Added argument parsing tests

chi_pet/chi.py

@@ -13,7 +13,7 @@
 import os
 from pathlib import Path
 # Main functions
-from .chi_parse import chi_parse
+from .chi_parse import parse_chi_options
 from .chi_run import ChiRun
 from .chi_node import ChiNode
 from . import chi_lib as clib
@@ -25,7 +25,7 @@ def __init__(self, opts):
 
         self.opts = opts
         self.read_opts()
-        self.run()
+        self.execute()
 
     def read_opts(self):
         if not self.opts.workdir:
@@ -35,7 +35,7 @@ def read_opts(self):
             yd = clib.create_dict_from_yaml_file(self.opts.args_file)
             self.opts.states = list(yd.keys())
 
-    def run(self):
+    def execute(self):
         if self.opts.command == "launch":
             # # If no sim dirs are given find them all in simulations
             # if self.opts.launch == []:
@@ -104,7 +104,7 @@ def run(self):
 def main():
     """Main function of chi_pet
     """
-    opts = chi_parse()
+    opts = parse_chi_options()
     chi = Chi(opts)
 
 

chi_pet/chi_parse.py

@@ -11,37 +11,37 @@
 
 from pathlib import Path
 
-# TODO NEXT add parser test
+# TODO NTEST add parser test
 
 
-def chi_parse():
-    parser = argparse.ArgumentParser(prog='chi_pet.py')
+def parse_chi_options():
+    parser = argparse.ArgumentParser(prog='chi.py')
 
-    parser.add_argument('-n', type=int, default=10,
-                        help='Number of different parameter sets used.')
-    parser.add_argument('-a', '--args_file', type=str,
-                        help='Name file that holds the program argument list.  (Used with --create option and --launch option)')
-    parser.add_argument('-d', '--workdir', type=str,
-                        help='Name of the working directory where simulation will be run. Used with --run option only)')
-    parser.add_argument('-s', '--states', nargs='+', type=str,
-                        help='Name of all the states the simulation will run eg. start, build, analyze, etc.')
+    parent_parser = argparse.ArgumentParser(add_help=False)
+
+    parent_parser.add_argument('-a', '--args_file', type=Path,
+                               help='Name file that holds the program argument list.  (Used with --create option and --launch option)')
+    parent_parser.add_argument('-d', '--workdir', type=Path,
+                               help='Name of the working directory where simulation will be run. Used with --run option only)')
+    parent_parser.add_argument('-s', '--states', nargs='+', type=str,
+                               help='Name of all the states the simulation will run eg. start, build, analyze, etc.')
 
     # TODO add prep functionality
     parser.add_argument('-P', '--prep', action='store_true',
                         help='Prepares simulationss to run with either states specified with -s or all argument states in --args_file.')
 
     # TODO add remove functionality
-    parser.add_argument('-rm', '--remove', nargs='+', metavar='FILE', type=str,
+    parser.add_argument('-rm', '--remove', nargs='+', metavar='FILE(s)', type=Path,
                         help='Removes FILEs from seed directories.')
 
     subparsers = parser.add_subparsers(dest='command')
 
     # CREATE options
     create_parser = subparsers.add_parser(
-        'create', help='Create a simulation directory structure using various strategies.')
+        'create', parents=[parent_parser], help='Create a simulation directory structure using various strategies.')
 
-    create_parser.add_argument('files',
-                               metavar='PARAM_FILE(S)', nargs='+', type=str, default=[],
+    create_parser.add_argument('param_files',
+                               metavar='PARAM_FILE(S)', nargs='+', type=Path, default=[],
                                help='List of yaml files to be combined into a single yaml file and varied using Chi-Pet.')
 
     # create_parser.add_argument('-A', '--algorithm', type=str, default='scan',
@@ -50,14 +50,14 @@ def chi_parse():
     create_parser.add_argument('-r', '--replace', default=False, action='store_true',
                                help='Replace simulation file instead of throwing and error if file already exists.(Used with create parser only)')
 
-    create_parser.add_argument('-ny', '--non_yaml', nargs='+', default=[], type=str,
+    create_parser.add_argument('-ny', '--non_yaml', nargs='+', default=[], type=Path,
                                help='Will add non-yaml files to seed directories when creating directory structure. (Used with create parser only)')
 
     run_parser = subparsers.add_parser(
-        'run', help='Run a simulation pipeline defined in args yaml file in a singular seed directory. Requires the --args_file option defined.')
+        'run', parents=[parent_parser], help='Run a simulation pipeline defined in args yaml file in a singular seed directory. Requires the --args_file option defined.')
 
     launch_parser = subparsers.add_parser(
-        'launch', help='Launch or create launching script to run simulations in seed directories.')
+        'launch', parents=[parent_parser], help='Launch or create launching script to run simulations in seed directories.')
 
     # parser.add_argument('-L', '--launch', nargs='*', default='NOLAUNCH', type=str, metavar='DIRS',
     #                     help='Launches all the seed directories in DIRS list. If no list is\
@@ -71,17 +71,9 @@ def chi_parse():
     #                     nargs='+', type=str, default=[],
     #                     help='Genetic Algorithm Optimization Creation. Creates seed directories with simulation structure that can be launched with ChiLaunch.py. PARAM_FILEs are copied into seed directories with ChiParams chosen according to the random distribution specified. Need -n to specify the number of random population members (default=10).')
 
-    # RUN options only
-    parser.add_argument('-R', '--run', action="store_true",
-                        help='Runs a singular seed directory. Need --args_file.')
-
     opts = parser.parse_args()
 
     if opts.command == 'run' and opts.args_file is None:
         parser.error("'run' requires the '--args_file' option.")
 
-    # If growing a chi tree, turn param file path strings into a pathlib list
-    if opts.command == 'create':
-        opts.param_file_paths = [opts.files]
-
     return opts

tests/test_chi_parse.py

@@ -0,0 +1,35 @@
+# -*- coding: utf-8 -*-
+"""Tests for `chi_pet` package."""
+
+import argparse
+from pathlib import Path
+import pytest
+import sys
+
+from unittest import mock
+from chi_pet.chi_parse import parse_chi_options
+
+# @pytest.mark.parametrize("command,arg_dict", [
+#     ('create', 'value1'),
+#     ('run', 'value2'),
+#     # Add more tuples for more test cases
+# ])
+
+
+def test_chi_create_argument_parsing():
+    # Setup
+    sys.argv = ['chi', 'create', 'param1.yaml',
+                'param2.yaml', '-a', 'args.yaml']
+    # Test
+    opts = parse_chi_options()
+    # Assert
+    assert opts.command == 'create'
+    for pf in sys.argv[2:4]:
+        assert Path(pf) in opts.param_files
+
+
+def test_chi_run_argument_parsing():
+    # Setup
+    sys.argv = ['chi', 'run', '-a',  'args.yaml']
+    opts = parse_chi_options()
+    assert opts.args_file == Path('args.yaml')