Merge pull request #207 from scverse/add_examples

Fixed bug 2.0.7 pl.obsm

Author: PauBadiaM

.readthedocs.yaml

@@ -12,7 +12,7 @@ build:
       - uv pip install .[doc,full]
     build:
       html:
-        - uv run sphinx-build -T -W -b html docs $READTHEDOCS_OUTPUT/html
+        - UV_LINK_MODE=copy uv run sphinx-build -T -W -b html docs $READTHEDOCS_OUTPUT/html
 
 submodules:
     include: all

CHANGELOG.md

@@ -8,7 +8,7 @@ and this project adheres to [Semantic Versioning][].
 [keep a changelog]: https://keepachangelog.com/en/1.0.0/
 [semantic versioning]: https://semver.org/spec/v2.0.0.html
 
-## 2.0.6
+## 2.0.8
 
 Major update to accomodate the scverse template {cite}`scverse`.
 

pyproject.toml

@@ -4,7 +4,7 @@ requires = [ "hatchling" ]
 
 [project]
 name = "decoupler"
-version = "2.0.7"
+version = "2.0.8"
 description = "Python package to perform enrichment analysis from omics data."
 readme = "README.md"
 license = { file = "LICENSE" }

src/decoupler/bm/_run.py

@@ -310,6 +310,16 @@ def benchmark(
     Returns
     -------
     Dataframe containing metric scores.
+
+    Example
+    -------
+    .. code-block:: python
+
+        import decoupler as dc
+
+        adata, net = dc.ds.toy_bench()
+        df = dc.bm.benchmark(adata=adata, net=net, kws_decouple={"tmin": 3})
+        df
     """
     # Validate
     assert isinstance(adata, AnnData), "adata must be anndata.AnnData"

src/decoupler/ds/_bulk.py

@@ -23,6 +23,15 @@ def hsctgfb(
     Returns
     -------
     AnnData object.
+
+    Example
+    -------
+    .. code-block:: python
+
+        import decoupler as dc
+
+        adata = dc.ds.hsctgfb()
+        adata
     """
     # Download
     url = (
@@ -70,6 +79,15 @@ def knocktf(
     Returns
     -------
     AnnData object.
+
+    Example
+    -------
+    .. code-block:: python
+
+        import decoupler as dc
+
+        adata = dc.ds.knocktf()
+        adata
     """
     assert isinstance(thr_fc, int | float) or thr_fc is None, "thr_fc must be numeric or None"
     # Download

src/decoupler/ds/_scell.py

@@ -50,6 +50,15 @@ def pbmc3k(
     Returns
     -------
     AnnData object.
+
+    Example
+    -------
+    .. code-block:: python
+
+        import decoupler as dc
+
+        adata = dc.ds.pbmc3k()
+        adata
     """
     url = "https://raw.githubusercontent.com/chanzuckerberg/cellxgene/main/example-dataset/pbmc3k.h5ad"
     adata = _download_anndata(url, verbose=verbose)
@@ -82,6 +91,15 @@ def covid5k(
     Returns
     -------
     AnnData object.
+
+    Example
+    -------
+    .. code-block:: python
+
+        import decoupler as dc
+
+        adata = dc.ds.covid5k()
+        adata
     """
     url = (
         "https://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/"
@@ -148,6 +166,15 @@ def erygast1k(
     Returns
     -------
     AnnData object.
+
+    Example
+    -------
+    .. code-block:: python
+
+        import decoupler as dc
+
+        adata = dc.ds.erygast1k()
+        adata
     """
     # How to process from scvelo:
     """

src/decoupler/ds/_spatial.py

@@ -29,6 +29,15 @@ def msvisium(
     Returns
     -------
     AnnData object.
+
+    Example
+    -------
+    .. code-block:: python
+
+        import decoupler as dc
+
+        adata = dc.ds.msvisium()
+        adata
     """
     url = "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM8563708&format=file&file=GSM8563708%5FMS377T%5F"
     # Download mat

src/decoupler/ds/_toy.py

@@ -47,6 +47,15 @@ def toy(
     Returns
     -------
     AnnData and net examples.
+
+    Example
+    -------
+    .. code-block:: python
+
+        import decoupler as dc
+
+        adata, net = dc.ds.toy()
+        adata, net
     """
     # Validate
     assert isinstance(nobs, int | float) and nobs >= 2, "nobs must be numeric and >= 2"
@@ -128,6 +137,15 @@ def toy_bench(shuffle_r: float = 0.25, seed: int = 42, verbose: bool = False, **
     Returns
     -------
     AnnData and net examples.
+
+    Example
+    -------
+    .. code-block:: python
+
+        import decoupler as dc
+
+        adata, net = dc.ds.toy_bench()
+        adata, net
     """
     # Validate
     assert isinstance(shuffle_r, int | float) and 0.0 <= shuffle_r <= 1.0, (

src/decoupler/ds/_utils.py

@@ -19,6 +19,14 @@ def ensmbl_to_symbol(
     Returns
     -------
     List of gene symbols
+
+    Example
+    -------
+    .. code-block:: python
+
+        import decoupler as dc
+
+        dc.ds.ensmbl_to_symbol(genes=["ENSG00000196092", "ENSG00000115415"], organism="hsapiens_gene_ensembl")
     """
     url = (
         'http://www.ensembl.org/biomart/martservice?query=<?xml version="1.0" encoding="UTF-8"?>'

src/decoupler/mt/_aucell.py

@@ -86,6 +86,15 @@ def _func_aucell(
         If ``None``, the top 5% of features based on their magnitude are selected.
 
     %(returns)s
+
+    Example
+    -------
+    .. code-block:: python
+
+        import decoupler as dc
+
+        adata, net = dc.ds.toy()
+        dc.mt.aucell(adata, net, tmin=3)
     """
     nobs, nvar = mat.shape
     nsrc = starts.size