Feature/project structure

.github/workflows/python-package.yml

@@ -1,40 +1,83 @@
-# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
-# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
-
-name: Python package
+name: Python Cluster Compare (pyCC)
 
 on:
   push:
-    branches: [ "master" ]
+    branches:
+      # - "*" # matches every branch that doesn't contain a '/'
+      # - "*/*" # matches every branch containing a single '/'
+      - "**" # matches every branch
+      # - "!main" # excludes master
   pull_request:
-    branches: [ "master" ]
+    branches: ["main"]
+
+concurrency:
+  group: ${{ github.ref }}
+  cancel-in-progress: ${{ github.ref != 'refs/heads/master' }}
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
 
     steps:
-    - 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 pip install flake8 pytest
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # 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
-    - name: Test with pytest
-      run: |
-        pytest
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Display Python version
+        run: python -c "import sys; print(sys.version)"
+        shell: bash
+
+      # - name: Install dependencies
+      #   run: |
+      #     python -m pip install --upgrade pip
+      #     # pip install .[dev]
+      #     pip install poetry
+      #     poetry install
+      #   shell: bash
+
+      # - name: Lint with ruff
+      #   run: |
+      #     poetry run ruff check .
+      #   shell: bash
+
+      #   # continue-on-error: true
+
+      # - name: Lint with mypy
+      #   run: |
+      #     poetry run mypy .
+      #   shell: bash
+
+      #   # continue-on-error: true
+
+      # - name: Build documentation
+      #   run: |
+      #     poetry run sphinx-build -b html docs/source docs/_build/html
+      #   shell: bash
+
+      # - name: Deploy to GitHub Pages
+      #   uses: peaceiris/actions-gh-pages@v3
+      #   if: github.ref == 'refs/heads/main'
+      #   with:
+      #     github_token: ${{ secrets.GITHUB_TOKEN }}
+      #     publish_dir: ./docs/_build/html
+
+      # - name: Test with pytest
+      #   run: |
+      #     python -m pip install pytest
+      #     python -m pip install pytest-cov
+      #     poetry run pytest -v -x
+      #   shell: bash
+
+      # - name: Test Coverage
+      #   run: |
+      #     python -m pip install coverage
+      #     poetry run coverage report
+      #     poetry run coverage html
+      #   shell: bash

.gitignore

@@ -3,12 +3,12 @@
 *.out
 *.tgz
 
-
 # xyz
-#*.xyz 
+#*.xyz
 
 # - IDE files/dir
-*.vscode/
+.vscode/*
+*.vscode/*
 
 # bash script to transfor output files to XYZ
 *geometry*.sh
@@ -18,8 +18,6 @@
 *org_files/
 
 # local files/directories
-.vscode/
-*.vscode/
 
 # Byte-compiled / optimized / DLL files
 __pycache__/