[med-svn] [Git][med-team/python-biom-format][master] 4 commits: use sphinx-build generate manpage.
Karsten Schöke (@karso)
gitlab at salsa.debian.org
Sat Aug 8 08:04:00 BST 2026
Karsten Schöke pushed to branch master at Debian Med / python-biom-format
Commits:
676c3512 by Karsten Schöke at 2026-08-07T10:00:46+02:00
use sphinx-build generate manpage.
- - - - -
6f7a8698 by Karsten Schöke at 2026-08-07T10:01:45+02:00
reconfigure sphings-build html doc
- - - - -
fcf15359 by Karsten Schöke at 2026-08-07T10:03:59+02:00
prepare 2.1.17-4 relaese.
- - - - -
d19f5cd3 by Karsten Schöke at 2026-08-07T10:07:05+02:00
Changes made by cme
- - - - -
10 changed files:
- − debian/biom.1
- debian/changelog
- debian/control
- − debian/create-manpages
- − debian/createmanpages
- − debian/manpages
- − debian/python-biom-format-doc.docs
- + debian/python-biom-format-doc.install
- + debian/python3-biom-format.install
- debian/rules
Changes:
=====================================
debian/biom.1 deleted
=====================================
@@ -1,51 +0,0 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.12.
-.TH BIOM "1" "July 2020" "biom 2.1.8" "User Commands"
-.SH NAME
-biom \- Biological Observation Matrix (BIOM) format (Python 3)
-.SH SYNOPSIS
-.B biom
-[\fI\,OPTIONS\/\fR] \fI\,COMMAND \/\fR[\fI\,ARGS\/\fR]...
-.SH OPTIONS
-.TP
-\fB\-\-version\fR
-Show the version and exit.
-.TP
-\fB\-h\fR, \fB\-\-help\fR
-Show this message and exit.
-.SS "Commands:"
-.TP
-add\-metadata
-Add metadata to a BIOM table.
-.TP
-convert
-Convert to/from the BIOM table format.
-.TP
-export\-metadata
-Export metadata as TSV.
-.TP
-from\-uc
-Create a BIOM table from a vsearch/uclust/usearch BIOM...
-.TP
-head
-Dump the first bit of a table.
-.TP
-normalize\-table
-Normalize a BIOM table.
-.TP
-show\-install\-info
-Provide information about the biom\-format installation.
-.TP
-subset\-table
-Subset a BIOM table.
-.TP
-summarize\-table
-Summarize sample or observation data in a BIOM table.
-.TP
-table\-ids
-Dump IDs in a table.
-.TP
-validate\-table
-Validate a BIOM\-formatted file.
-.SH AUTHOR
- This manpage was written by Nilesh Patra for the Debian distribution and
- can be used for any other usage of the program.
=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+python-biom-format (2.1.17-4) unstable; urgency=medium
+
+ * Team upload.
+ [ Andreas Tille ]
+ * Fix time traveling
+
+ [ Karsten Schöke ]
+ * use sphinx-build generate manpage.
+ * reconfigure sphings-build html doc
+ * Changes made by cme
+
+ -- Karsten Schöke <karsten.schoeke at geobasis-bb.de> Fri, 07 Aug 2026 10:04:50 +0200
+
python-biom-format (2.1.17-3) unstable; urgency=medium
* Fix removal of unwanted files in /usr/lib/python3.14
=====================================
debian/control
=====================================
@@ -7,8 +7,9 @@ Uploaders:
Section: python
Testsuite: autopkgtest-pkg-python
Build-Depends:
- debhelper-compat (= 13),
+ debhelper-compat (= 14),
dh-sequence-python3,
+ dh-sequence-sphinxdoc,
pybuild-plugin-pyproject,
help2man,
bash-completion,
=====================================
debian/create-manpages deleted
=====================================
@@ -1,37 +0,0 @@
-#!/bin/sh
-# Create manpages using help2man
-# When calling help2man at package build time this would require
-# the following Build-Depends:
-
-HELP2MANDEPENDS="help2man python-dateutil python-cogent"
-
-# Specifically the last one does not come really cheap on slow
-# architectures - so we build the manpages statically here
-
-missingdepends=`dpkg -l ${HELP2MANDEPENDS} | \
- grep -v -e "^ii" -e "^|" -e "^++" -e "^ " -e "^..[^[:space:]]" | \
- sed 's/^[a-z][a-z][[:space:]]\+\([^[:space:]]\+\)[[:space:]]\+.*/\1/'`
-if [ "$missingdepends" != "" ] ; then \
- echo "Please install the following packages to rebuild the upstream source tarball:"
- echo $missingdepends
- exit 1
-fi
-
-mandir=`dirname $0`
-bindir=`dirname ${mandir}`/scripts
-codedir=`dirname ${mandir}`/python-code
-version=`dpkg-parsechangelog -l${mandir}/changelog | grep Version: | cut -f2 -d' ' | cut -f1 -d- `
-
-mkdir -p ${mandir}
-# later we will strip .py extension - so we need to rename the scripts here as well
-ln -s ${bindir}/biom_validator.py biom_validator
-help2man --no-info --name='Test a biom file for adherence to the format specification' \
- --version-string="${version}" \
- biom_validator > ${mandir}/biom_validator.1
-rm biom_validator
-
-ln -s ${bindir}/convert_biom.py convert_biom
-PYTHONPATH=${codedir} \
-help2man --no-info --name='Script to convert biom formatted files' \
- convert_biom > ${mandir}/convert_biom.1
-rm convert_biom
=====================================
debian/createmanpages deleted
=====================================
@@ -1,29 +0,0 @@
-#!/bin/sh
-MANDIR=debian
-mkdir -p $MANDIR
-
-VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
-NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
-PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1`
-
-AUTHOR=".SH AUTHOR\n \
-This manpage was written by $DEBFULLNAME for the Debian distribution and\n \
-can be used for any other usage of the program.\
-"
-
-# If program name is different from package name or title should be
-# different from package short description change this here
-progname=biom
-help2man --no-info --no-discard-stderr --help-option="-h" \
- --name="$NAME" \
- --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
-echo $AUTHOR >> $MANDIR/${progname}.1
-
-echo "$MANDIR/*.1" > debian/manpages
-
-cat <<EOT
-Please enhance the help2man output.
-The following web page might be helpful in doing so:
- http://liw.fi/manpages/
-EOT
-
=====================================
debian/manpages deleted
=====================================
@@ -1 +0,0 @@
-debian/*.1
=====================================
debian/python-biom-format-doc.docs deleted
=====================================
@@ -1 +0,0 @@
-build/html
=====================================
debian/python-biom-format-doc.install
=====================================
@@ -0,0 +1 @@
+build/html usr/share/doc/python-biom-format-doc/
=====================================
debian/python3-biom-format.install
=====================================
@@ -0,0 +1 @@
+build/man/*.1 usr/share/man/man1
=====================================
debian/rules
=====================================
@@ -9,23 +9,24 @@ export PYBUILD_NAME=biom-format
export PYBUILD_DESTDIR=debian/python3-$(PYBUILD_NAME)
export PYBUILD_BEFORE_TEST=cp -r {dir}/examples {build_dir}
export PYBUILD_AFTER_TEST=rm -rf {build_dir}/examples
+export PYBUILD_AFTER_INSTALL= rm -fr {destdir}/usr/lib/python3*/dist-packages/biom_format*/top_level.txt \
+ rm -fr {destdir}/usr/lib/python3*/dist-packages/doc \
+ rm -fr {destdir}/usr/lib/python3*/dist-packages/licenses \
## When trying better hardening the build fails
# export DEB_BUILD_MAINT_OPTIONS = hardening=+all
export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow
%:
- dh $@ --with bash-completion,sphinxdoc,numpy3 --buildsystem=pybuild
+ dh $@ --with bash-completion,numpy3 --buildsystem=pybuild
-override_dh_auto_build:
- # arch
- USE_CYTHON=true dh_auto_build
- # indep:
- PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -b html doc build/html
- PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -b man doc build/man
-
-execute_after_dh_installdocs-indep:
- dh_sphinxdoc --indep
+execute_before_dh_install:
+ifeq (,$(findstring nodoc, $(DEB_BUILD_OPTIONS)))
+ PYTHONPATH=$(CURDIR)/debian/python3-biom-format/usr/lib/python$(shell py3versions -dv)/dist-packages \
+ http_proxy='127.0.0.1:9' sphinx-build -N -b html doc build/html
+ PYTHONPATH=$(CURDIR)/debian/python3-biom-format/usr/lib/python$(shell py3versions -dv)/dist-packages \
+ http_proxy='127.0.0.1:9' sphinx-build -N -b man doc build/man
+endif
execute_after_dh_fixperms:
find debian -name exercise_cli.sh -exec chmod +x \{\} \;
@@ -39,11 +40,3 @@ execute_after_dh_installexamples:
else \
find debian/python*$(PYBUILD_NAME) -name tests -type d | xargs rm -rf ; \
fi
-
-execute_after_dh_auto_install:
- find $(PYBUILD_DESTDIR) -name .coverage -delete
-
-execute_after_dh_python3-arch:
- rm -rf debian/*/usr/lib/python3.14/dist-packages/biom_format-2.1.17.dist-info
- rmdir debian/*/usr/lib/python3.14/dist-packages
- rmdir debian/*/usr/lib/python3.14
View it on GitLab: https://salsa.debian.org/med-team/python-biom-format/-/compare/42e120016e2f2f2bf3c822b6c0d1b7d6d9c5a060...d19f5cd3299950642835bd1cc1333906b0bd3406
--
View it on GitLab: https://salsa.debian.org/med-team/python-biom-format/-/compare/42e120016e2f2f2bf3c822b6c0d1b7d6d9c5a060...d19f5cd3299950642835bd1cc1333906b0bd3406
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