Coverage#107
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Link to the new ReadTheDocs site (https://tptbox.readthedocs.io) from the badge row and a short Documentation section so users landing on GitHub know the full API reference exists. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Adds three new test files increasing coverage of previously untested code paths in the NII wrapper, numpy utilities, and POI set operations: - test_nii_extended.py: 52 tests covering properties, dtype/copy ops, label manipulation, spatial transforms, smoothing, Euclidean morphology, reorientation, and rescaling. - test_nputils_extended.py: 36 tests covering np_is_empty, np_count_nonzero, np_unique*, np_bounding_boxes, np_contacts, np_region_graph, np_translate_arr, np_compute_surface, np_normalize_to_range, Euclidean erode/dilate, and label overlap. - test_poi_ops.py: 40 tests covering __len__/__contains__/__getitem__/ __setitem__, keys_region/subregion, items_2D/flatten, join_left/right, intersect, subtract, extract_subregion/region, remove, round, apply_all, calculate_distances_cord, and filter_points_inside_shape. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
README.md: insert a Modules table between the Documentation and Install sections linking each sub-package to its own README file. mkdocs.yml: add a Modules nav section (10 pages) and configure pymdownx.snippets base_path so wrappers can include source files from the repo root. docs/modules/: create thin wrapper pages for core, poi_fun, logger, mesh3d, registration, segmentation, spine, snapshot2d, spinestats, and stitching. Nine of them pull content via --8<-- snippets directly from the existing sub-package READMEs; the stitching wrapper is inlined to fix the relative image path to a GitHub raw URL. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Pull request overview
This PR improves project quality and discoverability by expanding unit test coverage for key core APIs (POI, np_utils, NII) and by adding a structured “Modules” section to the MkDocs documentation (plus a README documentation badge/link).
Changes:
- Added extended unit tests covering POI accessors/set operations, NumPy utility helpers, and NII label/spatial/morphology workflows.
- Expanded documentation: added ReadTheDocs badge + documentation section in
README.md, and added MkDocs “Modules” pages wired intomkdocs.yml. - Enabled MkDocs snippet includes from repository root via
pymdownx.snippets.base_path.
Reviewed changes
Copilot reviewed 15 out of 15 changed files in this pull request and generated 1 comment.
Show a summary per file
| File | Description |
|---|---|
| unit_tests/test_poi_ops.py | Adds unit tests for POI accessors, set-ops, filtering, and helpers. |
| unit_tests/test_nputils_extended.py | Adds unit tests for TPTBox.core.np_utils utilities (contacts, translate, surface, normalize, morphology). |
| unit_tests/test_nii_extended.py | Adds unit tests for NII properties, label ops, spatial ops, smoothing, and Euclidean morphology. |
| README.md | Adds documentation badge + new “Documentation” and “Modules” sections; small markdown cleanup. |
| mkdocs.yml | Adds Modules navigation section and configures pymdownx.snippets base path. |
| docs/modules/core.md | Includes TPTBox/core/README.md into MkDocs. |
| docs/modules/poi_fun.md | Includes TPTBox/core/poi_fun/README.md into MkDocs. |
| docs/modules/spine.md | Adds a spine module overview page with quick example and links to submodules. |
| docs/modules/snapshot2d.md | Includes TPTBox/spine/snapshot2D/README.md into MkDocs. |
| docs/modules/spinestats.md | Includes TPTBox/spine/spinestats/README.md into MkDocs. |
| docs/modules/registration.md | Includes TPTBox/registration/README.md into MkDocs. |
| docs/modules/segmentation.md | Includes TPTBox/segmentation/README.md into MkDocs. |
| docs/modules/mesh3d.md | Includes TPTBox/mesh3D/README.md into MkDocs. |
| docs/modules/stitching.md | Adds a MkDocs page documenting stitching usage and CLI/API. |
| docs/modules/logger.md | Includes TPTBox/logger/README.md into MkDocs. |
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Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
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