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parse: Prefer strain over name as sequence ID field #2840

parse: Prefer strain over name as sequence ID field

parse: Prefer strain over name as sequence ID field #2840

Workflow file for this run

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:
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')" >> "$GITHUB_ENV"
# While it may be tempting to install Augur using Conda to avoid hardcoding
# the list of dependencies here, installing just the dependencies not
# available on PyPI allows us to test against dependencies installed by pip,
# which may have slightly different versions compared to Conda counterparts.
- name: Install dependencies from Conda
uses: mamba-org/setup-micromamba@v1
with:
create-args: mafft raxml fasttree iqtree vcftools sqlite tsv-utils biopython=${{ 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@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: 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@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@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