From 945ee23e36a26119f6bcadcd2435114191cc67d4 Mon Sep 17 00:00:00 2001
From: Martin Larralde <martin.larralde@embl.de>
Date: Wed, 10 Jul 2024 13:41:11 +0200
Subject: [PATCH] Fix missing `api/hmmer/iter.rst` file and update styles
---
CONTRIBUTING.md | 2 +-
docs/api/hmmer/{jackhmmer.rst => iter.rst} | 0
docs/conf.py | 21 ++++++++-------------
3 files changed, 9 insertions(+), 14 deletions(-)
rename docs/api/hmmer/{jackhmmer.rst => iter.rst} (100%)
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index f20a2268..c35e0cfd 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -1,4 +1,4 @@
-# Contributing to pyHMMER
+# Contributing to PyHMMER
For bug fixes or new features, please file an issue before submitting a
pull request. If the change isn't trivial, it may be best to wait for
diff --git a/docs/api/hmmer/jackhmmer.rst b/docs/api/hmmer/iter.rst
similarity index 100%
rename from docs/api/hmmer/jackhmmer.rst
rename to docs/api/hmmer/iter.rst
diff --git a/docs/conf.py b/docs/conf.py
index daa4a5f4..3186ebca 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -27,16 +27,6 @@ if os.getenv("READTHEDOCS", "False") != "True":
sys.path.insert(0, project_dir)
-# -- Sphinx Setup ------------------------------------------------------------
-
-def setup(app):
- pass
- # Add custom stylesheet
- # app.add_css_file("css/main.css")
- # app.add_js_file("js/apitoc.js")
- # app.add_js_file("js/example-admonition.js")
-
-
# -- Project information -----------------------------------------------------
import pyhmmer
@@ -129,23 +119,28 @@ html_css_files = ["custom.css"]
# documentation.
#
html_theme_options = {
+ "external_links": [
+ {
+ "url": "https://doi.org/10.1093/bioinformatics/btad214",
+ "name": "Paper",
+ },
+ ],
"show_toc_level": 2,
"use_edit_page_button": True,
"icon_links": [
{
"name": "GitHub",
- "url": "https://github.com/pydata/pydata-sphinx-theme",
+ "url": "https://github.com/althonos/pyhmmer",
"icon": "fa-brands fa-github",
},
{
"name": "PyPI",
- "url": "https://pypi.org/project/pydata-sphinx-theme",
+ "url": "https://pypi.org/project/pyhmmer",
"icon": "fa-custom fa-pypi",
},
],
"logo": {
"text": "PyHMMER",
- "image_dark": "_images/logo.png",
},
"navbar_align": "left",
"footer_start": ["copyright"],
--
GitLab