[med-svn] [Git][med-team/umis][master] 5 commits: Fix Python3.12 string syntax Closes: #1087155

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / umis


Commits:
b2aa17c9 by Andreas Tille at 2024-12-12T13:02:10+01:00
Fix Python3.12 string syntax Closes: #1087155

- - - - -
5a635fdd by Andreas Tille at 2024-12-12T13:02:31+01:00
Standards-Version: 4.7.0 (routine-update)

- - - - -
9155061c by Andreas Tille at 2024-12-12T13:02:35+01:00
Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)

- - - - -
6d96efd5 by Andreas Tille at 2024-12-12T13:10:59+01:00
Ensure compatibility with current version of pandas

- - - - -
394923e5 by Andreas Tille at 2024-12-12T13:12:34+01:00
Upload to unstable

- - - - -


6 changed files:

- debian/changelog
- debian/control
- + debian/patches/pyhon3.12-syntax.patch
- + debian/patches/read_csv-no_squeeze.patch
- debian/patches/series
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+umis (1.0.9-2) unstable; urgency=medium
+
+  * Fix Python3.12 string syntax
+    Closes: #1087155
+  * Standards-Version: 4.7.0 (routine-update)
+  * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)
+  * Ensure compatibility with current version of pandas
+
+ -- Andreas Tille <tille at debian.org>  Thu, 12 Dec 2024 13:11:06 +0100
+
 umis (1.0.9-1) unstable; urgency=medium
 
   * New upstream version


=====================================
debian/control
=====================================
@@ -5,12 +5,12 @@ Uploaders: Andreas Tille <tille at debian.org>,
 Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 13),
-               dh-python,
+               dh-sequence-python3,
                cython3,
                python3-dev,
                python3-setuptools
 Build-Depends-Arch: python3-pysam
-Standards-Version: 4.6.2
+Standards-Version: 4.7.0
 Vcs-Browser: https://salsa.debian.org/med-team/umis
 Vcs-Git: https://salsa.debian.org/med-team/umis.git
 Homepage: https://github.com/vals/umis


=====================================
debian/patches/pyhon3.12-syntax.patch
=====================================
@@ -0,0 +1,19 @@
+Description: Fix Python3.12 string syntax
+Bug-Debian: https://bugs.debian.org/1087155
+Author: Andreas Tille <tille at debian.org>
+Last-Update: 2024-06-12
+
+--- a/umis/umis.py
++++ b/umis/umis.py
+@@ -158,9 +158,9 @@ def construct_transformed_regex(annotati
+         re_string += ":CELL_(?P<CB>.*)"
+     if "molecular" in annotations:
+         # Detect dual UMIs spaced with either _ or - if present
+-        re_string += ':UMI_(?P<MB>\w[-_\w]*)'
++        re_string += r':UMI_(?P<MB>\w[-_\w]*)'
+     if "sample" in annotations:
+-        re_string += ":SAMPLE_(?P<SB>\w*)"
++        re_string += r":SAMPLE_(?P<SB>\w*)"
+     if re_string == ".*":
+         logger.error("No annotation present on this file, aborting.")
+         sys.exit(1)


=====================================
debian/patches/read_csv-no_squeeze.patch
=====================================
@@ -0,0 +1,25 @@
+Description: Ensure compatibility with current version of pandas
+ pandas.read_csv() no longer supports the squeeze parameter in recent versions of pandas. This parameter was deprecated and then removed in pandas version 2.0
+Author: Andreas Tille <tille at debian.org>
+Last-Update: 2024-06-12
+
+--- a/umis/umis.py
++++ b/umis/umis.py
+@@ -499,7 +499,7 @@ def tagcount(sam, out, genemap, output_e
+     cb_hist = None
+     filter_cb = False
+     if cb_histogram:
+-        cb_hist = pd.read_csv(cb_histogram, index_col=0, header=None, squeeze=True, sep="\t")
++        cb_hist = pd.read_csv(cb_histogram, index_col=0, header=None, sep="\t").squeeze()
+         total_num_cbs = cb_hist.shape[0]
+         cb_hist = cb_hist[cb_hist > cb_cutoff]
+         logger.info('Keeping {} out of {} cellular barcodes.'.format(cb_hist.shape[0], total_num_cbs))
+@@ -772,7 +772,7 @@ def fasttagcount(sam, out, genemap, posi
+     cb_hist = None
+     filter_cb = False
+     if cb_histogram:
+-        cb_hist = pd.read_csv(cb_histogram, index_col=0, header=None, squeeze=True, sep="\t")
++        cb_hist = pd.read_csv(cb_histogram, index_col=0, header=None, sep="\t").squeeze()
+         total_num_cbs = cb_hist.shape[0]
+         cb_hist = cb_hist[cb_hist > cb_cutoff]
+         logger.info('Keeping {} out of {} cellular barcodes.'.format(cb_hist.shape[0], total_num_cbs))


=====================================
debian/patches/series
=====================================
@@ -1 +1,3 @@
+pyhon3.12-syntax.patch
 fix_bashism.patch
+read_csv-no_squeeze.patch


=====================================
debian/rules
=====================================
@@ -10,7 +10,7 @@ export PYBUILD_NAME=umis
 export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 
 %:
-	dh $@ --with python3 --buildsystem=pybuild
+	dh $@ --buildsystem=pybuild
 
 override_dh_install:
 	dh_install



View it on GitLab: https://salsa.debian.org/med-team/umis/-/compare/d6d2b8ca4c55bb149656d6e6bdc9c1b68730789a...394923e5fea3353d32893f0f5a969c187ff1ab17

-- 
View it on GitLab: https://salsa.debian.org/med-team/umis/-/compare/d6d2b8ca4c55bb149656d6e6bdc9c1b68730789a...394923e5fea3353d32893f0f5a969c187ff1ab17
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