Support psycopg 3.x (#268)

* Replace setup.cfg/.py with pyproject.toml

* Support linting with flake8 or ruff and fix some linting issues

* Fix test issues

* Update workflows

* Use uv in workflow for faster install

* Change default postgres username in workflow

* Delete STYLE.rst

* Update changelog

* Support psycopg 3.x

* Add documentation for the new connection flags

* Update changelog

* Make sdssdb.use_psycopg3 a boolean

CHANGELOG.rst

@@ -7,6 +7,7 @@ This document records the main changes to the ``sdssdb`` code.
 
 * :feature:`264` Add metadata for the ``sdss_id_to_catalog`` table.
 * :feature:`266` Support PEP 621.
+* :feature:`268` Allows to use `psycopy3 <https://www.psycopg.org/psycopg3/docs/>`__ as a driver for the Peewee database connection.
 * Add missing columns to the ``SDSS_ID_To_Catalog`` models (the columns were being completed via reflection).
 * Change ``reflection=False`` to ``use_reflection=False`` in many ``catalogdb`` models. The previous setting was incorrect and was causing the models to be reflected.
 * Add ``gortdb`` schema and models to ``lvmdb``. Moved ``lvmopsdb.overhead`` to ``gortdb``.

docs/sphinx/intro.rst

@@ -245,7 +245,7 @@ There are two database connections, ``SQLADatabaseConnection`` and ``PeeWeeDatab
 
 
 A note about passwords
-----------------------
+^^^^^^^^^^^^^^^^^^^^^^
 
 ``sdssdb`` does not allow you to pass plaintext passwords when creating a connection, or to store them in the profiles. Instead, you should use `pgpass <https://www.postgresql.org/docs/9.3/libpq-pgpass.html>`__ to set your passwords. A typical ``~/.pgpass`` file looks something like ::
 
@@ -256,6 +256,22 @@ A note about passwords
 where ``XXXX``, ``YYYY``, etc are the associated passwords for each set of parameters.
 
 
+Connection flags
+^^^^^^^^^^^^^^^^
+
+``sdssdb`` supports two flags that change the behaviour of the database connection.
+
+* **autoconnect**: if set to `False` the connection will not attempt to connect to the database when created. This is useful when you want to create a connection object but connect to the database later. ``autoconnect`` defaults to `True` and can be changed either by setting the environment variable ``SDSSDB_AUTOCONNECT=0`` before importing the model classes, or by doing ::
+
+        >>> import sdssdb
+        >>> sdssdb.autoconnect = False
+        ... import your model classes ...
+
+  When instantiating a `.DatabaseConnection` object manually, you can also pass the ``autoconnect=False`` keyword argument.
+
+* **use_psycopg3**: prefers to use `psycopg3 <https://www.psycopg.org/psycopg3/docs/>`__ instead of the default ``psycopg2``. If ``psycopg3`` is not installed, ``psycopg2`` will be used instead. This flag can be set via the environment variable ``SDSSDB_PSYCOPG3=1`` or by importing ``sdssdb`` and setting ``sdssdb.use_psycopg3 = True`` before importing the model classes.
+
+
 .. _profile:
 
 Supported Profiles

pyproject.toml

@@ -30,14 +30,15 @@ content-type = "text/markdown"
 
 [project.optional-dependencies]
 all = [
+    "psycopg[binary]",
     "progressbar2>=3.46.1",
     "pydot>=1.4.1",
     "astropy>=4.0.0",
     "pandas>=1.0.0",
     "inflect>=4.1.0",
     "h5py>=3.8.0",
     "sdssdb[dev]",
-    "sdssdb[docs]",
+    "sdssdb[docs]"
 ]
 dev = [
     "pytest>=5.2",
@@ -145,5 +146,8 @@ sdss = ["sdsstools"]
 sqla = ["sqlalchemy"]
 peewee = ["peewee", "playhouse"]
 
+[tool.ruff.format]
+preview = true
+
 [tool.coverage.run]
 branch = true

python/sdssdb/__init__.py

@@ -1,5 +1,6 @@
 # encoding: utf-8
 
+import os
 import warnings
 
 from sqlalchemy.exc import MovedIn20Warning
@@ -32,6 +33,8 @@
 config = get_config(NAME)
 
 autoconnect = True
+use_psycopg3 = os.environ.get("SDSSDB_PSYCOPG3", "false").lower() in ["true", "1"]
+
 
 from .connection import PeeweeDatabaseConnection  # noqa
 from .connection import SQLADatabaseConnection  # noqa

python/sdssdb/connection.py

@@ -13,6 +13,7 @@
 import os
 import re
 import socket
+import warnings
 
 import pgpasslib
 import six
@@ -23,18 +24,30 @@
 from sqlalchemy.orm import scoped_session, sessionmaker
 
 import peewee
-from peewee import OperationalError, PostgresqlDatabase
+from peewee import OperationalError
 from playhouse.postgres_ext import ArrayField
 from playhouse.reflection import Introspector, UnknownField
 
 import sdssdb
-from sdssdb import config, log
+from sdssdb import config, log, use_psycopg3
 from sdssdb.utils.internals import get_database_columns
 
 
 __all__ = ["DatabaseConnection", "PeeweeDatabaseConnection", "SQLADatabaseConnection"]
 
 
+if use_psycopg3 is True:
+    try:
+        import psycopg  # noqa
+        from playhouse.psycopg3_ext import Psycopg3Database as PostgresqlDatabase
+    except ImportError:
+        warnings.warn("psycopg3 is not installed. Using psycopg2.")
+        from peewee import PostgresqlDatabase
+
+else:
+    from peewee import PostgresqlDatabase
+
+
 def _should_autoconnect():
     """Determines whether we should autoconnect."""
 
@@ -62,7 +75,7 @@ def get_database_uri(
     else:
         auth: str = f"{user}:{password}@"
 
-    host_port: str = f"{host or ''}" if port is None else f"{host or ''}:{port}"
+    host_port: str = f"{host or ""}" if port is None else f"{host or ""}:{port}"
 
     if auth == "" and host_port == "":
         return f"postgresql://{dbname}"
@@ -132,7 +145,10 @@ def __init__(self, dbname=None, profile=None, autoconnect=None, dbversion=None):
 
     def __repr__(self):
         return "<{} (dbname={!r}, profile={!r}, connected={})>".format(
-            self.__class__.__name__, self.dbname, self.profile, self.connected
+            self.__class__.__name__,
+            self.dbname,
+            self.profile,
+            self.connected,
         )
 
     def set_profile(self, profile=None, connect=True, **params):