Merge pull request #1140 from nextgenusfs/bugfix_1139_pkgversion

remove use of pkg_version which is deprecated, bug #1139

Author: hyphaltip

funannotate/annotate.py

@@ -4,7 +4,6 @@
 
 import funannotate.library as lib
 from funannotate.aux_scripts.fasta2agp import parse_scaffolds_makeagp
-from pkg_resources import parse_version
 import sys
 import os
 import subprocess
@@ -1039,16 +1038,16 @@ def __init__(self, prog):
                 "--cpu",
                 str(args.cpus),
             ]
-            if parse_version(get_emapper_version()) >= parse_version("2.1.0"):
+            if packaging.version.parse(get_emapper_version()) >= packaging.version.parse("2.1.0"):
                 if not os.path.isdir(args.tmpdir):
                     os.makedirs(args.tmpdir)
                 if not os.path.isdir(scratch_dir):
                     os.makedirs(scratch_dir)
                 cmd += ["--scratch_dir", scratch_dir, "--temp_dir", args.tmpdir]
                 if lib.MemoryCheck() >= 48:
                     cmd.append("--dbmem")
-            if parse_version(get_emapper_version()) >= parse_version("2.1.4"):
-                if parse_version(lib.getDiamondVersion()) < parse_version("2.0.11"):
+            if packaging.version.parse(get_emapper_version()) >= packaging.version.parse("2.1.4"):
+                if packaging.version.parse(lib.getDiamondVersion()) < packaging.version.parse("2.0.11"):
                     cmd += ["--dmnd_iterate", "no"]
             lib.runSubprocess(cmd, os.path.join(outputdir, "annotate_misc"), lib.log)
             if os.path.isdir(scratch_dir):

funannotate/check.py

@@ -4,7 +4,7 @@
 import sys
 import os
 import re
-import pkg_resources
+import importlib.metadata
 import subprocess
 import errno
 import shutil
@@ -35,10 +35,11 @@ def checkPerlModule(mod):
 
 def checkPyModule(mod):
     try:
-        vers = pkg_resources.get_distribution(mod).version
-    except pkg_resources.DistributionNotFound:
-        vers = False
-    return vers
+        version = importlib.metadata.version(mod)
+    except importlib.metadata.PackageNotFoundError:
+        # Handle the case where the package metadata is not found
+        version = False
+    return version
 
 
 def mycmp(version1, version2):

funannotate/funannotate.py

@@ -8,12 +8,15 @@
 import importlib
 import subprocess
 import funannotate
-from pkg_resources import get_distribution
+import importlib.metadata
 
 global package_name
 global __version__
 package_name = 'funannotate'
-__version__ = get_distribution(package_name).version
+try:
+  __version__ = importlib.metadata.version(package_name)
+except importlib.metadata.PackageNotFoundError:
+  __version__ = "Unknown"
 
 default_help = """
 Usage:       {:} <command> <arguments>

funannotate/library.py

@@ -1092,9 +1092,11 @@ def getGeneBasename(fastafile):
 
 
 def get_version():
-    from pkg_resources import get_distribution
-
-    __version__ = get_distribution("funannotate").version
+    import importlib.metadata
+    try:
+        __version__ = importlib.metadata.version("funannotate")
+    except importlib.metadata.PackageNotFoundError:
+        __version__ = False
     return __version__
 
 

funannotate/train.py

@@ -13,7 +13,6 @@
 from collections import defaultdict
 from Bio.SeqIO.FastaIO import SimpleFastaParser
 from Bio.SeqIO.QualityIO import FastqGeneralIterator
-# from pkg_resources import parse_version
 
 
 def runTrimmomaticPE(left, right, cpus=1):