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Release Candidate 0.0.6 #175
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d6061cf
Added an 'extract_values' transform.
mmcdermott 5efbbcc
Updated mandatory types to be separate from mandatory MEDS columns
mmcdermott 6d6b318
Merge branch 'dev' into 57_extract_numeric_values
mmcdermott 10fedf0
Changed to 'categorical_value' and added better doctests
mmcdermott c463548
Added an integration test for extract_values -- it needs to wait for …
mmcdermott f8b260d
Merge branch 'dev' into 57_extract_numeric_values
mmcdermott 6ca0054
Merge branch 'dev' into 57_extract_numeric_values
mmcdermott 26db680
Merge branch 'dev' into 57_extract_numeric_values
mmcdermott f3da768
Merged dev
mmcdermott 350a82e
Merged to dev
mmcdermott f7d7e27
Merge branch 'dev' into 57_extract_numeric_values
mmcdermott 2d59ff2
Exit if there is no _metadata in the event configs
prenc d217885
Use a more precise message
prenc 1969ea1
Removed aggregate from default ETL and added dedicated test.
mmcdermott fc17317
Fixed a parent_codes schema error in vocabulary index
mmcdermott a751f72
Merge pull request #157 from mmcdermott/110_remove_agg_from_default_e…
mmcdermott d830d49
Merge branch 'dev' into 57_extract_numeric_values
mmcdermott df3517d
Corrected a typo in a doctest.
mmcdermott 87dde78
Everything but normalization succeeding -- I need to re-calculate exp…
mmcdermott 089ae24
Updated aggregations stage config syntax in mapper_fntr test.
mmcdermott 1fc2e4d
Added failing test to capture mapper_fntr bug with quantils when summ…
mmcdermott 6b7a6b8
Added tests and all are passing.
mmcdermott 9948bc9
Fixed normalization test.
mmcdermott 31e3652
Fixed tokenization test
mmcdermott 3cab512
Merge pull request #159 from mmcdermott/158_fix_typing_issue
mmcdermott 017d126
Merge branch 'dev' into 163_aggregation_test_and_mapper_bug
mmcdermott 497d411
Update type
mmcdermott 49fb1ce
Merge pull request #166 from mmcdermott/163_aggregation_test_and_mapp…
mmcdermott 9bb19bf
Separated input data preparation and renamed it to make tests cleaner…
mmcdermott 9cf0bc4
Making stage-name always be passed via the command line if it is used.
mmcdermott d5b0782
Updated test output syntax to support data and metadata checking and …
mmcdermott 138eb1e
Added a multi-stage test which currently, appropriately, fails due to…
mmcdermott 74d3ce1
Corrected #161. This makes the normalization error disappear, but mor…
mmcdermott 5911c90
Added a graceful exit mode for cases where shards are empty. Should s…
mmcdermott ff46645
Using more default parameters.
mmcdermott 9304bf7
Tests re-failing as I haven't added all the NRT tests, just the fully…
mmcdermott c7d56a9
Starting to track some of the intermediate outputs to identify the ta…
mmcdermott 210a9ce
Added capability to test intermediate files and started validating fu…
mmcdermott 747ce11
Tested outputs up to occlude outliers.
mmcdermott 8736279
Removed broken assert_no_other_outcomes
mmcdermott 6114c42
Validated fit normalization stage as well.
mmcdermott 3c5c7d9
Added test for final metadata stage
mmcdermott 4a466c0
Added normalization shard test.
mmcdermott 2a58ec1
Added tokenization schemas test.
mmcdermott aeedb9e
Added tokenized output validations.
mmcdermott 80b31fd
Tested tensorized outputs.
mmcdermott a27d361
Merge pull request #167 from mmcdermott/160-multi-stage-integration-t…
mmcdermott 7c55b34
Merge branch 'dev' into 125_metadata_extraction_crashes
mmcdermott 766f685
Added a test for the no metadata case.
mmcdermott 7f11b9e
Merge pull request #154 from mmcdermott/125_metadata_extraction_crashes
mmcdermott 0c4a942
Incorporating Ethan's update from #108 and fixing other issues with t…
mmcdermott 3fab90a
Added badges to the README.
mmcdermott 6046856
Fixed a typo in a badge link
mmcdermott 727f4bd
Fixed another typo in a badge link
mmcdermott 775ba5e
Merge pull request #171 from mmcdermott/170_badges
mmcdermott 4b2d10c
Set-up python 3.11 support.
mmcdermott 2f7382a
Made publishing workflow only use 3.12
mmcdermott 5a54e9a
Made code quality just use python 3.12
mmcdermott 1f80b15
Merge pull request #178 from mmcdermott/176_py311_support
mmcdermott 4ded5b0
Merge branch 'dev' into 57_extract_numeric_values
mmcdermott c4375c6
Fixed test (still errors, but now is due to proper issue.
mmcdermott 95e66fc
Added regex capabilities to parser.
mmcdermott 074237e
Added regex capabilities to matchers.
mmcdermott 64807c5
Added a possibly working additional match revise stage type and updat…
mmcdermott b15a8a1
Fixed things up to test config for extracting temp.
mmcdermott cd03fa9
Updated test outputs to be in the proper order and use the right rege…
mmcdermott 3f73a35
Merge pull request #121 from mmcdermott/57_extract_numeric_values
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1 change: 0 additions & 1 deletion
1
src/MEDS_transforms/configs/stage_configs/fit_vocabulary_indices.yaml
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,4 +1,3 @@ | ||
fit_vocabulary_indices: | ||
is_metadata: true | ||
ordering_method: "lexicographic" | ||
output_dir: "${cohort_dir}" |
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Avoid using mutable data structures for argument defaults.
Using mutable default arguments can lead to unexpected behavior. Set the default value to
None
and initialize within the function.Apply this diff to fix the issue:
Then, initialize the default value within the function:
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