From 31e2da1978326517d0c6007a0518f2f3f0d9e810 Mon Sep 17 00:00:00 2001
From: Mark Driver <mdd31@alumni.cam.ac.uk>
Date: Wed, 19 Feb 2020 12:19:41 +0000
Subject: [PATCH] doc update.
---
phasecalculator/phasecalculatorcli.py | 150 +++++++++++++++++++++++++-
1 file changed, 145 insertions(+), 5 deletions(-)
diff --git a/phasecalculator/phasecalculatorcli.py b/phasecalculator/phasecalculatorcli.py
index 63065f0..71e549f 100755
--- a/phasecalculator/phasecalculatorcli.py
+++ b/phasecalculator/phasecalculatorcli.py
@@ -35,6 +35,14 @@ LOGGER.setLevel(logging.WARN)
def main():
+ """Main function run when program called.
+
+ Returns
+ -------
+ None
+ Process result.
+
+ """
# Create parser
parser = create_phasecalculator_argparser()
# parse args
@@ -42,14 +50,51 @@ def main():
return process_args(args)
def process_args(args):
+ """Process CLI Arguments.
+
+ Parameters
+ ----------
+ args : argparse.Namespace
+ Arguments from reading command line.
+
+ Returns
+ -------
+ None
+ Process result.
+
+ """
return args.func(args)
def process_inputgen(args):
+ """Process arguments to run input file creation for phase calculation.
+
+ Parameters
+ ----------
+ args : argparse.Namespace
+ Arguments from reading command line.
+
+ Returns
+ -------
+ None.
+
+ """
output_filename = args.filename
system_collection = create_system_collection(args)
sysproc.write_system_collection_file(system_collection, output_filename)
def process_phasecalculator(args):
+ """Process arguments to run phase calculation.
+
+ Parameters
+ ----------
+ args : argparse.Namespace
+ Arguments from reading command line.
+
+ Returns
+ -------
+ None.
+
+ """
xml_filename = args.file
system_collection = read_calculator_xml(xml_filename)
if args.memreq is not None:
@@ -58,6 +103,19 @@ def process_phasecalculator(args):
run_system_collection(system_collection)
def create_system_collection(args):
+ """Create SystemCollection from input arguments
+
+ Parameters
+ ----------
+ args : argparse.Namespace
+ Arguments from argparse read of command line input.
+
+ Returns
+ -------
+ SystemCollection
+ SystemCollection.
+
+ """
phases = read_phasecsv(args.phases)
jar_path = args.jar
scratch_dir = args.scratch
@@ -72,22 +130,105 @@ def create_system_collection(args):
return SystemCollection([system])
def create_output_inf(fgip_output, similarity_output, similarity_output_type, vle_output):
+ """Create OutputInformation
+
+ Parameters
+ ----------
+ fgip_output : bool
+ FGIP output result.
+ similarity_output : bool
+ Similarity output result.
+ similarity_output_type : str
+ Output type, see schema for restriction.
+ vle_output : bool
+ VLE output result.
+
+ Returns
+ -------
+ OutputInformation
+ Output information for calculation.
+
+ """
return OutputInformation(fgip_output, similarity_output, similarity_output_type, vle_output)
def create_runtime_inf(jar_path, scratch_dir, output_dir):
+ """Create RuntimeInformation
+
+ Parameters
+ ----------
+ jar_path : str
+ Jar file location.
+ scratch_dir : str
+ Scratch directory path.
+ output_dir : str
+ Output directory path.
+
+ Returns
+ -------
+ RuntimeInformation
+ Runtime information for calculation.
+
+ """
return RuntimeInformation(jar_path, scratch_dir, output_dir)
def read_calculator_xml(xml_filename):
+ """Read SystemCollection XML.
+
+ Parameters
+ ----------
+ xml_filename : str
+ filename for SystemCollection XML.
+
+ Returns
+ -------
+ SystemCollection
+ System collection for calculations to run.
+
+ """
return sysproc.read_system_collection_file(xml_filename)
def read_phasecsv(csv_filename):
+ """Read CSV file containing phase infomration and create Phases object.
+
+ Parameters
+ ----------
+ csv_filename : str
+ phase information CSV file.
+
+ Returns
+ -------
+ Phases
+ Phases representation of information.
+
+ """
return csvconv.convert_csv_file_to_phases(csv_filename)
def run_system_collection(system_collection, **kwargs):
+ """Run all systems in collection.
+
+ Parameters
+ ----------
+ system_collection : SystemCollection
+ system collection.
+ memory_req : str, optional
+ Memory settings for jar executable. The default is None.
+
+ Returns
+ -------
+ None.
+
+ """
for system_info in system_collection.system_list:
phasecrun.run_all_analysis(system_info, **kwargs)
def create_phasecalculator_argparser():
+ """Create Argument parser for Phasecalculator module.
+
+ Returns
+ -------
+ ArgumentParser
+
+ """
description = """Phase Calculator provides methods to perform FGIP,
similarity and VLE analysis for solvents."""
epilog = """Example usage"""
@@ -96,19 +237,18 @@ similarity and VLE analysis for solvents."""
conflict_handler='resolve',
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
subparsers = phase_argparser.add_subparsers(title="commands", dest="command")
-
-
+
calc_description = """Calculation runner based on input System XML."""
calc_epilog = """"""
-
+
calc_argparser = subparsers.add_parser("calculate", description=calc_description,
epilog=calc_epilog,
help="calculate phase properties.",
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
calc_argparser.add_argument("-i", "-f","--file", type=str, required=True,
- help="")
+ help="filename for SystemCollectionXML")
calc_argparser.add_argument("--memreq", type=str, default=None,
- help="")
+ help="memory specifier for jar call. Defaults to system default.")
calc_argparser.set_defaults(func=process_phasecalculator)
inpgen_description = """Input SystemCollection XML generation."""
--
GitLab