MagnetDB · Trophime · Mar 20, 2026 · Mar 20, 2026 · Mar 20, 2026 · Mar 20, 2026
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -0,0 +1,51 @@
+name: Build and Deploy Docs
+
+on:
+  push:
+    branches: [ main ]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: pages
+  cancel-in-progress: false
+
+jobs:
+  build:
+    runs-on: ubuntu-24.04
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[docs]"
+
+      - name: Build docs
+        run: sphinx-build -W -b html docs docs/_build/html
+
+      - name: Upload pages artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: docs/_build/html
+
+  deploy:
+    needs: build
+    runs-on: ubuntu-24.04
+    environment:
+      name: github-pages
+      url: ${{ steps.deploy.outputs.page_url }}
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deploy
+        uses: actions/deploy-pages@v4
diff --git a/.gitignore b/.gitignore
@@ -140,3 +140,5 @@ ENV/
 # images
 *.png
 
+
+.envrc
diff --git a/.travis.yml b/.travis.yml
diff --git a/BREAKING_CHANGES.md b/BREAKING_CHANGES.md
@@ -1,12 +1,15 @@
-# API Breaking Changes - python_magnetgeo v1.0.0
+# API Breaking Changes - python_magnetgeo
 
 ## Overview
 
-This document details all API breaking changes introduced in version 1.0.0 compared to previous versions (0.3.x - 0.7.x). **No backward compatibility is provided.**
+This document details all API breaking changes introduced across versions. **No backward compatibility is provided.**
 
 ## Version History Summary
 
-### v1.0.0 (Current) - Major Architectural Overhaul
+### v1.0.1 (Current)
+- **`Chamfer` constructor**: parameter `l` renamed to `length` (see [v1.0.0 → v1.0.1](#v100--v101))
+
+### v1.0.0 - Major Architectural Overhaul
 - Complete rewrite with base class architecture
 - Enhanced type safety and validation system
 - **New Profile class** for bump profile management
@@ -41,6 +44,68 @@ This document details all API breaking changes introduced in version 1.0.0 compa
 
 ---
 
+## v1.0.0 → v1.0.1
+
+### Chamfer: parameter `l` renamed to `length`
+
+The `l` parameter of `Chamfer.__init__` was renamed to `length` to resolve the
+E741 linting error (ambiguous variable name).
+
+**Old:**
+```python
+Chamfer(name, side, rside, alpha=None, dr=None, l=None)
+```
+
+**New:**
+```python
+Chamfer(name, side, rside, alpha=None, dr=None, length=None)
+```
+
+**Migration — update any call that passes `l` as a keyword argument:**
+```python
+# Before
+chamfer = Chamfer("c1", "HP", "rext", alpha=45.0, l=10.0)
+
+# After
+chamfer = Chamfer("c1", "HP", "rext", alpha=45.0, length=10.0)
+```
+
+Positional calls (`Chamfer("c1", "HP", "rext", 45.0, None, 10.0)`) are
+unaffected. The YAML/JSON serialization key also changes from `"l"` to `"length"`.
+
+**YAML migration:**
+```yaml
+# Before
+!<Chamfer>
+name: c1
+side: HP
+rside: rext
+alpha: 45.0
+l: 10.0
+
+# After
+!<Chamfer>
+name: c1
+side: HP
+rside: rext
+alpha: 45.0
+length: 10.0
+```
+
+A helper script is provided to automate the YAML migration:
+
+```bash
+# Preview (no files written)
+python examples/migrate_chamfer_l_to_length.py --dry-run path/to/yaml/dir/
+
+# Apply
+python examples/migrate_chamfer_l_to_length.py path/to/yaml/dir/
+```
+
+---
+
+## v1.0.0 Breaking Changes
+
 ## 1. YAML Format Changes
 
 ### Evolution Across Versions
@@ -153,11 +218,10 @@ name: "HL-31_H1"
 axi:
   name: "HL-31.d"
   h: 86.51
-  turns: [2, 16, 2]
-  pitch: [...]
+  ...
 m3d:
-  cad: "HL-31_3D"
   ...
+shape:
 ```
 
 **New Format (v1.0.0):**
@@ -167,13 +231,25 @@ name: "HL-31_H1"
 modelaxi: !<ModelAxi>
   name: "HL-31.d"
   h: 86.51
-  turns: [2, 16, 2]
-  pitch: [...]
 model3d: !<Model3D>
-  cad: "HL-31_3D"
-  ...
+    ...
+shape: !<Shape>
+    ...
+
 ```
 
+#### Complete Field Name Migration History
+
+| Field (v0.5.x) | Field (v0.7.0) | Field (v1.0.0) | Status in v1.0.0 |
+|----------------|----------------|----------------|------------------|
+| `axi` | `modelaxi` | `modelaxi` | ✓ Required |
+| `m3d` | `model3d` | `model3d` | ✓ Required |
+| `shape` | `shape` | `shape` | ✓ Required |
+
+**Migration Notes:**
+- **v0.5.x → v0.7.0**: Rename field names
+- **v0.7.0 → v1.0.0**: Use nested objects with explicit type annotations
+
 **Breaking Changes:**
 - Nested objects require explicit type annotations
 - Helix field `axi` renamed to `modelaxi`

diff --git a/Makefile b/Makefile
@@ -63,15 +63,12 @@ coverage: ## check code coverage quickly with the default Python
 	$(BROWSER) htmlcov/index.html
 
 docs: ## generate Sphinx HTML documentation, including API docs
-	rm -f docs/python_magnetgeo.rst
-	rm -f docs/modules.rst
-	sphinx-apidoc -o docs/ python_magnetgeo
 	$(MAKE) -C docs clean
 	SPHINX_BUILD=1 $(MAKE) -C docs html
 	$(BROWSER) docs/_build/html/index.html
 
 servedocs: docs ## compile the docs watching for changes
-	watchmedo shell-command -p '*.rst' -c '$(MAKE) -C docs html' -R -D .
+	watchmedo shell-command -p '*.md' -c '$(MAKE) -C docs html' -R -D .
 
 release: dist ## package and upload a release
 	twine upload dist/*

diff --git a/README.md b/README.md
@@ -1,9 +1,8 @@
 # Python Magnet Geometry
 
 <!-- [![PyPI version](https://img.shields.io/pypi/v/python_magnetgeo.svg)](https://pypi.python.org/pypi/python_magnetgeo)
-[![Build Status](https://img.shields.io/travis/Trophime/python_magnetgeo.svg)](https://travis-ci.com/Trophime/python_magnetgeo)
 [![Documentation Status](https://readthedocs.org/projects/python-magnetgeo/badge/?version=latest)](https://python-magnetgeo.readthedocs.io/en/latest/?version=latest)
-[![Updates](https://pyup.io/repos/github/Trophime/python_magnetgeo/shield.svg)](https://pyup.io/repos/github/Trophime/python_magnetgeo/)
+[![Updates](https://pyup.io/repos/github/MagnetDB/python_magnetgeo/shield.svg)](https://pyup.io/repos/github/MagnetDB/python_magnetgeo/)
  -->
 Python Magnet Geometry contains magnet geometrical models for high-field magnet design and simulation.
 
@@ -41,7 +40,7 @@ poetry add python_magnetgeo@^1.0.0
 ### Development installation
 
 ```bash
-git clone https://github.com/Trophime/python_magnetgeo.git
+git clone https://github.com/MagnetDB/python_magnetgeo.git
 cd python_magnetgeo
 git checkout v1.0.0
 python -m venv --system-site-packages magnetgeo-env
@@ -487,7 +486,7 @@ python -m python_magnetgeo.xao HL-31-Axi.xao mesh --group CoolingChannels --geo
    - Enum types (e.g., `ShapePosition`)
    - Automatic YAML constructor registration
 
-**See [BREAKING_CHANGES.md](BREAKING_CHANGES.md) for complete migration guide and migration scripts.**
+**See [BREAKING_CHANGES.md](https://github.com/MagnetDB/python_magnetgeo/blob/main/BREAKING_CHANGES.md) for complete migration guide and migration scripts.**
 
 ### Version History
 
@@ -530,7 +529,7 @@ python -m python_magnetgeo.xao HL-31-Axi.xao mesh --group CoolingChannels --geo
 
 ### Quick Assessment: Which Version Are You Using?
 
-```python
+```yaml
 # Check your YAML files
 # If they look like this, you're on v0.5.x or earlier:
 name: "HL-31"
@@ -578,7 +577,7 @@ except ValidationError as e:
 
 ### Migration Path 2: From v0.5.x (or earlier) to v1.0.0
 
-Use the provided migration scripts in [BREAKING_CHANGES.md](BREAKING_CHANGES.md):
+Use the provided migration scripts in [BREAKING_CHANGES.md](https://github.com/MagnetDB/python_magnetgeo/blob/main/BREAKING_CHANGES.md):
 
 ```bash
 # Migrate a single YAML file
@@ -1476,7 +1475,7 @@ When reporting issues, please include:
 
 ## License
 
-MIT License - see [LICENSE](LICENSE) file for details.
+MIT License - see [LICENSE](https://github.com/Trophime/python_magnetgeo/blob/main/LICENSE) file for details.
 
 ## Documentation
 
@@ -1563,4 +1562,4 @@ If you use python_magnetgeo in your research, please cite:
 
 ---
 
-**Version 1.0.0** | Released: 2025 | [Changelog](CHANGELOG.md) | [Breaking Changes](BREAKING_CHANGES.md)
+**Version 1.0.0** | Released: 2025 | [Changelog](https://github.com/MagnetDB/python_magnetgeo/blob/main/HISTORY.md) | [Breaking Changes](https://github.com/MagnetDB/python_magnetgeo/blob/main/BREAKING_CHANGES.md)
diff --git a/archive.sh b/archive.sh
@@ -33,7 +33,7 @@ done
 shift $((OPTIND - 1))
 
 # add parameters
-: ${VERSION:="1.0.0"}
+: ${VERSION:="1.0.1"}
 : ${DIST:="trixie"}
 
 # cleanup source
@@ -52,6 +52,7 @@ tar \
     --exclude=.pc \
     --exclude=.devcontainer \
     --exclude=.vscode \
+    --exclude=.ruff_cache \
     --exclude=*.sif \
     --exclude=*.crt \
     --exclude=*.pem \

diff --git a/data/HL-31_H1.yaml b/data/HL-31_H1.yaml
@@ -59,10 +59,9 @@ model3d: !<Model3D>
   with_shapes: False
   with_channels: False
 shape: !<Shape>
-  name:
   profile: ""
   length: 0
   angle: 0
   onturns: 0
   position: ABOVE
-materials:
+
diff --git a/debian/changelog b/debian/changelog
@@ -1,10 +1,18 @@
-python-magnetgeo (1.0.0-7) UNRELEASED; urgency=medium
+python-magnetgeo (1.0.1-8) UNRELEASED; urgency=medium
+
+  * d/rules: overwrite dh_auto_test to skip coverage
+
+ -- Christophe Trophime <christophe.trophime@lncmi.cnrs.fr>  Thu, 07 May 2026 08:46:23 +0200
+
+python-magnetgeo (1.0.1-7) unstable; urgency=medium
 
   * add logging support
   * fix helper to create Profile from Shape_profile.dat
   * add helper to prepare helix YAML files for magnetdb
   * add helper to check yaml files
   * add support for lazzy loading
+  * add json_to_yaml helper to convert JSON objects to YAML
+  * fix Model3D.__repr__ and __init__ to handle optional name attribute
 
  -- Christophe Trophime <christophe.trophime@lncmi.cnrs.fr>  Tue, 03 Feb 2026 15:52:42 +0100
 

diff --git a/debian/rules b/debian/rules
@@ -8,6 +8,9 @@ export PYBUILD_NAME=magnetgeo
 %:
 	dh $@ --buildsystem=pybuild
 
+override_dh_auto_test:
+	PYBUILD_TEST_ARGS='--override-ini=addopts= -v --tb=short --strict-markers' dh_auto_test
+
 # If you need to rebuild the Sphinx documentation
 # Add sphinxdoc to the dh --with line
 #

diff --git a/docs/api_usage.md b/docs/api_usage.md
@@ -0,0 +1,9 @@
+# API Usage
+
+```{toctree}
+:maxdepth: 2
+
+dependency_analysis
+lazy_loading
+logging
+```
diff --git a/docs/authors.md b/docs/authors.md
@@ -0,0 +1,2 @@
+```{include} ../AUTHORS.md
+```
diff --git a/docs/authors.rst b/docs/authors.rst
diff --git a/docs/breaking_changes.md b/docs/breaking_changes.md
@@ -0,0 +1,2 @@
+```{include} ../BREAKING_CHANGES.md
+```
diff --git a/docs/conf.py b/docs/conf.py
@@ -31,7 +31,9 @@
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.viewcode']
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.viewcode', 'myst_parser']
+
+myst_heading_anchors = 4
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -40,7 +42,7 @@
 # You can specify multiple suffix as a list of string:
 #
 # source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+source_suffix = ['.rst', '.md']
 
 # The master toctree document.
 master_doc = 'index'

diff --git a/docs/contributing.md b/docs/contributing.md
@@ -0,0 +1,2 @@
+```{include} ../CONTRIBUTING.md
+```