ucam-department-of-psychiatry · martinburchell · Feb 26, 2024 · Feb 22, 2024 · Feb 22, 2024 · Feb 22, 2024
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -2,19 +2,22 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.2.0
+    rev: v4.5.0
     hooks:
     -   id: check-added-large-files
     -   id: check-json
-    -   id: check-yaml
+    -   id: check-shebang-scripts-are-executable
     -   id: check-xml
+    -   id: check-yaml
 -   repo: https://github.com/psf/black
+    # Use same version as in setup.py
     rev: 22.8.0
     hooks:
     -   id: black
         args:
           - --line-length=79
 -   repo: https://github.com/PyCQA/flake8
+    # Use same version as in setup.py
     rev: 5.0.4
     hooks:
     -   id: flake8
diff --git a/bug_reports/check_pycharm_generator_hint.py b/bug_reports/check_pycharm_generator_hint.py
diff --git a/crate_anon/__init__.py b/crate_anon/__init__.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/__init__.py
 

diff --git a/crate_anon/ancillary/timely_project/dd_criteria.py b/crate_anon/ancillary/timely_project/dd_criteria.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/ancillary/timely_project/dd_criteria.py
 

diff --git a/crate_anon/ancillary/timely_project/timely_filter.py b/crate_anon/ancillary/timely_project/timely_filter.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/ancillary/timely_project/timely_filter.py
 

diff --git a/crate_anon/ancillary/timely_project/timely_filter_cpft_rio.py b/crate_anon/ancillary/timely_project/timely_filter_cpft_rio.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/ancillary/timely_project/timely_filter_cpft_rio.py
 

diff --git a/crate_anon/ancillary/timely_project/timely_filter_systmone.py b/crate_anon/ancillary/timely_project/timely_filter_systmone.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/ancillary/timely_project/timely_filter_systmone.py
 

diff --git a/crate_anon/anonymise/__init__.py b/crate_anon/anonymise/__init__.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/anonymise/__init__.py
 

diff --git a/crate_anon/anonymise/altermethod.py b/crate_anon/anonymise/altermethod.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/anonymise/altermethod.py
 

diff --git a/crate_anon/anonymise/anonregex.py b/crate_anon/anonymise/anonregex.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/anonymise/anonregex.py
 

diff --git a/crate_anon/anonymise/anonymise.py b/crate_anon/anonymise/anonymise.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/anonymise/anonymise.py
 

diff --git a/crate_anon/anonymise/anonymise_cli.py b/crate_anon/anonymise/anonymise_cli.py
diff --git a/crate_anon/anonymise/check_text_extractor.py b/crate_anon/anonymise/check_text_extractor.py
@@ -69,3 +69,7 @@ def main() -> None:
             ext = None
         available = is_text_extractor_available(ext)
         print(f"Text extractor for extension {ext} present: {available}")
+
+
+if __name__ == "__main__":
+    main()
diff --git a/crate_anon/anonymise/config.py b/crate_anon/anonymise/config.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/anonymise/config.py
 

diff --git a/crate_anon/anonymise/config_singleton.py b/crate_anon/anonymise/config_singleton.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/anonymise/config_singleton.py
 

diff --git a/crate_anon/anonymise/constants.py b/crate_anon/anonymise/constants.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/anonymise/constants.py
 

diff --git a/crate_anon/anonymise/dbholder.py b/crate_anon/anonymise/dbholder.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/anonymise/dbholder.py
 

diff --git a/crate_anon/anonymise/dd.py b/crate_anon/anonymise/dd.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/anonymise/dd.py
 

diff --git a/crate_anon/anonymise/ddr.py b/crate_anon/anonymise/ddr.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/anonymise/ddr.py
 

diff --git a/crate_anon/anonymise/demo_config.py b/crate_anon/anonymise/demo_config.py
@@ -127,3 +127,7 @@ def main() -> None:
         else:
             contents = get_demo_config()
         print(contents, file=f)
+
+
+if __name__ == "__main__":
+    main()
diff --git a/crate_anon/anonymise/draft_dd.py b/crate_anon/anonymise/draft_dd.py
@@ -302,3 +302,7 @@ def main() -> None:
         systmone_alter_loaded_rows=args.systmone_alter_loaded_rows,
         systmone_table_info_in_comments=args.systmone_table_info_in_comments,
     )
+
+
+if __name__ == "__main__":
+    main()
diff --git a/crate_anon/anonymise/eponyms.py b/crate_anon/anonymise/eponyms.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/anonymise/eponyms.py
 

diff --git a/crate_anon/anonymise/fetch_wordlists.py b/crate_anon/anonymise/fetch_wordlists.py
diff --git a/crate_anon/anonymise/launch_multiprocess_anonymiser.py b/crate_anon/anonymise/launch_multiprocess_anonymiser.py
diff --git a/crate_anon/anonymise/models.py b/crate_anon/anonymise/models.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/anonymise/models.py
 

diff --git a/crate_anon/anonymise/patient.py b/crate_anon/anonymise/patient.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/anonymise/patient.py
 

diff --git a/crate_anon/anonymise/researcher_report.py b/crate_anon/anonymise/researcher_report.py
@@ -820,3 +820,7 @@ def main() -> None:
     )
 
     mk_researcher_report_pdf(reportcfg)
+
+
+if __name__ == "__main__":
+    main()
diff --git a/crate_anon/anonymise/scrub.py b/crate_anon/anonymise/scrub.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/anonymise/scrub.py
 

diff --git a/crate_anon/anonymise/show_counts.py b/crate_anon/anonymise/show_counts.py
@@ -133,3 +133,7 @@ def main() -> None:
     from crate_anon.anonymise.config_singleton import config  # delayed import
 
     show_record_counts(config)
+
+
+if __name__ == "__main__":
+    main()
diff --git a/crate_anon/anonymise/subset_db.py b/crate_anon/anonymise/subset_db.py
@@ -613,3 +613,7 @@ def main() -> None:
     )
     subsetter = Subsetter(subsetcfg)
     subsetter.subset_db()
+
+
+if __name__ == "__main__":
+    main()
diff --git a/crate_anon/anonymise/summarize_dd.py b/crate_anon/anonymise/summarize_dd.py
@@ -119,3 +119,7 @@ def main() -> None:
     from crate_anon.anonymise.config_singleton import config  # delayed import
 
     summarize_dd(config, args.output)
+
+
+if __name__ == "__main__":
+    main()
diff --git a/crate_anon/anonymise/test_anonymisation.py b/crate_anon/anonymise/test_anonymisation.py
diff --git a/crate_anon/anonymise/test_extract_text.py b/crate_anon/anonymise/test_extract_text.py
diff --git a/crate_anon/anonymise/tests/anonregex_tests.py b/crate_anon/anonymise/tests/anonregex_tests.py
diff --git a/crate_anon/anonymise/tests/scrub_tests.py b/crate_anon/anonymise/tests/scrub_tests.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/anonymise/tests/scrub_tests.py
 

diff --git a/crate_anon/common/__init__.py b/crate_anon/common/__init__.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/common/__init__.py
 

diff --git a/crate_anon/common/argparse_assist.py b/crate_anon/common/argparse_assist.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/common/argparse_assist.py
 

diff --git a/crate_anon/common/bugfix_flashtext.py b/crate_anon/common/bugfix_flashtext.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/common/bugfix_flashtext.py
 

diff --git a/crate_anon/common/constants.py b/crate_anon/common/constants.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/common/constants.py
 

diff --git a/crate_anon/common/dockerfunc.py b/crate_anon/common/dockerfunc.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/common/dockerfunc.py
 

diff --git a/crate_anon/common/exceptions.py b/crate_anon/common/exceptions.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/common/exceptions.py
 

diff --git a/crate_anon/common/extendedconfigparser.py b/crate_anon/common/extendedconfigparser.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/common/extendedconfigparser.py
 

diff --git a/crate_anon/common/file_io.py b/crate_anon/common/file_io.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/common/file_io.py
 

diff --git a/crate_anon/common/formatting.py b/crate_anon/common/formatting.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/common/formatting.py
 

diff --git a/crate_anon/common/inputfunc.py b/crate_anon/common/inputfunc.py
@@ -1,7 +1,5 @@
-#!/usr/bin/env python
-
 """
-crate_anon/nlp_manager/run_crate_nlp_demo.py
+crate_anon/common/inputfunc.py
 
 ===============================================================================
 

diff --git a/crate_anon/common/logfunc.py b/crate_anon/common/logfunc.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 r"""
 crate_anon/common/logfunc.py
 

diff --git a/crate_anon/common/memsize.py b/crate_anon/common/memsize.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/common/memsize.py
 

diff --git a/crate_anon/common/parallel.py b/crate_anon/common/parallel.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/common/parallel.py
 

diff --git a/crate_anon/common/profiling.py b/crate_anon/common/profiling.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/common/profiling.py
 

diff --git a/crate_anon/common/regex_helpers.py b/crate_anon/common/regex_helpers.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/common/regex_helpers.py
 

diff --git a/crate_anon/common/spreadsheet.py b/crate_anon/common/spreadsheet.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/common/spreadsheet.py
 

diff --git a/crate_anon/common/sql.py b/crate_anon/common/sql.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/common/sql.py
 

diff --git a/crate_anon/common/stringfunc.py b/crate_anon/common/stringfunc.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/common/stringfunc.py
 

diff --git a/crate_anon/common/tests/regex_helper_tests.py b/crate_anon/common/tests/regex_helper_tests.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/common/tests/regex_helper_tests.py
 

diff --git a/crate_anon/common/tests/spreadsheet_tests.py b/crate_anon/common/tests/spreadsheet_tests.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/common/tests/spreadsheet_tests.py
 

diff --git a/crate_anon/common/tests/sql_tests.py b/crate_anon/common/tests/sql_tests.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/common/tests/sql_tests.py
 

diff --git a/crate_anon/common/tests/stringfunc_tests.py b/crate_anon/common/tests/stringfunc_tests.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/common/tests/stringfunc_tests.py
 

diff --git a/crate_anon/conftest.py b/crate_anon/conftest.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/conftest.py
 

diff --git a/crate_anon/crateweb/__init__.py b/crate_anon/crateweb/__init__.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/crateweb/__init__.py
 

diff --git a/crate_anon/crateweb/anonymise_api/__init__.py b/crate_anon/crateweb/anonymise_api/__init__.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/crateweb/anonymise_api/__init__.py
 

diff --git a/crate_anon/crateweb/config/__init__.py b/crate_anon/crateweb/config/__init__.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/crateweb/config/__init__.py
 

diff --git a/crate_anon/crateweb/config/apps.py b/crate_anon/crateweb/config/apps.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/crateweb/config/apps.py
 

diff --git a/crate_anon/crateweb/config/constants.py b/crate_anon/crateweb/config/constants.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/crateweb/config/constants.py
 

diff --git a/crate_anon/crateweb/config/settings.py b/crate_anon/crateweb/config/settings.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/crateweb/config/settings.py
 

diff --git a/crate_anon/crateweb/config/test_settings.py b/crate_anon/crateweb/config/test_settings.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/crateweb/config/test_settings.py
 

diff --git a/crate_anon/crateweb/config/urls.py b/crate_anon/crateweb/config/urls.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/crateweb/config/urls.py
 

diff --git a/crate_anon/crateweb/config/wsgi.py b/crate_anon/crateweb/config/wsgi.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 crate_anon/crateweb/config/wsgi.py