Rename genomeAPCAT package to PanACoTA

bin/genomeAPCAT

-#!/usr/bin/env python3
-# coding: utf-8
-
-import sys
-from textwrap import dedent
-
-from genomeAPCAT import __version__ as version
-
-from genomeAPCAT.subcommands import annote
-from genomeAPCAT.subcommands import pangenome
-from genomeAPCAT.subcommands import corepers
-from genomeAPCAT.subcommands import align
-from genomeAPCAT.subcommands import tree
-
-
-def main():
-    """
-    Start program according to arguments given by user.
-    """
-    action, args = parse_arguments(sys.argv[1:])
-    action(args)
-
-
-def parse_arguments(argv):
-    """
-    Extract command-line arguments for different actions.
-    """
-    import argparse
-
-    # Create main parser
-
-    parser = argparse.ArgumentParser(
-                                epilog="For more details, visit the MacSyFinder website and see "
-                                       "the MacSyFinder documentation.",
-                                 formatter_class=argparse.RawDescriptionHelpFormatter,
-                                 description=dedent('''
-
-
-
- ___                 _____  ___         _____  _____
-(  _`\              (  _  )(  _`\      (_   _)(  _  )
-| |_) )  _ _   ___  | (_) || ( (_)   _   | |  | (_) |
-| ,__/'/'_` )/' _ `\|  _  || |  _  /'_`\ | |  |  _  |
-| |   ( (_| || ( ) || | | || (_( )( (_) )| |  | | | |
-(_)   `\__,_)(_) (_)(_) (_)(____/'`\___/'(_)  (_) (_)
-
-
-       Large scale comparative genomics tools
-
-     -------------------------------------------
-     ''') )
-
-
-    parser.add_argument('-V', '--version', action='version',
-                        version='genomeAPCAT - v. ' + str(version),
-                        help="Print the version number and exit")
-
-    # Create subparsers, for all submodules
-    subparsers = parser.add_subparsers(dest='subparser_called')
-    # dest: to be able to get the subparser called with args.subparser_called
-    actions = {}  # to add the action to do according to the subparser called
-    checks = {}  # to add the function to call to check the subparser arguments
-
-    # QC and annotation part
-    parser_annote = subparsers.add_parser('annotate',
-                                          help="Quality control and annotation of genomes",
-                                          add_help=False)
-    annote.build_parser(parser_annote)
-    actions["annotate"] = annote.main_from_parse
-    checks["annotate"] = annote.check_args
-
-    # Pan genome part
-    parser_pan = subparsers.add_parser('pangenome', help="Generate a pan-genome of your dataset",
-                                       add_help=False)
-    pangenome.build_parser(parser_pan)
-    actions["pangenome"] = pangenome.main_from_parse
-
-    # Persistent genome part
-    parser_corepers = subparsers.add_parser('corepers',
-                                            help="Compute a Core or Persistent genome of your "
-                                                 "dataset",
-                                            add_help=False)
-    corepers.build_parser(parser_corepers)
-    actions["corepers"] = corepers.main_from_parse
-    checks["corepers"] = corepers.check_args
-
-    # Alignment part
-    parser_align = subparsers.add_parser('align',
-                                         help="Align Core/Persistent familiest",
-                                         add_help=False)
-    align.build_parser(parser_align)
-    actions["align"] = align.main_from_parse
-
-    # tree part
-    parser_tree = subparsers.add_parser('tree',
-                                        help=("Infer phylogenetic tree based on "
-                                              "core/persistent genome"),
-                                        add_help=False)
-    tree.build_parser(parser_tree)
-    actions["tree"] = tree.main_from_parse
-    checks["tree"] = tree.check_args
-
-    # Parse arguments and execute corresponding action
-    arguments = parser.parse_args(argv)
-    arguments.argv = argv
-    action_called = arguments.subparser_called
-    # If checks are needed, do it (if some arguments are not compatible etc.)
-    if action_called in checks:
-        checks[action_called](parser, arguments)
-
-    # If subparser called does not exist, error
-    if action_called not in actions:
-        parser.error("too few arguments. Use '-h' to get help.")
-    return actions[action_called], arguments
-
-
-if __name__ == '__main__':
-    main()

make

@@ -46,11 +46,11 @@ def uninstall():
     Uninstall PanACoTA python package
     """
     logger.info("Uninstalling PanACoTA...")
-    cmd = "pip3 uninstall -y genomeAPCAT"
+    cmd = "pip3 uninstall -y PanACoTA"
     error = ("A problem occurred while trying to uninstall PanACoTA. If you have "
              "permission errors, try to add 'sudo' before your command line.")
     run_cmd(cmd, error)
-    link_dest = os.path.join(os.sep + "usr", "local", "bin", "genomeAPCAT")
+    link_dest = os.path.join(os.sep + "usr", "local", "bin", "PanACoTA")
     if os.path.exists(link_dest):
         os.remove(link_dest)
 
@@ -99,7 +99,7 @@ def install_all(install_dir, target, dev=False, user=False):
              "you do not have root access, install with the '--user' option")
     run_cmd(cmd, error, eof=True)
     if user:
-        gapcat_bin = os.path.join(os.getcwd(), "bin", "genomeAPCAT")
+        gapcat_bin = os.path.join(os.getcwd(), "bin", "PanACoTA")
         os.symlink(gapcat_bin, os.path.join(install_dir, os.path.basename(gapcat_bin)))
     if to_install_user:
         msg = ("Some dependencies needed for some subcommands of PanACoTA are not installed. "

setup.py

@@ -5,7 +5,7 @@
 Setup script
 """
 
-import genomeAPCAT
+import PanACoTA
 try:
     from setuptools import setup
     from setuptools.command.test import test as TestCommand
@@ -38,16 +38,16 @@ def parse_requirements(requirements):
                 and not l.startswith('#')]
 
 
-packages = ['genomeAPCAT', 'genomeAPCAT.annote_module',
-            'genomeAPCAT.pangenome_module', 'genomeAPCAT.corepers_module',
-            'genomeAPCAT.align_module', 'genomeAPCAT.tree_module', 'genomeAPCAT.subcommands']
+packages = ['PanACoTA', 'PanACoTA.annote_module',
+            'PanACoTA.pangenome_module', 'PanACoTA.corepers_module',
+            'PanACoTA.align_module', 'PanACoTA.tree_module', 'PanACoTA.subcommands']
 requires = parse_requirements("requirements.txt")
-scripts = ['bin/genomeAPCAT']
+scripts = ['bin/PanACoTA']
 
 classifiers = [
     "Environment :: Console",
     "Intended Audience :: Science/Research",
-    "License :: ???",
+    "License :: AGPL v3",
     "Programming Language :: Python :: 3",
     "Operating System :: OS Independent",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
@@ -57,9 +57,9 @@ with open('README.md') as f:
     long_description = f.read()
 
 setup(
-    name='genomeAPCAT',
+    name='PanACoTA',
     packages=packages,
-    version=genomeAPCAT.__version__,
+    version=PanACoTA.__version__,
     description="Large scale comparative genomics tools: annotate genomes, do pangenome, "
                 "core/persistent genome, align core/persistent families, infer phylogenetic tree.",
     long_description=long_description,