From df5690e1477301677d77de0d338f718627688b58 Mon Sep 17 00:00:00 2001
From: Danila Bredikhin <danila.bredikhin@embl.de>
Date: Wed, 26 May 2021 17:50:10 +0200
Subject: [PATCH] Improve docs

---
 docs/source/omics/multi.rst | 9 +++++++++
 muon/_core/preproc.py       | 9 ---------
 muon/rna.py                 | 1 +
 pyproject.toml              | 2 +-
 4 files changed, 11 insertions(+), 10 deletions(-)
 create mode 100644 muon/rna.py

diff --git a/docs/source/omics/multi.rst b/docs/source/omics/multi.rst
index e25fbd4..a79c419 100644
--- a/docs/source/omics/multi.rst
+++ b/docs/source/omics/multi.rst
@@ -75,3 +75,12 @@ Weighted nearest neighbours (WNN) is a procedure to define a neighbourhood graph
 	>>> mu.pp.neighbors(mdata)
 	>>> mu.tl.umap(mdata)
 
+
+Utility functions
+-----------------
+
+To manage the complexity of having to deal with multiple modalities, there is a handful of utility functions in `muon`. This includes in-place filtering: just as it works `for a single modality <uni.rst#in-place-filtering>`_, :func:`muon.pp.filter_obs` and :func:`muon.pp.filter_var` will filter observations or variables in each modality as well as in the attributes of the ``MuData`` object.
+
+In order to keep observations present in all the modalities, there is :func:`muon.pp.intersect_obs`. Using the in-place filtering under the hood, it will modify the ``MuData`` object and the contained modalities to only have the common observations:
+
+        >>> mu.pp.intersect_obs(mdata)
diff --git a/muon/_core/preproc.py b/muon/_core/preproc.py
index 1d5a522..39ae45b 100644
--- a/muon/_core/preproc.py
+++ b/muon/_core/preproc.py
@@ -612,9 +612,6 @@ def intersect_obs(mdata: MuData):
     Subset observations (samples or cells) in-place
     taking observations present only in all modalities.
 
-    This function is currently a draft, and it can be removed
-    or its behaviour might be changed in future.
-
     Parameters
     ----------
     mdata: MuData
@@ -646,9 +643,6 @@ def filter_obs(
     Filter observations (samples or cells) in-place
     using any column in .obs or in .X.
 
-    This function is currently a draft, and it can be removed
-    or its behaviour might be changed in future.
-
     Parameters
     ----------
     data: AnnData or MuData
@@ -765,9 +759,6 @@ def filter_var(
     Filter variables (features, e.g. genes) in-place
     using any column in .var or row in .X.
 
-    This function is currently a draft, and it can be removed
-    or its behaviour might be changed in future.
-
     Parameters
     ----------
     data: AnnData or MuData
diff --git a/muon/rna.py b/muon/rna.py
new file mode 100644
index 0000000..6bf4a15
--- /dev/null
+++ b/muon/rna.py
@@ -0,0 +1 @@
+from ._rna import *
diff --git a/pyproject.toml b/pyproject.toml
index bc26c79..c52a978 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -46,7 +46,7 @@ docs = [
 Documentation = "https://muon.readthedocs.io/en/latest/"
 
 [tool.flit.sdist]
-exclude = [".github"]
+exclude = [".github", "docs/build"]
 
 
 [tool.black]