[TST] Add test for command line commands.

setup.cfg

@@ -8,7 +8,8 @@ ignore = F401, # Imported but unused
         B028, # No explicit stacklevel keyword argument found
         W293, # blank line contains whitespace (I don't like this rule, interferes with good function indentation)
         C419, # Unnecessary list comprehension passed to all() prevents short-circuiting - rewrite as a generator 
-
+        E702, # Multiple statements on one line (semicolon)
+
 per-file-ignores = 
         # It poses no inconvenient to violate B006 in this file.
         tests/test_ageml/test_modelling.py: B006 

src/ageml/__main__.py

@@ -1,9 +1,10 @@
 import ageml
 
+
 def main():
     """Run age modelling interactive command line interface."""
 
-    ageml.ui.InteractiveCLI()
+    ageml.ui.CLI()
 
 
 if __name__ == '__main__':

src/ageml/commands.py

@@ -1,19 +1,33 @@
+"""Command line commands.
+
+Used in the AgeML project with poetry to create command line commands.
+
+Public classes:
+---------------
+ModelAge: Run age modelling with required parameters.
+FactorAnalysis: Run factor analysis with required parameters.
+ClinicalGroups: Run clinical analysis with age deltas with required parameters.
+ClinicalClassification: Run classification of groups based on age deltas with required parameters.
+
+
+Public functions:
+-----------------
+model_age(): Run ModelAge class.
+factor_analysis(): Run FactorAnalysis class.
+clinical_groups(): Run ClinicalGroups class.
+clinical_classify(): Run ClinicalClassification class.
+"""
+
 import argparse
 
 import ageml.messages as messages
 
 from ageml.ui import Interface
 from ageml.utils import convert
 
-class ModelAge(Interface):
-    """Read and parses user commands via command line.
-
-    Public methods:
-    ---------------
-    configure_parser(self): Configure parser with required arguments for processing.
 
-    configure_args(self, args): Configure arguments with required fromatting for modelling.
-    """
+class ModelAge(Interface):
+    """Run age modelling with required parameters."""
 
     def __init__(self):
         """Initialise variables."""
@@ -40,27 +54,27 @@ def configure_parser(self):
 
         # Required arguments
         self.parser.add_argument("-o", "--output", metavar="DIR", required=True,
-            help=messages.output_long_description,)
+                                 help=messages.output_long_description,)
         self.parser.add_argument("-f", "--features", metavar="FILE", required=True,
-            help=messages.features_long_description)
+                                 help=messages.features_long_description)
 
         # Parameter arguments with defaults
-        self.parser.add_argument("-m","--model", nargs="*", default=["linear"],
-            help=messages.model_long_description)
+        self.parser.add_argument("-m", "--model", nargs="*", default=["linear"],
+                                 help=messages.model_long_description)
         self.parser.add_argument("-s", "--scaler", nargs="*", default=["standard"],
-            help=messages.scaler_long_description)
+                                 help=messages.scaler_long_description)
         self.parser.add_argument("--cv", nargs="+", type=int, default=[5, 0],
-            help=messages.cv_long_description)
+                                 help=messages.cv_long_description)
 
         # Optional arguments
         self.parser.add_argument("--covariates", metavar="FILE",
-            help=messages.covar_long_description)
+                                 help=messages.covar_long_description)
         self.parser.add_argument("--covar_name", metavar="COVAR_NAME",
-            help=messages.covar_name_long_description)
+                                 help=messages.covar_name_long_description)
         self.parser.add_argument("--clinical", metavar="FILE",
-            help=messages.clinical_long_description)
+                                 help=messages.clinical_long_description)
         self.parser.add_argument("--systems", metavar="FILE",
-            help=messages.systems_long_description)
+                                 help=messages.systems_long_description)
 
     def configure_args(self, args):
         """Configure argumens with required fromatting for modelling.
@@ -117,13 +131,9 @@ def configure_args(self, args):
 
         return args
 
-class FactorAnalsyis(Interface):
-    """Read and parses user commands via command line.
 
-    Public methods:
-    ---------------
-    configure_parser(self): Configure parser with required arguments for processing.
-    """
+class FactorAnalsyis(Interface):
+    """Run factor analysis with required parameters."""
 
     def __init__(self):
         """Initialise variables."""
@@ -149,25 +159,21 @@ def configure_parser(self):
 
         # Required arguments
         self.parser.add_argument("-o", "--output", metavar="DIR", required=True,
-            help=messages.output_long_description,)
+                                 help=messages.output_long_description,)
         self.parser.add_argument("-a", "--ages", metavar="FILE", required=True,
-            help=messages.ages_long_description)
+                                 help=messages.ages_long_description)
         self.parser.add_argument("-f", "--factors", metavar="FILE", required=True,
-            help=messages.factors_long_description)
+                                 help=messages.factors_long_description)
 
         # Optional arguments
         self.parser.add_argument("--covariates", metavar="FILE",
-            help=messages.covar_long_description)
+                                 help=messages.covar_long_description)
         self.parser.add_argument("--clinical", metavar="FILE",
-            help=messages.clinical_long_description)
+                                 help=messages.clinical_long_description)
 
-class ClinicalGroups(Interface):
-    """Read and parses user commands via command line.
 
-    Public methods:
-    ---------------
-    configure_parser(self): Configure parser with required arguments for processing.
-    """
+class ClinicalGroups(Interface):
+    """Run clinical analysis with age deltas with required parameters."""
 
     def __init__(self):
         """Initialise variables."""
@@ -193,19 +199,15 @@ def configure_parser(self):
 
         # Required arguments
         self.parser.add_argument("-o", "--output", metavar="DIR", required=True,
-            help=messages.output_long_description,)
+                                 help=messages.output_long_description,)
         self.parser.add_argument("-a", "--ages", metavar="FILE", required=True,
-            help=messages.ages_long_description)
+                                 help=messages.ages_long_description)
         self.parser.add_argument("--clinical", metavar="FILE", required=True,
-            help=messages.clinical_long_description)
+                                 help=messages.clinical_long_description)
 
-class ClinicalClassification(Interface):
-    """Read and parses user commands via command line.
 
-    Public methods:
-    ---------------
-    configure_parser(self): Configure parser with required arguments for processing.
-    """
+class ClinicalClassification(Interface):
+    """Run classification of groups based on age deltas with required parameters."""
 
     def __init__(self):
         """Initialise variables."""
@@ -234,30 +236,36 @@ def configure_parser(self):
 
         # Required arguments
         self.parser.add_argument("-o", "--output", metavar="DIR", required=True,
-            help=messages.output_long_description,)
+                                 help=messages.output_long_description,)
         self.parser.add_argument("-a", "--ages", metavar="FILE", required=True,
-            help=messages.ages_long_description)
+                                 help=messages.ages_long_description)
         self.parser.add_argument("--clinical", metavar="FILE", required=True,
-            help=messages.clinical_long_description)
+                                 help=messages.clinical_long_description)
         self.parser.add_argument("--groups", nargs=2, metavar="GROUP", required=True,
-            help=messages.groups_long_description)
+                                 help=messages.groups_long_description)
+
+
+# Object wrappers
 
 def model_age():
-    """Run model_age class."""
+    """Run ModelAge class."""
 
     ModelAge()
 
+
 def factor_analysis():
-    """Run factor_analysis class."""
+    """Run FactorAnalysis class."""
 
     FactorAnalsyis()
 
+
 def clinical_groups():
-    """Run clinical_groups class."""
+    """Run ClinicalGroups class."""
 
     ClinicalGroups()
 
+
 def clinical_classify():
-    """Run clinical_classify class."""
+    """Run ClinicalClassification class."""
 
     ClinicalClassification()

src/ageml/ui.py

@@ -71,13 +71,13 @@ class Interface:
 
     run_wrapper(self, run): Wrapper for running modelling with log.
 
-    run_age(self): Run basic age modelling.
+    run_age(self): Run age modelling.
 
-    run_factor_analysis(self): Run age modelling with lifestyle factors.
+    run_factor_analysis(self): Factor analysis between deltas and factors.
 
-    run_clinical(self): Run age modelling with clinical factors.
+    run_clinical(self): Analyse differences between deltas in clinical groups.
 
-    run_classification(self): Run classification between two different clinical groups.
+    run_classification(self): Classify groups based on deltas.
     """
 
     def __init__(self, args):
@@ -553,7 +553,7 @@ def run_wrapper(self, run):
         run()
 
     def run_age(self):
-        """Run basic age modelling."""
+        """Run age modelling."""
 
         # Run age modelling
         print("Running age modelling...")
@@ -637,7 +637,7 @@ def run_age(self):
         self.df_ages.to_csv(os.path.join(self.dir_path, filename))
 
     def run_factor_analysis(self):
-        """Run age modelling with lifestyle factors."""
+        """Run factor analysis between deltas and factors."""
 
         print("Running lifestyle factors...")
 
@@ -667,7 +667,7 @@ def run_factor_analysis(self):
         self.factors_vs_deltas(dfs_ages, dfs_factors, groups, self.df_factors.columns.to_list())
 
     def run_clinical(self):
-        """Run age modelling with clinical factors."""
+        """Analyse differences between deltas in clinical groups."""
 
         print("Running clinical outcomes...")
 
@@ -727,7 +727,8 @@ def run_classification(self):
         self.set_classifier()
         self.classify(df_group1, df_group2, groups)
 
-class InteractiveCLI(Interface):
+
+class CLI(Interface):
 
     """Read and parses user commands via command line via an interactive interface