SQLAlchemy 1.4 (#54)

* change models for SQLA 1.4 * ci: add Debian 12, remove Debian 10 --------- Co-authored-by: Jacques Fize <[email protected]>
PnX-SI · Dec 6, 2023 · 4125f81 · 4125f81
1 parent f9102ca
commit 4125f81
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diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
@@ -18,28 +18,17 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        debian-version: [ "10", "11" ]
-        sqlalchemy-version: [ "1.3", "1.4" ]
+        debian-version: [ "11", "12" ]
+        sqlalchemy-version: [ "1.4" ]
         include:
-          - debian-version: "10"
-            python-version: "3.7"
-            postgres-version: 11
-            postgis-version: 2.5
           - debian-version: "11"
             python-version: "3.9"
-            postgres-version: 13
-            postgis-version: 3.2
-          - sqlalchemy-version: '1.3'
-            sqlalchemy-lt-version: '1.4'
-            flask-sqlalchemy-version: '2'
-            flask-sqlalchemy-lt-version: '3'
-          - sqlalchemy-version: '1.4'
-            sqlalchemy-lt-version: '2'
-            flask-sqlalchemy-version: '3'
-            flask-sqlalchemy-lt-version: '4'
-        exclude:
-          - debian-version: "10"
-            sqlalchemy-version: "1.4"
+            postgres-version: "13"
+            postgis-version: "3.2"
+          - debian-version: "12"
+            python-version: "3.11"
+            postgres-version: "15"
+            postgis-version: "3.3"
 
     name: Debian ${{ matrix.debian-version }} - SQLAlchemy ${{ matrix.sqlalchemy-version }}
 
@@ -59,14 +48,9 @@ jobs:
           --health-retries 5
 
     steps:
-    - name: Add postgis_raster database extension
-      if: ${{ matrix.postgis-version >= 3 }}
-      run: |
-        psql -h localhost -U postgres -d postgres -tc 'CREATE EXTENSION "postgis_raster";'
-      env:
-        PGPASSWORD: postgres
     - name: Add database extensions
       run: |
+        psql -h localhost -U postgres -d postgres -tc 'CREATE EXTENSION "postgis_raster";'
         psql -h localhost -U postgres -d postgres -tc 'CREATE EXTENSION "uuid-ossp";'
         psql -h localhost -U postgres -d postgres -tc 'CREATE EXTENSION "pg_trgm";'
       env:
@@ -86,9 +70,7 @@ jobs:
           -e .[tests] \
           -e file:dependencies/Utils-Flask-SQLAlchemy#egg=utils-flask-sqlalchemy \
           -e file:dependencies/TaxHub#egg=taxhub \
-          -e file:dependencies/UsersHub-authentification-module#egg=pypnusershub \
-          "sqlalchemy>=${{ matrix.sqlalchemy-version }},<${{ matrix.sqlalchemy-lt-version }}" \
-          "flask-sqlalchemy>=${{ matrix.flask-sqlalchemy-version }},<${{ matrix.flask-sqlalchemy-lt-version }}"
+          -e file:dependencies/UsersHub-authentification-module#egg=pypnusershub
     - name: Install database
       run: |
         flask db upgrade ref_geo@head -x local-srid=2154
@@ -104,7 +86,7 @@ jobs:
       env:
         NOMENCLATURE_SETTINGS: test_settings.py
     - name: Upload coverage to Codecov
-      if: ${{ matrix.debian-version == '11' && matrix.sqlalchemy-version == '1.4' }}
+      if: ${{ matrix.debian-version == '12' && matrix.sqlalchemy-version == '1.4' }}
       uses: codecov/codecov-action@v3
       with:
         flags: pytest
diff --git a/requirements.in b/requirements.in
@@ -7,7 +7,7 @@ psycopg2
 flask-marshmallow
 marshmallow-sqlalchemy
 shapely<2
-sqlalchemy>=1.3,<2
+sqlalchemy>=1.4,<2
 
 utils-flask-sqlalchemy>=0.3.0
 taxhub>=1.10.0

diff --git a/src/pypnnomenclature/models.py b/src/pypnnomenclature/models.py
@@ -47,7 +47,10 @@ class TNomenclatures(db.Model):
     id_type = db.Column(
         db.Integer, ForeignKey("ref_nomenclatures.bib_nomenclatures_types.id_type")
     )
-    nomenclature_type = relationship("BibNomenclaturesTypes", backref="nomenclatures")
+    nomenclature_type = relationship(
+        "BibNomenclaturesTypes",
+        backref="nomenclatures",
+    )
     cd_nomenclature = db.Column(db.Unicode)
     mnemonique = db.Column(db.Unicode)
     label_default = db.Column(db.Unicode)
@@ -73,14 +76,12 @@ class TNomenclatures(db.Model):
     @staticmethod
     def get_default_nomenclature(mnemonique, id_organism=0):
         q = select(
-            [
-                func.ref_nomenclatures.get_default_nomenclature_value(
-                    mnemonique, id_organism
-                ).label("default")
-            ]
+            func.ref_nomenclatures.get_default_nomenclature_value(mnemonique, id_organism).label(
+                "default"
+            )
         )
         result = db.session.execute(q)
-        return result.fetchone()["default"]
+        return result.fetchone().default
 
 
 class TNomenclatureTaxonomy(TNomenclatures):
@@ -127,7 +128,7 @@ def get_default_nomenclature(mnemonique, id_organism=0):
             ]
         )
         result = db.session.execute(q)
-        return result.fetchone()["default"]
+        return result.fetchone().default
 
 
 class BibNomenclaturesTypeTaxo(BibNomenclaturesTypes):
@@ -140,6 +141,7 @@ class BibNomenclaturesTypeTaxo(BibNomenclaturesTypes):
         primaryjoin="and_(TNomenclatureTaxonomy.id_type == BibNomenclaturesTypes.id_type, TNomenclatureTaxonomy.active == True)",
         lazy="joined",
         order_by="TNomenclatureTaxonomy.hierarchy",
+        viewonly=True,
     )