fix(rpfba): remove medium feature

.gitignore

@@ -11,4 +11,5 @@ node_modules
 _exclude
 /docsource/_build/
 /docsource/_autosummary
-cicd-toolkit
+cicd-toolkit
+*.egg-info

MANIFEST.in

@@ -3,4 +3,3 @@ graft rptools/rpthermo/data
 graft rptools/rpscore/models
 graft rptools/rpviz/data
 graft rptools/rpviz/templates
-graft rptools/rpfba/medium

rptools/rpfba/Args.py

@@ -3,95 +3,55 @@
     List,
 )
 from rptools._version import __version__
-from rptools.rpfba.medium import (
-    __MEDIUM_DEFAULT_ID,
-    __MEDIUM_PATH,
-    read_medium_ids
-)
 
-def add_arguments(
-    parser: ArgumentParser):
-    parser.add_argument(
-        'pathway_file',
-        type=str,
-        help='SBML file that contains an heterologous pathway'
-    )
-    parser.add_argument(
-        'model_file',
-        type=str,
-        help='GEM model file (SBML)'
-    )
+
+def add_arguments(parser: ArgumentParser):
     parser.add_argument(
-        'compartment_id',
-        type=str,
-        help='model compartment id to consider (e.g. \'c\' or \'MNXC3\')'
+        "pathway_file", type=str, help="SBML file that contains an heterologous pathway"
     )
+    parser.add_argument("model_file", type=str, help="GEM model file (SBML)")
     parser.add_argument(
-        'outfile',
+        "compartment_id",
         type=str,
-        help='output file'
+        help="model compartment id to consider (e.g. 'c' or 'MNXC3')",
     )
+    parser.add_argument("outfile", type=str, help="output file")
     parser.add_argument(
-        '--objective_rxn_id',
+        "--objective_rxn_id",
         type=str,
-        default='rxn_target',
-        help='reaction ID to optimise (default: rxn_target)'
+        default="rxn_target",
+        help="reaction ID to optimise (default: rxn_target)",
     )
     parser.add_argument(
-        '--biomass_rxn_id',
+        "--biomass_rxn_id",
         type=str,
-        default='biomass',
-        help='biomass reaction ID (default: biomass). Note: Only for \'fraction\' simulation'
+        default="biomass",
+        help="biomass reaction ID (default: biomass). Note: Only for 'fraction' simulation",
     )
     parser.add_argument(
-        '--sim',
+        "--sim",
         type=str,
-        choices=['fba', 'pfba', 'fraction'],
-        default='fraction',
-        help='type of simulation to use (default: fraction)'
+        choices=["fba", "pfba", "fraction"],
+        default="fraction",
+        help="type of simulation to use (default: fraction)",
     )
     parser.add_argument(
-        '--fraction_of',
+        "--fraction_of",
         type=float,
         default=0.75,
-        help='fraction of the optimum (default: 0.75). Note: this value is ignored is \'fba\' is used'
+        help="fraction of the optimum (default: 0.75). Note: this value is ignored is 'fba' is used",
     )
     parser.add_argument(
-        '--merge',
-        action='store_true',
+        "--merge",
+        action="store_true",
         default=False,
-        help='output the full merged model in addition of heterologous pathway only (default: False)'
+        help="output the full merged model in addition of heterologous pathway only (default: False)",
     )
     parser.add_argument(
-        '--ignore_orphan_species',
-        action='store_true',
+        "--ignore_orphan_species",
+        action="store_true",
         default=True,
-        help='ignore metabolites that are only consumed or produced (default: True)'
+        help="ignore metabolites that are only consumed or produced (default: True)",
     )
 
-    parser_medium = parser.add_argument_group('Medium', 'Medium modifications')
-    parser_medium.add_argument('--medium_compartment_id',
-        type=str,
-        default='MNXC2',
-        help='Model compartiment id corresponding to the extra-cellular compartment'
-    )
-    parser_medium.add_argument(
-        '--medium_file',
-        type=str,
-        help='Provide a csv file with an header as <coumpond_id>,<upper_bound>. \
-                This file provides information about metabolites (Metanetx Id) to add or remove (giving upper bound value)'
-    )
-    parser_medium.add_argument(
-        '--medium_id',
-        type=str,
-        default=__MEDIUM_DEFAULT_ID,
-        choices=[__MEDIUM_DEFAULT_ID] + read_medium_ids(__MEDIUM_PATH),
-        help='Use a base medium composition. Data can be add with the option --medium_file'
-    )
-    parser_medium.add_argument(
-        '--minimal_medium_file',
-        type=str,
-        help='Provide a path of a CSV file to output information about minimal medium'
-    )
-
     return parser

rptools/rpfba/__main__.py

@@ -1,66 +1,40 @@
 import pandas as pd
 
-from os import (
-  path as os_path,
-  makedirs as os_makedirs
-)
-from errno import (
-  EEXIST as errno_EEXIST
-)
-from logging import (
-  Logger,
-  getLogger
-)
-from typing import(
-  List,
-  Dict,
-  Tuple
-)
+from os import path as os_path, makedirs as os_makedirs
+from errno import EEXIST as errno_EEXIST
+from logging import Logger, getLogger
+from typing import List, Dict, Tuple
 from copy import deepcopy
 from rptools import build_args_parser
 from rptools.rpfba.Args import add_arguments
-from rptools.rpfba.medium import (
-    __MEDIUM_PATH,
-    load_compounds,
-)
-from rptools.rpfba import (
-    runFBA
-)
+from rptools.rpfba import runFBA
 from rptools.rplibs.rpPathway import rpPathway
 
 
 def entry_point():
     def _make_dir(filename):
         dirname = os_path.dirname(filename)
-        if dirname != '' and not os_path.exists(dirname):
+        if dirname != "" and not os_path.exists(dirname):
             try:
                 os_makedirs(dirname)
-            except OSError as exc: # Guard against race condition
+            except OSError as exc:  # Guard against race condition
                 if exc.errno != errno_EEXIST:
                     raise
+
     # Args.
     parser = build_args_parser(
-        prog = 'rpfba',
-        description='Process to Flux Balance Analysis',
-        m_add_args=add_arguments
+        prog="rpfba",
+        description="Process to Flux Balance Analysis",
+        m_add_args=add_arguments,
     )
     args = parser.parse_args()
 
+    # Init.
     from rptools.__main__ import init
-    logger = init(parser, args)
 
-    pathway = rpPathway.from_rpSBML(
-        infile=args.pathway_file,
-        logger=logger
-    )
+    logger = init(parser, args)
 
-    # Load compounds.
-    df_medium_base, df_medium_user = load_compounds(
-        medium_id=args.medium_id,
-        file_base=__MEDIUM_PATH,
-        file_user=args.medium_file,
-        logger=logger
-    )
+    pathway = rpPathway.from_rpSBML(infile=args.pathway_file, logger=logger)
 
     results = runFBA(
         pathway=pathway,
@@ -72,28 +46,17 @@ def _make_dir(filename):
         fraction_coeff=args.fraction_of,
         merge=args.merge,
         ignore_orphan_species=args.ignore_orphan_species,
-        medium_compartment_id=args.medium_compartment_id,
-        df_medium_base=df_medium_base,
-        df_medium_user=df_medium_user,
-        logger=logger
+        logger=logger,
     )
 
     if results is None:
-        logger.info('No results written. Exiting...')
+        logger.info("No results written. Exiting...")
     else:
-        logger.info('Writing into file...')
+        logger.info("Writing into file...")
         _make_dir(args.outfile)
         pathway.to_rpSBML().write_to_file(args.outfile)
-        logger.info('   |--> written in ' + args.outfile)
+        logger.info("   |--> written in " + args.outfile)
 
-        if args.minimal_medium_file:
-            minimal_medium = results.get(
-                'minimal_medium',
-                pd.DataFrame()
-            )
-            _make_dir(args.minimal_medium_file)
-            minimal_medium.to_csv(args.minimal_medium_file)
-            logger.info('   |--> written in ' + args.minimal_medium_file)
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     entry_point()