[med-svn] [Git][med-team/tombo][master] 5 commits: Fix Sphinx build Closes: #1135512
Andreas Tille (@tille)
gitlab at salsa.debian.org
Sun May 10 07:57:47 BST 2026
Andreas Tille pushed to branch master at Debian Med / tombo
Commits:
26fd0128 by Andreas Tille at 2026-05-10T08:52:12+02:00
Fix Sphinx build Closes: #1135512
- - - - -
1e2ac769 by Andreas Tille at 2026-05-10T08:54:14+02:00
d/watch: version=5
- - - - -
357074ea by Andreas Tille at 2026-05-10T08:54:45+02:00
Standards-Version: 4.7.4 (routine-update)
- - - - -
04cef555 by Andreas Tille at 2026-05-10T08:55:23+02:00
Changes made by cme
- - - - -
5a82549e by Andreas Tille at 2026-05-10T08:55:25+02:00
Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)
- - - - -
5 changed files:
- debian/changelog
- debian/control
- debian/patches/mathjax.patch
- debian/rules
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+tombo (1.5.1-9) UNRELEASED; urgency=medium
+
+ * Fix Sphinx build
+ Closes: #1135512
+ * d/watch: version=5
+ * Standards-Version: 4.7.4 (routine-update)
+ * Reflow Uploaders field (cme)
+ * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)
+
+ -- Andreas Tille <tille at debian.org> Sat, 09 May 2026 17:56:17 +0200
+
tombo (1.5.1-8) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -1,41 +1,46 @@
Source: tombo
+Standards-Version: 4.7.4
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
+Uploaders:
+ Andreas Tille <tille at debian.org>,
Section: science
-Build-Depends: cython3,
- debhelper-compat (= 13),
- dh-python,
- libjs-mathjax,
- python3-all-dev,
- python3-h5py <!nocheck>,
- python3-mappy <!nocheck>,
- python3-nose2 <!nocheck>,
- python3-numpy,
- python3-numpy-dev,
- python3-scipy <!nocheck>,
- python3-setuptools,
- python3-sphinx,
- python3-sphinx-argparse,
- python3-sphinx-rtd-theme,
- python3-tqdm <!nocheck>,
- sphinx-doc
-Standards-Version: 4.7.2
+Build-Depends:
+ cython3,
+ debhelper-compat (= 13),
+ dh-sequence-python3,
+ libjs-mathjax,
+ python3-all-dev,
+ python3-h5py <!nocheck>,
+ python3-mappy <!nocheck>,
+ python3-nose2 <!nocheck>,
+ python3-numpy,
+ python3-numpy-dev,
+ python3-scipy <!nocheck>,
+ python3-setuptools,
+ python3-sphinx,
+ python3-sphinx-argparse,
+ python3-sphinx-rtd-theme,
+ python3-tqdm <!nocheck>,
+ sphinx-doc,
Vcs-Browser: https://salsa.debian.org/med-team/tombo
Vcs-Git: https://salsa.debian.org/med-team/tombo.git
Homepage: https://github.com/nanoporetech/tombo
Package: tombo
Architecture: any
-Depends: python3-h5py,
- python3-mappy,
- python3-numpy,
- python3-packaging,
- python3-scipy,
- python3-tqdm,
- ${misc:Depends},
- ${python3:Depends},
- ${shlibs:Depends}
-Recommends: python3-pyfaidx, python3-rpy2
+Depends:
+ python3-h5py,
+ python3-mappy,
+ python3-numpy,
+ python3-packaging,
+ python3-scipy,
+ python3-tqdm,
+ ${misc:Depends},
+ ${python3:Depends},
+ ${shlibs:Depends},
+Recommends:
+ python3-pyfaidx,
+ python3-rpy2,
Description: identification of modified nucleotides from raw nanopore sequencing data
Tombo is a suite of tools primarily for the identification of modified
nucleotides from nanopore sequencing data. Tombo also provides tools for
@@ -43,9 +48,12 @@ Description: identification of modified nucleotides from raw nanopore sequencing
Package: tombo-doc
Architecture: all
-Section: doc
-Depends: libjs-mathjax, ${misc:Depends}, ${sphinxdoc:Depends}
Multi-Arch: foreign
+Section: doc
+Depends:
+ libjs-mathjax,
+ ${misc:Depends},
+ ${sphinxdoc:Depends},
Description: identification of modified nucleotides from raw nanopore sequencing data (doc)
Tombo is a suite of tools primarily for the identification of modified
nucleotides from nanopore sequencing data. Tombo also provides tools for
=====================================
debian/patches/mathjax.patch
=====================================
@@ -4,7 +4,7 @@ Description: Use Debian packaged MathJax
--- a/docs/conf.py
+++ b/docs/conf.py
-@@ -26,7 +26,7 @@ sys.path.insert(0, os.path.abspath('../t
+@@ -26,10 +26,10 @@ sys.path.insert(0, os.path.abspath('../t
extensions = ['sphinx.ext.autodoc', 'sphinx.ext.viewcode',
'sphinx.ext.intersphinx', 'sphinx.ext.mathjax', 'sphinxarg.ext',
'sphinx.ext.napoleon',]
@@ -12,4 +12,8 @@ Description: Use Debian packaged MathJax
+mathjax_path = "file:///usr/share/javascript/mathjax/MathJax.js?config=TeX-AMS-MML_HTMLorMML"
# don't include class inheritence in docs: https://stackoverflow.com/questions/46279030/how-can-i-prevent-sphinx-from-listing-object-as-a-base-class
- from sphinx.ext.autodoc import ClassDocumenter, _
+-from sphinx.ext.autodoc import ClassDocumenter, _
++from sphinx.ext.autodoc import ClassDocumenter
+ add_line = ClassDocumenter.add_line
+ def add_line_no_bases(self, text, *args, **kwargs):
+ if text.strip().startswith('Bases: '):
=====================================
debian/rules
=====================================
@@ -6,7 +6,7 @@ export http_proxy='127.0.0.1:9'
export DEB_BUILD_MAINT_OPTIONS=hardening=+all
%:
- dh $@ --with python3,sphinxdoc --buildsystem=pybuild
+ dh $@ --with sphinxdoc --buildsystem=pybuild
execute_after_dh_auto_clean:
rm -f tombo/_c_dynamic_programming.cpp tombo/_c_helper.cpp
=====================================
debian/watch
=====================================
@@ -1,4 +1,4 @@
-version=4
+Version: 5
-opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%" \
- https://github.com/nanoporetech/tombo/tags .*/v?@ANY_VERSION@\.tar\.gz
+Template: Github
+Dist: https://github.com/nanoporetech/tombo
View it on GitLab: https://salsa.debian.org/med-team/tombo/-/compare/6d85aaac469cf8bd2a1d3bc7fe530290e308f1c1...5a82549efb479dcdfb1f66aeddf64af9292d6068
--
View it on GitLab: https://salsa.debian.org/med-team/tombo/-/compare/6d85aaac469cf8bd2a1d3bc7fe530290e308f1c1...5a82549efb479dcdfb1f66aeddf64af9292d6068
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