From c556083f491342264143d39d6f0faf0876fa2e69 Mon Sep 17 00:00:00 2001 From: Forrest Collman Date: Tue, 28 Apr 2026 09:45:32 -0700 Subject: [PATCH 1/7] updating doc string Co-authored-by: Copilot --- dynamicannotationdb/annotation.py | 1 + 1 file changed, 1 insertion(+) diff --git a/dynamicannotationdb/annotation.py b/dynamicannotationdb/annotation.py index 0032d07..635ceb1 100644 --- a/dynamicannotationdb/annotation.py +++ b/dynamicannotationdb/annotation.py @@ -257,6 +257,7 @@ def insert_annotations(self, table_name: str, annotations: List[dict], user_id=N that meet the schema user_id : str, optional user id to fill in any auto_user_id fields in the schema, by default None + note: if user_id is None, auto_user_id fields will not be filled and will need to be provided in the annotation dicts Returns ------- From 27048f7d1be017d5ff45f19ea84a546d5348e4d6 Mon Sep 17 00:00:00 2001 From: Forrest Collman Date: Tue, 28 Apr 2026 09:53:50 -0700 Subject: [PATCH 2/7] trying to upgrade sqlalchemy --- pyproject.toml | 2 +- requirements.txt | 2 +- uv.lock | 8 ++++---- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 25d046f..a76240d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -21,7 +21,7 @@ requires-python = ">=3.8" dependencies = [ "marshmallow==3.5.1", "emannotationschemas>=5.26.0", - "sqlalchemy<1.4", + "sqlalchemy>=1.4,<2", "psycopg2-binary", "geoalchemy2", "pytz", diff --git a/requirements.txt b/requirements.txt index 9d75790..7b85643 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,6 +1,6 @@ marshmallow==3.5.1 emannotationschemas>=5.26.0 -sqlalchemy<1.4 +sqlalchemy>=1.4,<2 psycopg2-binary geoalchemy2 pytz diff --git a/uv.lock b/uv.lock index 1b944b0..1e2d993 100644 --- a/uv.lock +++ b/uv.lock @@ -574,7 +574,7 @@ wheels = [ [[package]] name = "dynamicannotationdb" -version = "5.13.1" +version = "5.14.1" source = { editable = "." } dependencies = [ { name = "alembic" }, @@ -601,7 +601,7 @@ dev = [ [package.metadata] requires-dist = [ { name = "alembic" }, - { name = "emannotationschemas", specifier = ">=5.4.0" }, + { name = "emannotationschemas", specifier = ">=5.26.0" }, { name = "geoalchemy2" }, { name = "jsonschema", specifier = "<4.0" }, { name = "marshmallow", specifier = "==3.5.1" }, @@ -620,7 +620,7 @@ dev = [ [[package]] name = "emannotationschemas" -version = "5.24.12" +version = "5.26.0" source = { registry = "https://pypi.org/simple" } dependencies = [ { name = "flask-cors" }, @@ -633,7 +633,7 @@ dependencies = [ { name = "shapely" }, { name = "sqlalchemy" }, ] -sdist = { url = "https://files.pythonhosted.org/packages/8d/60/2ccf0c3aa7d47f2fbda5d02ba023df5d88788ec1c579d7597702fca982f6/emannotationschemas-5.24.12.tar.gz", hash = "sha256:bd36cf0db1570e5098e3701c714ca1be20bb1de777f7624a9d37f0c805d3a5d0", size = 38327, upload-time = "2025-08-29T16:59:05.613Z" } +sdist = { url = "https://files.pythonhosted.org/packages/43/14/78090dfcc1ceef8abc207438fe768b15697db08655e55c642c0aeb71c7df/emannotationschemas-5.26.0.tar.gz", hash = "sha256:ab4ce6b699762396b5f0ad3f2134015fc4e4085f41292b14e598aeaeda9437b5", size = 39568, upload-time = "2026-04-28T16:24:13.056Z" } [[package]] name = "exceptiongroup" From 549a6e104332c10e00ff460c6c05881d71b02afa Mon Sep 17 00:00:00 2001 From: Forrest Collman Date: Tue, 28 Apr 2026 10:00:09 -0700 Subject: [PATCH 3/7] bumping EMannotationschemas --- pyproject.toml | 2 +- requirements.txt | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index a76240d..3427a82 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -20,7 +20,7 @@ classifiers = [ requires-python = ">=3.8" dependencies = [ "marshmallow==3.5.1", - "emannotationschemas>=5.26.0", + "emannotationschemas>=5.26.1", "sqlalchemy>=1.4,<2", "psycopg2-binary", "geoalchemy2", diff --git a/requirements.txt b/requirements.txt index 7b85643..dd3a8cb 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,5 +1,5 @@ marshmallow==3.5.1 -emannotationschemas>=5.26.0 +emannotationschemas>=5.26.1 sqlalchemy>=1.4,<2 psycopg2-binary geoalchemy2 From 04de28e6f159784df323c4c41922fa8519fabc37 Mon Sep 17 00:00:00 2001 From: Forrest Collman Date: Tue, 28 Apr 2026 10:04:19 -0700 Subject: [PATCH 4/7] fix import of DeclarativeMeta --- dynamicannotationdb/database.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dynamicannotationdb/database.py b/dynamicannotationdb/database.py index bf1ed60..76e87bc 100644 --- a/dynamicannotationdb/database.py +++ b/dynamicannotationdb/database.py @@ -5,7 +5,7 @@ from sqlalchemy import create_engine, func, inspect, or_ from sqlalchemy.ext.automap import automap_base -from sqlalchemy.ext.declarative.api import DeclarativeMeta +from sqlalchemy.orm import DeclarativeMeta from sqlalchemy.orm import Session, scoped_session, sessionmaker from sqlalchemy.orm.exc import NoResultFound from sqlalchemy.schema import MetaData From b5d315570fd324a90f1a662455e003d89dba74f8 Mon Sep 17 00:00:00 2001 From: Forrest Collman Date: Tue, 28 Apr 2026 10:29:28 -0700 Subject: [PATCH 5/7] bumipng EMAnnotationSchema deps --- pyproject.toml | 2 +- requirements.txt | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 3427a82..9deb3fa 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -20,7 +20,7 @@ classifiers = [ requires-python = ">=3.8" dependencies = [ "marshmallow==3.5.1", - "emannotationschemas>=5.26.1", + "emannotationschemas>=5.26.2", "sqlalchemy>=1.4,<2", "psycopg2-binary", "geoalchemy2", diff --git a/requirements.txt b/requirements.txt index dd3a8cb..d0ea03d 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,5 +1,5 @@ marshmallow==3.5.1 -emannotationschemas>=5.26.1 +emannotationschemas>=5.26.2 sqlalchemy>=1.4,<2 psycopg2-binary geoalchemy2 From 46faa7ffd8490d7f47969a259d12e7fc18c6b774 Mon Sep 17 00:00:00 2001 From: Forrest Collman Date: Tue, 28 Apr 2026 10:31:44 -0700 Subject: [PATCH 6/7] fixing tests --- tests/test_database.py | 2 +- tests/test_schema.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/test_database.py b/tests/test_database.py index f39935b..d9a65c7 100644 --- a/tests/test_database.py +++ b/tests/test_database.py @@ -3,7 +3,7 @@ import pytest from sqlalchemy import Table -from sqlalchemy.ext.declarative.api import DeclarativeMeta +from sqlalchemy.orm import DeclarativeMeta from emannotationschemas import type_mapping from dynamicannotationdb.errors import TableAlreadyExists diff --git a/tests/test_schema.py b/tests/test_schema.py index 719ee86..be7fd3d 100644 --- a/tests/test_schema.py +++ b/tests/test_schema.py @@ -1,7 +1,7 @@ import marshmallow from emannotationschemas.errors import UnknownAnnotationTypeException import pytest -from sqlalchemy.ext.declarative.api import DeclarativeMeta +from sqlalchemy.orm import DeclarativeMeta def test_get_schema(dadb_interface): From 6b2d6a5642c455063e2432024a58da6159968b63 Mon Sep 17 00:00:00 2001 From: Forrest Collman Date: Tue, 28 Apr 2026 11:01:53 -0700 Subject: [PATCH 7/7] bumping EMA dependancy --- pyproject.toml | 2 +- requirements.txt | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 9deb3fa..040ba19 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -20,7 +20,7 @@ classifiers = [ requires-python = ">=3.8" dependencies = [ "marshmallow==3.5.1", - "emannotationschemas>=5.26.2", + "emannotationschemas>=5.26.3", "sqlalchemy>=1.4,<2", "psycopg2-binary", "geoalchemy2", diff --git a/requirements.txt b/requirements.txt index d0ea03d..b965900 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,5 +1,5 @@ marshmallow==3.5.1 -emannotationschemas>=5.26.2 +emannotationschemas>=5.26.3 sqlalchemy>=1.4,<2 psycopg2-binary geoalchemy2