v0.20.5

ucam-department-of-psychiatry · Jun 26, 2024 · 1c735ee · 1c735ee
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diff --git a/crate_anon/version.py b/crate_anon/version.py
@@ -34,8 +34,8 @@
 # Constants
 # =============================================================================
 
-CRATE_VERSION = "0.20.4"
-CRATE_VERSION_DATE = "2024-05-21"
+CRATE_VERSION = "0.20.5"
+CRATE_VERSION_DATE = "2024-06-26"
 
 MINIMUM_PYTHON_VERSION = (3, 8)
 # Only other place that has this: install_virtualenv.py (which can't import

diff --git a/docker/dockerfiles/.env b/docker/dockerfiles/.env
@@ -22,7 +22,7 @@ CRATE_DOCKER_GATE_VERSION=9.0.1
 
 # Need to keep in sync with crate_anon/version.py
 # Use e.g. -rc1 suffix in development
-CRATE_DOCKER_IMAGE_TAG=crate:0.20.4
+CRATE_DOCKER_IMAGE_TAG=crate:0.20.5
 
 CRATE_DOCKER_MYSQL_CRATE_DATABASE_NAME=crate_web_db
 CRATE_DOCKER_MYSQL_CRATE_USER_NAME=crate_web_user

diff --git a/docs/source/anonymisation/_crate_anon_check_text_extractor.txt b/docs/source/anonymisation/_crate_anon_check_text_extractor.txt
@@ -1,7 +1,7 @@
 USAGE: crate_anon_check_text_extractor [-h] [checkextractor ...]
 
 Check availability of tools to extract text from different document formats.
-(CRATE version 0.20.4, 2024-05-21. Created by Rudolf Cardinal.)
+(CRATE version 0.20.5, 2024-06-26. Created by Rudolf Cardinal.)
 
 POSITIONAL ARGUMENTS:
   checkextractor  File extensions to check for availability of a text

diff --git a/docs/source/anonymisation/_crate_anon_demo_config_help.txt b/docs/source/anonymisation/_crate_anon_demo_config_help.txt
@@ -1,7 +1,7 @@
 USAGE: crate_anon_demo_config [-h] [--output OUTPUT] [--leave_placeholders]
 
-Print a demo config file for the CRATE anonymiser. (CRATE version 0.20.4,
-2024-05-21. Created by Rudolf Cardinal.)
+Print a demo config file for the CRATE anonymiser. (CRATE version 0.20.5,
+2024-06-26. Created by Rudolf Cardinal.)
 
 OPTIONS:
   -h, --help            show this help message and exit

diff --git a/docs/source/anonymisation/_crate_anon_draft_dd.txt b/docs/source/anonymisation/_crate_anon_draft_dd.txt
@@ -11,7 +11,7 @@ USAGE: crate_anon_draft_dd [-h] [--config CONFIG] [--verbose] [--incremental]
                            [--systmone_no_table_info_in_comments]
 
 Draft a data dictionary for the anonymiser, by scanning a source database.
-(CRATE version 0.20.4, 2024-05-21. Created by Rudolf Cardinal.)
+(CRATE version 0.20.5, 2024-06-26. Created by Rudolf Cardinal.)
 
 OPTIONS:
   -h, --help            show this help message and exit

diff --git a/docs/source/anonymisation/_crate_anon_show_counts_help.txt b/docs/source/anonymisation/_crate_anon_show_counts_help.txt
@@ -1,7 +1,7 @@
 USAGE: crate_anon_show_counts [-h] [--config CONFIG] [--verbose]
 
-Print record counts from source/destination databases. (CRATE version 0.20.4,
-2024-05-21. Created by Rudolf Cardinal.)
+Print record counts from source/destination databases. (CRATE version 0.20.5,
+2024-06-26. Created by Rudolf Cardinal.)
 
 OPTIONS:
   -h, --help       show this help message and exit

diff --git a/docs/source/anonymisation/_crate_anon_summarize_dd_help.txt b/docs/source/anonymisation/_crate_anon_summarize_dd_help.txt
@@ -2,8 +2,8 @@ USAGE: crate_anon_summarize_dd [-h] [--config CONFIG] [--verbose]
                                [--output OUTPUT]
 
 Summarize a data dictionary for the anonymiser. The resulting
-spreadsheet-style report has one row per source table. (CRATE version 0.20.4,
-2024-05-21. Created by Rudolf Cardinal.)
+spreadsheet-style report has one row per source table. (CRATE version 0.20.5,
+2024-06-26. Created by Rudolf Cardinal.)
 
 OPTIONS:
   -h, --help       show this help message and exit

diff --git a/docs/source/anonymisation/_crate_anonymise_help.txt b/docs/source/anonymisation/_crate_anonymise_help.txt
@@ -11,7 +11,7 @@ USAGE: crate_anonymise [-h] [--config CONFIG] [--version] [--verbose]
                        [--reportevery [REPORTEVERY]] [--debugscrubbers]
                        [--savescrubbers] [--echo]
 
-Database anonymiser. (CRATE version 0.20.4, 2024-05-21. Created by Rudolf
+Database anonymiser. (CRATE version 0.20.5, 2024-06-26. Created by Rudolf
 Cardinal.)
 
 OPTIONS:

diff --git a/docs/source/anonymisation/_crate_anonymise_multiprocess_help.txt b/docs/source/anonymisation/_crate_anonymise_multiprocess_help.txt
@@ -1,6 +1,6 @@
 USAGE: crate_anonymise_multiprocess [-h] [--nproc [NPROC]] [--verbose]
 
-Runs the CRATE anonymiser in parallel. Version 0.20.4 (2024-05-21). Note that
+Runs the CRATE anonymiser in parallel. Version 0.20.5 (2024-06-26). Note that
 all arguments not specified here are passed to the underlying script (see
 crate_anonymise --help).
 

diff --git a/docs/source/anonymisation/_crate_researcher_report_help.txt b/docs/source/anonymisation/_crate_researcher_report_help.txt
@@ -16,7 +16,7 @@ USAGE: crate_researcher_report [-h] [--config CONFIG] [--noconfig]
                                output
 
 Produce a researcher-oriented PDF report about a destination database.
-(CRATE version 0.20.4, 2024-05-21. Created by Rudolf Cardinal.)
+(CRATE version 0.20.5, 2024-06-26. Created by Rudolf Cardinal.)
 
 Note: if wkhtmtopdf reports 'Too many open files', see
 - https://stackoverflow.com/q/25355697;

diff --git a/docs/source/anonymisation/_crate_subset_db_help.txt b/docs/source/anonymisation/_crate_subset_db_help.txt
@@ -12,7 +12,7 @@ USAGE: crate_subset_db [-h] --src_db_url SRC_DB_URL --dst_db_url DST_DB_URL
                        [--exclude_table_filenames [EXCLUDE_TABLE_FILENAMES ...]]
                        [--verbose] [--echo]
 
-Create a simple subset of a database, copying one database to another while applying filters. You can filter by a standard column (e.g. one representing patient IDs), taking permitted filter values from the command line, from file(s), and/or from database(s). You can also decide which tables to include/exclude. (CRATE version 0.20.4, 2024-05-21. Created by Rudolf Cardinal.)
+Create a simple subset of a database, copying one database to another while applying filters. You can filter by a standard column (e.g. one representing patient IDs), taking permitted filter values from the command line, from file(s), and/or from database(s). You can also decide which tables to include/exclude. (CRATE version 0.20.5, 2024-06-26. Created by Rudolf Cardinal.)
 
 OPTIONS:
   -h, --help            show this help message and exit

diff --git a/docs/source/anonymisation/_specimen_anonymiser_config.ini b/docs/source/anonymisation/_specimen_anonymiser_config.ini
@@ -1,5 +1,5 @@
 # Configuration file for CRATE anonymiser (crate_anonymise).
-# Version 0.20.4 (2024-05-21).
+# Version 0.20.5 (2024-06-26).
 #
 # SEE HELP FOR DETAILS.
 

diff --git a/docs/source/autodoc_extra/_command_line_index.rst b/docs/source/autodoc_extra/_command_line_index.rst
@@ -123,4 +123,4 @@ Index of CRATE commands
 
 :ref:`crate_windows_service <crate_windows_service>`
 
-(Documentation built with CRATE 0.20.4.)
+(Documentation built with CRATE 0.20.5.)
diff --git a/docs/source/changelog.rst b/docs/source/changelog.rst
@@ -1656,11 +1656,14 @@ Changes
   The version of GATE used in the Docker image is configurable, defaulting to 9.0.1.
   https://github.com/ucam-department-of-psychiatry/crate/issues/149
 
-**0.20.5, in progress**
+**0.20.5, 2024-06-26**
 
 - When the Docker image is built, it is now possible to specify both a user ID and a group ID
   so that file systems shared between the host and the container have the correct permissions.
 
+**0.20.6, in progress**
+
+
 To do
 -----
 

diff --git a/docs/source/nlp/_crate_nlp_help.txt b/docs/source/nlp/_crate_nlp_help.txt
@@ -9,7 +9,7 @@ USAGE: crate_nlp [-h] [--config CONFIG] [--nlpdef NLPDEF] [-i | -f]
                  [--count] [--cloud] [--immediate] [--retrieve]
                  [--cancelrequest] [--cancelall] [--showqueue]
 
-NLP manager. Version 0.20.4 (2024-05-21). Created by Rudolf Cardinal.
+NLP manager. Version 0.20.5 (2024-06-26). Created by Rudolf Cardinal.
 
 OPTIONS:
   -h, --help            show this help message and exit

diff --git a/docs/source/nlp/_crate_nlp_multiprocess_help.txt b/docs/source/nlp/_crate_nlp_multiprocess_help.txt
@@ -1,7 +1,7 @@
 USAGE: crate_nlp_multiprocess [-h] --nlpdef NLPDEF [--nproc [NPROC]]
                               [--verbose]
 
-Runs the CRATE NLP manager in parallel. Version 0.20.4 (2024-05-21). Note that
+Runs the CRATE NLP manager in parallel. Version 0.20.5 (2024-06-26). Note that
 all arguments not specified here are passed to the underlying script (see
 crate_nlp --help).
 

diff --git a/docs/source/nlp/_specimen_nlp_config_file.ini b/docs/source/nlp/_specimen_nlp_config_file.ini
@@ -1,5 +1,5 @@
 # Configuration file for CRATE NLP manager (crate_nlp).
-# Version 0.20.4 (2024-05-21).
+# Version 0.20.5 (2024-06-26).
 #
 # PLEASE SEE THE HELP at https://crateanon.readthedocs.io/
 # Using defaults for Docker environment: False
Original file line number	Diff line number	Diff line change
Expand Up		@@ -123,4 +123,4 @@ Index of CRATE commands

		:ref:`crate_windows_service <crate_windows_service>`

		(Documentation built with CRATE 0.20.4.)
		(Documentation built with CRATE 0.20.5.)