Drop scVelo as hard dependency, add as optional pip extra

pyproject.toml

@@ -58,7 +58,6 @@ dependencies = [
   "scanpy>=1.11",
   "scikit-learn>=1.6",
   "scipy>=1.14",
-  "scvelo>=0.3",
   "seaborn>=0.13",
   "session-info2>=0.2",
   "wrapt>=1.16",
@@ -69,6 +68,7 @@ optional-dependencies.moscot = [ "moscot" ]
 optional-dependencies.petsc = [ "mpi4py", "petsc4py", "slepc4py" ]
 optional-dependencies.plot = [ "adjusttext" ]
 optional-dependencies.r = [ "rpy2>=3.3" ]
+optional-dependencies.scvelo = [ "scvelo>=0.3" ]
 urls."Bug Tracker" = "https://github.com/theislab/cellrank/issues"
 urls.Documentation = "https://cellrank.readthedocs.io"
 urls.Download = "https://cellrank.readthedocs.io/en/latest/installation.html"

src/cellrank/estimators/mixins/_lineage_drivers.py

@@ -286,7 +286,7 @@ def prepare_format(
         axes = np.ravel([axes])
 
         basis = kwargs.pop("basis", "umap")
-        # scvelo compat: "right" means "right margin" in scanpy
+        # "right" means "right margin" in scanpy
         if kwargs.get("legend_loc") == "right":
             kwargs["legend_loc"] = "right margin"
         _i = 0

src/cellrank/estimators/terminal_states/_term_states_estimator.py

@@ -443,7 +443,7 @@ def _plot_discrete(
 
         same_plot = same_plot or len(names) == 1
         kwargs.setdefault("legend_loc", "on data")
-        # scvelo compat: "right" means "right margin" in scanpy
+        # "right" means "right margin" in scanpy
         if kwargs.get("legend_loc") == "right":
             kwargs["legend_loc"] = "right margin"
         kwargs.pop("color_map", None)
@@ -580,13 +580,12 @@ def _plot_continuous(
             )
         elif mode == PlotMode.EMBEDDING:
             kwargs.setdefault("legend_loc", "on data")
-            # scvelo compat: "right" means "right margin" in scanpy
+            # "right" means "right margin" in scanpy
             if kwargs.get("legend_loc") == "right":
                 kwargs["legend_loc"] = "right margin"
 
             if same_plot:
                 if color:
-                    # https://github.com/theislab/scvelo/issues/673
                     logger.warning("Ignoring `color` when `mode='embedding'` and `same_plot=True`")
                 title = [_title] if title is None else title
                 _plot_color_gradients(self.adata, _data, basis=basis, title=title,

src/cellrank/kernels/_base_kernel.py

@@ -226,7 +226,7 @@ def plot_random_walks(
         %(parallel)s
         %(plotting)s
         kwargs
-            Keyword arguments for :func:`~scvelo.pl.scatter`.
+            Keyword arguments for :func:`~scanpy.pl.embedding`.
 
         Returns
         -------

src/cellrank/kernels/utils/_random_walk.py

@@ -239,7 +239,7 @@ def plot(
         # scVelo accepted color="none" to skip coloring; scanpy does not.
         if kwargs.get("color") == "none":
             kwargs.pop("color")
-        # scvelo compat: "right" means "right margin" in scanpy
+        # "right" means "right margin" in scanpy
         if kwargs.get("legend_loc") == "right":
             kwargs["legend_loc"] = "right margin"
         sc.pl.embedding(self._adata, basis=basis, show=False, ax=ax, **kwargs)

tests/_helpers.py

@@ -6,7 +6,6 @@
 import pytest
 import scanpy as sc
 import scipy.sparse as sp
-import scvelo as scv
 from anndata import AnnData
 from pandas.testing import assert_frame_equal, assert_series_equal
 from PIL import Image
@@ -26,6 +25,15 @@ def _jax_not_installed() -> bool:
         return True
 
 
+def _scvelo_not_installed() -> bool:
+    try:
+        import scvelo  # noqa
+
+        return False
+    except ImportError:
+        return True
+
+
 def _rpy2_mgcv_not_installed() -> bool:
     try:
         import rpy2
@@ -362,6 +370,8 @@ def _create_dummy_adata(n_obs: int) -> AnnData:
     -------
     The created adata object.
     """
+    import scvelo as scv
+
     np.random.seed(42)  # noqa: NPY002
     adata = scv.datasets.toy_data(n_obs=n_obs)
     adata.obs_names_make_unique()
@@ -396,6 +406,7 @@ def _create_dummy_adata(n_obs: int) -> AnnData:
 
 jax_not_installed_skip = pytest.mark.skipif(_jax_not_installed(), reason="JAX is not installed.")
 gamr_skip = pytest.mark.skipif(_rpy2_mgcv_not_installed(), reason="Cannot import `rpy2` or R's `mgcv` package.")
+scvelo_skip = pytest.mark.skipif(_scvelo_not_installed(), reason="scVelo is not installed.")
 
 if __name__ == "__main__":
     for size in [50, 100, 200]:

tests/test_kernels.py

@@ -41,6 +41,7 @@
     create_kernels,
     jax_not_installed_skip,
     random_transition_matrix,
+    scvelo_skip,
 )
 
 _rtol = 1e-6
@@ -950,6 +951,7 @@ def test_save_to_anndata(self, adata: AnnData, tmpdir):
         assert vk.params == bdata.uns[f"{key}_params"]["params"]
 
 
+@scvelo_skip
 class TestComputeProjection:
     def test_no_transition_matrix(self, adata: AnnData):
         with pytest.raises(RuntimeError, match=r"Compute transition matrix first as"):
@@ -1476,6 +1478,7 @@ def test_precomputed_autodetection(self, adata: AnnData, backward: bool):
         assert key in pk.params["origin"]
         np.testing.assert_array_equal(mat, pk.transition_matrix)
 
+    @scvelo_skip
     def test_projection_explicit_connectivities(self, adata: AnnData):
         mat = random_transition_matrix(adata.n_obs)
         pk = PrecomputedKernel(mat, adata=adata)

tests/test_plotting.py

@@ -24,6 +24,7 @@
     create_model,
     gamr_skip,
     resize_images_to_same_sizes,
+    scvelo_skip,
 )
 
 setup()
@@ -2253,6 +2254,7 @@ def test_gpcca_fate_probs_cont_same_clusters(self, mc: GPCCA, fpath: str):
     def test_gpcca_fate_probs_cont_not_same(self, mc: GPCCA, fpath: str):
         mc.plot_fate_probabilities(color="clusters", same_plot=False, dpi=DPI, save=fpath)
 
+    @scvelo_skip
     @compare(kind="gpcca")
     def test_scvelo_transition_matrix_projection(self, mc: GPCCA, fpath: str):
         mc.kernel.plot_projection(
@@ -3335,6 +3337,7 @@ def test_msc_legend_loc(self, mc: GPCCA, fpath: str):
         mc.plot_macrostate_composition("clusters_enlarged", dpi=DPI, save=fpath, legend_loc="upper left out")
 
 
+@scvelo_skip
 class TestProjectionEmbedding:
     @compare()
     def test_scvelo_connectivity_kernel_emb_stream(self, adata: AnnData, fpath: str):