Scripts and dependencies updates for Python 3.8 - 3.10 #102

Workflow file for this run

.github/workflows/starfish-prod-ci.yml at aba1a70


	name: starfish-prod-ci

	on:

	push:
	branches: [ master ]

	pull_request:
	branches: [ master ]

	jobs:

	lint:
	name: Lint
	runs-on: "ubuntu-latest"
	steps:
	- uses: actions/checkout@v2

	- name: Setup Python 3.8
	uses: actions/setup-python@v2
	with:
	python-version: 3.8

	- uses: actions/cache@v2
	with:
	path: ${{ env.pythonLocation }}
	key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}

	- name: Install Dependencies
	run: \|
	make install-dev

	- name: flake8 linting
	run: \|
	make lint mypy

	starfish-fast:
	name: Python-${{ matrix.python-version }}-${{ matrix.os }}
	needs: lint
	strategy:
	matrix:
	os: ["windows-latest", "ubuntu-latest"]
	python-version: ["3.8", "3.9", "3.10"]
	fail-fast: false
	runs-on: ${{ matrix.os }}
	steps:
	- uses: actions/checkout@v2

	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v2
	with:
	python-version: ${{ matrix.python-version }}

	- uses: actions/cache@v2
	with:
	path: ${{ env.pythonLocation }}
	key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}

	- name: Install dependencies
	run: \|
	make install-dev

	- name: Run tests
	run: \|
	make fast-test docs-html

	starfish-slow:
	name: Python-${{ matrix.python-version }}-${{ matrix.os }}
	needs: starfish-fast
	strategy:
	matrix:
	os: ["windows-latest", "ubuntu-latest"]
	python-version: ["3.8", "3.9", "3.10"]
	fail-fast: false
	runs-on: ${{ matrix.os }}
	steps:
	- uses: actions/checkout@v2

	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v2
	with:
	python-version: ${{ matrix.python-version }}

	- uses: actions/cache@v2
	with:
	path: ${{ env.pythonLocation }}
	key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}

	- name: Install dependencies
	run: \|
	make install-dev

	- name: Run tests
	run: \|
	make -j check-notebooks slow-test

	# Disabling napari tests for now since github actions runner has no
	# display so will need to modify tests to have napari run headless maybe?

	# napari-pinned:
	# name: Napari Pinned
	# runs-on: "ubuntu-latest"
	# steps:
	# - uses: actions/checkout@v2

	# - name: Install dependencies
	# run: \|
	# sudo apt-get install -y libgl1-mesa-glx libqt5x11extras5 xvfb
	# pip install -U pip==21.0.1
	# pip install -r requirements/REQUIREMENTS-NAPARI-CI.txt
	# make install-dev
	# pip freeze
	# export DISPLAY=:99
	# Xvfb $DISPLAY -ac -screen 0 1024x768x24 &
	# sleep 10

	# - name: Run tests
	# run: \|
	# python -c "import vispy; print(vispy.sys_info())"
	# make napari-test

	# napari-latest:
	# name: Napari Latest
	# needs: napari-pinned
	# runs-on: "ubuntu-latest"
	# steps:
	# - uses: actions/checkout@v2

	# - name: Install dependencies
	# run: \|
	# sudo apt-get install -y libgl1-mesa-glx libqt5x11extras5 xvfb
	# make install-dev
	# pip install .[napari] pytest-qt
	# pip freeze
	# export DISPLAY=:99
	# Xvfb $DISPLAY -ac -screen 0 1024x768x24 &
	# sleep 10

	# - name: Run tests
	# run: \|
	# python -c "import vispy; print(vispy.sys_info())"
	# make napari-test

	docker-smoketest:
	name: Docker Smoketest
	needs: starfish-slow
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v2

	- name: Build Docker Image
	run: \|
	docker build -f docker/Dockerfile -t spacetx/starfish .

	- name: Run Docker Smoketest
	run: \|
	docker run --rm spacetx/starfish starfish --help

	smfish-notebook:
	name: smFISH Notebook Test
	needs: starfish-slow
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v2

	- name: Setup Python 3.8
	uses: actions/setup-python@v2
	with:
	python-version: 3.8

	- uses: actions/cache@v2
	with:
	path: ${{ env.pythonLocation }}
	key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}

	- name: Install Dependencies
	run: \|
	make install-dev

	- name: Run Notebook Tests
	run: \|
	make notebooks/py/smFISH.py

	merfish-notebook:
	name: MERFISH Notebook Test
	needs: starfish-slow
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v2

	- name: Setup Python 3.8
	uses: actions/setup-python@v2
	with:
	python-version: 3.8

	- uses: actions/cache@v2
	with:
	path: ${{ env.pythonLocation }}
	key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}

	- name: Install Dependencies
	run: \|
	make install-dev

	- name: Run Notebook Tests
	run: \|
	make notebooks/py/MERFISH.py

	osmfish-notebook:
	name: osmFISH Notebook Test
	needs: starfish-slow
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v2

	- name: Setup Python 3.8
	uses: actions/setup-python@v2
	with:
	python-version: 3.8

	- uses: actions/cache@v2
	with:
	path: ${{ env.pythonLocation }}
	key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}

	- name: Install Dependencies
	run: \|
	make install-dev

	- name: Run Notebook Tests
	run: \|
	make notebooks/py/osmFISH.py

	dartfish-notebook:
	name: DARTFISH Notebook Test
	needs: starfish-slow
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v2

	- name: Setup Python 3.8
	uses: actions/setup-python@v2
	with:
	python-version: 3.8

	- uses: actions/cache@v2
	with:
	path: ${{ env.pythonLocation }}
	key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}

	- name: Install Dependencies
	run: \|
	make install-dev

	- name: Run Notebook Tests
	run: \|
	make notebooks/py/DARTFISH.py

	simulation-notebook:
	name: Simulation Notebook Test
	needs: starfish-slow
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v2

	- name: Setup Python 3.8
	uses: actions/setup-python@v2
	with:
	python-version: 3.8

	- uses: actions/cache@v2
	with:
	path: ${{ env.pythonLocation }}
	key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}

	- name: Install Dependencies
	run: \|
	make install-dev

	- name: Run Notebook Tests
	run: \|
	make notebooks/py/Starfish_simulation.py

	iss-notebook:
	name: ISS Notebook Test
	needs: starfish-slow
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v2

	- name: Setup Python 3.8
	uses: actions/setup-python@v2
	with:
	python-version: 3.8

	- uses: actions/cache@v2
	with:
	path: ${{ env.pythonLocation }}
	key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}

	- name: Install Dependencies
	run: \|
	make install-dev

	- name: Run Notebook Tests
	run: \|
	make notebooks/py/ISS.py

	baristaseq-notebook:
	name: BaristaSeq Notebook Test
	needs: starfish-slow
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v2

	- name: Setup Python 3.8
	uses: actions/setup-python@v2
	with:
	python-version: 3.8

	- uses: actions/cache@v2
	with:
	path: ${{ env.pythonLocation }}
	key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}

	- name: Install Dependencies
	run: \|
	make install-dev

	- name: Run Notebook Tests
	run: \|
	make notebooks/py/BaristaSeq.py

	seqfish-notebook:
	name: SeqFISH Notebook Test
	needs: starfish-slow
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v2

	- name: Setup Python 3.8
	uses: actions/setup-python@v2
	with:
	python-version: 3.8

	- uses: actions/cache@v2
	with:
	path: ${{ env.pythonLocation }}
	key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}

	- name: Install Dependencies
	run: \|
	make install-dev

	- name: Run Notebook Tests
	run: \|
	make notebooks/py/SeqFISH.py

	starmap-data-processing-example:
	name: STARmap Notebook Test
	needs: starfish-slow
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v2

	- name: Setpu Python 3.8
	uses: actions/setup-python@v2
	with:
	python-version: 3.8

	- uses: actions/cache@v2
	with:
	path: ${{ env.pythonLocation }}
	key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}

	- name: Install Dependencies
	run: \|
	make install-dev

	- name: Run Notebook Tests
	run: \|
	make notebooks/py/STARmap.py

	smfish-data-processing-example:
	name: 3D smFISH Data Processing Example
	needs: starfish-slow
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v2

	- name: Setup Python 3.8
	uses: actions/setup-python@v2
	with:
	python-version: 3.8

	- uses: actions/cache@v2
	with:
	path: ${{ env.pythonLocation }}
	key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}

	- name: Install Dependencies
	run: \|
	make install-dev

	- name: Run Data Processing Example Test
	run: \|
	make 3d_smFISH.py

	iss-pipeline-data-processing-example:
	name: iss_pipeline.py Data Processing Example
	needs: starfish-slow
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v2

	- name: Setup Python 3.8
	uses: actions/setup-python@v2
	with:
	python-version: 3.8

	- uses: actions/cache@v2
	with:
	path: ${{ env.pythonLocation }}
	key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}

	- name: Install Dependencies
	run: \|
	make install-dev

	- name: Run Data Processing Example Test
	run: \|
	make TESTING=1 iss_pipeline.py

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Scripts and dependencies updates for Python 3.8 - 3.10 #102

Workflow file

Scripts and dependencies updates for Python 3.8 - 3.10 #102

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Workflow file for this run