Remove output_assembled parameter. Update requirements.txt

docs/requirements.txt

@@ -1,9 +1,10 @@
 defusedxml>=0.7.1
-inflect>=5.5.1
+inflect>=6.0.2
 myst-parser>=0.18.1
-openpyxl>=3.0.9
+numpy>=1.21.6
+openpyxl>=3.1.0
 pandas>=1.3.5
-portalocker>=2.4.0
-semantic_version>=2.9.0
+portalocker>=2.7.0
+semantic_version>=2.10.0
 Sphinx>=5.2.2
 sphinx_rtd_theme>=1.0.0

hed/models/base_input.py

@@ -193,65 +193,45 @@ def expand_defs(self, hed_schema, def_dict):
         from df_util import expand_defs
         expand_defs(self._dataframe, hed_schema=hed_schema, def_dict=def_dict, columns=self._mapper.get_tag_columns())
 
-    def to_excel(self, file, output_assembled=False):
+    def to_excel(self, file):
         """ Output to an Excel file.
 
         Parameters:
             file (str or file-like):      Location to save this base input.
-            output_assembled (bool): Plug in categories and values from the sidecar directly.
         Raises:
             ValueError: if empty file object or file cannot be opened.
         """
         if not file:
             raise ValueError("Empty file name or object passed in to BaseInput.save.")
 
         dataframe = self._dataframe
-        old_columns = dataframe.columns
-
-        if output_assembled:
-            dataframe = self.dataframe_a
-            new_columns = dataframe.columns
-        else:
-            new_columns = old_columns
-
         if self._loaded_workbook:
-            column_mapping = {}  # assembled dataframe column number to original worksheet number
-            for new_c, column in enumerate(new_columns):
-                for old_c, old_column in enumerate(old_columns):
-                    if column == old_column:
-                        column_mapping[new_c] = old_c
-
             old_worksheet = self.get_worksheet(self._worksheet_name)
             # Excel spreadsheets are 1 based, then add another 1 for column names if present
             adj_row_for_col_names = 1
             if self._has_column_names:
                 adj_row_for_col_names += 1
             adj_for_one_based_cols = 1
-            for row_number in range(len(dataframe)):
-                for df_column_number, ws_column_number in column_mapping.items():
-                    cell_value = dataframe.iat[row_number, df_column_number]
-
+            for row_number, text_file_row in dataframe.iterrows():
+                for column_number, column_text in enumerate(text_file_row):
+                    cell_value = dataframe.iloc[row_number, column_number]
                     old_worksheet.cell(row_number + adj_row_for_col_names,
-                                       ws_column_number + adj_for_one_based_cols).value = cell_value
+                                       column_number + adj_for_one_based_cols).value = cell_value
+
             self._loaded_workbook.save(file)
         else:
             dataframe.to_excel(file, header=self._has_column_names)
 
-    def to_csv(self, file=None, output_assembled=False):
+    def to_csv(self, file=None):
         """ Write to file or return as a string.
 
         Parameters:
             file (str, file-like, or None): Location to save this file. If None, return as string.
-            output_assembled (bool): Plug in categories and values from the sidecar directly.
         Returns:
             None or str:  None if file is given or the contents as a str if file is None.
 
         """
         dataframe = self._dataframe
-
-        if output_assembled:
-            dataframe = self.dataframe_a
-
         csv_string_if_filename_none = dataframe.to_csv(file, '\t', index=False, header=self._has_column_names)
         return csv_string_if_filename_none
 

requirements.txt

@@ -1,6 +1,7 @@
 defusedxml>=0.7.1
-inflect>=5.5.1
-openpyxl>=3.0.9
+inflect>=6.0.2
+numpy>=1.21.6
+openpyxl>=3.1.0
 pandas>=1.3.5
-portalocker>=2.4.0
-semantic_version>=2.9.0
+portalocker>=2.7.0
+semantic_version>=2.10.0

tests/models/test_spreadsheet_input.py

@@ -32,7 +32,7 @@ def test_all(self):
         hed_input = self.default_test_file_name
         has_column_names = True
         column_prefix_dictionary = {1: 'Label/', 2: 'Description'}
-        tag_columns = [3]
+        tag_columns = [4]
         worksheet_name = 'LKT Events'
 
         file_input = SpreadsheetInput(hed_input, has_column_names=has_column_names, worksheet_name=worksheet_name,
@@ -50,7 +50,7 @@ def test_all2(self):
         hed_input = self.default_test_file_name
         has_column_names = True
         column_prefix_dictionary = {1: 'Label/', "Short label": 'Description'}
-        tag_columns = [3]
+        tag_columns = [4]
         worksheet_name = 'LKT Events'
 
         file_input = SpreadsheetInput(hed_input, has_column_names=has_column_names, worksheet_name=worksheet_name,
@@ -113,7 +113,7 @@ def test_to_excel_should_work(self):
                                        column_prefix_dictionary={1: 'Label/', 2: 'Description/'},
                                        name='ExcelOneSheet.xlsx')
         buffer = io.BytesIO()
-        spreadsheet.to_excel(buffer, output_assembled=True)
+        spreadsheet.to_excel(buffer)
         buffer.seek(0)
         v = buffer.getvalue()
         self.assertGreater(len(v), 0, "It should have a length greater than 0")
@@ -214,49 +214,21 @@ def test_to_excel_workbook(self):
                                       tag_columns=["HED tags"])
         test_output_name = self.base_output_folder + "ExcelMultipleSheets_resave_assembled.xlsx"
         excel_book.convert_to_long(self.hed_schema)
-        excel_book.to_excel(test_output_name, True)
+        excel_book.to_excel(test_output_name)
         reloaded_df = SpreadsheetInput(test_output_name, worksheet_name="LKT 8HED3")
 
         self.assertTrue(excel_book.dataframe.equals(reloaded_df.dataframe))
 
-        excel_book = SpreadsheetInput(self.default_test_file_name, worksheet_name="LKT 8HED3",
-                                      tag_columns=["HED tags"],
-                                      column_prefix_dictionary={
-                                          "Short label": "Label/",
-                                          "Description in text": "Description"
-                                      })
-        test_output_name = self.base_output_folder + "ExcelMultipleSheets_resave_assembled_prefix.xlsx"
-        excel_book.convert_to_long(self.hed_schema)
-        excel_book.to_excel(test_output_name, True)
-        reloaded_df = SpreadsheetInput(test_output_name, worksheet_name="LKT 8HED3",
-                                       tag_columns=["Short label", "Description in text", "HED tags"])
-
-        self.assertTrue(excel_book.dataframe_a.equals(reloaded_df.dataframe_a))
-
     def test_to_excel_workbook_no_col_names(self):
         excel_book = SpreadsheetInput(self.default_test_file_name, worksheet_name="LKT 8HED3",
                                       tag_columns=[4], has_column_names=False)
         test_output_name = self.base_output_folder + "ExcelMultipleSheets_resave_assembled_no_col_names.xlsx"
         excel_book.convert_to_long(self.hed_schema)
-        excel_book.to_excel(test_output_name, True)
+        excel_book.to_excel(test_output_name)
         reloaded_df = SpreadsheetInput(test_output_name, worksheet_name="LKT 8HED3", tag_columns=[4],
                                        has_column_names=False)
         self.assertTrue(excel_book.dataframe.equals(reloaded_df.dataframe))
 
-        excel_book = SpreadsheetInput(self.default_test_file_name, worksheet_name="LKT 8HED3", has_column_names=False,
-                                      tag_columns=[4],
-                                      column_prefix_dictionary={
-                                          1: "Label/",
-                                          3: "Description"
-                                      })
-        test_output_name = self.base_output_folder + "ExcelMultipleSheets_resave_assembled_prefix.xlsx"
-        excel_book.convert_to_long(self.hed_schema)
-        excel_book.to_excel(test_output_name, True)
-        reloaded_df = SpreadsheetInput(test_output_name, worksheet_name="LKT 8HED3", tag_columns=[1, 3, 4],
-                                       has_column_names=False)
-
-        self.assertTrue(excel_book.dataframe_a.equals(reloaded_df.dataframe_a))
-
 
 if __name__ == '__main__':
     unittest.main()