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Unfreeze SQLAlchemy #252

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Unfreeze SQLAlchemy #252

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898f0fd
Unfreeze SQLAlchemy
dnil May 13, 2024
6df0b56
Trying stepwise - unfreeze to 1.4 first..
dnil May 13, 2024
d967dd8
Merge branch 'master' into unfreeze_sqlalchemy
dnil May 13, 2024
c2e27f3
Merge branch 'master' into unfreeze_sqlalchemy
dnil May 13, 2024
29bd09e
Replace ruamel.yaml with pyyaml
May 13, 2024
5c08a01
Fixed test
May 13, 2024
50fcc3a
Unfreeze SQLAlchemy
dnil May 13, 2024
3df1f0d
Merge branch 'master' into unfreeze_sqlalchemy
northwestwitch May 13, 2024
cc49262
Fix test
dnil May 13, 2024
8cc4b45
explicit name import..
dnil May 13, 2024
cf9bd56
this one?
dnil May 13, 2024
db4267a
Merge branch 'master' into unfreeze_sqlalchemy
northwestwitch May 13, 2024
93002f0
changelog and some deprecations
dnil May 13, 2024
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2 changes: 1 addition & 1 deletion requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -6,4 +6,4 @@ toolz
pyyaml
importlib_metadata
pymysql
sqlalchemy==1.3.*
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@northwestwitch northwestwitch May 13, 2024 •
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sqlalchemy 2 can be quite different from v.1, there is even a migration guide: https://docs.sqlalchemy.org/en/20/changelog/migration_20.html

Just unfreezing like this seems risky..

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Yes, I realised a little while ago. 😊 It was useful to test the dependencies at least: nice to see that chanjo-report / scout did build and run ok with this configuration. But chanjo would likely bug out without changes..

sqlalchemy<2.0
6 changes: 3 additions & 3 deletions tests/store/test_store_api.py
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Expand Up @@ -4,7 +4,7 @@
from datetime import datetime

import pytest
from sqlalchemy.orm.exc import FlushError
from sqlalchemy.exc import IntegrityError
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💯


from chanjo.store.api import ChanjoDB
from chanjo.store.models import Sample
Expand Down Expand Up @@ -38,8 +38,8 @@ def test_save(chanjo_db):
# GIVEN sample already exists
conflict_sample = Sample(id=sample_id, group_id="ADMG2")
# WHEN saving it again with same id
# THEN error is raised _after_ rollback
with pytest.raises(FlushError):
# THEN an error is raised
with pytest.raises(IntegrityError):
chanjo_db.add(conflict_sample)
chanjo_db.save()

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