Fix some automated testing quirks

1) Upgrade GitHub Action workflow.

2) Remove support for Python 3.7 since champ/seaborn no longer supports it.

3) Add a few apt requirements and pip hacks in GitHub Action. These are needed
to support GitHub's broken handling of Python 3.10 (and even still, leidenalg
is currently broken on Python >3.9, so 3.10 testing cannot even be enabled
until that is fixed upstream).

Author: ragibson

.github/workflows/python-package.yml

@@ -15,30 +15,41 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.8', '3.9']
+        python-version: ["3.8", "3.9"]  # leidenalg breaks Python>3.9 at the moment
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        python -m venv env
-        source env/bin/activate
-        pip install Cython flake8 numpy pybind11 pytest pythran
-        sudo apt install bison build-essential flex libigraph0-dev libigraph0v5 libxml2 libxml2-dev python3-dev python3-igraph zlib1g-dev
-        python setup.py install
-    - name: Lint with flake8
-      run: |
-        source env/bin/activate
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics --exclude env/
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics --exclude env/
-    - name: Test with pytest
-      run: |
-        source env/bin/activate
-        pytest tests/
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m venv env
+          source env/bin/activate
+
+          # various build requirements for Python 3.10 Github Action
+          sudo apt install autoconf automake bison build-essential cython flex gcc gfortran libfreetype-dev \
+          libfreetype6 libfreetype6-dev libigraph0-dev libigraph0v5 liblapack-dev libopenblas-dev libxml2 \
+          libxml2-dev pkg-config python-dev python3-dev python3-freetype python3-igraph zlib1g-dev
+
+          pip install cython flake8 pytest
+
+          # the following don't seem to be handled correctly in pip dependency
+          # checking for the Python 3.10 GitHub Action?
+          # we don't even use pandas, but champ forces it
+          pip install igraph leidenalg louvain matplotlib numpy pandas pybind11 pythran scipy
+
+          python setup.py install
+      - name: Lint with flake8
+        run: |
+          source env/bin/activate
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics --exclude env/
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics --exclude env/
+      - name: Test with pytest
+        run: |
+          source env/bin/activate
+          pytest tests/

setup.py

@@ -24,20 +24,14 @@
         'Development Status :: 5 - Production/Stable',
         'Topic :: Scientific/Engineering :: Information Analysis',
         'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.7',
         'Programming Language :: Python :: 3.8',
         'Programming Language :: Python :: 3.9',
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3 :: Only',
         'License :: OSI Approved :: MIT License'
     ],
-    python_requires='>=3.7, <4',
-    install_requires=['champ', 'louvain', 'matplotlib',
-                      "numpy<1.22.0; python_version<'3.8'",
-                      "numpy; python_version>='3.8'",
-                      'psutil', 'python-igraph',
-                      "scipy<1.8; python_version<'3.8'",
-                      "scipy; python_version>='3.8'",
-                      'seaborn', 'sklearn']
+    python_requires='>=3.8, <4',
+    install_requires=['champ', 'louvain', 'matplotlib', "numpy", 'psutil',
+                      'python-igraph', "scipy", 'seaborn', 'sklearn']
 
 )