replaced pkg_resources by importlib.metadata

Author: trvinh

fdog/addTaxa.py

@@ -66,8 +66,8 @@ def parse_map_file(mapping_file, folIn):
 
 
 def main():
-    version = version("fdog")
-    parser = argparse.ArgumentParser(description='You are running fDOG version ' + str(version) + '.')
+    fdog_version = version("fdog")
+    parser = argparse.ArgumentParser(description='You are running fDOG version ' + str(fdog_version) + '.')
     required = parser.add_argument_group('required arguments')
     optional = parser.add_argument_group('optional arguments')
     required.add_argument('-i', '--input', help='Path to input folder', action='store', default='', required=True)

fdog/addTaxon.py

@@ -34,8 +34,8 @@
 
 
 def main():
-    version = version("fdog")
-    parser = argparse.ArgumentParser(description='You are running fDOG version ' + str(version) + '.')
+    fdog_version = version("fdog")
+    parser = argparse.ArgumentParser(description='You are running fDOG version ' + str(fdog_version) + '.')
     required = parser.add_argument_group('required arguments')
     optional = parser.add_argument_group('optional arguments')
     required.add_argument('-f', '--fasta', help='FASTA file of input taxon', action='store', default='', required=True)

fdog/checkData.py

@@ -418,8 +418,8 @@ def run_check(args):
     return(caution)
 
 def main():
-    version = version("fdog")
-    parser = argparse.ArgumentParser(description='You are running fDOG version ' + str(version) + '.')
+    fdog_version = version("fdog")
+    parser = argparse.ArgumentParser(description='You are running fDOG version ' + str(fdog_version) + '.')
     parser.add_argument('-s', '--searchTaxa_dir', help='Path to search taxa directory (e.g. fdog_dataPath/searchTaxa_dir)', action='store', default='')
     parser.add_argument('-c', '--coreTaxa_dir', help='Path to blastDB directory (e.g. fdog_dataPath/coreTaxa_dir)', action='store', default='')
     parser.add_argument('-a', '--annotation_dir', help='Path to feature annotation directory (e.g. fdog_dataPath/annotation_dir)', action='store', default='')

fdog/mergeOutput.py

@@ -37,8 +37,8 @@ def createConfigPP(phyloprofile, domains_0, ex_fasta, directory, out):
 
 
 def main():
-    version = version("fdog")
-    parser = argparse.ArgumentParser(description='You are running fDOG version ' + str(version) + '.')
+    fdog_version = version("fdog")
+    parser = argparse.ArgumentParser(description='You are running fDOG version ' + str(fdog_version) + '.')
     parser.add_argument('-i', '--input',
                         help='Input directory, where all single output (.extended.fa, .phyloprofile, _forward.domains, _reverse.domains) can be found',
                         action='store', default='', required=True)

fdog/removefDog.py

@@ -48,8 +48,8 @@ def query_yes_no(question, default='yes'):
 
 
 def main():
-    version = version("fdog")
-    parser = argparse.ArgumentParser(description='You are running fDOG version ' + str(version) + '.')
+    fdog_version = version("fdog")
+    parser = argparse.ArgumentParser(description='You are running fDOG version ' + str(fdog_version) + '.')
     parser.add_argument('--all', help='Remove fdog together with all files/data within the installed fdog directory', action='store_true', default=False)
     args = parser.parse_args()
     data = args.all

fdog/runMulti.py

@@ -161,8 +161,8 @@ def join_outputs(outpath, jobName, seeds, keep, silentOff):
 
 
 def main():
-    version = version("fdog")
-    parser = argparse.ArgumentParser(description='You are running fDOG version ' + str(version) + '.',
+    fdog_version = version("fdog")
+    parser = argparse.ArgumentParser(description='You are running fDOG version ' + str(fdog_version) + '.',
                                      epilog="For more information on certain options, please refer to the wiki pages "
                                             "on github: https://github.com/BIONF/fDOG/wiki")
     required = parser.add_argument_group('Required arguments')

fdog/runSingle.py

@@ -33,8 +33,8 @@
 
 
 def main():
-    version = version("fdog")
-    parser = argparse.ArgumentParser(description='You are running fDOG version ' + str(version) + '.',
+    fdog_version = version("fdog")
+    parser = argparse.ArgumentParser(description='You are running fDOG version ' + str(fdog_version) + '.',
                                      epilog="For more information on certain options, please refer to the wiki pages "
                                             "on github: https://github.com/BIONF/fDOG/wiki")
     required = parser.add_argument_group('Required arguments')

fdog/setPaths.py

@@ -65,8 +65,8 @@ def check_data(searchpath, corepath, annopath):
 
 
 def main():
-    version = version("fdog")
-    parser = argparse.ArgumentParser(description='You are running fDOG version ' + str(version) + '.')
+    fdog_version = version("fdog")
+    parser = argparse.ArgumentParser(description='You are running fDOG version ' + str(fdog_version) + '.')
     required = parser.add_argument_group('required arguments')
     optional = parser.add_argument_group('optional arguments')
     required.add_argument('--searchpath', help='Path to search taxa folder (e.g. fdog_data/searchTaxa_dir)', action='store', default='', required=True)

fdog/setupfDog.py

@@ -201,8 +201,8 @@ def write_pathconfig(fdogPath, dataPath):
 
 
 def main():
-    version = version("fdog")
-    parser = argparse.ArgumentParser(description='You are running fDOG version ' + str(version) + '.')
+    fdog_version = version("fdog")
+    parser = argparse.ArgumentParser(description='You are running fDOG version ' + str(fdog_version) + '.')
     required = parser.add_argument_group('required arguments')
     optional = parser.add_argument_group('optional arguments')
     required.add_argument('-d', '--dataPath', help='Output path for fDOG data', action='store', default='', required=True)