Release 0.2.0: CI, packaging, docs, and assets

.github/workflows/lint.yml

@@ -23,7 +23,7 @@ jobs:
           python-version: "3.11"
           environment-file: environment.yml
           activate-environment: plotlymol
-          auto-activate: plotlymol
+          auto-activate: false
           miniforge-version: latest
           conda-solver: libmamba
 
@@ -45,7 +45,7 @@ jobs:
           python-version: "3.11"
           environment-file: environment.yml
           activate-environment: plotlymol
-          auto-activate: plotlymol
+          auto-activate: false
           miniforge-version: latest
           conda-solver: libmamba
 

.github/workflows/publish.yml

@@ -0,0 +1,61 @@
+name: Publish to PyPI
+
+on:
+  push:
+    tags:
+      - "v*.*.*"
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Build distribution
+        run: |
+          pip install build
+          python -m build
+
+      - name: Check distribution metadata
+        run: |
+          pip install twine
+          twine check dist/*
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  publish-testpypi:
+    needs: build
+    runs-on: ubuntu-latest
+    environment: testpypi
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+
+  publish-pypi:
+    needs: publish-testpypi
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/security.yml

@@ -27,7 +27,7 @@ jobs:
           python-version: "3.11"
           environment-file: environment.yml
           activate-environment: plotlymol
-          auto-activate: plotlymol
+          auto-activate: false
           miniforge-version: latest
           conda-solver: libmamba
 
@@ -70,7 +70,7 @@ jobs:
           python-version: "3.11"
           environment-file: environment.yml
           activate-environment: plotlymol
-          auto-activate: plotlymol
+          auto-activate: false
           miniforge-version: latest
           conda-solver: libmamba
 

.github/workflows/test.yml

@@ -34,7 +34,7 @@ jobs:
           python-version: ${{ matrix.python-version }}
           environment-file: environment.yml
           activate-environment: plotlymol
-          auto-activate: plotlymol
+          auto-activate: false
           miniforge-version: latest
           conda-solver: libmamba
 
@@ -46,9 +46,9 @@ jobs:
 
       - name: Upload coverage to Codecov
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.11'
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
         with:
-          file: ./coverage.xml
+          files: ./coverage.xml
           flags: unittests
           name: codecov-umbrella
           fail_ci_if_error: false

.pre-commit-config.yaml

@@ -9,6 +9,7 @@ repos:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: check-yaml
+        args: [--unsafe]
       - id: check-added-large-files
       - id: check-merge-conflict
       - id: debug-statements

CHANGELOG.md

@@ -7,33 +7,37 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [0.2.0] - 2026-04-04
+
 ### Added
 - **Vibrational Mode Visualization** - Complete system for visualizing molecular vibrations from quantum chemistry calculations
   - Three file format parsers: Gaussian (.log), ORCA (.out), Molden (.molden) with auto-detection
   - Three visualization modes:
     - Static displacement arrows using Plotly Cone traces
     - Animated vibrations with interactive controls (play/pause, frame slider)
     - Heatmap coloring by displacement magnitude
-  - New `vibrations.py` module (~1000 lines) with comprehensive dataclasses and functions
-  - Streamlit "📊 Vibration Settings" section with file upload and interactive controls
+  - New `vibrations.py` module with comprehensive dataclasses and functions
+  - Streamlit "Vibration Settings" section with file upload and interactive controls
   - 21 new tests achieving ~95% coverage of vibration module
   - Test fixtures for all three file formats (water molecule examples)
 - Exported vibration functions in `__init__.py` for public API access
-- Comprehensive vibration documentation in README with code examples
 - Symbol-to-atomic-number mapping (`symbol_to_number`) in `atomProperties.py`
+- Conda environment (`environment.yml`) replacing venv-based setup
+- Security CI workflow: `pip-audit` dependency scanning + CodeQL static analysis
+- Dependabot configuration for automated dependency updates
+- Branch protection rules (required status checks, no force-push)
+- PyPI publishing checklist (`docs/PYPI_PUBLISHING.md`)
 
 ### Changed
-- Enhanced Streamlit app with vibration file uploader and parameter controls
-- Updated README with vibration visualization examples and available parsers
+
+- Aromatic bond rendering now uses ring-center geometry for correct dashed bond offset direction
+- Displacement arrows auto-scaled relative to molecular size for consistent visibility
+- Animation caching replaced `@st.cache_data` with session-state caching and live progress bar
+- Longer dashes (75% vs 60%) for aromatic bond rendering
+- Updated README installation instructions for conda workflow
 - Expanded test suite from 26 to 47 tests
-- Updated CLAUDE.md with vibration module documentation and architecture details
-
-### Previous Changes
-- Expanded README with badges, features list, quick start, orbital example, and GUI instructions.
-- Added this changelog.
-- Applied Black formatting and Ruff auto-fixes across plotlymol3d and tests.
-- Switched to a src/ layout and moved demos into examples/.
-- Consolidated dev and runtime dependencies into a single requirements.txt.
+- Bumped `requires-python` from `>=3.8` to `>=3.9`
+- Fixed repo URLs in `pyproject.toml` (now correctly point to NCCU-Schultz-Lab org)
 
 ## [0.1.0] - 2026-01-31
 

mkdocs.yml

@@ -37,8 +37,8 @@ theme:
     - content.code.annotate
   icon:
     repo: fontawesome/brands/github
-  logo: assets/logo.png
-  favicon: assets/favicon.png
+  logo: assets/logo.svg
+  favicon: assets/logo.svg
 
 extra_css:
   - stylesheets/extra.css

pyproject.toml

@@ -4,23 +4,23 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "plotlymol"
-version = "0.1.0"
+version = "0.2.0"
 description = "A package to create interactive molecular visualizations using Plotly"
 readme = "README.md"
 authors = [
     {name = "Jonathan Schultz", email = "jonathanschultzNU@users.noreply.github.com"},
     {name = "Benjamin Lear"}
 ]
 license = {text = "MIT"}
-requires-python = ">=3.8"
+requires-python = ">=3.9"
+keywords = ["chemistry", "molecular visualization", "plotly", "rdkit", "3d", "cheminformatics", "quantum chemistry", "vibrational modes"]
 classifiers = [
     "Development Status :: 3 - Alpha",
     "Intended Audience :: Science/Research",
     "Topic :: Scientific/Engineering :: Chemistry",
     "Topic :: Scientific/Engineering :: Visualization",
     "License :: OSI Approved :: MIT License",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
@@ -37,17 +37,21 @@ dependencies = [
 dev = [
     "pytest>=7.0.0",
     "pytest-cov>=4.0.0",
-    "black>=23.0.0",
+    "black>=24.3.0",
     "ruff>=0.1.0",
     "flake8>=6.0.0",
     "mypy>=1.0.0",
     "pre-commit>=3.0.0",
 ]
+gui = [
+    "streamlit>=1.30.0",
+]
 
 [project.urls]
-Homepage = "https://github.com/jonathanschultzNU/plotlyMol"
-Repository = "https://github.com/jonathanschultzNU/plotlyMol"
-Issues = "https://github.com/jonathanschultzNU/plotlyMol/issues"
+Homepage = "https://github.com/NCCU-Schultz-Lab/plotlyMol"
+Repository = "https://github.com/NCCU-Schultz-Lab/plotlyMol"
+Issues = "https://github.com/NCCU-Schultz-Lab/plotlyMol/issues"
+Documentation = "https://nccu-schultz-lab.github.io/plotlyMol"
 
 [tool.setuptools]
 packages = ["plotlymol3d"]

src/plotlymol3d/app.py

@@ -942,7 +942,7 @@ def set_random_smiles():
 
     st.sidebar.markdown("---")
     st.sidebar.caption(
-        "plotlyMol3D v0.1.0 | [GitHub](https://github.com/jonathanschultzNU/plotlyMol)"
+        "plotlyMol3D v0.2.0 | [GitHub](https://github.com/NCCU-Schultz-Lab/plotlyMol)"
     )