Merge pull request #425 from dgasmith/cleanup

Cleanup

.lgtm.yml

@@ -13,4 +13,6 @@ path_classifiers:
   generated:
     - qcfractal/_version.py
 queries:
-- exclude: py/not-named-self # Blocks Pydantic's @validator not accepting `self` until a better fix can be found
+- exclude:
+   - py/not-named-self # Blocks Pydantic's @validator not accepting `self` until a better fix can be found
+   - py/missing-call-to-init

qcfractal/__init__.py

@@ -3,18 +3,16 @@
 """
 
 from . import interface
-
-# Import modules
-from .storage_sockets import storage_socket_factory
-
+# Handle versioneer
+from .extras import get_information
 # Handle top level object imports
 from .postgres_harness import PostgresHarness, TemporaryPostgres
+from .queue import QueueManager
 from .server import FractalServer
 from .snowflake import FractalSnowflake, FractalSnowflakeHandler
-from .queue import QueueManager
+# Import modules
+from .storage_sockets import storage_socket_factory
 
-# Handle versioneer
-from .extras import get_information
 __version__ = get_information('version')
 __git_revision__ = get_information('git_revision')
 del get_information

qcfractal/_version.py

@@ -75,12 +75,11 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=
         try:
             dispcmd = str([c] + args)
             # remember shell=False, so use git.cmd on windows, not just git
-            p = subprocess.Popen(
-                [c] + args,
-                cwd=cwd,
-                env=env,
-                stdout=subprocess.PIPE,
-                stderr=(subprocess.PIPE if hide_stderr else None))
+            p = subprocess.Popen([c] + args,
+                                 cwd=cwd,
+                                 env=env,
+                                 stdout=subprocess.PIPE,
+                                 stderr=(subprocess.PIPE if hide_stderr else None))
             break
         except EnvironmentError:
             e = sys.exc_info()[1]

qcfractal/alembic/env.py

@@ -1,15 +1,12 @@
 
 from logging.config import fileConfig
 
-from sqlalchemy import engine_from_config
-from sqlalchemy import pool
+import yaml
+from sqlalchemy import engine_from_config, pool
 
 from alembic import context
-
-from qcfractal.storage_sockets.models import Base
-
-import yaml
 from qcfractal.config import FractalConfig
+from qcfractal.storage_sockets.models import Base
 
 # this is the Alembic Config object, which provides
 # access to the values within the .ini file in use.

qcfractal/cli/cli_utils.py

@@ -7,9 +7,10 @@
 import importlib
 import json
 import signal
-import yaml
 from functools import partial
 
+import yaml
+
 
 def import_module(module, package=None):
     """Protected import of a module

qcfractal/cli/qcfractal_dashboard.py

@@ -35,5 +35,6 @@ def main(args=None):
 
     dashboard_app.run_server(debug=True)
 
+
 if __name__ == '__main__':
     main()

qcfractal/cli/qcfractal_server.py

@@ -90,7 +90,11 @@ def parse_args():
 
     ### Config subcommands
     info = subparsers.add_parser('info', help="Manage users and permissions on a QCFractal server instance.")
-    info.add_argument("category", nargs="?", default="config", choices=["config", "alembic"], help="The config category to show.")
+    info.add_argument("category",
+                      nargs="?",
+                      default="config",
+                      choices=["config", "alembic"],
+                      help="The config category to show.")
     info.add_argument("--base-folder", **FractalConfig.help_info("base_folder"))
 
     ### User subcommands
@@ -101,9 +105,16 @@ def parse_args():
 
     user_add = user_subparsers.add_parser("add", help="Add a user to the QCFractal server.")
     user_add.add_argument("username", default=None, type=str, help="The username to add.")
-    user_add.add_argument("--password", default=None, type=str, required=False,
+    user_add.add_argument("--password",
+                          default=None,
+                          type=str,
+                          required=False,
                           help="The password for the user. If None, a default one will be created and printed.")
-    user_add.add_argument("--permissions", nargs='+', default=None, type=str, required=True,
+    user_add.add_argument("--permissions",
+                          nargs='+',
+                          default=None,
+                          type=str,
+                          required=True,
                           help="Permissions for the user. Allowed values: read, write, queue, compute, admin.")
 
     user_show = user_subparsers.add_parser("info", help="Show the user's current permissions.")
@@ -112,12 +123,21 @@ def parse_args():
     user_modify = user_subparsers.add_parser("modify", help="Change a user's password or permissions.")
     user_modify.add_argument("username", default=None, type=str, help="The username to modify.")
     user_modify_password = user_modify.add_mutually_exclusive_group()
-    user_modify_password.add_argument("--password", type=str, default=None, required=False,
+    user_modify_password.add_argument("--password",
+                                      type=str,
+                                      default=None,
+                                      required=False,
                                       help="Change the user's password to the specified value.")
-    user_modify_password.add_argument("--reset-password", action='store_true',
+    user_modify_password.add_argument("--reset-password",
+                                      action='store_true',
                                       help="Reset the user's password. A new password will be generated and printed.")
-    user_modify.add_argument("--permissions", nargs='+', default=None, type=str, required=False,
-                             help="Change the users's permissions. Allowed values: read, write, compute, queue, admin.")
+    user_modify.add_argument(
+        "--permissions",
+        nargs='+',
+        default=None,
+        type=str,
+        required=False,
+        help="Change the users's permissions. Allowed values: read, write, compute, queue, admin.")
 
     user_remove = user_subparsers.add_parser("remove", help="Remove a user.")
     user_remove.add_argument("username", default=None, type=str, help="The username to remove.")
@@ -385,7 +405,9 @@ def server_user(args, config):
     try:
         if args["user_command"] == "add":
             print("\n>>> Adding new user...")
-            success, pw = storage.add_user(args["username"], password=args["password"], permissions=args["permissions"])
+            success, pw = storage.add_user(args["username"],
+                                           password=args["password"],
+                                           permissions=args["permissions"])
             if success:
                 print(f"\n>>> New user successfully added, password:\n{pw}")
                 if config.fractal.security is None:
@@ -404,9 +426,7 @@ def server_user(args, config):
                 print(permissions)
         elif args["user_command"] == "modify":
             print(f"\n>>> Modifying user '{args['username']}'...")
-            success, message = storage.modify_user(args["username"],
-                                                   args["password"],
-                                                   args["reset_password"],
+            success, message = storage.modify_user(args["username"], args["password"], args["reset_password"],
                                                    args["permissions"])
             if success:
                 info = "Successfully modified user\n"

qcfractal/cli/tests/test_cli.py

@@ -2,16 +2,15 @@
 Tests for QCFractals CLI
 """
 import os
-import time
 import tempfile
+import time
 
 import pytest
+import yaml
 
 import qcfractal
-
 from qcfractal import testing
 from qcfractal.cli.cli_utils import read_config_file
-import yaml
 
 # def _run_tests()
 _options = {"coverage": True, "dump_stdout": True}
@@ -26,8 +25,7 @@ def qcfractal_base_init():
 
     args = [
         "qcfractal-server", "init", "--base-folder",
-        str(tmpdir.name), "--db-own=False", "--clear-database",
-        f"--db-port={storage.config.database.port}"
+        str(tmpdir.name), "--db-own=False", "--clear-database", f"--db-port={storage.config.database.port}"
     ]
     assert testing.run_process(args, **_options)
 
@@ -55,8 +53,10 @@ def test_cli_user_add(qcfractal_base_init):
     args = ["qcfractal-server", "user", qcfractal_base_init, "add", "test_user_add_1", "--permissions", "admin"]
     assert testing.run_process(args, **_options) is False
 
-    args = ["qcfractal-server", "user", qcfractal_base_init, "add", "test_user_add_2", "--password", "foo",
-            "--permissions", "admin"]
+    args = [
+        "qcfractal-server", "user", qcfractal_base_init, "add", "test_user_add_2", "--password", "foo",
+        "--permissions", "admin"
+    ]
     assert testing.run_process(args, **_options)
 
     args = ["qcfractal-server", "user", qcfractal_base_init, "add", "test_user_add_3"]
@@ -80,16 +80,16 @@ def test_cli_user_modify(qcfractal_base_init):
     args = ["qcfractal-server", "user", qcfractal_base_init, "add", "test_user_modify", "--permissions", "read"]
     assert testing.run_process(args, **_options)
 
-    args = ["qcfractal-server", "user", qcfractal_base_init, "modify", "test_user_modify",
-            "--permissions", "read", "write", "--reset-password"]
+    args = [
+        "qcfractal-server", "user", qcfractal_base_init, "modify", "test_user_modify", "--permissions", "read",
+        "write", "--reset-password"
+    ]
     assert testing.run_process(args, **_options)
 
-    args = ["qcfractal-server", "user", qcfractal_base_init, "modify", "test_user_modify",
-            "--password", "foopass"]
+    args = ["qcfractal-server", "user", qcfractal_base_init, "modify", "test_user_modify", "--password", "foopass"]
     assert testing.run_process(args, **_options)
 
-    args = ["qcfractal-server", "user", qcfractal_base_init, "modify", "test_user_modify",
-            "--permissions", "read"]
+    args = ["qcfractal-server", "user", qcfractal_base_init, "modify", "test_user_modify", "--permissions", "read"]
     assert testing.run_process(args, **_options)
 
     args = ["qcfractal-server", "user", qcfractal_base_init, "modify", "badname_1234"]
@@ -136,8 +136,7 @@ def test_with_api_logging(postgres_server, log_apis):
 
     args = [
         "qcfractal-server", "init", "--base-folder",
-        str(tmpdir.name), "--db-own=False", "--clear-database",
-        f"--db-port={postgres_server.config.database.port}",
+        str(tmpdir.name), "--db-own=False", "--clear-database", f"--db-port={postgres_server.config.database.port}",
         f"--log-apis={log_apis}"
     ]
     assert testing.run_process(args, **_options)
@@ -272,4 +271,3 @@ def test_cli_managers_skel(tmp_path):
     config = tmp_path / "config.yaml"
     args = ["qcfractal-manager", "--skel", config.as_posix()]
     testing.run_process(args, **_options)
-

qcfractal/config.py

@@ -7,8 +7,8 @@
 from pathlib import Path
 from typing import Optional
 
-from pydantic import Schema, validator
 import yaml
+from pydantic import Schema, validator
 
 from .interface.models import AutodocBaseSettings
 
@@ -86,10 +86,11 @@ class FractalServerSettings(ConfigSettings):
                                      description="Compress REST responses or not, should be True unless behind a "
                                      "proxy.")
     allow_read: bool = Schema(True, description="Always allows read access to record tables.")
-    security: str = Schema(None, description="Optional user authentication. Specify 'local' to enable "
-                                             "authentication through locally stored usernames. "
-                                             "User permissions may be manipulated through the ``qcfractal-server "
-                                             "user`` CLI.")
+    security: str = Schema(None,
+                           description="Optional user authentication. Specify 'local' to enable "
+                           "authentication through locally stored usernames. "
+                           "User permissions may be manipulated through the ``qcfractal-server "
+                           "user`` CLI.")
 
     query_limit: int = Schema(1000, description="The maximum number of records to return per query.")
     logfile: Optional[str] = Schema("qcfractal_server.log", description="The logfile to write server logs.")

qcfractal/dashboard/app.py

@@ -5,4 +5,3 @@
 server = app.server
 app.config.suppress_callback_exceptions = True
 app.server.config.from_mapping(DATABASE_URI="mongodb://localhost", DATABASE_NAME="QCFractal Server")
-

qcfractal/dashboard/connection.py

@@ -1,4 +1,5 @@
 from flask import current_app, g
+
 from ..storage_sockets import storage_socket_factory
 
 

qcfractal/dashboard/dash_managers.py

@@ -1,16 +1,16 @@
-import dash_table
+## Functions to call on the fly when page loads
+import pandas as pd
+
+import dash_bootstrap_components as dbc
 import dash_core_components as dcc
 import dash_html_components as html
-import dash_bootstrap_components as dbc
+import dash_table
 from dash.dependencies import Input, Output
 
 from .app import app
 from .connection import get_socket
 from .navbar import navbar
 
-## Functions to call on the fly when page loads
-import pandas as pd
-
 
 def managers_table(status):
     socket = get_socket()
@@ -77,4 +77,4 @@ def overview_graph(status):
     Output('manager-overview', 'figure'),
  [Input('manager-overview-groupby', 'value')])
 def update_overview_graph(status):
-    return overview_graph(status)
+    return overview_graph(status)

qcfractal/dashboard/dash_queue.py

@@ -1,16 +1,16 @@
-import dash_table
+## Functions to call on the fly when page loads
+import pandas as pd
+
+import dash_bootstrap_components as dbc
 import dash_core_components as dcc
 import dash_html_components as html
-import dash_bootstrap_components as dbc
+import dash_table
 from dash.dependencies import Input, Output
 
 from .app import app
 from .connection import get_socket
 from .navbar import navbar
 
-## Functions to call on the fly when page loads
-import pandas as pd
-
 
 def queue_counts(status):
     socket = get_socket()
@@ -29,5 +29,3 @@ def queue_counts(status):
 ])
 
 layout = lambda: html.Div([navbar, body()])
-
-

qcfractal/dashboard/dash_service.py

@@ -1,16 +1,16 @@
-import dash_table
+## Functions to call on the fly when page loads
+import pandas as pd
+
+import dash_bootstrap_components as dbc
 import dash_core_components as dcc
 import dash_html_components as html
-import dash_bootstrap_components as dbc
+import dash_table
 from dash.dependencies import Input, Output
 
 from .app import app
 from .connection import get_socket
 from .navbar import navbar
 
-## Functions to call on the fly when page loads
-import pandas as pd
-
 
 def service_counts(status):
     socket = get_socket()
@@ -29,5 +29,3 @@ def service_counts(status):
 ])
 
 layout = lambda: html.Div([navbar, body()])
-
-

qcfractal/dashboard/index.py

@@ -1,15 +1,12 @@
+import dash_bootstrap_components as dbc
 import dash_core_components as dcc
 import dash_html_components as html
-import dash_bootstrap_components as dbc
 from dash.dependencies import Input, Output
 
+from . import dash_managers, dash_queue, dash_service
 from .app import app
 from .navbar import navbar
 
-from . import dash_managers
-from . import dash_queue
-from . import dash_service
-
 body = dbc.Container(
     [
         dbc.Row([

qcfractal/dashboard/navbar.py

@@ -16,4 +16,3 @@
     brand_href="/",
     sticky="top",
 )
-

qcfractal/extras.py

@@ -56,4 +56,4 @@ def provenance_stamp(routine):
         'creator': 'QCFractal',
         'version': get_information('version'),
         'routine': routine,
-    }
+    }