Improve error messages and formatting

asreviewcontrib/makita/entrypoint.py

@@ -16,7 +16,7 @@ def get_template_fp(name):
 
 
 def is_valid_template(fp):
-    if Path(fp).is_file():
+    if fp and Path(fp).is_file():
         return True
     else:
         raise ValueError(f"Template {fp} not found")
@@ -53,9 +53,11 @@ def execute(self, argv):  # noqa: C901
                 self._template(args_name, args_program)
             except Exception as err:
                 print(f"\u001b[31mERROR: {err}\u001b[0m")
-
         elif args_program.tool == "add-script":
-            self._add_script(args_name, args_program)
+            try:
+                self._add_script(args_name, args_program)
+            except Exception as err:
+                print(f"\u001b[31mERROR: {err}\u001b[0m")
         else:
             parser = _parse_arguments_program(self.version, add_help=True)
             parser.parse_args(argv)
@@ -98,7 +100,9 @@ def _template(self, args_name, args_program):
         args = parser.parse_args(args_name)
 
         # check if a custom template is used, otherwise use the default template
-        fp_template = args.template or get_template_fp(args_template.name)
+        fp_template = args.template or (
+            args_template.name and get_template_fp(args_template.name)
+        )
         is_valid_template(fp_template)
 
         # load datasets

asreviewcontrib/makita/template_arfi.py

@@ -53,17 +53,15 @@ def render_jobs_arfi(
             }
         )
 
-    # Instantiate a ConfigTemplate object, initializing a Jinja2 environment and 
+    # Instantiate a ConfigTemplate object, initializing a Jinja2 environment and
     # setting up template variables and extensions.
     template = ConfigTemplate(fp_template)
 
     # render scripts
     if template.scripts is not None:
         for s in template.scripts:
             t_script = file_handler.render_file_from_template(
-                s, 
-                "script", 
-                output_folder=output_folder
+                s, "script", output_folder=output_folder
             )
             export_fp = Path(scripts_folder, s)
             file_handler.add_file(t_script, export_fp)
@@ -75,9 +73,7 @@ def render_jobs_arfi(
                 s,
                 "doc",
                 datasets=datasets,
-                template_name=template.name
-                if template.name == "ARFI"
-                else "custom",
+                template_name=template.name if template.name == "ARFI" else "custom",
                 template_name_long=template.name_long,
                 template_scripts=template.scripts,
                 output_folder=output_folder,
@@ -101,7 +97,6 @@ def render_jobs_arfi(
     )
 
 
-
 def _get_priors(dataset, init_seed, n_priors):
     """Sample priors."""
     asdata = ASReviewData.from_file(dataset)
@@ -127,4 +122,3 @@ def _get_priors(dataset, init_seed, n_priors):
         priors.append(list(map(str, priors_list)))
 
     return priors
-

asreviewcontrib/makita/template_basic.py

@@ -51,17 +51,15 @@ def render_jobs_basic(
             }
         )
 
-    # Instantiate a ConfigTemplate object, initializing a Jinja2 environment and 
+    # Instantiate a ConfigTemplate object, initializing a Jinja2 environment and
     # setting up template variables and extensions.
     template = ConfigTemplate(fp_template)
 
     # render scripts
     if template.scripts is not None:
         for s in template.scripts:
             t_script = file_handler.render_file_from_template(
-                s, 
-                "script", 
-                output_folder=output_folder
+                s, "script", output_folder=output_folder
             )
             export_fp = Path(scripts_folder, s)
             file_handler.add_file(t_script, export_fp)
@@ -73,9 +71,7 @@ def render_jobs_basic(
                 s,
                 "doc",
                 datasets=datasets,
-                template_name=template.name
-                if template.name == "basic"
-                else "custom",
+                template_name=template.name if template.name == "basic" else "custom",
                 template_name_long=template.name_long,
                 template_scripts=template.scripts,
                 output_folder=output_folder,

asreviewcontrib/makita/template_multiple_models.py

@@ -62,17 +62,15 @@ def render_jobs_multiple_models(
             }
         )
 
-    # Instantiate a ConfigTemplate object, initializing a Jinja2 environment and 
+    # Instantiate a ConfigTemplate object, initializing a Jinja2 environment and
     # setting up template variables and extensions.
     template = ConfigTemplate(fp_template)
 
     # render scripts
     if template.scripts is not None:
         for s in template.scripts:
             t_script = file_handler.render_file_from_template(
-                s, 
-                "script", 
-                output_folder=output_folder
+                s, "script", output_folder=output_folder
             )
             export_fp = Path(scripts_folder, s)
             file_handler.add_file(t_script, export_fp)

asreviewcontrib/makita/utils.py

@@ -8,7 +8,7 @@
 
 class FileHandler:
     """
-    The FileHandler class handles file operations such as adding files and rendering 
+    The FileHandler class handles file operations such as adding files and rendering
     scripts.
     """
 
@@ -22,7 +22,7 @@ def add_file(self, content, export_fp):
 
         Args:
         content (str): The content to be written into the file.
-        export_fp (Path): A Path object that specifies the directory where the file 
+        export_fp (Path): A Path object that specifies the directory where the file
         should be added.
         """
 

examples/arfi_example/scripts/merge_descriptives.py

@@ -35,31 +35,32 @@ def create_table_descriptives(datasets):
 
     for ds in datasets:
         with open(ds) as f:
-            data = json.load(f)['data']['items']
+            data = json.load(f)["data"]["items"]
             values = {}
             for item in data:
-                values[item['id']] = item['value']
+                values[item["id"]] = item["value"]
             stats.append(values)
 
     df = pd.DataFrame(stats, index=[Path(ds).name for ds in datasets])
     return df
 
 
 if __name__ == "__main__":
-
     parser = argparse.ArgumentParser(
         description="Merge descriptives of multiple files into single table."
     )
     parser.add_argument(
         "-s",
         type=str,
         default="output/simulation/*/descriptives/",
-        help="Datasets location")
+        help="Datasets location",
+    )
     parser.add_argument(
         "-o",
         type=str,
         default="output/tables/data_descriptives_all.csv",
-        help="Output table location")
+        help="Output table location",
+    )
     args = parser.parse_args()
 
     # load datasets
@@ -75,4 +76,4 @@ def create_table_descriptives(datasets):
     # store result in output folder
     Path(args.o).parent.mkdir(parents=True, exist_ok=True)
     result.to_csv(Path(args.o))
-    result.to_excel(Path(args.o).with_suffix('.xlsx'))
+    result.to_excel(Path(args.o).with_suffix(".xlsx"))

examples/arfi_example/scripts/merge_metrics.py

@@ -33,38 +33,36 @@ def create_table_state_metrics(metric_files):
 
     for metric in metric_files:
         with open(metric) as f:
-            data = json.load(f)['data']['items']
+            data = json.load(f)["data"]["items"]
             values = {}
-            values['file_name'] = Path(metric).name
+            values["file_name"] = Path(metric).name
             for item in data:
-                if item['id'] == 'td':
+                if item["id"] == "td":
                     continue
                 # check if value is a list
-                if item['value'] is not None and isinstance(item['value'], list):
-                    for value in item['value']:
-                        values[item['id'] + "_" + str(value[0])] = value[1]
+                if item["value"] is not None and isinstance(item["value"], list):
+                    for value in item["value"]:
+                        values[item["id"] + "_" + str(value[0])] = value[1]
                 else:
-                    values[item['id']] = item['value']
+                    values[item["id"]] = item["value"]
             metrics.append(values)
 
     return pd.DataFrame(metrics)
 
 
 if __name__ == "__main__":
-
     parser = argparse.ArgumentParser(
         description="Merge metrics of multiple states into single table."
     )
     parser.add_argument(
-        "-s",
-        type=str,
-        default="output/simulation/*/metrics/",
-        help="states location")
+        "-s", type=str, default="output/simulation/*/metrics/", help="states location"
+    )
     parser.add_argument(
         "-o",
         type=str,
         default="output/tables/metrics_sim_all.csv",
-        help="Output table location")
+        help="Output table location",
+    )
     args = parser.parse_args()
 
     # load metric files
@@ -80,4 +78,4 @@ def create_table_state_metrics(metric_files):
     # store result in output folder
     Path(args.o).parent.mkdir(parents=True, exist_ok=True)
     result.to_csv(Path(args.o))
-    result.to_excel(Path(args.o).with_suffix('.xlsx'))
+    result.to_excel(Path(args.o).with_suffix(".xlsx"))

examples/arfi_example/scripts/merge_tds.py

@@ -35,17 +35,21 @@ def create_table_state_tds(metrics):
 
     for metric in metrics:
         with open(metric) as f:
-            i = next(filter(lambda x: x['id'] == 'td', json.load(f)['data']['items']))['value']  # noqa
+            i = next(filter(lambda x: x["id"] == "td", json.load(f)["data"]["items"]))[
+                "value"
+            ]  # noqa
             values.extend((item[0], item[1], file_counter) for item in i)
             file_counter += 1
 
-    df = pd.DataFrame(values, columns=['record_id', 'td', 'metric_file'])
-    pivoted = df.pivot_table(index='record_id',
-                             columns='metric_file',
-                             values='td',
-                             aggfunc='first',
-                             fill_value=0)
-    pivoted.columns = [f'td_sim_{col}' for col in pivoted.columns]
+    df = pd.DataFrame(values, columns=["record_id", "td", "metric_file"])
+    pivoted = df.pivot_table(
+        index="record_id",
+        columns="metric_file",
+        values="td",
+        aggfunc="first",
+        fill_value=0,
+    )
+    pivoted.columns = [f"td_sim_{col}" for col in pivoted.columns]
     return pivoted
 
 
@@ -54,15 +58,14 @@ def create_table_state_tds(metrics):
         description="Merge tds of multiple metrics into single table."
     )
     parser.add_argument(
-        "-s",
-        type=str,
-        default="output/simulation/*/metrics/",
-        help="metrics location")
+        "-s", type=str, default="output/simulation/*/metrics/", help="metrics location"
+    )
     parser.add_argument(
         "-o",
         type=str,
         default="output/tables/tds_sim_all.csv",
-        help="Output table location")
+        help="Output table location",
+    )
     args = parser.parse_args()
 
     # load metric files
@@ -77,4 +80,4 @@ def create_table_state_tds(metrics):
     # store table
     Path(args.o).parent.mkdir(parents=True, exist_ok=True)
     states_table.to_csv(Path(args.o))
-    states_table.to_excel(Path(args.o).with_suffix('.xlsx'))
+    states_table.to_excel(Path(args.o).with_suffix(".xlsx"))

examples/basic_example/scripts/merge_descriptives.py

@@ -35,31 +35,32 @@ def create_table_descriptives(datasets):
 
     for ds in datasets:
         with open(ds) as f:
-            data = json.load(f)['data']['items']
+            data = json.load(f)["data"]["items"]
             values = {}
             for item in data:
-                values[item['id']] = item['value']
+                values[item["id"]] = item["value"]
             stats.append(values)
 
     df = pd.DataFrame(stats, index=[Path(ds).name for ds in datasets])
     return df
 
 
 if __name__ == "__main__":
-
     parser = argparse.ArgumentParser(
         description="Merge descriptives of multiple files into single table."
     )
     parser.add_argument(
         "-s",
         type=str,
         default="output/simulation/*/descriptives/",
-        help="Datasets location")
+        help="Datasets location",
+    )
     parser.add_argument(
         "-o",
         type=str,
         default="output/tables/data_descriptives_all.csv",
-        help="Output table location")
+        help="Output table location",
+    )
     args = parser.parse_args()
 
     # load datasets
@@ -75,4 +76,4 @@ def create_table_descriptives(datasets):
     # store result in output folder
     Path(args.o).parent.mkdir(parents=True, exist_ok=True)
     result.to_csv(Path(args.o))
-    result.to_excel(Path(args.o).with_suffix('.xlsx'))
+    result.to_excel(Path(args.o).with_suffix(".xlsx"))