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Update config, issue templates, editor/IDE settings, and docs templates to match the scverse template v0.7.0. No source code or CI changes. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Switch from optional-dependencies to dependency-groups (PEP 735) - Add hatch environments (default, docs, hatch-test matrix) - Add build.yaml CI workflow (uv build + twine check) - Replace prettier with biome, add pyproject-fmt and pre-commit-hooks - Switch docs from mathjax to KaTeX, add sphinx-tabs and opengraph - Update .readthedocs.yaml to use hatch docs:build - Rewrite contributing.md with hatch/uv/pip tabs, keep plot-testing guide - Add [tool.cruft] skip list for future template syncs - Keep pixi config, html_logo, full intersphinx mappings, nitpicky=False Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Dynamic test matrix extracted from pyproject.toml via hatch env show - Add hatch-test env config with dependency-groups, scripts, and pre-release matrix - Add concurrency control, check job (alls-green), and bi-monthly cron schedule - Switch coverage upload to Codecov OIDC - Keep visual test artifact upload, MPLBACKEND=agg, and tag triggers Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Replace secret-based PyPI token with OIDC trusted publishing - Use uv for building instead of pip/hatch dual build - Split into build + publish jobs with artifact handoff - Add pypi environment for deployment protection - Update actions to v5 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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Superseded — pushing directly to #528 instead. |
Workaround for pypa/hatch#2193 — hatch is incompatible with virtualenv 21+. Same fix used by scanpy and squidpy. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
The old RTD config had fail_on_warning: false. Upstream libraries (xarray, geopandas) emit harmless import warnings that -W promotes to fatal errors. Remove -W to match previous behavior. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Codecov Report✅ All modified and coverable lines are covered by tests.
Additional details and impacted files@@ Coverage Diff @@
## main #548 +/- ##
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- Coverage 84.01% 73.66% -10.35%
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Files 9 9
Lines 2608 2616 +8
Branches 0 623 +623
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- Hits 2191 1927 -264
- Misses 417 422 +5
- Partials 0 267 +267 🚀 New features to boost your workflow:
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Suppress sphinx-autodoc-typehints warnings from upstream libraries: - ColorType forward reference from matplotlib.figure.Figure - Guarded iris import from xarray.core.dataarray - Guarded folium import from geopandas.geodataframe These are optional deps of upstream packages, not our issue. Restores -W (warnings as errors) to match the scverse template. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
coverage couldn't map site-packages/spatialdata_plot back to src/spatialdata_plot, resulting in ~15% reported coverage. Add paths.source mapping, enable branch and parallel coverage. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Remove .vscode/ from tracking and set ide_integration: false in cruft.json - Add .vscode/ back to .gitignore - Fix set_constrained_layout deprecation (use set_layout_engine) - Fix SettingWithCopyWarning in test_render_labels.py Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Coverage requires serial execution (coverage run doesn't instrument xdist workers). Mirror squidpy's approach: run-cov without -n auto on one env (py3.14-stable), run with -n auto on all others. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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Summary
Brings the repository in line with cookiecutter-scverse v0.7.0, superseding #528.
[dependency-groups](PEP 735), add hatch environments (default, docs, hatch-test matrix with pre-release testing), add[tool.cruft]skip list, pyproject-fmt normalizedpypienvironment, replacing secret-based tokenKept as spatialdata-plot-specific
[tool.pixi.*]config (local dev workflow)html_logo(spatialdata branding)exclude_patternsfor tutorial pathsnitpicky = False