From f9432f82cabfeec6220aca4d438d182b325536cd Mon Sep 17 00:00:00 2001 From: Jonas Freimuth Date: Mon, 16 Mar 2026 23:32:26 +0100 Subject: [PATCH 1/5] refactor: Move plugin module to src dir For consistency with current plugin template. --- .../snakemake_executor_plugin_cluster_generic}/__init__.py | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename {snakemake_executor_plugin_cluster_generic => src/snakemake_executor_plugin_cluster_generic}/__init__.py (100%) diff --git a/snakemake_executor_plugin_cluster_generic/__init__.py b/src/snakemake_executor_plugin_cluster_generic/__init__.py similarity index 100% rename from snakemake_executor_plugin_cluster_generic/__init__.py rename to src/snakemake_executor_plugin_cluster_generic/__init__.py From e77f45a22881b277a249b269be546dac034d8ef0 Mon Sep 17 00:00:00 2001 From: Jonas Freimuth Date: Mon, 16 Mar 2026 22:41:59 +0100 Subject: [PATCH 2/5] chore: Use pixi infra from current scaffold For ease of development. Done by copying current Snakedeploy scaffolding. This also means using different pacakges for dev tasks. Due to the latter, test coverage seems to have gone down to just above 68.9. --- .gitattributes | 2 + .github/workflows/ci.yml | 78 +- .github/workflows/release-please.yml | 39 +- .gitignore | 4 +- pixi.lock | 1430 ++++++++++++++++++++++++++ pyproject.toml | 58 +- tests/{tests.py => test_plugin.py} | 0 7 files changed, 1513 insertions(+), 98 deletions(-) create mode 100644 .gitattributes create mode 100644 pixi.lock rename tests/{tests.py => test_plugin.py} (100%) diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..997504b --- /dev/null +++ b/.gitattributes @@ -0,0 +1,2 @@ +# SCM syntax highlighting & preventing 3-way merges +pixi.lock merge=binary linguist-language=YAML linguist-generated=true -diff diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index b2de6f9..393c6f0 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -13,80 +13,46 @@ jobs: - name: Check out the code uses: actions/checkout@v4 - - uses: actions/setup-python@v5 - with: - python-version: "3.11" - - - name: Install poetry - run: pip install poetry - - - name: Determine dependencies - run: poetry lock - - - uses: actions/setup-python@v5 - with: - python-version: "3.11" - cache: poetry - - - name: Install Dependencies using Poetry - run: poetry install + - name: Setup pixi + uses: prefix-dev/setup-pixi@v0 - name: Check formatting - run: poetry run black --check . + run: pixi run format --check linting: runs-on: ubuntu-latest steps: - name: Check out the code - uses: actions/checkout@v3 - - - uses: actions/setup-python@v4 - with: - python-version: "3.11" - - - name: Install poetry - run: pip install poetry - - - name: Determine dependencies - run: poetry lock + uses: actions/checkout@v6 - - uses: actions/setup-python@v4 - with: - python-version: "3.11" - cache: poetry - - - name: Install Dependencies using Poetry - run: poetry install + - name: Setup pixi + uses: prefix-dev/setup-pixi@v0 - name: Check code - run: poetry run flake8 + run: pixi run lint - testing: + typecheck: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 - - - uses: actions/setup-python@v5 - with: - python-version: "3.11" + - name: Check out the code + uses: actions/checkout@v6 - - name: Install poetry - run: pip install poetry + - name: Setup pixi + uses: prefix-dev/setup-pixi@v0 - - name: Determine dependencies - run: poetry lock + - name: Check code + run: pixi run typecheck - - uses: actions/setup-python@v5 - with: - python-version: "3.11" - cache: poetry + test: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v6 - - name: Install dependencies - run: | - poetry install + - name: Setup pixi + uses: prefix-dev/setup-pixi@v0 - name: Run pytest - run: poetry run coverage run -m pytest tests/tests.py + run: pixi run test -v - name: Run Coverage - run: poetry run coverage report -m + run: pixi run coverage-report diff --git a/.github/workflows/release-please.yml b/.github/workflows/release-please.yml index d41a7ad..d46f703 100644 --- a/.github/workflows/release-please.yml +++ b/.github/workflows/release-please.yml @@ -5,16 +5,20 @@ on: name: release-please +env: + PYTHON_VERSION: "3.11" + jobs: release-please: runs-on: ubuntu-latest outputs: release_created: ${{ steps.release.outputs.release_created }} steps: - - uses: googleapis/release-please-action@v4 + - uses: GoogleCloudPlatform/release-please-action@v3 id: release with: release-type: python + package-name: snakemake-executor-plugin-cluster-generic token: ${{ secrets.RELEASE_PLEASE_PR_CI_TOKEN }} publish: @@ -22,28 +26,21 @@ jobs: needs: release-please if: ${{ needs.release-please.outputs.release_created }} steps: - - uses: actions/checkout@v4 + - name: Check out the code + uses: actions/checkout@v4 - - uses: actions/setup-python@v5 + - name: Setup pixi + uses: prefix-dev/setup-pixi@v0 with: - python-version: "3.11" - - - name: Install poetry - run: pip install poetry + cache: true + python-version: ${{ env.PYTHON_VERSION }} - - name: Determine dependencies - run: poetry lock + - name: Build source and wheel distribution + check build + run: | + pixi run -e dev check-build - - uses: actions/setup-python@v5 + - name: Publish to PyPI + uses: pypa/gh-action-pypi-publish@release/v1 with: - python-version: "3.11" - cache: poetry - - - name: Install Dependencies using Poetry - run: poetry install - - - name: Publish to PyPi - env: - PYPI_USERNAME: __token__ - PYPI_PASSWORD: ${{ secrets.PYPI_TOKEN }} - run: poetry publish --build --username $PYPI_USERNAME --password $PYPI_PASSWORD + user: __token__ + password: ${{ secrets.PYPI_TOKEN }} diff --git a/.gitignore b/.gitignore index bcc3d59..0334294 100644 --- a/.gitignore +++ b/.gitignore @@ -159,4 +159,6 @@ cython_debug/ # option (not recommended) you can uncomment the following to ignore the entire idea folder. #.idea/ -poetry.lock \ No newline at end of file +# pixi environments +.pixi/* +!.pixi/config.toml diff --git a/pixi.lock b/pixi.lock new file mode 100644 index 0000000..3099178 --- /dev/null +++ b/pixi.lock @@ -0,0 +1,1430 @@ +version: 6 +environments: + default: + channels: + - url: https://conda.anaconda.org/conda-forge/ + indexes: + - https://pypi.org/simple + options: + pypi-prerelease-mode: if-necessary-or-explicit + packages: + linux-64: + - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda + - 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"Failed to obtain job status. " - "See above for error message." + "Failed to obtain job status. See above for error message." ) ret = ret.strip().split("\n") From e0d18f0129b93fabcec2273b038ee8e3c5e0d6ff Mon Sep 17 00:00:00 2001 From: Jonas Freimuth Date: Mon, 16 Mar 2026 22:14:07 +0100 Subject: [PATCH 4/5] ci: Rename actions for consistency Using names from current SnakeDeploy template. --- .github/workflows/ci.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 393c6f0..7e4601f 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -7,7 +7,7 @@ on: pull_request: jobs: - formatting: + format: runs-on: ubuntu-latest steps: - name: Check out the code @@ -19,7 +19,7 @@ jobs: - name: Check formatting run: pixi run format --check - linting: + lint: runs-on: ubuntu-latest steps: - name: Check out the code From 40c24c23ddf76baa0526a439b1588d9895a70c25 Mon Sep 17 00:00:00 2001 From: Jonas Freimuth Date: Mon, 16 Mar 2026 22:23:10 +0100 Subject: [PATCH 5/5] ci: Use checkout action v6 Just for consistency. --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 7e4601f..3e3bc74 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out the code - uses: actions/checkout@v4 + uses: actions/checkout@v6 - name: Setup pixi uses: prefix-dev/setup-pixi@v0