Merge pull request #4 from NsquaredLab/dev_add-spindle

Improve everything

Author: RaulSimpetru

.github/workflows/sphinx.yml

@@ -14,7 +14,7 @@ jobs:
     - name: Set up Python 3.12
       uses: actions/setup-python@v4
       with:
-        python-version: 3.12.7
+        python-version: 3.12.8
 
     - name: Install dependencies
       run: |
@@ -25,15 +25,15 @@ jobs:
         python -m pip install --upgrade pip
         python -m pip install uv
         uv sync --group docs
+        uv run poe setup_myogen
 
     - name: Build the docs
       run: |
         source .venv/bin/activate
-        python -c "from myogen.utils import setup_myogen; setup_myogen()"
-        python -c "import myogen.simulator"
         cd docs
         make clean
         make html
+        make html
         cd ..
 
     - name: Deploy

.gitignore

@@ -74,6 +74,8 @@ docs/_build/
 docs/source/auto_examples/
 docs/source/generated/
 docs/source/sg_execution_times.rst
+docs/source/index.md  # Auto-generated from root README.md
+docs/source/index.rst.backup  # Backup of original index.rst
 
 # PyBuilder
 .pybuilder/
@@ -170,3 +172,15 @@ examples/results/
 results/
 test_*.png
 *.code-workspace
+
+myogen/simulator/neuron/_cython/*.c
+myogen/simulator/nmodl_files/x86_64/
+myogen/simulator/x86_64/
+myogen/simulator/nmodl_files/*.c
+myogen/simulator/nmodl_files/*.o
+myogen/simulator/nmodl_files/*.dll
+
+data/
+# Note: examples/data/ is NOT ignored - it contains pre-generated static data for docs
+examples/finetune/experimental_results/
+sandbox/

.python-version

@@ -1 +1 @@
-3.12
+3.12

.vscode/extensions.json

@@ -0,0 +1,6 @@
+{
+    "recommendations": [
+        "imatlopez.vscode-neuron",
+        "vincent-templier.vscode-netron"
+    ]
+}

.vscode/settings.json

@@ -17,11 +17,11 @@
     "python.analysis.autoImportCompletions": true,
     "editor.fontSize": 16,
     "editor.fontLigatures": true,
-    "svg.preview.background": "dark-transparent",
-    "cursorpyright.analysis.autoImportCompletions": true,
-    "cursorpyright.analysis.extraPaths": [
-        "${workspaceFolder}",
-        "C:/nrn/lib/python"
-    ],
-    "cursorpyright.analysis.typeCheckingMode": "basic"
+    
+    "editor.formatOnSave": true,
+    "editor.defaultFormatter": "charliermarsh.ruff",
+    "markdown.validate.enabled": true,
+    "[markdown]": {
+        "editor.defaultFormatter": "DavidAnson.vscode-markdownlint"
+    },
 }

CHANGELOG.md

@@ -13,7 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - **Type System Enhancement**: New `RECRUITMENT_THRESHOLDS__ARRAY` custom type alias for 1D recruitment threshold arrays with runtime validation via Beartype
 - **Development Guidelines**: Comprehensive `CLAUDE.md` with development protocols:
   - Git workflow with logical commit chunking and co-authorship requirements
-  - Example development guidelines with plt.xkcd() usage and Sphinx Gallery format
+  - Example development guidelines with professional plotting styles and Sphinx Gallery format
   - API testing requirements and font warning suppression protocols
   - CHANGELOG.md update requirements for all changes
 - **Naming Standards**: Enhanced CLAUDE.md with comprehensive naming conventions: