Release 0.10.0 (#148)

* adds back function

* updates to scanpy 1.10

* minor docs fixes

* fixes 2 links

docs/api/scanpy_gpu.md

@@ -1,6 +1,6 @@
 # scanpy-GPU
 
-These functions offer accelerated near drop-in replacements for common tools porvided by {mod}`scanpy`.
+These functions offer accelerated near drop-in replacements for common tools porvided by [`scanpy`](https://scanpy.readthedocs.io/en/stable/api/index.html).
 
 ## Preprocessing `pp`
 Filtering of highly-variable genes, batch-effect correction, per-cell normalization.

docs/release-notes/0.9.1.md

@@ -4,7 +4,7 @@
 ```{rubric} Features
 ```
 * added batchsize for {func}`~rapids_singlecell.tl.embedding_density` {pr}`67` {smaller}`S Dicks`
-* adds subclustering and brings {func}`~rapids_singlecell.tl.leiden` and {func}`~rapids_singlecell.tl.louvain` closer to feature parity with {mod}`scanpy` {pr}`68` {smaller}`S Dicks`
+* adds subclustering and brings {func}`~rapids_singlecell.tl.leiden` and {func}`~rapids_singlecell.tl.louvain` closer to feature parity with [`scanpy`](https://scanpy.readthedocs.io/en/stable/api/index.html) {pr}`68` {smaller}`S Dicks`
 
 ```{rubric} Misc
 ```

pyproject.toml

@@ -13,7 +13,7 @@ dynamic = ["version"]
 
 dependencies = [
     "anndata>=0.10.0",
-    "scanpy>=1.10.0rc2",
+    "scanpy>=1.10.0",
     "numpy>=1.17.0",
     "decoupler>=1.3.2",
     "scipy>=1.4",

src/rapids_singlecell/preprocessing/_scrublet/__init__.py

@@ -108,7 +108,7 @@ def scrublet(
         at the specified rate.
     knn_dist_metric
         Distance metric used when finding nearest neighbors. For list of
-        valid values, see the documentation cuml.neighbors.NearestNeighbors.
+        valid values, see the documentation :class:`cuml.neighbors.NearestNeighbors`.
     normalize_variance
         If True, normalize the data such that each gene has a variance of 1.
         :class:`cuml.decomposition.tsvd.TruncatedSVD` will be used for dimensionality
@@ -124,7 +124,7 @@ def scrublet(
         Number of principal components used to embed the transcriptomes prior
         to k-nearest-neighbor graph construction.
     use_approx_neighbors
-        Does not affect the results, just here to stay consistent with :mod:`scanpy`.
+        Does not affect the results, just here to stay consistent with :func:`scanpy.pp.scrublet`.
     get_doublet_neighbor_parents
         If True, return (in .uns) the parent transcriptomes that generated the
         doublet neighbors of each observed transcriptome. This information can
@@ -172,7 +172,7 @@ def scrublet(
     --------
     :func:`~rapids_singlecell.pp.scrublet_simulate_doublets`: Run Scrublet's doublet
         simulation separately for advanced usage.
-    `scanpy.pl.scrublet_score_distribution`: Plot histogram of doublet
+    :func:`~scanpy.pl.scrublet_score_distribution`: Plot histogram of doublet
         scores for observed transcriptomes and simulated doublets.
     """
 
@@ -350,7 +350,7 @@ def _scrublet_call_doublets(
         Number of principal components used to embed the transcriptomes prior
         to k-nearest-neighbor graph construction.
     use_approx_neighbors
-        Does not affect the results, just here to stay consistent with :mod:`scanpy`.
+        Does not affect the results, just here to stay consistent with :func:`scanpy.pp.scrublet`.
     knn_dist_metric
         Distance metric used when finding nearest neighbors. For list of
         valid values, see the documentation cuml.neighbors.NearestNeighbors.
@@ -539,7 +539,7 @@ def scrublet_simulate_doublets(
     --------
     :func:`~rapids_singlecell.pp.scrublet`: Main way of running Scrublet, runs
         preprocessing, doublet simulation (this function) and calling.
-    `scanpy.pl.scrublet_score_distribution`: Plot histogram of doublet
+    :func:`~scanpy.pl.scrublet_score_distribution`: Plot histogram of doublet
         scores for observed transcriptomes and simulated doublets.
     """
 

src/rapids_singlecell/tools/_diffmap.py

@@ -26,7 +26,7 @@ def diffmap(
 
     The width ("sigma") of the connectivity kernel is implicitly determined by
     the number of neighbors used to compute the single-cell graph in
-    :func:`~scanpy.pp.neighbors`.
+    :func:`scanpy.pp.neighbors` or :func:`~rapids_singlecell.pp.neighbors`.
 
     Parameters
     ----------