Unfreeze SQLAlchemy

CHANGELOG.md

@@ -11,6 +11,7 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 ### Fixed
 - Add missing brew path to GitHub action. It has been removed from PATH variable in Ubuntu
 - Badges on README page
+- Unfreeze SQLAlchemy again, allowing >=1.3 as the limitation in chanjo-report is being fixed
 
 ## [4.6.1] - 2021-07-08
 ### Fixed

chanjo/init/bootstrap.py

@@ -42,4 +42,4 @@ def pull(target_dir, force=False):  # pragma: no cover
         logger.info('removing BED archive...')
         bed_zip_path.remove_p()
     else:
-        logger.warn('file already exists, skipping: %s', final_bed)
+        logger.warning('file already exists, skipping: %s', final_bed)

chanjo/init/demo.py

@@ -30,7 +30,7 @@ def setup_demo(location, force=False):
         # we can copy the directory(tree)
         demo_dir.copytree(target_dir)
     except OSError as error:
-        log.warn('location must be a non-existing directory')
+        log.warning('location must be a non-existing directory')
         raise error
 
     # inform the user

requirements.txt

@@ -6,4 +6,4 @@ toolz
 pyyaml
 importlib_metadata
 pymysql
-sqlalchemy==1.3.*
+sqlalchemy<2.0

tests/conftest.py

@@ -13,7 +13,7 @@
 from chanjo.load.link import link_elements
 
 
-@pytest.yield_fixture
+@pytest.fixture
 def reset_path():
     """Reset PATH environment variable temporarily."""
     path_env = os.environ['PATH']
@@ -22,15 +22,15 @@ def reset_path():
     os.environ['PATH'] = path_env
 
 
-@pytest.yield_fixture(scope='function')
+@pytest.fixture(scope='function')
 def chanjo_db():
     _chanjo_db = ChanjoDB('sqlite://')
     _chanjo_db.set_up()
     yield _chanjo_db
     _chanjo_db.tear_down()
 
 
-@pytest.yield_fixture(scope='function')
+@pytest.fixture(scope='function')
 def existing_db(tmpdir):
     db_path = tmpdir.join('coverage.sqlite3')
     chanjo_db = ChanjoDB(str(db_path))
@@ -39,7 +39,7 @@ def existing_db(tmpdir):
     chanjo_db.tear_down()
 
 
-@pytest.yield_fixture(scope='function')
+@pytest.fixture(scope='function')
 def popexist_db(existing_db, exon_lines):
     result = link_elements(exon_lines)
     existing_db.add(*result.models)
@@ -50,7 +50,7 @@ def popexist_db(existing_db, exon_lines):
     yield existing_db
 
 
-@pytest.yield_fixture(scope='function')
+@pytest.fixture(scope='function')
 def populated_db(chanjo_db, exon_lines):
     exon_lines = list(exon_lines)
     result = link_elements(exon_lines)

tests/store/test_store_api.py

@@ -4,7 +4,7 @@
 from datetime import datetime
 
 import pytest
-from sqlalchemy.orm.exc import FlushError
+from sqlalchemy.exc import IntegrityError
 
 from chanjo.store.api import ChanjoDB
 from chanjo.store.models import Sample
@@ -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()