Merge pull request #32 from quadbio/docs/update

Update to the docs

Author: Marius1311

CHANGELOG.md

@@ -10,6 +10,11 @@ and this project adheres to [Semantic Versioning][].
 
 ## [Unreleased]
 
+## [v0.1.4]
+### Changed
+- Rename mapping methods to `map_obs`, `map_obsm`, and `map_layers`, and improve support for numerical `.obs` annotations {pr}`30`.
+
+
 ## [v0.1.3]
 
 ### Added

README.md

@@ -5,12 +5,14 @@
 [![Pre-commit.ci][badge-pre-commit]][pre-commit]
 [![PyPI][badge-pypi]][pypi]
 [![Documentation][badge-docs]][docs]
+[![Downloads][badge-downloads]][downloads]
 
 [badge-tests]: https://github.com/quadbio/cellmapper/actions/workflows/test.yaml/badge.svg
 [badge-coverage]: https://codecov.io/gh/quadbio/cellmapper/branch/main/graph/badge.svg
 [badge-pre-commit]: https://results.pre-commit.ci/badge/github/quadbio/cellmapper/main.svg
 [badge-pypi]: https://img.shields.io/pypi/v/cellmapper.svg
 [badge-docs]: https://img.shields.io/readthedocs/cellmapper
+[badge-downloads]: https://static.pepy.tech/badge/cellmapper
 
 k-NN-based mapping of cells across representations to tranfer labels, embeddings and expression values. Works for millions of cells, on CPU and GPU, across molecular modalities, between spatial and non-spatial data, for arbitrary query and reference datasets. Using [faiss][] to compute k-NN graphs, CellMapper takes about 30 seconds to transfer cell type labels from 1.5M cells to 1.5M cells on a single RTX 4090 with 60 GB CPU memory.
 
@@ -84,6 +86,7 @@ Please cite this GitHub repo if you find CellMapper useful for your research.
 [coverage]: https://codecov.io/gh/quadbio/cellmapper
 [pre-commit]: https://results.pre-commit.ci/latest/github/quadbio/cellmapper/main
 [pypi]: https://pypi.org/project/cellmapper/
+[downloads]: https://pepy.tech/project/cellmapper
 
 [faiss]: https://github.com/facebookresearch/faiss
 [pynndescent]: https://github.com/lmcinnes/pynndescent

docs/_static/images/cellmapper_logo_dark.svg

@@ -128,6 +128,10 @@
     "use_repository_button": True,
     "path_to_docs": "docs/",
     "navigation_with_keys": False,
+    "logo": {
+        "image_light": "_static/images/cellmapper_logo_light.svg",  # Logo for light mode
+        "image_dark": "_static/images/cellmapper_logo_dark.svg",  # Logo for dark mode
+    },
 }
 
 pygments_style = "default"

docs/_static/images/cellmapper_logo_light.svg

@@ -118,7 +118,9 @@ def compute_fast_cca(
         )
 
         # Concatenate with inner join on genes
-        joint = ad.concat([self.reference, self.query], join="inner", label="batch", keys=["reference", "query"])
+        joint = ad.concat(
+            [self.reference, self.query], join="inner", label="batch", keys=["reference", "query"], merge="same"
+        )
 
         # Potentially subset along the features
         mask_var = _check_mask(joint, mask_var, "var")