Refactor CI pipeline and update to latest Apptainers

.github/workflows/apptainer.yml

@@ -0,0 +1,61 @@
+name: Apptainer Run
+
+on:
+  push:
+    branches:
+      - main
+      - dev
+  pull_request:
+    branches-ignore: []
+  schedule:
+    - cron: '0 0 * * SUN'
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 5
+      matrix:
+        python: [3.8, '3.10']
+      fail-fast: false
+
+
+    steps:
+
+    - name: precleanup
+      run: |
+        sudo rm -rf /usr/share/dotnet
+        sudo rm -rf "$AGENT_TOOLSDIRECTORY"
+    - name: install graphviz
+      run: |
+        sudo apt update
+        sudo apt-get install -y graphviz software-properties-common
+        sudo add-apt-repository -y ppa:apptainer/ppa
+        sudo apt update
+        sudo apt install -y apptainer
+
+    - name: checkout git repo
+      uses: actions/checkout@v3
+
+    - name: Set up Python 3.X
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python }}
+
+    - name: Install dependencies
+      run: |
+        pip install .[testing]
+
+    - name: install package itself
+      run: |
+         pip install .
+
+    - name: testing
+      run: |
+
+        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
+
+
+
+
+

.github/workflows/main.yml

@@ -3,57 +3,61 @@ name: Tests
 on:
   push:
     branches:
-      - master
+      - main
+      - dev
+  workflow_dispatch:
   pull_request:
     branches-ignore: []
+  schedule:
+    - cron: '0 0 2 * *'
 
 jobs:
   build-linux:
     runs-on: ubuntu-latest
     strategy:
       max-parallel: 5
       matrix:
-        python: [3.7,3.8,3.9]
+        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: Set up Python 3.X
-      uses: actions/setup-python@v2
+    - name: conda/mamba
+      uses: mamba-org/setup-micromamba@v2
       with:
-        python-version: ${{ matrix.python }}
-
-    - name: Add conda to system path
-      run: |
-        # $CONDA is an environment variable pointing to the root of the miniconda directory
-        echo $CONDA/bin >> $GITHUB_PATH
-        conda update ruamel_yaml
+          environment-file: environment.yml
+          create-args: >-
+            python=${{ matrix.python }}
+          cache-environment: true
+          cache-downloads: true
 
-    - name: conda
+    - name: install package itself
+      shell: bash -l {0}
       run: |
-        conda install -c conda-forge --quiet mamba  python=${{ matrix.python }}
-        mamba install -c bioconda -c conda-forge --quiet -y bowtie samtools bamtools pigz bedtools
+        pip install .
 
     - name: Install dependencies
+      shell: bash -l {0}
       run: |
         pip install coveralls pytest-cov pytest pytest-xdist
 
-    - name: install package itself
-      run: |
-         pip install .
-
     - name: testing
+      shell: bash -l {0}
       run: |
         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
         coveralls --service=github

.github/workflows/pypi.yml

@@ -8,32 +8,33 @@ on:
 jobs:
   build-n-publish:
     name: Build and publish to PyPI and TestPyPI
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
     steps:
-    - uses: actions/checkout@master
+    - uses: actions/checkout@v4
     - name: Set up Python 3.7
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.7
+        python-version: 3.8
 
-    - name: Install package
+    - name: Install package 
       run: |
-          pip install build
+          pip install build poetry
 
     - name: Build source tarball
       run: |
           rm -rf dist;
-          python setup.py sdist
-
+          poetry build
+ 
     - name: Publish distribution to Test PyPI
+      if: startsWith(github.ref, 'refs/tags')
       uses: pypa/gh-action-pypi-publish@master
       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@master
+      uses: pypa/gh-action-pypi-publish@release/v1
       with:
-        user: __token__
         password: ${{ secrets.PYPI_API_TOKEN }}

README.rst

@@ -9,6 +9,10 @@
 .. 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-3.11%20%7C%203.12-blue.svg
+    :target: https://pypi.python.org/pypi/sequana_ribofinder
+    :alt: Python 3.11 | 3.12
+
 
 This is is the **ribofinder** pipeline from the `Sequana <https://sequana.readthedocs.org>`_ project
 
@@ -62,8 +66,10 @@ Requirements
 
 This pipelines requires the following executable(s):
 
-- bowtie1
+- bowtie1 >= 1.3.0
+- bedtools
 - samtools
+- bamtools
 - pigz
 
 .. image:: https://raw.githubusercontent.com/sequana/ribofinder/master/sequana_pipelines/ribofinder/dag.png
@@ -102,6 +108,12 @@ Changelog
 ========= ====================================================================
 Version   Description
 ========= ====================================================================
+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
+1.0.0     * use graphviz apptainer and latest wrappers
+0.13.0    * add  final apptainers and update CI actions
+0.12.0    * set singularity containers
 0.11.1    * Fix config file (removing hard-coded path)
 0.11.0    * Fix multiqc plot using same fix as in sequna_rnaseq pipelines
           * add utility plot to check rate of  ribosomal per sequence and also

environment.yml

@@ -0,0 +1,14 @@
+name: sequana_ribofinder
+
+channels:
+- conda-forge
+- bioconda
+- defaults
+- r
+
+dependencies:
+- 'bowtie>=1.3.0'
+- samtools>1.7
+- bamtools
+- bedtools
+- pigz

pyproject.toml

@@ -0,0 +1,52 @@
+[build-system]
+requires = ["poetry-core>=1.0.0"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.poetry]
+name = "sequana-ribofinder"
+version = "1.1.1"
+description = "A multi-sample identification of ribosomal content"
+authors = ["Sequana Team"]
+license = "BSD-3"
+repository = "https://github.com/sequana/ribofinder"
+readme = "README.rst"
+keywords = ["snakemake", "ribosomal", "rRNA", "sequana"]
+classifiers = [
+        "Development Status :: 5 - Production/Stable",
+        "Intended Audience :: Education",
+        "Intended Audience :: End Users/Desktop",
+        "Intended Audience :: Developers",
+        "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",
+        "Topic :: Software Development :: Libraries :: Python Modules",
+        "Topic :: Scientific/Engineering :: Bio-Informatics",
+        "Topic :: Scientific/Engineering :: Information Analysis",
+]
+
+packages = [
+    {include = "sequana_pipelines"}
+]
+
+
+[tool.poetry.dependencies]
+python = ">=3.8,<4.0"
+sequana = ">=0.15.0"
+sequana_pipetools = ">=0.16.0"
+click-completion = "^0.5.2"
+
+
+[tool.poetry.scripts]
+sequana_ribofinder = "sequana_pipelines.ribofinder.main:main"
+
+
+[tool.poetry.group.dev.dependencies]
+black = "^23.7.0"
+pytest = "^7.4.0"
+mock = "^5.1.0"
+pytest-mock = "^3.11.1"
+pytest-cov = "^4.1.0"
+

sequana_pipelines/ribofinder/__init__.py

@@ -1,6 +1,11 @@
-import pkg_resources
-try:
-    version = pkg_resources.require("sequana_ribofinder")[0].version
-except:
-    version = ">=0.8.0"
+import importlib.metadata as metadata
+
+def get_package_version(package_name):
+    try:
+        version = metadata.version(package_name)
+        return version
+    except metadata.PackageNotFoundError:
+        return f"{package_name} not found"
+
+version = get_package_version("sequana-ribofinder")
 

sequana_pipelines/ribofinder/config.yaml

@@ -7,6 +7,8 @@
 # If input_directory provided, use it otherwise if input_pattern provided,
 # use it, otherwise use input_samples.
 # ============================================================================
+sequana_wrappers: "v23.11.18"
+
 input_directory:
 input_readtag: _R[12]_
 input_pattern: '*fastq.gz'
@@ -37,10 +39,16 @@ general:
     rRNA_file: ''
     rRNA_feature: rRNA
     genbank_file: ''
-    gff_file: 
-    reference_file: 
-
+    gff_file:
+    reference_file:
 
+apptainers:
+    sequana_ribofinder: "https://zenodo.org/record/7348115/files/sequana_ribofinder_0.12.0.img"
+    pigz: "https://zenodo.org/record/7346805/files/pigz_2.4.0.img"
+    bedtools: "https://zenodo.org/record/7346774/files/bedtools_2.30.0.img"
+    samtools: "https://zenodo.org/record/7215278/files/samtools_1.15.0.img"
+    graphviz:  "https://zenodo.org/record/7928262/files/graphviz_7.0.5.img"
+    multiqc: "https://zenodo.org/record/10205070/files/multiqc_1.16.0.img"
 
 #############################################################################
 # bowtie1_mapping_rna used to align reads against ribosomal RNA