Drop scVelo as hard dependency, add as optional pip extra#1314
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Marius1311 merged 2 commits intomainfrom Mar 9, 2026
Merged
Drop scVelo as hard dependency, add as optional pip extra#1314Marius1311 merged 2 commits intomainfrom
Marius1311 merged 2 commits intomainfrom
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- Remove `scvelo>=0.3` from `[project] dependencies` - Add `optional-dependencies.scvelo = ["scvelo>=0.3"]` for velocity embedding stream/grid plots (already import-guarded in _projection.py) - Keep scVelo in `[dependency-groups] test` for projection tests - Fix stale docstring ref `scvelo.pl.scatter` → `scanpy.pl.embedding` in _base_kernel.py - Drop `scvelo compat:` prefix from 4 legend_loc comments — the code now uses scanpy directly - Remove `scvelo/issues/673` URL comment (bug is in CellRank's own code) - Move top-level `import scvelo` in tests/_helpers.py inside `_create_dummy_adata()` (only used for offline data regeneration)
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Final step of the scVelo removal: drop scVelo from hard dependencies and make it an optional pip extra for velocity embedding stream/grid plots.
Changes
pyproject.tomlscvelo>=0.3from[project] dependenciesoptional-dependencies.scvelo = ["scvelo>=0.3"]— used byTmatProjection.plot()forscv.pl.velocity_embedding_stream/grid(already import-guarded via_check_module_importable)scvelo>=0.3in[dependency-groups] test— needed for 5 projection testsSource docstrings & comments
scvelo.pl.scatter→scanpy.pl.embeddingref in_base_kernel.pyrandom walk kwargs docstringscvelo compat:prefix from 4 legend-loc normalization comments (code uses scanpy directly now)scvelo/issues/673URL comment from_term_states_estimator.py(bug is in CellRank's own code)Tests
import scvelointests/_helpers.pyinside_create_dummy_adata()— only used for offline test data regeneration, never at test runtimeWhat stays
docs/conf.pyintersphinx mapping for scvelo — projection docstrings still cross-reference ittests/conftest.pytry/except scvelo import — sets figdir for projection teststests/test_plotting.pytest_scvelo_*test names — historical, functionalCloses the scVelo removal plan (
.github/prompts/PLAN_scvelo_removal.md).Follows #1301 and #1302.