feat(ancestral): make --genes optional when reconstructing translations, if omitted, translate all genes in annotation #2997
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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: | |
workflow_call: | |
inputs: | |
version: | |
required: true | |
type: string | |
jobs: | |
mypy: | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/setup-python@v5 | |
- uses: actions/checkout@v4 | |
- run: pip install .[dev] | |
- run: mypy | |
pyright: | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/setup-python@v5 | |
- uses: actions/checkout@v4 | |
- run: npx pyright --stats | |
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')" >> "$GITHUB_ENV" | |
# While it may be tempting to install Augur using Conda to avoid hardcoding | |
# the list of dependencies here, installing just the dependencies not | |
# available on PyPI allows us to test against dependencies installed by pip, | |
# which may have slightly different versions compared to Conda counterparts. | |
- name: Install dependencies from Conda | |
uses: mamba-org/setup-micromamba@v2 | |
with: | |
create-args: mafft raxml fasttree iqtree vcftools sqlite tsv-utils biopython=${{ 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 --cov=augur | |
- run: cram tests/ | |
env: | |
AUGUR: coverage run -a ${{ github.workspace }}/bin/augur | |
# Only upload coverage for one job | |
- if: matrix.python-version == '3.11' && matrix.biopython-version == '' | |
uses: actions/upload-artifact@v4 | |
with: | |
name: coverage | |
include-hidden-files: true | |
path: "${{ env.COVERAGE_FILE }}" | |
# Replicating pathogen-repo-ci workflow because we decided not to support | |
# local versions of Augur in the centralized workflow | |
# <https://github.com/nextstrain/.github/issues/66> | |
# This job is for pathogen repos _do_ follow standard pathogen repo structure | |
# and new pathogens should be added here. | |
pathogen-repo-ci: | |
runs-on: ubuntu-latest | |
continue-on-error: true | |
strategy: | |
matrix: | |
pathogen: | |
- dengue | |
- lassa | |
- measles | |
- mpox | |
- seasonal-cov | |
- 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@v2 | |
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: Verify nextstrain-pathogen.yaml file | |
run: > | |
if [[ ! -f './pathogen-repo/nextstrain-pathogen.yaml' ]]; then | |
echo "To use this workflow, there must be a 'nextstrain-pathogen.yaml' file present in the repository root"; | |
exit 1; | |
fi | |
- name: Run ingest | |
if: hashFiles('./pathogen-repo/ingest/Snakefile') && hashFiles('./pathogen-repo/ingest/build-configs/ci/config.yaml') | |
id: ingest | |
run: nextstrain build --ambient ./pathogen-repo/ingest --configfile build-configs/ci/config.yaml | |
- name: Run phylogenetic | |
if: hashFiles('./pathogen-repo/phylogenetic/Snakefile') && hashFiles('./pathogen-repo/phylogenetic/build-configs/ci/config.yaml') && !cancelled() | |
id: phylogenetic | |
run: nextstrain build --ambient ./pathogen-repo/phylogenetic --configfile build-configs/ci/config.yaml | |
- name: Run nextclade | |
if: hashFiles('./pathogen-repo/nextclade/Snakefile') && hashFiles('./pathogen-repo/nextclade/build-configs/ci/config.yaml') && !cancelled() | |
id: nextclade | |
run: nextstrain build --ambient ./pathogen-repo/nextclade --configfile build-configs/ci/config.yaml | |
- if: always() | |
uses: actions/upload-artifact@v4 | |
with: | |
name: output-${{ matrix.pathogen }} | |
if-no-files-found: ignore | |
path: | | |
./pathogen-repo/ingest/.snakemake/log/ | |
./pathogen-repo/ingest/auspice/ | |
./pathogen-repo/ingest/benchmarks/ | |
./pathogen-repo/ingest/logs/ | |
./pathogen-repo/ingest/results/ | |
./pathogen-repo/phylogenetic/.snakemake/log/ | |
./pathogen-repo/phylogenetic/auspice/ | |
./pathogen-repo/phylogenetic/benchmarks/ | |
./pathogen-repo/phylogenetic/logs/ | |
./pathogen-repo/phylogenetic/results/ | |
./pathogen-repo/nextclade/.snakemake/log/ | |
./pathogen-repo/nextclade/auspice/ | |
./pathogen-repo/nextclade/benchmarks/ | |
./pathogen-repo/nextclade/logs/ | |
./pathogen-repo/nextclade/results/ | |
- if: always() | |
name: Verify a workflow ran | |
env: | |
# "outcome" is success/failure/cancelled/skipped _before_ | |
# "continue-on-error" is applied to calculate "conclusion"; we no | |
# longer use continue-on-error for these steps, but even so, | |
# conceptually here what we want is outcome not conclusion. | |
ingest: ${{ steps.ingest.outcome }} | |
phylogenetic: ${{ steps.phylogenetic.outcome }} | |
nextclade: ${{ steps.nextclade.outcome }} | |
run: | | |
# Show step outcomes in job logs… | |
echo "ingest $ingest" | tee -a "$GITHUB_STEP_SUMMARY" | |
echo "phylogenetic $phylogenetic" | tee -a "$GITHUB_STEP_SUMMARY" | |
echo "nextclade $nextclade"| tee -a "$GITHUB_STEP_SUMMARY" | |
# Assert status; we're good if we see at least one success and the | |
# rest are success or skipped. | |
[[ | |
($ingest == success || $phylogenetic == success || $nextclade == success) | |
&& ($ingest == success || $ingest == skipped) | |
&& ($phylogenetic == success || $phylogenetic == skipped) | |
&& ($nextclade == success || $nextclade == skipped) | |
]] | |
# Replicating pathogen-repo-ci-v0 workflow because we decided not to support | |
# local versions of Augur in the centralized workflow | |
# <https://github.com/nextstrain/.github/issues/66> | |
# This particular jobs is for pathogen repos that do not follow the standard | |
# pathogen repo structure and is not expected to be updated. | |
# Any new pathogen repos should be added to the job replicating the latest version | |
# of the pathogen-repo-ci above. | |
pathogen-repo-ci-v0: | |
runs-on: ubuntu-latest | |
continue-on-error: true | |
env: | |
repodata_use_zst: true | |
strategy: | |
matrix: | |
include: | |
- { pathogen: avian-flu, build-args: --configfile config/gisaid.yaml -pf test_target } | |
- { pathogen: ebola } | |
- { pathogen: mumps } | |
- { | |
pathogen: ncov, | |
build-args: all_regions -j 2 --profile nextstrain_profiles/nextstrain-ci, | |
} | |
- { pathogen: rsv } | |
- { | |
pathogen: seasonal-flu, | |
build-args: --configfile profiles/ci/builds.yaml -p, | |
} | |
- { pathogen: tb } | |
name: pathogen-repo-ci-v0 (${{ 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@v2 | |
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@v4 | |
with: | |
token: ${{ secrets.CODECOV_TOKEN }} | |
fail_ci_if_error: false | |
build-docs: | |
uses: nextstrain/.github/.github/workflows/docs-ci.yaml@master | |
with: | |
docs-directory: docs/ | |
pip-install-target: .[dev] | |
check-docs: | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/setup-python@v5 | |
- uses: actions/checkout@v4 | |
- run: pip install .[dev] | |
- run: ./devel/regenerate-developer-api-docs | |
- name: Check for changes | |
run: | | |
if [[ -n $(git status --porcelain) ]]; then | |
git add . | |
git diff --staged >&2 | |
echo "There are changes that affect the developer API docs. Please update: <https://github.com/nextstrain/augur/blob/-/docs/contribute/DEV_DOCS.md#regenerating-developer-api-docs>" >&2 | |
echo "If there are changes to the Augur CLI, please manually adjust files under 'docs/usage/cli/'." >&2 | |
exit 1 | |
fi | |
release: | |
# Only run when called by the release workflow on the default branch | |
if: github.event_name == 'workflow_call' && github.workflow_ref == format('{0}/.github/workflows/release.yaml@refs/heads/{1}', github.repository, github.event.repository.default_branch) | |
needs: [pytest-cram] | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v4 | |
with: | |
# Fetch all branches and tags. | |
fetch-depth: 0 | |
- uses: actions/setup-python@v5 | |
with: | |
python-version: '3.10' | |
- name: Set Nextstrain bot as git user | |
run: | | |
git config --global user.email "hello@nextstrain.org" | |
git config --global user.name "Nextstrain bot" | |
- run: python3 -m pip install --upgrade build twine | |
- run: devel/release ${{ github.event.inputs.version }} | |
- uses: actions/upload-artifact@v4 | |
with: | |
name: dist | |
path: dist/ | |
- run: git push origin master tag ${{ github.event.inputs.version }} | |
- name: Publish to PyPI | |
run: twine upload dist/* | |
env: | |
TWINE_USERNAME: __token__ | |
TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }} | |
TWINE_REPOSITORY_URL: https://upload.pypi.org/legacy/ | |
- name: Create GitHub Release | |
run: ./devel/create-github-release "${{github.event.inputs.version }}" dist/* | |
env: | |
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
rebuild-docker-image: | |
needs: [release] | |
runs-on: ubuntu-latest | |
steps: | |
# Delay for 10 minutes to allow the PyPI package to be available. | |
# See https://github.com/nextstrain/docker-base/issues/128 | |
- name: Sleep for 10 minutes | |
run: sleep 600 | |
shell: bash | |
- run: gh workflow run ci.yml --repo nextstrain/docker-base | |
env: | |
GITHUB_TOKEN: ${{ secrets.GH_TOKEN_NEXTSTRAIN_BOT_WORKFLOW_DISPATCH }} |