From c520c7ee965a740bfc05f7610808eca0ce7307fa Mon Sep 17 00:00:00 2001 From: "m.fab" Date: Sat, 28 Sep 2024 19:08:02 -0700 Subject: [PATCH] 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 | 2 +- .readthedocs.yml | 16 ++++++++++++++-- CITATION.cff | 4 ++-- setup.py | 4 ++-- weblogo/htdocs/index.html | 2 +- weblogo/htdocs/weblogo_changelog.txt | 4 ++++ 6 files changed, 24 insertions(+), 8 deletions(-) diff --git a/.github/workflows/python-build.yml b/.github/workflows/python-build.yml index 309dccf6..8a79afa2 100644 --- a/.github/workflows/python-build.yml +++ b/.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 diff --git a/.readthedocs.yml b/.readthedocs.yml index 493fa24c..e446146d 100644 --- a/.readthedocs.yml +++ b/.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 diff --git a/CITATION.cff b/CITATION.cff index 8cfe1570..f53487f5 100644 --- a/CITATION.cff +++ b/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" diff --git a/setup.py b/setup.py index 7fd843c4..e77fe7f9 100755 --- a/setup.py +++ b/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", diff --git a/weblogo/htdocs/index.html b/weblogo/htdocs/index.html index 00dc9291..804d8dc4 100644 --- a/weblogo/htdocs/index.html +++ b/weblogo/htdocs/index.html @@ -71,7 +71,7 @@

WebLogo - is a web-based application designed to make the generation of sequence logos easy and painless. WebLogo has been featured in over 10000 scientific publications. + is a web-based application designed to make the generation of sequence logos easy and painless. WebLogo has been featured in over 12000 scientific publications.

A sequence logo 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.

diff --git a/weblogo/htdocs/weblogo_changelog.txt b/weblogo/htdocs/weblogo_changelog.txt index c3c8288a..cddbe2af 100644 --- a/weblogo/htdocs/weblogo_changelog.txt +++ b/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]