From b2a7d54ee27d80ad36df843119570cc01cefc00a Mon Sep 17 00:00:00 2001
From: Oliver Beckstein <orbeckst@gmail.com>
Date: Thu, 10 Oct 2024 11:31:12 -0700
Subject: [PATCH] RTD with own conda environment

- new devtools/conda-envs/readthedocs.yaml
- update RTD config with new env file
- update sphinx config (intersphinx, put authors into variable)
- blackened sphinx conf.py
---
 .readthedocs.yaml                    |  2 +-
 devtools/conda-envs/readthedocs.yaml | 26 +++++++++++++++++++++
 doc/sphinx/source/conf.py            | 34 +++++++++++++---------------
 3 files changed, 43 insertions(+), 19 deletions(-)
 create mode 100644 devtools/conda-envs/readthedocs.yaml

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 31c7bb8d..4ee85489 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -25,5 +25,5 @@ python:
         path: .
 
 conda:
-    environment: devtools/conda-envs/test_env.yaml
+    environment: devtools/conda-envs/readthedocs.yaml
 
diff --git a/devtools/conda-envs/readthedocs.yaml b/devtools/conda-envs/readthedocs.yaml
new file mode 100644
index 00000000..a9d7747b
--- /dev/null
+++ b/devtools/conda-envs/readthedocs.yaml
@@ -0,0 +1,26 @@
+name: readthedocs
+channels:
+- conda-forge
+dependencies:
+- python >=3.10
+- six
+- numpy
+- scipy >=1.11.0
+- matplotlib-base
+- pandas
+- scikit-learn
+- pyyaml
+- mdanalysis >=2
+- numkit
+- gromacswrapper
+- alchemlyb >=2
+- pymbar >=4
+- rdkit
+- seaborn
+- svgutils
+- cairosvg
+- pypdf
+
+# sphinx and RTD
+- sphinx
+- sphinx_rtd_theme
\ No newline at end of file
diff --git a/doc/sphinx/source/conf.py b/doc/sphinx/source/conf.py
index b55c6df5..df741327 100644
--- a/doc/sphinx/source/conf.py
+++ b/doc/sphinx/source/conf.py
@@ -55,9 +55,8 @@
 # General information about the project.
 project = "MDPOW"
 now = datetime.datetime.now()
-copyright = "2010–{}, Shujie Fan, Ian Kenney, Alia Lescoulie, Bogdan Iorga, and Oliver Beckstein".format(
-    now.year
-)
+authors = "Shujie Fan, Ian Kenney, Alia Lescoulie, Bogdan Iorga, and Oliver Beckstein"
+copyright = "2010–{}, ".format(now.year) + authors
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -220,16 +219,16 @@
 latex_documents = [
     (
         "index",
-        "MDpow.tex",
-        "MDpow Documentation",
-        "Ian Kenney, Bogdan Iorga, and Oliver Beckstein",
+        "MDPOW.tex",
+        "MDPOW Documentation",
+        authors,
         "manual",
     ),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
 # the title page.
-# latex_logo = None
+latex_logo = html_logo
 
 # For "manual" documents, if this is true, then toplevel headings are parts,
 # not chapters.
@@ -250,17 +249,16 @@
 # intersphinx: reference standard lib and RecSQL
 # http://sphinx.pocoo.org/latest/ext/intersphinx.html
 intersphinx_mapping = {
-    "https://docs.python.org/": None,
-    "https://numpy.org/doc/stable/": None,
-    "https://docs.scipy.org/doc/scipy/reference/": None,
-    "https://gromacswrapper.readthedocs.io/en/latest": None,
-    "https://docs.mdanalysis.org/stable/": None,
-    "https://www.rdkit.org/docs/": None,
-    "https://pandas.pydata.org/docs/": None,
-    "https://seaborn.pydata.org": None,
-    "https://cairosvg.org/documentation/": None,
-    "https://svgutils.readthedocs.io/en/latest/": None,
-    "https://pypdf.readthedocs.io/en/stable/": None,
+    "python": ("https://docs.python.org/3", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy", None),
+    "GromacsWrapper": ("https://gromacswrapper.readthedocs.io/en/latest", None),
+    "MDAnalysis": ("https://docs.mdanalysis.org/stable/", None),
+    "RDKit": ("https://www.rdkit.org/docs/", None),
+    "pandas": ("https://pandas.pydata.org/docs/", None),
+    "seaborn": ("https://seaborn.pydata.org", None),
+    "svgutils": ("https://svgutils.readthedocs.io/en/latest/", None),
+    "pypdf": ("https://pypdf.readthedocs.io/en/stable/", None),
 }