[med-svn] [Git][med-team/cnvkit][master] 3 commits: Re-diff patches (refresh)
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Fri Oct 15 07:52:34 BST 2021
Nilesh Patra pushed to branch master at Debian Med / cnvkit
Commits:
df777caa by Nilesh Patra at 2021-10-15T11:45:26+05:30
Re-diff patches (refresh)
- - - - -
7c63182b by Nilesh Patra at 2021-10-15T12:11:02+05:30
d/rules: do not run tests in parallel
- - - - -
01d66663 by Nilesh Patra at 2021-10-15T12:11:42+05:30
Upload to unstable
- - - - -
6 changed files:
- debian/changelog
- debian/patches/controldir
- debian/patches/no-py-ext
- debian/patches/python3compat.patch
- debian/patches/spelling
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+cnvkit (0.9.9-2) unstable; urgency=medium
+
+ * Team Upload.
+ * Re-diff patches (refresh)
+ * d/rules: do not run tests in parallel
+
+ -- Nilesh Patra <nilesh at debian.org> Fri, 15 Oct 2021 12:11:06 +0530
+
cnvkit (0.9.9-1) unstable; urgency=medium
* Fix watchfile to detect new versions on github (routine-update)
=====================================
debian/patches/controldir
=====================================
@@ -5,9 +5,9 @@ Author: Olivier Sallou <osallou at debian.org>
Bug: 925568
Forwarded: no
Last-Updated: 2019-03-27
---- cnvkit.orig/cnvlib/commands.py
-+++ cnvkit/cnvlib/commands.py
-@@ -1439,8 +1439,9 @@
+--- a/cnvlib/commands.py
++++ b/cnvlib/commands.py
+@@ -1452,8 +1452,9 @@
'anti' if 'antitarget' in fname else ''))
if args.output_dir:
if not os.path.isdir(args.output_dir):
=====================================
debian/patches/no-py-ext
=====================================
@@ -1,8 +1,8 @@
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Description: Remove .py extensions as per Debian policy
---- cnvkit.orig/setup.py
-+++ cnvkit/setup.py
-@@ -39,7 +39,7 @@
+--- a/setup.py
++++ b/setup.py
+@@ -46,7 +46,7 @@
'skgenome',
'skgenome.tabio',
],
=====================================
debian/patches/python3compat.patch
=====================================
@@ -1,6 +1,6 @@
Description: enable building with Python3
---- cnvkit.orig/test/Makefile
-+++ cnvkit/test/Makefile
+--- a/test/Makefile
++++ b/test/Makefile
@@ -3,7 +3,9 @@
# Dependency: pdfunite (poppler-utils)
# (Otherwise, all-scatters.pdf and all-diagrams.pdf will be empty files.)
@@ -29,88 +29,88 @@ Description: enable building with Python3
# ------------------------------------------------------------------------------
---- cnvkit.orig/test/test_cnvlib.py
-+++ cnvkit/test/test_cnvlib.py
+--- a/test/test_cnvlib.py
++++ b/test/test_cnvlib.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""Unit tests for the CNVkit library, cnvlib."""
import unittest
---- cnvkit.orig/test/test_genome.py
-+++ cnvkit/test/test_genome.py
+--- a/test/test_genome.py
++++ b/test/test_genome.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""Unit tests for the 'genome' sub-package."""
import random
import unittest
---- cnvkit.orig/test/test_io.py
-+++ cnvkit/test/test_io.py
+--- a/test/test_io.py
++++ b/test/test_io.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""Unit tests for the CNVkit library, cnvlib."""
import unittest
---- cnvkit.orig/test/test_r.py
-+++ cnvkit/test/test_r.py
+--- a/test/test_r.py
++++ b/test/test_r.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""Unit tests for CNVkit that require an R installation."""
import unittest
import logging
---- cnvkit.orig/cnvkit.py
-+++ cnvkit/cnvkit.py
+--- a/cnvkit.py
++++ b/cnvkit.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/python3
"""Command-line interface for CNVkit, the Copy Number Variation toolkit."""
import logging
from cnvlib import commands
---- cnvkit.orig/scripts/cnv_annotate.py
-+++ cnvkit/scripts/cnv_annotate.py
+--- a/scripts/cnv_annotate.py
++++ b/scripts/cnv_annotate.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""Update gene names in CNVkit .cnn/.cnr files.
"""
import argparse
---- cnvkit.orig/scripts/cnv_updater.py
-+++ cnvkit/scripts/cnv_updater.py
+--- a/scripts/cnv_updater.py
++++ b/scripts/cnv_updater.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""Update .cnn/.cnr files from older CNVkit versions to match current defaults.
CNVkit v0.8.0 and later uses a 'depth' column in the *.targetcoverage.cnn and
---- cnvkit.orig/scripts/guess_baits.py
-+++ cnvkit/scripts/guess_baits.py
+--- a/scripts/guess_baits.py
++++ b/scripts/guess_baits.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""Guess the coordinates of captured regions from sample read depths.
Two approaches available:
---- cnvkit.orig/scripts/reference2targets.py
-+++ cnvkit/scripts/reference2targets.py
+--- a/scripts/reference2targets.py
++++ b/scripts/reference2targets.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""Extract target and antitarget BED files from a CNVkit reference file.
Once you have a stable CNVkit reference for your platform, you can use this
---- cnvkit.orig/scripts/skg_convert.py
-+++ cnvkit/scripts/skg_convert.py
+--- a/scripts/skg_convert.py
++++ b/scripts/skg_convert.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""Convert between tabular formats using scikit-genome I/O."""
import argparse
import logging
---- cnvkit.orig/scripts/cnv_expression_correlate.py
-+++ cnvkit/scripts/cnv_expression_correlate.py
+--- a/scripts/cnv_expression_correlate.py
++++ b/scripts/cnv_expression_correlate.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
=====================================
debian/patches/spelling
=====================================
@@ -1,7 +1,7 @@
From: Michael R. Crusoe <michael.crusoe at gmail.com>
Subject: Fix typos
---- cnvkit.orig/cnvlib/commands.py
-+++ cnvkit/cnvlib/commands.py
+--- a/cnvlib/commands.py
++++ b/cnvlib/commands.py
@@ -176,7 +176,7 @@
parallel. Without an argument, use the maximum number of
available CPUs. [Default: process each BAM in serial]""")
@@ -11,7 +11,7 @@ Subject: Fix typos
Use this option to specify a non-default R installation.
[Default: %(default)s]""")
-@@ -696,7 +696,7 @@
+@@ -709,7 +709,7 @@
Set to 0 for no outlier filtering.
[Default: %(default)g]""")
P_segment.add_argument("--rscript-path", metavar="PATH", default="Rscript",
=====================================
debian/rules
=====================================
@@ -44,8 +44,8 @@ override_dh_auto_install:
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
- cd test && ${MAKE} -j$(shell nproc)
- cd test && ${MAKE} -j$(shell nproc) clean || /bin/true
+ cd test && ${MAKE}
+ cd test && ${MAKE} clean || /bin/true
rm -Rf test/build test/*.tsv
endif
View it on GitLab: https://salsa.debian.org/med-team/cnvkit/-/compare/2ee1721d6565c8fba2fa4575d64ae2e0417c8a3e...01d666636b2e846266dec9699f7b5b365e53f9d6
--
View it on GitLab: https://salsa.debian.org/med-team/cnvkit/-/compare/2ee1721d6565c8fba2fa4575d64ae2e0417c8a3e...01d666636b2e846266dec9699f7b5b365e53f9d6
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