fix CI/CD workflows for modern GitHub Actions

- Update actions/checkout to v4
- Update conda-incubator/setup-miniconda to v3
- Update Python versions to 3.9, 3.10, 3.11, 3.12
- Remove deprecated libgcc and libstdcxx-ng packages
- Fix shell configuration for proper conda activation
- Use python -m build instead of setup.py

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Author: SvenSerneels

.github/workflows/python-package.yml

@@ -10,43 +10,43 @@ jobs:
   build:
     runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
-        python-version: [3.8, "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+
+    defaults:
+      run:
+        shell: bash -el {0}
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       with:
         auto-update-conda: true
         python-version: ${{ matrix.python-version }}
         activate-environment: testenv
-        environment-file: ""
         auto-activate-base: false
 
     - name: Install dependencies
-      shell: bash -l {0}
       run: |
-        conda install -y -c conda-forge \
-          libstdcxx-ng libgcc=5.2.0 scikit-learn pandas numpy statsmodels dcor sympy matplotlib cyipopt flake8 pytest
-        # Optionally, install extra pip dependencies here, e.g.:
-        # pip install -r requirements.txt
+        conda install -y -c conda-forge scikit-learn pandas numpy statsmodels dcor sympy matplotlib cyipopt flake8 pytest
 
     - name: Conda info
-      shell: bash -l {0}
       run: conda info
 
     - name: Conda list
-      shell: bash -l {0}
       run: conda list
 
+    - name: Install package
+      run: |
+        pip install -e .
+
     - name: Lint with flake8
-      shell: bash -l {0}
       run: |
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         flake8 . --count --exit-zero --max-complexity=15 --max-line-length=127 --statistics
 
     - name: Test with pytest
-      shell: bash -l {0}
       run: pytest

.github/workflows/python-publish.yml

@@ -1,4 +1,4 @@
-# This workflows will upload a Python Package using Twine when a release is created
+# This workflow will upload a Python Package using Twine when a release is created
 # For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
 
 name: Upload Python Package
@@ -24,53 +24,41 @@ on:
         description: "The version portion to increment"
         required: true
         type: string
-  push:
-    branches:
-      - master
-    paths-ignore:
-      - '.github/**'
-      - 'README.md'
-      - '.gitignore'
-      - 'CHANGELOG.md'
-  pull_request:
-    branches:
-      - master
 
 jobs:
   deploy:
     runs-on: ubuntu-latest
 
+    defaults:
+      run:
+        shell: bash -el {0}
+
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Set up Python
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       with:
         auto-update-conda: true
-        python-version: 3.9
+        python-version: "3.11"
         activate-environment: pubenv
-        environment-file: ""
         auto-activate-base: false
 
     - name: Install dependencies
-      shell: bash -l {0}
       run: |
-        conda install -y -c conda-forge \
-          libstdcxx-ng libgcc=5.2.0 scikit-learn pandas numpy statsmodels dcor sympy matplotlib cyipopt setuptools wheel twine
+        conda install -y -c conda-forge scikit-learn pandas numpy statsmodels dcor sympy matplotlib cyipopt
 
     - name: Conda info
-      shell: bash -l {0}
       run: conda info
 
     - name: Conda list
-      shell: bash -l {0}
       run: conda list
 
     - name: Build and publish
-      shell: bash -l {0}
       env:
         TWINE_USERNAME: ${{ secrets.PYPIUID }}
         TWINE_PASSWORD: ${{ secrets.PYPIPWD }}
       run: |
-        python setup.py sdist bdist_wheel
+        pip install build twine
+        python -m build
         twine upload dist/*