HDXDSYS-409 Update all libraries to latest build stack

.config/pre-commit-config.yaml → .pre-commit-config.yaml

@@ -12,10 +12,9 @@ repos:
     hooks:
       # Run the linter.
       - id: ruff
-        args: [--config, .config/ruff.toml, --fix]
+        args: [ --fix ]
       # Run the formatter.
       - id: ruff-format
-        args: [--config, .config/ruff.toml]
   - repo: https://github.com/astral-sh/uv-pre-commit
     rev: 0.6.5
     hooks:

documentation/mkdocs.yaml

@@ -12,5 +12,7 @@ plugins:
 nav:
   - Home: index.md
   - API Documentation:
-    - Database: $src/hdx.database.database.*
+    - Database:
+      - $src/hdx.database.Database
+      - $src/hdx.database.DatabaseError
     - PostgreSQL specific: $src/hdx.database.postgresql.*

hatch.toml

@@ -0,0 +1,34 @@
+# Build
+
+[build.targets.wheel]
+packages = ["src/hdx"]
+
+[build.hooks.vcs]
+version-file = "src/hdx/database/_version.py"
+
+# Versioning
+
+[version]
+source = "vcs"
+
+[version.raw-options]
+local_scheme = "no-local-version"
+version_scheme = "python-simplified-semver"
+
+# Tests
+
+[envs.hatch-test]
+features = ["test"]
+
+[[envs.hatch-test.matrix]]
+python = ["3.12"]
+
+[envs.hatch-test.scripts]
+run = """
+       pytest --rootdir=. --junitxml=test-results.xml --cov --no-cov-on-fail \
+       --cov-report=lcov --cov-report=term-missing
+       """
+
+[envs.hatch-static-analysis]
+config-path = "none"
+dependencies = ["ruff==0.9.10"]

pyproject.toml

@@ -48,52 +48,6 @@ Homepage = "https://github.com/OCHA-DAP/hdx-python-database"
 [project.optional-dependencies]
 sshtunnel = ["sshtunnel"]
 postgresql = ["psycopg[binary]"]
-test = ["pytest", "pytest-cov"]
+test = ["sshtunnel", "psycopg[binary]", "pytest", "pytest-cov"]
 dev = ["pre-commit"]
 docs = ["mkapi"]
-
-
-#########
-# Hatch #
-#########
-
-# Build
-
-[tool.hatch.build.targets.wheel]
-packages = ["src/hdx"]
-
-[tool.hatch.build.hooks.vcs]
-version-file = "src/hdx/database/_version.py"
-
-# Versioning
-
-[tool.hatch.version]
-source = "vcs"
-
-[tool.hatch.version.raw-options]
-local_scheme = "no-local-version"
-version_scheme = "python-simplified-semver"
-
-# Tests
-
-[tool.hatch.envs.hatch-test]
-features = ["sshtunnel", "postgresql", "test"]
-
-[[tool.hatch.envs.hatch-test.matrix]]
-python = ["3.12"]
-
-[tool.hatch.envs.hatch-test.scripts]
-run = """
-       pytest -c .config/pytest.ini --rootdir=. --junitxml=test-results.xml \
-       --cov --cov-config=.config/coveragerc --no-cov-on-fail \
-       --cov-report=lcov --cov-report=term-missing
-       """
-
-[tool.hatch.envs.hatch-static-analysis]
-dependencies = ["ruff==0.9.10"]
-
-[tool.hatch.envs.hatch-static-analysis.scripts]
-format-check = ["ruff format --config .config/ruff.toml --check --diff {args:.}",]
-format-fix = ["ruff format --config .config/ruff.toml {args:.}",]
-lint-check = ["ruff check --config .config/ruff.toml {args:.}",]
-lint-fix = ["ruff check --config .config/ruff.toml --fix {args:.}",]

.config/pytest.ini → pytest.ini

@@ -1,4 +1,4 @@
 [pytest]
-pythonpath = ../src
+pythonpath = src
 addopts = "--color=yes"
 log_cli = 1

requirements.txt

@@ -1,83 +1,78 @@
 # This file was autogenerated by uv via the following command:
 #    uv pip compile pyproject.toml --resolver=backtracking --all-extras -o requirements.txt
-astdoc==1.1.5
+astdoc==1.2.1
     # via mkapi
 babel==2.17.0
     # via mkdocs-material
 backrefs==5.8
     # via mkdocs-material
 bcrypt==4.3.0
     # via paramiko
-certifi==2025.1.31
+certifi==2025.4.26
     # via requests
 cffi==1.17.1
     # via
     #   cryptography
     #   pynacl
 cfgv==3.4.0
     # via pre-commit
-charset-normalizer==3.4.1
+charset-normalizer==3.4.2
     # via requests
 click==8.1.8
     # via mkdocs
 colorama==0.4.6
     # via mkdocs-material
-coverage==7.7.0
+coverage==7.8.0
     # via pytest-cov
-cryptography==44.0.2
+cryptography==44.0.3
     # via paramiko
 distlib==0.3.9
     # via virtualenv
 filelock==3.18.0
     # via virtualenv
 ghp-import==2.1.0
     # via mkdocs
-greenlet==3.1.1
+greenlet==3.2.1
     # via sqlalchemy
-identify==2.6.9
+identify==2.6.10
     # via pre-commit
 idna==3.10
     # via requests
-iniconfig==2.0.0
+iniconfig==2.1.0
     # via pytest
 jinja2==3.1.6
     # via
     #   mkapi
     #   mkdocs
     #   mkdocs-material
-markdown==3.7
+markdown==3.8
     # via
-    #   astdoc
     #   mkdocs
     #   mkdocs-material
     #   pymdown-extensions
-markdown-it-py==3.0.0
-    # via rich
 markupsafe==3.0.2
     # via
     #   jinja2
     #   mkdocs
-mdurl==0.1.2
-    # via markdown-it-py
 mergedeep==1.3.4
     # via
     #   mkdocs
     #   mkdocs-get-deps
-mkapi==4.1.3
+mkapi==4.3.2
     # via hdx-python-database (pyproject.toml)
 mkdocs==1.6.1
     # via
     #   mkapi
     #   mkdocs-material
 mkdocs-get-deps==0.2.0
     # via mkdocs
-mkdocs-material==9.6.8
+mkdocs-material==9.6.12
     # via mkapi
 mkdocs-material-extensions==1.3.1
     # via mkdocs-material
 nodeenv==1.9.1
     # via pre-commit
-packaging==24.2
+packaging==25.0
     # via
     #   mkdocs
     #   pytest
@@ -87,33 +82,31 @@ paramiko==3.5.1
     # via sshtunnel
 pathspec==0.12.1
     # via mkdocs
-platformdirs==4.3.6
+platformdirs==4.3.7
     # via
     #   mkdocs-get-deps
     #   virtualenv
 pluggy==1.5.0
     # via pytest
-pre-commit==4.1.0
+pre-commit==4.2.0
     # via hdx-python-database (pyproject.toml)
-psycopg==3.2.6
+psycopg==3.2.7
     # via hdx-python-database (pyproject.toml)
-psycopg-binary==3.2.6
+psycopg-binary==3.2.7
     # via psycopg
 pycparser==2.22
     # via cffi
 pygments==2.19.1
-    # via
-    #   mkdocs-material
-    #   rich
-pymdown-extensions==10.14.3
+    # via mkdocs-material
+pymdown-extensions==10.15
     # via mkdocs-material
 pynacl==1.5.0
     # via paramiko
 pytest==8.3.5
     # via
     #   hdx-python-database (pyproject.toml)
     #   pytest-cov
-pytest-cov==6.0.0
+pytest-cov==6.1.1
     # via hdx-python-database (pyproject.toml)
 python-dateutil==2.9.0.post0
     # via ghp-import
@@ -128,21 +121,19 @@ pyyaml-env-tag==0.1
     # via mkdocs
 requests==2.32.3
     # via mkdocs-material
-rich==13.9.4
-    # via mkapi
 six==1.17.0
     # via python-dateutil
-sqlalchemy==2.0.39
+sqlalchemy==2.0.40
     # via hdx-python-database (pyproject.toml)
 sshtunnel==0.4.0
     # via hdx-python-database (pyproject.toml)
-typing-extensions==4.12.2
+typing-extensions==4.13.2
     # via
     #   psycopg
     #   sqlalchemy
-urllib3==2.3.0
+urllib3==2.4.0
     # via requests
-virtualenv==20.29.3
+virtualenv==20.31.1
     # via pre-commit
 watchdog==6.0.0
     # via mkdocs

.config/ruff.toml → ruff.toml

@@ -1,4 +1,3 @@
-line-length = 79
 exclude = ["_version.py"]
 
 [lint]

src/hdx/database/database.py

@@ -281,9 +281,7 @@ def create_session(
             engine = create_engine(db_uri, poolclass=NullPool, echo=False)
         if reflect:
             Base = automap_base(declarative_base=table_base)
-            Base.prepare(
-                autoload_with=engine, reflection_options={"views": True}
-            )
+            Base.prepare(autoload_with=engine, reflection_options={"views": True})
             table_base = Base
         else:
             table_base.metadata.create_all(engine)
@@ -307,9 +305,7 @@ def recreate_schema(engine: Engine, schema_name: str = "public") -> bool:
                     DropSchema(schema_name, cascade=True, if_exists=True)
                 )
                 connection.commit()
-                connection.execute(
-                    CreateSchema(schema_name, if_not_exists=True)
-                )
+                connection.execute(CreateSchema(schema_name, if_not_exists=True))
                 connection.commit()
                 return True
         except SQLAlchemyError:

src/hdx/database/utils.py

@@ -13,7 +13,5 @@ def camel_to_snake_case(string: str) -> str:
     Returns:
         str: String in snake case
     """
-    string = re.sub(
-        r"((?<=[a-z0-9])[A-Z]|(?!^)[A-Z](?=[a-z]))", r"_\1", string
-    )
+    string = re.sub(r"((?<=[a-z0-9])[A-Z]|(?!^)[A-Z](?=[a-z]))", r"_\1", string)
     return string.lower().lstrip("_")

tests/hdx/database/test_database.py

@@ -45,9 +45,7 @@ def prepare_fn():
             now = datetime(2023, 10, 20, 22, 35, 55, tzinfo=timezone.utc)
             rows = [{"test_date": now}]
             dbdatabase.batch_populate(rows, DBTestDate)
-            dbtestdate = (
-                dbsession.execute(select(DBTestDate)).all()[1][0].test_date
-            )
+            dbtestdate = dbsession.execute(select(DBTestDate)).all()[1][0].test_date
             assert dbtestdate == now
 
         remove(dbpath)

tests/hdx/database/test_dburi.py

@@ -17,9 +17,7 @@ class TestDBURI:
         "dialect": "postgresql",
         "driver": "psycopg",
     }
-    connection_uri_pg = (
-        "postgresql+psycopg://myuser:mypass@myserver:1234/mydatabase"
-    )
+    connection_uri_pg = "postgresql+psycopg://myuser:mypass@myserver:1234/mydatabase"
     params_pg_no_driver = {
         "database": "mydatabase",
         "host": "myserver",
@@ -37,9 +35,7 @@ class TestDBURI:
         "dialect": "postgresql",
         "driver": None,
     }
-    connection_uri_pg_no_driver = (
-        "postgresql://myuser:mypass@myserver:1234/mydatabase"
-    )
+    connection_uri_pg_no_driver = "postgresql://myuser:mypass@myserver:1234/mydatabase"
     params_sq_no_driver = {
         "database": "mydatabase",
         "host": "myserver",
@@ -67,19 +63,15 @@ def test_get_params_from_connection_uri(self):
             include_driver=False,
         )
         assert result == TestDBURI.params_pg_no_driver
-        result = get_params_from_connection_uri(
-            TestDBURI.connection_uri_pg_no_driver
-        )
+        result = get_params_from_connection_uri(TestDBURI.connection_uri_pg_no_driver)
         assert result == TestDBURI.params_pg_driver_none
         result = get_params_from_connection_uri(TestDBURI.connection_uri_sq)
         assert result == TestDBURI.params_sq_driver_none
 
     def test_get_connection_uri(self):
         result = get_connection_uri(**TestDBURI.params_pg)
         assert result == TestDBURI.connection_uri_pg
-        result = get_connection_uri(
-            **TestDBURI.params_pg, include_driver=False
-        )
+        result = get_connection_uri(**TestDBURI.params_pg, include_driver=False)
         assert result == TestDBURI.connection_uri_pg_no_driver
         result = get_connection_uri(**TestDBURI.params_pg_no_driver)
         assert result == TestDBURI.connection_uri_pg

tests/hdx/database/test_ssh.py

@@ -53,9 +53,7 @@ def test_get_session_ssh(
             )
             assert dbdatabase._base == NoTZBase
 
-        with Database(
-            ssh_host="mysshhost", ssh_port=25, **params
-        ) as dbdatabase:
+        with Database(ssh_host="mysshhost", ssh_port=25, **params) as dbdatabase:
             dbsession = dbdatabase.get_session()
             assert (
                 str(dbsession.bind.engine.url)