Fix CI (micromamba v2) and bump apptainer URLs

.github/workflows/main.yml

@@ -17,32 +17,34 @@ 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 +56,7 @@ 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

@@ -8,11 +8,13 @@ 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 3.7
+      uses: actions/setup-python@v5
       with:
         python-version: 3.8
 
@@ -26,14 +28,13 @@ jobs:
           poetry build
 
     - name: Publish distribution to Test PyPI
-      uses: pypa/gh-action-pypi-publish@release/v1
+      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@release/v1
       with:
-        user: __token__
         password: ${{ secrets.PYPI_API_TOKEN }}

README.rst

@@ -9,10 +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
-    :target: https://pypi.python.org/pypi/sequana
-    :alt: Python 3.8 | 3.9 | 3.10
-
+.. 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

test/test_main.py

@@ -34,7 +34,7 @@ def test_full_rRNA_file():
         cmd = f"sequana_ribofinder --input-directory {sharedir} "
         cmd += f"--working-directory {wk}  --force --rRNA-file {sharedir}/feature.fasta"
         subprocess.call(cmd.split())
-        stat = subprocess.call("sh ribofinder.sh".split(), cwd=wk)
+        stat = subprocess.call("bash ribofinder.sh".split(), cwd=wk)
         assert os.path.exists(wk + "/summary.html")
 
 def test_full_rRNA_extract():
@@ -43,15 +43,8 @@ def test_full_rRNA_extract():
         cmd = f"sequana_ribofinder --input-directory {sharedir} "
         cmd += f"--working-directory {wk}  --force --reference-file {sharedir}/Lepto.fa --gff-file {sharedir}/Lepto.gff"
         subprocess.call(cmd.split())
-        stat = subprocess.call("sh ribofinder.sh".split(), cwd=wk)
-
-
-        if os.path.exists(wk + "/summary.html"):
-            pass
-        else:
-            with open(f"{wk}/indexing/bowtie_rRNA.log", "r") as fout: 
-                print(fout.read())
-            raise IOError
+        stat = subprocess.call("bash ribofinder.sh".split(), cwd=wk)
+        assert os.path.exists(wk + "/summary.html")
 
 def test_version():
     cmd = "sequana_ribofinder --version"