Fix circular definition

benchmark/Arguments.py

@@ -11,137 +11,3 @@ ALL_METRICS = (
 )
 
 
-class EnvData:
-    @staticmethod
-    def load():
-        args = {}
-        with open(Files.dot_env) as f:
-            for line in f.read().splitlines():
-                if line == "" or line.startswith("#"):
-                    continue
-                key, value = line.split("=")
-                args[key] = value
-        return args
-
-
-class EnvDefault(argparse.Action):
-    # Thanks to https://stackoverflow.com/users/445507/russell-heilling
-    def __init__(self, envvar, required=True, default=None, **kwargs):
-        self._args = EnvData.load()
-        default = self._args[envvar]
-        required = False
-        super(EnvDefault, self).__init__(
-            default=default, required=required, **kwargs
-        )
-
-    def __call__(self, parser, namespace, values, option_string=None):
-        setattr(namespace, self.dest, values)
-
-
-class Arguments:
-    def __init__(self):
-        self.ap = argparse.ArgumentParser()
-        models_data = Models.define_models(random_state=0)
-        models = "{" + ", ".join(models_data) + "}"
-        self.parameters = {
-            "best": [
-                ("-b", "--best"),
-                {
-                    "type": str,
-                    "required": False,
-                    "help": "best results of models",
-                },
-            ],
-            "color": [],
-            "compare": [
-                ("-c", "--compare"),
-                {
-                    "type": bool,
-                    "required": False,
-                    "help": "Compare accuracy with best results",
-                },
-            ],
-            "dataset": [],
-            "excel": [
-                ("-x", "--excel"),
-                {
-                    "type": bool,
-                    "required": False,
-                    "default": False,
-                    "help": "Generate Excel File",
-                },
-            ],
-            "file": [
-                ("-f", "--file"),
-                {"type": str, "required": False, "help": "Result file"},
-            ],
-            "grid": [
-                ("-g", "--grid"),
-                {
-                    "type": str,
-                    "required": False,
-                    "help": "grid results of model",
-                },
-            ],
-            "grid_paramfile": [],
-            "hidden": [],
-            "hyperparameters": [],
-            "key": [],
-            "lose": [],
-            "model": [
-                ("-m", "--model"),
-                {
-                    "type": str,
-                    "required": True,
-                    "choices": list(models_data),
-                    "help": f"model name: {models}",
-                },
-            ],
-            "model1": [],
-            "model2": [],
-            "nan": [],
-            "number": [],
-            "n_folds": [],
-            "paramfile": [],
-            "platform": [],
-            "quiet": [],
-            "report": [],
-            "score": [
-                ("-s", "--score"),
-                {
-                    "action": EnvDefault,
-                    "envvar": "score",
-                    "type": str,
-                    "required": True,
-                    "choices": ALL_METRICS,
-                },
-            ],
-            "sql": [
-                ("-q", "--sql"),
-                {"type": bool, "required": False, "help": "Generate SQL File"},
-            ],
-            "stratified": [],
-            "tex_output": [
-                ("-t", "--tex-output"),
-                {
-                    "type": bool,
-                    "required": False,
-                    "default": False,
-                    "help": "Generate Tex file with the table",
-                },
-            ],
-            "title": [],
-            "win": [],
-        }
-
-    def xset(self, *arg_name, **kwargs):
-        print("parameters", arg_name[0])
-        names, default = self.parameters[arg_name[0]]
-        self.ap.add_argument(
-            *names,
-            **{**default, **kwargs},
-        )
-        return self
-
-    def parse(self):
-        return self.ap.parse_args()

benchmark/Experiments.py

@@ -14,8 +14,7 @@ from sklearn.model_selection import (
     cross_validate,
 )
 from .Utils import Folders, Files
-from .Arguments import EnvData
-from .Models import Models
+from .Models import Models, EnvData
 
 
 class Randomized:

benchmark/Models.py

@@ -1,3 +1,4 @@
+import argparse
 from statistics import mean
 from sklearn.tree import DecisionTreeClassifier, ExtraTreeClassifier
 from sklearn.ensemble import (
@@ -11,6 +12,15 @@ from stree import Stree
 from wodt import Wodt
 from odte import Odte
 from xgboost import XGBClassifier
+from .Utils import Files
+
+ALL_METRICS = (
+    "accuracy",
+    "f1-macro",
+    "f1-micro",
+    "f1-weighted",
+    "roc-auc-ovr",
+)
 
 
 class Models:
@@ -89,3 +99,139 @@ class Models:
             nodes, leaves = result.nodes_leaves()
             depth = result.depth_ if hasattr(result, "depth_") else 0
         return nodes, leaves, depth
+
+
+class EnvData:
+    @staticmethod
+    def load():
+        args = {}
+        with open(Files.dot_env) as f:
+            for line in f.read().splitlines():
+                if line == "" or line.startswith("#"):
+                    continue
+                key, value = line.split("=")
+                args[key] = value
+        return args
+
+
+class EnvDefault(argparse.Action):
+    # Thanks to https://stackoverflow.com/users/445507/russell-heilling
+    def __init__(self, envvar, required=True, default=None, **kwargs):
+        self._args = EnvData.load()
+        default = self._args[envvar]
+        required = False
+        super(EnvDefault, self).__init__(
+            default=default, required=required, **kwargs
+        )
+
+    def __call__(self, parser, namespace, values, option_string=None):
+        setattr(namespace, self.dest, values)
+
+
+class Arguments:
+    def __init__(self):
+        self.ap = argparse.ArgumentParser()
+        models_data = Models.define_models(random_state=0)
+        self.parameters = {
+            "best": [
+                ("-b", "--best"),
+                {
+                    "type": str,
+                    "required": False,
+                    "help": "best results of models",
+                },
+            ],
+            "color": [],
+            "compare": [
+                ("-c", "--compare"),
+                {
+                    "type": bool,
+                    "required": False,
+                    "help": "Compare accuracy with best results",
+                },
+            ],
+            "dataset": [],
+            "excel": [
+                ("-x", "--excel"),
+                {
+                    "type": bool,
+                    "required": False,
+                    "default": False,
+                    "help": "Generate Excel File",
+                },
+            ],
+            "file": [
+                ("-f", "--file"),
+                {"type": str, "required": False, "help": "Result file"},
+            ],
+            "grid": [
+                ("-g", "--grid"),
+                {
+                    "type": str,
+                    "required": False,
+                    "help": "grid results of model",
+                },
+            ],
+            "grid_paramfile": [],
+            "hidden": [],
+            "hyperparameters": [],
+            "key": [],
+            "lose": [],
+            "model": [
+                ("-m", "--model"),
+                {
+                    "type": str,
+                    "required": True,
+                    "choices": list(models_data),
+                    "action": EnvDefault,
+                    "envvar": "model",
+                    "help": f"model name",
+                },
+            ],
+            "model1": [],
+            "model2": [],
+            "nan": [],
+            "number": [],
+            "n_folds": [],
+            "paramfile": [],
+            "platform": [],
+            "quiet": [],
+            "report": [],
+            "score": [
+                ("-s", "--score"),
+                {
+                    "action": EnvDefault,
+                    "envvar": "score",
+                    "type": str,
+                    "required": True,
+                    "choices": ALL_METRICS,
+                },
+            ],
+            "sql": [
+                ("-q", "--sql"),
+                {"type": bool, "required": False, "help": "Generate SQL File"},
+            ],
+            "stratified": [],
+            "tex_output": [
+                ("-t", "--tex-output"),
+                {
+                    "type": bool,
+                    "required": False,
+                    "default": False,
+                    "help": "Generate Tex file with the table",
+                },
+            ],
+            "title": [],
+            "win": [],
+        }
+
+    def xset(self, *arg_name, **kwargs):
+        names, default = self.parameters[arg_name[0]]
+        self.ap.add_argument(
+            *names,
+            **{**default, **kwargs},
+        )
+        return self
+
+    def parse(self):
+        return self.ap.parse_args()

benchmark/Utils.py

@@ -2,13 +2,6 @@ import os
 import subprocess
 
 BEST_ACCURACY_STREE = 40.282203
-ALL_METRICS = (
-    "accuracy",
-    "f1-macro",
-    "f1-micro",
-    "f1-weighted",
-    "roc-auc-ovr",
-)
 
 
 class Folders:

benchmark/__init__.py

@@ -1,6 +1,6 @@
 from .Experiments import Experiment, Datasets, DatasetsSurcov, DatasetsTanveer
 from .Results import Report, Summary
-from .Arguments import EnvDefault
+from .Models import EnvDefault
 
 __author__ = "Ricardo Montañana Gómez"
 __copyright__ = "Copyright 2020-2022, Ricardo Montañana Gómez"

benchmark/scripts/be_benchmark

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 from benchmark.Results import Benchmark
 from benchmark.Utils import Files
-from benchmark.Arguments import Arguments
+from benchmark.Models import Arguments
 
 
 arguments = Arguments()

benchmark/scripts/be_report

@@ -6,7 +6,7 @@ from benchmark.Utils import (
     Files,
     TextColor,
 )
-from benchmark.Arguments import Arguments
+from benchmark.Models import Arguments
 
 
 """Build report on screen of a result file, optionally generate excel and sql
@@ -44,7 +44,9 @@ def default_report():
 if __name__ == "__main__":
     arguments = Arguments()
     arguments.xset("file").xset("excel").xset("sql").xset("compare")
-    arguments.xset("best").xset("grid").xset("model").xset("score")
+    arguments.xset("best").xset("grid").xset("model", required=False).xset(
+        "score"
+    )
     args = arguments.parse()
 
     if args.grid: