Update depricated Bio.Applications from Biopython

Main update is the substitution of Bio.Applications from Biopython for subprocess calls to blast and samtools.

Other updates include:

CI workflow now tests multiple pyhton versions.
pybedtools 0.12.0 test
relaxed Biopython version allowed

Author: milnus

.github/workflows/Compile_paper.yml

@@ -6,15 +6,15 @@ jobs:
     name: Paper Draft
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       - name: Build draft PDF
         uses: openjournals/openjournals-draft-action@master
         with:
           journal: joss
           # This should be the path to the paper within your repo.
           paper-path: paper/paper.md
       - name: Upload
-        uses: actions/upload-artifact@v1
+        uses: actions/upload-artifact@v4
         with:
           name: paper
           # This is the output path where Pandoc will write the compiled

.github/workflows/Mapghi_test_suite.yml

@@ -7,31 +7,18 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@main
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v1
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.13
+      uses: actions/setup-python@v6
       with:
-        python-version: 3.9
+        python-version: '3.13'
+        cache: 'pip'
     - name: Install pypa/build
-      run: >-
-        python -m
-        pip install
-        build
-        --user
-    - name: Build a binary wheel and a source tarball
-      run: >-
-        python -m
-        build
-        --sdist
-        --wheel
-        --outdir dist/
-#    - name: Publish distribution 📦 to Test PyPI
-#      uses: pypa/gh-action-pypi-publish@master
-#      with:
-#        password: ${{ secrets.TEST_PYPI_TOKEN_CICD }}
-#        repository_url: https://test.pypi.org/legacy/
+      run: python -m pip install build --user
+    - name: Publish distribution 📦 to Test PyPI
+      run: python -m build --sdist --wheel --outdir dist/
     - 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:
         password: ${{ secrets.PYPI_API_TOKEN_SECRET }}

.github/workflows/build_n_publish.yml

@@ -1,17 +1,54 @@
-name: 'Test'
+name: Test
+
 on:
   push:
+    branches: [main, dev]
   pull_request:
-    branches:
-      - main
+    branches: [main]
+
 jobs:
   test:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.9', '3.10', '3.11', '3.12']
+
     steps:
-      - uses: actions/checkout@v2
-      - name: 'Build Docker image'
-        run: docker build -t magphi .
-      - name: 'Run unit tests'
-        run: docker run --entrypoint /Magphi/.travis/unit-test.sh magphi
-      - name: 'Run functional tests'
-        run: docker run --entrypoint /Magphi/functional_tests/Magphi-test.sh magphi -p Magphi -d /Magphi/functional_tests/test_data -v
+      - uses: actions/checkout@v5
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+
+      - name: Install system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y bedtools samtools ncbi-blast+
+
+      - name: Install Python dependencies
+        run: |
+          pip install --upgrade pip
+          pip install setuptools
+          pip install .
+          pip install -r requirements-dev.txt
+
+      - name: Verify installation
+        run: |
+          which Magphi
+          Magphi --check
+          blastn -version
+          samtools --version | head -1
+          bedtools --version
+
+      - name: Run unit tests
+        working-directory: unit_tests
+        run: python Magphi_test.py
+
+      - name: Run pylint
+        run: pylint -E Magphi/*.py
+
+      - name: Run functional tests
+        run: bash functional_tests/Magphi-test.sh -p Magphi -d functional_tests/test_data -v

.github/workflows/test.yml

@@ -7,3 +7,6 @@ code_to_transfer/
 extractor.yml
 functional_tests/test_data/test_folder/
 venv/
+CLAUDE.md
+build/
+Magphi.egg-info/

.gitignore

@@ -1 +1 @@
-*.pyc
+*.pyc

.travis.yml

@@ -16,9 +16,9 @@
 import logging
 from sys import argv
 from math import ceil
-import pkg_resources
 import concurrent.futures
 from tempfile import TemporaryDirectory
+from importlib.metadata import version, PackageNotFoundError
 
 try:
     from Magphi.commandline_interface import get_commandline_arguments
@@ -79,8 +79,8 @@
 
 
 try:
-    PROGRAM_VERSION = pkg_resources.require(PROGRAM_NAME)[0].version
-except pkg_resources.DistributionNotFound:
+    PROGRAM_VERSION = version(PROGRAM_NAME)
+except PackageNotFoundError:
     PROGRAM_VERSION = "undefined_version"