depends on deprecated pkg_resources module

[emollier]

Hi,

As initially reported in Debian bug #1083762, scoary depends on pkg_resources which is deprecated and on a course to be removed. I intend to workaround the issue with the below patch, but I'm not 100% it is suitable in every situations, notably outside Debian context. Anyway, in case you find something useful:

--- 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

Have a nice day, :)
Étienne.