[med-svn] [Git][med-team/virulencefinder][master] 5 commits: Standards-Version: 4.6.2

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / virulencefinder


Commits:
84c65934 by Andreas Tille at 2024-02-02T11:40:17+01:00
Standards-Version: 4.6.2

- - - - -
2a1a80ac by Andreas Tille at 2024-02-02T11:41:21+01:00
Build-Depends: s/dh-python/dh-sequence-python3/

- - - - -
04df4d68 by Andreas Tille at 2024-02-02T11:42:39+01:00
Install run-unit-test script to user docs

- - - - -
2e01ee1e by Andreas Tille at 2024-02-02T11:43:48+01:00
Port to Python3.12 by removing distutils

- - - - -
13e201e8 by Andreas Tille at 2024-02-02T11:45:41+01:00
Upload to unstable

- - - - -


7 changed files:

- debian/README.test
- debian/changelog
- debian/control
- + debian/patches/python3.12.patch
- debian/patches/series
- debian/rules
- debian/virulencefinder.docs


Changes:

=====================================
debian/README.test
=====================================
@@ -3,6 +3,7 @@ Notes on how this package can be tested.
 
 This package can be tested by running the provided test:
 
+    sudo apt install virulencefinder-examples
     sh run-unit-test
 
 in order to confirm its integrity.


=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+virulencefinder (2.0.4-4) unstable; urgency=medium
+
+  * Standards-Version: 4.6.2
+  * Build-Depends: s/dh-python/dh-sequence-python3/
+  * Install run-unit-test script to user docs
+  * Port to Python3.12 by removing distutils
+    Closes: #1061856
+
+ -- Andreas Tille <tille at debian.org>  Fri, 02 Feb 2024 11:44:04 +0100
+
 virulencefinder (2.0.4-3) unstable; urgency=medium
 
   * d/control: add myself to uploaders.


=====================================
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,
                python3,
                python3-tabulate,
                python3-cgecore,
                ncbi-blast+ <!nocheck>
-Standards-Version: 4.6.1
+Standards-Version: 4.6.2
 Vcs-Browser: https://salsa.debian.org/med-team/virulencefinder
 Vcs-Git: https://salsa.debian.org/med-team/virulencefinder.git
 Homepage: https://bitbucket.org/genomicepidemiology/virulencefinder


=====================================
debian/patches/python3.12.patch
=====================================
@@ -0,0 +1,34 @@
+Description: Port to Python3.12 by removing distutils
+Bug-Debian: https://bugs.debian.org/1061856
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Fri, 02 Feb 2024 11:10:47 +0100
+
+--- a/virulencefinder.py
++++ b/virulencefinder.py
+@@ -4,7 +4,7 @@ from argparse import ArgumentParser
+ from tabulate import tabulate
+ from cgecore.blaster import Blaster
+ from cgecore.cgefinder import CGEFinder
+-from distutils.spawn import find_executable
++import shutil
+ import sys
+ import os
+ import time
+@@ -322,7 +322,7 @@ file_format = get_file_format(infile)
+ if file_format == "fastq":
+     if not method_path:
+         method_path = "kma"
+-    if find_executable(method_path) is None:
++    if shutil.which(method_path) is None:
+         sys.exit("No valid path to a kma program was provided. Use the -mp "
+                  "flag to provide the path.")
+ 
+@@ -351,7 +351,7 @@ if file_format == "fastq":
+ elif file_format == "fasta":
+     if not method_path:
+         method_path = "blastn"
+-    if find_executable(method_path) is None:
++    if shutil.which(method_path) is None:
+         sys.exit("No valid path to a blastn program was provided. Use the "
+                  "-mp flag to provide the path.")
+ 


=====================================
debian/patches/series
=====================================
@@ -1 +1,2 @@
 reproducible_build.patch
+python3.12.patch


=====================================
debian/rules
=====================================
@@ -7,7 +7,7 @@ export PYBUILD_CLEAN_ARGS=rm -rf test/Hit_in_genome_seq.fsa test/Virulence_genes
 export PYBUILD_AFTER_TEST=rm -rf test/Hit_in_genome_seq.fsa test/Virulence_genes.fsa test/data.json test/tmp test/results_tab.tsv test/results.txt
 
 %:
-	dh $@ --with python3 --buildsystem=pybuild
+	dh $@ --buildsystem=pybuild
 
 override_dh_auto_test:
 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))


=====================================
debian/virulencefinder.docs
=====================================
@@ -1 +1,3 @@
 README*
+debian/README.test
+debian/tests/run-unit-test



View it on GitLab: https://salsa.debian.org/med-team/virulencefinder/-/compare/400e5052b61187bf42535591e1fe6bc83e32daea...13e201e80cd2cd995d0bef811ebcffe96d036da6

-- 
View it on GitLab: https://salsa.debian.org/med-team/virulencefinder/-/compare/400e5052b61187bf42535591e1fe6bc83e32daea...13e201e80cd2cd995d0bef811ebcffe96d036da6
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