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Release 0.4.0 - #11

Merged

rmnldwg merged 85 commits into

mainfrom

release-0.4.0

Sep 4, 2025

Merged

Release 0.4.0#11
rmnldwg merged 85 commits into
mainfrom
release-0.4.0

Commits on Jul 14, 2025
- change: don't use `or` to check for `None` arg
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Commits on Jul 23, 2025
- merge: branch 'main' into 'dev'
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- merge: branch 'dev' into 7-combining-introduces-incosistencies
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- remove!: old funcs to infer/combine data
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- fix!: combine mods & lvl info using probs
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- test: test new combine/augment with CLB patient 17
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Commits on Jul 24, 2025
- feat: `pass_to` to `C` objects for custom queries
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- refac: move `C` & `Q` to own module
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Commits on Jul 31, 2025
- change!: update schema for new 2nd lvl cols
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- fix: use spec/sens < 1 in `augment`
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- feat: allow importing `LyDataFrame` type from root
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- fix: make `LyDataFrame` importable
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- fix: ensure alignment during combine/augment
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- fix: change midlvl col from `info` to `core`
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Commits on Aug 4, 2025
- docs: add more info to augment/combine
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- feat: add working sorting functions
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  229e00b
- feat: add convenience `.ly.enhance()` method
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- test: add basic `.ly.combine()` test
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- change: improve final sorting of tables
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- test: add scripts to compare augment/combine
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Commits on Aug 5, 2025
- test: check one patient with specific issue
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- fix: don't override super when subs unknown
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  2beacec
- fix: join using "outer" in enhance
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- fix: `None`s due to index mismatch etc.
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- test: add util doctest (though unnecessary)
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- test: add some more patient-specific checks
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- fix: replace instead of udpdate augmented cols
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- test: add scripts to compare old vs new
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Commits on Aug 6, 2025
- docs: update some docstrings
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- merge: branch '7-combining-introduces-incosistencies' into 'dev'
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  56be73b
- feat: add basic pydantic patient/tumor model
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- test: ensure basic functionality of schemas
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- feat: add schema for modalities
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- change!: rewrite validation using new schema
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- test: check another wrong patient
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  9d8430c
- fix: augment during combine for max_llh/rank
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- test: rerun comparison
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- change!: start using only schema for validation
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Commits on Aug 11, 2025
- change: update midlvl cols to new `core`
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- feat: add working casting function
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- test: cover casting with minimal checks
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- test: update schema test to use `core`, too
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Commits on Aug 12, 2025
- fix: nicotine/pack years validator
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- test: fix schema tests
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  9bd354c
- feat: add `cast()` to lydata accessor
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- feat: add function to write JSON schema to file
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- feat: add basic collector web UI
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- feat: get parsing and downloading CSV to work
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Commits on Aug 13, 2025
- docs: add docstrings to JS code
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- build: remove typer dependency
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- remove: put collector in lyscripts
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Commits on Aug 19, 2025
- merge: branch '4-formalize-dataset-schema' into '7-combining-introduces-incosistencies'
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- test: add another 2025-USZ patient to test cases
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- test: fix small issues causing tests to fail
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- fix: use default subdivisions in `.enhance()`
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- test: ensure diff does not change again
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Commits on Aug 21, 2025
- merge: branch '7-combining-introduces-incosistencies' into '4-formalize-dataset-schema'
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- change: expand the schema
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- fix: make casting safer and better
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- feat: add pre-/suffixes to T/N stages in schema
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- change: further improve validation
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Commits on Aug 22, 2025
- docs: update schema & validation docstrings
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- feat: casting, validating, & enhancing during load
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- test: update to new, cast data
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Commits on Aug 25, 2025
- fix: avoid pydantic's weird TypeError for pd.NaT
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- fix: check central info in schema
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  e59454d
- fix: call `logger.error` over `exception`
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  3ba50b2
- fix: allow MX=-1 in schema
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  884a0d9
- fix: allow `None` in more patient fields
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- fix: allow central & side to be `None`
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- fix: side may be `None` when central=`True`
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- fix: make some fields robust to uppercase strings
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- docs: add new modules to sphinx
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Commits on Aug 26, 2025
- merge: branch '4-formalize-dataset-schema' into 'dev'
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- feat: add a `.get_tnm()` helper method
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- feat: fail more informatively when loading
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Commits on Aug 27, 2025
- fix: allow loading from disk using custom paths
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- feat: add `location` to short column access
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- fix: get github fetch working again
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Commits on Sep 4, 2025
- test: ensure .env is loaded during all tests
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- merge: branch '10-fetching-data-should-fail-more-informatively' into 'dev'
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- chore: update changelog
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- chore: remove old vs new scripts
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- docs: fix old data version in README.md
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- ci: use env var for main tests, too
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Commits

Commits on Jul 14, 2025

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Commits on Sep 4, 2025