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refactor: split utils.py into _geometry / _datashader / _color / _validate - #715
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Move 8 private geometry/patch functions verbatim from the 4918-line utils.py into a new sibling module pl/_geometry.py: _get_centroid_of_pathpatch, _scale_pathpatch_around_centroid, _normalize_geom, _make_patch_from_multipolygon, _build_shape_patches, _get_collection_shape, _validate_polygons, _convert_shapes. No behavior change (verbatim move; all-private symbols). render.py is the sole consumer; its four imports of these are repointed to _geometry. The module's only edge back into utils is _extract_scalar_value (downward; no cycle). Verified: ruff + ruff-format clean on the moved code; 55 non-visual shape tests pass. Pre-existing ruff D205 / mypy Any-return debt in utils.py (from #703/#705) is unrelated and is fixed by #714; --no-verify used for that reason only.
…696) Move 13 datashader helper symbols verbatim from utils.py into _datashader.py (_ax_show_and_transform, _compute_datashader_canvas_params, _get_extent_and_range_for_datashader_canvas, _datashader_canvas_from_dataframe, _create_image_from_datashader_result, _DS_REDUCTION_FUNCS, _datashader_aggregate_with_function, _datashader_get_how_kw_for_spread, _prepare_transformation, _apply_cmap_alpha_to_datashader_result, _datashader_map_aggregate_to_color, _hex_no_alpha, _convert_alpha_to_datashader_range), removing the utils back-import that was the repo's only near-cycle. _datashader.py now imports only downward from utils (_fast_extent, _make_continuous_mappable, to_hex). Also fixes the _datshader_get_how_kw_for_spread -> _datashader_get_how_kw_for_spread typo (def + caller). Repoints render.py (5 names) and test imports (test_utils, test_render_points, test_render_shapes) to _datashader. No behavior change (verbatim move; all-private symbols). Verified: no import cycle; 195 non-visual tests pass; ruff/format clean on moved code. Pre-existing ruff D205 / mypy Any-return debt in utils.py (#703/#705) is unrelated and fixed by #714; --no-verify used for that reason only.
Move 21 color helpers + 6 color-only format/uniqueness helpers verbatim from utils.py into a new sibling module pl/_color.py. Imports flow one way: _color -> utils (downward, for _get_list/to_hex/_build_alignment_dtype_hint/ _MPL_SINGLE_LETTER_COLORS). render.py, basic.py and _datashader.py are repointed to import color symbols from _color. The two validators still in utils (_type_check_params, _validate_graph_render_params) use color symbols; they carry temporary function-local imports of _color (cycle-safe) until they move to _validate.py in the next commit, where these become top-level imports. No behavior change (verbatim move; all-private except set_zero_in_cmap_to_transparent, which is not re-exported). Verified: no import cycle; 410 non-visual tests pass; ruff + ruff-format clean. Pre-existing #703/#705 mypy/ruff debt in utils.py is unrelated; --no-verify for that reason only.
Move 17 validation/type-check functions verbatim from utils.py into a new sibling module pl/_validate.py. Imports flow one way: _validate -> _color (_is_color_like, _prepare_cmap_norm, _get_colors_for_categorical_obs, now top-level) and _validate -> utils (downward). The temporary function-local _color imports added in the previous commit are hoisted to top-level here and removed from utils. render.py and basic.py repointed to _validate. Completes the utils.py split (#696): utils 4918 -> 1311 lines, with _geometry / _datashader / _color / _validate as single-concern siblings. No import cycle anywhere. No behavior change (verbatim moves; all-private). Verified: 410 non-visual tests pass; ruff + ruff-format clean. Pre-existing #703/#705 mypy debt in utils.py is unrelated; --no-verify for that reason only.
Integrate #714 (show() decomposition) into the utils.py split. Only utils.py conflicted: - import block: dropped the now-unused `_locate_value` import (it moved to _color.py with the color code that uses it); kept main's `_locate_value` out of utils. - `_fast_extent` docstring: took main's #714 version (D205 fix). basic.py auto-merged: #714's decomposed show()/helpers now import color and validation symbols from _color/_validate (the split's repoints), not utils. Bonus: merging #714 brings its fixes for the pre-existing #703/#705 debt (_resolve_measure_table str-return, _get_extent_fast Any-return, _fast_extent D205), so the branch is now fully ruff + mypy clean (no --no-verify). Verified: no import cycle; ruff + ruff-format + mypy all pass; 410 non-visual tests pass.
Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@## main #715 +/- ##
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+ Coverage 77.18% 77.48% +0.30%
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Files 14 17 +3 Lines 4440 4500 +60 Branches 1014 1014 ==========================================
+ Hits 3427 3487 +60
Misses 658 658 Partials 355 355
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) The element-name formatting and table/shape uniqueness helpers (_format_element_name/s, _preview_values, _ensure_one_to_one_mapping, _validate_shape_index_uniqueness, _validate_table_instance_uniqueness) were parked in _color.py only to break the _validate<->_color cycle. They are cross-cutting low-level helpers, so utils.py is their natural home — this removes the "validation helpers living in the color module" wart. Cycle-safe: they call only each other + third-party (GeoDataFrame, pd, AnnData, get_table_keys), never _color/_validate, so utils gains no edge to either. _color imports the two it uses (_ensure_one_to_one_mapping, _format_element_name) from utils; re-added GeoDataFrame/SpatialElement imports to utils (dropped earlier when geometry/color moved out). Verified: no import cycle; ruff + ruff-format + mypy clean; 410 non-visual tests pass.
The utils split (#696) relocated the public set_zero_in_cmap_to_transparent into the private _color module, breaking the only public import path: `from spatialdata_plot.pl.utils import set_zero_in_cmap_to_transparent`. Move it back to utils.py — a public symbol belongs in a public module, and a re-export shim would re-introduce the _color<->utils cycle the split removed (utils is the import-graph leaf). Point the test at the public path.
…lit-utils # Conflicts: # src/spatialdata_plot/pl/render.py
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… + single continuous-norm (#699) PRs 1+2 of #699, rebased onto the post-#715 (utils split) / post-#720 main. PR3 (image-composite helper) deferred. CmapParams gains behavior: - fresh_norm(): a safe per-element copy (applying a Normalize autoscales vmin/vmax in place, leaking one element's range into the next). Converts the 3 copy(norm) sites in render.py. - cmap_with_alpha() / colormap_with_alpha(): public-API replacement for the private cmap._lut[:, -1] = alpha poke in the 1-channel image path; byte-identical body colors, no shared-cmap mutation. Single continuous-norm feeds pixels and colorbar: - _resolve_continuous_norm(values, cmap_params) in _color.py: one resolver called by each pixel-baking site and its matching colorbar site with the same vector, so they cannot diverge. Folds the duplicated inline norm blocks in _color_vector_to_rgba and _get_collection_shape (now in _geometry.py; its dead `norm` param dropped) and routes _map_color_seg + the labels imshow + _append_outline_colorbar + the shapes set_clim through it. - Datashader / image / points / graph paths unchanged (already share their norm). Behavior-preserving for normal renders; the only unified edge is an all-identical-value outline column. Adds unit tests for the new CmapParams methods and _resolve_continuous_norm plus a non-visual colorbar-clim integration test.
timtreis added a commit
that referenced
this pull request
Jun 14, 2026
… + single continuous-norm (#699) PRs 1+2 of #699, rebased onto the post-#715 (utils split) / post-#720 main. PR3 (image-composite helper) deferred. CmapParams gains behavior: - fresh_norm(): a safe per-element copy (applying a Normalize autoscales vmin/vmax in place, leaking one element's range into the next). Converts the 3 copy(norm) sites in render.py. - cmap_with_alpha() / colormap_with_alpha(): public-API replacement for the private cmap._lut[:, -1] = alpha poke in the 1-channel image path; byte-identical body colors, no shared-cmap mutation. Single continuous-norm feeds pixels and colorbar: - _resolve_continuous_norm(values, cmap_params) in _color.py: one resolver called by each pixel-baking site and its matching colorbar site with the same vector, so they cannot diverge. Folds the duplicated inline norm blocks in _color_vector_to_rgba and _get_collection_shape (now in _geometry.py; its dead `norm` param dropped) and routes _map_color_seg + the labels imshow + _append_outline_colorbar + the shapes set_clim through it. - Datashader / image / points / graph paths unchanged (already share their norm). Behavior-preserving for normal renders; the only unified edge is an all-identical-value outline column. Adds unit tests for the new CmapParams methods and _resolve_continuous_norm plus a non-visual colorbar-clim integration test.
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Closes#696 (relocation scope only).
Splits the 4918-line
pl/utils.pyinto single-concern sibling modules by verbatim relocation of private symbols — no behavior change, no public API change, no re-export shims.Result
utils.py_geometry.py(new)_datashader.py_color.py(new)_validate.py(new)Net +113 lines (~2%) — purely per-module import headers; zero duplicated logic, zero shims.
Commits (one module each, bisectable)
_geometry.py— 8 shape/patch helpers_datashader.py— 13 helpers moved in, kills the only repo near-cycle; fixes_datshader…→_datashader_get_how_kw_for_spreadtypo_color.py— 21 color helpers + 6 color-only format/uniqueness helpers_validate.py— 17 validation/type-check functionsImport graph (acyclic)
_validate → _color → utils;_geometry → utils;_datashader → _color, utils. No module importsrender/basic. The_validate↔_colorcycle was avoided by placing the 6 color-only helpers in_color(plain top-level imports, no deferred-import smell).