fix: pyproject.toml was originally created from the conda.yaml which was an...

See merge request meldb/concepts-processing!13

docs: added documentation directory structure, and initial tests ok mkdocs but...

Closes #10

See merge request meldb/concepts-processing!12

docs: added documentation directory structure, and initial tests ok mkdocs but that's another issue. Closes #10

started the precommit hook work, but seems more complex as it requires some...

Closes #21

See merge request meldb/concepts-processing!11

test: add hatch run check to pyproject.toml to run all of the tools rather than precommit hook. This will do for now. closes #21

started the precommit hook work, but seems more complex as it requires some download from github etc with usernames and passwords #21

refactor: tidied up the action code for categories but still not opimimal as...

Closes #27

See merge request meldb/concepts-processing!10

refactor: tidied up the action code for categories but still not opimimal as the action is distributed across multipel functions. Closes #27

refactor: completed refactoring of config to combine codes within concept...

Closes #3

See merge request meldb/concepts-processing!9

refactor: completed refactoring of config to combine codes within concept sets. This optimisation will shorten to file overall, even though for things like hanlon it will be longer. Makes understanding of the file easier as no separate links bewteen concept sets and the code definition. Closes #3.

test: added new config3.yaml that includes hanlon. had to refactor phen map to...

Closes #22

See merge request meldb/concepts-processing!8

test: added new config3.yaml that includes hanlon. had to refactor phen map to handle new format and there's some weird code in the processing of the concept categories that needs further attention. The hanlon also includes an action to divide columns. #22

refactor: converted all examples to yaml and added test for config2. Updated...

Closes #19

See merge request meldb/concepts-processing!7

refactor: converted all examples to yaml and added test for config2. Updated readme. Fixed but in diff that assumed all csv files in map directory where map files when some where error files if no codes exists, moved error files to errors directory in the map directory to avoid this. Closes #19

refactor: converted all examples to yaml and added test for config2. Updated readme. Fixed but in diff that assumed all csv files in map directory where map files when some where error files if no codes exists, moved error files to errors directory in the map directory to avoid this.

added gitignore to phen init. closes #4

Closes #4

See merge request meldb/concepts-processing!6

test: run mypc to check types and add annotations. run black and reformatted...

Closes #20

See merge request meldb/concepts-processing!5

test: run mypc to check types and add annotations. run black and reformatted all python files. run tests and still pass. Closes #20

test: run mypc to check types and add annotations. run black and reformatted all python files. run tests and still pass

refactor:trud and omop versions are now written in yaml format. When map is...

Closes #5

See merge request meldb/concepts-processing!4

refactor:trud and omop versions are now written in yaml format. When map is created a version file is written (also in yaml) to the phen directory vocab_version.yaml including acmc, trud and omop version data. Closes #5.

Merge branch '18-pyarrow-19-0-0-requires-numpy-2-which-may-cause-conflicts-in-the-future' into 'dev'

fix: pyproject.toml was originally created from the conda.yaml which was an...

Closes #18

See merge request meldb/concepts-processing!3

fix: pyproject.toml was originally created from the conda.yaml which was an export of a conda environment. This provided libraries with specific versions on dependency packages. We don't need to pin the packages to specific versions. We are also not using hatch which handles dependencies between packages well. Remvoed all versions from the dependancies and numpy is now v2.2.3 and all tests pass. Closes #18.

Resolve "Document the development environment"

Closes #7

See merge request meldb/concepts-processing!2

Resolve "Document git workflow"

See merge request meldb/concepts-processing!1