v2.4.0 - #29
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Align module, docs, citations, and config references with SlicerMorphoWeave, keeping a legacy ATLAS alias for existing configs. Co-authored-by: Cursor <cursoragent@cursor.com>
Co-authored-by: Cursor <cursoragent@cursor.com>
Merge pull request Imageomics#28 from calcharp/main
Prevents Slurm/YAML jobs with name: ATLAS from silently falling back to Shell after the rename. Co-authored-by: Cursor <cursoragent@cursor.com>
Configs must use name: MorphoWeave; a one-line rename is clearer than fragile silent remapping. Co-authored-by: Cursor <cursoragent@cursor.com>
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Pull request overview
This PR completes the MorphoWeave renaming across the add-on by updating morphospace identifiers, module APIs, and all user-facing documentation/navigation to consistently refer to “MorphoWeave” instead of “ATLAS”.
Changes:
- Renamed the MorphoWeave morphospace implementation API surface (functions/classes/logging) to MorphoWeave naming.
- Updated morphospace discovery ordering and operator/docstrings to reference MorphoWeave.
- Updated MkDocs navigation and all documentation pages to reflect the new morphospace name and resources.
Reviewed changes
Copilot reviewed 21 out of 25 changed files in this pull request and generated no comments.
Show a summary per file
| File | Description |
|---|---|
| traitblender/ui/operators/imaging_pipeline_op.py | Updates inline comment to reference MorphoWeave PCA alignment. |
| traitblender/ui/operators/generate_morphospace_sample_op.py | Updates inline comment to reference MorphoWeave trait column behavior. |
| traitblender/mkdocs.yml | Renames nav entry from ATLAS to MorphoWeave and points to morphoweave.md. |
| traitblender/docs/morphospaces/overview.md | Updates morphospace list and naming examples to MorphoWeave. |
| traitblender/docs/morphospaces/morphoweave.md | Updates/refreshes MorphoWeave morphospace documentation and assets. |
| traitblender/docs/getting-started/quick-start.md | Updates quick-start references and links to MorphoWeave. |
| traitblender/docs/configuration/config-files.md | Updates config documentation and examples to recommend MorphoWeave wording. |
| traitblender/docs/api/scene-assets.md | Updates API reference text for orient_before_export recommendation. |
| traitblender/core/morphospaces/trait_params.py | Updates docstring example reference to MorphoWeave. |
| traitblender/core/morphospaces/list_morphospaces.py | Updates GUI ordering tuple to include MorphoWeave. |
| traitblender/core/helpers/orientation_helpers.py | Updates comment reference to MorphoWeave Default orientation behavior. |
| traitblender/core/datasets/traitblender_dataset.py | Updates docstring reference to MorphoWeave n_components behavior. |
| traitblender/core/config/templates/meshes.py | Updates UI description string to reference MorphoWeave PCA-aligned frame. |
| traitblender/assets/morphospace_modules/MorphoWeave/orientations/init.py | Renames internal orientation helpers from atlas_* to morphoweave_*. |
| traitblender/assets/morphospace_modules/MorphoWeave/morphospace/morphoweave_morphospace.py | Renames MorphoWeave generator function, imports, and logging prefix. |
| traitblender/assets/morphospace_modules/MorphoWeave/morphospace/morphoweave_morphospace_sample.py | Renames morphospace sample class to MorphoWeaveMorphospaceSample. |
| traitblender/assets/morphospace_modules/MorphoWeave/morphospace/morphoweave_core.py | Renames PCA coefficient helper and updates call sites. |
| traitblender/assets/morphospace_modules/MorphoWeave/morphospace/init.py | Adds package exports for MorphoWeave morphospace module API. |
| traitblender/assets/morphospace_modules/MorphoWeave/init.py | Updates morphospace NAME, sample defaults, and exported symbols to MorphoWeave. |
| traitblender/assets/morphospace_modules/ATLAS/morphospace/init.py | Removes the old ATLAS morphospace package export file. |
| README.md | Updates README morphospace bullet to MorphoWeave and associated link/description. |
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Include references and related_identifiers for Blender 5.1, Shell papers (Crossref-verified), and MorphoWeave; correct Shell author/title in docs. Co-authored-by: Cursor <cursoragent@cursor.com>
egrace479
approved these changes
Jul 29, 2026
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MorphoWeave renaming is fixed