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Update readthedocs.yml

Update readthedocs.yml #109

Workflow file for this run

.github/workflows/starfish-prod-ci.yml at 256c14d
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