Migrate quality_control pipeline to modern sequana standards

.github/workflows/apptainer.yml

@@ -0,0 +1,90 @@
+name: Apptainer Run
+
+on:
+  push:
+    branches:
+      - main
+      - dev
+  workflow_dispatch:
+  pull_request:
+    branches-ignore: []
+  schedule:
+    - cron: '0 0 1 * *'
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 5
+      matrix:
+        python: ['3.11']
+      fail-fast: false
+
+    steps:
+
+    # Clean up unnecessary preinstalled packages to free disk space
+    - name: Pre-cleanup
+      run: |
+        sudo rm -rf /usr/share/dotnet
+        sudo rm -rf "$AGENT_TOOLSDIRECTORY"
+
+    # Cache APT .deb packages
+    - name: Cache APT archives
+      uses: actions/cache@v3
+      with:
+        path: /var/cache/apt/archives
+        key: ${{ runner.os }}-apt-cache-v1
+
+    # Cache Apptainer installation
+    - name: Cache Apptainer install
+      id: cache-apptainer
+      uses: actions/cache@v3
+      with:
+        path: |
+          /usr/bin/apptainer
+          /usr/lib/apptainer
+          /etc/apptainer
+        key: ${{ runner.os }}-apptainer-v1
+
+    # Install Apptainer only if not cached
+    - name: Install Apptainer
+      if: steps.cache-apptainer.outputs.cache-hit != 'true'
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y software-properties-common
+        sudo add-apt-repository -y ppa:apptainer/ppa
+        sudo apt-get update
+        sudo apt-get install -y apptainer
+
+    # Cache Apptainer image cache (~/.apptainer/cache)
+    - name: Cache Apptainer images
+      uses: actions/cache@v3
+      with:
+        path: ~/.apptainer/cache
+        key: ${{ runner.os }}-apptainer-images-v1
+
+    # Checkout repository
+    - name: Checkout repo
+      uses: actions/checkout@v4
+
+    # Set up Python
+    - name: Set up Python ${{ matrix.python }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python }}
+
+    # Install dependencies
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install .[testing]
+
+    # Install package
+    - name: Install package itself
+      run: |
+        pip install .
+
+    # Run tests using Apptainer
+    - name: Run Apptainer tests
+      run: |
+        sequana_quality_control --input-directory test/data/ --apptainer-prefix ~/.apptainer/cache && cd quality_control && bash quality_control.sh

.github/workflows/main.yml

@@ -17,46 +17,48 @@ jobs:
     strategy:
       max-parallel: 5
       matrix:
-        python: [3.8,3.9,'3.10']
+        python: ['3.11','3.12']
       fail-fast: false
 
 
     steps:
 
     - name: install graphviz
       run: |
+        sudo apt-get update -qq
         sudo apt-get install -y graphviz
 
     - name: checkout git repo
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
 
     - name: conda/mamba
-      uses: mamba-org/setup-micromamba@v1
+      uses: mamba-org/setup-micromamba@v2
       with:
-          micromamba-version: '1.3.1-0'
           environment-file: environment.yml
-          create-args: |
+          create-args: >-
             python=${{ matrix.python }}
           cache-environment: true
           cache-downloads: true
+          generate-run-shell: true
 
     - name: install package itself
-      shell: bash -el {0}
+      shell: micromamba-shell {0}
       run: |
         pip install .
 
     - name: Install dependencies
-      shell: bash -el {0}
+      shell: micromamba-shell {0}
       run: |
         pip install coveralls pytest-cov pytest pytest-xdist
 
     - name: testing
-      shell: bash -el {0}
+      shell: micromamba-shell {0}
       run: |
         pytest -v --cov-report term-missing --cov=sequana_pipelines.quality_control
 
     - name: coveralls
-      shell: bash -l {0}
+      continue-on-error: true
+      shell: micromamba-shell {0}
       run: |
         echo $COVERALLS_REPO_TOKEN
         coveralls --service=github

.github/workflows/pypi.yml

@@ -1,5 +1,5 @@
 name: Publish to PyPI
-on: 
+on:
   workflow_dispatch:
   push:
     tags:
@@ -8,32 +8,33 @@ on:
 jobs:
   build-n-publish:
     name: Build and publish to PyPI and TestPyPI
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
     steps:
-    - uses: actions/checkout@main
-    - name: Set up Python 3.8
-      uses: actions/setup-python@v2
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.8
+        python-version: '3.11'
 
-    - name: Install package 
+    - name: Install package
       run: |
           pip install build poetry
 
     - name: Build source tarball
       run: |
           rm -rf dist;
           poetry build
- 
+
     - name: Publish distribution to Test PyPI
+      if: startsWith(github.ref, 'refs/tags')
       uses: pypa/gh-action-pypi-publish@release/v1
       with:
-        user: __token__
         password: ${{ secrets.TEST_PYPI_API_TOKEN }}
-        repository_url: https://test.pypi.org/legacy/
+        repository-url: https://test.pypi.org/legacy/
     - name: Publish distribution to PyPI
       if: startsWith(github.ref, 'refs/tags')
       uses: pypa/gh-action-pypi-publish@release/v1
       with:
-        user: __token__
         password: ${{ secrets.PYPI_API_TOKEN }}

README.rst

@@ -9,8 +9,12 @@
 .. image:: https://github.com/sequana/quality_control/actions/workflows/main.yml/badge.svg
    :target: https://github.com/sequana/quality_control/actions/workflows
 
+.. image:: https://img.shields.io/badge/python-3.11%20%7C%203.12-blue.svg
+    :target: https://pypi.python.org/pypi/sequana_quality_control
+    :alt: Python 3.11 | 3.12
 
-This pipeline is not maintained anymore but should be functional. It is a short-read quality control pipeline
+
+**This pipeline is not maintained anymore but should be functional**. It is a short-read quality control pipeline
 from the `Sequana <https://sequana.readthedocs.org>`_ project. We would recommend to use the fastqc, demultiplex,
 and multitax pipelines instead.
 
@@ -89,8 +93,8 @@ ChangeLog
 ========= ====================================================================
 Version   Description
 ========= ====================================================================
-0.11.0    * switch to click, pyproject. remove kraken (see multitax pipeline
-            instead)
+1.0.0    * switch to click, pyproject. remove kraken (see multitax pipeline
+            instead). Uses new convention. 
 0.10.0    * add missing MANIFEST
 0.9.0     * remove design_file for cutadapt to reflect changes in
             sequana 0.12.0

environment.yml

@@ -1,19 +1,17 @@
-name: mapper
-
+name: quality_control
 channels:
-  - conda-forge
-  - bioconda
-  - defaults
-
+- conda-forge
+- bioconda
+- defaults
 dependencies:
-  - bwa
-  - samtools
-  - pigz
-  - fastqc
-  - sambamba
-  - pip:
-    - sequana
-    - cutadapt
-    - atropos
-
-
+- bwa
+- samtools
+- pigz
+- fastqc
+- sambamba
+- graphviz
+- pulp>=2.8
+- pip:
+  - sequana
+  - cutadapt
+  - atropos