From c03f9c509c90e7b142f907c7c536c35046ad0bd8 Mon Sep 17 00:00:00 2001
From: Mark Driver <mdd31@alumni.cam.ac.uk>
Date: Thu, 26 Mar 2020 22:48:16 +0000
Subject: [PATCH] update to CLI adding extra subparser and updating help
information.
---
phasecalculator/phasecalculatorcli.py | 54 +++++++++++++++++++++++++--
1 file changed, 50 insertions(+), 4 deletions(-)
diff --git a/phasecalculator/phasecalculatorcli.py b/phasecalculator/phasecalculatorcli.py
index 183dd17..d9d479a 100755
--- a/phasecalculator/phasecalculatorcli.py
+++ b/phasecalculator/phasecalculatorcli.py
@@ -22,17 +22,21 @@ Script with CLI for phasecalculator.
import logging
import argparse
+import textwrap
import phasecalculator.runners.phasecalculatorrunner as phasecrun
import phasecalculator.io.systemcollectionprocessor as sysproc
import phasecalculator.io.phasecsvconverter as csvconv
from phasecalculator.classes.runtimeinformation import RuntimeInformation
from phasecalculator.classes.outputinformation import OutputInformation
from phasecalculator.classes.system import System, SystemCollection
+import puresolventinformation.information as pureinf
logging.basicConfig()
LOGGER = logging.getLogger(__name__)
LOGGER.setLevel(logging.WARN)
+INFO_LOGGER = logging.getLogger(__name__)
+INFO_LOGGER.setLevel(logging.INFO)
def main():
"""Main function run when program called.
@@ -236,6 +240,27 @@ def run_system_collection(system_collection, **kwargs):
for system_info in system_collection.system_list:
phasecrun.run_all_analysis(system_info, **kwargs)
+def get_acceptable_solvent_names():
+ """Get Acceptable solvent names.
+
+ Returns
+ -------
+ Str
+ Solvent names, formatted 1 per line.
+
+ """
+ solvent_names = pureinf.get_name_inchikey_mapping().keys()
+ return "\n".join(solvent_names)
+
+def solvent_names(args):
+ """Output solvent names by using a logger.
+
+ Returns
+ -------
+ None.
+
+ """
+ INFO_LOGGER.info("Solvent names:\n%s", get_acceptable_solvent_names())
def create_phasecalculator_argparser():
"""Create Argument parser for Phasecalculator module.
@@ -247,7 +272,7 @@ def create_phasecalculator_argparser():
"""
description = """Phase Calculator provides methods to perform FGIP,
similarity and VLE analysis for solvents."""
- epilog = """Example usage"""
+ epilog = """For example usage see submodule help"""
phase_argparser = argparse.ArgumentParser(
description=description,
epilog=epilog,
@@ -257,7 +282,11 @@ similarity and VLE analysis for solvents."""
subparsers = phase_argparser.add_subparsers(title="commands", dest="command")
calc_description = """Calculation runner based on input System XML."""
- calc_epilog = """"""
+ calc_epilog = textwrap.dedent("""Example Usage:
+
+python -m phasecalculator calculate -f systemcollection.xml
+
+Where systemcollection.xml was generated with inpgen. For large phase sets you need to set memreq to match your current hardware limit.""")
calc_argparser = subparsers.add_parser(
"calculate",
@@ -283,7 +312,13 @@ similarity and VLE analysis for solvents."""
calc_argparser.set_defaults(func=process_phasecalculator)
inpgen_description = """Input SystemCollection XML generation."""
- inpgen_epilog = """"""
+ inpgen_epilog = textwrap.dedent("""\
+ Example usage:
+
+ python -m phasecalculator inpgen -p $CONDA_PREFIX/lib/python3.7/site-packages/phasecalculator/test/resources/examplephasecomp.csv -f -j PATH_TO_JAR
+
+ Where PATH_TO_JAR is replaced with the SSIP phasetransfer jar file location.
+""")
inpgen_argparser = subparsers.add_parser(
"inpgen",
@@ -323,7 +358,18 @@ similarity and VLE analysis for solvents."""
"-v", "--vle", action="store_true", help="Calculate VLE for input solvents"
)
inpgen_argparser.add_argument(
- "--filename", type=str, default="systemcollection.xml"
+ "--filename", type=str, default="systemcollection.xml",
+ help="filename for XML file.",
)
inpgen_argparser.set_defaults(func=process_inputgen)
+ solvname_description = """Display acceptable solvent molecule names for inclusion in a phases csv file."""
+ solvnames_epilog = "Solvent molecule names:\n" + get_acceptable_solvent_names() + "\n"
+ solvent_nameparser = subparsers.add_parser(
+ "solventnames",
+ description=solvname_description,
+ epilog=solvnames_epilog,
+ help="Get list of aceptable pure solvent names.",
+ formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+ )
+ solvent_nameparser.set_defaults(func=solvent_names)
return phase_argparser
--
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