From 5fc3d9a30d89412b2582b9be5403418e42609128 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= <bouysset.cedric@gmail.com>
Date: Fri, 11 Jun 2021 12:31:10 +0200
Subject: [PATCH] fix sphinx warnings

---
 README.rst                 |  3 +++
 prolif/fingerprint.py      | 16 +++++++++-------
 prolif/plotting/network.py |  4 ++--
 3 files changed, 14 insertions(+), 9 deletions(-)

diff --git a/README.rst b/README.rst
index 4e05f8e..9783502 100644
--- a/README.rst
+++ b/README.rst
@@ -32,6 +32,9 @@ Documentation
 
 The installation instructions, documentation and tutorials can be found online on `ReadTheDocs <https://prolif.readthedocs.io/en/latest/>`_.
 
+| ⚠ Do not ``pip install prolif`` yet ⚠
+| Please refer to the installation instructions instead (and `this comment <https://github.com/chemosim-lab/ProLIF/issues/6#issue-784313798>`__ if you want to know the details)
+
 Issues
 ------
 
diff --git a/prolif/fingerprint.py b/prolif/fingerprint.py
index 09b96a1..b946fd4 100644
--- a/prolif/fingerprint.py
+++ b/prolif/fingerprint.py
@@ -218,10 +218,10 @@ def bitvector_atoms(self, res1, res2):
             A list containing indices for the protein atoms responsible for
             each interaction
 
-
         .. versionchanged:: 0.3.2
-            Returns atom indices as two separate lists instead of a single list
-            of tuples
+            Atom indices are returned as two separate lists instead of a single
+            list of tuples
+
         """
         bitvector = []
         lig_atoms = []
@@ -334,6 +334,7 @@ def run(self, traj, lig, prot, residues=None, progress=True):
         .. versionchanged:: 0.3.2
             Moved the ``return_atoms`` parameter from the ``run`` method to the
             dataframe conversion code
+
         """
         iterator = tqdm(traj) if progress else traj
         if residues == "all":
@@ -387,14 +388,15 @@ def run_from_iterable(self, lig_iterable, prot_mol, residues=None,
             >>> fp = plf.Fingerprint()
             >>> fp.run_from_iterable(lig_iter, prot)
 
-        Notes
-        -----
-        See :meth:`~Fingerprint.generate` to generate the fingerprint between
-        two single structures
+        .. seealso::
+
+            :meth:`Fingerprint.generate` to generate the fingerprint between
+            two single structures
 
         .. versionchanged:: 0.3.2
             Moved the ``return_atoms`` parameter from the ``run_from_iterable``
             method to the dataframe conversion code
+
         """
         iterator = tqdm(lig_iterable) if progress else lig_iterable
         if residues == "all":
diff --git a/prolif/plotting/network.py b/prolif/plotting/network.py
index fb0d303..edca756 100644
--- a/prolif/plotting/network.py
+++ b/prolif/plotting/network.py
@@ -2,6 +2,8 @@
 Plot a Ligand Interaction Network --- :mod:`prolif.plotting.network`
 ====================================================================
 
+.. versionadded:: 0.3.2
+
 .. autoclass:: LigNetwork
    :members:
 
@@ -71,8 +73,6 @@ class LigNetwork:
     You can customize the diagram by tweaking :attr:`LigNetwork.COLORS` and
     :attr:`LigNetwork.RESIDUE_TYPES` by adding or modifying the
     dictionaries inplace.
-
-    .. versionadded:: 0.3.2
     """
     COLORS = {
         "interactions": {