[med-svn] [Git][med-team/nanosv][master] 8 commits: Bump standards version to 4.7.0 (no changes needed)

Ananthu C V (@weepingclown) gitlab at salsa.debian.org
Fri Dec 6 15:39:37 GMT 2024 


Ananthu C V pushed to branch master at Debian Med / nanosv


Commits:
c37bcdba by Ananthu C V at 2024-12-06T20:33:13+05:30
Bump standards version to 4.7.0 (no changes needed)

- - - - -
44901512 by Ananthu C V at 2024-12-06T20:34:57+05:30
Update patch header metadata

- - - - -
93fd51b4 by Ananthu C V at 2024-12-06T20:37:37+05:30
Use execute_after_* hooks instead of overrides in d/rules

- - - - -
d9ba7eee by Ananthu C V at 2024-12-06T20:38:43+05:30
Use dh-sequence-python3 and run wrap-and-sort

- - - - -
a01a29c4 by Ananthu C V at 2024-12-06T20:40:54+05:30
Add repository fields to upstream metadata

- - - - -
996339dc by Ananthu C V at 2024-12-06T20:48:20+05:30
Add patch to fix syntaxwarnings (Closes: #1085733)

- - - - -
88b8c207 by Ananthu C V at 2024-12-06T20:58:42+05:30
Fix deprecated dash separated option in setup.cfg

- - - - -
9a794f3a by Ananthu C V at 2024-12-06T21:00:01+05:30
Upload to unstable

- - - - -


12 changed files:

- debian/changelog
- debian/control
- debian/copyright
- debian/docs
- + debian/patches/fix-invalid-dash-seperation.patch
- debian/patches/fix_setup.patch
- debian/patches/python3_has_buildin_configparser.patch
- debian/patches/series
- + debian/patches/use-raw-strings.patch
- debian/rules
- debian/tests/control
- debian/upstream/metadata


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+nanosv (1.2.4+git20190409.c1ae30c-7) unstable; urgency=medium
+
+  * Team upload.
+  * Bump standards version to 4.7.0 (no changes needed)
+  * Update patch header metadata
+  * Use execute_after_* hooks instead of overrides in d/rules
+  * Use dh-sequence-python3 and run wrap-and-sort
+  * Add repository fields to upstream metadata
+  * Add patch to fix syntaxwarnings (Closes: #1085733)
+  * Fix deprecated dash separated option in setup.cfg
+
+ -- Ananthu C V <weepingclown at disroot.org>  Fri, 06 Dec 2024 20:59:53 +0530
+
 nanosv (1.2.4+git20190409.c1ae30c-6) unstable; urgency=medium
 
   * Team Upload.


=====================================
debian/control
=====================================
@@ -4,12 +4,12 @@ Uploaders: Steffen Moeller <moeller at debian.org>
 Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 13),
-               dh-python,
-               python3-setuptools,
-               python3-all,
+               dh-sequence-python3,
                help2man,
-               python3-vcf,
-Standards-Version: 4.6.0
+               python3-all,
+               python3-setuptools,
+               python3-vcf
+Standards-Version: 4.7.0
 Vcs-Browser: https://salsa.debian.org/med-team/nanosv
 Vcs-Git: https://salsa.debian.org/med-team/nanosv.git
 Homepage: https://github.com/mroosmalen/nanosv
@@ -18,10 +18,7 @@ Rules-Requires-Root: no
 Package: nanosv
 Architecture: all
 Recommends: sambamba
-Depends: ${python3:Depends},
-         ${misc:Depends},
-         python3-pysam,
-         python3-vcf
+Depends: python3-pysam, python3-vcf, ${misc:Depends}, ${python3:Depends}
 Description: structural variant caller for nanopore data
  NanoSV is a software package that can be used to identify structural
  genomic variations in long-read sequencing data, such as data produced


=====================================
debian/copyright
=====================================
@@ -28,5 +28,3 @@ License: MIT
  CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
  TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
  SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-
- 


=====================================
debian/docs
=====================================
@@ -1,3 +1,3 @@
 README.md
 debian/README*
-debian/tests/run-unit-test
\ No newline at end of file
+debian/tests/run-unit-test


=====================================
debian/patches/fix-invalid-dash-seperation.patch
=====================================
@@ -0,0 +1,11 @@
+Description: fix deprecated dash separated option in setup.cfg
+Author: Ananthu C V <weepingclown at debian.org>
+Last-Update: 2024-12-06
+--- a/setup.cfg
++++ b/setup.cfg
+@@ -1,2 +1,2 @@
+ [metadata]
+-description-file = README.md
+\ No newline at end of file
++description_file = README.md
+\ No newline at end of file


=====================================
debian/patches/fix_setup.patch
=====================================
@@ -1,7 +1,7 @@
 Author: Steffen Möller
-Last-Update: 2020-06-07 17:34:55 +0200
+Last-Update: 2020-06-07
 Description: Fix typo in setup.py
-Reported-Upstream: https://github.com/mroosmalen/nanosv/pull/67
+Forwarded: https://github.com/mroosmalen/nanosv/pull/67
 
 --- nanosv-1.2.4.orig/setup.py
 +++ nanosv-1.2.4/setup.py


=====================================
debian/patches/python3_has_buildin_configparser.patch
=====================================
@@ -1,5 +1,5 @@
 Author: Andreas Tille <tille at debian.org>
-Last-Update: Mon, 08 Jun 2020 14:23:48 +0200
+Last-Update: 2020-01-08
 Description: Do not require configparser which is part of Python3
 
 --- a/setup.py


=====================================
debian/patches/series
=====================================
@@ -1,2 +1,4 @@
 fix_setup.patch
 python3_has_buildin_configparser.patch
+use-raw-strings.patch
+fix-invalid-dash-seperation.patch


=====================================
debian/patches/use-raw-strings.patch
=====================================
@@ -0,0 +1,33 @@
+Description: use raw strings to avoid illegal escape sequences
+Author: Ananthu C V <weepingclown at debian.org>
+Last-Update: 2024-12-06
+--- a/nanosv/utils/parse_bam.py
++++ b/nanosv/utils/parse_bam.py
+@@ -42,3 +42,3 @@
+     else:
+-        sample_name = re.sub('(\.sorted)?\.bam$', '', str(NanoSV.opts_bam))
++        sample_name = re.sub(r'(\.sorted)?\.bam$', '', str(NanoSV.opts_bam))
+ 
+@@ -205,3 +205,3 @@
+         if j > 0:
+-            pattern_list[i] += '[' + str(int(NanoSV.opts_min_indel_size[i]) + 1) + '-9]\d{' + str(j) + ',}'
++            pattern_list[i] += '[' + str(int(NanoSV.opts_min_indel_size[i]) + 1) + r'-9]\d{' + str(j) + ',}'
+         for k in range(i + 1, len(pattern_list)):
+@@ -209,3 +209,3 @@
+     pattern_list[-1] += '[' + str(int(NanoSV.opts_min_indel_size[-1])) + '-9]'
+-    pattern_list.append("\d{" + str(len(NanoSV.opts_min_indel_size) + 1) + ",}")
++    pattern_list.append(r"\d{" + str(len(NanoSV.opts_min_indel_size) + 1) + ",}")
+     pattern = re.compile(r'' + "(" + "|".join(pattern_list) + ")([DI])" + '')
+@@ -391,3 +391,3 @@
+     global tmp_variants
+-    md_tag = re.split("\^\D+", md)
++    md_tag = re.split(r"\^\D+", md)
+     read_cursor = 0
+@@ -415,5 +415,5 @@
+         if tuple[0] == 0:
+-            if re.search("\D+", md_tag[md_cursor]):
++            if re.search(r"\D+", md_tag[md_cursor]):
+                 if md_string == '':
+-                    for m in re.split("\D", md_tag[md_cursor]):
++                    for m in re.split(r"\D", md_tag[md_cursor]):
+                         if md_string != '':


=====================================
debian/rules
=====================================
@@ -4,17 +4,15 @@ export DH_VERBOSE = 1
 export PYBUILD_NAME=nanosv
 
 %:
-	dh $@ --with python3 --buildsystem=pybuild
+	dh $@ --buildsystem=pybuild
 
-override_dh_auto_install:
-	dh_auto_install
+execute_after_dh_auto_install:
 	find $(CURDIR)/debian -name "*.bed" -o -name "*.ini" | xargs -r chmod -x
 	PYTHONPATH=./debian/nanosv/usr/lib/$(shell py3versions -d)/dist-packages/ help2man --include=debian/NanoSV.h2m ./debian/nanosv/usr/bin/NanoSV > $(CURDIR)/debian/NanoSV.1
 
 override_dh_auto_test:
 	echo "I: Do nothing"
 
-override_dh_auto_clean:
-	dh_auto_clean
+execute_after_dh_auto_clean:
 	rm -rf $(CURDIR)/debian/python3-nanosv*
 	rm -f $(CURDIR)/debian/NanoSV.1


=====================================
debian/tests/control
=====================================
@@ -1,3 +1,3 @@
 Tests: run-unit-test
-Depends: @, sambamba, samtools, bedtools
+Depends: bedtools, sambamba, samtools, @
 Restrictions: allow-stderr, skip-not-installable


=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,5 @@
+Repository: https://github.com/mroosmalen/nanosv.git
+Repository-Browse: https://github.com/mroosmalen/nanosv
 Bug-Database: https://github.com/mroosmalen/nanosv/issues
 Bug-Submit: https://github.com/mroosmalen/nanosv/issues/new
 Reference:



View it on GitLab: https://salsa.debian.org/med-team/nanosv/-/compare/964cf74e84bc978c14e467097d6329c01b7e4940...9a794f3a19f82ae980d460421768d25b5c7e28d4

-- 
View it on GitLab: https://salsa.debian.org/med-team/nanosv/-/compare/964cf74e84bc978c14e467097d6329c01b7e4940...9a794f3a19f82ae980d460421768d25b5c7e28d4
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