hbat 2.2.0__tar.gz → 2.2.3__tar.gz

{hbat-2.2.0 → hbat-2.2.3}/.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-2.2.3}/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-2.2.3}/PKG-INFO

@@ -1,55 +1,73 @@
 Metadata-Version: 2.4
 Name: hbat
-Version: 2.2.0
+Version: 2.2.3
 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-2.2.3}/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

hbat-2.2.3/build_standalone_linux.py

@@ -0,0 +1,384 @@
+#!/usr/bin/env python3
+"""
+Build script for HBAT standalone Linux executables.
+
+This script creates standalone Linux executables using PyInstaller and AppImage.
+Run this from the project root directory on Linux.
+"""
+
+import os
+import shutil
+import subprocess
+import sys
+import urllib.request
+from pathlib import Path
+
+
+def install_dependencies():
+    """Install build dependencies."""
+    print("Installing build dependencies...")
+    try:
+        subprocess.run(
+            [
+                sys.executable,
+                "-m",
+                "pip",
+                "install",
+                "pyinstaller>=5.0.0",
+                "setuptools-scm>=6.2.0",
+            ],
+            check=True,
+        )
+        return True
+    except subprocess.CalledProcessError:
+        print("Failed to install dependencies")
+        return False
+
+
+def clean_build():
+    """Clean previous build artifacts."""
+    print("Cleaning previous builds...")
+    paths_to_clean = ["build", "dist", "__pycache__"]
+
+    for path in paths_to_clean:
+        if os.path.exists(path):
+            shutil.rmtree(path)
+            print(f"  Removed {path}")
+
+
+def build_gui():
+    """Build GUI executable for Linux."""
+    print("Building Linux GUI executable...")
+
+    cmd = [
+        "pyinstaller",
+        "--onefile",
+        "--windowed",
+        "--name",
+        "HBAT-GUI",
+        "--add-data",
+        "example_pdb_files:example_pdb_files",
+        "--add-data",
+        "example_presets:example_presets",
+        "--add-data",
+        "hbat.png:.",
+        "--add-data",
+        "README.md:.",
+        "--hidden-import",
+        "tkinter",
+        "--hidden-import",
+        "matplotlib.backends.backend_tkagg",
+        "--hidden-import",
+        "networkx",
+        "--exclude-module",
+        "PyQt5",
+        "--exclude-module",
+        "PyQt6",
+        "--clean",
+        "--distpath",
+        "dist/linux",
+        "hbat_gui.py",
+    ]
+
+    # Add icon if available
+    if os.path.exists("hbat.png"):
+        cmd.extend(["--icon", "hbat.png"])
+
+    try:
+        subprocess.run(cmd, check=True)
+        print("✓ Linux GUI executable built successfully")
+        return True
+    except subprocess.CalledProcessError as e:
+        print(f"✗ Linux GUI build failed: {e}")
+        return False
+
+
+def build_cli():
+    """Build CLI executable for Linux."""
+    print("Building Linux CLI executable...")
+
+    cmd = [
+        "pyinstaller",
+        "--onefile",
+        "--console",
+        "--name",
+        "hbat",
+        "--add-data",
+        "example_pdb_files:example_pdb_files",
+        "--add-data",
+        "example_presets:example_presets",
+        "--hidden-import",
+        "matplotlib",
+        "--hidden-import",
+        "networkx",
+        "--clean",
+        "--distpath",
+        "dist/linux",
+        "hbat_cli.py",
+    ]
+
+    try:
+        subprocess.run(cmd, check=True)
+        print("✓ Linux CLI executable built successfully")
+        return True
+    except subprocess.CalledProcessError as e:
+        print(f"✗ Linux CLI build failed: {e}")
+        return False
+
+
+def create_appimage():
+    """Create AppImage for better Linux distribution."""
+    print("\nCreating AppImage...")
+
+    # Create AppDir structure
+    appdir = Path("HBAT.AppDir")
+    if appdir.exists():
+        shutil.rmtree(appdir)
+
+    appdir.mkdir()
+    (appdir / "usr" / "bin").mkdir(parents=True)
+    (appdir / "usr" / "share" / "applications").mkdir(parents=True)
+    (appdir / "usr" / "share" / "icons" / "hicolor" / "256x256" / "apps").mkdir(
+        parents=True
+    )
+
+    # Copy executables
+    if os.path.exists("dist/linux/HBAT-GUI"):
+        shutil.copy2("dist/linux/HBAT-GUI", appdir / "usr" / "bin" / "HBAT-GUI")
+        os.chmod(appdir / "usr" / "bin" / "HBAT-GUI", 0o755)
+
+    if os.path.exists("dist/linux/hbat"):
+        shutil.copy2("dist/linux/hbat", appdir / "usr" / "bin" / "hbat")
+        os.chmod(appdir / "usr" / "bin" / "hbat", 0o755)
+
+    # Copy icon
+    if os.path.exists("hbat.png"):
+        shutil.copy2(
+            "hbat.png",
+            appdir
+            / "usr"
+            / "share"
+            / "icons"
+            / "hicolor"
+            / "256x256"
+            / "apps"
+            / "hbat.png",
+        )
+
+    # Create desktop file
+    desktop_content = """[Desktop Entry]
+Name=HBAT
+Comment=Hydrogen Bond Analysis Tool
+Exec=HBAT-GUI
+Icon=hbat
+Type=Application
+Categories=Science;Chemistry;
+Terminal=false
+"""
+
+    with open(appdir / "usr" / "share" / "applications" / "hbat.desktop", "w") as f:
+        f.write(desktop_content)
+
+    # Create AppRun script
+    apprun_content = """#!/bin/bash
+SELF=$(readlink -f "$0")
+HERE=${SELF%/*}
+export PATH="${HERE}/usr/bin:${PATH}"
+
+if [ "$1" = "cli" ]; then
+    shift
+    exec "${HERE}/usr/bin/hbat" "$@"
+else
+    exec "${HERE}/usr/bin/HBAT-GUI" "$@"
+fi
+"""
+
+    with open(appdir / "AppRun", "w") as f:
+        f.write(apprun_content)
+    os.chmod(appdir / "AppRun", 0o755)
+
+    # Download appimagetool if not present
+    appimagetool = "appimagetool-x86_64.AppImage"
+    if not os.path.exists(appimagetool):
+        print("Downloading appimagetool...")
+        try:
+            urllib.request.urlretrieve(
+                "https://github.com/AppImage/AppImageKit/releases/download/continuous/appimagetool-x86_64.AppImage",
+                appimagetool,
+            )
+            os.chmod(appimagetool, 0o755)
+        except Exception as e:
+            print(f"Failed to download appimagetool: {e}")
+            return False
+
+    # Build AppImage
+    try:
+        env = os.environ.copy()
+        env["ARCH"] = "x86_64"
+        subprocess.run(
+            [f"./{appimagetool}", "HBAT.AppDir", "dist/HBAT-x86_64.AppImage"],
+            check=True,
+            env=env,
+        )
+        shutil.rmtree(appdir)
+        print("✓ AppImage created successfully")
+        return True
+    except subprocess.CalledProcessError:
+        print("✗ Failed to create AppImage")
+        return False
+
+
+def create_deb_package():
+    """Create .deb package for Debian/Ubuntu."""
+    print("\nCreating .deb package...")
+
+    # Create debian package structure
+    debdir = Path("hbat-deb")
+    if debdir.exists():
+        shutil.rmtree(debdir)
+
+    # Create directory structure
+    (debdir / "DEBIAN").mkdir(parents=True)
+    (debdir / "usr" / "bin").mkdir(parents=True)
+    (debdir / "usr" / "share" / "applications").mkdir(parents=True)
+    (debdir / "usr" / "share" / "icons" / "hicolor" / "256x256" / "apps").mkdir(
+        parents=True
+    )
+
+    # Copy executables
+    if os.path.exists("dist/linux/HBAT-GUI"):
+        shutil.copy2("dist/linux/HBAT-GUI", debdir / "usr" / "bin" / "hbat-gui")
+        os.chmod(debdir / "usr" / "bin" / "hbat-gui", 0o755)
+
+    if os.path.exists("dist/linux/hbat"):
+        shutil.copy2("dist/linux/hbat", debdir / "usr" / "bin" / "hbat")
+        os.chmod(debdir / "usr" / "bin" / "hbat", 0o755)
+
+    # Copy icon
+    if os.path.exists("hbat.png"):
+        shutil.copy2(
+            "hbat.png",
+            debdir
+            / "usr"
+            / "share"
+            / "icons"
+            / "hicolor"
+            / "256x256"
+            / "apps"
+            / "hbat.png",
+        )
+
+    # Create desktop file
+    desktop_content = """[Desktop Entry]
+Name=HBAT
+Comment=Hydrogen Bond Analysis Tool
+Exec=hbat-gui
+Icon=hbat
+Type=Application
+Categories=Science;Chemistry;
+Terminal=false
+"""
+
+    with open(debdir / "usr" / "share" / "applications" / "hbat.desktop", "w") as f:
+        f.write(desktop_content)
+
+    # Create control file
+    control_content = """Package: hbat
+Version: 1.0.0
+Section: science
+Priority: optional
+Architecture: amd64
+Maintainer: HBAT Team
+Description: Hydrogen Bond Analysis Tool
+ A comprehensive tool for analyzing hydrogen bonds in molecular structures.
+"""
+
+    with open(debdir / "DEBIAN" / "control", "w") as f:
+        f.write(control_content)
+
+    # Build .deb package
+    try:
+        subprocess.run(
+            ["dpkg-deb", "--build", "hbat-deb", "dist/hbat_1.0.0_amd64.deb"], check=True
+        )
+        shutil.rmtree(debdir)
+        print("✓ .deb package created successfully")
+        return True
+    except (subprocess.CalledProcessError, FileNotFoundError):
+        print("✗ Failed to create .deb package (dpkg-deb not found)")
+        if debdir.exists():
+            shutil.rmtree(debdir)
+        return False
+
+
+def main():
+    """Main build function."""
+    print("HBAT Linux Build Script")
+    print("=" * 40)
+
+    # Check we're in the right directory
+    if not os.path.exists("hbat_gui.py"):
+        print("Error: Please run this script from the HBAT project root directory")
+        return 1
+
+    # Check if running on Linux
+    if sys.platform != "linux":
+        print("Warning: This script is designed for Linux.")
+        print("Cross-compilation may not work properly.")
+
+    # Install dependencies
+    if not install_dependencies():
+        return 1
+
+    # Clean previous builds
+    clean_build()
+
+    # Build executables
+    gui_success = build_gui()
+    cli_success = build_cli()
+
+    if not (gui_success or cli_success):
+        print("All builds failed!")
+        return 1
+
+    # Try to create packages
+    appimage_success = create_appimage()
+    deb_success = create_deb_package()
+
+    print("\n" + "=" * 40)
+    print("Build Summary")
+    print("=" * 40)
+
+    if gui_success:
+        print("✓ GUI: dist/linux/HBAT-GUI")
+    else:
+        print("✗ GUI build failed")
+
+    if cli_success:
+        print("✓ CLI: dist/linux/hbat")
+    else:
+        print("✗ CLI build failed")
+
+    if appimage_success:
+        print("✓ AppImage: dist/HBAT-x86_64.AppImage")
+    else:
+        print("✗ AppImage creation skipped/failed")
+
+    if deb_success:
+        print("✓ DEB Package: dist/hbat_1.0.0_amd64.deb")
+    else:
+        print("✗ DEB package creation skipped/failed")
+
+    print("\nUsage:")
+    if gui_success:
+        print("  GUI: ./dist/linux/HBAT-GUI")
+    if cli_success:
+        print("  CLI: ./dist/linux/hbat")
+    if appimage_success:
+        print("  AppImage: ./dist/HBAT-x86_64.AppImage")
+
+    return 0
+
+
+if __name__ == "__main__":
+    sys.exit(main())