The-Schultz-Lab · NCCU-Schultz-Lab · Apr 18, 2026 · Apr 18, 2026
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,10 +7,23 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [0.2.1] - 2026-04-18
+
 ### Changed
 - GUI migrated from Streamlit to Dash — launch with `python examples/gui_app.py`
 - `gui` optional dependency updated: `dash>=2.14.0` + `dash-bootstrap-components>=1.5.0` (replaces `streamlit`)
 - `launch_app.bat` and `stop_app.bat` updated for Dash process management
+- Bumped `black` minimum from `>=23.0.0` to `>=24.3.0` in `requirements.txt`
+
+### Fixed
+- Removed stale `streamlit` dependency from `requirements.txt` and `environment.yml`
+- Corrected all remaining Streamlit references in docs to Dash (`about.md`, `installation.md`, `contributing.md`, `tutorials/index.md`)
+- Updated version number from 0.1.0 to 0.2.0 in `docs/about.md` (including BibTeX citation)
+- Fixed Python minimum version in `docs/installation.md` (3.8 → 3.9)
+- Updated author contact email to `The-Schultz-Lab@users.noreply.github.com` in `docs/about.md`
+- Replaced broken `docs/ROADMAP.md` and `docs/PERFORMANCE_TESTING_GUIDE.md` links in `README.md` and `docs/contributing.md`
+- Updated stale Streamlit cache reference in `tests/test_performance.py`
+- Fixed logo not rendering on PyPI by replacing relative `logo.svg` path with absolute raw GitHub URL
 
 ## [0.2.0] - 2026-04-04
 

diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
 # plotlyMol
 
 <p align="center">
-  <img src="logo.svg" alt="plotlyMol Logo" width="300"/>
+  <img src="https://raw.githubusercontent.com/The-Schultz-Lab/plotlyMol/main/logo.svg" alt="plotlyMol Logo" width="300"/>
 </p>
 
 [![Tests](https://github.com/The-Schultz-Lab/plotlyMol/actions/workflows/test.yml/badge.svg)](https://github.com/The-Schultz-Lab/plotlyMol/actions/workflows/test.yml)
@@ -20,11 +20,15 @@ Interactive molecular visualizations with Plotly. Supports SMILES, XYZ, MOL/PDB,
   - Static displacement arrows
   - Animated vibrations with interactive controls
   - Heatmap coloring by displacement magnitude
-- Streamlit GUI for interactive exploration
+- Dash GUI for interactive exploration
 
 ## Installation
 
-### From source (recommended for now)
+```bash
+pip install plotlymol
+```
+
+### From source (for development)
 
 ```bash
 git clone https://github.com/The-Schultz-Lab/plotlyMol.git
@@ -68,13 +72,13 @@ fig.show()
 from plotlymol3d import draw_3D_rep
 
 fig = draw_3D_rep(
-	cubefile="path/to/file.cube",
-	molfile="path/to/file.mol",
-	mode="ball+stick",
-	ambient=0.1,
-	cubedraw="orbitals",
-	orbital_opacity=0.25,
-	orbital_colors=["darkorange", "darkblue"],
+    cubefile="path/to/file.cube",
+    molfile="path/to/file.mol",
+    mode="ball+stick",
+    ambient=0.1,
+    cubedraw="orbitals",
+    orbital_opacity=0.25,
+    orbital_colors=["darkorange", "darkblue"],
 )
 fig.show()
 ```
@@ -167,10 +171,10 @@ for mode in vib_data.modes:
 
 ## GUI
 
-Launch the Streamlit app for interactive controls:
+Launch the Dash app for interactive controls:
 
 ```bash
-streamlit run examples/gui_app.py
+python examples/gui_app.py
 ```
 
 ## Examples
@@ -213,7 +217,7 @@ python tests/test_performance.py
 jupyter notebook examples/performance_benchmarking.ipynb
 ```
 
-**Full guide:** [Performance Testing Guide](docs/PERFORMANCE_TESTING_GUIDE.md)
+**Full guide:** `docs/PERFORMANCE_TESTING_GUIDE.md` (coming soon)
 
 **Key metrics tracked:**
 
@@ -227,7 +231,7 @@ Use these tools to identify bottlenecks and optimize GUI responsiveness.
 
 ## Repository layout
 
-```
+```text
 plotlyMol/
 ├─ src/
 │  └─ plotlymol3d/        # Library package code + sample data files
@@ -241,4 +245,4 @@ plotlyMol/
 
 ## Roadmap
 
-See the current roadmap in [docs/ROADMAP.md](docs/ROADMAP.md).
+See [GitHub Issues](https://github.com/The-Schultz-Lab/plotlyMol/issues) for planned features and upcoming work.
diff --git a/docs/about.md b/docs/about.md
@@ -9,7 +9,7 @@ plotlyMol is an open-source Python package for creating interactive 3D molecular
 **Jonathan Schultz**
 North Carolina Central University, Assistant Professor of Chemistry
 
-**Benjamin Lear**
+**[Benjamin Lear](https://github.com/ProfLear)**
 (The Pennsylvania State University, Professor of Chemistry)
 
 ## Motivation
@@ -51,7 +51,7 @@ plotlyMol is built on industry-standard scientific Python libraries:
 
 ### Optional Components
 
-- **[Streamlit](https://streamlit.io/)** - Web app framework for GUI
+- **[Dash](https://dash.plotly.com/)** - Web app framework for GUI
 - **[Kaleido](https://github.com/plotly/Kaleido)** - Static image export
 - **pytest** - Testing framework
 - **black/ruff** - Code quality tools
@@ -61,6 +61,7 @@ plotlyMol is built on industry-standard scientific Python libraries:
 ### Simplicity
 
 Simple things should be simple:
+
 ```python
 from plotlymol3d import draw_3D_rep
 fig = draw_3D_rep(smiles="CCO")
@@ -70,6 +71,7 @@ fig.show()
 ### Flexibility
 
 Complex things should be possible:
+
 ```python
 fig = draw_3D_rep(
     cubefile="orbital.cube",
@@ -139,7 +141,7 @@ Initial development by Prof. Lear focused on creating a modern molecular visuali
 
 ## Project Status
 
-**Current Version**: 0.1.0 (Development)
+**Current Version**: 0.2.0 (Development)
 
 **Status**: Pre-release
 
@@ -194,7 +196,7 @@ Thanks to the developers of:
 
 plotlyMol is released under the [MIT License](https://github.com/The-Schultz-Lab/plotlyMol/blob/main/LICENSE).
 
-```
+```text
 MIT License
 
 Copyright (c) 2026 Jonathan Schultz & Benjamin Lear
@@ -214,7 +216,6 @@ copies or substantial portions of the Software.
 
 - **GitHub Issues**: [Report issues or request features](https://github.com/The-Schultz-Lab/plotlyMol/issues)
 - **GitHub Discussions**: [Ask questions or share ideas](https://github.com/The-Schultz-Lab/plotlyMol/discussions)
-- **Email**: jonathanschultzNU@users.noreply.github.com
 
 ## Citation
 
@@ -226,7 +227,7 @@ If you use plotlyMol in your research, please cite:
   author = {Schultz, Jonathan and Lear, Benjamin},
   year = {2026},
   url = {https://github.com/The-Schultz-Lab/plotlyMol},
-  note = {Version 0.1.0}
+  note = {Version 0.2.0}
 }
 ```
 

diff --git a/docs/contributing.md b/docs/contributing.md
@@ -4,7 +4,7 @@ Thank you for your interest in contributing to plotlyMol! This guide will help y
 
 ## Ways to Contribute
 
-###  Report Bugs
+### Report Bugs
 
 Found a bug? Please [open an issue](https://github.com/The-Schultz-Lab/plotlyMol/issues/new) with:
 
@@ -14,15 +14,15 @@ Found a bug? Please [open an issue](https://github.com/The-Schultz-Lab/plotlyMol
 - System information (OS, Python version)
 - Minimal code example
 
-###  Suggest Features
+### Suggest Features
 
 Have an idea? We'd love to hear it! [Open an issue](https://github.com/The-Schultz-Lab/plotlyMol/issues/new) describing:
 
 - The feature and its use case
 - Why it would be valuable
 - Possible implementation approach (optional)
 
-###  Improve Documentation
+### Improve Documentation
 
 Documentation improvements are always welcome:
 
@@ -31,7 +31,7 @@ Documentation improvements are always welcome:
 - Improve API documentation
 - Translate documentation (future)
 
-###  Submit Code
+### Submit Code
 
 Ready to code? Great! Follow the guidelines below.
 
@@ -213,11 +213,13 @@ pre-commit run --all-files
 All pull requests must pass CI checks:
 
 #### Test Workflow
+
 - Runs on Ubuntu, macOS, Windows
 - Tests Python 3.9, 3.10, 3.11, 3.12
 - Runs full test suite with coverage
 
 #### Lint Workflow
+
 - Black formatting check
 - Ruff linting
 - Mypy type checking
@@ -297,6 +299,7 @@ Your PR should:
 To add support for a new file format:
 
 1. Add parser function in `plotlyMol3D.py`:
+
    ```python
    def newformat_to_rdkitmol(filepath: str) -> Chem.Mol:
        """Parse new format file to RDKit Mol."""
@@ -320,10 +323,10 @@ To add new visualization features:
 
 #### 3. GUI Features
 
-To enhance the Streamlit GUI:
+To enhance the Dash GUI:
 
 1. Modify `src/plotlymol3d/app.py`
-2. Test manually with `streamlit run`
+2. Test manually with `python examples/gui_app.py`
 3. Update user guide
 
 ## Documentation
@@ -397,7 +400,7 @@ We use [Semantic Versioning](https://semver.org/):
 
 ## Development Roadmap
 
-See [ROADMAP.md](roadmap.md) for planned features and improvements.
+See [GitHub Issues](https://github.com/The-Schultz-Lab/plotlyMol/issues) for planned features and improvements.
 
 ## Recognition
 

diff --git a/docs/installation.md b/docs/installation.md
@@ -2,7 +2,7 @@
 
 ## Requirements
 
-plotlyMol requires **Python 3.8 or higher**.
+plotlyMol requires **Python 3.9 or higher**.
 
 ## Install from Source
 
@@ -50,7 +50,7 @@ This includes:
 - **black** - Code formatting
 - **ruff** - Fast linting
 - **mypy** - Type checking
-- **streamlit** - GUI application
+- **dash** + **dash-bootstrap-components** - GUI application
 
 ## Verify Installation
 

diff --git a/docs/tutorials/index.md b/docs/tutorials/index.md
@@ -87,7 +87,7 @@ Comprehensive tutorials are currently in development! Check back soon for:
     - Embedding visualizations
     - Building web apps
     - API integration
-    - Streamlit deployment
+    - Dash deployment
 
 ## Jupyter Notebooks
 

diff --git a/environment.yml b/environment.yml
@@ -11,7 +11,8 @@ dependencies:
   - numpy>=1.20.0
 
   # GUI
-  - streamlit>=1.30.0
+  - dash>=2.14.0
+  - dash-bootstrap-components>=1.5.0
 
   # Testing
   - pytest>=7.0.0

diff --git a/pyproject.toml b/pyproject.toml
@@ -4,11 +4,11 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "plotlymol"
-version = "0.2.0"
+version = "0.2.1"
 description = "A package to create interactive molecular visualizations using Plotly"
 readme = "README.md"
 authors = [
-    {name = "Jonathan Schultz", email = "jonathanschultzNU@users.noreply.github.com"},
+    {name = "Jonathan Schultz"},
     {name = "Benjamin Lear"}
 ]
 license = {text = "MIT"}
@@ -154,7 +154,7 @@ ignore = [
 ]
 
 [tool.ruff.lint.per-file-ignores]
-"tests/*" = ["ARG", "S101"]
+"tests/*" = ["ARG", "S101", "E402"]
 "src/plotlymol3d/__init__.py" = ["F403"]
 "src/plotlymol3d/test.py" = ["ALL"]
 "src/plotlymol3d/Cube_to_Blender*" = ["ALL"]

diff --git a/requirements.txt b/requirements.txt
@@ -9,7 +9,7 @@ pytest>=7.0.0
 pytest-cov>=4.0.0
 
 # Linting and Formatting
-black>=23.0.0
+black>=24.3.0
 ruff>=0.1.0
 flake8>=6.0.0
 
@@ -19,8 +19,9 @@ mypy>=1.0.0
 # Optional: Pre-commit hooks
 pre-commit>=3.0.0
 
-# GUI for visual testing
-streamlit>=1.30.0
+# GUI
+dash>=2.14.0
+dash-bootstrap-components>=1.5.0
 
 # Documentation
 mkdocs>=1.5.0

diff --git a/tests/test_performance.py b/tests/test_performance.py
@@ -515,10 +515,10 @@ def analyze_performance_results(results: dict[str, pd.DataFrame]):
 
     # General recommendations
     print("\n6. GENERAL RECOMMENDATIONS:")
-    print("   For GUI/Streamlit Performance:")
+    print("   For GUI/Dash Performance:")
     print("   • Use resolution=16 for interactive preview (2-3x faster)")
     print("   • Switch to resolution=32 for final figures")
-    print("   • Cache parsed vibration files with @st.cache_resource")
+    print("   • Cache parsed vibration files using session state")
     print("   • Use 'stick' mode for molecules >50 atoms")
     print("   • Limit animations to 20-30 frames during development")
     print("   • Consider 'vdw' mode for very large systems (>100 atoms)")