Added python 3.12 support, dropped 3.8

* Update python-build.yml

add python 3.12, dropped 3.8

* Update .readthedocs.yml

update readthedocs.yml

* Update weblogo_changelog.txt

update change log with new python version, dropping python 3.8 support. noting updates around ghostscript deprecation

* Update setup.py

add python version 3.12 and update minimum python version

* Update index.html

update citation count to 12k

* Update CITATION.cff

update version to 3.8 and date of release

.github/workflows/python-build.yml

@@ -16,7 +16,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
 
     steps:
     - uses: actions/checkout@v3

.readthedocs.yml

@@ -1,8 +1,20 @@
+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
 version: 2
-formats: []
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+
+# Build documentation in the "docs/" directory with Sphinx
 sphinx:
   configuration: docs/conf.py
+
+
 python:
-  version: 3.7
   install:
     - requirements: requirements.txt

CITATION.cff

@@ -17,8 +17,8 @@ preferred-citation:
   end: 1190
   year: 2004
   doi: 10.1101/gr.849004
-version: 3.7
-date-released: 2019-03-04
+version: 3.8
+date-released: 2024-03-03
 license: MIT
 url: "http://weblogo.threeplusone.com/"
 repository-code: "https://github.com/WebLogo/weblogo"

setup.py

@@ -17,7 +17,7 @@
 
 setup(
     name="weblogo",
-    python_requires=">=3.8",
+    python_requires=">=3.9",
     install_requires=["numpy", "scipy", "setuptools"],
     use_scm_version=True,
     setup_requires=["setuptools_scm"],
@@ -40,10 +40,10 @@
         # Specify the Python versions you support here. In particular, ensure
         # that you indicate whether you support Python 2, Python 3 or both.
         "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
         "Programming Language :: Python :: 3.11",
+        "Programming Language :: Python :: 3.12",
     ],
     packages=[
         "weblogo",

weblogo/htdocs/index.html

@@ -71,7 +71,7 @@
 
               <p class="lead">
               <a href="http://weblogo.berkeley.edu/"><strong>WebLogo</strong></a>
-              is a web-based application designed to make the generation of sequence logos easy and painless. WebLogo has been featured in over <a href="https://scholar.google.com/citations?view_op=view_citation&hl=en&user=zXkYKVEAAAAJ&citation_for_view=zXkYKVEAAAAJ:u5HHmVD_uO8C"> 10000 </a>scientific publications.
+              is a web-based application designed to make the generation of sequence logos easy and painless. WebLogo has been featured in over <a href="https://scholar.google.com/citations?view_op=view_citation&hl=en&user=zXkYKVEAAAAJ&citation_for_view=zXkYKVEAAAAJ:u5HHmVD_uO8C"> 12000 </a>scientific publications.
               </p>
 
               <p>A <a href="https://alum.mit.edu/www/toms/sequencelogo.html">sequence&nbsp;logo</a> is a graphical representation of an amino acid or nucleic acid multiple sequence alignment. Each logo consists of stacks of symbols, one stack for each position in the sequence. The overall height of the stack indicates the sequence conservation at that position, while the height of symbols within the stack indicates the relative frequency of each amino or nucleic acid at that position. In general, a sequence logo provides a richer and more precise description of, for example, a binding site, than would a consensus sequence. </p>

weblogo/htdocs/weblogo_changelog.txt

@@ -1,4 +1,8 @@
 WebLogo Release Notes
+3.8 (2024-03-03) [Gavin Crooks, Melissa Fabros]
+* fixes for Ghostscript deprecation
+* remove support for python 3.8
+Weblogo 3.8 runs under python 3.9, 3.10, 3.11, 3.12
 
 
 3.7.11 (2022-05-26) [Gavin Crooks, Melissa Fabros]