Merge pull request #20 from UW-Macrostrat/import-sorting

Add import sorting with isort

Makefile

@@ -9,5 +9,9 @@ install:
 publish:
 	poetry run mono publish
 
+format:
+	poetry run isort .
+	poetry run black .
+
 test:
 	poetry run pytest -s -x --failed-first

app-frame/macrostrat/app_frame/__init__.py

@@ -1,4 +1,4 @@
-from .core import Application
 from .compose import compose
-from .subsystems import SubsystemManager, Subsystem, SubsystemError
+from .core import Application
 from .exc import ApplicationError
+from .subsystems import Subsystem, SubsystemError, SubsystemManager

app-frame/macrostrat/app_frame/compose.py

@@ -1,6 +1,7 @@
-from macrostrat.utils import cmd, get_logger
 from rich.console import Console
 
+from macrostrat.utils import cmd, get_logger
+
 console = Console()
 
 log = get_logger(__name__)

app-frame/macrostrat/app_frame/control_command.py

@@ -6,11 +6,12 @@
 import click
 import typer
 from click import Group
-from macrostrat.utils import get_logger
 from typer import Context, Typer
 from typer.core import TyperGroup
 from typer.models import TyperInfo
 
+from macrostrat.utils import get_logger
+
 from .compose import check_status, compose
 from .core import Application
 from .follow_logs import Result, command_stream, follow_logs

app-frame/macrostrat/app_frame/core.py

@@ -1,11 +1,12 @@
-from rich.console import Console
-from typing import Optional, Callable
-from macrostrat.utils import setup_stderr_logs, get_logger
 import logging
 from os import environ
 from pathlib import Path
+from typing import Callable, Optional
+
 from dotenv import load_dotenv
+from rich.console import Console
 
+from macrostrat.utils import get_logger, setup_stderr_logs
 
 log = get_logger(__name__)
 

app-frame/macrostrat/app_frame/follow_logs.py

@@ -3,11 +3,11 @@
 import sys
 import termios
 from contextlib import contextmanager
+from datetime import datetime
 from enum import Enum
 from subprocess import Popen
 from time import sleep
 from typing import Generator
-from datetime import datetime
 
 from macrostrat.utils import get_logger
 

app-frame/macrostrat/app_frame/subsystems/__init__.py

@@ -1,14 +1,14 @@
-from toposort import toposort_flatten
-from ..core import ApplicationBase
+from typing import Optional
+
 from packaging.specifiers import InvalidSpecifier, SpecifierSet
 from packaging.version import Version
-from typing import Optional
+from toposort import toposort_flatten
 
 from macrostrat.utils.logs import get_logger
 
+from ..core import ApplicationBase
 from .defs import Subsystem, SubsystemError
 
-
 log = get_logger(__name__)
 
 

app-frame/test_app/__init__.py

@@ -1,6 +1,6 @@
 from pathlib import Path
-from macrostrat.app_frame import Application
 
+from macrostrat.app_frame import Application
 
 APP_ROOT = Path(__file__).parent
 

conftest.py

@@ -1,11 +1,13 @@
-from pytest import fixture
 from os import environ
-from macrostrat.dinosaur.upgrade_cluster.utils import database_cluster, get_unused_port
-from dotenv import load_dotenv
+
 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.dinosaur.upgrade_cluster.utils import database_cluster, get_unused_port
+
 load_dotenv()
 
 

database/macrostrat/database/__init__.py

@@ -2,23 +2,17 @@
 from contextlib import contextmanager
 from typing import Optional
 
-from sqlalchemy import create_engine, inspect, MetaData, text
-from sqlalchemy.orm import sessionmaker, scoped_session, Session
+from sqlalchemy import MetaData, create_engine, inspect, text
 from sqlalchemy.exc import IntegrityError
-from macrostrat.utils import get_logger
 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 .utils import (
-    run_sql,
-    get_or_create,
-    reflect_table,
-    get_dataframe,
-)
 from .mapper import DatabaseMapper
-from .postgresql import prefix_inserts, on_conflict  # noqa
-
+from .postgresql import on_conflict, prefix_inserts  # noqa
+from .utils import get_dataframe, get_or_create, reflect_table, run_sql
 
 metadata = MetaData()
 

database/macrostrat/database/mapper/__init__.py

@@ -1,20 +1,21 @@
 from distutils.log import warn
-from macrostrat.database.utils import reflect_table
-from sqlalchemy.ext.automap import generate_relationship
-from macrostrat.utils.logs import get_logger
 from warnings import warn
 
 # Drag in geographic types for database reflection
-from geoalchemy2 import Geometry, Geography
+from geoalchemy2 import Geography, Geometry
+from sqlalchemy.ext.automap import generate_relationship
+
+from macrostrat.database.utils import reflect_table
+from macrostrat.utils.logs import get_logger
 
 from .cache import DatabaseModelCache
 from .utils import (
     ModelCollection,
     TableCollection,
-    classname_for_table,
     _classname_for_table,
-    name_for_scalar_relationship,
+    classname_for_table,
     name_for_collection_relationship,
+    name_for_scalar_relationship,
 )
 
 log = get_logger(__name__)

database/macrostrat/database/mapper/cache.py

@@ -1,8 +1,10 @@
+from os import makedirs, path
+from pickle import dump, load
+
 from sqlalchemy.ext.automap import automap_base
-from os import path, makedirs
+
 from macrostrat.utils.logs import get_logger
-from sqlalchemy.ext.automap import automap_base
-from pickle import load, dump
+
 from .base import ModelHelperMixins
 
 log = get_logger(__name__)

database/macrostrat/database/postgresql.py

@@ -2,15 +2,13 @@
 
 from contextlib import contextmanager
 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.dialects import postgresql
-import psycopg2
-
-
-from typing import TYPE_CHECKING
 
 if TYPE_CHECKING:
     from ..database import Database

database/macrostrat/database/utils.py

@@ -1,22 +1,28 @@
+from contextlib import contextmanager
+from pathlib import Path
+from re import search
+from time import sleep
+from typing import IO, Union
+from warnings import warn
+
 from click import echo, secho
-from sqlalchemy.exc import ProgrammingError, IntegrityError, InternalError
-from sqlparse import split, format
-from sqlalchemy.sql.elements import TextClause, ClauseElement
+from psycopg2.sql import SQL, Composable, Composed
+from sqlalchemy import MetaData, create_engine, text
+from sqlalchemy.engine import Connection, Engine
+from sqlalchemy.exc import (
+    IntegrityError,
+    InternalError,
+    InvalidRequestError,
+    ProgrammingError,
+)
 from sqlalchemy.orm import sessionmaker
-from sqlalchemy.engine import Engine, Connection
 from sqlalchemy.schema import Table
-from sqlalchemy import MetaData, create_engine, text
-from contextlib import contextmanager
+from sqlalchemy.sql.elements import ClauseElement, TextClause
 from sqlalchemy_utils import create_database, database_exists, drop_database
-from sqlalchemy.exc import InvalidRequestError
+from sqlparse import format, split
+
 from macrostrat.utils import cmd, get_logger
-from time import sleep
-from typing import Union, IO
-from pathlib import Path
-from warnings import warn
-from psycopg2.sql import SQL, Composable, Composed
-from re import search
-from macrostrat.utils import get_logger
+
 from .postgresql import _setup_psycopg2_wait_callback
 
 log = get_logger(__name__)

database/test-scripts/test-long-running-query

@@ -3,10 +3,11 @@
 Run a long-running query to test if we can interrupt it.
 """
 
-from macrostrat.database import Database
 from sys import argv, exit
+
 from sqlalchemy.exc import OperationalError
 
+from macrostrat.database import Database
 
 db_conn = argv[1]
 print(f"Connecting to {db_conn}")

database/test_database.py

@@ -1,17 +1,17 @@
 # Skeletal testing file
+from os import environ
 from pathlib import Path
-from pytest import fixture
+
 from dotenv import load_dotenv
 from psycopg2.sql import SQL, Identifier, Literal, Placeholder
+from pytest import fixture, mark, raises, warns
 from sqlalchemy.exc import ProgrammingError
 from sqlalchemy.sql import text
 
-from macrostrat.utils import relative_path, get_logger
 from macrostrat.database import Database, run_sql
-from macrostrat.database.utils import temp_database, infer_is_sql_text
 from macrostrat.database.postgresql import table_exists
-from pytest import warns, raises, mark
-from os import environ
+from macrostrat.database.utils import infer_is_sql_text, temp_database
+from macrostrat.utils import get_logger, relative_path
 
 load_dotenv()
 
@@ -215,6 +215,7 @@ def test_close_connection(conn):
     """
 
     import threading
+
     from psycopg2.extensions import QueryCanceledError
     from sqlalchemy.exc import DBAPIError
 
@@ -240,8 +241,8 @@ def test_sigint_cancel(db):
     by sending a SIGINT.
     """
 
-    import subprocess
     import signal
+    import subprocess
     import time
 
     db_url = str(db.engine.url)

dinosaur/macrostrat/dinosaur/__init__.py

@@ -1,25 +1,21 @@
 import os
 import sys
 from contextlib import contextmanager, redirect_stdout
+from typing import Callable
 
-from sqlalchemy.exc import ProgrammingError, IntegrityError, DataError
-from schemainspect import get_inspector
+import docker
 from migra import Migration
 from migra.statements import check_for_drop
-from sqlalchemy import text
 from rich import print
-from typing import Callable
-import docker
+from schemainspect import get_inspector
+from sqlalchemy import text
+from sqlalchemy.exc import DataError, IntegrityError, ProgrammingError
 
-from macrostrat.utils import get_logger, cmd
 from macrostrat.database import Database
-from macrostrat.database.utils import (
-    run_sql,
-    temp_database,
-    connection_args,
-)
-from .upgrade_cluster.utils import wait_for_cluster, wait_for_ready
+from macrostrat.database.utils import connection_args, run_sql, temp_database
+from macrostrat.utils import cmd, get_logger
 
+from .upgrade_cluster.utils import wait_for_cluster, wait_for_ready
 
 log = get_logger(__name__)
 

dinosaur/macrostrat/dinosaur/upgrade_cluster/__init__.py

@@ -1,19 +1,21 @@
+from typing import List
+
 from docker.client import DockerClient
-from macrostrat.utils import get_logger
 from rich.console import Console
-from typing import List
 
+from macrostrat.utils import get_logger
+
+from .describe import (
+    check_database_cluster_version,
+    check_database_exists,
+    count_database_tables,
+)
+from .restore import pg_restore
 from .utils import (
     database_cluster,
     ensure_empty_docker_volume,
-    replace_docker_volume,
     get_unused_port,
-)
-from .restore import pg_restore
-from .describe import (
-    check_database_exists,
-    count_database_tables,
-    check_database_cluster_version,
+    replace_docker_volume,
 )
 
 log = get_logger(__name__)

dinosaur/macrostrat/dinosaur/upgrade_cluster/describe.py

@@ -1,8 +1,9 @@
-from docker.models.containers import Container
+from pathlib import Path
 from subprocess import CalledProcessError
-from docker.errors import ContainerError
+
 from docker.client import DockerClient
-from pathlib import Path
+from docker.errors import ContainerError
+from docker.models.containers import Container
 
 from macrostrat.utils import get_logger
 

dinosaur/macrostrat/dinosaur/upgrade_cluster/restore.py

@@ -1,8 +1,8 @@
 import asyncio
+
 from docker.models.containers import Container
 from rich.console import Console
 
-
 console = Console()