Fix CI

.github/workflows/apptainer.yml

@@ -5,6 +5,7 @@ on:
     branches:
       - main
       - dev
+  workflow_dispatch:
   pull_request:
     branches-ignore: []
   schedule:
@@ -21,35 +22,69 @@ jobs:
 
     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
         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
+    # Checkout repository
+    - name: Checkout repo
       uses: actions/checkout@v4
 
-    - name: Set up Python 3.X
+    # 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 "snakemake>=8" .[testing]
 
-    - name: install package itself
+    # Install package
+    - name: Install package itself
       run: |
         pip install .
 
-    - name: testing
+    # Run tests using Apptainer
+    - name: Run Apptainer tests
       run: |
-        sequana_chipseq --design-file test/data/design.csv --input-directory test/data/ --apptainer-prefix ~/images --genome-directory test/data/ecoli_MG1655 && cd chipseq && bash chipseq.sh
+        sequana_chipseq --design-file test/data/design.csv --input-directory test/data/ --use-apptainer --apptainer-prefix ~/.apptainer/cache --genome-directory test/data/ecoli_MG1655 && cd chipseq && bash chipseq.sh

.github/workflows/main.yml

@@ -9,57 +9,55 @@ on:
   pull_request:
     branches-ignore: []
   schedule:
-    - cron: '0 0 21 * *'
+    - cron: '0 0 2 * *'
 
 jobs:
   build-linux:
     runs-on: ubuntu-latest
     strategy:
       max-parallel: 5
       matrix:
-        python: ['3.10', '3.11', '3.12']
+        python: ['3.11', '3.12']
       fail-fast: false
 
-
     steps:
 
     - name: install graphviz
       run: |
+        sudo apt-get update -qq
         sudo apt-get install -y graphviz
-        sudo apt-get install libopenblas-dev # for scipy
 
     - name: checkout git repo
       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: |
+          generate-run-shell: true
+          create-args: >-
             python=${{ matrix.python }}
           cache-environment: true
           cache-downloads: 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.chipseq
 
     - name: coveralls
       continue-on-error: true
-      shell: bash -l {0}
+      shell: micromamba-shell {0}
       run: |
         echo $COVERALLS_REPO_TOKEN
         coveralls --service=github

README.rst

@@ -1,16 +1,16 @@
 
 .. image:: https://badge.fury.io/py/sequana-chipseq.svg
-     :target: https://pypi.python.org/pypi/sequana_chipseq
+     :target: https://pypi.python.org/pypi/sequana-chipseq
 
 .. image:: https://github.com/sequana/chipseq/actions/workflows/main.yml/badge.svg
-   :target: https://github.com/sequana/chipseq/actions/workflows/main.yml
+   :target: https://github.com/sequana/chipseq/actions/workflows
 
 .. image:: https://img.shields.io/badge/python-3.10%20%7C%203.11%20%7C%203.12-blue.svg
-    :target: https://pypi.python.org/pypi/sequana
+    :target: https://pypi.python.org/pypi/sequana-chipseq
     :alt: Python 3.10 | 3.11 | 3.12
 
-.. image:: http://joss.theoj.org/papers/10.21105/joss.00352/status.svg
-    :target: http://joss.theoj.org/papers/10.21105/joss.00352
+.. image:: https://joss.theoj.org/papers/10.21105/joss.00352/status.svg
+    :target: https://joss.theoj.org/papers/10.21105/joss.00352
     :alt: JOSS (journal of open source software) DOI
 
 This is the **chipseq** pipeline from the `Sequana <https://sequana.readthedocs.org>`_ project.
@@ -75,7 +75,7 @@ Example::
 **4. Run the pipeline**::
 
     cd chipseq
-    sh chipseq.sh
+    bash chipseq.sh
 
 
 Usage
@@ -126,16 +126,12 @@ Run every tool inside pre-built containers — no local tool installation needed
         --input-directory DATAPATH \
         --genome-directory /path/to/genome \
         --design-file design.csv \
-        --use-apptainer
-
-Store images in a shared location to avoid re-downloading::
-
-    sequana_chipseq ... --use-apptainer --apptainer-prefix ~/.sequana/apptainers
+        --apptainer-prefix ~/.sequana/apptainers
 
 Then run as usual::
 
     cd chipseq
-    sh chipseq.sh
+    bash chipseq.sh
 
 
 Requirements
@@ -206,6 +202,13 @@ Changelog
 ========= ====================================================================
 Version   Description
 ========= ====================================================================
+0.13.0    * Migrate to standard importlib.metadata version pattern
+          * Remove click_completion dependency
+          * Add snakemake, pulp dependencies to pyproject.toml
+          * Add dot2svg to localrules
+          * Fix CI: use generate-run-shell and micromamba-shell
+          * Update environment.yml: add graphviz, pulp, sequana_pipetools
+          * Fix README badges and apptainer usage
 0.12.0    * Fix ``macs3``, ``self_pseudo_replicate_peaks``, and
             ``pseudo_replicate_peaks`` rules: macs3 exits non-zero on sparse
             CI data; added ``|| true`` + conditional ``touch`` so the pipeline

environment.yml

@@ -1,11 +1,8 @@
 name: sequana_chipseq
-
 channels:
 - conda-forge
 - bioconda
 - defaults
-- r
-
 dependencies:
 - samtools>1.7
 - bamtools
@@ -20,8 +17,10 @@ dependencies:
 - homer
 - macs3
 - multiqc
+- graphviz
 - snakemake-minimal
+- pulp>=2.8
 - pip:
-  - sequana
-  - sequana-wrappers>=26.3.21
-
+  - sequana>=0.21.0
+  - sequana_pipetools>=1.5.3
+  - sequana-wrappers>=26.4.1

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "sequana-chipseq"
-version = "0.12.0"
+version = "0.13.0"
 description = "A ChIP-seq pipeline from raw reads to peaks"
 authors = ["Sequana Team"]
 license = "BSD-3"
@@ -36,9 +36,10 @@ packages = [
 python = ">=3.10,<4.0"
 sequana = ">=0.21.0"
 sequana_pipetools = ">=1.5.3"
-sequana_wrappers = ">=26.3.21"
-click-completion = "^0.5.2"
+sequana-wrappers = ">=26.4.1"
 idrix = ">=2.1.0"
+snakemake = ">=7.32"
+pulp = ">=2.8"
 
 
 [tool.poetry.scripts]

sequana_pipelines/chipseq/__init__.py

@@ -1,6 +1,3 @@
-from importlib.metadata import PackageNotFoundError, version
+import importlib.metadata
 
-try:
-    version = version("sequana-chipseq")
-except PackageNotFoundError:
-    version = "unknown"
+version = importlib.metadata.version("sequana-chipseq")