Skip to content
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

Revise model classes #20

Merged
merged 52 commits into from
Jun 28, 2023
Merged

Revise model classes #20

merged 52 commits into from
Jun 28, 2023

Conversation

lnrekerle
Copy link
Collaborator

update develop to be the most accurate branch

ielis and others added 30 commits April 25, 2023 15:01
@ielis
Start revising the model classes.
a50579f
@ielis
Work on disease, phenotype, variant and proteins.
5968e49
@lnrekerle
worked further on changing class structuring
b19016c
@ielis
Update __init__.py
d0252ea
@ielis
Update disease creator
da84b05
@ielis
Revise phenotype creator.
d5038ee
@ielis
Protein metadata must be valid when an instance is created.
4cf36e7
@ielis
Start working on the variant data model.
8608cb8
@ielis
Fix typo in PhenopacketVariantCoordinateFinder, add TODOs for the n…
9db8468 
…ext session.
@lnrekerle
finished Variant and made test for VEP/Caching
308ab34
@ielis
Create variant module, setup tests for `variant.verify_start_end_co…
d2d163c 
…ordinates`.
@lnrekerle
Updated cohort and patient classes
1a7f60a
@ielis
Abstract away the details from PhenopacketPatientCreator, assemble …
a704126 
…the first part of the future workflow. Implement stubs for predicates. Require `hpo-toolkit>=0.1.5`.
@lnrekerle
Added Caching for Proteins
80f43ab
@lnrekerle
Merge branch 'revise_model_classes' into outline_workflow
2494dc5
@lnrekerle
Update _annotators.py
10951a5 
Missed a spot when fixing merge conflicts
@lnrekerle
Merge pull request #18 from monarch-initiative/outline_workflow
d71e234 
Outline gpc workflow
@ielis
Add type annotations in PhenopacketPatientCreator, make the tests f…
34c43b0 
…or `PhenopacketVariantCoordinateFinder` run.
@lnrekerle
notebook updates
4daf985
@lnrekerle
reworked for given tx id and protein id
c1444e6
@lnrekerle
Added comments and fixed a couple bugs
ef93ddb
@lnrekerle
Updated Notebook
28c2258
@ielis
Add notes.
92ba75c
@lnrekerle
now creates a cohort
dbb1806
@lnrekerle
Merge branch 'revise_model_classes' into lnrekerle_dev
02f9d57
@ielis
Remove the extra tx_id parameter in the FunctionalAnnotator signa…
0fec9be 
…ture.
@ielis
set is not a typing.Sequence but a tuple is.
d3fe3e2
@ielis
Remove redundant instance check.
6d1d58b
@ielis
Enable tests on my machine.
5a48158
@ielis
Remove old TODO - we have the tests now.
e59e72b
ielis and others added 22 commits June 5, 2023 17:30
@ielis
Remove another TODO - we do not need MANE transcript at the point of …
8695817 
…annotation (at least now).
@lnrekerle
fixed changes as suggested by Daniel
f4c8508
@lnrekerle
missed a change
741d4c0
@ielis
Simplify creation of the counter dict.
f5b2b3c
@ielis
Use add instead of update when updating the set with a singular v…
bb3632f 
…alue.
@ielis
We do not need the entire MinimalTerm to back Phenotype. The `Ter…
f48d42a 
…mId` is enough.
@ielis
Update the doc string - we provide coordinates in a tuple, not in a l…
495bcca 
…ist.
@ielis
Generally, it is easier to understand the if/else branches with synta…
f107ebc 
…x "if x is None then ... else ...", as compared with "if x is not None then ... else ...".
@ielis
Add TODOs for the future.
6056179
@ielis
I actually thought Union and not Optional.
f3085bd
@ielis
Revert back the test error that I introduced a few weeks ago.
4871739
@ielis
Setup GitHub action for running tests.
6f94cd9
@lnrekerle
Merge pull request #19 from monarch-initiative/lnrekerle_dev
35f077e 
now creates a cohort
@lnrekerle
Added Multiple tests!
df4581c
@lnrekerle
Fixed Testing
c388c7d
@lnrekerle
Merge pull request #21 from monarch-initiative/cohort_testing
2e0a195 
Added Multiple tests!
@lnrekerle
ignoring incomplete tests
ac23ac4
@lnrekerle
ignoring incomplete tests
41cd8ef
@ielis
Update the project setup. Clean up dependencies and create a test s…
663310c 
…ection for running tests. Update the links.
@ielis
Update the CI script.
a2eccb5
@lnrekerle
Merge pull request #23 from monarch-initiative/update_project_and_ci
37cc964 
Update project and CI
@lnrekerle
Fixed var == None and printed divide by 0 errors.
cee3b33
@lnrekerle lnrekerle merged commit 238c397 into develop Jun 28, 2023
3 checks passed
@lnrekerle lnrekerle deleted the revise_model_classes branch June 28, 2023 17:50
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
@lnrekerle @ielis