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merging into master from develop to make a new release #573

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merging into master from develop to make a new release #573

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proccaserra
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this is to address issues with isa-tab parser and many improvements

proccaserra and others added 30 commits September 21, 2022 17:57
@proccaserra
ld-refactor updating isa-jsonschemas, updating model classes to add t…
6f52763 
…o_ld method
@proccaserra
Merge branch 'develop' of github.com:ISA-tools/isa-api into develop
db01962
@proccaserra
adding tests to test-create
ff576f3
@proccaserra
upgrading from develop
1b1663d
@proccaserra
bring develop up to test
cacdf87
@proccaserra
Merge branch 'develop' of github.com:ISA-tools/isa-api into develop
d6cc5a5
@proccaserra
working on upgrading isa model json schema
a125347
@proccaserra
claarifying the meaning of an attribute for isatab validator , replac…
8456ebb 
…ing mzml argument with origin
@proccaserra
porting isa model json-schema to latest json schema specification
a7a0a91
@proccaserra
cleanup of isa model json schema - related to issue469
2d0ddb3
@terazus
Merge pull request #493 from ISA-tools/master
5235dda 
Merge from master
@terazus
Merge pull request #495 from ISA-tools/master
6ce0008 
merge from master
@proccaserra
adding field Performer, associated test
27c5797
@proccaserra
fixing issue497
42b5d4b
@proccaserra
synching develop on master
05f49df
@proccaserra
Merge branch 'develop' of github.com:ISA-tools/isa-api into develop
a82f7f3
@proccaserra
fixing assertion error in test
b900691
@proccaserra
Merge branch 'master' of github.com:ISA-tools/isa-api into develop
a2a5a98
@proccaserra
upgrading github action to clear error message
b265303
@proccaserra
upgrade to second github action
b2ecfb0
@proccaserra
merging develop into issue-497-fix
4f41ecd
@proccaserra
Merge pull request #507 from ISA-tools/issue-497-fix
d246d77 
Issue 497 fix
@proccaserra
should fix issue 511
c9859d4
@proccaserra
corrections, test passing (new test)
195cf71
@proccaserra
minor edit
34f9291
@proccaserra
fixes issue #512
2f489f5
@proccaserra
fixes issue #512
034291f
@proccaserra
adding a test to check if comments on assay declaration are properly …
818332d 
…serialized in isatab2json conversion
@proccaserra
fixes issue #506 - updating to ols4
324bcd4
@proccaserra
minor fix to test
1ec71db
proccaserra and others added 23 commits July 21, 2024 19:18
@proccaserra
bringing compatibility with python 3.12.4 by reviewing requirements.t…
2632c33 
…xt and setup
@proccaserra
adding python 3.12 support to buildandtest github action, dropping py…
d1c558c 
…thon 3.8
@proccaserra
tuning requirements for py3.12 support
169c372
@proccaserra
more tweaks
f658f56
@proccaserra
Merge pull request #564 from ISA-tools/issue562-python312
00c2f63 
Issue562 python312
@proccaserra
adjusting bh23 workbook, and model class
339db38
@knirirr
Mocked one test, mock seems to apply to others. #557
f0b765f
@knirirr
Mocked tests and fixed test_isatools_utils #557
a0adc99
@knirirr
Merge branch 'develop' into mock_pubmed_557
fc63569
@knirirr
Removed tests not needed due to mocking. #557
7467ffb
@knirirr
Fix ols test.
0b4afe6
@knirirr
Merge pull request #567 from ISA-tools/mock_pubmed_557
11913a7 
Mock pubmed 557
@proccaserra
fixes #569
95a788c
@proccaserra
adding a check on parameter values in write_study and write_assay met…
5a69357 
…hods
@proccaserra
Merge pull request #565 from ISA-tools/prs-patch-2
d6c182c 
adjusting bh23 workbook, and model class
@proccaserra
restoring old jpnb
70b0e24
@proccaserra
downgrading to SQLAlchemy 1.4.52 as migrating to 2 or higher brakes b…
25b21a4 
…uild, but altering the models to clear some of the errors identified during the migration attempt
@proccaserra
cleaning up refs
b9f9de8
@proccaserra
updating setup.py
89d6aa1
@proccaserra
pinning SQLAlchemy version so it does build with 2.0 or higher for now
87e1331
@proccaserra
temporary removal w4m test
572a69a
@proccaserra
minor corrections to clear warnings when running the test, fixing und…
8c969d8 
…erlying test data associated with tests
@proccaserra
bumping release version to 0.14.3
983fe15
@proccaserra proccaserra requested a review from knirirr March 6, 2025 10:07
@proccaserra proccaserra self-assigned this Mar 6, 2025
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Coverage Status

coverage: 81.279% (-3.0%) from 84.305%
when pulling 983fe15 on develop
into 972f4d8 on master.

knirirr
knirirr reviewed Mar 27, 2025
View reviewed changes
.github/workflows/buildandtestpython.yml
@@ -10,12 +10,12 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: [3.8, 3.9, '3.10', '3.11']
python-version: [3.9, '3.10', '3.11', '3.12']
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Can 3.13 be added here or would the changes in requirements.txt be too much of a nuisance?

knirirr
knirirr reviewed Mar 27, 2025
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I've looked through this and would benefit from further discussion if time permits.

@knirirr knirirr self-requested a review March 27, 2025 13:38
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@proccaserra @coveralls @knirirr @terazus @ptth222