url = https://gitlab.com/openflexure/openflexure-microscope-jsclient.git
+	branch = frame

.tarignore

@@ -0,0 +1,80 @@
+Distribution archive rules
+node_modules
+.gitlab-ci.yml
+./dist
+!openflexure_microscope/api/static/dist
+.tarignore
+
+# Pyenv files
+.python-version
+.venv*
+.env*
+
+# Byte-compiled / optimized / DLL files
+__pycache__
+*.py[cod]
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Pytho
+env/
+build
+develop-eggs
+downloads
+eggs
+lib
+lib64
+parts
+sdist
+var
+*.egg-info
+.installed.cfg
+*.egg
+pip-wheel-metadata
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov
+.tox
+.coverage
+.cache
+nosetests.xml
+coverage.xml
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+
+# Sphinx documentation
+docs/_build
+
+# PyBuilder
+target
+
+#Big-o files
+capture
+record
+*.data
+
+#IDE files
+.vscode
+.idea
+activate
+
+# UML diagrams
+classes.png
+packages.png

README.md

@@ -9,6 +9,15 @@ This includes basic installation instructions suitable for most users.
 Full developer documentation can be found on [**ReadTheDocs**](https://openflexure-microscope-software.readthedocs.io/en/stable/). 
 This includes installing the server in a mode better suited for active development.
 
+## Installation
+* `git clone --recurse-submodules https://gitlab.com/openflexure/openflexure-microscope-server.git`
+* `poetry install`
+* `poetry run build_static`
+
+### Distributing
+* `mkdir -p dist`
+* `tar -c --exclude-vcs --exclude-from .tarignore -vzf dist/openflexure-microscope-server.tar.gz .`
+
 ## Build-system
 As of 1.0.0b0, we're using [Poetry](https://github.com/sdispater/poetry) to manage dependencies, build, and distribute the package. All package information and dependencies are found in `pyproject.toml`, in line with [PEP 518](https://www.python.org/dev/peps/pep-0518/). If you're developing this package, make use of `poetry.lock` to ensure you're using the latest locked dependency list.
 

openflexure_microscope/api/app.py

@@ -65,8 +65,8 @@ app, labthing = create_app(
     title=f"OpenFlexure Microscope {api_microscope.name}",
     description="Test LabThing-based API for OpenFlexure Microscope",
     types=["org.openflexure.microscope"],
-    version=pkg_resources.get_distribution("openflexure_microscope").version,
-    flask_kwargs={"static_url_path": ""},
+    version=pkg_resources.get_distribution("openflexure-microscope-server").version,
+    flask_kwargs={"static_url_path": "", "static_folder": "static/dist"},
 )
 
 # Enable CORS for some routes outside of LabThings

openflexure_microscope/api/static

@@ -0,0 +1 @@
+Subproject commit df7169ba6833fa213f497ff71594dc4330af0792

openflexure_microscope/api/static/css/chunk-vendors.1800c649.css

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:8605f70737729f74f48d3183b30b4a2f50706f4f750cd208aeb8c136253f7d01
-size 772

openflexure_microscope/api/static/css/main.24f9722e.css

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:e68506e72389393d35cc47e5184459fff9a23bedea8c9ee96491f66c88e71954
-size 1375875

openflexure_microscope/api/static/favicon-16x16.png

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:ee944cc13be0a52ce48a81a09c179dac70729bd7580a516ccc8ac10b4cfa3f98
-size 1310

openflexure_microscope/api/static/favicon-32x32.png

@@ -1,3 +0,0 @@
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-oid sha256:710327f8b3d83c83019ed2c4b27de8caf8e4e923c9148f93c1c0a2662f683f26
-size 1659

openflexure_microscope/api/static/favicon.ico

@@ -1,3 +0,0 @@
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-oid sha256:0405ef60ab42df1c2e8721bf1f500c8c7d9e1afae130307101b8f77925ffdac1
-size 1150

openflexure_microscope/api/static/fonts/MaterialIcons-Regular.012cf6a1.woff

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:c4a1baec300d09e03a8380b85918267ee80faae8e00c6c56b48e2e74b1d9b38d
-size 57620

openflexure_microscope/api/static/fonts/MaterialIcons-Regular.570eb838.woff2

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:a87d66c91b2e7dc5530aef76c03bd6a3d25ea5826110bf4803b561b811cc8726
-size 44300

openflexure_microscope/api/static/fonts/MaterialIcons-Regular.a37b0c01.ttf

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:b7f4a3ab562048f28dd1fa691601bc43363a61d0f876d16d8316c52e4f32d696
-size 128180

openflexure_microscope/api/static/fonts/MaterialIcons-Regular.e79bfd88.eot

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:8c998b4a9c0acbb9fe5dd572c206a5a33fdd5ca2b58db87fc3b893beac85068d
-size 143258

openflexure_microscope/api/static/index.html

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:463bfdbd635ddff1d00df38b1149ffd3947b492d71cfb546549dffebd311b090
-size 843

openflexure_microscope/api/static/js/chunk-vendors.3b7762c4.js

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:a536bfa88fd1bf69284804285c5cf1da33cf05f164f175eb4085f7d057ff4f17
-size 378133

openflexure_microscope/api/static/js/chunk-vendors.3b7762c4.js.map

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:996b19391845b7cf1810f1181d935aad524897763da4c36847c7715f762b63fa
-size 1597950

openflexure_microscope/api/static/js/main.eaa8787b.js

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:0a77d7d2e5e4220883bc1491a627435cc80d0b2574d51972bcd6b12add7a4a94
-size 116850

openflexure_microscope/api/static/js/main.eaa8787b.js.map

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:1404c938e8f60b1694dd48357d486d919f5b1e32c9f226ca26fc0ee399019542
-size 395811

openflexure_microscope/api/static/titleicon.svg

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:187e61d8f6171eebf611502412556c707fab1d837f8763b2b60ce3915303f0ad
-size 1734

openflexure_microscope/install.py

@@ -0,0 +1,14 @@
+from pynpm import NPMPackage
+import os 
+
+dir_path = os.path.dirname(os.path.realpath(__file__))
+pkg_path = os.path.join(dir_path, "api", "static", "package.json")
+
+pkg = NPMPackage(pkg_path)
+
+def install():
+    pkg.install()
+
+def build():
+    pkg.install()
+    pkg.run_script('build')

openflexure_microscope/microscope.py

@@ -15,7 +15,8 @@ from openflexure_microscope.stage.sanga import SangaStage
 
 try:
     from openflexure_microscope.camera.pi import PiCameraStreamer
-except ImportError:
+except Exception as e:
+    logging.error(e)
     logging.warning("Unable to import PiCameraStreamer")
 from openflexure_microscope.camera.mock import MissingCamera
 

poetry.lock

@@ -389,19 +389,19 @@ six = "*"
 category = "main"
 description = "A pure Python interface for the Raspberry Pi camera module."
 name = "picamera"
-optional = true
+optional = false
 python-versions = "*"
 version = "1.13.2b0"
 
 [package.extras]
 array = ["numpy"]
 doc = ["sphinx"]
-test = ["pillow", "coverage", "mock", "numpy", "pytest"]
+test = ["coverage", "pytest", "mock", "pillow", "numpy"]
 
 [package.source]
-reference = "e50a34826fc8691e9f8554c529a1700662724ade"
-type = "git"
-url = "https://github.com/rwb27/picamera.git"
+reference = ""
+type = "url"
+url = "https://github.com/rwb27/picamera/releases/download/v1.13.2b0/picamera-1.13.2b0-py3-none-any.whl"
 [[package]]
 category = "main"
 description = "Python Imaging Library (Fork)"
@@ -453,6 +453,19 @@ isort = ">=4.2.5,<5"
 mccabe = ">=0.6,<0.7"
 toml = ">=0.7.1"
 
+[[package]]
+category = "main"
+description = "Python interface to your NPM and package.json."
+name = "pynpm"
+optional = false
+python-versions = "*"
+version = "0.1.2"
+
+[package.extras]
+all = ["Sphinx (>=1.5.1)", "check-manifest (>=0.25)", "coverage (>=4.0)", "isort (>=4.2.2)", "pydocstyle (>=1.0.0)", "pytest-cache (>=1.0)", "pytest-cov (>=1.8.0)", "pytest-pep8 (>=1.0.6)", "pytest (>=2.8.0)"]
+docs = ["Sphinx (>=1.5.1)"]
+tests = ["check-manifest (>=0.25)", "coverage (>=4.0)", "isort (>=4.2.2)", "pydocstyle (>=1.0.0)", "pytest-cache (>=1.0)", "pytest-cov (>=1.8.0)", "pytest-pep8 (>=1.0.6)", "pytest (>=2.8.0)"]
+
 [[package]]
 category = "dev"
 description = "Python parsing module"
@@ -744,10 +757,10 @@ version = "0.26.1"
 ifaddr = "*"
 
 [extras]
-rpi = ["picamera", "RPi.GPIO"]
+rpi = ["RPi.GPIO"]
 
 [metadata]
-content-hash = "7fbc27aa162c3acb7f1775b974ed87d3261e4038e0999904e9d1cf0f80ec98a2"
+content-hash = "e62efd90867a69b3385fb417a0cd0a9124fb4d23a36177ebef27903b4e78eb77"
 python-versions = "^3.6"
 
 [metadata.files]
@@ -1140,6 +1153,10 @@ pylint = [
     {file = "pylint-2.5.2-py3-none-any.whl", hash = "sha256:dd506acce0427e9e08fb87274bcaa953d38b50a58207170dbf5b36cf3e16957b"},
     {file = "pylint-2.5.2.tar.gz", hash = "sha256:b95e31850f3af163c2283ed40432f053acbc8fc6eba6a069cb518d9dbf71848c"},
 ]
+pynpm = [
+    {file = "pynpm-0.1.2-py2.py3-none-any.whl", hash = "sha256:3f03fbf667549f8b8b7e0419eef88d1b21833ce288f96de66fbb761b9f4c4061"},
+    {file = "pynpm-0.1.2.tar.gz", hash = "sha256:8a6d3f9423760cf3c142db3bf9bda5a075e8a91837e7d2e2b0a3de5be5e26da2"},
+]
 pyparsing = [
     {file = "pyparsing-2.4.7-py2.py3-none-any.whl", hash = "sha256:ef9d7589ef3c200abe66653d3f1ab1033c3c419ae9b9bdb1240a85b024efc88b"},
     {file = "pyparsing-2.4.7.tar.gz", hash = "sha256:c203ec8783bf771a155b207279b9bccb8dea02d8f0c9e5f8ead507bc3246ecc1"},

pyproject.toml

@@ -3,8 +3,8 @@ requires = ["poetry>=0.12"]
 build-backend = "poetry.masonry.api"
 
 [tool.poetry]
-name = "openflexure_microscope"
-version = "2.1.0-dev"
+name = "openflexure-microscope-server"
+version = "2.1.0-beta"
 description = "Python module, and Flask-based web API, to run the OpenFlexure Microscope."
 
 authors = [
@@ -22,6 +22,12 @@ keywords = ['raspberry pi', 'arduino', 'microscope']
 
 license = "GPL-3.0"
 
+exclude = ["**/node_modules/"]
+
+packages = [
+    { include = "openflexure_microscope" },
+]
+
 [tool.poetry.dependencies]
 python = "^3.6"
 Flask = "^1.0"
@@ -29,8 +35,9 @@ numpy = "1.18.2"
 Pillow = "^5.4"
 scipy = "1.4.1" # Exact version so we can guarantee a wheel
 
-picamera = { git = "https://github.com/rwb27/picamera.git", branch = "master", optional = true }  # Lens shading requires >1.14 or RWB fork, lens-shading branch.
 "RPi.GPIO" = { version = "^0.6.5", optional = true }
+picamera = {url = "https://github.com/rwb27/picamera/releases/download/v1.13.2b0/picamera-1.13.2b0-py3-none-any.whl" }
+
 pyserial = "^3.4" # Used for sangaboard (basic_serial_instrument) until we move to sangaboard pip library
 
 python-dateutil = "^2.8"
@@ -40,9 +47,13 @@ opencv-python-headless = [
     {version = "4.2.0.34", python = "^3.8"}  # Latest for Py38 systems
 ]
 labthings = "0.6.1"
+pynpm = "^0.1.2"
 
 [tool.poetry.extras]
-rpi = ["picamera", "RPi.GPIO"]
+rpi = ["RPi.GPIO"]
+
+[tool.poetry.scripts]
+build_static = 'openflexure_microscope.install:build'
 
 [tool.poetry.dev-dependencies]
 sphinxcontrib-httpdomain = "^1.7"