update CI #205
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
name: Test and deploy code | |
on: [push] | |
jobs: | |
test: | |
runs-on: ${{ matrix.os }} | |
strategy: | |
fail-fast: false | |
matrix: | |
os: ["ubuntu-latest"] | |
python-version: ["3.8", "3.9", "3.10"] | |
defaults: # Needed for conda | |
run: | |
shell: bash -l {0} | |
steps: | |
- uses: actions/checkout@v3 | |
with: | |
lfs: true | |
submodules: true | |
- uses: conda-incubator/setup-miniconda@v2 | |
with: | |
auto-update-conda: true | |
python-version: ${{ matrix.python-version }} | |
use-mamba: true | |
miniforge-variant: Mambaforge | |
channels: acellera,conda-forge,defaults | |
- name: Install HTMD conda deps # psfgen should not be included by default in HTMD due to licensing | |
run: | | |
mamba install --file package/htmd-deps/DEPENDENCIES python=${{ matrix.python-version }} -y | |
- name: Install pip dependencies | |
run: | | |
pip install flake8 pytest | |
pip install . | |
- name: Lint with flake8 | |
run: | | |
# stop the build if there are Python syntax errors or undefined names | |
flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
- name: Test | |
run: | | |
export HTMD_NONINTERACTIVE=1 | |
pytest --verbose --durations=10 ./htmd/ | |
deploy: | |
if: startsWith(github.event.ref, 'refs/tags/') | |
needs: test | |
runs-on: ${{ matrix.os }} | |
defaults: # Needed for conda | |
run: | |
shell: bash -l {0} | |
strategy: | |
fail-fast: false | |
matrix: | |
os: ["ubuntu-latest"] | |
python-version: ["3.8", "3.9", "3.10"] | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Set version envvar | |
run: echo "BUILD_VERSION=${{ github.ref_name }}" >> $GITHUB_ENV | |
- name: Check version envvar | |
run: echo "Building version $BUILD_VERSION" | |
- uses: conda-incubator/setup-miniconda@v2 | |
with: | |
activate-environment: writedeps | |
auto-update-conda: true | |
python-version: ${{ matrix.python-version }} | |
uses-mamba: true | |
miniforge-variant: Mambaforge | |
channels: acellera,conda-forge,defaults | |
- name: Dump exact dependencies yaml file | |
run: | | |
mamba install --file package/htmd-deps/DEPENDENCIES python=${{ matrix.python-version }} -y | |
python package/htmd-deps/write_meta_yaml.py package/htmd-deps | |
- uses: conda-incubator/setup-miniconda@v2 | |
with: | |
auto-activate-base: true | |
activate-environment: build | |
python-version: ${{ matrix.python-version }} | |
uses-mamba: true | |
miniforge-variant: Mambaforge | |
- name: Build htmd-deps conda package | |
run: | | |
echo "Building version $BUILD_VERSION" | |
mamba install anaconda-client conda-build python=${{ matrix.python-version }} boa | |
conda mambabuild --python ${{ matrix.python-version }} package/htmd-deps --output-folder ./pkg/ --no-include-recipe --no-anaconda-upload -c acellera -c conda-forge | |
- name: Build htmd conda package | |
run: | | |
echo "Building version $BUILD_VERSION" | |
conda mambabuild --python ${{ matrix.python-version }} package/htmd --output-folder ./pkg/ --no-include-recipe --no-anaconda-upload -c acellera -c conda-forge | |
- name: Upload to conda | |
run: | | |
anaconda -t ${{ secrets.ANACONDA_TOKEN_BASIC }} upload -u acellera ./pkg/*/htmd-*.tar.bz2 |