new version: complete changes to the APIs and implementations.

Author: HFooladi

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -7,7 +7,7 @@ body:
     attributes:
       value: |
         Thanks for taking the time to fill out this bug report!
-        
+
   - type: textarea
     id: what-happened
     attributes:
@@ -16,7 +16,7 @@ body:
       placeholder: Tell us what you see!
     validations:
       required: true
-      
+
   - type: textarea
     id: reproduction
     attributes:
@@ -28,32 +28,31 @@ body:
         3. See error
     validations:
       required: true
-      
+
   - type: textarea
     id: logs
     attributes:
       label: Relevant log output
       description: Please copy and paste any relevant log output. This will be automatically formatted into code.
       render: shell
-      
+
   - type: input
     id: version
     attributes:
       label: Version
       description: What version of THEMAP are you running?
     validations:
       required: true
-      
+
   - type: dropdown
     id: python-version
     attributes:
       label: Python Version
       description: What version of Python are you using?
       options:
-        - Python 3.8
-        - Python 3.9
         - Python 3.10
+        - Python 3.11
+        - Python 3.12
         - Other (specify in description)
     validations:
       required: true
-      

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -7,7 +7,7 @@ body:
     attributes:
       value: |
         Thanks for taking the time to suggest a new feature!
-        
+
   - type: textarea
     id: problem
     attributes:
@@ -16,23 +16,23 @@ body:
       placeholder: I'm always frustrated when [...]
     validations:
       required: true
-      
+
   - type: textarea
     id: solution
     attributes:
       label: Describe the solution you'd like
       description: A clear and concise description of what you want to happen.
     validations:
       required: true
-      
+
   - type: textarea
     id: alternatives
     attributes:
       label: Describe alternatives you've considered
       description: A clear and concise description of any alternative solutions or features you've considered.
-      
+
   - type: textarea
     id: context
     attributes:
       label: Additional context
-      description: Add any other context about the feature request here.
+      description: Add any other context about the feature request here.

.github/dependabot.yml

@@ -16,4 +16,4 @@ updates:
     open-pull-requests-limit: 10
     labels:
       - "dependencies"
-      - "github_actions" 
+      - "github_actions"

.github/workflows/lint.yml

@@ -10,31 +10,32 @@ on:
 jobs:
   lint:
     runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+
     steps:
     - uses: actions/checkout@v3
-    - name: Set up Python
+    - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v4
       with:
-        python-version: "3.10"
+        python-version: ${{ matrix.python-version }}
         cache: 'pip'
 
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install ruff black isort mypy
+        pip install ruff mypy
 
     - name: Lint with ruff
       run: |
         ruff check .
 
-    - name: Check formatting with black
-      run: |
-        black --check .
-
-    - name: Check imports with isort
+    - name: Check formatting with ruff
       run: |
-        isort --check .
+        ruff format --check .
 
     - name: Type check with mypy
       run: |
-        mypy themap 
+        mypy themap

.github/workflows/publish.yml

@@ -8,27 +8,30 @@ on:
 jobs:
   deploy:
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
     steps:
     - uses: actions/checkout@v3
       with:
         fetch-depth: 0
-    
-    - name: Set up Python
+
+    - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v4
       with:
-        python-version: '3.10'
-    
+        python-version: ${{ matrix.python-version }}
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install build twine
-    
+
     - name: Build and package
       run: |
         python -m build
-    
+
     - name: Publish to PyPI
       if: github.event_name == 'release' && startsWith(github.ref, 'refs/tags')
       uses: pypa/gh-action-pypi-publish@release/v1
       with:
-        password: ${{ secrets.PYPI_API_TOKEN }} 
+        password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/test.yml

@@ -13,7 +13,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10"]
+        python-version: ["3.10", "3.11", "3.12"]
 
     steps:
     - uses: actions/checkout@v3
@@ -71,4 +71,30 @@ jobs:
 
     - name: Build documentation
       run: |
-        mkdocs build --strict 
+        mkdocs build --strict
+
+  publish:
+    runs-on: ubuntu-latest
+    needs: [test, docs]
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.10"
+        cache: 'pip'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Build package
+      run: |
+        python -m build
+    - name: Publish to Test PyPI
+      if: github.event_name == 'workflow_dispatch'
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        repository-url: https://test.pypi.org/legacy/
+        password: ${{ secrets.TEST_PYPI_API_TOKEN }}

.gitignore

@@ -166,7 +166,7 @@ cython_debug/
 datasets/fsmol_hardness/
 
 # ignore assets folder
-assets/
+# assets/
 
 # ignore dev notebook
-notebooks/dev.ipynb
+notebooks/dev.ipynb

.gitmodules

@@ -1,6 +0,0 @@
-[submodule "third_party/FS-Mol"]
-	path = third_party/FS-Mol
-	url = git@github.com:HFooladi/FS-Mol.git
-[submodule "third_party/otdd"]
-	path = third_party/otdd
-	url = git@github.com:HFooladi/otdd.git

.pre-commit-config.yaml

@@ -1,7 +1,42 @@
 repos:
--   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.9  # This should match your pyproject.toml version
+  # Ruff - replaces flake8, isort, black, and more
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.12.4  # Use latest stable version
     hooks:
-    -   id: ruff
-        args: [--fix]
-    -   id: ruff-format
+      - id: ruff
+        args: [--fix]  # Automatically fix what can be fixed
+      - id: ruff-format
+
+  # Type checking
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.17.0
+    hooks:
+      - id: mypy
+        additional_dependencies: [types-requests]
+        args: [--ignore-missing-imports]
+        exclude: ^(scripts/|third_party/|themap/models/otdd/)
+
+  # Basic file checks
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-toml
+      - id: check-merge-conflict
+      - id: check-case-conflict
+      - id: check-added-large-files
+        args: ['--maxkb=1000']  # Prevent large files
+
+  # Optional: Run tests (can be slow, consider making it optional)
+  # Uncomment if you want tests to run on every commit
+  # - repo: local
+  #   hooks:
+  #     - id: pytest
+  #       name: pytest
+  #       entry: pytest
+  #       language: system
+  #       types: [python]
+  #       args: [tests/, --maxfail=1, -x]  # Stop on first failure
+  #       pass_filenames: false