hbat 2.2.0__tar.gz → 2.2.4__tar.gz

hbat-2.2.4/.github/workflows/cleanup-prereleases.yml

@@ -0,0 +1,77 @@
+name: Cleanup Pre-releases
+
+on:
+  schedule:
+    # Run daily at 2 AM UTC
+    - cron: '0 2 * * *'
+  workflow_dispatch:
+    inputs:
+      days_to_keep:
+        description: 'Number of days to keep pre-releases'
+        required: false
+        default: '7'
+        type: string
+
+jobs:
+  cleanup:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    
+    steps:
+    - uses: actions/checkout@v4
+    
+    - name: Clean up old pre-releases
+      uses: actions/github-script@v7
+      with:
+        script: |
+          const daysToKeep = parseInt('${{ github.event.inputs.days_to_keep || '7' }}');
+          const cutoffDate = new Date();
+          cutoffDate.setDate(cutoffDate.getDate() - daysToKeep);
+          
+          console.log(`Cleaning up pre-releases older than ${daysToKeep} days (before ${cutoffDate.toISOString()})`);
+          
+          // Get all releases
+          const releases = await github.rest.repos.listReleases({
+            owner: context.repo.owner,
+            repo: context.repo.repo,
+            per_page: 100
+          });
+          
+          let deletedCount = 0;
+          
+          for (const release of releases.data) {
+            // Only process pre-releases with PR tags
+            if (release.prerelease && release.tag_name.includes('-pr')) {
+              const releaseDate = new Date(release.created_at);
+              
+              if (releaseDate < cutoffDate) {
+                console.log(`Deleting pre-release: ${release.tag_name} (created: ${releaseDate.toISOString()})`);
+                
+                try {
+                  // Delete the release
+                  await github.rest.repos.deleteRelease({
+                    owner: context.repo.owner,
+                    repo: context.repo.repo,
+                    release_id: release.id
+                  });
+                  
+                  // Delete the tag
+                  await github.rest.git.deleteRef({
+                    owner: context.repo.owner,
+                    repo: context.repo.repo,
+                    ref: `tags/${release.tag_name}`
+                  });
+                  
+                  deletedCount++;
+                  console.log(`✓ Deleted: ${release.tag_name}`);
+                } catch (error) {
+                  console.error(`✗ Failed to delete ${release.tag_name}:`, error.message);
+                }
+              } else {
+                console.log(`Keeping: ${release.tag_name} (created: ${releaseDate.toISOString()})`);
+              }
+            }
+          }
+          
+          console.log(`Cleanup complete. Deleted ${deletedCount} pre-releases.`);

hbat-2.2.4/.github/workflows/pr-prerelease.yml

@@ -0,0 +1,324 @@
+name: PR Pre-release
+
+on:
+  pull_request:
+    types: [opened, synchronize, reopened]
+    branches: [ main ]
+
+jobs:
+  generate-prerelease-tag:
+    runs-on: ubuntu-latest
+    outputs:
+      prerelease_tag: ${{ steps.generate_tag.outputs.prerelease_tag }}
+      github_tag: ${{ steps.generate_tag.outputs.github_tag }}
+      version: ${{ steps.generate_tag.outputs.version }}
+      pr_number: ${{ github.event.number }}
+      pr_head_sha: ${{ github.event.pull_request.head.sha }}
+      pr_title: ${{ github.event.pull_request.title }}
+      pr_head_ref: ${{ github.event.pull_request.head.ref }}
+    
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+    
+    - name: Generate pre-release tag
+      id: generate_tag
+      run: |
+        # Get base version from latest tag or default to 0.0.0
+        BASE_VERSION=$(git describe --tags --abbrev=0 2>/dev/null | sed 's/^v//' || echo "0.0.0")
+        
+        # Generate PEP 440 compatible pre-release version
+        SHORT_SHA=$(git rev-parse --short HEAD)
+        PR_NUMBER=${{ github.event.number }}
+        
+        # Use PEP 440 compatible format: {base_version}.dev{pr_number}+{sha}
+        PRERELEASE_VERSION="${BASE_VERSION}.dev${PR_NUMBER}+${SHORT_SHA}"
+        PRERELEASE_TAG="v${PRERELEASE_VERSION}"
+        
+        # Also create a simple tag for GitHub release (without +sha which can cause issues)
+        GITHUB_TAG="v${BASE_VERSION}-pr${PR_NUMBER}.${SHORT_SHA}"
+        
+        echo "Base version: $BASE_VERSION"
+        echo "Pre-release version: $PRERELEASE_VERSION"
+        echo "Pre-release tag: $PRERELEASE_TAG"
+        echo "GitHub tag: $GITHUB_TAG"
+        
+        echo "prerelease_tag=$PRERELEASE_TAG" >> $GITHUB_OUTPUT
+        echo "version=$PRERELEASE_VERSION" >> $GITHUB_OUTPUT
+        echo "github_tag=$GITHUB_TAG" >> $GITHUB_OUTPUT
+
+  build-prerelease:
+    needs: generate-prerelease-tag
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      pull-requests: write
+    
+    steps:
+    - uses: actions/checkout@v4
+    
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.11'
+    
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements-dev.txt
+        pip install -e .
+    
+    - name: Set version for setuptools-scm
+      run: |
+        git config user.name "GitHub Actions"
+        git config user.email "actions@github.com"
+        # Create a temporary tag for building
+        git tag -a "${{ needs.generate-prerelease-tag.outputs.prerelease_tag }}" -m "Pre-release ${{ needs.generate-prerelease-tag.outputs.prerelease_tag }}"
+        echo "Created temporary tag: ${{ needs.generate-prerelease-tag.outputs.prerelease_tag }}"
+    
+    - name: Build package
+      run: make build
+    
+    - name: Upload build artifacts
+      uses: actions/upload-artifact@v4
+      with:
+        name: prerelease-build-artifacts-${{ needs.generate-prerelease-tag.outputs.pr_number }}
+        path: dist/*
+        retention-days: 30
+    
+    - name: Create pre-release
+      uses: softprops/action-gh-release@v2
+      with:
+        token: ${{ secrets.GITHUB_TOKEN }}
+        files: |
+            dist/hbat-${{ needs.generate-prerelease-tag.outputs.version }}-py3-none-any.whl
+            dist/hbat-${{ needs.generate-prerelease-tag.outputs.version }}.tar.gz
+        tag_name: ${{ needs.generate-prerelease-tag.outputs.github_tag }}
+        name: Pre-release ${{ needs.generate-prerelease-tag.outputs.github_tag }}
+        body: |
+          🚧 **Pre-release build for PR #${{ needs.generate-prerelease-tag.outputs.pr_number }}**
+          
+          **Branch:** `${{ needs.generate-prerelease-tag.outputs.pr_head_ref }}`
+          **Commit:** ${{ needs.generate-prerelease-tag.outputs.pr_head_sha }}
+          **Title:** ${{ needs.generate-prerelease-tag.outputs.pr_title }}
+          
+          This is an automated pre-release build. Use for testing purposes only.
+          
+          **Install with pip:**
+          ```bash
+          pip install https://github.com/${{ github.repository }}/releases/download/${{ needs.generate-prerelease-tag.outputs.github_tag }}/hbat-${{ needs.generate-prerelease-tag.outputs.version }}-py3-none-any.whl
+          ```
+        prerelease: true
+        draft: false
+    
+    - name: Comment on PR
+      uses: actions/github-script@v7
+      with:
+        script: |
+          const prNumber = ${{ needs.generate-prerelease-tag.outputs.pr_number }};
+          const tag = '${{ needs.generate-prerelease-tag.outputs.github_tag }}';
+          const version = '${{ needs.generate-prerelease-tag.outputs.version }}';
+          
+          const comment = `## 🚧 Pre-release Ready
+          
+          A pre-release has been created for this PR: **${tag}**
+          
+          ### Quick Install
+          \`\`\`bash
+          pip install https://github.com/${{ github.repository }}/releases/download/${tag}/hbat-${version}-py3-none-any.whl
+          \`\`\`
+          
+          ### Available Artifacts
+          - Python wheel: \`hbat-${version}-py3-none-any.whl\`
+          - Source distribution: \`hbat-${version}.tar.gz\`
+          - macOS DMG: \`hbat-${version}.dmg\`
+          - Conda package: \`hbat-${version}.tar.bz2\` or \`hbat-${version}.conda\`
+          
+          ### Install Options
+          **Pip:**
+          \`\`\`bash
+          pip install https://github.com/${{ github.repository }}/releases/download/${tag}/hbat-${version}-py3-none-any.whl
+          \`\`\`
+          
+          **Conda:** Download the conda package from the release and install locally
+          
+          View all artifacts at: https://github.com/${{ github.repository }}/releases/tag/${tag}
+          `;
+          
+          github.rest.issues.createComment({
+            issue_number: prNumber,
+            owner: context.repo.owner,
+            repo: context.repo.repo,
+            body: comment
+          });
+
+  build-macos-prerelease:
+    needs: generate-prerelease-tag
+    runs-on: macos-latest
+    
+    steps:
+    - uses: actions/checkout@v4
+    
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.11'
+    
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements-dev.txt
+        pip install -e .
+        # Install tkinter on macOS
+        brew install python-tk create-dmg
+    
+    - name: Set version for setuptools-scm
+      run: |
+        git config user.name "GitHub Actions"
+        git config user.email "actions@github.com"
+        git tag -a "${{ needs.generate-prerelease-tag.outputs.prerelease_tag }}" -m "Pre-release ${{ needs.generate-prerelease-tag.outputs.prerelease_tag }}"
+        echo "Created temporary tag: ${{ needs.generate-prerelease-tag.outputs.prerelease_tag }}"
+    
+    - name: Build standalone macOS app
+      run: make build-standalone
+
+    - name: Ad-hoc sign the app
+      run: |
+        echo "Signing app with ad-hoc signature..."
+        codesign --force --deep --sign - dist/HBAT-GUI.app
+        codesign --verify --verbose dist/HBAT-GUI.app
+
+    - name: Remove HBAT-GUI folder
+      run: |
+        echo "Contents of dist directory:"
+        ls -la dist/
+        cd dist && rm -rf HBAT-GUI
+    
+    - name: Create DMG installer
+      run: |
+        create-dmg \
+          --volname "HBAT Pre-release Installer" \
+          --window-pos 200 120 \
+          --window-size 800 400 \
+          --icon-size 100 \
+          --icon "HBAT-GUI.app" 200 190 \
+          --hide-extension "HBAT-GUI.app" \
+          --app-drop-link 600 185 \
+          "hbat-${{ needs.generate-prerelease-tag.outputs.version }}.dmg" \
+          "dist/"
+        mv hbat-${{ needs.generate-prerelease-tag.outputs.version }}.dmg dist/
+    
+    - name: Upload macOS app artifact
+      uses: actions/upload-artifact@v4
+      with:
+        name: prerelease-macos-app-${{ needs.generate-prerelease-tag.outputs.pr_number }}
+        path: dist/hbat-${{ needs.generate-prerelease-tag.outputs.version }}.dmg
+        retention-days: 30
+
+  build-conda-prerelease:
+    needs: generate-prerelease-tag
+    runs-on: ubuntu-latest
+    
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+    
+    - name: Create pre-release tag (simulate conda-release.yml workflow)
+      run: |
+        git config user.name "GitHub Actions"
+        git config user.email "actions@github.com"
+        # Create tag to simulate the release process that conda build expects
+        git tag -a "${{ needs.generate-prerelease-tag.outputs.prerelease_tag }}" -m "Pre-release ${{ needs.generate-prerelease-tag.outputs.prerelease_tag }}"
+        echo "Created tag for conda build: ${{ needs.generate-prerelease-tag.outputs.prerelease_tag }}"
+    
+    - name: Setup Miniconda
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        auto-update-conda: true
+        python-version: 3.11
+        channels: conda-forge,defaults
+        channel-priority: true
+    
+    - name: Install conda-build and dependencies
+      shell: bash -l {0}
+      run: |
+        conda install -y conda-build conda-verify
+        # Disable automatic upload (simulate conda-release.yml process without uploading)
+        conda config --set anaconda_upload no
+    
+    - name: Build conda package (simulate conda-release.yml workflow)
+      shell: bash -l {0}
+      run: |
+        # Export the pre-release tag (same as main conda-release workflow process)
+        export GIT_DESCRIBE_TAG=${{ needs.generate-prerelease-tag.outputs.prerelease_tag }}
+        echo "Building conda package with version: ${GIT_DESCRIBE_TAG}"
+        echo "Simulating conda-release.yml workflow without uploading to conda channels"
+        
+        # Use same build command as conda-release workflow
+        conda build conda --output-folder conda-build-output
+        
+        # List built packages
+        echo "Built conda packages:"
+        ls -la conda-build-output/noarch/
+        
+        # Show package info for verification
+        PACKAGE_PATH=$(find conda-build-output -name "hbat-*.tar.bz2" -o -name "hbat-*.conda" | head -n 1)
+        if [ -n "$PACKAGE_PATH" ]; then
+          echo "Package details:"
+          echo "Package file: $PACKAGE_PATH"
+          echo "Package size: $(du -h "$PACKAGE_PATH" | cut -f1)"
+          echo "File type: $(file "$PACKAGE_PATH")"
+        else
+          echo "Warning: No package found!"
+          ls -la conda-build-output/
+        fi
+    
+    - name: Upload conda package as artifact
+      uses: actions/upload-artifact@v4
+      with:
+        name: prerelease-conda-package-${{ needs.generate-prerelease-tag.outputs.pr_number }}
+        path: conda-build-output/noarch/hbat-*.*
+        retention-days: 30
+
+  update-prerelease:
+    needs: [generate-prerelease-tag, build-prerelease, build-macos-prerelease, build-conda-prerelease]
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    
+    steps:
+    - name: Download build artifacts
+      uses: actions/download-artifact@v4
+      with:
+        name: prerelease-build-artifacts-${{ needs.generate-prerelease-tag.outputs.pr_number }}
+        path: dist/
+    
+    - name: Download macOS app
+      uses: actions/download-artifact@v4
+      with:
+        name: prerelease-macos-app-${{ needs.generate-prerelease-tag.outputs.pr_number }}
+        path: dist/
+    
+    - name: Download conda package
+      uses: actions/download-artifact@v4
+      with:
+        name: prerelease-conda-package-${{ needs.generate-prerelease-tag.outputs.pr_number }}
+        path: dist/
+    
+    - name: List dist directory contents
+      run: |
+        echo "Contents of dist directory:"
+        ls -la dist/
+    
+    - name: Update pre-release with all artifacts
+      uses: softprops/action-gh-release@v2
+      with:
+        token: ${{ secrets.GITHUB_TOKEN }}
+        files: |
+            dist/hbat-${{ needs.generate-prerelease-tag.outputs.version }}.dmg
+            dist/hbat-*.tar.bz2
+            dist/hbat-*.conda
+        tag_name: ${{ needs.generate-prerelease-tag.outputs.github_tag }}
+        prerelease: true

{hbat-2.2.0 → hbat-2.2.4}/.github/workflows/test.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
 
     steps:
     - uses: actions/checkout@v4

{hbat-2.2.0 → hbat-2.2.4}/Makefile

@@ -186,6 +186,17 @@ build-standalone:
 	@echo "Building standalone executables with PyInstaller..."
 	python build_standalone.py
 
+build-standalone-windows:
+	@echo "Building Windows standalone executables..."
+	python build_standalone_windows.py
+
+build-standalone-linux:
+	@echo "Building Linux standalone executables..."
+	python build_standalone_linux.py
+
+build-standalone-all: build-standalone build-standalone-windows build-standalone-linux
+	@echo "All standalone builds completed"
+
 # Package validation
 check:
 	@echo "Checking package..."
@@ -193,6 +204,87 @@ check:
 	@echo "Package structure:"
 	@find dist/ -name "*.whl" -exec unzip -l {} \; 2>/dev/null | head -20
 
+# Test built package
+test-build:
+	@echo "Building and testing package in isolated environment..."
+	@# Clean up any existing environments
+	@if [ -d "hbat-build" ]; then rm -rf hbat-build; fi
+	@if [ -d "hbat-test-build" ]; then rm -rf hbat-test-build; fi
+	
+	@# Create fresh build environment
+	@echo "Creating build environment..."
+	@python -m venv hbat-build
+	@echo "Host Python: $$(which python)"
+	@echo "Build environment: ./hbat-build"
+	
+	@# Install build dependencies
+	@echo "Installing build dependencies..."
+	@if [ -f "./hbat-build/bin/pip" ]; then \
+		./hbat-build/bin/pip install --upgrade pip && \
+		./hbat-build/bin/pip install build setuptools wheel setuptools-scm; \
+	else \
+		./hbat-build/Scripts/pip.exe install --upgrade pip && \
+		./hbat-build/Scripts/pip.exe install build setuptools wheel setuptools-scm; \
+	fi
+	
+	@# Build the package
+	@echo "Building package..."
+	@if [ -f "./hbat-build/bin/python" ]; then \
+		./hbat-build/bin/python -m build; \
+	else \
+		./hbat-build/Scripts/python.exe -m build; \
+	fi
+	@echo "✓ Package built successfully!"
+	
+	@# Clean up build environment
+	@rm -rf hbat-build
+	
+	@# Create fresh test environment
+	@echo "\nCreating test environment..."
+	@python -m venv hbat-test-build
+	@echo "Test environment: ./hbat-test-build"
+	
+	@# Install the built package
+	@echo "Installing built package..."
+	@WHEEL_FILE=$$(ls -t dist/*.whl 2>/dev/null | head -1); \
+	if [ -z "$$WHEEL_FILE" ]; then \
+		echo "Error: No wheel file found in dist/."; \
+		exit 1; \
+	fi; \
+	echo "Installing $$WHEEL_FILE..."; \
+	if [ -f "./hbat-test-build/bin/pip" ]; then \
+		./hbat-test-build/bin/pip install --upgrade pip && \
+		./hbat-test-build/bin/pip install "$$WHEEL_FILE" && \
+		echo "Installing pdbfixer from Git..." && \
+		./hbat-test-build/bin/pip install git+https://github.com/openmm/pdbfixer.git && \
+		HBAT_CMD="./hbat-test-build/bin/hbat"; \
+	else \
+		./hbat-test-build/Scripts/pip.exe install --upgrade pip && \
+		./hbat-test-build/Scripts/pip.exe install "$$WHEEL_FILE" && \
+		echo "Installing pdbfixer from Git..." && \
+		./hbat-test-build/Scripts/pip.exe install git+https://github.com/openmm/pdbfixer.git && \
+		HBAT_CMD="./hbat-test-build/Scripts/hbat.exe"; \
+	fi; \
+	echo "\nTesting package imports..."; \
+	if [ -f "./hbat-test-build/bin/python" ]; then \
+		PYTHON_CMD="./hbat-test-build/bin/python"; \
+	else \
+		PYTHON_CMD="./hbat-test-build/Scripts/python.exe"; \
+	fi; \
+	$$PYTHON_CMD -c "import pdbreader; print('✓ pdbreader:', pdbreader)" && \
+	$$PYTHON_CMD -c "import openbabel; print('✓ openbabel:', openbabel)" && \
+	$$PYTHON_CMD -c "import pdbfixer; print('✓ pdbfixer:', pdbfixer)" && \
+	$$PYTHON_CMD -c "import mmcif; print('✓ mmcif:', mmcif)" && \
+	$$PYTHON_CMD -c "import mmcif; print('  mmcif version:', mmcif.__version__)" && \
+	$$PYTHON_CMD -c "import hbat; print('✓ hbat version:', hbat.__version__)" && \
+	echo "\nTesting hbat CLI with 6RSA.pdb..."; \
+	$$HBAT_CMD example_pdb_files/6RSA.pdb --summary-only
+	
+	@echo "\n✓ Package build and installation test passed!"
+	@echo "Cleaning up test environment..."
+	@rm -rf hbat-test-build
+	@echo "Test completed successfully!"
+
 # Upload to test PyPI
 upload-test:
 	@echo "Uploading to Test PyPI..."

{hbat-2.2.0 → hbat-2.2.4}/PKG-INFO

@@ -1,55 +1,73 @@
 Metadata-Version: 2.4
 Name: hbat
-Version: 2.2.0
+Version: 2.2.4
 Summary: Hydrogen Bond Analysis Tool for PDB structures
 Author-email: Abhishek Tiwari <abhishek_twr@yahoo.com>
-License: MIT
+License-Expression: MIT
 Project-URL: Homepage, https://github.com/abhishektiwari/hbat
 Project-URL: Bug Reports, https://github.com/abhishektiwari/hbat/issues
 Project-URL: Source, https://github.com/abhishektiwari/hbat
-Keywords: bioinformatics,chemistry,hydrogen bonds,protein structure
+Keywords: bioinformatics,chemistry,hydrogen bonds,halogen bonds,protein structure,PDB,mmCIF
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Science/Research
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Topic :: Scientific/Engineering :: Chemistry
-Classifier: License :: OSI Approved :: MIT License
 Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Classifier: Operating System :: OS Independent
-Requires-Python: >=3.7
+Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: pdbreader>=0.1.0
+Requires-Dist: numpy>=1.20.0
 Requires-Dist: networkx>=2.5.0
 Requires-Dist: matplotlib>=3.3.0
+Requires-Dist: openbabel-wheel>=3.1.1.22
+Requires-Dist: pybel>=0.15.5
+Requires-Dist: mmcif-pdbx>=2.0.1
+Requires-Dist: mmcif>=0.92.0
 Provides-Extra: dev
 Requires-Dist: pytest>=6.0.0; extra == "dev"
 Requires-Dist: pytest-cov>=2.8.0; extra == "dev"
 Requires-Dist: pytest-mock>=3.0.0; extra == "dev"
 Requires-Dist: black>=21.0.0; extra == "dev"
 Requires-Dist: flake8>=3.8.0; extra == "dev"
+Requires-Dist: isort>=5.0.0; extra == "dev"
 Requires-Dist: mypy>=0.800; extra == "dev"
 Requires-Dist: pre-commit>=2.10.0; extra == "dev"
 Requires-Dist: coverage>=5.0.0; extra == "dev"
+Requires-Dist: types-setuptools>=57.0.0; extra == "dev"
+Requires-Dist: types-requests>=2.0.0; extra == "dev"
+Requires-Dist: types-Pillow>=8.0.0; extra == "dev"
+Requires-Dist: pandas-stubs>=1.0.0; extra == "dev"
 Provides-Extra: build
 Requires-Dist: build>=0.8.0; extra == "build"
 Requires-Dist: twine>=4.0.0; extra == "build"
 Requires-Dist: pyinstaller>=5.0.0; extra == "build"
 Requires-Dist: setuptools-scm>=6.2.0; extra == "build"
+Provides-Extra: docs
+Requires-Dist: sphinx>=3.0.0; extra == "docs"
+Requires-Dist: sphinx-rtd-theme>=0.5.0; extra == "docs"
+Requires-Dist: sphinx-toolbox>=4.0.0; extra == "docs"
+Requires-Dist: sphinxcontrib-bibtex>=2.0.0; extra == "docs"
+Requires-Dist: sphinx-sitemap>=2.7.2; extra == "docs"
+Requires-Dist: sphinx-autodoc-typehints>=1.10.0; extra == "docs"
 Provides-Extra: gui
-Requires-Dist: tkinter; python_version >= "3.7" and extra == "gui"
+Requires-Dist: tkinter; python_version >= "3.8" and extra == "gui"
 Provides-Extra: advanced-viz
 Requires-Dist: seaborn>=0.11.0; extra == "advanced-viz"
-Requires-Dist: numpy>=1.19.0; extra == "advanced-viz"
 Requires-Dist: plotly>=5.0.0; extra == "advanced-viz"
 Provides-Extra: export
 Requires-Dist: pandas>=1.1.0; extra == "export"
 Requires-Dist: openpyxl>=3.0.0; extra == "export"
 Requires-Dist: xlwt>=1.3.0; extra == "export"
 Provides-Extra: all
-Requires-Dist: hbat[advanced-viz,export,gui]; extra == "all"
+Requires-Dist: hbat[advanced-viz,docs,export,gui]; extra == "all"
 Dynamic: license-file
 
 ![HBAT](https://github.com/abhishektiwari/hbat/raw/main/hbat.svg)
@@ -106,6 +124,12 @@ pip install hbat
 
 Run HBAT Command-Line Interface (CLI) using `hbat` or launch HBAT GUI using `hbat-gui`.
 
+**Recommended**: For [fixing missing Hydrogen Atoms](https://hbat.abhishek-tiwari.com/pdbfixing), install PDBFixer (preferred over OpenBabel).
+
+```bash
+pip install git+https://github.com/openmm/pdbfixer.git
+```
+
 ### Option 2: Install from Source
 
 ```bash
@@ -114,6 +138,12 @@ cd hbat
 pip install -e .
 ```
 
+Alternatively,  
+
+```bash
+pip install git+https://github.com/abhishektiwari/hbat.git
+```
+
 Run HBAT Command-Line Interface (CLI) using `hbat` or launch HBAT GUI using `hbat-gui`.
 
 ### Option 3: Install from Conda

{hbat-2.2.0 → hbat-2.2.4}/README.md

@@ -52,6 +52,12 @@ pip install hbat
 
 Run HBAT Command-Line Interface (CLI) using `hbat` or launch HBAT GUI using `hbat-gui`.
 
+**Recommended**: For [fixing missing Hydrogen Atoms](https://hbat.abhishek-tiwari.com/pdbfixing), install PDBFixer (preferred over OpenBabel).
+
+```bash
+pip install git+https://github.com/openmm/pdbfixer.git
+```
+
 ### Option 2: Install from Source
 
 ```bash
@@ -60,6 +66,12 @@ cd hbat
 pip install -e .
 ```
 
+Alternatively,  
+
+```bash
+pip install git+https://github.com/abhishektiwari/hbat.git
+```
+
 Run HBAT Command-Line Interface (CLI) using `hbat` or launch HBAT GUI using `hbat-gui`.
 
 ### Option 3: Install from Conda