feat: make finalise non-interactive by default (#309)

* make interactivity optional in finalise(); add more tests

* update demo to make finalise interactive

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* linting

* more linting

* really annoying how the checks are different in pre-commit and on GitHub

* Update acro/acro.py

Co-authored-by: Richard Preen <rpreen@gmail.com>
Signed-off-by: Jim-smith <jim-smith@users.noreply.github.com>

* addressing reviewer comments

---------

Signed-off-by: Jim-smith <jim-smith@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Richard Preen <rpreen@gmail.com>

Author: 3 people

acro/acro.py

@@ -78,7 +78,9 @@ def __init__(self, config: str = "default", suppress: bool = False) -> None:
         # set globals for survival analysis
         acro_tables.SURVIVAL_THRESHOLD = self.config["survival_safe_threshold"]
 
-    def finalise(self, path: str = "outputs", ext="json") -> Records | None:
+    def finalise(
+        self, path: str = "outputs", ext: str = "json", interactive: bool = False
+    ) -> Records | None:
         """Create a results file for checking.
 
         Parameters
@@ -87,6 +89,8 @@ def finalise(self, path: str = "outputs", ext="json") -> Records | None:
             Name of a folder to save outputs.
         ext : str
             Extension of the results file. Valid extensions: {json, xlsx}.
+        interactive : bool
+            Whether to prompt the user to request exceptions for failing outputs.
 
         Returns
         -------
@@ -101,7 +105,7 @@ def finalise(self, path: str = "outputs", ext="json") -> Records | None:
                 path,
             )
             return None
-        self.results.finalise(path, ext)
+        self.results.finalise(path, ext, interactive)
         config_filename: str = os.path.normpath(f"{path}/config.json")
         try:
             with open(config_filename, "w", newline="", encoding="utf-8") as file:

acro/acro_tables.py

@@ -214,6 +214,7 @@ def crosstab(  # pylint: disable=too-many-arguments,too-many-locals
                     )
 
         # record output
+
         self.results.add(
             status=status,
             output_type="table",
@@ -225,6 +226,11 @@ def crosstab(  # pylint: disable=too-many-arguments,too-many-locals
             output=[table],
             comments=comments,
         )
+        if self.suppress:
+            justadded = f"output_{self.results.output_id - 1}"
+            self.results.add_exception(
+                justadded, "Suppression automatically applied where needed"
+            )
         return table
 
     def pivot_table(  # pylint: disable=too-many-arguments,too-many-locals
@@ -398,6 +404,11 @@ def pivot_table(  # pylint: disable=too-many-arguments,too-many-locals
             output=[table],
             comments=comments,
         )
+        if self.suppress:
+            justadded = f"output_{self.results.output_id - 1}"
+            self.results.add_exception(
+                justadded, "Suppression automatically applied where needed"
+            )
         return table
 
     def surv_func(  # pylint: disable=too-many-arguments,too-many-locals
@@ -1367,7 +1378,7 @@ def create_dataframe(index, columns) -> DataFrame:
             index_df = pd.concat(index, axis=1)
         elif isinstance(index, pd.Series):
             index_df = pd.DataFrame({index.name: index})
-    except ValueError:
+    except (ValueError, TypeError):
         index_df = empty_dataframe
 
     columns_df = empty_dataframe
@@ -1376,12 +1387,12 @@ def create_dataframe(index, columns) -> DataFrame:
             columns_df = pd.concat(columns, axis=1)
         elif isinstance(columns, pd.Series):
             columns_df = pd.DataFrame({columns.name: columns})
-    except ValueError:
+    except (ValueError, TypeError):
         columns_df = empty_dataframe
 
     try:
         data = pd.concat([index_df, columns_df], axis=1)
-    except ValueError:
+    except (ValueError, TypeError):
         data = empty_dataframe
 
     return data

acro/record.py

@@ -430,7 +430,7 @@ def validate_outputs(self) -> None:
                 )
                 record.exception = input("")
 
-    def finalise(self, path: str, ext: str) -> None:
+    def finalise(self, path: str, ext: str, interactive: bool = False) -> None:
         """Create a results file for checking.
 
         Parameters
@@ -439,9 +439,12 @@ def finalise(self, path: str, ext: str) -> None:
             Name of a folder to save outputs.
         ext : str
             Extension of the results file. Valid extensions: {json, xlsx}.
+        interactive : Bool
+            Whether to prompt the user to request exceptions for failing outputs.
         """
         logger.debug("finalise()")
-        self.validate_outputs()
+        if interactive:
+            self.validate_outputs()
         if ext == "json":
             self.finalise_json(path)
         elif ext == "xlsx":