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adding a separeated cli module for the comand line
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,109 @@ | ||
| #!/usr/bin/env python3 | ||
| # -*- coding: utf-8 -*- | ||
| """For information of MolDrug: | ||
| Docs: https://moldrug.readthedocs.io/en/latest/ | ||
| Source Code: https://github.com/ale94mleon/moldrug | ||
| """ | ||
| from moldrug import utils, __version__ | ||
| import yaml, argparse, inspect, importlib | ||
| def moldrug_cmd(): | ||
| parser = argparse.ArgumentParser(description=__doc__, | ||
| formatter_class=argparse.RawTextHelpFormatter) | ||
| parser.add_argument( | ||
| help='The configuration yaml file', | ||
| dest='yaml_file', | ||
| type=str) | ||
| parser.add_argument( | ||
| '-v', '--version', | ||
| action='version', | ||
| version=f"moldrug: {__version__}") | ||
| parser.add_argument('-f', '--fitness', | ||
| help="The path to the user-custom fitness module; inside of which the given custom cost function must be implemented. "\ | ||
| "See the docs for how to do it properly. E.g. my/awesome/fitness_module.py."\ | ||
| "By default will look in the moldrug.fitness module.", | ||
| dest='fitness', | ||
| default=None, | ||
| type=str) | ||
| args = parser.parse_args() | ||
|
|
||
| with open(args.yaml_file, 'r') as c: | ||
| Config = yaml.safe_load(c) | ||
|
|
||
| # Checking how many jobs are defined: Main and follows jobs | ||
| MainConfig = Config.pop(list(Config.keys())[0]) | ||
| FollowConfig = Config | ||
|
|
||
| if args.fitness: | ||
| spec=importlib.util.spec_from_file_location('fitness', args.fitness) | ||
| fitness = importlib.util.module_from_spec(spec) | ||
| spec.loader.exec_module(fitness) | ||
| Cost = dict(inspect.getmembers(fitness))[MainConfig['costfunc']] | ||
| else: | ||
| from moldrug import fitness | ||
| Cost = dict(inspect.getmembers(fitness))[MainConfig['costfunc']] | ||
|
|
||
| if MainConfig['type'].lower() == 'ga': | ||
| TypeOfRun = utils.GA | ||
| elif MainConfig['type'].lower() == 'local': | ||
| TypeOfRun = utils.Local | ||
| else: | ||
| raise RuntimeError(f"\"{MainConfig['type']}\" it is not a possible type. Select from: GA or Local") | ||
| InitArgs = MainConfig.copy() | ||
|
|
||
| # Modifying InitArgs | ||
| [InitArgs.pop(key, None) for key in ['type', 'njobs']] | ||
| InitArgs['costfunc'] = Cost | ||
|
|
||
| # Checking for follow jobs and sanity check on the arguments | ||
| if FollowConfig: | ||
| # Defining the possible mutable arguments with its default values | ||
| mutable_args = { | ||
| 'njobs': MainConfig['njobs'], | ||
| 'crem_db_path': InitArgs['crem_db_path'], | ||
| 'maxiter': InitArgs['maxiter'], | ||
| 'popsize': InitArgs['popsize'], | ||
| 'beta': InitArgs['beta'], | ||
| 'pc': InitArgs['pc'], | ||
| 'get_similar': InitArgs['get_similar'], | ||
| # This one it will update with the default values of crem rather thant the previous one. | ||
| 'mutate_crem_kwargs': InitArgs['mutate_crem_kwargs'], | ||
| 'save_pop_every_gen': InitArgs['save_pop_every_gen'], | ||
| 'deffnm': InitArgs['deffnm'], | ||
| } | ||
| # Sanity check | ||
| for job in FollowConfig: | ||
| for arg in FollowConfig[job]: | ||
| if arg not in mutable_args: | ||
| raise ValueError(f"The job: {job} has a non-valid argument \"{arg}\". For now only the following are accepted: {list(mutable_args.keys())}") | ||
|
|
||
| # Initialize the class | ||
| ResultsClass = TypeOfRun(**InitArgs) | ||
| # Call the class | ||
| print(f'The main job is being executed.') | ||
| ResultsClass(MainConfig['njobs']) | ||
| # Save final data | ||
| ResultsClass.pickle(f"{InitArgs['deffnm']}_result", compress=True) | ||
| # Saving final sdf file always | ||
| utils.make_sdf(ResultsClass.pop, sdf_name = f"{InitArgs['deffnm']}_pop") | ||
| print(f'The main job finished!.') | ||
| # In case that follows jobs were defined | ||
| if FollowConfig: | ||
| for job in FollowConfig: | ||
| print(f"The follow job {job} started.") | ||
|
|
||
| # Updating arguments | ||
| mutable_args.update(FollowConfig[job]) | ||
| InitArgs = mutable_args.copy() | ||
| njobs = InitArgs.pop('njobs') | ||
|
|
||
| # Changing the attributes values | ||
| for arg in InitArgs: | ||
| setattr(ResultsClass, arg, InitArgs[arg]) | ||
|
|
||
| # Call the class again | ||
| ResultsClass(njobs) | ||
| # Save final data | ||
| ResultsClass.pickle(f"{InitArgs['deffnm']}_result", compress=True) | ||
| # Saving final sdf file always | ||
| utils.make_sdf(ResultsClass.pop, sdf_name = f"{InitArgs['deffnm']}_pop") | ||
| print(f'The job {job} finished!.') |
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