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 <[email protected]> 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 <[email protected]>, 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 <[email protected]> +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 <[email protected]> +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 You're receiving this email because of your account on salsa.debian.org.
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