[med-svn] [Git][med-team/qcat][master] remove usage of python3-six

[Alexandre Detiste (@detiste-guest)]

Alexandre Detiste pushed to branch master at Debian Med / qcat


Commits:
ae352645 by Alexandre Detiste at 2024-01-08T06:31:26+01:00
remove usage of python3-six

- - - - -


3 changed files:

- debian/control
- + debian/patches/remove_six.patch
- debian/patches/series


Changes:

=====================================
debian/control
=====================================
@@ -7,7 +7,6 @@ Build-Depends: debhelper-compat (= 13),
                dh-python,
                python3,
                python3-setuptools,
-               python3-six <!nocheck>,
                python3-pytest-runner <!nocheck>,
                python3-pytest <!nocheck>,
                python3-pytest-cov <!nocheck>,


=====================================
debian/patches/remove_six.patch
=====================================
@@ -0,0 +1,59 @@
+From: Alexandre Detiste <tchet at debian.org>
+Subject: remove trivial usage of python3-six
+Forwarded: no, project is archived
+
+--- a/qcat/cli.py
++++ b/qcat/cli.py
+@@ -4,7 +4,6 @@
+ import time
+ import sys
+ import os
+-import six
+ 
+ from Bio.SeqIO.FastaIO import SimpleFastaParser
+ from Bio.SeqIO.QualityIO import FastqGeneralIterator
+@@ -385,7 +384,7 @@
+ 
+ def print_barcode_hist(barcode_dist, adapter_dist, total_reads):
+     adapters_detected = 0
+-    for key, value in six.iteritems(adapter_dist):
++    for key, value in adapter_dist.items():
+         if key != "none":
+             adapters_detected += value
+     logging.info("Adapters detected in %d of %d reads" % (adapters_detected, total_reads))
+@@ -395,7 +394,7 @@
+                                      int(perc / 5) * "#", "{:.2f}".format(perc)))
+ 
+     barcodes_detected = 0
+-    for key, value in six.iteritems(barcode_dist):
++    for key, value in barcode_dist.items():
+         if key != "none":
+             barcodes_detected += value
+     logging.info("Barcodes detected in %d of %d adapters" % (barcodes_detected, total_reads))
+--- a/qcat/eval.py
++++ b/qcat/eval.py
+@@ -5,7 +5,6 @@
+ import sys
+ import os
+ 
+-from six.moves import zip
+ from argparse import ArgumentParser, RawDescriptionHelpFormatter
+ 
+ from qcat import cli
+--- a/setup.py
++++ b/setup.py
+@@ -18,7 +18,6 @@
+     install_requires=[
+         'biopython',
+         'parasail',
+-        'six',
+         'pyyaml'
+     ],
+     extras_require={
+@@ -42,4 +41,4 @@
+                                       'qcat-eval = qcat.eval:main',
+                                       'qcat-roc = qcat.eval_roc:main',
+                                       'qcat-eval-truth = qcat.eval_full:main']}
+-)
+\ No newline at end of file
++)


=====================================
debian/patches/series
=====================================
@@ -1 +1,2 @@
 yaml_safe_load.patch
+remove_six.patch



View it on GitLab: https://salsa.debian.org/med-team/qcat/-/commit/ae3526451550cdb7a3b40de36d607655134a333c

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View it on GitLab: https://salsa.debian.org/med-team/qcat/-/commit/ae3526451550cdb7a3b40de36d607655134a333c
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