add mol fingerprint methods ✋ (#724) #4319
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| # This workflow will check for Black formating, install Python dependencies using Anaconda, and then run tests with a single version of Python. | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| # | |
| # We also use a third-party action(s) for setting up our conda environment. See: | |
| # conda: https://github.com/marketplace/actions/setup-miniconda | |
| # mamba: https://github.com/mamba-org/provision-with-micromamba | |
| name: Test | |
| on: | |
| push: | |
| branches: [main] | |
| pull_request: | |
| branches: [main] | |
| schedule: | |
| # Runs the schedule every day at 5:30 and at 17:30 UTC | |
| - cron: "30 5,17 * * *" | |
| jobs: | |
| lint-and-test: | |
| # Establishes the combination of all OS and python versions | |
| # for us to test. The "steps" below will be ran for each | |
| # of these combinations. | |
| name: Python ${{ matrix.python-version }} (${{ matrix.os }}) | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| # setup-miniconda not compatible with macos-latest | |
| # https://github.com/conda-incubator/setup-miniconda/issues/344 | |
| os: ["ubuntu-latest", "macos-12", "windows-latest"] | |
| python-version: ["3.10", "3.11"] | |
| steps: | |
| - name: Initial setup | |
| uses: actions/checkout@v3 | |
| - name: Check code format with Black | |
| uses: psf/black@stable | |
| # This action seems poorly-maintained -- as it fails on MacOS and also | |
| # directly installs isort (unlike the action used for Black). I therefore | |
| # disable this for now. | |
| # - name: Check import format with iSort | |
| # uses: isort/isort-action@master | |
| - name: Create conda env and install deps | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| environment-file: envs/conda/dev.yaml | |
| python-version: ${{ matrix.python-version }} | |
| auto-activate-base: false | |
| channels: conda-forge | |
| activate-environment: simmate_dev | |
| channel-priority: strict | |
| # The lines "shell: bash -l {0}" ensure we use the created env below | |
| - name: Install Simmate | |
| shell: bash -l {0} | |
| run: | | |
| pip install -e . | |
| # --editable is needed because we need test files too | |
| # note: we want to skip installing the deps (--no-deps) because they were | |
| # done in last step, but we repeat this because of a bug: | |
| # "maggma 0.57.0 has requirement ruamel.yaml<0.18, but you have ruamel-yaml 0.18.5." | |
| # Run checks to see that simmate & deps are installed correctly | |
| - name: Check conda info | |
| shell: bash -l {0} | |
| run: | | |
| conda info | |
| conda list | |
| # DISABLED BC OF https://github.com/jacksund/simmate/issues/669 | |
| # - name: Check dependencies | |
| # shell: bash -l {0} | |
| # run: | | |
| # pip check | |
| - name: Run default tests | |
| shell: bash -l {0} | |
| run: | | |
| pytest -vv --durations=15 | |
| # "-vv" makes the pytest output verbose so errors are more useful | |
| # and "duration=0" has pytest print how long every test took. We ask for | |
| # the 15 slowest ones. | |
| docker-build: | |
| name: Docker | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| image-name: ["bader", "simmate", "quantum_espresso"] | |
| permissions: | |
| contents: read | |
| packages: write | |
| steps: | |
| - name: Initial setup | |
| uses: actions/checkout@v3 | |
| - name: Build Docker image | |
| uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc | |
| with: | |
| context: . | |
| file: ./envs/docker/${{ matrix.image-name }}.dockerfile | |
| push: false |