[med-svn] [Git][med-team/pychopper][master] 6 commits: d/watch: Rewrite in v5 format.
Andreas Tille (@tille)
gitlab at salsa.debian.org
Thu Apr 16 16:35:51 BST 2026
Andreas Tille pushed to branch master at Debian Med / pychopper
Commits:
3267d30f by Karsten Schöke at 2026-04-16T15:49:26+02:00
d/watch: Rewrite in v5 format.
- - - - -
62e54bd9 by Karsten Schöke at 2026-04-16T15:51:17+02:00
d/control: Bump Standards-Version to 4.7.4
- drop Priority: tag
- drop "Rules-Requires-Root: no": it is the default now
- - - - -
2c54725f by Karsten Schöke at 2026-04-16T15:55:34+02:00
rebuild patch queue.
- - - - -
ca1449e9 by Karsten Schöke at 2026-04-16T15:56:51+02:00
Modernization test.
- - - - -
5fc2e172 by Karsten Schöke at 2026-04-16T16:26:42+02:00
prepare 2.7.10-2 release.
- - - - -
66324e88 by Andreas Tille at 2026-04-16T17:35:47+02:00
Merge branch 'karso' into 'master'
Modernization tests and bug fixing
See merge request med-team/pychopper!1
- - - - -
9 changed files:
- debian/changelog
- debian/control
- + debian/patches/fix-sphinx-scripts-path.patch
- debian/patches/fixTests.patch
- debian/patches/series
- debian/rules
- − debian/tests/control
- − debian/tests/run-unit-test
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,15 @@
+pychopper (2.7.10-2) UNRELEASED; urgency=medium
+
+ * d/watch: Rewrite in v5 format.
+ * d/control: Bump Standards-Version to 4.7.4
+ - drop Priority: tag
+ - drop "Rules-Requires-Root: no": it is the default now
+ * rebuild patch queue.
+ * Modernization test.
+ (Closes: #1121065, #1082368, #1122177)
+
+ -- Karsten Schöke <karsten.schoeke at geobasis-bb.de> Thu, 16 Apr 2026 15:57:45 +0200
+
pychopper (2.7.10-1) unstable; urgency=medium
* Team upload
=====================================
debian/control
=====================================
@@ -1,10 +1,10 @@
Source: pychopper
Section: science
-Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Steffen Moeller <moeller at debian.org>
Build-Depends: debhelper-compat (= 13),
dh-sequence-python3,
+ pybuild-plugin-pyproject,
python3-setuptools,
python3-sphinx <!nodoc>,
python3-sphinx-argparse <!nodoc>,
@@ -30,12 +30,11 @@ Build-Depends: debhelper-compat (= 13),
python3-pysam <!nocheck>,
python3-zombie-imp <!nodoc>,
xonsh <!nocheck>
-Standards-Version: 4.6.2
+Standards-Version: 4.7.4
Homepage: https://github.com/epi2me-labs/pychopper
Vcs-Browser: https://salsa.debian.org/med-team/pychopper
Vcs-Git: https://salsa.debian.org/med-team/pychopper.git
Testsuite: autopkgtest-pkg-python
-Rules-Requires-Root: no
Package: python3-pychopper
Architecture: all
=====================================
debian/patches/fix-sphinx-scripts-path.patch
=====================================
@@ -0,0 +1,34 @@
+From: =?utf-8?q?Karsten_Sch=C3=B6ke?= <karsten.schoeke at geobasis-bb.de>
+Date: Thu, 16 Apr 2026 15:03:47 +0200
+Subject: fix-sphinx-scripts-path
+
+Fix Sphinx documentation build by correcting the script discovery path in
+docs/cmd_tools.py.
+
+The original code assumes a top-level "scripts/" directory, but the Debian
+package layout places scripts under "pychopper/scripts/". This mismatch
+causes Sphinx to load and import pychopper.py incorrectly, leading to
+circular import errors during documentation generation.
+
+This patch updates the script directory reference to match the actual
+package structure and prevents Sphinx from treating the CLI script as a
+top-level Python module.
+
+---
+ docs/cmd_tools.py | 3 ++-
+ 1 file changed, 2 insertions(+), 1 deletion(-)
+
+diff --git a/docs/cmd_tools.py b/docs/cmd_tools.py
+index f8c5e89..deec45c 100755
+--- a/docs/cmd_tools.py
++++ b/docs/cmd_tools.py
+@@ -36,7 +36,8 @@ for script in scripts:
+
+ try:
+ mod_name = '{}.{}'.format(scripts_rel, script_name)
+- #mod = __import__(mod_name, globals(), locals(), [attr_name])
++ if script_name == "pychopper":
++ continue
+ mod = imp.load_source(script_name, os.path.join(scripts_abs, script))
+ script = script.replace('.py', '')
+
=====================================
debian/patches/fixTests.patch
=====================================
@@ -1,7 +1,17 @@
-Author: Steffen Möller <moeller at debian.org>, Nilesh Patra <nilesh at debian.org>
+From: "moeller at debian.org" <moeller at debian.org>
+Date: Thu, 16 Apr 2026 14:46:57 +0200
+Subject: Force Python3 in tests
+
Last-Update: 2022-11-16 20:11:23 +0530
-Description: Force Python3 in tests
+---
+ docs/cmd_tools.py | 2 +-
+ docs/conf.py | 2 +-
+ evaluation/scripts/regplot.py | 2 +-
+ pychopper/scripts/pychopper.py | 2 +-
+ 4 files changed, 4 insertions(+), 4 deletions(-)
+diff --git a/docs/cmd_tools.py b/docs/cmd_tools.py
+index 4187d2f..f8c5e89 100755
--- a/docs/cmd_tools.py
+++ b/docs/cmd_tools.py
@@ -1,4 +1,4 @@
@@ -10,6 +20,8 @@ Description: Force Python3 in tests
"""Helper script to generate cmd_line.rst file for all scripts in bin which
have and parser object defined in their global scope - taken from tang
+diff --git a/docs/conf.py b/docs/conf.py
+index 7958113..0cd35f2 100755
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -1,4 +1,4 @@
@@ -18,6 +30,8 @@ Description: Force Python3 in tests
# -*- coding: utf-8 -*-
#
# sphinx-quickstart on Tue Jul 9 22:26:36 2013.
+diff --git a/evaluation/scripts/regplot.py b/evaluation/scripts/regplot.py
+index 2ce35f9..371e2bf 100755
--- a/evaluation/scripts/regplot.py
+++ b/evaluation/scripts/regplot.py
@@ -1,4 +1,4 @@
@@ -26,6 +40,8 @@ Description: Force Python3 in tests
import sys
import pandas as pd
+diff --git a/pychopper/scripts/pychopper.py b/pychopper/scripts/pychopper.py
+index 2a86c7a..f8978da 100755
--- a/pychopper/scripts/pychopper.py
+++ b/pychopper/scripts/pychopper.py
@@ -1,4 +1,4 @@
=====================================
debian/patches/series
=====================================
@@ -1 +1,2 @@
fixTests.patch
+fix-sphinx-scripts-path.patch
=====================================
debian/rules
=====================================
@@ -1,43 +1,20 @@
#!/usr/bin/make -f
-export DH_VERBOSE = 1
+#export DH_VERBOSE = 1
export PYBUILD_NAME=pychopper
-export PYBUILD_BEFORE_TEST=cp -av $(CURDIR)/pychopper/tests/ {build_dir}/pychopper/
-DEF_PY=$(shell py3versions -d)
-DEF_BUILDDIR3 := $(shell pybuild --print build_dir --interpreter python3)
+export PYBUILD_TEST_ARGS = {dir}/pychopper/tests
+export PYBUILD_AFTER_INSTALL=rm -fr {destdir}/usr/lib/python3*/dist-packages/pychopper-*/top_level.txt \
+ rm -fr {destdir}/usr/lib/python3*/dist-packages/pychopper.pdf \
+ rm -fr {destdir}/usr/lib/python3*/dist-packages/pychopper.tsv
%:
dh $@ --buildsystem=pybuild
-
-override_dh_auto_build:
- dh_auto_build
- cd docs && PYTHONPATH=.. make man
-
execute_after_dh_auto_build:
- for py in `py3versions -s`; do \
- builddir=$$(pybuild --print build_dir --interpreter $$py); \
- mv $$builddir/pychopper/scripts/pychopper.py $$builddir/pychopper/scripts/pychopper; \
- done
-
-override_dh_auto_clean:
- dh_auto_clean
- make clean
- cd docs && make clean # fails
-
-override_dh_auto_test:
-ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
- dh_auto_test -- --system=custom --test-args="export PATH=$(DEF_BUILDDIR3)/pychopper/scripts:$$PATH; \
- chmod +x $(DEF_BUILDDIR3)/pychopper/scripts/pychopper; PYTHONPATH={build_dir} {interpreter} -m pytest -v"
- set -e; \
- for py in `py3versions -sv`; do \
- rm -rf ".pybuild/cpython3_$${py}_$(PYBUILD_NAME)/pychopper/tests/"; \
- done
-endif
+ cd docs && PYTHONPATH=.. $(MAKE) man
-execute_after_dh_auto_install:
- find debian/ -name .gitignore -delete
+execute_before_dh_auto_build:
+ ln -sfn pychopper/scripts scripts
-override_dh_fixperms:
- dh_fixperms
+execute_after_dh_fixperms:
find debian/ -name PCS111_primers.fas -exec chmod -x '{}' \;
=====================================
debian/tests/control deleted
=====================================
@@ -1,3 +0,0 @@
-Tests: run-unit-test
-Depends: @, python3-all, python3-pytest, python3-edlib
-Restrictions: allow-stderr
=====================================
debian/tests/run-unit-test deleted
=====================================
@@ -1,8 +0,0 @@
-#!/bin/bash
-set -e
-
-for py in $(py3versions -s 2> /dev/null)
-do
- $py -m pytest -v
-done
-
=====================================
debian/watch
=====================================
@@ -1,4 +1,5 @@
-version=4
-opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%pychopper-$1.tar.gz%" \
- https://github.com/epi2me-labs/pychopper/tags \
- (?:.*?/)?v?(\d[\d.]*)\.tar\.gz
+Version: 5
+
+Template: Github
+Owner: epi2me-labs
+Project: pychopper
View it on GitLab: https://salsa.debian.org/med-team/pychopper/-/compare/6c0057c668509221ab5d660be909d906d151b16e...66324e88d440e779a59e6d060256757ba22c781c
--
View it on GitLab: https://salsa.debian.org/med-team/pychopper/-/compare/6c0057c668509221ab5d660be909d906d151b16e...66324e88d440e779a59e6d060256757ba22c781c
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