diff --git a/.gitignore b/.gitignore
index b6e4761..10cf3b7 100644
--- a/.gitignore
+++ b/.gitignore
@@ -27,6 +27,9 @@ share/python-wheels/
*.egg
MANIFEST
+# Jetbrains stuff
+.idea
+
# PyInstaller
# Usually these files are written by a python script from a template
# before PyInstaller builds the exe, so as to inject date/other infos into it.
diff --git a/.idea/misc.xml b/.idea/misc.xml
index 3a2a2ad..0d0f1d3 100644
--- a/.idea/misc.xml
+++ b/.idea/misc.xml
@@ -4,7 +4,7 @@
-
+
\ No newline at end of file
diff --git a/.idea/python-libraries.iml b/.idea/python-libraries.iml
index 92fb703..1d67f67 100644
--- a/.idea/python-libraries.iml
+++ b/.idea/python-libraries.iml
@@ -1,5 +1,10 @@
+
+
+
+
+
@@ -18,6 +23,7 @@
+
diff --git a/Makefile b/Makefile
index 22b2f89..927f4ef 100644
--- a/Makefile
+++ b/Makefile
@@ -14,4 +14,4 @@ format:
poetry run black .
test:
- poetry run pytest -s -x
\ No newline at end of file
+ poetry run pytest -s -x
diff --git a/auth-system/poetry.lock b/auth-system/poetry.lock
index 336e7a4..9135f1d 100644
--- a/auth-system/poetry.lock
+++ b/auth-system/poetry.lock
@@ -48,39 +48,63 @@ trio = ["trio (<0.22)"]
[[package]]
name = "bcrypt"
-version = "4.2.0"
+version = "4.3.0"
description = "Modern password hashing for your software and your servers"
optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
groups = ["main"]
files = [
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]
[package.extras]
@@ -89,107 +113,124 @@ typecheck = ["mypy"]
[[package]]
name = "certifi"
-version = "2024.8.30"
+version = "2025.11.12"
description = "Python package for providing Mozilla's CA Bundle."
optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
groups = ["main"]
files = [
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- {file = "certifi-2024.8.30.tar.gz", hash = "sha256:bec941d2aa8195e248a60b31ff9f0558284cf01a52591ceda73ea9afffd69fd9"},
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]
[[package]]
name = "cffi"
-version = "1.17.1"
+version = "2.0.0"
description = "Foreign Function Interface for Python calling C code."
optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
groups = ["main"]
markers = "platform_python_implementation != \"PyPy\""
files = [
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+greenlet = {version = ">=1", markers = "platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\""}
typing-extensions = ">=4.6.0"
[package.extras]
-aiomysql = ["aiomysql (>=0.2.0)", "greenlet (!=0.4.17)"]
-aioodbc = ["aioodbc", "greenlet (!=0.4.17)"]
-aiosqlite = ["aiosqlite", "greenlet (!=0.4.17)", "typing_extensions (!=3.10.0.1)"]
-asyncio = ["greenlet (!=0.4.17)"]
-asyncmy = ["asyncmy (>=0.2.3,!=0.2.4,!=0.2.6)", "greenlet (!=0.4.17)"]
+aiomysql = ["aiomysql (>=0.2.0)", "greenlet (>=1)"]
+aioodbc = ["aioodbc", "greenlet (>=1)"]
+aiosqlite = ["aiosqlite", "greenlet (>=1)", "typing_extensions (!=3.10.0.1)"]
+asyncio = ["greenlet (>=1)"]
+asyncmy = ["asyncmy (>=0.2.3,!=0.2.4,!=0.2.6)", "greenlet (>=1)"]
mariadb-connector = ["mariadb (>=1.0.1,!=1.1.2,!=1.1.5,!=1.1.10)"]
mssql = ["pyodbc"]
mssql-pymssql = ["pymssql"]
@@ -1192,7 +1292,7 @@ mysql-connector = ["mysql-connector-python"]
oracle = ["cx_oracle (>=8)"]
oracle-oracledb = ["oracledb (>=1.0.1)"]
postgresql = ["psycopg2 (>=2.7)"]
-postgresql-asyncpg = ["asyncpg", "greenlet (!=0.4.17)"]
+postgresql-asyncpg = ["asyncpg", "greenlet (>=1)"]
postgresql-pg8000 = ["pg8000 (>=1.29.1)"]
postgresql-psycopg = ["psycopg (>=3.0.7)"]
postgresql-psycopg2binary = ["psycopg2-binary"]
@@ -1232,20 +1332,19 @@ url = ["furl (>=0.4.1)"]
[[package]]
name = "sqlparse"
-version = "0.4.4"
+version = "0.5.3"
description = "A non-validating SQL parser."
optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.8"
groups = ["main"]
files = [
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]
[package.extras]
-dev = ["build", "flake8"]
+dev = ["build", "hatch"]
doc = ["sphinx"]
-test = ["pytest", "pytest-cov"]
[[package]]
name = "starlette"
@@ -1267,50 +1366,106 @@ full = ["httpx (>=0.22.0)", "itsdangerous", "jinja2", "python-multipart", "pyyam
[[package]]
name = "tomli"
-version = "2.0.2"
+version = "2.3.0"
description = "A lil' TOML parser"
optional = false
python-versions = ">=3.8"
groups = ["dev"]
markers = "python_version < \"3.11\""
files = [
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- {file = "tomli-2.0.2.tar.gz", hash = "sha256:d46d457a85337051c36524bc5349dd91b1877838e2979ac5ced3e710ed8a60ed"},
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]
[[package]]
name = "typing-extensions"
-version = "4.12.2"
-description = "Backported and Experimental Type Hints for Python 3.8+"
+version = "4.15.0"
+description = "Backported and Experimental Type Hints for Python 3.9+"
optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
+groups = ["main", "dev"]
+files = [
+ {file = "typing_extensions-4.15.0-py3-none-any.whl", hash = "sha256:f0fa19c6845758ab08074a0cfa8b7aecb71c999ca73d62883bc25cc018c4e548"},
+ {file = "typing_extensions-4.15.0.tar.gz", hash = "sha256:0cea48d173cc12fa28ecabc3b837ea3cf6f38c6d1136f85cbaaf598984861466"},
+]
+markers = {dev = "python_version < \"3.11\""}
+
+[[package]]
+name = "typing-inspection"
+version = "0.4.2"
+description = "Runtime typing introspection tools"
+optional = false
+python-versions = ">=3.9"
groups = ["main"]
files = [
- {file = "typing_extensions-4.12.2-py3-none-any.whl", hash = "sha256:04e5ca0351e0f3f85c6853954072df659d0d13fac324d0072316b67d7794700d"},
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+ {file = "typing_inspection-0.4.2-py3-none-any.whl", hash = "sha256:4ed1cacbdc298c220f1bd249ed5287caa16f34d44ef4e9c3d0cbad5b521545e7"},
+ {file = "typing_inspection-0.4.2.tar.gz", hash = "sha256:ba561c48a67c5958007083d386c3295464928b01faa735ab8547c5692e87f464"},
]
+[package.dependencies]
+typing-extensions = ">=4.12.0"
+
[[package]]
name = "webargs"
-version = "8.6.0"
+version = "8.7.1"
description = "Declarative parsing and validation of HTTP request objects, with built-in support for popular web frameworks, including Flask, Django, Bottle, Tornado, Pyramid, Falcon, and aiohttp."
optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
groups = ["main"]
files = [
- {file = "webargs-8.6.0-py3-none-any.whl", hash = "sha256:83da4d7105643d0a50499b06d98a6ade1a330ce66d039eaa51f715172c704aba"},
- {file = "webargs-8.6.0.tar.gz", hash = "sha256:b8d098ab92bd74c659eca705afa31d681475f218cb15c1e57271fa2103c0547a"},
+ {file = "webargs-8.7.1-py3-none-any.whl", hash = "sha256:a184aed9d2509e6e14ab99ee3e9dc3a614c7070affe94cd4dfdb0d002e0a6e5f"},
+ {file = "webargs-8.7.1.tar.gz", hash = "sha256:799bf9039c76c23fd8dc1951107a75a9e561203c15d6ae8f89c1e46e234636c1"},
]
[package.dependencies]
-marshmallow = ">=3.0.0"
+marshmallow = ">=3.13.0,<5.0.0"
packaging = ">=17.0"
[package.extras]
-dev = ["pre-commit (>=3.5,<4.0)", "tox", "webargs[tests]"]
-docs = ["Sphinx (==8.0.2)", "furo (==2024.8.6)", "sphinx-issues (==4.1.0)", "webargs[frameworks]"]
+dev = ["pre-commit (>=3.5,<5.0)", "tox", "webargs[tests]"]
+docs = ["Sphinx (==8.2.3)", "furo (==2025.9.25)", "sphinx-issues (==5.0.1)", "webargs[frameworks]"]
frameworks = ["Django (>=2.2.0)", "Flask (>=0.12.5)", "aiohttp (>=3.0.8)", "bottle (>=0.12.13)", "falcon (>=2.0.0)", "pyramid (>=1.9.1)", "tornado (>=4.5.2)"]
-tests = ["pytest", "pytest-aiohttp (>=0.3.0)", "pytest-asyncio", "webargs[frameworks]", "webtest (==3.0.1)", "webtest-aiohttp (==2.0.0)"]
+tests = ["packaging (>=17.0)", "pytest", "pytest-aiohttp (>=0.3.0)", "pytest-asyncio", "webargs[frameworks]", "webtest (==3.0.7)", "webtest-aiohttp (==2.0.0)"]
[[package]]
name = "webargs-starlette"
@@ -1337,14 +1492,14 @@ tests = ["mock", "pytest", "webtest (>=2.0.32,<2.1.0)", "webtest-asgi (>=1.1.0,<
[[package]]
name = "werkzeug"
-version = "3.0.4"
+version = "3.1.3"
description = "The comprehensive WSGI web application library."
optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
groups = ["main"]
files = [
- {file = "werkzeug-3.0.4-py3-none-any.whl", hash = "sha256:02c9eb92b7d6c06f31a782811505d2157837cea66aaede3e217c7c27c039476c"},
- {file = "werkzeug-3.0.4.tar.gz", hash = "sha256:34f2371506b250df4d4f84bfe7b0921e4762525762bbd936614909fe25cd7306"},
+ {file = "werkzeug-3.1.3-py3-none-any.whl", hash = "sha256:54b78bf3716d19a65be4fceccc0d1d7b89e608834989dfae50ea87564639213e"},
+ {file = "werkzeug-3.1.3.tar.gz", hash = "sha256:60723ce945c19328679790e3282cc758aa4a6040e4bb330f53d30fa546d44746"},
]
[package.dependencies]
@@ -1356,4 +1511,4 @@ watchdog = ["watchdog (>=2.3)"]
[metadata]
lock-version = "2.1"
python-versions = "^3.10"
-content-hash = "9d5953de48e4ccca5f42268a24572fc1967911213611bc92072343f746f2c7b4"
+content-hash = "0a2f4336e1c7d4ea80181d376d271e8eb0b10f53437f246ab11b114ca4f819cb"
diff --git a/auth-system/pyproject.toml b/auth-system/pyproject.toml
index 7e8e894..a930bfb 100644
--- a/auth-system/pyproject.toml
+++ b/auth-system/pyproject.toml
@@ -8,7 +8,7 @@ packages = [{ include = "macrostrat" }]
[tool.poetry.dependencies]
python = "^3.10"
-"macrostrat.database" = "^3.3.1"
+"macrostrat.database" = "^3.3.1||^4.0.0"
"macrostrat.utils" = "^1.2.0"
PyJWT = "^1.7.1 || ^2.0"
werkzeug = "^2.3.7 || ^3.0"
diff --git a/conftest.py b/conftest.py
index ddc9691..8ff65bb 100644
--- a/conftest.py
+++ b/conftest.py
@@ -3,9 +3,9 @@
from docker.client import DockerClient
from dotenv import load_dotenv
from pytest import fixture
-from sqlalchemy import create_engine
from sqlalchemy.exc import OperationalError
+from macrostrat.database.utils import create_engine
from macrostrat.dinosaur.upgrade_cluster.utils import database_cluster, get_unused_port
load_dotenv()
diff --git a/database/CHANGELOG.md b/database/CHANGELOG.md
index 22a1560..5c9d334 100644
--- a/database/CHANGELOG.md
+++ b/database/CHANGELOG.md
@@ -1,5 +1,19 @@
# Changelog
+## [4.0.0] - Unreleased
+
+- Upgrade to `psycopg` version 3 instead of Psycopg2
+- `psycopg`'s new
+ [adaptation system](https://www.psycopg.org/psycopg3/docs/advanced/adapt.html)
+ means that parameter binding has changed substantially. Consequently, `AsIs`
+ and other parameter-binding extensions are no longer supported.
+- `psycopg`'s new
+ [async mode](https://www.psycopg.org/psycopg3/docs/advanced/async.html#interrupting-async-operations)
+ allows us to remove the `set_wait_callback` approach to waiting for
+ long-running operations
+- This is a major breaking change, but it should be mostly transparent, except
+ for a need to update custom parameter binding code.
+
## [3.5.3] - 2024-12-23
- Fix errors and add tests for `run_sql` changes
diff --git a/database/macrostrat/database/__init__.py b/database/macrostrat/database/__init__.py
index 2e43812..123a92c 100644
--- a/database/macrostrat/database/__init__.py
+++ b/database/macrostrat/database/__init__.py
@@ -3,16 +3,15 @@
from pathlib import Path
from typing import Optional, Union
-from psycopg2.errors import InvalidSavepointSpecification
-from psycopg2.sql import Identifier
-from sqlalchemy import URL, Engine, MetaData, create_engine, inspect
-from sqlalchemy.exc import IntegrityError, InternalError
+from psycopg.errors import InvalidSavepointSpecification
+from psycopg.sql import Identifier
+from sqlalchemy import URL, Engine, MetaData, inspect
+from sqlalchemy.exc import IntegrityError, OperationalError
from sqlalchemy.ext.compiler import compiles
from sqlalchemy.orm import Session, scoped_session, sessionmaker
from sqlalchemy.sql.expression import Insert
from macrostrat.utils import get_logger
-
from .mapper import DatabaseMapper
from .postgresql import on_conflict, prefix_inserts # noqa
from .utils import ( # noqa
@@ -25,6 +24,7 @@
run_fixtures,
run_query,
run_sql,
+ create_engine,
)
metadata = MetaData()
@@ -60,12 +60,8 @@ def __init__(self, db_conn: Union[str, URL, Engine], *, echo_sql=False, **kwargs
self.instance_params = kwargs.pop("instance_params", {})
- if isinstance(db_conn, Engine):
- log.info(f"Set up database connection with engine {db_conn.url}")
- self.engine = db_conn
- else:
- log.info(f"Setting up database connection with URL '{db_conn}'")
- self.engine = create_engine(db_conn, echo=echo_sql, **kwargs)
+ self.engine = create_engine(db_conn, echo=echo_sql, **kwargs)
+
self.metadata = kwargs.get("metadata", metadata)
# Scoped session for database
@@ -334,6 +330,7 @@ def savepoint(self, name=None, rollback="on-error", connection=None):
if connection is None:
connection = self.session.connection()
+
params = {"name": Identifier(name)}
run_query(connection, "SAVEPOINT {name}", params)
should_rollback = rollback == "always"
@@ -356,7 +353,7 @@ def _clear_savepoint(connection, name, rollback=True):
run_query(connection, "ROLLBACK TO SAVEPOINT {name}", params)
else:
run_query(connection, "RELEASE SAVEPOINT {name}", params)
- except InternalError as err:
+ except OperationalError as err:
if isinstance(err.orig, InvalidSavepointSpecification):
log.warning(
f"Savepoint {name} does not exist; we may have already rolled back."
diff --git a/database/macrostrat/database/postgresql.py b/database/macrostrat/database/postgresql.py
index cf3ec2b..046e030 100644
--- a/database/macrostrat/database/postgresql.py
+++ b/database/macrostrat/database/postgresql.py
@@ -4,11 +4,11 @@
from contextvars import ContextVar
from typing import TYPE_CHECKING
-import psycopg2
from sqlalchemy.dialects import postgresql
from sqlalchemy.exc import CompileError
from sqlalchemy.ext.compiler import compiles
-from sqlalchemy.sql.expression import Insert, text
+from sqlalchemy.sql.dml import Insert
+from sqlalchemy.sql.expression import text
if TYPE_CHECKING:
from ..database import Database
@@ -26,9 +26,10 @@ def on_conflict(action="restrict"):
_insert_mode.reset(token)
-# @compiles(Insert, "postgresql")
+@compiles(Insert, "postgresql")
def prefix_inserts(insert, compiler, **kw):
"""Conditionally adapt insert statements to use on-conflict resolution (a PostgreSQL feature)"""
+
if insert._post_values_clause is not None:
return compiler.visit_insert(insert, **kw)
@@ -63,7 +64,7 @@ def prefix_inserts(insert, compiler, **kw):
def table_exists(db: Database, table_name: str, schema: str = "public") -> bool:
"""Check if a table exists in a PostgreSQL database."""
sql = """SELECT EXISTS (
- SELECT FROM information_schema.tables
+ SELECT FROM information_schema.tables
WHERE table_schema = :schema
AND table_name = :table_name
);"""
diff --git a/database/macrostrat/database/utils.py b/database/macrostrat/database/utils.py
index 2676d22..a7dab76 100644
--- a/database/macrostrat/database/utils.py
+++ b/database/macrostrat/database/utils.py
@@ -4,18 +4,17 @@
from pathlib import Path
from re import search
from sys import stderr
-from time import sleep
from typing import IO, Union
from warnings import warn
-import psycopg2.errors
from click import echo, secho
-from psycopg2.extensions import set_wait_callback
-from psycopg2.extras import wait_select
-from psycopg2.sql import SQL, Composable, Composed
+from psycopg.errors import QueryCanceled
+from psycopg.sql import SQL, Composable, Composed
from rich.console import Console
-from sqlalchemy import MetaData, create_engine, text
+from sqlalchemy import MetaData, text
+from sqlalchemy import create_engine as base_create_engine
from sqlalchemy.engine import Connection, Engine
+from sqlalchemy.engine.url import make_url
from sqlalchemy.exc import (
IntegrityError,
InternalError,
@@ -29,6 +28,7 @@
from sqlalchemy_utils import create_database as _create_database
from sqlalchemy_utils import database_exists, drop_database
from sqlparse import format, split
+from time import sleep
from macrostrat.utils import cmd, get_logger
@@ -196,6 +196,8 @@ def _get_cursor(connectable):
while hasattr(conn, "driver_connection") or hasattr(conn, "connection"):
if hasattr(conn, "driver_connection"):
conn = conn.driver_connection
+ elif conn.connection == conn:
+ break
else:
conn = conn.connection
if callable(conn):
@@ -296,7 +298,7 @@ def _run_sql(connectable, sql, params=None, **kwargs):
if pre_bind_params is not None:
if not isinstance(query, SQL):
query = SQL(query)
- # Pre-bind the parameters using PsycoPG2
+ # Pre-bind the parameters using psycopg
query = query.format(**pre_bind_params)
if isinstance(query, (SQL, Composed)):
@@ -328,9 +330,6 @@ def _run_sql(connectable, sql, params=None, **kwargs):
)
continue
- # This only does something for postgresql, but it's harmless to run it for other engines
- set_wait_callback(wait_select)
-
try:
trans = connectable.begin()
except InvalidRequestError:
@@ -360,7 +359,7 @@ def _run_sql(connectable, sql, params=None, **kwargs):
_print_error(sql_text, err, file=output_file)
finally:
- set_wait_callback(None)
+ pass
def _should_raise_query_error(err):
@@ -379,7 +378,7 @@ def _should_raise_query_error(err):
# database backends.
# Ideally we could handle operational errors more gracefully
if (
- isinstance(orig_err, psycopg2.errors.QueryCanceled)
+ isinstance(orig_err, QueryCanceled)
or getattr(orig_err, "pgcode", None) == "57014"
):
return True
@@ -602,6 +601,26 @@ def create_database(url, **kwargs):
_create_database(url, **kwargs)
+def create_engine(db_conn, **kwargs):
+ if isinstance(db_conn, Engine):
+ log.info(f"Set up database connection with engine {db_conn.url}")
+ if db_conn.driver == "psycopg2":
+ log.warning(
+ "The psycopg2 driver is deprecated. Please use psycopg3 instead."
+ )
+ return db_conn
+ else:
+ log.info(f"Setting up database connection with URL '{db_conn}'")
+ url = db_conn
+ if isinstance(url, str):
+ url = make_url(url)
+ # Set the driver to psycopg if not already set
+ if url.drivername != "postgresql+psycopg":
+ url = url.set(drivername="postgresql+psycopg")
+
+ return base_create_engine(url, **kwargs)
+
+
def connection_args(engine):
"""Get PostgreSQL connection arguments for an engine"""
_psql_flags = {"-U": "username", "-h": "host", "-p": "port", "-P": "password"}
@@ -617,15 +636,24 @@ def connection_args(engine):
return flags, engine.url.database
-def db_isready(engine_or_url):
- args, _ = connection_args(engine_or_url)
- c = cmd("pg_isready", args, capture_output=True)
- return c.returncode == 0
+def db_isready(engine_or_url, use_shell_command=False):
+ if use_shell_command:
+ args, _ = connection_args(engine_or_url)
+ c = cmd("pg_isready", args, capture_output=True)
+ return c.returncode == 0
+ # Use a more typical sqlalchemy connection approach
+ engine = create_engine(engine_or_url)
+ try:
+ with engine.connect() as conn:
+ conn.execute(text("SELECT 1"))
+ return True
+ except OperationalError:
+ return False
-def wait_for_database(engine_or_url, quiet=False):
+def wait_for_database(engine_or_url, *, quiet=False, use_shell_command=False):
msg = "Waiting for database..."
- while not db_isready(engine_or_url):
+ while not db_isready(engine_or_url, use_shell_command=use_shell_command):
if not quiet:
echo(msg, err=True)
log.info(msg)
diff --git a/database/poetry.lock b/database/poetry.lock
index dce0f77..ab06ce2 100644
--- a/database/poetry.lock
+++ b/database/poetry.lock
@@ -12,16 +12,28 @@ files = [
{file = "aiofiles-23.2.1.tar.gz", hash = "sha256:84ec2218d8419404abcb9f0c02df3f34c6e0a68ed41072acfb1cef5cbc29051a"},
]
+[[package]]
+name = "annotated-types"
+version = "0.7.0"
+description = "Reusable constraint types to use with typing.Annotated"
+optional = false
+python-versions = ">=3.8"
+groups = ["main", "dev"]
+files = [
+ {file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"},
+ {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"},
+]
+
[[package]]
name = "click"
-version = "8.1.3"
+version = "8.3.1"
description = "Composable command line interface toolkit"
optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.10"
groups = ["main"]
files = [
- {file = "click-8.1.3-py3-none-any.whl", hash = "sha256:bb4d8133cb15a609f44e8213d9b391b0809795062913b383c62be0ee95b1db48"},
- {file = "click-8.1.3.tar.gz", hash = "sha256:7682dc8afb30297001674575ea00d1814d808d6a36af415a82bd481d37ba7b8e"},
+ {file = "click-8.3.1-py3-none-any.whl", hash = "sha256:981153a64e25f12d547d3426c367a4857371575ee7ad18df2a6183ab0545b2a6"},
+ {file = "click-8.3.1.tar.gz", hash = "sha256:12ff4785d337a1bb490bb7e9c2b1ee5da3112e94a8622f26a6c77f5d2fc6842a"},
]
[package.dependencies]
@@ -42,14 +54,14 @@ markers = {main = "platform_system == \"Windows\" or sys_platform == \"win32\"",
[[package]]
name = "colorlog"
-version = "6.7.0"
+version = "6.10.1"
description = "Add colours to the output of Python's logging module."
optional = false
python-versions = ">=3.6"
groups = ["main", "dev"]
files = [
- {file = "colorlog-6.7.0-py2.py3-none-any.whl", hash = "sha256:0d33ca236784a1ba3ff9c532d4964126d8a2c44f1f0cb1d2b0728196f512f662"},
- {file = "colorlog-6.7.0.tar.gz", hash = "sha256:bd94bd21c1e13fac7bd3153f4bc3a7dc0eb0974b8bc2fdf1a989e474f6e582e5"},
+ {file = "colorlog-6.10.1-py3-none-any.whl", hash = "sha256:2d7e8348291948af66122cff006c9f8da6255d224e7cf8e37d8de2df3bad8c9c"},
+ {file = "colorlog-6.10.1.tar.gz", hash = "sha256:eb4ae5cb65fe7fec7773c2306061a8e63e02efc2c72eba9d27b0fa23c94f1321"},
]
[package.dependencies]
@@ -79,82 +91,72 @@ shapely = ["Shapely (>=1.7)"]
[[package]]
name = "greenlet"
-version = "2.0.2"
+version = "3.2.4"
description = "Lightweight in-process concurrent programming"
optional = false
-python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*"
+python-versions = ">=3.9"
groups = ["main"]
markers = "platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\""
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+typing-extensions = ">=4.6.0"
[package.extras]
-aiomysql = ["aiomysql (>=0.2.0)", "greenlet (!=0.4.17)"]
-aioodbc = ["aioodbc", "greenlet (!=0.4.17)"]
-aiosqlite = ["aiosqlite", "greenlet (!=0.4.17)", "typing_extensions (!=3.10.0.1)"]
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-mariadb-connector = ["mariadb (>=1.0.1,!=1.1.2,!=1.1.5)"]
+aiomysql = ["aiomysql (>=0.2.0)", "greenlet (>=1)"]
+aioodbc = ["aioodbc", "greenlet (>=1)"]
+aiosqlite = ["aiosqlite", "greenlet (>=1)", "typing_extensions (!=3.10.0.1)"]
+asyncio = ["greenlet (>=1)"]
+asyncmy = ["asyncmy (>=0.2.3,!=0.2.4,!=0.2.6)", "greenlet (>=1)"]
+mariadb-connector = ["mariadb (>=1.0.1,!=1.1.2,!=1.1.5,!=1.1.10)"]
mssql = ["pyodbc"]
mssql-pymssql = ["pymssql"]
mssql-pyodbc = ["pyodbc"]
@@ -462,7 +543,7 @@ mysql-connector = ["mysql-connector-python"]
oracle = ["cx_oracle (>=8)"]
oracle-oracledb = ["oracledb (>=1.0.1)"]
postgresql = ["psycopg2 (>=2.7)"]
-postgresql-asyncpg = ["asyncpg", "greenlet (!=0.4.17)"]
+postgresql-asyncpg = ["asyncpg", "greenlet (>=1)"]
postgresql-pg8000 = ["pg8000 (>=1.29.1)"]
postgresql-psycopg = ["psycopg (>=3.0.7)"]
postgresql-psycopg2binary = ["psycopg2-binary"]
@@ -473,14 +554,14 @@ sqlcipher = ["sqlcipher3_binary"]
[[package]]
name = "sqlalchemy-utils"
-version = "0.41.1"
+version = "0.41.2"
description = "Various utility functions for SQLAlchemy."
optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
groups = ["main"]
files = [
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password = ["passlib (>=1.6,<2.0)"]
pendulum = ["pendulum (>=2.0.5)"]
phone = ["phonenumbers (>=5.9.2)"]
-test = ["Jinja2 (>=2.3)", "Pygments (>=1.2)", "backports.zoneinfo ; python_version < \"3.9\"", "docutils (>=0.10)", "flake8 (>=2.4.0)", "flexmock (>=0.9.7)", "isort (>=4.2.2)", "pg8000 (>=1.12.4)", "psycopg (>=3.1.8)", "psycopg2 (>=2.5.1)", "psycopg2cffi (>=2.8.1)", "pymysql", "pyodbc", "pytest (>=2.7.1)", "python-dateutil (>=2.6)", "pytz (>=2014.2)"]
-test-all = ["Babel (>=1.3)", "Jinja2 (>=2.3)", "Pygments (>=1.2)", "arrow (>=0.3.4)", "backports.zoneinfo ; python_version < \"3.9\"", "colour (>=0.0.4)", "cryptography (>=0.6)", "docutils (>=0.10)", "flake8 (>=2.4.0)", "flexmock (>=0.9.7)", "furl (>=0.4.1)", "intervals (>=0.7.1)", "isort (>=4.2.2)", "passlib (>=1.6,<2.0)", "pendulum (>=2.0.5)", "pg8000 (>=1.12.4)", "phonenumbers (>=5.9.2)", "psycopg (>=3.1.8)", "psycopg2 (>=2.5.1)", "psycopg2cffi (>=2.8.1)", "pymysql", "pyodbc", "pytest (>=2.7.1)", "python-dateutil", "python-dateutil (>=2.6)", "pytz (>=2014.2)"]
+test = ["Jinja2 (>=2.3)", "Pygments (>=1.2)", "backports.zoneinfo ; python_version < \"3.9\"", "docutils (>=0.10)", "flake8 (>=2.4.0)", "flexmock (>=0.9.7)", "isort (>=4.2.2)", "pg8000 (>=1.12.4)", "psycopg (>=3.1.8)", "psycopg2 (>=2.5.1)", "psycopg2cffi (>=2.8.1)", "pymysql", "pyodbc", "pytest (==7.4.4)", "python-dateutil (>=2.6)", "pytz (>=2014.2)"]
+test-all = ["Babel (>=1.3)", "Jinja2 (>=2.3)", "Pygments (>=1.2)", "arrow (>=0.3.4)", "backports.zoneinfo ; python_version < \"3.9\"", "colour (>=0.0.4)", "cryptography (>=0.6)", "docutils (>=0.10)", "flake8 (>=2.4.0)", "flexmock (>=0.9.7)", "furl (>=0.4.1)", "intervals (>=0.7.1)", "isort (>=4.2.2)", "passlib (>=1.6,<2.0)", "pendulum (>=2.0.5)", "pg8000 (>=1.12.4)", "phonenumbers (>=5.9.2)", "psycopg (>=3.1.8)", "psycopg2 (>=2.5.1)", "psycopg2cffi (>=2.8.1)", "pymysql", "pyodbc", "pytest (==7.4.4)", "python-dateutil", "python-dateutil (>=2.6)", "pytz (>=2014.2)"]
timezone = ["python-dateutil"]
url = ["furl (>=0.4.1)"]
[[package]]
name = "sqlparse"
-version = "0.5.1"
+version = "0.5.3"
description = "A non-validating SQL parser."
optional = false
python-versions = ">=3.8"
groups = ["main"]
files = [
- {file = "sqlparse-0.5.1-py3-none-any.whl", hash = "sha256:773dcbf9a5ab44a090f3441e2180efe2560220203dc2f8c0b0fa141e18b505e4"},
- {file = "sqlparse-0.5.1.tar.gz", hash = "sha256:bb6b4df465655ef332548e24f08e205afc81b9ab86cb1c45657a7ff173a3a00e"},
+ {file = "sqlparse-0.5.3-py3-none-any.whl", hash = "sha256:cf2196ed3418f3ba5de6af7e82c694a9fbdbfecccdfc72e281548517081f16ca"},
+ {file = "sqlparse-0.5.3.tar.gz", hash = "sha256:09f67787f56a0b16ecdbde1bfc7f5d9c3371ca683cfeaa8e6ff60b4807ec9272"},
]
[package.extras]
@@ -518,17 +599,45 @@ doc = ["sphinx"]
[[package]]
name = "typing-extensions"
-version = "4.5.0"
-description = "Backported and Experimental Type Hints for Python 3.7+"
+version = "4.15.0"
+description = "Backported and Experimental Type Hints for Python 3.9+"
optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.9"
groups = ["main", "dev"]
files = [
- {file = "typing_extensions-4.5.0-py3-none-any.whl", hash = "sha256:fb33085c39dd998ac16d1431ebc293a8b3eedd00fd4a32de0ff79002c19511b4"},
- {file = "typing_extensions-4.5.0.tar.gz", hash = "sha256:5cb5f4a79139d699607b3ef622a1dedafa84e115ab0024e0d9c044a9479ca7cb"},
+ {file = "typing_extensions-4.15.0-py3-none-any.whl", hash = "sha256:f0fa19c6845758ab08074a0cfa8b7aecb71c999ca73d62883bc25cc018c4e548"},
+ {file = "typing_extensions-4.15.0.tar.gz", hash = "sha256:0cea48d173cc12fa28ecabc3b837ea3cf6f38c6d1136f85cbaaf598984861466"},
+]
+
+[[package]]
+name = "typing-inspection"
+version = "0.4.2"
+description = "Runtime typing introspection tools"
+optional = false
+python-versions = ">=3.9"
+groups = ["main", "dev"]
+files = [
+ {file = "typing_inspection-0.4.2-py3-none-any.whl", hash = "sha256:4ed1cacbdc298c220f1bd249ed5287caa16f34d44ef4e9c3d0cbad5b521545e7"},
+ {file = "typing_inspection-0.4.2.tar.gz", hash = "sha256:ba561c48a67c5958007083d386c3295464928b01faa735ab8547c5692e87f464"},
+]
+
+[package.dependencies]
+typing-extensions = ">=4.12.0"
+
+[[package]]
+name = "tzdata"
+version = "2025.2"
+description = "Provider of IANA time zone data"
+optional = false
+python-versions = ">=2"
+groups = ["main"]
+markers = "sys_platform == \"win32\""
+files = [
+ {file = "tzdata-2025.2-py2.py3-none-any.whl", hash = "sha256:1a403fada01ff9221ca8044d701868fa132215d84beb92242d9acd2147f667a8"},
+ {file = "tzdata-2025.2.tar.gz", hash = "sha256:b60a638fcc0daffadf82fe0f57e53d06bdec2f36c4df66280ae79bce6bd6f2b9"},
]
[metadata]
lock-version = "2.1"
python-versions = "^3.10"
-content-hash = "88da8bdaf1e3811925c85bb0bcc65cd3e19fa2a743045e5cc5f5744f5df26b90"
+content-hash = "d97bf5c79a67f46b826ecaf436e4b0cf3a9973f209406dc3c2c7ffd5d07cb478"
diff --git a/database/pyproject.toml b/database/pyproject.toml
index f0e1d50..2ca9567 100644
--- a/database/pyproject.toml
+++ b/database/pyproject.toml
@@ -3,7 +3,7 @@ authors = ["Daven Quinn "]
description = "A SQLAlchemy-based database toolkit."
name = "macrostrat.database"
packages = [{ include = "macrostrat" }]
-version = "3.5.4"
+version = "4.0.0"
[tool.poetry.dependencies]
GeoAlchemy2 = "^0.15.2"
@@ -11,11 +11,12 @@ SQLAlchemy = "^2.0.18"
SQLAlchemy-Utils = "^0.41.1"
click = "^8.1.3"
"macrostrat.utils" = "^1.3.0"
-psycopg2-binary = "^2.9.6"
python = "^3.10"
sqlparse = "^0.5.1"
aiofiles = "^23.2.1"
rich = "^13.7.1"
+psycopg = "^3.2.1"
+psycopg2 = "^2.9.11"
[tool.poetry.group.dev.dependencies]
"macrostrat.utils" = { path = "../utils", develop = true }
diff --git a/database/tests/scripts/test-long-running-query b/database/tests/scripts/test-long-running-query
index 24e37bc..eeb5b62 100755
--- a/database/tests/scripts/test-long-running-query
+++ b/database/tests/scripts/test-long-running-query
@@ -3,9 +3,7 @@
Run a long-running query to test if we can interrupt it.
"""
-from sys import argv, exit
-
-from sqlalchemy.exc import OperationalError
+from sys import argv
from macrostrat.database import Database
@@ -14,9 +12,5 @@ print(f"Connecting to {db_conn}")
db = Database(db_conn)
-try:
- db.run_sql("SELECT pg_sleep(10);")
-except OperationalError as e:
- if "canceling statement due to user request" in str(e):
- print("Query canceled due to user request.")
- exit(1)
+db.run_sql("SELECT pg_sleep(10);")
+
diff --git a/database/tests/test_database.py b/database/tests/test_database.py
index b70a2ef..f233e07 100644
--- a/database/tests/test_database.py
+++ b/database/tests/test_database.py
@@ -9,13 +9,6 @@
from sys import stdout
from dotenv import load_dotenv
-from psycopg2.errors import SyntaxError
-from psycopg2.extensions import AsIs
-from psycopg2.sql import SQL, Identifier, Literal, Placeholder
-from pytest import fixture, raises, warns
-from sqlalchemy.exc import ProgrammingError
-from sqlalchemy.sql import text
-
from macrostrat.database import Database, run_sql
from macrostrat.database.postgresql import table_exists
from macrostrat.database.utils import (
@@ -25,6 +18,12 @@
temp_database,
)
from macrostrat.utils import get_logger, relative_path
+from psycopg.errors import SyntaxError
+from psycopg.sql import SQL, Identifier, Literal, Placeholder
+from pytest import fixture, raises, warns
+from pytest import mark
+from sqlalchemy.exc import ProgrammingError
+from sqlalchemy.sql import text
load_dotenv()
@@ -249,7 +248,7 @@ def test_server_bound_parameters_mixed(db):
def test_server_bound_parameters_invalid(db):
sql = "SELECT name FROM %(table_name)s WHERE name = %(name)s"
- with raises(KeyError):
+ with raises(ProgrammingError):
db.run_query(sql, {"name": "Test", "table_name": Identifier("sample")})
@@ -273,7 +272,9 @@ def test_server_bound_parameters_invalid_3(db):
assert False
+@mark.skip(reason="This is based on older, psycopg2-style parameter binding.")
def test_server_bound_parameters_dbapi_extensions(db):
+ # from psycopg2.extensions import AsIs
sql = "SELECT name FROM %(table_name)s WHERE name = %(name)s"
res = db.run_query(sql, {"name": "Test", "table_name": AsIs("sample")})
assert res.scalar() == "Test"
@@ -291,7 +292,7 @@ def test_server_parameters_function_def(db):
END;
$$ LANGUAGE plpgsql;
"""
- with raises(TypeError):
+ with raises(ProgrammingError):
db.run_sql(sql, raise_errors=True)
# This should not raise
db.run_sql(sql, raise_errors=True, has_server_binds=False)
@@ -333,7 +334,7 @@ def test_copy_statement(db):
pg_conn = db.engine.connect().connection
cur = pg_conn.cursor()
- cur.copy_expert("COPY sample (name) TO STDOUT", stdout)
+ cur.copy("COPY sample (name) TO STDOUT", stdout)
def test_close_connection(conn):
@@ -344,7 +345,7 @@ def test_close_connection(conn):
import threading
- from psycopg2.extensions import QueryCanceledError
+ from psycopg.errors import QueryCanceled
from sqlalchemy.exc import DBAPIError
sql = text("SELECT pg_sleep(10)")
@@ -357,7 +358,7 @@ def test_close_connection(conn):
conn.execute(sql)
assert False
except DBAPIError as e:
- if type(e.orig) == QueryCanceledError:
+ if type(e.orig) == QueryCanceled:
print("Long running query was cancelled.")
assert True
t.cancel()
@@ -385,14 +386,15 @@ def test_sigint_cancel(db):
str(script),
db_url,
],
+ stdout=subprocess.PIPE,
)
time.sleep(0.5)
p.send_signal(signal.SIGINT)
p.wait()
- assert p.returncode == 1
# Make sure it didn't take too long
dT = time.time() - start
assert dT < 2
+ assert p.returncode != 0
def test_check_table_exists(db):
diff --git a/database/tests/test_database_fixtures.py b/database/tests/test_database_fixtures.py
index dc31f62..0692fff 100644
--- a/database/tests/test_database_fixtures.py
+++ b/database/tests/test_database_fixtures.py
@@ -1,6 +1,6 @@
from pathlib import Path
-from psycopg2.sql import Literal
+from psycopg.sql import Literal
from pytest import fixture, mark, raises
from sqlalchemy.exc import StatementError
@@ -83,7 +83,7 @@ def test_nested_savepoint(db):
def test_savepoint_failing_query(db):
"""This works to rollback the savepoint, but is awkward."""
- with db.savepoint():
+ with db.savepoint(rollback="on-error"):
db.run_fixtures(fixture_dir)
# This query will fail without a cascade
try:
diff --git a/dinosaur/macrostrat/dinosaur/upgrade_cluster/utils.py b/dinosaur/macrostrat/dinosaur/upgrade_cluster/utils.py
index 2a518cd..59fa330 100644
--- a/dinosaur/macrostrat/dinosaur/upgrade_cluster/utils.py
+++ b/dinosaur/macrostrat/dinosaur/upgrade_cluster/utils.py
@@ -1,14 +1,14 @@
import socket
-import time
from contextlib import contextmanager
from typing import Mapping, Optional
import docker
+import time
from docker.client import DockerClient
from docker.models.containers import Container
-from sqlalchemy import create_engine
from sqlalchemy.exc import OperationalError
+from macrostrat.database.utils import create_engine
from macrostrat.utils import get_logger
log = get_logger(__name__)
diff --git a/dinosaur/poetry.lock b/dinosaur/poetry.lock
index e4fc392..7495bfd 100644
--- a/dinosaur/poetry.lock
+++ b/dinosaur/poetry.lock
@@ -12,113 +12,163 @@ files = [
{file = "aiofiles-23.2.1.tar.gz", hash = "sha256:84ec2218d8419404abcb9f0c02df3f34c6e0a68ed41072acfb1cef5cbc29051a"},
]
+[[package]]
+name = "annotated-types"
+version = "0.7.0"
+description = "Reusable constraint types to use with typing.Annotated"
+optional = false
+python-versions = ">=3.8"
+groups = ["main", "dev"]
+files = [
+ {file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"},
+ {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"},
+]
+
[[package]]
name = "certifi"
-version = "2023.5.7"
+version = "2025.11.12"
description = "Python package for providing Mozilla's CA Bundle."
optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
groups = ["main"]
files = [
- {file = "certifi-2023.5.7-py3-none-any.whl", hash = "sha256:c6c2e98f5c7869efca1f8916fed228dd91539f9f1b444c314c06eef02980c716"},
- {file = "certifi-2023.5.7.tar.gz", hash = "sha256:0f0d56dc5a6ad56fd4ba36484d6cc34451e1c6548c61daad8c320169f91eddc7"},
+ {file = "certifi-2025.11.12-py3-none-any.whl", hash = "sha256:97de8790030bbd5c2d96b7ec782fc2f7820ef8dba6db909ccf95449f2d062d4b"},
+ {file = "certifi-2025.11.12.tar.gz", hash = "sha256:d8ab5478f2ecd78af242878415affce761ca6bc54a22a27e026d7c25357c3316"},
]
[[package]]
name = "charset-normalizer"
-version = "3.1.0"
+version = "3.4.4"
description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
optional = false
-python-versions = ">=3.7.0"
+python-versions = ">=3.7"
groups = ["main"]
files = [
- {file = "charset-normalizer-3.1.0.tar.gz", hash = "sha256:34e0a2f9c370eb95597aae63bf85eb5e96826d81e3dcf88b8886012906f509b5"},
- {file = "charset_normalizer-3.1.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:e0ac8959c929593fee38da1c2b64ee9778733cdf03c482c9ff1d508b6b593b2b"},
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name = "click"
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description = "Composable command line interface toolkit"
optional = false
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groups = ["main", "dev"]
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+version = "6.10.1"
description = "Add colours to the output of Python's logging module."
optional = false
python-versions = ">=3.6"
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description = "Lightweight in-process concurrent programming"
optional = false
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-typing-extensions = ">=4.2.0"
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+typing-extensions = ">=4.6.0"
[package.extras]
-aiomysql = ["aiomysql (>=0.2.0)", "greenlet (!=0.4.17)"]
-aioodbc = ["aioodbc", "greenlet (!=0.4.17)"]
-aiosqlite = ["aiosqlite", "greenlet (!=0.4.17)", "typing_extensions (!=3.10.0.1)"]
-asyncio = ["greenlet (!=0.4.17)"]
-asyncmy = ["asyncmy (>=0.2.3,!=0.2.4,!=0.2.6)", "greenlet (!=0.4.17)"]
-mariadb-connector = ["mariadb (>=1.0.1,!=1.1.2,!=1.1.5)"]
+aiomysql = ["aiomysql (>=0.2.0)", "greenlet (>=1)"]
+aioodbc = ["aioodbc", "greenlet (>=1)"]
+aiosqlite = ["aiosqlite", "greenlet (>=1)", "typing_extensions (!=3.10.0.1)"]
+asyncio = ["greenlet (>=1)"]
+asyncmy = ["asyncmy (>=0.2.3,!=0.2.4,!=0.2.6)", "greenlet (>=1)"]
+mariadb-connector = ["mariadb (>=1.0.1,!=1.1.2,!=1.1.5,!=1.1.10)"]
mssql = ["pyodbc"]
mssql-pymssql = ["pymssql"]
mssql-pyodbc = ["pyodbc"]
@@ -713,7 +863,7 @@ mysql-connector = ["mysql-connector-python"]
oracle = ["cx_oracle (>=8)"]
oracle-oracledb = ["oracledb (>=1.0.1)"]
postgresql = ["psycopg2 (>=2.7)"]
-postgresql-asyncpg = ["asyncpg", "greenlet (!=0.4.17)"]
+postgresql-asyncpg = ["asyncpg", "greenlet (>=1)"]
postgresql-pg8000 = ["pg8000 (>=1.29.1)"]
postgresql-psycopg = ["psycopg (>=3.0.7)"]
postgresql-psycopg2binary = ["psycopg2-binary"]
@@ -724,14 +874,14 @@ sqlcipher = ["sqlcipher3_binary"]
[[package]]
name = "sqlalchemy-utils"
-version = "0.41.1"
+version = "0.41.2"
description = "Various utility functions for SQLAlchemy."
optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
groups = ["main", "dev"]
files = [
- {file = "SQLAlchemy-Utils-0.41.1.tar.gz", hash = "sha256:a2181bff01eeb84479e38571d2c0718eb52042f9afd8c194d0d02877e84b7d74"},
- {file = "SQLAlchemy_Utils-0.41.1-py3-none-any.whl", hash = "sha256:6c96b0768ea3f15c0dc56b363d386138c562752b84f647fb8d31a2223aaab801"},
+ {file = "SQLAlchemy-Utils-0.41.2.tar.gz", hash = "sha256:bc599c8c3b3319e53ce6c5c3c471120bd325d0071fb6f38a10e924e3d07b9990"},
+ {file = "SQLAlchemy_Utils-0.41.2-py3-none-any.whl", hash = "sha256:85cf3842da2bf060760f955f8467b87983fb2e30f1764fd0e24a48307dc8ec6e"},
]
[package.dependencies]
@@ -746,8 +896,8 @@ intervals = ["intervals (>=0.7.1)"]
password = ["passlib (>=1.6,<2.0)"]
pendulum = ["pendulum (>=2.0.5)"]
phone = ["phonenumbers (>=5.9.2)"]
-test = ["Jinja2 (>=2.3)", "Pygments (>=1.2)", "backports.zoneinfo ; python_version < \"3.9\"", "docutils (>=0.10)", "flake8 (>=2.4.0)", "flexmock (>=0.9.7)", "isort (>=4.2.2)", "pg8000 (>=1.12.4)", "psycopg (>=3.1.8)", "psycopg2 (>=2.5.1)", "psycopg2cffi (>=2.8.1)", "pymysql", "pyodbc", "pytest (>=2.7.1)", "python-dateutil (>=2.6)", "pytz (>=2014.2)"]
-test-all = ["Babel (>=1.3)", "Jinja2 (>=2.3)", "Pygments (>=1.2)", "arrow (>=0.3.4)", "backports.zoneinfo ; python_version < \"3.9\"", "colour (>=0.0.4)", "cryptography (>=0.6)", "docutils (>=0.10)", "flake8 (>=2.4.0)", "flexmock (>=0.9.7)", "furl (>=0.4.1)", "intervals (>=0.7.1)", "isort (>=4.2.2)", "passlib (>=1.6,<2.0)", "pendulum (>=2.0.5)", "pg8000 (>=1.12.4)", "phonenumbers (>=5.9.2)", "psycopg (>=3.1.8)", "psycopg2 (>=2.5.1)", "psycopg2cffi (>=2.8.1)", "pymysql", "pyodbc", "pytest (>=2.7.1)", "python-dateutil", "python-dateutil (>=2.6)", "pytz (>=2014.2)"]
+test = ["Jinja2 (>=2.3)", "Pygments (>=1.2)", "backports.zoneinfo ; python_version < \"3.9\"", "docutils (>=0.10)", "flake8 (>=2.4.0)", "flexmock (>=0.9.7)", "isort (>=4.2.2)", "pg8000 (>=1.12.4)", "psycopg (>=3.1.8)", "psycopg2 (>=2.5.1)", "psycopg2cffi (>=2.8.1)", "pymysql", "pyodbc", "pytest (==7.4.4)", "python-dateutil (>=2.6)", "pytz (>=2014.2)"]
+test-all = ["Babel (>=1.3)", "Jinja2 (>=2.3)", "Pygments (>=1.2)", "arrow (>=0.3.4)", "backports.zoneinfo ; python_version < \"3.9\"", "colour (>=0.0.4)", "cryptography (>=0.6)", "docutils (>=0.10)", "flake8 (>=2.4.0)", "flexmock (>=0.9.7)", "furl (>=0.4.1)", "intervals (>=0.7.1)", "isort (>=4.2.2)", "passlib (>=1.6,<2.0)", "pendulum (>=2.0.5)", "pg8000 (>=1.12.4)", "phonenumbers (>=5.9.2)", "psycopg (>=3.1.8)", "psycopg2 (>=2.5.1)", "psycopg2cffi (>=2.8.1)", "pymysql", "pyodbc", "pytest (==7.4.4)", "python-dateutil", "python-dateutil (>=2.6)", "pytz (>=2014.2)"]
timezone = ["python-dateutil"]
url = ["furl (>=0.4.1)"]
@@ -775,14 +925,14 @@ pg = ["psycopg2"]
[[package]]
name = "sqlparse"
-version = "0.5.1"
+version = "0.5.3"
description = "A non-validating SQL parser."
optional = false
python-versions = ">=3.8"
groups = ["main", "dev"]
files = [
- {file = "sqlparse-0.5.1-py3-none-any.whl", hash = "sha256:773dcbf9a5ab44a090f3441e2180efe2560220203dc2f8c0b0fa141e18b505e4"},
- {file = "sqlparse-0.5.1.tar.gz", hash = "sha256:bb6b4df465655ef332548e24f08e205afc81b9ab86cb1c45657a7ff173a3a00e"},
+ {file = "sqlparse-0.5.3-py3-none-any.whl", hash = "sha256:cf2196ed3418f3ba5de6af7e82c694a9fbdbfecccdfc72e281548517081f16ca"},
+ {file = "sqlparse-0.5.3.tar.gz", hash = "sha256:09f67787f56a0b16ecdbde1bfc7f5d9c3371ca683cfeaa8e6ff60b4807ec9272"},
]
[package.extras]
@@ -791,35 +941,63 @@ doc = ["sphinx"]
[[package]]
name = "typing-extensions"
-version = "4.5.0"
-description = "Backported and Experimental Type Hints for Python 3.7+"
+version = "4.15.0"
+description = "Backported and Experimental Type Hints for Python 3.9+"
optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.9"
groups = ["main", "dev"]
files = [
- {file = "typing_extensions-4.5.0-py3-none-any.whl", hash = "sha256:fb33085c39dd998ac16d1431ebc293a8b3eedd00fd4a32de0ff79002c19511b4"},
- {file = "typing_extensions-4.5.0.tar.gz", hash = "sha256:5cb5f4a79139d699607b3ef622a1dedafa84e115ab0024e0d9c044a9479ca7cb"},
+ {file = "typing_extensions-4.15.0-py3-none-any.whl", hash = "sha256:f0fa19c6845758ab08074a0cfa8b7aecb71c999ca73d62883bc25cc018c4e548"},
+ {file = "typing_extensions-4.15.0.tar.gz", hash = "sha256:0cea48d173cc12fa28ecabc3b837ea3cf6f38c6d1136f85cbaaf598984861466"},
+]
+
+[[package]]
+name = "typing-inspection"
+version = "0.4.2"
+description = "Runtime typing introspection tools"
+optional = false
+python-versions = ">=3.9"
+groups = ["main", "dev"]
+files = [
+ {file = "typing_inspection-0.4.2-py3-none-any.whl", hash = "sha256:4ed1cacbdc298c220f1bd249ed5287caa16f34d44ef4e9c3d0cbad5b521545e7"},
+ {file = "typing_inspection-0.4.2.tar.gz", hash = "sha256:ba561c48a67c5958007083d386c3295464928b01faa735ab8547c5692e87f464"},
+]
+
+[package.dependencies]
+typing-extensions = ">=4.12.0"
+
+[[package]]
+name = "tzdata"
+version = "2025.2"
+description = "Provider of IANA time zone data"
+optional = false
+python-versions = ">=2"
+groups = ["main", "dev"]
+markers = "sys_platform == \"win32\""
+files = [
+ {file = "tzdata-2025.2-py2.py3-none-any.whl", hash = "sha256:1a403fada01ff9221ca8044d701868fa132215d84beb92242d9acd2147f667a8"},
+ {file = "tzdata-2025.2.tar.gz", hash = "sha256:b60a638fcc0daffadf82fe0f57e53d06bdec2f36c4df66280ae79bce6bd6f2b9"},
]
[[package]]
name = "urllib3"
-version = "2.0.2"
+version = "2.5.0"
description = "HTTP library with thread-safe connection pooling, file post, and more."
optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.9"
groups = ["main"]
files = [
- {file = "urllib3-2.0.2-py3-none-any.whl", hash = "sha256:d055c2f9d38dc53c808f6fdc8eab7360b6fdbbde02340ed25cfbcd817c62469e"},
- {file = "urllib3-2.0.2.tar.gz", hash = "sha256:61717a1095d7e155cdb737ac7bb2f4324a858a1e2e6466f6d03ff630ca68d3cc"},
+ {file = "urllib3-2.5.0-py3-none-any.whl", hash = "sha256:e6b01673c0fa6a13e374b50871808eb3bf7046c4b125b216f6bf1cc604cff0dc"},
+ {file = "urllib3-2.5.0.tar.gz", hash = "sha256:3fc47733c7e419d4bc3f6b3dc2b4f890bb743906a30d56ba4a5bfa4bbff92760"},
]
[package.extras]
brotli = ["brotli (>=1.0.9) ; platform_python_implementation == \"CPython\"", "brotlicffi (>=0.8.0) ; platform_python_implementation != \"CPython\""]
-secure = ["certifi", "cryptography (>=1.9)", "idna (>=2.0.0)", "pyopenssl (>=17.1.0)", "urllib3-secure-extra"]
+h2 = ["h2 (>=4,<5)"]
socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
zstd = ["zstandard (>=0.18.0)"]
[metadata]
lock-version = "2.1"
python-versions = "^3.10"
-content-hash = "ef72e309040a01b37eeb97928305c566f0cede0430cdbb5747481e0f7d076753"
+content-hash = "b53b56dbe3f9b6e1c5be13b8aff54ce1ae45f31895fbfd469a0f1a4cb54aff1b"
diff --git a/dinosaur/pyproject.toml b/dinosaur/pyproject.toml
index b860d4b..aadea29 100644
--- a/dinosaur/pyproject.toml
+++ b/dinosaur/pyproject.toml
@@ -3,17 +3,18 @@ authors = ["Daven Quinn "]
description = "Diff-based database migrations"
name = "macrostrat.dinosaur"
packages = [{ include = "macrostrat" }]
-version = "3.2.0"
+version = "3.3.0"
[tool.poetry.dependencies]
SQLAlchemy = "^2.0.0"
docker = "^7.0.0"
-"macrostrat.database" = "^3.4.1"
-"macrostrat.utils" = "^1.2.1"
+"macrostrat.database" = "^3.3.0||^4.0.0"
+"macrostrat.utils" = "^1.3.0"
migra = "^3.0.1621480950"
-psycopg2-binary = "^2.9.1"
python = "^3.10"
schemainspect = "^3.0.1616029793"
+# Add an explicit dependency on setuptools for Python 3.12 compatibility
+setuptools = "^78.1.0"
[tool.poetry.group.dev.dependencies]
"macrostrat.database" = { path = "../database", develop = true }
diff --git a/dinosaur/tests/test_upgrade_cluster.py b/dinosaur/tests/test_upgrade_cluster.py
index 82fba0e..9ddbb48 100644
--- a/dinosaur/tests/test_upgrade_cluster.py
+++ b/dinosaur/tests/test_upgrade_cluster.py
@@ -2,14 +2,13 @@
PostgreSQL/PostGIS cluster upgrade tests reliant onto Docker.
"""
import random
-import time
from os import environ
from pathlib import Path
from re import match
from docker.client import DockerClient
from pytest import fixture
-from sqlalchemy import create_engine, inspect, text
+from sqlalchemy import inspect, text
from macrostrat.database import Database
from macrostrat.database.utils import run_sql_file
@@ -21,7 +20,6 @@
random_hex = lambda: "%08x" % random.randrange(16**8)
from macrostrat.dinosaur.upgrade_cluster import (
- default_version_images,
upgrade_database_cluster,
)
from macrostrat.dinosaur.upgrade_cluster.describe import check_database_cluster_version
diff --git a/package-tools/macrostrat/package_tools/install.py b/package-tools/macrostrat/package_tools/install.py
index a3baac2..ac2de02 100644
--- a/package-tools/macrostrat/package_tools/install.py
+++ b/package-tools/macrostrat/package_tools/install.py
@@ -4,7 +4,6 @@
from rich import print
from macrostrat.utils import cmd
-
from .dependencies import get_local_dependencies, load_poetry_config
diff --git a/poetry.lock b/poetry.lock
index f4d9a99..ba5d994 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -14,14 +14,14 @@ files = [
[[package]]
name = "annotated-types"
-version = "0.7.0"
+version = "0.6.0"
description = "Reusable constraint types to use with typing.Annotated"
optional = false
python-versions = ">=3.8"
groups = ["dev"]
files = [
- {file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"},
- {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"},
+ {file = "annotated_types-0.6.0-py3-none-any.whl", hash = "sha256:0641064de18ba7a25dee8f96403ebc39113d0cb953a01429249d5c7564666a43"},
+ {file = "annotated_types-0.6.0.tar.gz", hash = "sha256:563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d"},
]
[[package]]
@@ -48,14 +48,14 @@ trio = ["trio (<0.22)"]
[[package]]
name = "babel"
-version = "2.16.0"
+version = "2.14.0"
description = "Internationalization utilities"
optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.7"
groups = ["dev"]
files = [
- {file = "babel-2.16.0-py3-none-any.whl", hash = "sha256:368b5b98b37c06b7daf6696391c3240c938b37767d4584413e8438c5c435fa8b"},
- {file = "babel-2.16.0.tar.gz", hash = "sha256:d1f3554ca26605fe173f3de0c65f750f5a42f924499bf134de6423582298e316"},
+ {file = "Babel-2.14.0-py3-none-any.whl", hash = "sha256:efb1a25b7118e67ce3a259bed20545c29cb68be8ad2c784c83689981b7a57287"},
+ {file = "Babel-2.14.0.tar.gz", hash = "sha256:6919867db036398ba21eb5c7a0f6b28ab8cbc3ae7a73a44ebe34ae74a4e7d363"},
]
[package.extras]
@@ -63,37 +63,63 @@ dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
[[package]]
name = "bcrypt"
-version = "4.2.1"
+version = "4.3.0"
description = "Modern password hashing for your software and your servers"
optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
groups = ["dev"]
files = [
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- {file = "bcrypt-4.2.1-cp37-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:b1ee315739bc8387aa36ff127afc99120ee452924e0df517a8f3e4c0187a0f5f"},
- {file = "bcrypt-4.2.1-cp37-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:8dbd0747208912b1e4ce730c6725cb56c07ac734b3629b60d4398f082ea718ad"},
- {file = "bcrypt-4.2.1-cp37-abi3-manylinux_2_28_aarch64.whl", hash = "sha256:aaa2e285be097050dba798d537b6efd9b698aa88eef52ec98d23dcd6d7cf6fea"},
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@@ -137,14 +163,14 @@ uvloop = ["uvloop (>=0.15.2)"]
[[package]]
name = "certifi"
-version = "2024.12.14"
+version = "2024.2.2"
description = "Python package for providing Mozilla's CA Bundle."
optional = false
python-versions = ">=3.6"
groups = ["dev"]
files = [
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[[package]]
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groups = ["dev"]
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+version = "6.8.2"
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@@ -644,14 +648,14 @@ test = ["objgraph", "psutil"]
[[package]]
name = "griffe"
-version = "1.5.1"
+version = "0.42.1"
description = "Signatures for entire Python programs. Extract the structure, the frame, the skeleton of your project, to generate API documentation or find breaking changes in your API."
optional = false
-python-versions = ">=3.9"
+python-versions = ">=3.8"
groups = ["dev"]
files = [
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@@ -718,19 +722,16 @@ socks = ["socksio (==1.*)"]
[[package]]
name = "idna"
-version = "3.10"
+version = "3.6"
description = "Internationalized Domain Names in Applications (IDNA)"
optional = false
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groups = ["dev"]
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-
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name = "iniconfig"
version = "2.0.0"
@@ -760,14 +761,14 @@ colors = ["colorama (>=0.4.6)"]
[[package]]
name = "jinja2"
-version = "3.1.5"
+version = "3.1.3"
description = "A very fast and expressive template engine."
optional = false
python-versions = ">=3.7"
groups = ["dev"]
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fastapi = "^0.104.0"
httpx = "^0.25.0"
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PyJWT = "^1.7.1 || ^2.0"
python-jose = {version = "^3.3.0", extras = ["cryptography"]}
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[[package]]
name = "macrostrat-database"
-version = "3.5.4"
+version = "4.0.0"
description = "A SQLAlchemy-based database toolkit."
optional = false
python-versions = "^3.10"
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click = "^8.1.3"
GeoAlchemy2 = "^0.15.2"
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rich = "^13.7.1"
SQLAlchemy = "^2.0.18"
SQLAlchemy-Utils = "^0.41.1"
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[[package]]
name = "macrostrat-dinosaur"
-version = "3.2.0"
+version = "3.3.0"
description = "Diff-based database migrations"
optional = false
python-versions = "^3.10"
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migra = "^3.0.1621480950"
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schemainspect = "^3.0.1616029793"
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SQLAlchemy = "^2.0.0"
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[[package]]
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+version = "3.6"
description = "Python implementation of John Gruber's Markdown."
optional = false
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description = "A lightweight library for converting complex datatypes to and from native Python datatypes."
optional = false
python-versions = ">=3.9"
groups = ["dev"]
files = [
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[[package]]
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name = "mkdocs"
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description = "Project documentation with Markdown."
optional = false
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ghp-import = ">=1.0"
jinja2 = ">=2.11.1"
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markupsafe = ">=2.0.1"
mergedeep = ">=1.3.4"
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packaging = ">=20.5"
pathspec = ">=0.11.1"
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pyyaml = ">=5.1"
pyyaml-env-tag = ">=0.1"
watchdog = ">=2.0"
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name = "mkdocs-autorefs"
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description = "Automatically link across pages in MkDocs."
optional = false
python-versions = ">=3.8"
groups = ["dev"]
files = [
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markupsafe = ">=2.0.1"
mkdocs = ">=1.1"
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name = "mkdocs-material"
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description = "Documentation that simply works"
optional = false
python-versions = ">=3.8"
groups = ["dev"]
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colorama = ">=0.4,<1.0"
jinja2 = ">=3.0,<4.0"
markdown = ">=3.2,<4.0"
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mkdocs-material-extensions = ">=1.3,<2.0"
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[[package]]
name = "regex"
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description = "Alternative regular expression module, to replace re."
optional = false
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