Merge pull request #19 from quadbio/docs/tutorial

Write a tutorial

Author: Marius1311

.gitignore

@@ -18,3 +18,7 @@ __pycache__/
 # docs
 /docs/generated/
 /docs/_build/
+.ipynb_checkpoints/
+
+# datasets
+*.h5ad

CHANGELOG.md

@@ -14,6 +14,8 @@ and this project adheres to [Semantic Versioning][].
 - Included tests for the `check` module, and more tests for the main classes {pr}`15`.
 - Implemented the computation of presence scores, following HNOCA-tools {pr}`16`.
 - Add a `groupby` parameter to expression transfer evaluation {pr}`16`.
+- Add a `test_var_key` parameter to expression transfer evaluation {pr}`19`.
+- Add a tutorial on spatial mapping {pr}`19`.
 
 ## [v0.1.1]
 

README.md

@@ -14,7 +14,7 @@
 
 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.
 
-Inspired by scanpy's [ingest][] and the [HNOCA-tools][] packages. Check out the [docs][] to learn more.
+Inspired by scanpy's [ingest][] and the [HNOCA-tools][] packages. Check out the [docs][] to learn more, in particular our [tutorials][].
 
 ## Installation
 
@@ -69,6 +69,7 @@ Please cite this GitHub repo if you find CellMapper useful for your research.
 [tests]: https://github.com/quadbio/cellmapper/actions/workflows/test.yaml
 [changelog]: https://cellmapper.readthedocs.io/en/latest/changelog.html
 [docs]: https://cellmapper.readthedocs.io/
+[tutorials]: https://cellmapper.readthedocs.io/en/latest/notebooks/tutorials/index.html
 [pypi]: https://pypi.org/project/cellmapper
 [coverage]: https://codecov.io/gh/quadbio/cellmapper
 [pre-commit]: https://results.pre-commit.ci/latest/github/quadbio/cellmapper/main

docs/index.md

@@ -11,5 +11,5 @@ changelog.md
 contributing.md
 references.md
 
-notebooks/example
+notebooks/tutorials/index
 ```

docs/notebooks/example.ipynb

@@ -0,0 +1,9 @@
+Tutorials
+=========
+This section contains tutorials showcasing use cases for k-NN based mapping of cells across representations with :mod:`cellmapper`.
+
+.. toctree::
+    :maxdepth: 1
+    :glob:
+
+    *