[med-svn] [Git][med-team/pycoqc][master] 11 commits: disable-pkg-resources.patch: new: workaround uses of pkg_resources.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Thu Feb 5 19:29:32 GMT 2026
Étienne Mollier pushed to branch master at Debian Med / pycoqc
Commits:
890eed63 by Étienne Mollier at 2026-02-05T20:06:48+01:00
disable-pkg-resources.patch: new: workaround uses of pkg_resources.
- - - - -
59627457 by Étienne Mollier at 2026-02-05T20:07:32+01:00
d/control: drop python3-pkg-resources.
Closes: #1125838
- - - - -
cb2ea9df by Étienne Mollier at 2026-02-05T20:08:15+01:00
d/s/lintian-overrides: delete: remove mismatched overrides.
- - - - -
be3c628b by Étienne Mollier at 2026-02-05T20:08:34+01:00
remove_non_free_part_of_documentation.patch:
Normalize the Last-Update timestamp.
- - - - -
51892b01 by Étienne Mollier at 2026-02-05T20:09:13+01:00
d/control: drop redundant Rules-Requires-Root: no.
- - - - -
7c083070 by Étienne Mollier at 2026-02-05T20:09:37+01:00
d/control: drop redundant Priority: optional.
- - - - -
c52ec99a by Étienne Mollier at 2026-02-05T20:11:36+01:00
d/*.1: fix typos caught by lintian.
- - - - -
17e686fb by Étienne Mollier at 2026-02-05T20:12:45+01:00
remove_non_free_part_of_documentation.patch:
Declare forwarding not-needed.
- - - - -
7a95b93f by Étienne Mollier at 2026-02-05T20:13:11+01:00
d/control: declare compliance to standards version 4.7.3.
- - - - -
52eae2db by Étienne Mollier at 2026-02-05T20:28:24+01:00
d/watch: convert to v5 Github template.
- - - - -
ad0e3467 by Étienne Mollier at 2026-02-05T20:29:09+01:00
d/changelog: ready for upload to unstable.
- - - - -
10 changed files:
- debian/Barcode_split.1
- debian/Fast5_to_seq_summary.1
- debian/changelog
- debian/control
- + debian/patches/disable-pkg-resources.patch
- debian/patches/remove_non_free_part_of_documentation.patch
- debian/patches/series
- debian/pycoQC.1
- − debian/source/lintian-overrides
- debian/watch
Changes:
=====================================
debian/Barcode_split.1
=====================================
@@ -38,7 +38,7 @@ current dir
.TP
\fB\-\-output_unclassified\fR, \fB\-u\fR
If given, unclassified barcodes are also written in a
-file. By default they are skiped
+file. By default they are skipped
.TP
\fB\-\-min_barcode_percent\fR MIN_BARCODE_PERCENT, \fB\-p\fR MIN_BARCODE_PERCENT
Minimal percent of total reads to retain barcode
=====================================
debian/Fast5_to_seq_summary.1
=====================================
@@ -40,7 +40,7 @@ the reader and 1 for the writer. Minimum 3 (default:
.TP
\fB\-\-basecall_id\fR BASECALL_ID
id of the basecalling group. By default leave to 0,
-but if you perfome multiple basecalling on the same
+but if you perform multiple basecalling on the same
fast5 files, this can be used to indicate the
corresponding group (1, 2 ...) (default: 0)
.TP
=====================================
debian/changelog
=====================================
@@ -1,3 +1,20 @@
+pycoqc (2.5.2+dfsg-5) unstable; urgency=medium
+
+ * Team upload.
+ * disable-pkg-resources.patch: new: workaround uses of pkg_resources.
+ * d/control: drop python3-pkg-resources. (Closes: #1125838)
+ * d/control: drop redundant Rules-Requires-Root: no.
+ * d/control: drop redundant Priority: optional.
+ * d/control: declare compliance to standards version 4.7.3.
+ * d/s/lintian-overrides: delete: remove mismatched overrides.
+ * remove_non_free_part_of_documentation.patch:
+ Normalize the Last-Update timestamp.
+ Declare forwarding not-needed.
+ * d/*.1: fix typos caught by lintian.
+ * d/watch: convert to v5 Github template.
+
+ -- Étienne Mollier <emollier at debian.org> Thu, 05 Feb 2026 20:28:50 +0100
+
pycoqc (2.5.2+dfsg-4) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -2,22 +2,19 @@ Source: pycoqc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Andreas Tille <tille at debian.org>
Section: science
-Priority: optional
Build-Depends: debhelper-compat (= 13),
dh-sequence-python3,
python3,
python3-setuptools
-Standards-Version: 4.6.0
+Standards-Version: 4.7.3
Vcs-Browser: https://salsa.debian.org/med-team/pycoqc
Vcs-Git: https://salsa.debian.org/med-team/pycoqc.git
Homepage: https://github.com/a-slide/pycoQC
-Rules-Requires-Root: no
Package: pycoqc
Architecture: all
Depends: ${python3:Depends},
${misc:Depends},
- python3-pkg-resources,
python3-numpy,
python3-scipy,
python3-pandas,
=====================================
debian/patches/disable-pkg-resources.patch
=====================================
@@ -0,0 +1,48 @@
+Description: workaround to remove python3-pkg-resources.
+ This patch works around the use of pkg_resources.resource_filename by
+ hardwiring the expected file name, since it is going to land at a known
+ location. Such workaround is not suitable for forwarding upstream.
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1125838
+Forwarded: not-needed
+Last-Update: 2026-02-05
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- pycoqc.orig/pycoQC/__main__.py
++++ pycoqc/pycoQC/__main__.py
+@@ -6,7 +6,6 @@
+ import argparse
+ import sys
+ import textwrap
+-from pkg_resources import resource_filename
+
+ # Third party imports
+ from jinja2 import Environment, PackageLoader, Template
+@@ -96,7 +95,7 @@
+
+ # Print the default config parameters and exit
+ if args.default_config:
+- config_file = resource_filename("pycoQC", "templates/pycoQC_config.json")
++ config_file = "/usr/lib/python3/dist-packages/pycoQC/templates/pycoQC_config.json"
+ with open (config_file) as fp:
+ sys.stdout.write(fp.read())
+ sys.exit()
+--- pycoqc.orig/pycoQC/pycoQC_report.py
++++ pycoqc/pycoQC/pycoQC_report.py
+@@ -4,7 +4,6 @@
+ #~~~~~~~~~~~~~~IMPORTS~~~~~~~~~~~~~~#
+ # Standard library imports
+ import json
+-from pkg_resources import resource_filename
+ import datetime
+ import os
+
+@@ -170,7 +169,7 @@
+
+ # Last use the default harcoded config_dict
+ self.logger.debug ("\tRead default configuration file")
+- config_file = resource_filename("pycoQC", "templates/pycoQC_config.json")
++ config_file = "/usr/lib/python3/dist-packages/pycoQC/templates/pycoQC_config.json"
+ with open(config_file, 'r') as cf:
+ return json.load(cf)
+
=====================================
debian/patches/remove_non_free_part_of_documentation.patch
=====================================
@@ -1,8 +1,9 @@
Author: Andreas Tille <tille at debian.org>
-Last-Update: Wed, 22 Apr 2020 12:54:02 +0200
+Last-Update: 2020-04-22
Description: The file docs/pycoQC/API_usage.ipynb contains compressed JS and had
to be removed from the source tarball. Make sure it is not used inside the doc
which is refereing to an online replacement anyway
+Forwarded: not-needed
--- a/docs/pycoQC/usage.md
+++ b/docs/pycoQC/usage.md
=====================================
debian/patches/series
=====================================
@@ -1 +1,2 @@
remove_non_free_part_of_documentation.patch
+disable-pkg-resources.patch
=====================================
debian/pycoQC.1
=====================================
@@ -86,7 +86,7 @@ basecaller are removed (default: False)
.TP
\fB\-\-filter_duplicated\fR
If given, duplicated read_ids are removed but the
-first occurence is kept (Guppy sometimes outputs the
+first occurrence is kept (Guppy sometimes outputs the
same read multiple times) (default: False)
.TP
\fB\-\-min_barcode_percent\fR MIN_BARCODE_PERCENT
@@ -119,7 +119,7 @@ transcriptome (default: False)
.TP
\fB\-\-sample\fR SAMPLE
If not None a n number of reads will be randomly
-selected instead of the entire dataset for ploting
+selected instead of the entire dataset for plotting
function (deterministic sampling) (default: 100000)
.TP
\fB\-\-default_config\fR, \fB\-d\fR
=====================================
debian/source/lintian-overrides deleted
=====================================
@@ -1,4 +0,0 @@
-# The rendered sample results are no JS without source
-pycoqc source: source-is-missing docs/pycoQC/results*
-pycoqc source: very-long-line-length-in-source-file docs/pycoQC/results*
-pycoqc source: source-contains-prebuilt-javascript-object docs/pycoQC/results*
=====================================
debian/watch
=====================================
@@ -1,4 +1,9 @@
-version=4
+Version: 5
-opts="repacksuffix=+dfsg,dversionmangle=auto,repack,compression=xz,filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%" \
-https://github.com/a-slide/pycoQC/tags .*/v?@ANY_VERSION@\.tar\.gz
+Template: Github
+Owner: a-slide
+Project: pycoQC
+Compression: xz
+Dversionmangle: auto
+Repack: yes
+Repacksuffix: +dfsg
View it on GitLab: https://salsa.debian.org/med-team/pycoqc/-/compare/f584d2e190a9cca9dfe459302e58f160e5186c35...ad0e3467814e3f18e328ac517e5634c1e7a7223a
--
View it on GitLab: https://salsa.debian.org/med-team/pycoqc/-/compare/f584d2e190a9cca9dfe459302e58f160e5186c35...ad0e3467814e3f18e328ac517e5634c1e7a7223a
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