Skip to content

Release 0.4.0 #11

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Merged
rmnldwg merged 85 commits into from
Sep 4, 2025
Merged

Release 0.4.0 #11

rmnldwg merged 85 commits into from
Sep 4, 2025

Conversation

@rmnldwg
Copy link
Contributor

@rmnldwg rmnldwg commented Sep 4, 2025

No description provided.

rmnldwg added 30 commits July 14, 2025 16:25
@rmnldwg
change: don't use or to check for None arg
2d76ff8
@rmnldwg
merge: branch 'main' into 'dev'
ff8a01d
@rmnldwg
merge: branch 'dev' into 7-combining-introduces-incosistencies
2ba9d41
@rmnldwg
remove!: old funcs to infer/combine data
2518817
@rmnldwg
fix!: combine mods & lvl info using probs
f23b07f 
Fixes: #7
@rmnldwg
test: test new combine/augment with CLB patient 17
11c6161 
Related: #7
@rmnldwg
feat: pass_to to C objects for custom queries
7412c06
@rmnldwg
refac: move C & Q to own module
d4658b7
@rmnldwg
change!: update schema for new 2nd lvl cols
90ef414
@rmnldwg
fix: use spec/sens < 1 in augment
f7f41a0 
Not sure this is necessary, but I've got the feeling there may be edge
cases where it could cause errors.
@rmnldwg
feat: allow importing LyDataFrame type from root
eef4bd3
@rmnldwg
fix: make LyDataFrame importable
9d52456
@rmnldwg
fix: ensure alignment during combine/augment
374b256
@rmnldwg
fix: change midlvl col from info to core
2a1b20c
@rmnldwg
docs: add more info to augment/combine
6b8c41b
@rmnldwg
feat: add working sorting functions
229e00b
@rmnldwg
feat: add convenience .ly.enhance() method
4635820
@rmnldwg
test: add basic .ly.combine() test
cebbacd
@rmnldwg
change: improve final sorting of tables
aff4c79
@rmnldwg
test: add scripts to compare augment/combine
c89275d
@rmnldwg
test: check one patient with specific issue
fce13ba
@rmnldwg
fix: don't override super when subs unknown
2beacec
@rmnldwg
fix: join using "outer" in enhance
dba7666
@rmnldwg
fix: Nones due to index mismatch etc.
a2c157c
@rmnldwg
test: add util doctest (though unnecessary)
382aa46
@rmnldwg
test: add some more patient-specific checks
9952c31
@rmnldwg
fix: replace instead of udpdate augmented cols
01a62ec
@rmnldwg
test: add scripts to compare old vs new
116a70b
@rmnldwg
docs: update some docstrings
3ac9338
@rmnldwg
merge: branch '7-combining-introduces-incosistencies' into 'dev'
56be73b
rmnldwg added 22 commits August 22, 2025 13:36
@rmnldwg
docs: update schema & validation docstrings
b18ef3e
@rmnldwg
feat: casting, validating, & enhancing during load
9490b0b
@rmnldwg
test: update to new, cast data
8163d9e
@rmnldwg
fix: avoid pydantic's weird TypeError for pd.NaT
02f7a8e
@rmnldwg
fix: check central info in schema
e59454d
@rmnldwg
fix: call logger.error over exception
3ba50b2 
This deduplicates the output.
@rmnldwg
fix: allow MX=-1 in schema
884a0d9
@rmnldwg
fix: allow None in more patient fields
1e22f1b
@rmnldwg
fix: allow central & side to be None
a60a8af
@rmnldwg
fix: side may be None when central=True
c5c6ad3
@rmnldwg
fix: make some fields robust to uppercase strings
93aac55
@rmnldwg
docs: add new modules to sphinx
1e6196b
@rmnldwg
merge: branch '4-formalize-dataset-schema' into 'dev'
e5a08d1 
Fixes: #4
@rmnldwg
feat: add a .get_tnm() helper method
8469a26
@rmnldwg
feat: fail more informatively when loading
6812761 
Fixes: #10
@rmnldwg
fix: allow loading from disk using custom paths
d3b8e06
@rmnldwg
feat: add location to short column access
371970f
@rmnldwg
fix: get github fetch working again
0c82338
@rmnldwg
test: ensure .env is loaded during all tests
5cc6a22
@rmnldwg
merge: branch '10-fetching-data-should-fail-more-informatively' into …
b65a65f 
…'dev'

Fixes: #10
@rmnldwg
chore: update changelog
26414d0
@rmnldwg
chore: remove old vs new scripts
53bb4ad
@github-actions
Copy link

github-actions bot commented Sep 4, 2025 •
edited
Loading

Coverage report

Click to see where and how coverage changed

FileStatementsMissingCoverageCoverage
(new stmts)		Lines missing
  src/lydata
  __init__.py
  _version.py
  accessor.py 200, 270, 275, 493, 563-565, 577-579
  augmentor.py 80, 130, 219
  loader.py 58-61, 76-79, 134-142, 194, 234, 248-260, 290
  querier.py 175, 179
  schema.py 183, 286, 292, 300, 306, 312, 442-452, 456-459
  types.py
  utils.py 263, 293, 296, 302, 311, 319, 322, 352, 361, 364
  validator.py 81-98, 186-193, 199-211
Project Total  

This report was generated by python-coverage-comment-action

@rmnldwg rmnldwg merged commit f66fe8d into main Sep 4, 2025
4 checks passed
@rmnldwg rmnldwg deleted the release-0.4.0 branch September 4, 2025 09:21
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

No reviews

Assignees

No one assigned

Labels

None yet

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

2 participants

@rmnldwg