From d750aa703c768fe5b66a4f390c81d55053f6ac71 Mon Sep 17 00:00:00 2001
From: James Graham <j.graham@soton.ac.uk>
Date: Wed, 25 Nov 2020 19:50:41 +0000
Subject: [PATCH] refactor: add --no option for boolean arguments
---
pycgtool/__main__.py | 48 +++++++++++++++++++++++++++-----------------
1 file changed, 30 insertions(+), 18 deletions(-)
diff --git a/pycgtool/__main__.py b/pycgtool/__main__.py
index 0e3e138..7c31421 100755
--- a/pycgtool/__main__.py
+++ b/pycgtool/__main__.py
@@ -107,6 +107,18 @@ def full_run(config):
measure_bonds(cg_frame, mapping, config)
+class BooleanAction(argparse.Action):
+ """Set up a boolean argparse argument with matching `--no` argument.
+
+ Based on https://thisdataguy.com/2017/07/03/no-options-with-argparse-and-python/
+ """
+ def __init__(self, option_strings, dest, nargs=None, **kwargs):
+ super().__init__(option_strings, dest, nargs=0, **kwargs)
+
+ def __call__(self, parser, namespace, values, option_string=None):
+ setattr(namespace, self.dest, not option_string.startswith('--no-'))
+
+
def parse_arguments(arg_list):
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
@@ -129,33 +141,33 @@ def parse_arguments(arg_list):
input_files.add_argument('-i', '--itp', type=str,
help="GROMACS ITP file")
input_files.add_argument('--begin', type=int, default=0,
- help="Frame number to begin")
+ help="Trajectory frame number to begin")
input_files.add_argument('--end', type=int, default=None,
- help="Frame number to end")
+ help="Trajectory frame number to end")
# Output files
output_files = parser.add_argument_group("output files")
output_files.add_argument('--out-dir', default='.', type=str,
help="Directory where output files should be placed")
- output_files.add_argument('--output-xtc', default=False, action='store_true',
- help="Output a pseudo-CG trajectory")
output_files.add_argument("--output-name", default="out",
help="Base name of output files")
+ output_files.add_argument('--output-xtc', '--no-output-xtc', default=False, action=BooleanAction,
+ help="Output a pseudo-CG trajectory?")
output_files.add_argument("--output", default="gro",
help="Coordinate output format")
- output_files.add_argument("--output-forcefield", default=False, action='store_true',
+ output_files.add_argument("--output-forcefield", '--no-output-forcefield', default=False, action=BooleanAction,
help="Output GROMACS forefield directory?")
- output_files.add_argument("--dump-measurements", default=False, action="store_true",
- help="Whether to output bond measurements")
+ output_files.add_argument("--dump-measurements", '--no-dump-measurements', default=False, action=BooleanAction,
+ help="Output sample of bond measurements?")
output_files.add_argument("--dump-n-values", type=int, default=10000,
- help="How many measurements to output")
+ help="Size of sample of measurements to output")
# Mapping options
mapping_options = parser.add_argument_group("mapping options")
- mapping_options.add_argument("--map-only", default=False, action="store_true",
- help="Run in mapping-only mode")
+ mapping_options.add_argument("--map-only", '--no-map-only', default=False, action=BooleanAction,
+ help="Run in mapping-only mode?")
mapping_options.add_argument("--map-center", default="geom",
choices=["geom", "mass", "first"],
help="Mapping method")
@@ -167,15 +179,15 @@ def parse_arguments(arg_list):
bond_options = parser.add_argument_group("bond options")
bond_options.add_argument("--constr_threshold", type=float, default=100000,
- help="Convert stiff bonds to contraints over [value]")
+ help="Convert bonds with force constants over [value] to constraints")
bond_options.add_argument("--temperature", type=float, default=310,
help="Temperature of reference simulation")
- bond_options.add_argument("--default-fc", default=False, action='store_true',
+ bond_options.add_argument("--default-fc", '--no-default-fc', default=False, action=BooleanAction,
help="Use default MARTINI force constants?")
- bond_options.add_argument("--generate-angles", default=True, action='store_false',
- help="Generate angles from bonds")
- bond_options.add_argument("--generate-dihedrals", default=False, action="store_true",
- help="Generate dihedrals from bonds")
+ bond_options.add_argument("--generate-angles", '--no-generate-angles', default=True, action=BooleanAction,
+ help="Generate angles from bonds?")
+ bond_options.add_argument("--generate-dihedrals", '--no-generate-dihedrals', default=False, action=BooleanAction,
+ help="Generate dihedrals from bonds?")
bond_options.add_argument("--length-form", default="Harmonic",
help="Form of bond potential")
bond_options.add_argument("--angle-form", default="CosHarmonic",
@@ -186,8 +198,8 @@ def parse_arguments(arg_list):
# Run options
run_options = parser.add_argument_group("run options")
- run_options.add_argument('--profile', default=False, action='store_true',
- help="Profile performance")
+ run_options.add_argument('--profile', '--no-profile', default=False, action=BooleanAction,
+ help="Profile performance?")
# yapf: enable
args = parser.parse_args(arg_list)
--
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