beykyle · kylegodbey · Aug 11, 2025 · Aug 11, 2025
diff --git a/.github/workflows/gh-pages.yml b/.github/workflows/gh-pages.yml
@@ -0,0 +1,37 @@
+name: Deploy Docs to GitHub Pages
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install .[docs]
+
+      - name: Build docs
+        run: mkdocs build --site-dir site
+
+      - name: Deploy to GitHub Pages
+        # Uncomment the following line to deploy only from the main branch
+        # if: github.ref == 'refs/heads/main'
+
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./site
diff --git a/SUMMARY.md b/SUMMARY.md
@@ -0,0 +1,7 @@
+* [data](docs/api/jitr/data.md)
+* [optical_potentials](docs/api/jitr/optical_potentials/index.md)
+* [reactions](docs/api/jitr/reactions/index.md)
+* [utils](docs/api/jitr/utils/index.md)
+* [quadrature](docs/api/jitr/quadrature/index.md)
+* [xs](docs/api/jitr/xs/index.md)
+* [rmatrix](docs/api/jitr/rmatrix/index.md)
diff --git a/api/compute/compute.md b/api/compute/compute.md
@@ -0,0 +1,7 @@
+# jitr.compute
+
+::: jitr.compute
+    options:
+      show_root_heading: true
+      show_root_toc_entry: true
+      show_root_full_path: false
diff --git a/api/configuration/config.md b/api/configuration/config.md
@@ -0,0 +1,7 @@
+# jitr.config
+
+::: jitr.config
+    options:
+      show_root_heading: true
+      show_root_toc_entry: true
+      show_root_full_path: false
diff --git a/api/data/data.md b/api/data/data.md
@@ -0,0 +1,7 @@
+# jitr.data
+
+::: jitr.data
+    options:
+      show_root_heading: true
+      show_root_toc_entry: true
+      show_root_full_path: false
diff --git a/api/jitr/data.md b/api/jitr/data.md
@@ -0,0 +1,8 @@
+# `jitr.data`
+
+::: jitr.data
+    options:
+      show_root_heading: true
+      show_root_toc_entry: true
+      show_root_full_path: false
+      heading_level: 2
diff --git a/api/jitr/optical_potentials/index.md b/api/jitr/optical_potentials/index.md
@@ -0,0 +1,9 @@
+# `jitr.optical_potentials`
+
+::: jitr.optical_potentials
+    options:
+      show_root_heading: true
+      show_root_toc_entry: true
+      show_root_full_path: false
+      heading_level: 2
+      show_submodules: true
diff --git a/api/jitr/quadrature/index.md b/api/jitr/quadrature/index.md
@@ -0,0 +1,9 @@
+# `jitr.quadrature`
+
+::: jitr.quadrature
+    options:
+      show_root_heading: true
+      show_root_toc_entry: true
+      show_root_full_path: false
+      heading_level: 2
+      show_submodules: true
diff --git a/api/jitr/reactions/index.md b/api/jitr/reactions/index.md
@@ -0,0 +1,9 @@
+# `jitr.reactions`
+
+::: jitr.reactions
+    options:
+      show_root_heading: true
+      show_root_toc_entry: true
+      show_root_full_path: false
+      heading_level: 2
+      show_submodules: true
diff --git a/api/jitr/rmatrix/index.md b/api/jitr/rmatrix/index.md
@@ -0,0 +1,9 @@
+# `jitr.rmatrix`
+
+::: jitr.rmatrix
+    options:
+      show_root_heading: true
+      show_root_toc_entry: true
+      show_root_full_path: false
+      heading_level: 2
+      show_submodules: true
diff --git a/api/jitr/utils/index.md b/api/jitr/utils/index.md
@@ -0,0 +1,9 @@
+# `jitr.utils`
+
+::: jitr.utils
+    options:
+      show_root_heading: true
+      show_root_toc_entry: true
+      show_root_full_path: false
+      heading_level: 2
+      show_submodules: true
diff --git a/api/jitr/xs/index.md b/api/jitr/xs/index.md
@@ -0,0 +1,9 @@
+# `jitr.xs`
+
+::: jitr.xs
+    options:
+      show_root_heading: true
+      show_root_toc_entry: true
+      show_root_full_path: false
+      heading_level: 2
+      show_submodules: true
diff --git a/api/reaction/elastic.md b/api/reaction/elastic.md
@@ -0,0 +1,7 @@
+# jitr.xs.elastic
+
+::: jitr.xs.elastic
+    options:
+      show_root_heading: true
+      show_root_toc_entry: true
+      show_root_full_path: false
diff --git a/api/reaction/quasielastic_pn.md b/api/reaction/quasielastic_pn.md
@@ -0,0 +1,7 @@
+# jitr.xs.quasielastic_pn
+
+::: jitr.xs.quasielastic_pn
+    options:
+      show_root_heading: true
+      show_root_toc_entry: true
+      show_root_full_path: false
diff --git a/api/visualization/visualize.md b/api/visualization/visualize.md
@@ -0,0 +1,7 @@
+# jitr.visualize
+
+::: jitr.visualize
+    options:
+      show_root_heading: true
+      show_root_toc_entry: true
+      show_root_full_path: false
diff --git a/docs/api/jitr/data.md b/docs/api/jitr/data.md
@@ -0,0 +1,8 @@
+# `jitr.data`
+
+::: jitr.data
+    options:
+      show_root_heading: true
+      show_root_toc_entry: true
+      show_root_full_path: false
+      heading_level: 2
diff --git a/docs/api/jitr/optical_potentials/index.md b/docs/api/jitr/optical_potentials/index.md
@@ -0,0 +1,9 @@
+# `jitr.optical_potentials`
+
+::: jitr.optical_potentials
+    options:
+      show_root_heading: true
+      show_root_toc_entry: true
+      show_root_full_path: false
+      heading_level: 2
+      show_submodules: true
diff --git a/docs/api/jitr/quadrature/index.md b/docs/api/jitr/quadrature/index.md
@@ -0,0 +1,9 @@
+# `jitr.quadrature`
+
+::: jitr.quadrature
+    options:
+      show_root_heading: true
+      show_root_toc_entry: true
+      show_root_full_path: false
+      heading_level: 2
+      show_submodules: true
diff --git a/docs/api/jitr/reactions/index.md b/docs/api/jitr/reactions/index.md
@@ -0,0 +1,9 @@
+# `jitr.reactions`
+
+::: jitr.reactions
+    options:
+      show_root_heading: true
+      show_root_toc_entry: true
+      show_root_full_path: false
+      heading_level: 2
+      show_submodules: true
diff --git a/docs/api/jitr/rmatrix/index.md b/docs/api/jitr/rmatrix/index.md
@@ -0,0 +1,9 @@
+# `jitr.rmatrix`
+
+::: jitr.rmatrix
+    options:
+      show_root_heading: true
+      show_root_toc_entry: true
+      show_root_full_path: false
+      heading_level: 2
+      show_submodules: true
diff --git a/docs/api/jitr/utils/index.md b/docs/api/jitr/utils/index.md
@@ -0,0 +1,9 @@
+# `jitr.utils`
+
+::: jitr.utils
+    options:
+      show_root_heading: true
+      show_root_toc_entry: true
+      show_root_full_path: false
+      heading_level: 2
+      show_submodules: true
diff --git a/docs/api/jitr/xs/index.md b/docs/api/jitr/xs/index.md
@@ -0,0 +1,9 @@
+# `jitr.xs`
+
+::: jitr.xs
+    options:
+      show_root_heading: true
+      show_root_toc_entry: true
+      show_root_full_path: false
+      heading_level: 2
+      show_submodules: true
diff --git a/docs/api/reaction.md b/docs/api/reaction.md
@@ -0,0 +1,15 @@
+# Reaction Modules
+
+## `jitr.xs.elastic`
+::: jitr.xs.elastic
+    options:
+      show_root_heading: true
+      show_root_toc_entry: true
+      show_root_full_path: false
+
+## `jitr.xs.quasielastic_pn`
+::: jitr.xs.quasielastic_pn
+    options:
+      show_root_heading: true
+      show_root_toc_entry: true
+      show_root_full_path: false
diff --git a/docs/assets/jitr_logo.png b/docs/assets/jitr_logo.png
diff --git a/docs/contributing.md b/docs/contributing.md
@@ -0,0 +1,38 @@
+# Contributing to jitr
+
+We welcome contributions! Here's how to get started:
+
+## Development Setup
+
+1. Clone the repository:
+```bash
+git clone git@github.com:beykyle/jitr.git
+```
+
+2. Install dependencies:
+```bash
+pip install -r requirements.txt
+```
+
+3. Install jitr in editable mode:
+```bash
+pip install -e .
+```
+
+## Running Tests
+
+Execute the test suite with:
+```bash
+pytest jitr
+```
+
+## Contribution Guidelines
+
+- Fork the repository and create a new branch for your feature or fix
+- Add tests for any new functionality
+- Ensure all tests pass and code meets quality standards
+- Submit a pull request with a clear description of changes
+
+## Report Issues
+
+Open an issue on GitHub if you encounter any problems or have suggestions.
diff --git a/docs/examples/index.md b/docs/examples/index.md
@@ -0,0 +1,21 @@
+# Examples & Tutorials
+
+Explore practical implementations of jitr through these interactive notebooks:
+
+| Notebook | Description | Key Topics |
+|----------|-------------|------------|
+| [Built-in OMPs UQ](notebooks/builtin_omps_uq.ipynb) | Uncertainty quantification for optical model potentials | OMP parameters, uncertainty propagation, sensitivity analysis |
+| [Reaction Modeling](notebooks/reaction.ipynb) | Modeling nuclear reactions with R-matrix formalism | Cross section calculation, resonance analysis, channel coupling |
+| [How to Define Your Interaction](notebooks/how_to_define_your_interaction.ipynb) | Creating custom nuclear potentials | Potential definition, parameterization, validation |
+| [Mass Exploration](notebooks/mass_exploration.ipynb) | Exploring nuclear mass models | Mass tables, systematics, model comparison |
+| [Validation Studies](notebooks/chex_jitr_validation.ipynb) | Validating jitr against experimental data | Data comparison, uncertainty analysis, model accuracy |
+| [Comparison to Runge Kutta](notebooks/Comparison_to_Runge_Kutta.ipynb) | Numerical method comparisons | Solver accuracy, performance benchmarking |
+| [Integration Techniques](notebooks/integration.ipynb) | Advanced integration methods | Numerical integration, mesh optimization |
+
+## Running Examples Locally
+1. Install jitr: `pip install jitr`
+2. Launch Jupyter: `jupyter notebook`
+3. Navigate to `examples/notebooks/`
+4. Open and run any notebook
+
+> Note: Some notebooks may require additional data files from the `data/` directory
diff --git a/...notebooks/Comparison_to_Runge_Kutta.ipynb → ...notebooks/Comparison_to_Runge_Kutta.ipynb b/...notebooks/Comparison_to_Runge_Kutta.ipynb → ...notebooks/Comparison_to_Runge_Kutta.ipynb
diff --git a/examples/notebooks/builtin_omps_uq.ipynb → .../examples/notebooks/builtin_omps_uq.ipynb b/examples/notebooks/builtin_omps_uq.ipynb → .../examples/notebooks/builtin_omps_uq.ipynb
diff --git a/...ples/notebooks/chex_jitr_validation.ipynb → ...ples/notebooks/chex_jitr_validation.ipynb b/...ples/notebooks/chex_jitr_validation.ipynb → ...ples/notebooks/chex_jitr_validation.ipynb
diff --git a/examples/notebooks/chex_qepn_xs.txt → docs/examples/notebooks/chex_qepn_xs.txt b/examples/notebooks/chex_qepn_xs.txt → docs/examples/notebooks/chex_qepn_xs.txt
diff --git a/examples/notebooks/chuq_kduq_comp.ipynb → docs/examples/notebooks/chuq_kduq_comp.ipynb b/examples/notebooks/chuq_kduq_comp.ipynb → docs/examples/notebooks/chuq_kduq_comp.ipynb
diff --git a/...ooks/how_to_define_your_interaction.ipynb → ...ooks/how_to_define_your_interaction.ipynb b/...ooks/how_to_define_your_interaction.ipynb → ...ooks/how_to_define_your_interaction.ipynb
diff --git a/examples/notebooks/integration.ipynb → docs/examples/notebooks/integration.ipynb b/examples/notebooks/integration.ipynb → docs/examples/notebooks/integration.ipynb
diff --git a/examples/notebooks/jitr_logo.ipynb → docs/examples/notebooks/jitr_logo.ipynb b/examples/notebooks/jitr_logo.ipynb → docs/examples/notebooks/jitr_logo.ipynb
diff --git a/examples/notebooks/jitr_logo.png → docs/examples/notebooks/jitr_logo.png b/examples/notebooks/jitr_logo.png → docs/examples/notebooks/jitr_logo.png
diff --git a/examples/notebooks/mass_exploration.ipynb → ...examples/notebooks/mass_exploration.ipynb b/examples/notebooks/mass_exploration.ipynb → ...examples/notebooks/mass_exploration.ipynb
diff --git a/examples/notebooks/reaction.ipynb → docs/examples/notebooks/reaction.ipynb b/examples/notebooks/reaction.ipynb → docs/examples/notebooks/reaction.ipynb
diff --git a/...tebooks/rose_vs_jitr_validation_nPb.ipynb → ...tebooks/rose_vs_jitr_validation_nPb.ipynb b/...tebooks/rose_vs_jitr_validation_nPb.ipynb → ...tebooks/rose_vs_jitr_validation_nPb.ipynb
diff --git a/...tebooks/rose_vs_jitr_validation_pCa.ipynb → ...tebooks/rose_vs_jitr_validation_pCa.ipynb b/...tebooks/rose_vs_jitr_validation_pCa.ipynb → ...tebooks/rose_vs_jitr_validation_pCa.ipynb
diff --git a/examples/notebooks/solver.pkl → docs/examples/notebooks/solver.pkl b/examples/notebooks/solver.pkl → docs/examples/notebooks/solver.pkl
diff --git a/.../notebooks/test_coupled_single_dwba.ipynb → .../notebooks/test_coupled_single_dwba.ipynb b/.../notebooks/test_coupled_single_dwba.ipynb → .../notebooks/test_coupled_single_dwba.ipynb
diff --git a/examples/notebooks/test_wavefunction.ipynb → ...xamples/notebooks/test_wavefunction.ipynb b/examples/notebooks/test_wavefunction.ipynb → ...xamples/notebooks/test_wavefunction.ipynb
diff --git a/docs/gen_api_docs.py b/docs/gen_api_docs.py
@@ -0,0 +1,56 @@
+import os
+import mkdocs_gen_files
+from pathlib import Path
+
+nav = mkdocs_gen_files.Nav()
+
+# Base package name
+package = "jitr"
+
+# Get all Python modules and subpackages
+src_path = Path("src") / package
+modules = []
+subpackages = []
+
+for item in src_path.iterdir():
+    if item.is_file() and item.suffix == ".py" and not item.name.startswith("__"):
+        modules.append(f"{package}.{item.stem}")
+    elif item.is_dir() and not item.name.startswith("__"):
+        subpackages.append(f"{package}.{item.name}")
+
+# Generate API documentation for modules
+for module in modules:
+    doc_path = f"docs/api/{module.replace('.', '/')}.md"
+    os.makedirs(os.path.dirname(doc_path), exist_ok=True)
+    with open(doc_path, "w") as f:
+        f.write(f"# `{module}`\n\n")
+        f.write(f"::: {module}\n")
+        f.write("    options:\n")
+        f.write("      show_root_heading: true\n")
+        f.write("      show_root_toc_entry: true\n")
+        f.write("      show_root_full_path: false\n")
+        f.write("      heading_level: 2\n")
+
+    nav[module.split(".")[-1]] = doc_path
+
+# Generate API documentation for subpackages
+for subpackage in subpackages:
+    doc_path = f"docs/api/{subpackage.replace('.', '/')}/index.md"
+    os.makedirs(os.path.dirname(doc_path), exist_ok=True)
+    with open(doc_path, "w") as f:
+        f.write(f"# `{subpackage}`\n\n")
+        f.write(f"::: {subpackage}\n")
+        f.write("    options:\n")
+        f.write("      show_root_heading: true\n")
+        f.write("      show_root_toc_entry: true\n")
+        f.write("      show_root_full_path: false\n")
+        f.write("      heading_level: 2\n")
+        f.write("      show_submodules: true\n")
+
+    nav[subpackage.split(".")[-1]] = doc_path
+
+# Write navigation file
+with open("SUMMARY.md", "w") as nav_file:
+    nav_file.writelines(nav.build_literate_nav())
+
+print("API documentation generated successfully!")