chore!: change --data-type into --chemical-space, args in functions as well

Author: breakthewall

rr_cache/Args.py

@@ -9,7 +9,7 @@
 CONFIG_PATH = os_path.join(HERE, 'config')
 # Default values for the arguments
 DEFAULTS = {
-    'data_type': 'mnx3.1',
+    'cspace': 'mnx3.1',
     'interactive': False,
     'do_not_dwnl_cache': False,
 }
@@ -43,16 +43,17 @@ def add_arguments(parser: ArgumentParser) -> ArgumentParser:
     parser = add_logger_args(parser)
 
     parser.add_argument(
-        '--data-type',
-        default=DEFAULTS['data_type'],
+        '--chemical-space',
+        dest='cspace',
+        default=DEFAULTS['cspace'],
         type=str,
-        help='Type of data to use (e.g. mnx3.1, mnx4.0...). Determines which configuration files and folders to use both the cache and the input cache (default: %(default)s).'
+        help='chemical space to use (e.g. mnx3.1, mnx4.0...). Determines which configuration files and folders to use both the cache and the input cache (default: %(default)s).'
     )
     parser.add_argument(
-        '--list-data-types',
+        '--list-chemical-spaces',
         default=None,
         action='store_true',
-        help='list available data types and exits'
+        help='list available chemical spaces and exits'
     )
     parser.add_argument(
         '--build',

rr_cache/__main__.py

@@ -76,28 +76,28 @@ def entry_point():
 
     logger = init(parser, args)
 
-    if args.list_data_types:
+    if args.list_chemical_spaces:
         # list config_*.json files in CONFIG_PATH
         import os
         files = os.listdir(CONFIG_PATH)
-        data_types = []
+        cspaces = []
         for file in files:
             if file.startswith('config_') and file.endswith('.json'):
-                data_types.append(file[len('config_'):-len('.json')])
+                cspaces.append(file[len('config_'):-len('.json')])
         print(
-            '{color}{typo}Available data types:{rst}{color}{rst}\n'.format(
+            '{color}{typo}Available chemical spaces:{rst}{color}{rst}\n'.format(
                 color=fg('white'),
                 typo=attr('bold'),
                 rst=attr('reset')
             )
         )
-        for dt in data_types:
+        for dt in cspaces:
             print(f'- {dt}')
         print()
         exit(0)
 
     cache = rrCache(
-        data_type=args.data_type,
+        cspace=args.cspace,
         interactive=args.interactive,
         do_not_dwnl_cache=args.do_not_dwnl_cache,
         load=False,

rr_cache/rr_cache.py

@@ -87,15 +87,15 @@ class rrCache:
     ## Cache constructor
     def __init__(
         self,
-        data_type: str = DEFAULTS['data_type'],
+        cspace: str = DEFAULTS['cspace'],
         interactive: bool = DEFAULTS['interactive'],
         do_not_dwnl_cache: bool = DEFAULTS['do_not_dwnl_cache'],
         load: bool = True,
         logger: Logger = getLogger(__name__)
     ) -> 'rrCache':
         """Constructor for the class
         Args:
-            data_type (str): Version of MetaNetX to use.
+            cspace (str): Chemical space to use (e.g. mnx3.1, mnx4.4...).
             interactive (bool): Whether to ask the user for confirmation before overwriting existing files.
             do_not_dwnl_cache (bool): Whether to download the cache files from the internet.
             load (bool): Whether to load the cache files into memory.
@@ -104,24 +104,24 @@ def __init__(
 
         self.logger = logger
         self.logger.debug('New instance of rrCache')
-        self.logger.debug('data_type: '+str(data_type))
+        self.logger.debug('cspace: '+str(cspace))
         self.logger.debug('interactive: '+str(interactive))
         self.logger.debug('do_not_dwnl_cache: '+str(do_not_dwnl_cache))
         self.logger.debug('load: '+str(load))
 
-        self.__data_type = data_type
+        self.__cspace = cspace
 
         # Cache config
         cache_cfg_file = os_path.join(
-            CONFIG_PATH, f'config_{self.__data_type}.json'
+            CONFIG_PATH, f'config_{self.__cspace}.json'
         )
         try:
             with open(cache_cfg_file, 'r') as f:
                 cache_cfg = json_load(f)
                 rrCache.__cache_sources = cache_cfg['sources']
                 rrCache.__cache = cache_cfg['cache']
         except FileNotFoundError:
-            logger.error(f'Cache config file {cache_cfg_file} not found, please check the data_type argument')
+            logger.error(f'Cache config file {cache_cfg_file} not found, please check the --chemical-space argument')
             logger.error('Exiting...')
             exit(1)
 
@@ -137,9 +137,9 @@ def __init__(
             except FileNotFoundError:
                 rrCache.__convertMNXM = {}
 
-        self.logger.info(f'Using {self.__data_type}')
-        self.__input__cache_dir = os_path.join(HERE, 'input-cache', self.__data_type)
-        self.__cache_dir = os_path.join(HERE, 'cache', self.__data_type)
+        self.logger.info(f'Using {self.__cspace}')
+        self.__input__cache_dir = os_path.join(HERE, 'input-cache', self.__cspace)
+        self.__cache_dir = os_path.join(HERE, 'cache', self.__cspace)
         if load:
             self.Load(attrs=rrCache.__attributes_list, interactive=interactive, do_not_dwnl_cache=do_not_dwnl_cache)
 
@@ -343,7 +343,6 @@ def Build(
     ) -> None:
         """Generate the cache files and store them to disk.
         Args:
-            data_type (str): Version of MetaNetX to use.
             interactive (bool): Whether to ask the user for confirmation before overwriting existing files.
             logger (Logger): Logger instance for logging messages.
         """

tests/test_rrCache.py

@@ -25,9 +25,9 @@
 
 class Test_rrCache(TestCase):
 
-    data_type = 'mnx3.1'
-    outdir = f'cache-{data_type}'
-    cache = rrCache(data_type=data_type, interactive=False)
+    cspace = 'mnx3.1'
+    outdir = f'cache-{cspace}'
+    cache = rrCache(cspace=cspace, interactive=False)
 
     # Not possible to compare hashes since
     # files contain dict that have to be sorted
@@ -44,7 +44,7 @@ def setUp(self, logger: Logger = None):
             with open(os_path.join(DATA_PATH, f'{elem}.json'), 'r') as f:
                 setattr(self, f'{elem}', json_load(f))
         for elem in ['compounds', 'metrics']:
-            with open(os_path.join(DATA_PATH, f'{elem}_{self.data_type}.json'), 'r') as f:
+            with open(os_path.join(DATA_PATH, f'{elem}_{self.cspace}.json'), 'r') as f:
                 setattr(self, f'{elem}', json_load(f))
 
     def test_all_attr(self):
@@ -53,7 +53,7 @@ def test_all_attr(self):
         Method: Load a full rrCache in 'file' store mode. Then, for each
         attribute, compare its length with it is supposed to be.
         """
-        cache = rrCache(data_type=self.data_type, interactive=False, logger=self.logger)
+        cache = rrCache(cspace=self.cspace, interactive=False, logger=self.logger)
         for attr in self.metrics:
             length = self.metrics[attr]['length']
             with self.subTest(attr=attr, length=length):
@@ -68,7 +68,7 @@ def test_single_attr_file(self):
         for attr in self.metrics:
             length = self.metrics[attr]['length']
             with self.subTest(attr=attr, length=length):
-                cache = rrCache(data_type=self.data_type, interactive=False, logger=self.logger)
+                cache = rrCache(cspace=self.cspace, interactive=False, logger=self.logger)
                 self.assertEqual(len(cache.get(attr)), length)
 
     def test_generate_cache(self):