From 2b2af1fbfa873c3f656aaecefc3d4463b8435aa5 Mon Sep 17 00:00:00 2001 From: Severin Dicks <37635888+Intron7@users.noreply.github.com> Date: Tue, 26 Mar 2024 17:06:53 +0100 Subject: [PATCH] Release 0.10.0 (#148) * adds back function * updates to scanpy 1.10 * minor docs fixes * fixes 2 links --- docs/api/scanpy_gpu.md | 2 +- docs/release-notes/0.9.1.md | 2 +- pyproject.toml | 2 +- .../preprocessing/_scrublet/__init__.py | 10 +++++----- src/rapids_singlecell/tools/_diffmap.py | 2 +- 5 files changed, 9 insertions(+), 9 deletions(-) diff --git a/docs/api/scanpy_gpu.md b/docs/api/scanpy_gpu.md index cebbfa23..7416c91b 100644 --- a/docs/api/scanpy_gpu.md +++ b/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. diff --git a/docs/release-notes/0.9.1.md b/docs/release-notes/0.9.1.md index ae11024a..5e0f911a 100644 --- a/docs/release-notes/0.9.1.md +++ b/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 ``` diff --git a/pyproject.toml b/pyproject.toml index 9d207956..b7cadbff 100644 --- a/pyproject.toml +++ b/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", diff --git a/src/rapids_singlecell/preprocessing/_scrublet/__init__.py b/src/rapids_singlecell/preprocessing/_scrublet/__init__.py index 5bfb3e6c..ab6dc6db 100644 --- a/src/rapids_singlecell/preprocessing/_scrublet/__init__.py +++ b/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. """ diff --git a/src/rapids_singlecell/tools/_diffmap.py b/src/rapids_singlecell/tools/_diffmap.py index 4dc6973b..3034f5eb 100644 --- a/src/rapids_singlecell/tools/_diffmap.py +++ b/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 ----------