Remove redundant Scanpy functions (#1276)

- Remove import statements
- Update docs accordingly

docs/source/api.rst

@@ -8,22 +8,12 @@ Import scVelo as::
    import scvelo as scv
 
 
-After reading the data (``scv.read``) or loading an in-built dataset (``scv.datasets.*``),
+After reading the data or loading an in-built dataset (``scv.datasets.*``),
 the typical workflow consists of subsequent calls of
 preprocessing (``scv.pp.*``), analysis tools (``scv.tl.*``) and plotting (``scv.pl.*``).
 Further, several utilities (``scv.utils.*``) are provided to facilitate data analysis.
 
 
-Read / Load
------------
-
-.. autosummary::
-   :toctree: .
-
-   read
-   read_loom
-
-
 Preprocessing (pp)
 ------------------
 
@@ -51,15 +41,6 @@ Preprocessing (pp)
 Tools (tl)
 ----------
 
-**Clustering and embedding**
-(more at `scanpy-docs <https://scanpy.readthedocs.io/en/stable/api/>`_)
-
-.. autosummary::
-   :toctree: .
-
-   tl.louvain
-   tl.umap
-
 **Velocity estimation**
 
 .. autosummary::

scvelo/__init__.py

@@ -1,6 +1,5 @@
 """scvelo - RNA velocity generalized through dynamical modeling."""
 from anndata import AnnData
-from scanpy import read, read_loom
 
 from scvelo import datasets, logging
 from scvelo import plotting as pl
@@ -44,9 +43,7 @@
     "Neighbors",
     "pl",
     "pp",
-    "read",
     "read_csv",
-    "read_loom",
     "round",
     "run_all",
     "set_figure_params",

scvelo/plotting/__init__.py

@@ -1,5 +1,3 @@
-from scanpy.plotting import paga_compare, rank_genes_groups
-
 from .gridspec import gridspec
 from .heatmap import heatmap
 from .paga import paga
@@ -21,12 +19,10 @@
     "heatmap",
     "hist",
     "paga",
-    "paga_compare",
     "pca",
     "phate",
     "plot",
     "proportions",
-    "rank_genes_groups",
     "scatter",
     "simulation",
     "summary",

scvelo/tools/__init__.py

@@ -1,5 +1,3 @@
-from scanpy.tools import diffmap, dpt, louvain, tsne, umap
-
 from ._em_model import ExpectationMaximizationModel
 from ._em_model_core import (
     align_dynamics,
@@ -25,12 +23,9 @@
 __all__ = [
     "align_dynamics",
     "differential_kinetic_test",
-    "diffmap",
-    "dpt",
     "DynamicsRecovery",
     "eigs",
     "latent_time",
-    "louvain",
     "paga",
     "rank_dynamical_genes",
     "rank_velocity_genes",
@@ -39,8 +34,6 @@
     "score_genes_cell_cycle",
     "terminal_states",
     "transition_matrix",
-    "tsne",
-    "umap",
     "velocity",
     "velocity_clusters",
     "velocity_confidence",