From 9b1eb1f4f94cdf5db3624b150eb2039654db251c Mon Sep 17 00:00:00 2001
From: Jason Kai <tkai@uwo.ca>
Date: Fri, 20 Oct 2023 09:26:52 -0400
Subject: [PATCH] Fix plotting documentation

Issue with matplotlib installation that prevented the plotting page to
be loaded. This was due to a `poetry` installation command.

Also added intersphinx mappings for plotting functionality and made some
text changes to docstrings.
---
 .gitignore              | 3 ++-
 .readthedocs.yml        | 4 +++-
 afids_utils/metrics.py  | 2 +-
 afids_utils/plotting.py | 7 +++----
 docs/api/transform.md   | 2 +-
 docs/conf.py            | 4 ++++
 6 files changed, 14 insertions(+), 8 deletions(-)

diff --git a/.gitignore b/.gitignore
index 53ed9238..c12c944b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,7 +1,8 @@
 # Directories
 __pycache__/
+_build/
 
 # Testing
 .hypothesis
 .ruff_cache
-.pytest_cache
\ No newline at end of file
+.pytest_cache
diff --git a/.readthedocs.yml b/.readthedocs.yml
index 8fa269db..821e1af7 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -17,9 +17,11 @@ formats: [pdf]
 build:
   os: ubuntu-20.04
   tools:
-    python: '3.10'
+    python: "3.10"
 python:
   install:
     - requirements: docs/requirements.txt
     - method: pip
       path: .
+      extra_requirements:
+        - plotting
diff --git a/afids_utils/metrics.py b/afids_utils/metrics.py
index f7977e82..ce7e4289 100644
--- a/afids_utils/metrics.py
+++ b/afids_utils/metrics.py
@@ -65,7 +65,7 @@ def mean_distances(
     template_afid_set: AfidSet,
     component: str = "distance",
 ) -> list[float]:
-    """Calculate the average distance for a given spatial component betweeen
+    """Calculate the average distance for a given spatial component between
     a collection of ``AfidSet`` objects and a common / template ``AfidSet``.
 
     Parameters
diff --git a/afids_utils/plotting.py b/afids_utils/plotting.py
index 4dc77b61..2d8c626a 100644
--- a/afids_utils/plotting.py
+++ b/afids_utils/plotting.py
@@ -87,11 +87,11 @@ def plot_ortho(
     nii_img: nib.nifti1.Nifti1Image,
     opacity: float = 1,
 ) -> StatMapView:
-    """Generate interactive, html ortho view of the slices. Uses ``nilearn``
-    to generate the figures.
+    """Generate interactive, html ortho view of the slices. Uses
+    ``nilearn.plotting`` to generate the figures.
 
     The generated view can either be opened interactively or saved as a figure
-    per ``nilearn`` functionality:
+    per ``nilearn.plotting`` functionality:
         * Interactive view - ``view.open_in_browser()``
         * Save - ``view.save_as_html(file_name.html)``
 
@@ -108,7 +108,6 @@ def plot_ortho(
 
     opacity:
         Opacity value [0 - transparent, 1 - opaque] of overlaid AFIDs
-        (default: 0.8)
 
     Returns
     -------
diff --git a/docs/api/transform.md b/docs/api/transform.md
index b7f280db..e2901992 100644
--- a/docs/api/transform.md
+++ b/docs/api/transform.md
@@ -3,4 +3,4 @@
 ```{eval-rst}
     .. automodule:: afids_utils.transforms
         :members:
-```
\ No newline at end of file
+```
diff --git a/docs/conf.py b/docs/conf.py
index 1a5b573b..0bef26bf 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -80,7 +80,11 @@
 
 intersphinx_mapping = {
     "python": ("https://docs.python.org/3", None),
+    "matplotlib": ("https://matplotlib.org/stable", None),
+    "nibabel": ("https://nipy.org/nibabel", None),
+    "nilearn": ("https://nilearn.github.io/stable/plotting", None),
     "numpy": ("https://numpy.org/doc/1.24", None),
+    "plotly": ("https://plotly.com/python", None),
 }