Fix Parameters, Tests and Freezing UI on large PDB files (#23)

* Add async loop for large PDB files
* Fix the progress bar on the PDB structure
* Adding descriptors for atom and interactions
* Cleaning docs and badges
* Fixing the release notes
* Refactoring tests - moving in unit test, integration test, performance test, and e2e 
* Enabled Codecov generation and upload for Github Action

Author: abhishektiwari

.github/workflows/release.yml

@@ -419,21 +419,28 @@ jobs:
             - `hbat_${{ needs.generate-version.outputs.version }}_amd64.deb` - Debian package
           
           ### Conda Package
-          - `hbat-${{ needs.generate-version.outputs.version }}.tar.bz2` or `.conda`
+          - `hbat-${{ needs.generate-version.outputs.version }}-py0.conda`
           
           ### Documentation
           - `hbat-docs-${{ needs.generate-version.outputs.version }}.zip` - Full HTML documentation
           
           ## Installation
           
-          **pip:**
+          **PIP:**
           ```bash
           pip install https://github.com/${{ github.repository }}/releases/download/${{ needs.generate-version.outputs.github_tag }}/hbat-${{ needs.generate-version.outputs.version }}-py3-none-any.whl
           ```
           
-          ${{ needs.generate-version.outputs.is_prerelease == 'false' && '**PyPI:**\n```bash\npip install hbat\n```' || '' }}
+          ${{ needs.generate-version.outputs.is_prerelease == 'false' && '**PyPI:**
+          ```bash
+          pip install hbat
+          ```' || '' }}
           
-          ${{ needs.generate-version.outputs.is_prerelease == 'false' && '**Conda:**\n```bash\nconda install -c ${{ secrets.ANACONDA_ORG }} hbat\n```' || '**Conda:** Download the package and install locally' }}
+          ${{ needs.generate-version.outputs.is_prerelease == 'false' && '**Conda:**
+          ```bash
+          conda install -c ${{ secrets.ANACONDA_ORG }} hbat
+          ```' || '**Conda:**
+          Download the package and install locally' }}
         prerelease: ${{ needs.generate-version.outputs.is_prerelease == 'true' }}
         draft: false
 

.github/workflows/test.yml

@@ -38,11 +38,19 @@ jobs:
 
     - name: Run coverage
       run: make test-coverage
-      if: matrix.python-version == '3.9'
+      if: matrix.python-version == '3.10'
 
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v3
-      if: matrix.python-version == '3.9'
+      uses: codecov/codecov-action@v5
+      if: matrix.python-version == '3.10'
       with:
-        file: ./tests/htmlcov/coverage.xml
-        fail_ci_if_error: false
+        fail_ci_if_error: false
+        files: ./coverage.xml
+        token: ${{ secrets.CODECOV_TOKEN }}
+
+    - name: Upload test results to Codecov
+      if: ${{ !cancelled() }}
+      uses: codecov/test-results-action@v1
+      with:
+        files: ./junit.xml
+        token: ${{ secrets.CODECOV_TOKEN }}

.gitignore

@@ -240,4 +240,11 @@ experiments/*
 # CCD
 ccd-data/*
 !ccd-data/.gitkeep
-!ccd-data/README.md
+!ccd-data/README.md
+
+# Ignore config files
+hbat/config/*
+
+# XML files
+junit.xml
+coverage.xml

Makefile

@@ -1,6 +1,6 @@
 # HBAT Development Makefile
 
-.PHONY: help install install-dev test test-fast test-legacy test-pytest test-core test-cli test-gui test-coverage test-ccd clean lint format type-check docs generate-ccd-bonds
+.PHONY: help install install-dev test test-all test-fast test-legacy test-pytest test-unit test-integration test-e2e test-performance test-cli test-gui test-coverage test-ccd clean lint format type-check docs generate-ccd-bonds
 
 # Default target
 help:
@@ -9,11 +9,15 @@ help:
 	@echo "  install-dev   Install with development dependencies"
 	@echo ""
 	@echo "Testing:"
-	@echo "  test          Run comprehensive test suite (recommended)"
+	@echo "  test          Run comprehensive test suite (excludes slow tests)"
+	@echo "  test-all      Run ALL tests including slow performance tests"
 	@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-unit     Run unit tests only (fast, isolated)"
+	@echo "  test-integration Run integration tests only (component interactions)"
+	@echo "  test-e2e      Run end-to-end workflow tests only"
+	@echo "  test-performance Run performance benchmark 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"
@@ -32,6 +36,7 @@ help:
 	@echo "Development:"
 	@echo "  clean         Clean build artifacts"
 	@echo "  docs          Build documentation"
+	@echo "  docs-watch    Build docs with auto-reload and open browser"
 	@echo "  run-gui       Launch GUI application"
 	@echo "  run-cli       Run CLI with test file"
 	@echo "  generate-ccd-bonds Generate residue bond constants from CCD files"
@@ -46,36 +51,52 @@ install-dev:
 
 # Testing
 test:
-	@echo "Running additional pytest tests if available..."
-	-pytest tests/ -v
+	@echo "Running all tests except slow ones..."
+	pytest tests/ -v -m "not slow"
 
 test-fast:
 	@echo "Running fast tests only..."
 	cd tests && python run_tests.py --fast
 
+test-all:
+	@echo "Running ALL tests including slow ones..."
+	pytest tests/ -v
+
 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
+	pytest tests/cli/ -v -m "cli"
 
 test-coverage:
-	@echo "Running tests with coverage..."
-	cd tests && python run_tests.py --coverage
+	@echo "Running tests with coverage...(excludes slow tests)"
+	pytest tests/ -v -m "not slow" --cov --cov-branch --cov-report=xml --junitxml=junit.xml -o junit_family=legacy 
 
 test-gui:
 	@echo "Running GUI tests..."
-	cd tests && python run_tests.py --gui --fast
+	pytest tests/gui/ -v -m "gui"
+
+test-unit:
+	@echo "Running unit tests..."
+	pytest tests/unit/ -v -m "unit"
+
+test-integration:
+	@echo "Running integration tests..."
+	pytest tests/integration/ -v -m "integration"
+
+test-e2e:
+	@echo "Running end-to-end tests..."
+	pytest tests/e2e/ -v -m "e2e"
+
+test-performance:
+	@echo "Running performance tests..."
+	pytest tests/performance/ -v -m "performance"
 
 test-ccd:
 	@echo "Running CCD performance tests..."
-	pytest tests/core/test_ccd_performance.py -v -m "ccd"
+	pytest tests/performance/test_ccd_performance.py -v -m "ccd"
 
 # Code quality
 lint:
@@ -125,6 +146,10 @@ docs-serve:
 		echo "Documentation not built. Run 'make docs' first."; \
 	fi
 
+docs-watch:
+	@echo "Building and watching documentation with auto-reload (requires sphinx-autobuild)..."
+	sphinx-autobuild docs/source/ docs/build/html/ --open-browser
+
 # Development runners
 run-gui:
 	python hbat_gui.py

README.md

@@ -15,8 +15,8 @@ A Python package to automate the analysis of potential hydrogen bonds and simila
 ![License](https://img.shields.io/github/license/abhishektiwari/hbat)
 ![GitHub Downloads (all assets, all releases)](https://img.shields.io/github/downloads/abhishektiwari/hbat/total?label=GitHub%20Downloads)
 ![SourceForge Downloads](https://img.shields.io/sourceforge/dt/hbat?label=SourceForge%20Downloads)
-
-
+![PyPI Downloads](https://img.shields.io/pypi/dm/hbat?label=PyPI%20Downloads)
+[![codecov](https://codecov.io/gh/abhishektiwari/hbat/graph/badge.svg?token=QSKYLB3M1V)](https://codecov.io/gh/abhishektiwari/hbat)
 
 ## Background
 

build_standalone_linux.py

@@ -38,7 +38,13 @@ def install_dependencies():
 def clean_build():
     """Clean previous build artifacts."""
     print("Cleaning previous builds...")
-    paths_to_clean = ["build", "dist", "__pycache__", "appimagetool-extracted", "squashfs-root"]
+    paths_to_clean = [
+        "build",
+        "dist",
+        "__pycache__",
+        "appimagetool-extracted",
+        "squashfs-root",
+    ]
 
     for path in paths_to_clean:
         if os.path.exists(path):
@@ -129,9 +135,9 @@ def build_cli():
 def create_appimage():
     """Create AppImage for better Linux distribution."""
     print("\nCreating AppImage...")
-    
+
     # Get version from environment or use default
-    version = os.environ.get('HBAT_VERSION', '2.0.0')
+    version = os.environ.get("HBAT_VERSION", "2.0.0")
 
     # Create AppDir structure
     appdir = Path("HBAT.AppDir")
@@ -183,7 +189,7 @@ def create_appimage():
 
     with open(appdir / "usr" / "share" / "applications" / "hbat.desktop", "w") as f:
         f.write(desktop_content)
-    
+
     # Also create desktop file at root for appimagetool
     with open(appdir / "hbat.desktop", "w") as f:
         f.write(desktop_content)
@@ -209,7 +215,7 @@ def create_appimage():
     # Download and extract appimagetool if not present
     appimagetool = "appimagetool-x86_64.AppImage"
     appimagetool_dir = "appimagetool-extracted"
-    
+
     if not os.path.exists(appimagetool_dir):
         if not os.path.exists(appimagetool):
             print("Downloading appimagetool...")
@@ -222,13 +228,16 @@ def create_appimage():
             except Exception as e:
                 print(f"Failed to download appimagetool: {e}")
                 return False
-        
+
         # Extract appimagetool to avoid FUSE requirement
         print("Extracting appimagetool...")
         try:
             # Extract quietly to avoid verbose output
-            result = subprocess.run([f"./{appimagetool}", "--appimage-extract"], 
-                                  capture_output=True, text=True)
+            result = subprocess.run(
+                [f"./{appimagetool}", "--appimage-extract"],
+                capture_output=True,
+                text=True,
+            )
             if result.returncode != 0 and "squashfs-root" not in result.stdout:
                 print(f"Failed to extract appimagetool: {result.stderr}")
                 return False
@@ -246,13 +255,13 @@ def create_appimage():
         env = os.environ.copy()
         env["ARCH"] = "x86_64"
         appimage_name = f"dist/HBAT-{version}-x86_64.AppImage"
-        
+
         # Check if desktop file exists at root (required by appimagetool)
         desktop_file = appdir / "hbat.desktop"
         if not desktop_file.exists():
             print(f"Error: Desktop file not found at {desktop_file}")
             return False
-            
+
         # Use the extracted AppRun instead of the AppImage
         print(f"Building AppImage with {appimagetool_dir}/AppRun...")
         result = subprocess.run(
@@ -261,12 +270,12 @@ def create_appimage():
             text=True,
             env=env,
         )
-        
+
         if result.returncode != 0:
             print(f"AppImage build failed: {result.stderr}")
             print(f"stdout: {result.stdout}")
             return False
-            
+
         shutil.rmtree(appdir)
         print(f"✓ AppImage created successfully: HBAT-{version}-x86_64.AppImage")
         return True
@@ -278,9 +287,9 @@ def create_appimage():
 def create_deb_package():
     """Create .deb package for Debian/Ubuntu."""
     print("\nCreating .deb package...")
-    
+
     # Get version from environment or use default
-    version = os.environ.get('HBAT_VERSION', '2.0.0')
+    version = os.environ.get("HBAT_VERSION", "2.0.0")
 
     # Create debian package structure
     debdir = Path("hbat-deb")
@@ -349,7 +358,8 @@ def create_deb_package():
     # Build .deb package
     try:
         subprocess.run(
-            ["dpkg-deb", "--build", "hbat-deb", f"dist/hbat_{version}_amd64.deb"], check=True
+            ["dpkg-deb", "--build", "hbat-deb", f"dist/hbat_{version}_amd64.deb"],
+            check=True,
         )
         shutil.rmtree(debdir)
         print(f"✓ .deb package created successfully: hbat_{version}_amd64.deb")
@@ -365,9 +375,9 @@ def main():
     """Main build function."""
     print("HBAT Linux Build Script")
     print("=" * 40)
-    
+
     # Get version from environment or use default
-    version = os.environ.get('HBAT_VERSION', '2.0.0')
+    version = os.environ.get("HBAT_VERSION", "2.0.0")
     print(f"Building version: {version}")
 
     # Check we're in the right directory

docs/source/conf.py

@@ -35,6 +35,7 @@
     'sphinx.ext.githubpages',
     'sphinx_toolbox.shields',
     'sphinx_sitemap',
+    'sphinx_copybutton',
 ]
 
 # Mock imports for modules that might not be available in CI
@@ -56,7 +57,7 @@
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.
-html_theme = 'sphinx_rtd_theme'
+html_theme = 'sphinx_book_theme'
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
@@ -107,6 +108,7 @@
 html_theme_options = {
     'canonical_url': '',
     'analytics_id': '',
+    'google_analytics_id': 'G-PLZNCJY1B7',
     'logo_only': False,
     'prev_next_buttons_location': 'bottom',
     'style_external_links': False,
@@ -116,7 +118,39 @@
     'sticky_navigation': True,
     'navigation_depth': 4,
     'includehidden': True,
-    'titles_only': False
+    'titles_only': False,
+    "repository_url": "https://github.com/abhishektiwari/hbat",
+    "repository_provider": "github",
+    "repository_branch": "main",
+    "path_to_docs": "docs/source",
+    "use_issues_button": True,
+    "use_repository_button": True,
+    "use_edit_page_button": True,
+    "use_download_button": False,
+    "use_fullscreen_button": True,
+    "use_search_button": True,
+    "use_sidenotes": True,
+    "icon_links_label": "Quick Links",
+    "icon_links": [
+        {
+            "name": "GitHub",
+            "url": "https://github.com/abhishektiwari/hbat",
+            "icon": "fa-brands fa-square-github",
+            "type": "fontawesome",
+        },
+        {
+            "name": "Abhishek Tiwari",
+            "url": "https://www.abhishek-tiwari.com",
+            "icon": "https://www.abhishek-tiwari.com/images/logo.svg",
+            "type": "local",
+        },
+        {
+            "name": "PyPI",
+            "url": "https://pypi.org/project/hbat/",
+            "icon": "fa-brands fa-python",
+            "type": "fontawesome",
+        },
+   ]
 }
 
 # The version info for the project you're documenting, acts as replacement for