Update to use new layout

.github/workflows/apptainer.yml

@@ -5,57 +5,91 @@ on:
     branches:
       - main
       - dev
+  workflow_dispatch:
   pull_request:
     branches-ignore: []
   schedule:
-    - cron: '0 0 * * SUN'
+    - cron: '0 0 1 * *'
 
 jobs:
   build-linux:
     runs-on: ubuntu-latest
     strategy:
       max-parallel: 5
       matrix:
-        python: [3.8, '3.10']
+        python: ['3.11']
       fail-fast: false
 
-
     steps:
 
-    - name: precleanup
+    # Clean up unnecessary preinstalled packages to free disk space
+    - name: Pre-cleanup
       run: |
         sudo rm -rf /usr/share/dotnet
         sudo rm -rf "$AGENT_TOOLSDIRECTORY"
-    - name: install graphviz
+
+    # 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 update
-        sudo apt-get install -y graphviz software-properties-common
+        sudo apt-get update
+        sudo apt-get install -y software-properties-common graphviz
         sudo add-apt-repository -y ppa:apptainer/ppa
-        sudo apt update
-        sudo apt install -y apptainer
+        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
 
-    - name: checkout git repo
-      uses: actions/checkout@v3
+    # Checkout repository
+    - name: Checkout repo
+      uses: actions/checkout@v4
 
-    - name: Set up Python 3.X
-      uses: actions/setup-python@v3
+    # 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: |
-        pip install .[testing]
+        python -m pip install --upgrade pip
+        pip install .
 
-    - name: install package itself
+    # Install pinned pulp
+    - name: Install pinned pulp
       run: |
-         pip install .
+        pip install "pulp>=2.8" --no-deps
 
-    - name: testing
+    # Run tests using Apptainer
+    - name: Run Apptainer tests
       run: |
+        sequana_ribofinder --input-directory test/data \
+          --reference-file test/data/Lepto.fa \
+          --gff-file test/data/Lepto.gff \
+          --use-apptainer --apptainer-prefix ~/.apptainer/cache
 
-        sequana_ribofinder --input-directory test/data --reference-file test/data/Lepto.fa --gff-file test/data/Lepto.gff --use-apptainer && cd ribofinder && sh ribofinder.sh
-
-
-
-
-
+        cd ribofinder && bash ribofinder.sh

.github/workflows/main.yml

@@ -17,32 +17,33 @@ 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/provision-with-micromamba@main
+      uses: mamba-org/setup-micromamba@v2
       with:
           environment-file: environment.yml
-          extra-specs: |
+          create-args: >-
             python=${{ matrix.python }}
+          cache-environment: true
+          cache-downloads: true
 
     - name: install package itself
       shell: bash -l {0}
       run: |
         pip install .
 
-
     - name: Install dependencies
       shell: bash -l {0}
       run: |
@@ -54,6 +55,7 @@ jobs:
         pytest -v --cov-report term-missing --cov=sequana_pipelines.ribofinder
 
     - name: coveralls
+      continue-on-error: true
       shell: bash -l {0}
       run: |
         echo $COVERALLS_REPO_TOKEN

.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

@@ -9,9 +9,9 @@
 .. image:: https://github.com/sequana/ribofinder/actions/workflows/main.yml/badge.svg
    :target: https://github.com/sequana/ribofinder/actions/workflows/main.yml
 
-.. image:: https://img.shields.io/badge/python-3.8%20%7C%203.9%20%7C3.10-blue.svg
+.. image:: https://img.shields.io/badge/python-3.9%20%7C%203.10%20%7C%203.11%20%7C%203.12-blue.svg
     :target: https://pypi.python.org/pypi/sequana
-    :alt: Python 3.8 | 3.9 | 3.10
+    :alt: Python 3.9 | 3.10 | 3.11 | 3.12
 
 
 
@@ -67,12 +67,16 @@ Requirements
 
 This pipelines requires the following executable(s):
 
-- bowtie1 >= 1.3.0
+- bowtie2 >= 2.4.0
+- bwa
+- sambamba
 - bedtools
 - samtools
-- bamtools
 - pigz
 
+The aligner is selectable at the command line with ``--aligner bowtie2`` (default)
+or ``--aligner bwa``. You only need to install the one(s) you intend to use.
+
 .. image:: https://raw.githubusercontent.com/sequana/ribofinder/master/sequana_pipelines/ribofinder/dag.png
 
 Details
@@ -109,6 +113,23 @@ Changelog
 ========= ====================================================================
 Version   Description
 ========= ====================================================================
+1.2.0     * Replace bowtie1 with bowtie2 (default) and bwa as aligner options
+            for rRNA mapping; the aligner is now user-selectable via
+            ``--aligner bowtie2|bwa``.
+          * Drop the bowtie1-specific ``fix_bowtie1_log`` workaround and the
+            standalone ``bam_indexing`` / ``samtools_faidx`` rules; the new
+            sequana-wrappers already produce sorted+indexed BAMs and a
+            faidx'ed reference.
+          * For bwa, feed multiqc with ``samtools stats`` output (bwa has no
+            native multiqc module); the mapping-rate plot in the HTML report
+            is built from ``multiqc_samtools_stats.txt``.
+          * For bowtie2, the HTML summary uses ``sequana.multiqc.plots.Bowtie2``
+            which handles both single-end and paired-end outputs.
+          * Rewrite the HTML summary introduction to explain what the
+            pipeline does, how it works step-by-step, and how to interpret
+            each of the three plots (mapping rate, per-sequence proportions,
+            per-sequence RPKM).
+            (``bowtie2``, ``bwa``, ``sambamba`` replace ``bowtie``/``bamtools``).
 1.1.1     * hotfix for running on HPC (slurm)
 1.1.0     * Uses click (refactoring of sequana_pipetools)
 1.0.1     * add sequana_wrappers in the config/pipeline

environment.yml

@@ -7,8 +7,10 @@ channels:
 - r
 
 dependencies:
-- 'bowtie>=1.3.0'
+- 'bowtie2>=2.4.0'
+- bwa
+- sambamba
 - samtools>1.7
-- bamtools
 - bedtools
 - pigz
+- graphviz

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "sequana-ribofinder"
-version = "1.1.1"
+version = "1.2.0"
 description = "A multi-sample identification of ribosomal content"
 authors = ["Sequana Team"]
 license = "BSD-3"
@@ -19,9 +19,9 @@ classifiers = [
         "Intended Audience :: Science/Research",
         "License :: OSI Approved :: BSD License",
         "Operating System :: POSIX :: Linux",
-        "Programming Language :: Python :: 3.8",
-        "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
+        "Programming Language :: Python :: 3.11",
+        "Programming Language :: Python :: 3.12",
         "Topic :: Software Development :: Libraries :: Python Modules",
         "Topic :: Scientific/Engineering :: Bio-Informatics",
         "Topic :: Scientific/Engineering :: Information Analysis",
@@ -33,20 +33,29 @@ packages = [
 
 
 [tool.poetry.dependencies]
-python = ">=3.8,<4.0"
-sequana = ">=0.15.0"
-sequana_pipetools = ">=0.16.0"
+python = ">=3.9,<4.0"
+sequana = ">=0.18.0"
+sequana_pipetools = ">=1.5.4"
+sequana-wrappers = ">=26.3.19"
 click-completion = "^0.5.2"
-
+snakemake = ">=7.32"
+pulp = ">=2.8"
 
 [tool.poetry.scripts]
 sequana_ribofinder = "sequana_pipelines.ribofinder.main:main"
 
 
 [tool.poetry.group.dev.dependencies]
 black = "^23.7.0"
-pytest = "^7.4.0"
+pytest = "^8.0.0"
 mock = "^5.1.0"
 pytest-mock = "^3.11.1"
 pytest-cov = "^4.1.0"
 
+[tool.pytest.ini_options]
+filterwarnings = [
+    "ignore::pytest.PytestDeprecationWarning",
+    "ignore::DeprecationWarning:click_completion",
+    "ignore::DeprecationWarning:importlib",
+]
+asyncio_mode = "auto"