hbat 2.0.8079654__tar.gz

hbat-2.0.8079654/.github/workflows/release.yml

@@ -0,0 +1,169 @@
+name: Release
+
+on:
+  workflow_run:
+    workflows: ["Tests"]
+    types:
+      - completed
+    branches: [ main ]
+
+jobs:
+  generate-tag:
+    runs-on: ubuntu-latest
+    if: ${{ github.event.workflow_run.conclusion == 'success' }}
+    outputs:
+      release_tag: ${{ steps.generate_tag.outputs.tag }}
+      version: ${{ steps.generate_tag.outputs.version }}
+    
+    steps:
+    - uses: actions/checkout@v4
+    
+    - name: Generate release tag
+      id: generate_tag
+      run: |
+        GIT_HASH=$(git rev-parse --short=7 HEAD)
+        # Convert git hash to a numeric value to make it PEP 440 compliant
+        # This uses the decimal representation of the first 6 hex chars
+        NUMERIC_HASH=$(printf "%d" 0x${GIT_HASH:0:6})
+        VERSION="2.0.${NUMERIC_HASH}"
+        TAG="v${VERSION}"
+        echo "version=$VERSION" >> $GITHUB_OUTPUT
+        echo "tag=$TAG" >> $GITHUB_OUTPUT
+        echo "Generated VERSION: $VERSION (from git hash: $GIT_HASH)"
+        echo "Generated TAG: $TAG"
+
+  release:
+    needs: generate-tag
+    runs-on: ubuntu-latest
+    
+    steps:
+    - uses: actions/checkout@v4
+    
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.11'
+    
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements-dev.txt
+        pip install -e .
+    
+    - name: Set version for setuptools-scm
+      run: |
+        git config user.name "GitHub Actions"
+        git config user.email "actions@github.com"
+        git tag -a "${{ needs.generate-tag.outputs.release_tag }}" -m "Release ${{ needs.generate-tag.outputs.release_tag }}"
+        echo "Created tag: ${{ needs.generate-tag.outputs.release_tag }}"
+    
+    - name: Build package
+      run: make build
+    
+    - name: Upload build artifacts
+      uses: actions/upload-artifact@v4
+      with:
+        name: build-artifacts
+        path: dist/*
+    
+    - name: Publish to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        password: ${{ secrets.PYPI_API_TOKEN }}
+        skip-existing: true
+
+  build-macos:
+    needs: generate-tag
+    runs-on: macos-latest
+    
+    steps:
+    - uses: actions/checkout@v4
+    
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.11'
+    
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements-dev.txt
+        pip install -e .
+        # Install tkinter on macOS
+        brew install python-tk create-dmg
+    
+    - name: Set version for setuptools-scm
+      run: |
+        git config user.name "GitHub Actions"
+        git config user.email "actions@github.com"
+        git tag -a "${{ needs.generate-tag.outputs.release_tag }}" -m "Release ${{ needs.generate-tag.outputs.release_tag }}"
+        echo "Created tag: ${{ needs.generate-tag.outputs.release_tag }}"
+    
+    - name: Build standalone macOS app
+      run: make build-standalone
+
+    - name: Ad-hoc sign the app
+      run: |
+        echo "Signing app with ad-hoc signature..."
+        codesign --force --deep --sign - dist/HBAT-GUI.app
+        codesign --verify --verbose dist/HBAT-GUI.app
+
+    - name: Remove HBAT-GUI folder
+      run: |
+        echo "Contents of dist directory:"
+        ls -la dist/
+        cd dist && rm -rf HBAT-GUI
+    
+    - name: Create DMG installer
+      run: |
+        create-dmg \
+          --volname "HBAT Installer" \
+          --window-pos 200 120 \
+          --window-size 800 400 \
+          --icon-size 100 \
+          --icon "HBAT-GUI.app" 200 190 \
+          --hide-extension "HBAT-GUI.app" \
+          --app-drop-link 600 185 \
+          "hbat-${{ needs.generate-tag.outputs.version }}.dmg" \
+          "dist/"
+        mv hbat-${{ needs.generate-tag.outputs.version }}.dmg dist/
+    
+    - name: Upload macOS app artifact
+      uses: actions/upload-artifact@v4
+      with:
+        name: macos-app
+        path: dist/hbat-${{ needs.generate-tag.outputs.version }}.dmg
+  
+  create-release:
+    needs: [generate-tag, release, build-macos]
+    runs-on: ubuntu-latest
+    
+    steps:
+    - name: Download build artifacts
+      uses: actions/download-artifact@v4
+      with:
+        name: build-artifacts
+        path: dist/
+    
+    - name: Download macOS app
+      uses: actions/download-artifact@v4
+      with:
+        name: macos-app
+        path: dist/
+    
+    - name: List dist directory contents
+      run: |
+        echo "Contents of dist directory:"
+        ls -la dist/
+    
+    - name: Create Release
+      uses: softprops/action-gh-release@v2
+      with:
+        token: ${{ secrets.GITHUB_TOKEN }}
+        files: |
+            dist/hbat-${{ needs.generate-tag.outputs.version }}-py3-none-any.whl
+            dist/hbat-${{ needs.generate-tag.outputs.version }}.tar.gz
+            dist/hbat-${{ needs.generate-tag.outputs.version }}.dmg
+        tag_name: ${{ needs.generate-tag.outputs.release_tag }}
+        name: Release ${{ needs.generate-tag.outputs.release_tag }}
+        body: ${{ github.event.head_commit.message }}

hbat-2.0.8079654/.github/workflows/test.yml

@@ -0,0 +1,48 @@
+name: Tests
+
+on:
+  push:
+    branches: [ main]
+  pull_request:
+    branches: [ main]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11"]
+
+    steps:
+    - uses: actions/checkout@v4
+    
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements-dev.txt
+        pip install -e .
+    
+    - name: Format code
+      run: make format
+    
+    - name: Run type check
+      run: make type-check
+    
+    - name: Run tests
+      run: make test
+    
+    - name: Run coverage
+      run: make test-coverage
+      if: matrix.python-version == '3.9'
+    
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v3
+      if: matrix.python-version == '3.9'
+      with:
+        file: ./tests/htmlcov/coverage.xml
+        fail_ci_if_error: false

hbat-2.0.8079654/CITATION.cff

@@ -0,0 +1,28 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+- family-names: "Tiwari"
+  given-names: "Abhishek"
+  orcid: "https://orcid.org/0000-0003-2222-2395"
+- family-names: "Panigrahi"
+  given-names: "Sunil Kumar"
+title: "HBAT: Hydrogen Bond Analysis Tool (v2)"
+version: 2.0.4
+doi: 10.3233/ISI-2007-003
+date-released: 2017-12-18
+url: "https://github.com/abhishektiwari/hbat"
+preferred-citation:
+  type: article
+  authors:
+  - family-names: "Tiwari"
+    given-names: "Abhishek"
+    orcid: "https://orcid.org/0000-0003-2222-2395"
+  - family-names: "Panigrahi"
+    given-names: "Sunil Kumar"
+  doi: "10.3233/ISI-2007-00337"
+  journal: "In Silico Biology"
+  month: 12
+  year: 2007
+  title: "HBAT: A Complete Package for Analysing Strong and Weak Hydrogen Bonds in Macromolecular Crystal Structures"
+  issue: 6
+  volume: 7

hbat-2.0.8079654/CLAUDE.md

@@ -0,0 +1,27 @@
+# Development Guidelines
+
+## Core Development Rules
+
+1. Testing Requirements
+
+    - When updating existing functions or classes must update the existing test cases
+    - When adding a new feature must create a new test case
+
+2.  Documentation Requirements
+
+    - When changing in `core` module must update `logic.rst`
+    - When adding new file to `hbat` or `tests` must update `development.rst`
+
+3. Code Quality
+
+   - Type hints required for all code in `core` module
+   - All public APIs in `core`, `cli`, and `gui` module must have Sphinx docstring format
+   - Run formatters before type checks
+   - Format code using `make format`
+   - Perform type check using `make type-check`
+   - Fix type checking errors by adding type hint
+   - For typing support install required package type stubs if available
+
+4. Requirements management
+
+    - After installing new packages add them to requirements files

hbat-2.0.8079654/CODE_OF_CONDUCT.md

@@ -0,0 +1,133 @@
+# Contributor Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+``pwessel at hawaii dot edu``, ``leouieda at gmail dot com``, or
+``meghanj at hawaii dot edu``. All complaints will be reviewed and investigated
+promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
+
+For answers to common questions about this code of conduct, see the FAQ at
+[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at
+[https://www.contributor-covenant.org/translations][translations].
+
+[homepage]: https://www.contributor-covenant.org
+[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
+[Mozilla CoC]: https://github.com/mozilla/diversity
+[FAQ]: https://www.contributor-covenant.org/faq
+[translations]: https://www.contributor-covenant.org/translations

hbat-2.0.8079654/CONTRIBUTING.md

@@ -0,0 +1,30 @@
+# Contributing Guidelines
+
+:tada: **First off, thank you for considering contributing to our project!** :tada:
+
+This is a community-driven project, so it's people like you that make it useful and
+successful. These are some of the many ways to contribute:
+
+* :bug: Submitting bug reports and feature requests
+* :memo: Writing tutorials or examples
+* :mag: Fixing typos and improving the documentation
+* :bulb: Writing code for everyone to use
+* :people_holding_hands: Community engagement and outreach
+
+If you get stuck at any point you can create an
+[issue](https://github.com/abhishektiwari/hbat/issues) on GitHub.
+
+For more information on contributing to open source projects,
+[GitHub's own guide](https://opensource.guide/how-to-contribute)
+is a great starting point if you are new to version control. Also, checkout the
+[Zen of Scientific Software Maintenance](https://jrleeman.github.io/ScientificSoftwareMaintenance/)
+for some guiding principles on how to create high quality scientific software
+contributions.
+
+
+## Ground Rules
+
+The goal is to maintain a diverse community that's pleasant for everyone.
+**Please be considerate and respectful of others**. Everyone must abide by our
+[Code of Conduct](/CODE_OF_CONDUCT.md)
+and we encourage all to read it carefully.

hbat-2.0.8079654/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Abhishek Tiwari
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

hbat-2.0.8079654/MANIFEST.in

@@ -0,0 +1,44 @@
+# MANIFEST.in - Include additional files in distribution package
+
+# Documentation files
+include README.md
+include LICENSE
+include CONTRIBUTING.md
+include CODE_OF_CONDUCT.md
+
+# Configuration files
+include pyproject.toml
+include pytest.ini
+include requirements*.txt
+include Makefile
+
+# Icon and graphics files
+include *.ico
+include *.png
+include *.svg
+
+# Example files
+recursive-include example_pdb_files *.pdb
+recursive-include example_presets *.hbat
+
+# Test files and documentation
+recursive-include tests *.py
+recursive-include tests *.md
+exclude tests/htmlcov/*
+
+# Executable scripts
+include hbat_cli.py
+include hbat_gui.py
+
+# Exclude development and build artifacts
+global-exclude *.pyc
+global-exclude *.pyo
+global-exclude __pycache__
+global-exclude .git*
+global-exclude .DS_Store
+global-exclude *.so
+global-exclude .coverage
+global-exclude .pytest_cache
+prune build
+prune dist
+prune *.egg-info

hbat-2.0.8079654/Makefile

@@ -0,0 +1,164 @@
+# HBAT Development Makefile
+
+.PHONY: help install install-dev test test-fast test-legacy test-pytest test-core test-cli test-gui test-coverage clean lint format type-check docs
+
+# Default target
+help:
+	@echo "HBAT Development Commands:"
+	@echo "  install       Install package in development mode"
+	@echo "  install-dev   Install with development dependencies"
+	@echo ""
+	@echo "Testing:"
+	@echo "  test          Run comprehensive test suite (recommended)"
+	@echo "  test-fast     Run fast tests only (skip slow integration tests)"
+	@echo "  test-legacy   Run legacy test runner"
+	@echo "  test-pytest   Run tests with pytest (if available)"
+	@echo "  test-core     Run core module tests only"
+	@echo "  test-cli      Run CLI tests only"
+	@echo "  test-gui      Run GUI tests only (requires display)"
+	@echo "  test-coverage Generate test coverage report"
+	@echo ""
+	@echo "Code Quality:"
+	@echo "  lint          Run code linting"
+	@echo "  format        Format code with black and isort"
+	@echo "  type-check    Run type checking with mypy"
+	@echo ""
+	@echo "Development:"
+	@echo "  clean         Clean build artifacts"
+	@echo "  docs          Build documentation"
+	@echo "  run-gui       Launch GUI application"
+	@echo "  run-cli       Run CLI with test file"
+
+# Installation
+install:
+	pip install -e .
+
+install-dev:
+	pip install -r requirements-dev.txt
+	pip install -e .
+
+# Testing
+test:
+	@echo "Running additional pytest tests if available..."
+	-pytest tests/ -v
+
+test-fast:
+	@echo "Running fast tests only..."
+	cd tests && python run_tests.py --fast
+
+test-pytest:
+	@echo "Running tests with pytest..."
+	pytest tests/ -v
+
+test-cli:
+	@echo "Running CLI tests..."
+	cd tests && python run_tests.py --cli --fast
+
+test-core:
+	@echo "Running core tests..."
+	cd tests && python run_tests.py --core --fast
+
+test-coverage:
+	@echo "Running tests with coverage..."
+	cd tests && python run_tests.py --coverage
+
+test-gui:
+	@echo "Running GUI tests..."
+	cd tests && python run_tests.py --gui --fast
+
+# Code quality
+lint:
+	@echo "Running flake8..."
+	-flake8 hbat/ *.py
+	@echo "Running pylint..."
+	-pylint hbat/
+
+format:
+	@echo "Formatting with black..."
+	-black hbat/ *.py
+	@echo "Sorting imports with isort..."
+	-isort hbat/ *.py
+
+type-check:
+	@echo "Type checking with mypy..."
+	-mypy hbat/core/ hbat/cli/
+
+# Cleanup
+clean:
+	rm -rf build/
+	rm -rf dist/
+	rm -rf *.egg-info/
+	rm -rf __pycache__/
+	rm -rf */__pycache__/
+	rm -rf */*/__pycache__/
+	rm -rf .pytest_cache/
+	rm -rf .mypy_cache/
+	rm -rf .coverage
+	rm -rf htmlcov/
+	rm -rf docs/build/
+	find . -name "*.pyc" -delete
+	find . -name "*.pyo" -delete
+
+# Documentation
+docs:
+	@echo "Building documentation (requires sphinx)..."
+	-sphinx-build -b html docs/source/ docs/build/html/
+
+docs-serve:
+	@echo "Serving documentation locally..."
+	@if [ -f docs/build/html/index.html ]; then \
+		echo "Opening documentation at http://localhost:8000"; \
+		cd docs/build/html && python -m http.server 8000; \
+	else \
+		echo "Documentation not built. Run 'make docs' first."; \
+	fi
+
+# Development runners
+run-gui:
+	python hbat_gui.py
+
+run-cli:
+	python hbat_cli.py example_pdb_files/6RSA.pdb --verbose --summary-only
+
+# Example analysis
+example:
+	@echo "Running example analysis with 6RSA.pdb..."
+	python hbat_cli.py example_pdb_files/6RSA.pdb --json example_results.json --csv example_results.csv --verbose --summary-only
+	@echo "Results saved to example_results.json and example_results.csv"
+
+# Package building
+build:
+	@echo "Building package with modern build system..."
+	python -m build
+
+build-legacy:
+	@echo "Building with legacy setup.py..."
+	python setup.py sdist bdist_wheel
+
+# Standalone executables
+build-standalone:
+	@echo "Building standalone executables with PyInstaller..."
+	python build_standalone.py
+
+# Package validation
+check:
+	@echo "Checking package..."
+	-twine check dist/*
+	@echo "Package structure:"
+	@find dist/ -name "*.whl" -exec unzip -l {} \; 2>/dev/null | head -20
+
+# Upload to test PyPI
+upload-test:
+	@echo "Uploading to Test PyPI..."
+	twine upload --repository testpypi dist/*
+
+# Upload to PyPI
+upload:
+	@echo "Uploading to PyPI..."
+	twine upload dist/*
+
+# Development environment setup
+setup-dev:
+	python -m venv venv
+	@echo "Activate virtual environment with: source venv/bin/activate (Linux/Mac) or venv\\Scripts\\activate (Windows)"
+	@echo "Then run: make install-dev"