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feat: upgrade to use bgcflow wrapper v0.5.0 with use Snakemake v8.25.5 #1017

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feat: upgrade to use bgcflow wrapper v0.5.0 with use Snakemake v8.25.5

feat: upgrade to use bgcflow wrapper v0.5.0 with use Snakemake v8.25.5 #1017

Workflow file for this run

.github/workflows/push.yml at c9cb61c
name: snakemake-actions
on: [push]
jobs:
formatting:
runs-on: ubuntu-latest
steps:
- name: Checkout repository and submodules
uses: actions/checkout@v4
with:
submodules: recursive
- name: Formatting
uses: github/super-linter@v5
env:
VALIDATE_ALL_CODEBASE: false
DEFAULT_BRANCH: main
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
VALIDATE_SNAKEMAKE_SNAKEFMT: true
linting:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Linting
uses: ezherman/snakemake-github-action@5027c0e706ada924ab91e0501bd92185fc98de3c
with:
directory: .tests
snakefile: workflow/Snakefile
stagein: "conda config --set channel_priority strict"
args: "--lint"
dry-run:
runs-on: ubuntu-latest
needs:
- linting
- formatting
steps:
- name: Checkout repository and submodules
uses: actions/checkout@v4
with:
submodules: recursive
- name: Dry-run workflow
uses: ezherman/snakemake-github-action@5027c0e706ada924ab91e0501bd92185fc98de3c
with:
directory: .tests
snakefile: workflow/Snakefile
stagein: "conda config --set channel_priority strict"
args: "--use-conda --show-failed-logs --cores 2 --conda-cleanup-pkgs cache -n"
dry-run-report:
runs-on: ubuntu-latest
needs:
- linting
- formatting
steps:
- name: Checkout repository and submodules
uses: actions/checkout@v4
with:
submodules: recursive
- name: Dry-run workflow
uses: ezherman/snakemake-github-action@5027c0e706ada924ab91e0501bd92185fc98de3c
with:
directory: .tests
snakefile: workflow/Report
stagein: "conda config --set channel_priority strict"
args: "--use-conda --show-failed-logs --cores 2 --conda-cleanup-pkgs cache -n"
dry-run-metabase:
runs-on: ubuntu-latest
needs:
- linting
- formatting
steps:
- name: Checkout repository and submodules
uses: actions/checkout@v4
with:
submodules: recursive
- name: Dry-run workflow
uses: ezherman/snakemake-github-action@5027c0e706ada924ab91e0501bd92185fc98de3c
with:
directory: .tests
snakefile: workflow/Metabase
stagein: "conda config --set channel_priority strict"
args: "--use-conda --show-failed-logs --cores 2 --conda-cleanup-pkgs cache -n"
dry-run-bgc:
runs-on: ubuntu-latest
needs:
- linting
- formatting
steps:
- name: Checkout repository and submodules
uses: actions/checkout@v4
with:
submodules: recursive
- name: Dry-run workflow
uses: ezherman/snakemake-github-action@5027c0e706ada924ab91e0501bd92185fc98de3c
with:
directory: .tests
snakefile: workflow/BGC
stagein: "conda config --set channel_priority strict"
args: "--use-conda --show-failed-logs --cores 2 --conda-cleanup-pkgs cache -n"
dry-run-ppanggolin:
runs-on: ubuntu-latest
needs:
- linting
- formatting
steps:
- name: Checkout repository and submodules
uses: actions/checkout@v4
with:
submodules: recursive
- name: Dry-run workflow
uses: ezherman/snakemake-github-action@5027c0e706ada924ab91e0501bd92185fc98de3c
with:
directory: .tests
snakefile: workflow/ppanggolin
stagein: "conda config --set channel_priority strict"
args: "--use-conda --show-failed-logs --cores 2 --conda-cleanup-pkgs cache -n"
dry-run-lsabgc:
runs-on: ubuntu-latest
needs:
- linting
- formatting
steps:
- name: Checkout repository and submodules
uses: actions/checkout@v4
with:
submodules: recursive
- name: Dry-run workflow
uses: ezherman/snakemake-github-action@5027c0e706ada924ab91e0501bd92185fc98de3c
with:
directory: .tests
snakefile: workflow/lsabgc
stagein: "conda config --set channel_priority strict"
args: "--use-conda --show-failed-logs --cores 2 --conda-cleanup-pkgs cache -n"
unit-test:
runs-on: ubuntu-latest
needs:
- dry-run
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v5
with:
python-version: 3.11
- run: pip install "bgcflow_wrapper>=0.5.0"
- run: pip install pytest-cov
- run: pip install alive-progress
- name: Test coverage
run: pytest --cov=.tests/unit .tests/unit/
- name: Build coverage file
run: pytest --cov=.tests/unit .tests/unit/ > pytest-coverage.txt
- name: Comment coverage
uses: coroo/pytest-coverage-commentator@v1.0.2
with:
pytest-coverage: pytest-coverage.txt