WIP [refine] unique internal node names #2317
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name: CI | |
on: | |
push: | |
branches: | |
- master | |
# Routinely check that tests pass with new versions of dependencies. | |
schedule: | |
# Every day at 17:42 UTC / 9:42 Seattle (winter) / 10:42 Seattle (summer) | |
- cron: "42 17 * * *" | |
pull_request: | |
workflow_dispatch: | |
jobs: | |
pytest-cram: | |
name: test (python=${{ matrix.python-version }} biopython=${{ matrix.biopython-version || 'latest' }}) | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
python-version: | |
- '3.8' | |
- '3.9' | |
- '3.10' | |
- '3.11' | |
biopython-version: | |
# list of Biopython versions with support for a new Python version | |
# from https://github.com/biopython/biopython/blob/master/NEWS.rst | |
- '1.80' # first to support Python 3.10 and 3.11 | |
- '' # latest | |
defaults: | |
run: | |
shell: bash -l {0} | |
env: | |
COVERAGE_FILE: ${{ github.workspace }}/.coverage@python=${{ matrix.python-version }},biopython=${{ matrix.biopython-version || 'latest' }} | |
COVERAGE_RCFILE: ${{ github.workspace }}/.coveragerc | |
steps: | |
- uses: actions/checkout@v4 | |
- name: Set cache key | |
run: echo "DATE=$(date +'%Y-%m-%d')" >> "$GITHUB_ENV" | |
# While it may be tempting to install Augur using Conda to avoid hardcoding | |
# the list of dependencies here, installing just the dependencies not | |
# available on PyPI allows us to test against dependencies installed by pip, | |
# which may have slightly different versions compared to Conda counterparts. | |
- name: Install dependencies from Conda | |
uses: mamba-org/setup-micromamba@v1 | |
with: | |
create-args: mafft raxml fasttree iqtree vcftools biopython=${{ matrix.biopython-version }} python=${{ matrix.python-version }} | |
condarc: | | |
channels: | |
- conda-forge | |
- bioconda | |
channel_priority: strict | |
cache-environment: true | |
cache-environment-key: ${{ env.DATE }} | |
environment-name: augur | |
# Replace the Conda Augur installation with the local version. | |
- run: pip install .[dev] | |
- run: conda info | |
- run: conda list | |
- run: pytest -c pytest.python3.ini --cov=augur | |
- run: cram tests/ | |
env: | |
AUGUR: coverage run -a ${{ github.workspace }}/bin/augur | |
# Only upload coverage for one job | |
- if: matrix.python-version == '3.11' && matrix.biopython-version == '' | |
uses: actions/upload-artifact@v4 | |
with: | |
name: coverage | |
path: "${{ env.COVERAGE_FILE }}" | |
# TODO: Use the central pathogen-repo-ci workflow¹. Currently, this is not | |
# possible because it only supports "stock" docker and conda runtimes. | |
# ¹ https://github.com/nextstrain/.github/blob/-/.github/workflows/pathogen-repo-ci.yaml | |
pathogen-repo-ci: | |
runs-on: ubuntu-latest | |
continue-on-error: true | |
env: | |
repodata_use_zst: true | |
strategy: | |
matrix: | |
include: | |
- { pathogen: avian-flu, build-args: auspice/avian-flu_h5n1_ha.json } | |
- { pathogen: ebola } | |
- { pathogen: lassa } | |
- { pathogen: mumps } | |
- { | |
pathogen: ncov, | |
build-args: all_regions -j 2 --profile nextstrain_profiles/nextstrain-ci, | |
} | |
- { pathogen: rsv } | |
- { | |
pathogen: seasonal-flu, | |
build-args: --configfile profiles/ci/builds.yaml -p, | |
} | |
- { pathogen: tb } | |
# Disable some pathogens until pathogen-repo-ci supports custom build directories | |
# See issue https://github.com/nextstrain/.github/issues/63 | |
# - { pathogen: mpox } | |
# - { pathogen: zika } | |
name: pathogen-repo-ci (${{ matrix.pathogen }}) | |
defaults: | |
run: | |
shell: bash -l {0} | |
steps: | |
- uses: actions/checkout@v4 | |
with: | |
path: ./augur | |
- name: Set cache key | |
run: echo "DATE=$(date +'%Y-%m-%d')" >> "$GITHUB_ENV" | |
# Set up a Conda environment that replicates Nextstrain's Conda runtime. | |
- name: Install nextstrain-base from Conda | |
uses: mamba-org/setup-micromamba@v1 | |
with: | |
create-args: nextstrain-base | |
condarc: | | |
channels: | |
- nextstrain | |
- conda-forge | |
- bioconda | |
channel_priority: strict | |
cache-environment: true | |
cache-environment-key: ${{ env.DATE }} | |
environment-name: augur | |
# Replace the Conda Augur installation with the local version. | |
- run: pip install ./augur | |
- uses: actions/checkout@v4 | |
with: | |
repository: nextstrain/${{ matrix.pathogen }} | |
path: ./pathogen-repo | |
- name: Copy example data | |
working-directory: ./pathogen-repo | |
run: | | |
if [[ -d example_data ]]; then | |
mkdir -p data/ | |
cp -r -v example_data/* data/ | |
else | |
echo No example data to copy. | |
fi | |
- run: nextstrain build --ambient ./pathogen-repo ${{ matrix.build-args }} | |
- if: always() | |
uses: actions/upload-artifact@v4 | |
with: | |
name: output-${{ matrix.pathogen }} | |
path: | | |
./pathogen-repo/auspice/ | |
./pathogen-repo/results/ | |
./pathogen-repo/benchmarks/ | |
./pathogen-repo/logs/ | |
./pathogen-repo/.snakemake/log/ | |
codecov: | |
if: github.repository == 'nextstrain/augur' | |
needs: [pytest-cram] | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v4 | |
- uses: actions/setup-python@v5 | |
- run: pip install coverage | |
- uses: actions/download-artifact@v4 | |
with: | |
name: coverage | |
- run: coverage combine .coverage@* | |
- run: coverage xml | |
- uses: codecov/codecov-action@v3 | |
with: | |
fail_ci_if_error: false | |
build-docs: | |
uses: nextstrain/.github/.github/workflows/docs-ci.yaml@master | |
with: | |
docs-directory: docs/ | |
pip-install-target: .[dev] |