From 2fef21dcb4d08513dc03fcf171e4d1b753c63989 Mon Sep 17 00:00:00 2001
From: Mark Driver <mdd31@alumni.cam.ac.uk>
Date: Fri, 14 Feb 2020 16:44:29 +0000
Subject: [PATCH] update to add CLI.
---
phasecalculator/__main__.py | 26 ++++++
phasecalculator/phasecalculatorcli.py | 109 +++++++++++++++++++++++---
2 files changed, 125 insertions(+), 10 deletions(-)
diff --git a/phasecalculator/__main__.py b/phasecalculator/__main__.py
index e69de29..0558d70 100644
--- a/phasecalculator/__main__.py
+++ b/phasecalculator/__main__.py
@@ -0,0 +1,26 @@
+# -*- coding: utf-8 -*-
+# phasecalculator calculates FGIPs, solvent similarity and VLE with SSIMPLE.
+# Copyright (C) 2019 Mark D. Driver
+#
+# phasecalculator is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+"""
+Main script to be called for module level operation.
+
+@author: Mark
+"""
+
+from phasecalculator.phasecalculatorcli import main
+
+if __name__ == '__main__':
+ main()
\ No newline at end of file
diff --git a/phasecalculator/phasecalculatorcli.py b/phasecalculator/phasecalculatorcli.py
index 0e0ef74..63065f0 100755
--- a/phasecalculator/phasecalculatorcli.py
+++ b/phasecalculator/phasecalculatorcli.py
@@ -22,7 +22,12 @@ Script with CLI for phasecalculator.
import logging
import argparse
-
+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
logging.basicConfig()
LOGGER = logging.getLogger(__name__)
@@ -30,22 +35,106 @@ LOGGER.setLevel(logging.WARN)
def main():
- # Create parser
- parser = create_argparser()
+ # Create parser
+ parser = create_phasecalculator_argparser()
# parse args
args = parser.parse_args()
return process_args(args)
-def process_args():
+def process_args(args):
+ return args.func(args)
+
+def process_inputgen(args):
+ output_filename = args.filename
+ system_collection = create_system_collection(args)
+ sysproc.write_system_collection_file(system_collection, output_filename)
+
+def process_phasecalculator(args):
+ xml_filename = args.file
+ system_collection = read_calculator_xml(xml_filename)
+ if args.memreq is not None:
+ run_system_collection(system_collection, memory_req=args.memreq)
+ else:
+ run_system_collection(system_collection)
+
+def create_system_collection(args):
+ phases = read_phasecsv(args.phases)
+ jar_path = args.jar
+ scratch_dir = args.scratch
+ output_dir = args.out_dir
+ run_inf = create_runtime_inf(jar_path, scratch_dir, output_dir)
+ fgip_output = args.fgip
+ similarity_output = args.sim
+ similarity_output_type = args.sim_type if similarity_output else None
+ vle_output = args.vle
+ out_inf = create_output_inf(fgip_output, similarity_output, similarity_output_type, vle_output)
+ system = System(phases, run_inf, out_inf)
+ return SystemCollection([system])
+
+def create_output_inf(fgip_output, similarity_output, similarity_output_type, vle_output):
+ return OutputInformation(fgip_output, similarity_output, similarity_output_type, vle_output)
+
+def create_runtime_inf(jar_path, scratch_dir, output_dir):
+ return RuntimeInformation(jar_path, scratch_dir, output_dir)
-def create_calculator_xml():
+def read_calculator_xml(xml_filename):
+ return sysproc.read_system_collection_file(xml_filename)
+
+def read_phasecsv(csv_filename):
+ return csvconv.convert_csv_file_to_phases(csv_filename)
+
+def run_system_collection(system_collection, **kwargs):
+ for system_info in system_collection.system_list:
+ phasecrun.run_all_analysis(system_info, **kwargs)
+
+def create_phasecalculator_argparser():
+ description = """Phase Calculator provides methods to perform FGIP,
+similarity and VLE analysis for solvents."""
+ epilog = """Example usage"""
+ phase_argparser= argparse.ArgumentParser(description=description,
+ epilog=epilog,
+ conflict_handler='resolve',
+ formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+ subparsers = phase_argparser.add_subparsers(title="commands", dest="command")
-def read_calculator_xml():
-def run_system_collection():
+ calc_description = """Calculation runner based on input System XML."""
+ calc_epilog = """"""
-def create_phasecalculator_argparser():
+ 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="")
+ calc_argparser.add_argument("--memreq", type=str, default=None,
+ help="")
+ calc_argparser.set_defaults(func=process_phasecalculator)
+
+ inpgen_description = """Input SystemCollection XML generation."""
+ inpgen_epilog = """"""
-def create_calculate_argparser():
+ inpgen_argparser = subparsers.add_parser("inpgen", description=inpgen_description,
+ epilog=inpgen_epilog,
+ help="create system input xml.",
+ formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+ inpgen_argparser.add_argument("-p", "--phases", type=str,
+ help="")
+ inpgen_argparser.add_argument("-j", "--jar", type=str, required=True,
+ help="Phasetransfer jar path.")
+ inpgen_argparser.add_argument("-x", "--scratch", type=str, default="scratch",
+ help="scratch directory path.")
+ inpgen_argparser.add_argument("-o", "--out_dir", type=str, default="output",
+ help="output directory for calculation results")
-def create_inputgen_argparser():
\ No newline at end of file
+ inpgen_argparser.add_argument("-f", "--fgip", action='store_true',
+ help="Calculate FGIPs for input solvents")
+ inpgen_argparser.add_argument("-s","--sim", action='store_true',
+ help="Calculate similarity for input solvents")
+ inpgen_argparser.add_argument("--sim_type", type=str, default="all",
+ help="similarity output type.")
+ inpgen_argparser.add_argument("-v","--vle", action='store_true',
+ help="Calculate VLE for input solvents")
+ inpgen_argparser.add_argument("--filename", type=str, default="systemcollection.xml")
+ inpgen_argparser.set_defaults(func=process_inputgen)
+ return phase_argparser
--
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