Change pkg_ressource to importlib.metadata

VERSION

@@ -1 +1 @@
-1.2.185
+1.2.186

ppanggolin/formats/writeBinaries.py

@@ -6,7 +6,7 @@
 from collections import Counter, defaultdict
 import statistics
 from typing import Tuple
-import pkg_resources
+from importlib.metadata import distribution
 
 # installed libraries
 from tqdm import tqdm
@@ -668,7 +668,7 @@ def write_status(pangenome: Pangenome, h5f: tables.File):
     status_group._v_attrs.spots = True if pangenome.status["spots"] in ["Computed", "Loaded", "inFile"] else False
     status_group._v_attrs.modules = True if pangenome.status["modules"] in ["Computed", "Loaded", "inFile"] else False
     status_group._v_attrs.metadata = write_metadata_status(pangenome, h5f, status_group)
-    status_group._v_attrs.version = pkg_resources.get_distribution("ppanggolin").version
+    status_group._v_attrs.version = distribution("ppanggolin").version
 
 
 def write_info(pangenome: Pangenome, h5f: tables.File):

ppanggolin/formats/writeFlat.py

@@ -8,7 +8,7 @@
 from collections import Counter, defaultdict
 from pathlib import Path
 from typing import TextIO
-import pkg_resources
+from importlib.metadata import distribution
 from statistics import median, mean, stdev
 import os
 
@@ -214,7 +214,7 @@ def write_gexf_header(gexf: TextIO, light: bool = True):
             gexf.write(f'      <attribute id="{org_idx + len(index) + shift}" title="{org.name}" type="long" />\n')
     gexf.write('    </attributes>\n')
     gexf.write('    <meta>\n')
-    gexf.write(f'      <creator>PPanGGOLiN {pkg_resources.get_distribution("ppanggolin").version}</creator>\n')
+    gexf.write(f'      <creator>PPanGGOLiN {distribution("ppanggolin").version}</creator>\n')
     gexf.write('    </meta>\n')
 
 

ppanggolin/utils.py

@@ -12,7 +12,7 @@
 from typing import TextIO, Union, BinaryIO, Tuple, List, Set, Iterable
 
 import networkx as nx
-import pkg_resources
+from importlib.metadata import distribution
 from numpy import repeat
 from collections.abc import Callable
 
@@ -158,8 +158,7 @@ def set_verbosity_level(args):
                                 format=str_format,
                                 datefmt=datefmt)
         logging.getLogger("PPanGGOLiN").info("Command: " + " ".join([arg for arg in sys.argv]))
-        logging.getLogger("PPanGGOLiN").info(
-            "PPanGGOLiN version: " + pkg_resources.get_distribution("ppanggolin").version)
+        logging.getLogger("PPanGGOLiN").info(f"PPanGGOLiN version: {distribution('ppanggolin').version}")
 
 
 def jaccard_similarities(mat: csc_matrix, jaccard_similarity_th) -> csc_matrix: