Fixed bug 2.0.7 pl.obsm

.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

src/decoupler/mt/_consensus.py

@@ -106,6 +106,16 @@ def consensus(
     Returns
     -------
     Consensus enrichment scores and p-values.
+
+    Example
+    -------
+    .. code-block:: python
+
+        import decoupler as dc
+
+        adata, net = dc.ds.toy()
+        dc.mt.decouple(adata, net, tmin=3)
+        dc.mt.consensus(adata)
     """
     # Validate
     assert isinstance(result, dict | AnnData), "scores must be dict or anndata.AnnData"

src/decoupler/mt/_decouple.py

@@ -33,6 +33,19 @@ def decouple(
     %(empty)s
     %(bsize)s
     %(verbose)s
+
+    Returns
+    -------
+    Dictionary of results or as ``.obsm`` keys in the provided AnnData.
+
+    Example
+    -------
+    .. code-block:: python
+
+        import decoupler as dc
+
+        adata, net = dc.ds.toy()
+        dc.mt.decouple(adata, net, tmin=3)
     """
     # Validate
     _mdict = {m.name: m for m in _methods}

src/decoupler/mt/_gsea.py

@@ -224,6 +224,14 @@ def _func_gsea(
     %(seed)s
 
     %(returns)s
+
+    Example
+    -------
+    .. code-block:: python
+
+        import decoupler as dc
+        adata, net = dc.ds.toy()
+        dc.mt.gsea(adata, net, tmin=3)
     """
     nobs, nvar = mat.shape
     assert isinstance(times, int | float) and times >= 0, "times must be numeric and >= 0"

src/decoupler/mt/_gsva.py

@@ -362,6 +362,14 @@ def _func_gsva(
         will be regarded as 'highly' activated.
 
     %(returns)s
+
+    Example
+    -------
+    .. code-block:: python
+
+        import decoupler as dc
+        adata, net = dc.ds.toy()
+        dc.mt.gsva(adata, net, tmin=3)
     """
     if isinstance(mat, sps.csr_matrix):
         m = "gsva - Converting sparse matrix to dense format before density transformation"

src/decoupler/mt/_mdt.py

@@ -45,6 +45,15 @@ def _func_mdt(
     kwargs
         All other keyword arguments are passed to ``xgboost.XGBRegressor``.
     %(returns)s
+
+    Example
+    -------
+    .. code-block:: python
+
+        import decoupler as dc
+
+        adata, net = dc.ds.toy()
+        dc.mt.mdt(adata, net, tmin=3)
     """
     _check_import(xgboost, "xgboost")
     nobs = mat.shape[0]

src/decoupler/mt/_mlm.py

@@ -93,6 +93,15 @@ def _func_mlm(
     %(tval)s
 
     %(returns)s
+
+    Example
+    -------
+    .. code-block:: python
+
+        import decoupler as dc
+
+        adata, net = dc.ds.toy()
+        dc.mt.mlm(adata, net, tmin=3)
     """
     # Get dims
     n_features, n_fsets = adj.shape

src/decoupler/mt/_ora.py

@@ -240,6 +240,15 @@ def _func_ora(
         Number indicating the background size.
 
     %(returns)s
+
+    Example
+    -------
+    .. code-block:: python
+
+        import decoupler as dc
+
+        adata, net = dc.ds.toy()
+        dc.mt.ora(adata, net, tmin=3)
     """
     nobs, nvar = mat.shape
     nsrc = starts.size

src/decoupler/mt/_udt.py

@@ -49,6 +49,15 @@ def _func_udt(
     kwargs
         All other keyword arguments are passed to ``xgboost.XGBRegressor``.
     %(returns)s
+
+    Example
+    -------
+    .. code-block:: python
+
+        import decoupler as dc
+
+        adata, net = dc.ds.toy()
+        dc.mt.udt(adata, net, tmin=3)
     """
     _check_import(xgboost, "xgboost")
     nobs = mat.shape[0]

src/decoupler/mt/_ulm.py

@@ -82,6 +82,15 @@ def _func_ulm(
     %(tval)s
 
     %(returns)s
+
+    Example
+    -------
+    .. code-block:: python
+
+        import decoupler as dc
+
+        adata, net = dc.ds.toy()
+        dc.mt.ulm(adata, net, tmin=3)
     """
     # Get degrees of freedom
     n_var, n_src = adj.shape

src/decoupler/mt/_viper.py

@@ -283,6 +283,14 @@ def _func_viper(
         If ``pleiotropy``, number higher than 1 indicating the penalty for the pleiotropic interactions. 1 = no penalty.
 
     %(returns)s
+
+    Example
+    -------
+    .. code-block:: python
+
+        import decoupler as dc
+        adata, net = dc.ds.toy()
+        dc.mt.viper(adata, net, tmin=3)
     """
     # Get number of batches
     n_samples = mat.shape[0]

src/decoupler/mt/_waggr.py

@@ -207,6 +207,15 @@ def _func_waggr(
     %(seed)s
 
     %(returns)s
+
+    Example
+    -------
+    .. code-block:: python
+
+        import decoupler as dc
+
+        adata, net = dc.ds.toy()
+        dc.mt.waggr(adata, net, tmin=3)
     """
     assert isinstance(fun, str) or callable(fun), "fun must be str or callable"
     if isinstance(fun, str):

src/decoupler/mt/_zscore.py

@@ -56,6 +56,15 @@ def _func_zscore(
         Which flavor to use when calculating the z-score, either KSEA or RoKAI.
 
     %(returns)s
+
+    Example
+    -------
+    .. code-block:: python
+
+        import decoupler as dc
+
+        adata, net = dc.ds.toy()
+        dc.mt.zscore(adata, net, tmin=3)
     """
     assert isinstance(flavor, str) and flavor in ["KSEA", "RoKAI"], "flavor must be str and KSEA or RoKAI"
     nobs, nvar = mat.shape