[med-svn] [Git][med-team/qcat][master] 6 commits: Add patch to replace yaml.load instances with yaml.safe_load
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Sun Nov 6 18:23:56 GMT 2022
Nilesh Patra pushed to branch master at Debian Med / qcat
Commits:
7cb77259 by Nilesh Patra at 2022-11-06T21:53:10+05:30
Add patch to replace yaml.load instances with yaml.safe_load
- - - - -
a5049c35 by Nilesh Patra at 2022-11-06T21:53:10+05:30
Bump Standards-Version to 4.6.1 (no changes needed)
- - - - -
1f05dfb8 by Nilesh Patra at 2022-11-06T21:53:10+05:30
Upload to unstable
- - - - -
4e54fde0 by Nilesh Patra at 2022-11-06T16:30:56+00:00
Update manpages
- - - - -
7ee6b168 by Nilesh Patra at 2022-11-06T22:01:35+05:30
Upload to unstable
- - - - -
3f569d65 by Nilesh Patra at 2022-11-06T18:10:24+00:00
Fix manpage properly
- - - - -
10 changed files:
- debian/changelog
- debian/control
- debian/createmanpages
- debian/man/qcat-eval-truth.1
- debian/man/qcat-eval.1
- debian/man/qcat-roc.1
- debian/man/qcat.1
- + debian/manpages
- + debian/patches/series
- + debian/patches/yaml_safe_load.patch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+qcat (1.1.0-5) unstable; urgency=medium
+
+ * Team Upload.
+ * Add patch to replace yaml.load instances
+ with yaml.safe_load (Closes: #1022451)
+ * Bump Standards-Version to 4.6.1 (no changes needed)
+ * Update manpages
+
+ -- Nilesh Patra <nilesh at debian.org> Sun, 06 Nov 2022 21:43:01 +0530
+
qcat (1.1.0-4) unstable; urgency=medium
* Team Upload.
=====================================
debian/control
=====================================
@@ -14,7 +14,7 @@ Build-Depends: debhelper-compat (= 13),
python3-biopython <!nocheck>,
python3-parasail <!nocheck>,
python3-yaml <!nocheck>
-Standards-Version: 4.6.0
+Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/qcat
Vcs-Git: https://salsa.debian.org/med-team/qcat.git
Homepage: https://github.com/nanoporetech/qcat
=====================================
debian/createmanpages
=====================================
@@ -6,11 +6,6 @@ VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*:
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 $DEBFULLNAME for the Debian distribution and\n \
-can be used for any other usage of the program.\
-"
-
# If program name is different from package name or title should be
# different from package short description change this here
progname=${PROGNAME}
=====================================
debian/man/qcat-eval-truth.1
=====================================
@@ -1,5 +1,5 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.13.
-.TH QCAT-EVAL-TRUTH "1" "April 2020" "qcat-eval-truth 1.1.0" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.48.5.
+.TH QCAT-EVAL-TRUTH "1" "November 2022" "qcat-eval-truth 1.1.0" "User Commands"
.SH NAME
qcat-eval-truth \- Command line interface to barcode detection library
.SH DESCRIPTION
@@ -10,7 +10,7 @@ Command line interface to barcode detection library
.SS "positional arguments:"
.IP
FASTQ
-.SS "optional arguments:"
+.SS "options:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
@@ -22,6 +22,4 @@ show this help message and exit
\fB\-g\fR GENOMES, \fB\-\-genomes\fR GENOMES
.HP
\fB\-\-max\fR MAX
-.SH AUTHOR
- This manpage was written by Andreas Tille for the Debian distribution and
- can be used for any other usage of the program.
+
=====================================
debian/man/qcat-eval.1
=====================================
@@ -1,5 +1,5 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.13.
-.TH QCAT-EVAL "1" "April 2020" "qcat-eval 1.1.0" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.48.5.
+.TH QCAT-EVAL "1" "November 2022" "qcat-eval 1.1.0" "User Commands"
.SH NAME
qcat-eval \- Command line interface to barcode detection library
.SH DESCRIPTION
@@ -12,7 +12,7 @@ Command line interface to barcode detection library
.SS "positional arguments:"
.IP
FASTQ
-.SS "optional arguments:"
+.SS "options:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
@@ -28,6 +28,4 @@ show this help message and exit
\fB\-g\fR GUPPY, \fB\-\-guppy_summary\fR GUPPY
.HP
\fB\-i\fR INCORRECT, \fB\-\-get\-incorrect\fR INCORRECT
-.SH AUTHOR
- This manpage was written by Andreas Tille for the Debian distribution and
- can be used for any other usage of the program.
+
=====================================
debian/man/qcat-roc.1
=====================================
@@ -1,5 +1,5 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.13.
-.TH QCAT-ROC "1" "April 2020" "qcat-roc 1.1.0" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.48.5.
+.TH QCAT-ROC "1" "November 2022" "qcat-roc 1.1.0" "User Commands"
.SH NAME
qcat-roc \- Command line interface to barcode detection library
.SH DESCRIPTION
@@ -9,10 +9,8 @@ Command line interface to barcode detection library
.SS "positional arguments:"
.IP
FASTQ
-.SS "optional arguments:"
+.SS "options:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
-.SH AUTHOR
- This manpage was written by Andreas Tille for the Debian distribution and
- can be used for any other usage of the program.
+
=====================================
debian/man/qcat.1
=====================================
@@ -1,5 +1,5 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.13.
-.TH QCAT "1" "April 2020" "qcat 1.1.0" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.48.5.
+.TH QCAT "1" "November 2022" "qcat 1.1.0" "User Commands"
.SH NAME
qcat \- demultiplexing Oxford Nanopore reads from FASTQ files
.SH DESCRIPTION
@@ -7,13 +7,15 @@ usage: qcat [\-h] [\-V] [\-l LOG] [\-\-quiet] [\-f FASTQ] [\-b BARCODE_DIR]
.IP
[\-o OUTPUT] [\-\-min\-score MIN_QUAL] [\-\-detect\-middle] [\-t THREADS]
[\-\-min\-read\-length MIN_LENGTH] [\-\-tsv] [\-\-trim]
-[\-k {Auto,RAB204/RAB214,PBC001,NBD103/NBD104,RAB214,RPB004/RLB001,NBD114,NBD104/NBD114,PBK004/LWB001,DUAL,RAB204,RBK004,PBC096,RBK001,VMK001}]
+[\-k {Auto,RAB204,RPB004/RLB001,NBD104/NBD114,
+ RAB204/RAB214,VMK001,NBD103/NBD104,PBC001,PBK004/LWB001,
+ RAB214,RBK004,PBC096,RBK001,NBD114,DUAL}]
[\-\-list\-kits] [\-\-guppy | \fB\-\-epi2me\fR | \fB\-\-dual\fR | \fB\-\-simple]\fR
[\-\-no\-batch] [\-\-filter\-barcodes]
[\-\-simple\-barcodes SIMPLE_BARCODES]
.PP
Python command\-line tool for demultiplexing Oxford Nanopore reads from FASTQ files
-.SS "optional arguments:"
+.SS "options:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
@@ -61,7 +63,9 @@ read to stdout.
\fB\-\-trim\fR
Remove adapter and barcode sequences from reads.
.TP
-\fB\-k\fR {Auto,RAB204/RAB214,PBC001,NBD103/NBD104,RAB214,RPB004/RLB001,NBD114,NBD104/NBD114,PBK004/LWB001,DUAL,RAB204,RBK004,PBC096,RBK001,VMK001}, \fB\-\-kit\fR {Auto,RAB204/RAB214,PBC001,NBD103/NBD104,RAB214,RPB004/RLB001,NBD114,NBD104/NBD114,PBK004/LWB001,DUAL,RAB204,RBK004,PBC096,RBK001,VMK001}
+\fB\-k\fR, \fB\-\-kit\fR {Auto,RAB204,RPB004/RLB001,NBD104/NBD114,RAB204/RAB214,
+ VMK001,NBD103/NBD104,PBC001,PBK004/LWB001,RAB214,RBK004,PBC096,
+ RBK001,NBD114,DUAL}
Sequencing kit. Specifying the correct kit will
improve sensitivity and specificity and runtime
(default: auto)
@@ -96,6 +100,4 @@ Filter rare barcode calls when run in batch mode
\fB\-\-simple\-barcodes\fR SIMPLE_BARCODES
Use 12 (standard) or 96 (extended) barcodes for
demultiplexing
-.SH AUTHOR
- This manpage was written by Andreas Tille for the Debian distribution and
- can be used for any other usage of the program.
+
=====================================
debian/manpages
=====================================
@@ -0,0 +1 @@
+debian/man/*.1
=====================================
debian/patches/series
=====================================
@@ -0,0 +1 @@
+yaml_safe_load.patch
=====================================
debian/patches/yaml_safe_load.patch
=====================================
@@ -0,0 +1,41 @@
+Description: Replace instances of yaml.load with yaml.safe_load
+Author: Nilesh Patra <nilesh at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1022451
+Last-Update: 2022-11-06
+--- a/qcat/adapters.py
++++ b/qcat/adapters.py
+@@ -34,7 +34,7 @@
+ def yaml2adapter(filename):
+ with open(filename, 'r') as stream:
+ try:
+- data = yaml.load(stream)
++ data = yaml.safe_load(stream)
+ return data
+ except yaml.YAMLError as exc:
+ print(exc)
+@@ -77,10 +77,10 @@
+ try:
+ try:
+ # Python 3
+- data = yaml.load(stream, Loader=yaml.FullLoader)
++ data = yaml.safe_load(stream)
+ except AttributeError:
+ # Python 2
+- data = yaml.load(stream)
++ data = yaml.safe_load(stream)
+
+ if not data.get('active', True):
+ return None
+@@ -126,10 +126,10 @@
+ try:
+ try:
+ # Python 3
+- data = yaml.load(stream, Loader=yaml.FullLoader)
++ data = yaml.safe_load(stream)
+ except AttributeError:
+ # Python 2
+- data = yaml.load(stream)
++ data = yaml.safe_load(stream)
+ return read_barcode_set(data.get('barcode_set_1', []))
+ except yaml.YAMLError as exc:
+ print(exc)
View it on GitLab: https://salsa.debian.org/med-team/qcat/-/compare/d1900639209679610d372a1e79c4bb7abd06c0e1...3f569d6544ac14d268cecb58e0bb524b0d33dae8
--
View it on GitLab: https://salsa.debian.org/med-team/qcat/-/compare/d1900639209679610d372a1e79c4bb7abd06c0e1...3f569d6544ac14d268cecb58e0bb524b0d33dae8
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20221106/f03a87e6/attachment-0001.htm>
More information about the debian-med-commit
mailing list