Add table_base parameter

Bring requirements up to date
Bring precommit config up to date

.config/pre-commit-config.yaml

@@ -2,23 +2,22 @@ default_language_version:
     python: python3.11
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: check-ast
-  - repo: https://github.com/psf/black
-    rev: 23.3.0
-    hooks:
-      - id: black
-        args: [--config, .config/black.toml]
-  - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.267
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.14
     hooks:
+      # Run the linter.
       - id: ruff
-        args: [--config, .config/ruff.toml, --fix, --exit-non-zero-on-fix]
+        args: [--config, .config/ruff.toml, --fix]
+      # Run the formatter.
+      - id: ruff-format
+        args: [--config, .config/ruff.toml]
   - repo: https://github.com/jazzband/pip-tools
-    rev: 6.13.0
+    rev: 7.3.0
     hooks:
       - id: pip-compile
         name: pip-compile requirements.txt

.config/ruff.toml

@@ -1,14 +1,16 @@
 line-length = 79
 exclude = ["_version.py"]
-ignore = [
-    "E501" # Line too long
-]
-# List of rules: https://beta.ruff.rs/docs/rules/
+
+[lint]
+# List of rules: https://docs.astral.sh/ruff/rules/
 select = [
   "E",   # pycodestyle - default
   "F",   # pyflakes - default
   "I"    # isort
 ]
+ignore = [
+    "E501" # Line too long
+]
 
-[isort]
+[lint.isort]
 known-local-folder = ["hdx"]

CONTRIBUTING.md

@@ -21,14 +21,13 @@ you make a git commit:
     pre-commit install
 
 The configuration file for this project is in a
-non-start location. Thus, you will need to edit your
+non-standard location. Thus, you will need to edit your
 `.git/hooks/pre-commit` file to reflect this. Change
 the line that begins with `ARGS` to:
 
     ARGS=(hook-impl --config=.config/pre-commit-config.yaml --hook-type=pre-commit)
 
 With pre-commit, all code is formatted according to
-[black]("https://github.com/psf/black") and
 [ruff]("https://github.com/charliermarsh/ruff") guidelines.
 
 To check if your changes pass pre-commit without committing, run:
@@ -41,7 +40,7 @@ To run the tests and view coverage, execute:
 
     pytest -c .config/pytest.ini --cov hdx --cov-config .config/coveragerc
 
-Follow the example set out already in ``api.rst`` as you write the documentation.
+Follow the example set out already in ``documentation/main.md`` as you write the documentation.
 
 ## Packages
 

pyproject.toml

@@ -86,22 +86,14 @@ test = """
        """
 
 [[tool.hatch.envs.test.matrix]]
-python = ["3.11"]
+python = ["3.12"]
 
 [tool.hatch.envs.lint]
 detached = true
-dependencies = [
-  "black",
-  "ruff",
-]
+dependencies = ["ruff"]
 
 [tool.hatch.envs.lint.scripts]
 style = [
-  "ruff --config .config/ruff.toml {args:.}",
-  "black --config .config/black.toml --check --diff {args:.}",
-]
-# Not used for anything at the moment
-fmt = [
-  "black --config .config/black.toml {args:.}",
-  "ruff --config .config/ruff.toml --fix {args:.}",
+  "ruff check --config .config/ruff.toml --diff {args:.}",
+  "ruff format --config .config/ruff.toml --diff {args:.}",
 ]

requirements.txt

@@ -4,65 +4,65 @@
 #
 #    pip-compile --all-extras --output-file=requirements.txt --resolver=backtracking pyproject.toml
 #
-bcrypt==4.0.1
+bcrypt==4.1.2
     # via paramiko
 cffi==1.16.0
     # via
     #   cryptography
     #   pynacl
 cfgv==3.4.0
     # via pre-commit
-coverage[toml]==7.3.2
+coverage[toml]==7.4.1
     # via pytest-cov
-cryptography==41.0.4
+cryptography==42.0.2
     # via paramiko
-distlib==0.3.7
+distlib==0.3.8
     # via virtualenv
-filelock==3.12.4
+filelock==3.13.1
     # via virtualenv
-greenlet==3.0.0
+greenlet==3.0.3
     # via sqlalchemy
-identify==2.5.30
+identify==2.5.34
     # via pre-commit
 iniconfig==2.0.0
     # via pytest
 nodeenv==1.8.0
     # via pre-commit
 packaging==23.2
     # via pytest
-paramiko==3.3.1
+paramiko==3.4.0
     # via sshtunnel
-platformdirs==3.11.0
+platformdirs==4.2.0
     # via virtualenv
-pluggy==1.3.0
+pluggy==1.4.0
     # via pytest
-pre-commit==3.4.0
+pre-commit==3.6.1
     # via hdx-python-database (pyproject.toml)
-psycopg[binary]==3.1.12
+psycopg[binary]==3.1.18
     # via hdx-python-database (pyproject.toml)
-psycopg-binary==3.1.12
+psycopg-binary==3.1.18
     # via psycopg
 pycparser==2.21
     # via cffi
 pynacl==1.5.0
     # via paramiko
-pytest==7.4.2
+pytest==8.0.0
     # via
     #   hdx-python-database (pyproject.toml)
     #   pytest-cov
 pytest-cov==4.1.0
     # via hdx-python-database (pyproject.toml)
 pyyaml==6.0.1
     # via pre-commit
-sqlalchemy==2.0.21
+sqlalchemy==2.0.27
     # via hdx-python-database (pyproject.toml)
 sshtunnel==0.4.0
     # via hdx-python-database (pyproject.toml)
-typing-extensions==4.8.0
+typing-extensions==4.9.0
     # via
     #   psycopg
     #   sqlalchemy
-virtualenv==20.24.5
+virtualenv==20.25.0
     # via pre-commit
 
 # The following packages are considered to be unsafe in a requirements file:

src/hdx/database/__init__.py

@@ -23,7 +23,7 @@ class Database:
     reflected classes. db_has_tz which defaults to False indicates whether
     database datetime columns have timezones. If not, conversion occurs between
     Python datetimes with timezones to timezoneless database columns (but not
-    when using reflection).
+    when using reflection). If table_base is supplied, db_has_tz is ignored.
 
     Args:
         database (Optional[str]): Database name
@@ -34,6 +34,7 @@ class Database:
         dialect (str): Database dialect. Defaults to "postgresql".
         driver (Optional[str]): Database driver. Defaults to None (psycopg if postgresql or None)
         db_has_tz (bool): True if db datetime columns have timezone. Defaults to False.
+        table_base (Optional[Type[DeclarativeBase]]): Override table base. Defaults to None.
         reflect (bool): Whether to reflect existing tables. Defaults to False.
         **kwargs: See below
         ssh_host (str): SSH host (the server to connect to)
@@ -55,6 +56,7 @@ def __init__(
         dialect: str = "postgresql",
         driver: Optional[str] = None,
         db_has_tz: bool = False,
+        table_base: Optional[Type[DeclarativeBase]] = None,
         reflect: bool = False,
         **kwargs: Any,
     ) -> None:
@@ -98,10 +100,11 @@ def __init__(
         )
         if dialect == "postgresql":
             wait_for_postgresql(db_uri)
-        if db_has_tz:
-            table_base = TZBase
-        else:
-            table_base = NoTZBase
+        if not table_base:
+            if db_has_tz:
+                table_base = TZBase
+            else:
+                table_base = NoTZBase
         self.session = self.get_session(
             db_uri, table_base=table_base, reflect=reflect
         )

tests/hdx/database/test_database.py

@@ -140,3 +140,11 @@ def test_get_session_ssh(self, mock_psycopg, mock_SSHTunnelForwarder):
                 == "postgresql+psycopg://myuser@0.0.0.0:12345/mydatabase"
             )
             assert TestDatabase.table_base == TZBase
+        with Database(
+            ssh_host="mysshhost", ssh_port=25, table_base=TZBase, **params
+        ) as dbsession:
+            assert (
+                str(dbsession.bind.engine.url)
+                == "postgresql+psycopg://myuser@0.0.0.0:12345/mydatabase"
+            )
+            assert TestDatabase.table_base == TZBase