[med-svn] [Git][med-team/scoary][master] 3 commits: rm-pkg_resources.patch: new: reimplement uses of pkg_resources.

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / scoary


Commits:
3222d4ad by Étienne Mollier at 2024-10-16T17:18:20+02:00
rm-pkg_resources.patch: new: reimplement uses of pkg_resources.

- - - - -
9cdaea23 by Étienne Mollier at 2024-10-16T17:18:45+02:00
d/control: remove dependency on python3-pkg-resources.

Closes: #1083762

- - - - -
17f85885 by Étienne Mollier at 2024-10-16T17:19:16+02:00
Ready for upload to unstable.

- - - - -


4 changed files:

- debian/changelog
- debian/control
- + debian/patches/rm-pkg_resources.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+scoary (1.6.16-9) unstable; urgency=medium
+
+  * rm-pkg_resources.patch: new: reimplement uses of pkg_resources.
+  * d/control: remove dependency on python3-pkg-resources. (Closes: #1083762)
+
+ -- Étienne Mollier <emollier at debian.org>  Wed, 16 Oct 2024 17:19:08 +0200
+
 scoary (1.6.16-8) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/control
=====================================
@@ -20,7 +20,6 @@ Package: scoary
 Architecture: all
 Depends: ${misc:Depends},
          ${python3:Depends},
-         python3-pkg-resources,
          python3-scipy
 Suggests: roary
 Description: pangenome-wide association studies


=====================================
debian/patches/rm-pkg_resources.patch
=====================================
@@ -0,0 +1,71 @@
+Description: workaround removal of pkg_resources.
+Author: Étienne Mollier <emollier at debian.org>
+Bug: https://github.com/AdmiralenOla/Scoary/issues/112
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1083762
+Last-Update: 2024-10-16
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- scoary.orig/scoary/GUI.py
++++ scoary/scoary/GUI.py
+@@ -61,7 +61,7 @@
+ except ImportError:
+     sys.exit("Could not find the main Scoary executable") 
+ 
+-from pkg_resources import resource_string, resource_filename
++from importlib.metadata import distribution
+ 
+ class ScoaryGUI(Tkinter.Tk):
+     """
+@@ -617,11 +617,12 @@
+         """
+         Sets all variables corresponding to --test in the methods script
+         """
++        scoary_dist = distribution('scoary')
+         self.GPAentryVariable.set(
+-            str(os.path.join(resource_filename(__name__, 'exampledata'),
++            str(os.path.join(scoary_dist.locate_file('scoary'), 'exampledata',
+                              'Gene_presence_absence.csv')))
+         self.TraitsentryVariable.set(
+-            str(os.path.join(resource_filename(__name__, 'exampledata'),
++            str(os.path.join(scoary_dist.locate_file('scoary'), 'exampledata',
+                              'Tetracycline_resistance.csv')))
+         self.TreeentryVariable.set("")
+         self.RestrictVariable.set("")
+--- scoary.orig/scoary/methods.py
++++ scoary/scoary/methods.py
+@@ -27,7 +27,7 @@
+ #import scoary
+ 
+ import os
+-from pkg_resources import resource_string, resource_filename
++from importlib.metadata import distribution
+ 
+ #SCOARY_VERSION = scoary.__version__
+ SCOARY_VERSION = __version__
+@@ -69,9 +69,10 @@
+     if args.test:
+         args.correction = ['I','EPW']
+         args.delimiter = ','
+-        args.genes = os.path.join(
+-            resource_filename(__name__, 'exampledata'), 
+-            'Gene_presence_absence.csv')
++        scoary_dist = distribution('scoary')
++        args.genes = os.path.join(scoary_dist.locate_file('scoary'),
++                                  'exampledata',
++                                  'Gene_presence_absence.csv')
+         args.grabcols = []
+         args.max_hits = None
+         args.newicktree = None
+@@ -82,9 +83,9 @@
+         args.restrict_to = None
+         args.start_col = 15
+         args.threads = 4
+-        args.traits = os.path.join(
+-            resource_filename(__name__, 'exampledata'),
+-            'Tetracycline_resistance.csv')
++        args.traits = os.path.join(scoary_dist.locate_file('scoary'),
++                                   'exampledata',
++                                   'Tetracycline_resistance.csv')
+         args.upgma_tree = True
+         args.write_reduced = False
+         args.no_time = False


=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
 python3.11.patch
 scipy-1.12.0.patch
 remove_six.patch
+rm-pkg_resources.patch



View it on GitLab: https://salsa.debian.org/med-team/scoary/-/compare/b4a9b51dbbefb50b52ef476fe874f4065d30aea5...17f8588573d2ff6ee1caf0223d4714c5ecea81aa

-- 
View it on GitLab: https://salsa.debian.org/med-team/scoary/-/compare/b4a9b51dbbefb50b52ef476fe874f4065d30aea5...17f8588573d2ff6ee1caf0223d4714c5ecea81aa
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