add dark logo, doc fixes

Author: trichter

.github/workflows/logo.yml

@@ -27,7 +27,7 @@ jobs:
         run: |
           python create_sugar_logo.py sugar_logo.png
           python create_sugar_logo.py sugar_logo_transparent.png --transparent
-          python create_sugar_logo.py sugar_logo_dark.png --transparent --color1 0.9 --color2 0.5
+          python create_sugar_logo.py sugar_logo_dark.png --transparent --color1 0.8 --color2 0.5
       - name: commit logo
         run: |
           git config --global user.name 'trichter'

docs/conf.py

@@ -35,11 +35,11 @@ def parse_version():
 #     return sorted(modules)
 
 
-def download_logo():
+def download_logo(modifier=''):
     from pathlib import Path
     import urllib.request
-    logo = Path(__file__).parent / '_static/sugar_logo.png'
-    url = 'https://raw.githubusercontent.com/rnajena/sugar/logo/sugar_logo.png'
+    logo = Path(__file__).parent / f'_static/sugar_logo{modifier}.png'
+    url = f'https://raw.githubusercontent.com/rnajena/sugar/logo/sugar_logo{modifier}.png'
     urllib.request.urlretrieve(url, logo)
     return logo.name
 
@@ -76,6 +76,7 @@ def write_table(what):
 .. _biopython: https://biopython.org
 .. _biotite: https://www.biotite-python.org
 .. _DNAFeaturesViewer: https://edinburgh-genome-foundry.github.io/DnaFeaturesViewer
+.. _Clustal: https://en.wikipedia.org/wiki/Clustal
 """
 
 extensions = ['sphinx.ext.autodoc',
@@ -103,9 +104,11 @@ def write_table(what):
 html_theme = 'furo'
 html_static_path = ['_static']
 html_title = f'S*R for your RNA <br>v{release} docs'
-html_logo = '_static/' + download_logo()
+#html_logo = '_static/' + download_logo()
 html_show_sphinx  = True
 html_theme_options = {
+    'light_logo': download_logo(),
+    'dark_logo': download_logo('_dark'),
     'footer_icons' : [],
     "source_edit_link": "https://github.com/rnajena/sugar/edit/master/docs/{filename}",
     #"source_view_link": "_sources/src/{filename}.txt",

src/sugar/_io/clustal.py

@@ -1,6 +1,6 @@
 # (C) 2024, Tom Eulenfeld, MIT license
 """
-`Clustal`_ reader
+`Clustal`_ IO
 """
 from warnings import warn
 from sugar import BioBasket, BioSeq, __version__

src/sugar/core/cane.py

@@ -381,8 +381,8 @@ def find_orfs(seq, rf='all', start='start', stop='stop', need_start='always', ne
         You can attach these features to sequences using `.BioSeq.add_fts()` or `.BioBasket.add_fts()`.
         Use the `.BioSeq.fts` and `.BioBasket.fts` properties to overwrite features with the found ORFs.
 
-    ..note::
-        Python's `python:re.matchall()` is used internally to find start and stop codons.
+    .. note::
+        Python's :func:`python:re.finditer` is used internally to find start and stop codons.
         The limitations of this function apply; for example, matches cannot overlap.
         Care must be taken in special cases.
         For instance, if ORFs do not need to start with a start codon,