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From 82484016be1462d45478186fd15330ad54307b07 Mon Sep 17 00:00:00 2001
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From: Chris Markiewicz <effigies@gmail.com>
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Date: Mon, 24 Apr 2023 09:29:11 -0400
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Subject: [PATCH 1/3] FIX: Import declarative_base from correct location
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---
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bids/layout/models.py | 8 ++++++--
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setup.cfg | 2 +-
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2 files changed, 7 insertions(+), 3 deletions(-)
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diff --git a/bids/layout/models.py b/bids/layout/models.py
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index be1534bb..fff3d1ff 100644
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--- a/bids/layout/models.py
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+++ b/bids/layout/models.py
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@@ -9,12 +9,16 @@ from copy import deepcopy
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from itertools import chain
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from functools import lru_cache
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-from sqlalchemy.ext.declarative import declarative_base
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from sqlalchemy.ext.associationproxy import association_proxy
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from sqlalchemy.orm.collections import attribute_mapped_collection
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-from sqlalchemy import (Column, String, Boolean, ForeignKey, Table)
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+from sqlalchemy import Column, String, Boolean, ForeignKey, Table
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from sqlalchemy.orm import reconstructor, relationship, backref, object_session
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+try:
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+ from sqlalchemy.orm import declarative_base
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+except ImportError: # sqlalchemy < 1.4
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+ from sqlalchemy.ext.declarative import declarative_base
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+
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from ..utils import listify
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from .writing import build_path, write_to_file
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from ..config import get_option
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diff --git a/setup.cfg b/setup.cfg
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index 5a901aa6..8d23fa8c 100644
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--- a/setup.cfg
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+++ b/setup.cfg
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@@ -27,7 +27,7 @@ install_requires =
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nibabel >=2.1
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pandas >=0.23
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formulaic >=0.2.4, <0.4 # Tested on 0.2.4 and 0.3.2
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- sqlalchemy <1.4.0.dev0
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+ sqlalchemy
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bids-validator
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num2words
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click >=8.0
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--
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2.39.2
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From d167ba66c01352fedc59fc50d04967c0cd13d8cd Mon Sep 17 00:00:00 2001
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From: Chris Markiewicz <effigies@gmail.com>
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Date: Mon, 24 Apr 2023 09:44:12 -0400
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Subject: [PATCH 2/3] FIX: Accept more precise proxied error for duplicate
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config
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---
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bids/layout/tests/test_models.py | 3 ++-
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1 file changed, 2 insertions(+), 1 deletion(-)
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diff --git a/bids/layout/tests/test_models.py b/bids/layout/tests/test_models.py
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index 2f7862fa..0e1e5b59 100644
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--- a/bids/layout/tests/test_models.py
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+++ b/bids/layout/tests/test_models.py
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@@ -179,7 +179,8 @@ def test_load_existing_config():
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session.commit()
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from sqlalchemy.orm.exc import FlushError
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- with pytest.raises(FlushError):
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+ from sqlalchemy.exc import DBAPIError
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+ with pytest.raises((FlushError, DBAPIError)):
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second = Config.load({"name": "dummy"})
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session.add(second)
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session.commit()
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--
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2.39.2
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From 4c91c328cf500a2acc0a3908411f210bf20e57d4 Mon Sep 17 00:00:00 2001
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From: Chris Markiewicz <effigies@gmail.com>
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Date: Mon, 24 Apr 2023 09:44:27 -0400
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Subject: [PATCH 3/3] TEST: Yield from fixture to avoid session going out of
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scope
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---
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bids/layout/tests/test_writing.py | 2 +-
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1 file changed, 1 insertion(+), 1 deletion(-)
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diff --git a/bids/layout/tests/test_writing.py b/bids/layout/tests/test_writing.py
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index dde6b3a1..ad74785a 100644
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--- a/bids/layout/tests/test_writing.py
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+++ b/bids/layout/tests/test_writing.py
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@@ -37,7 +37,7 @@ def writable_file(tmpdir):
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session.add_all(list(ents.values()) + tags + [bf])
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session.commit()
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- return bf
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+ yield bf
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@pytest.fixture(scope='module')
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--
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2.39.2
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