merge origin/main

.ci.condarc

@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+channel_priority: strict

.github/actions/conda-cache/action.yml

@@ -0,0 +1,38 @@
+name: 'Install/Cache conda'
+description: 'Install or retrieve a conda environment from cache'
+inputs:
+  python-version:
+    required: true
+    type: string
+  environment-file:
+    required: true
+    type: string
+  cache-number:
+    required: false
+    type: number
+    default: 1
+
+defaults:
+  run:
+    shell: bash -el {0}
+
+runs:
+  using: "composite"
+  steps:
+    - name: Setup conda
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        activate-environment: ci_test_conda
+        python-version: ${{ inputs.python-version }}
+
+    - name: Cache conda
+      uses: actions/cache@v3
+      with:
+        path: ${{ env.CONDA }}/envs
+        key: ${{ runner.os }}-conda-${{ inputs.cache-number }}-${{ hashFiles(inputs.environment-file) }}
+      id: cache
+
+    - name: Update conda environment
+      shell: bash -el {0}
+      if: steps.cache.outputs.cache-hit != 'true'
+      run: conda env update -n ci_test_conda -f ${{ inputs.environment-file }}

.github/dependabot.yml

@@ -0,0 +1,11 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  - package-ecosystem: "pip" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"

.github/workflows/ci-e2e.yml

@@ -42,39 +42,64 @@ on:
       - 'snappy_wrappers/wrappers/somatic_variant_filtration/**'
       - 'snappy_wrappers/wrappers/vep/**'
 
+defaults:
+  run:
+    shell: bash -el {0}
 
 jobs:
 
   Dryrun_Tests:
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version:
+          - "3.12"
     steps:
     - uses: actions/checkout@v4
       with:
         lfs: 'true'
+
+    - name: Setup conda
+      uses: ./.github/actions/conda-cache
+      with:
+        python-version: ${{ matrix.python-version }}
+        environment-file: environment.yml
+
     - name: Test workflow (local FASTQs)
-      uses: snakemake/snakemake-github-action@v1
+      uses: snakemake/snakemake-github-action@cebcb23c87aa3a23efddff3f79b3a4bd143d4120
       with:
         directory: .tests/test-workflow
         snakefile: .tests/test-workflow/workflow/Snakefile
         args: "--configfile .tests/test-workflow/config/config.yaml --use-conda --show-failed-logs -j 2 --conda-cleanup-pkgs cache --dryrun"
         show-disk-usage-on-error: true
+        snakemake-version: 7.32.4
 
 
   Tests:
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version:
+          - "3.12"
     needs:
       - Dryrun_Tests
     steps:
-    - name: update apt
-      run: sudo apt-get update
     - uses: actions/checkout@v4
       with:
         lfs: 'true'
+
+    - name: Setup conda
+      uses: ./.github/actions/conda-cache
+      with:
+        python-version: ${{ matrix.python-version }}
+        environment-file: environment.yml
+
     - name: Test workflow (local FASTQs)
-      uses: snakemake/snakemake-github-action@v1
+      uses: snakemake/snakemake-github-action@cebcb23c87aa3a23efddff3f79b3a4bd143d4120
       with:
         directory: .tests/test-workflow
         snakefile: .tests/test-workflow/workflow/Snakefile
         args: "--configfile .tests/test-workflow/config/config.yaml --use-conda --show-failed-logs -j 2 --conda-cleanup-pkgs cache"
         show-disk-usage-on-error: true
+        snakemake-version: 7.32.4
 

.github/workflows/ci.yml

@@ -7,7 +7,12 @@ on:
   pull_request:
     branches_ignore: []
 
+defaults:
+  run:
+    shell: bash -el {0}
+
 jobs:
+
   cancel-previous:
     runs-on: ubuntu-latest
     if: github.ref != 'refs/heads/main'
@@ -20,13 +25,18 @@ jobs:
 
   linting:
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version:
+          - "3.12"
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v4
 
-      - name: Install Python
-        uses: actions/setup-python@v2
+      - name: Setup conda
+        uses: ./.github/actions/conda-cache
         with:
-          python-version: "3.12"
+          python-version: ${{ matrix.python-version }}
+          environment-file: environment.yml
 
       - name: Install dependencies
         run: |
@@ -49,26 +59,6 @@ jobs:
             You can trigger all lints locally by running `make lint`
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
-  sphinx-docs:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-
-      - name: Install Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: "3.12"
-
-      - name: Install dependencies
-        run: |
-            pip install -e ".[docs]"
-            pip freeze
-
-      - name: Build documentation
-        run: |
-          cd docs
-          make html
-
   testing:
     runs-on: ubuntu-latest
     strategy:
@@ -77,34 +67,21 @@ jobs:
           - "3.12"
     needs: linting
     steps:
-      - name: Install Python via conda
-        uses: s-weigand/setup-conda@v1
-        with:
-          python-version: ${{ matrix.python-version }}
-          conda-channels: defaults,bioconda,conda-forge
       - name: Checkout repository
         uses: actions/checkout@v4
         with:
           lfs: true
           fetch-depth: 2
-      - name: Install mamba
-        run: conda install -y mamba>=1.0.0
-      - name: Prepare environment.yml file
-        run: >
-          cp environment.yml /tmp/environment.yml && sed -i -e
-          's/- python=.*/- python=${{ matrix.python-version }}/'
-          /tmp/environment.yml
-      - name: Update environment using mamba
-        run: mamba env update --name root --file /tmp/environment.yml
-      - name: Fail early on htslib etc. problems
-        run: |
-          set -euo pipefail
-          bgzip -c /dev/null >/dev/null
-          samtools version
-          bcftools version
+
+      - name: Setup conda
+        uses: ./.github/actions/conda-cache
+        with:
+          python-version: ${{ matrix.python-version }}
+          environment-file: environment.yml
+
+      - run: which pip
       - name: Install some more dependencies via pip
-        # Workaround - see https://github.com/pytest-dev/pytest/issues/10420#issuecomment-1290697849
-        run: pip install ".[test]"; pip install --ignore-installed py
+        run: pip install '.[test]'  # 'pyproject.toml[test]'
       - name: Run tests
         run: pytest
         env:

.gitignore

@@ -87,3 +87,4 @@ docs/step/DEFAULT_CONFIG_*.rst
 
 # Test directory
 work/
+.tests/

.pre-commit-config.yaml

@@ -1,12 +1,12 @@
 repos:
   - repo: https://github.com/charliermarsh/ruff-pre-commit
     # Ruff version.
-    rev: v0.4.8
+    rev: v0.9.1
     hooks:
       - id: ruff
         args: [ --fix ]
       - id: ruff-format
   - repo: https://github.com/snakemake/snakefmt
-    rev: v0.8.5 # https://github.com/snakemake/snakefmt/releases
+    rev: v0.10.2 # https://github.com/snakemake/snakefmt/releases
     hooks:
       - id: snakefmt

.readthedocs.yaml

@@ -0,0 +1,23 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+   os: ubuntu-22.04
+   tools:
+     python: "3.12"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/conf.py
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs