Merge pull request #225 from hjkgrp/fix_rtd #117
Workflow file for this run
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name: Pytest | |
on: | |
push: | |
branches: | |
- "master" | |
- "main" | |
pull_request: | |
branches: | |
- "master" | |
- "main" | |
jobs: | |
pytest_conda: | |
name: Pytest (conda) on ${{ matrix.os }}, Python ${{ matrix.python-version }} | |
runs-on: ${{ matrix.os }} | |
strategy: | |
matrix: | |
os: ["ubuntu-latest"] | |
python-version: ["3.7", "3.8"] | |
defaults: | |
run: | |
shell: bash -l {0} | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Additional info about the build | |
run: | | |
uname -a | |
df -h | |
ulimit -a | |
# Get date for the cache key | |
- name: Get current time | |
uses: josStorer/get-current-time@v2.0.2 | |
id: current-time | |
- name: Cache conda env | |
uses: actions/cache@v3 | |
id: cache | |
env: | |
# Increase this value to reset cache if mols.yml has not changed | |
CACHE_NUMBER: 0 | |
with: | |
path: ~/conda_pkgs_dir | |
key: | |
# Key contains current year and month to ensure it is updated once a month | |
${{ runner.os }}-py${{ matrix.python-version }}-conda-${{ steps.current-time.outputs.year }}-${{ | |
steps.current-time.outputs.month }}-${{ hashFiles('devtools/conda-envs/mols.yml') }}-${{ | |
env.CACHE_NUMBER }} | |
# More info on the whole conda setup: https://github.com/conda-incubator/setup-miniconda | |
- name: Setup Conda | |
uses: conda-incubator/setup-miniconda@v2 | |
id: conda-setup | |
with: | |
# mamba-version: "*" # uncomment to activate mamba | |
python-version: ${{ matrix.python-version }} | |
miniforge-variant: Mambaforge | |
channels: conda-forge,defaults | |
environment-file: devtools/conda-envs/mols.yml | |
activate-environment: molsimp | |
use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly! | |
- name: Install package | |
run: | | |
pip install -e . --no-deps | |
pip install pytest-cov | |
conda list | |
- name: Run tests | |
run: | | |
pytest -v --cov=molSimplify --cov-report=xml | |
- name: Run doctest | |
# For now still excluding several subfolders and files | |
run: | | |
pytest --doctest-modules --ignore=molSimplify/Informatics/MOF --ignore=molSimplify/Informatics/protein --ignore=molSimplify/Scripts/in_b3lyp_usetc.py --ignore=molSimplify/Informatics/jupyter_vis.py --ignore=molSimplify/Informatics/macrocycle_synthesis.py --ignore=molSimplify/Informatics/organic_fingerprints.py molSimplify | |
- name: Upload coverage report to codecov | |
uses: codecov/codecov-action@v3 | |
with: | |
token: ${{ secrets.CODECOV_TOKEN }} | |
directory: ./coverage/reports/ | |
env_vars: OS,PYTHON | |
files: ./coverage.xml | |
flags: unittests | |
name: codecov-umbrella | |
verbose: true | |
- name: Report Status | |
# Slack notifications only on the main repo | |
if: ${{job.status == 'failure' && github.event_name != 'pull_request' && github.repository == 'hjkgrp/molSimplify' }} | |
#uses: ravsamhq/notify-slack-action@v1 | |
uses: 8398a7/action-slack@v3 | |
with: | |
job_name: Pytest (conda) on ${{ matrix.os }}, Python ${{ matrix.python-version }} | |
fields: message,commit,author,workflow,job,took | |
status: ${{ job.status }} | |
env: | |
SLACK_WEBHOOK_URL: ${{secrets.SLACK_WEBHOOK}} | |
#MATRIX_CONTEXT: ${{ toJson(matrix) }} # required | |
pytest_pip: | |
name: Pytest (pip) on ${{ matrix.os }}, Python ${{ matrix.python-version }} | |
runs-on: ${{ matrix.os }} | |
strategy: | |
matrix: | |
os: ["ubuntu-latest"] | |
python-version: ["3.8"] | |
steps: | |
- uses: actions/checkout@v4 | |
- name: Set up Python ${{ matrix.python-version }} | |
uses: actions/setup-python@v4 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- name: Install package | |
run: | | |
pip install -e .[dev] | |
- name: Run pytest | |
run: | | |
pytest -v |