Blackify & optimize imports

MolSSI · May 14, 2024 · 2513d5d · 2513d5d
1 parent f389c67
commit 2513d5d
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Showing 162 changed files with 281 additions and 177 deletions.
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -4,13 +4,12 @@
 # list see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
-# Import the package for version info
-import qcfractal
-
 # Other packages
-import os
 import datetime
 
+# Import the package for version info
+import qcfractal
+
 # -- Path setup --------------------------------------------------------------
 
 # If extensions (or modules to document with autodoc) are in another directory,
@@ -24,9 +23,11 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'QCArchive'
-copyright = f'2018-{datetime.datetime.today().year}, The Molecular Sciences Software Institute'
-author = 'Molecular Sciences Software Institute'
+project = "QCArchive"
+copyright = (
+    f"2018-{datetime.datetime.today().year}, The Molecular Sciences Software Institute"
+)
+author = "Molecular Sciences Software Institute"
 
 # The short X.Y version
 version = qcfractal.__version__
@@ -40,83 +41,81 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.autosummary',
-    'sphinx.ext.viewcode',
-    'sphinx.ext.napoleon',
-    'sphinx.ext.extlinks',
-    'sphinx_design',
-    'sphinxcontrib.autodoc_pydantic',
-    'sphinx_copybutton',
-    'myst_nb',
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.extlinks",
+    "sphinx_design",
+    "sphinxcontrib.autodoc_pydantic",
+    "sphinx_copybutton",
+    "myst_nb",
 ]
 
 # Some options
 add_module_names = False
 autoclass_content = "both"
-autodoc_typehints = 'description'
+autodoc_typehints = "description"
 autodoc_default_options = {
-    'members': True,
-    'undoc-members': True,
-    'inherited-members': "BaseModel",
-    'show-inheritance': True,
-    'member-order': 'bysource',
+    "members": True,
+    "undoc-members": True,
+    "inherited-members": "BaseModel",
+    "show-inheritance": True,
+    "member-order": "bysource",
 }
 autodoc_pydantic_model_show_json = False
 autodoc_pydantic_settings_show_json = False
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates', ]
+templates_path = [
+    "_templates",
+]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ['.ipynb_checkpoints/*']
+exclude_patterns = [".ipynb_checkpoints/*"]
 
 
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'pydata_sphinx_theme'
+html_theme = "pydata_sphinx_theme"
 
 html_theme_options = {
     "github_url": "https://github.com/MolSSI/QCFractal",
-
     "logo": {
-      "image_light": "qcarchive_logo.svg",
-      "image_dark": "qcarchive_logo_inverted.svg",
-      "text": "QCArchive",
-      "molssi_light": "molssi_main_logo.png",
-      "molssi_dark": "molssi_main_logo_inverted_white.png",
+        "image_light": "qcarchive_logo.svg",
+        "image_dark": "qcarchive_logo_inverted.svg",
+        "text": "QCArchive",
+        "molssi_light": "molssi_main_logo.png",
+        "molssi_dark": "molssi_main_logo_inverted_white.png",
     },
     "show_toc_level": 2,
     "header_links_before_dropdown": 6,
-    "external_links": [
-      {"name": "MolSSI", "url": "https://molssi.org"}
-  ],
-
+    "external_links": [{"name": "MolSSI", "url": "https://molssi.org"}],
     "secondary_sidebar_items": ["page-toc", "sourcelink"],
-    "footer_start": [ "molssi_footer" ],
+    "footer_start": ["molssi_footer"],
     "footer_end": [],
 }
 
-html_css_files = ['css/custom.css']
+html_css_files = ["css/custom.css"]
 
 html_context = {
-    'extrahead': '<link href="https://fonts.googleapis.com/css?family=Roboto:400,700&display=swap" rel="stylesheet">'
+    "extrahead": '<link href="https://fonts.googleapis.com/css?family=Roboto:400,700&display=swap" rel="stylesheet">'
 }
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 # -- extlinks extension ----------------------------------------------------
 
 extlinks = {
-    'issue': ('https://github.com/MolSSI/QCFractal/issues/%s', 'Issue %s'),
-    'pr': ('https://github.com/MolSSI/QCFractal/pull/%s', 'PR %s'),
-    'contrib': ('https://github.com/%s', '@%s'),
+    "issue": ("https://github.com/MolSSI/QCFractal/issues/%s", "Issue %s"),
+    "pr": ("https://github.com/MolSSI/QCFractal/pull/%s", "PR %s"),
+    "contrib": ("https://github.com/%s", "@%s"),
 }
diff --git a/qcarchivetesting/qcarchivetesting/helpers.py b/qcarchivetesting/qcarchivetesting/helpers.py
@@ -1,6 +1,7 @@
 """
 Contains testing infrastructure for QCFractal.
 """
+
 from __future__ import annotations
 
 import json

diff --git a/qcarchivetesting/qcarchivetesting/test_full_neb.py b/qcarchivetesting/qcarchivetesting/test_full_neb.py
@@ -3,10 +3,10 @@
 import time
 from typing import TYPE_CHECKING
 
+from qcarchivetesting import load_molecule_data
 from qcportal.neb import NEBKeywords
 from qcportal.optimization import OptimizationSpecification
 from qcportal.record_models import RecordStatusEnum
-from qcarchivetesting import load_molecule_data
 from qcportal.singlepoint import QCSpecification
 
 if TYPE_CHECKING:

diff --git a/qcarchivetesting/qcarchivetesting/testing_fixtures.py b/qcarchivetesting/qcarchivetesting/testing_fixtures.py
@@ -1,6 +1,7 @@
 """
 Pytest fixtures for QCArchive
 """
+
 from __future__ import annotations
 
 import secrets

diff --git a/qcfractal/qcfractal/alembic/env.py b/qcfractal/qcfractal/alembic/env.py
@@ -4,7 +4,7 @@
 from sqlalchemy import engine_from_config, pool
 
 from qcfractal.db_socket import BaseORM
-from qcfractal.components import register_all
+from qcfractal.components import register_all  # noqa
 
 # this is the Alembic Config object, which provides
 # access to the values within the .ini file in use.

diff --git a/qcfractal/qcfractal/alembic/versions/2019-07-02-d28e52d86633_add_username_to_manager.py b/qcfractal/qcfractal/alembic/versions/2019-07-02-d28e52d86633_add_username_to_manager.py
@@ -5,6 +5,7 @@
 Create Date: 2019-07-02 22:51:25.613742
 
 """
+
 from alembic import op
 import sqlalchemy as sa
 

diff --git a/qcfractal/qcfractal/alembic/versions/2019-07-09-6adeb5d3032e_service_ordering.py b/qcfractal/qcfractal/alembic/versions/2019-07-09-6adeb5d3032e_service_ordering.py
@@ -5,9 +5,9 @@
 Create Date: 2019-07-09 12:02:39.164203
 
 """
-from alembic import op
-import sqlalchemy as sa
 
+import sqlalchemy as sa
+from alembic import op
 
 # revision identifiers, used by Alembic.
 revision = "6adeb5d3032e"

diff --git a/qcfractal/qcfractal/alembic/versions/2019-07-23-26cfd7b0439e_add_access_logs_table.py b/qcfractal/qcfractal/alembic/versions/2019-07-23-26cfd7b0439e_add_access_logs_table.py
@@ -5,9 +5,9 @@
 Create Date: 2019-07-23 16:06:28.766128
 
 """
-from alembic import op
-import sqlalchemy as sa
 
+import sqlalchemy as sa
+from alembic import op
 
 # revision identifiers, used by Alembic.
 revision = "26cfd7b0439e"

diff --git a/...cfractal/alembic/versions/2019-07-26-4bb79efa9855_add_queue_manager_id_to_base_results.py b/...cfractal/alembic/versions/2019-07-26-4bb79efa9855_add_queue_manager_id_to_base_results.py
@@ -5,6 +5,7 @@
 Create Date: 2019-07-26 15:31:14.811337
 
 """
+
 from alembic import op
 import sqlalchemy as sa
 

diff --git a/qcfractal/qcfractal/alembic/versions/2019-08-10-963822c28879_molecule_msgpack_1.py b/qcfractal/qcfractal/alembic/versions/2019-08-10-963822c28879_molecule_msgpack_1.py
@@ -5,17 +5,16 @@
 Create Date: 2019-08-10 17:41:15.520300
 
 """
-from alembic import op
-import sqlalchemy as sa
-import numpy as np
 
 import os
 import sys
 
+import numpy as np
+
 sys.path.insert(1, os.path.dirname(os.path.abspath(__file__)))
 
 from migration_helpers import msgpack_migrations
-from qcelemental.util import msgpackext_dumps, msgpackext_loads
+from qcelemental.util import msgpackext_dumps
 
 # revision identifiers, used by Alembic.
 revision = "963822c28879"

diff --git a/qcfractal/qcfractal/alembic/versions/2019-08-11-05ceea11b78a_base_records_msgpack_2.py b/qcfractal/qcfractal/alembic/versions/2019-08-11-05ceea11b78a_base_records_msgpack_2.py
@@ -5,15 +5,12 @@
 Create Date: 2019-08-11 22:30:51.453746
 
 """
-from alembic import op
-import sqlalchemy as sa
 
 import os
 import sys
 
 sys.path.insert(1, os.path.dirname(os.path.abspath(__file__)))
 from migration_helpers import msgpack_migrations
-from qcelemental.util import msgpackext_dumps, msgpackext_loads
 
 # revision identifiers, used by Alembic.
 revision = "05ceea11b78a"

diff --git a/qcfractal/qcfractal/alembic/versions/2019-08-11-1134312ad4a3_results_msgpack_2.py b/qcfractal/qcfractal/alembic/versions/2019-08-11-1134312ad4a3_results_msgpack_2.py
@@ -5,8 +5,6 @@
 Create Date: 2019-08-11 17:21:43.328492
 
 """
-from alembic import op
-import sqlalchemy as sa
 
 import os
 import sys

diff --git a/qcfractal/qcfractal/alembic/versions/2019-08-11-84c94a48e491_results_msgpack_1.py b/qcfractal/qcfractal/alembic/versions/2019-08-11-84c94a48e491_results_msgpack_1.py
@@ -5,16 +5,16 @@
 Create Date: 2019-08-11 17:21:40.264688
 
 """
-from alembic import op
-import sqlalchemy as sa
-import numpy as np
 
 import os
 import sys
 
+import numpy as np
+import sqlalchemy as sa
+
 sys.path.insert(1, os.path.dirname(os.path.abspath(__file__)))
 from migration_helpers import msgpack_migrations
-from qcelemental.util import msgpackext_dumps, msgpackext_loads
+from qcelemental.util import msgpackext_dumps
 
 # revision identifiers, used by Alembic.
 revision = "84c94a48e491"

diff --git a/qcfractal/qcfractal/alembic/versions/2019-08-11-8b0cd9accaf2_base_records_msgpack_1.py b/qcfractal/qcfractal/alembic/versions/2019-08-11-8b0cd9accaf2_base_records_msgpack_1.py
@@ -5,6 +5,7 @@
 Create Date: 2019-08-11 22:30:27.613722
 
 """
+
 from alembic import op
 import sqlalchemy as sa
 

diff --git a/qcfractal/qcfractal/alembic/versions/2019-08-11-d56ac42b9a43_molecule_msgpack_2.py b/qcfractal/qcfractal/alembic/versions/2019-08-11-d56ac42b9a43_molecule_msgpack_2.py
@@ -5,8 +5,6 @@
 Create Date: 2019-08-11 16:17:23.856255
 
 """
-from alembic import op
-import sqlalchemy as sa
 
 import os
 import sys

diff --git a/qcfractal/qcfractal/alembic/versions/2019-08-12-da7c6f141bcb_extras_msgpack_1.py b/qcfractal/qcfractal/alembic/versions/2019-08-12-da7c6f141bcb_extras_msgpack_1.py
@@ -5,15 +5,13 @@
 Create Date: 2019-08-12 10:12:46.478628
 
 """
-from alembic import op
-import sqlalchemy as sa
 
 import os
 import sys
 
 sys.path.insert(1, os.path.dirname(os.path.abspath(__file__)))
 from migration_helpers import msgpack_migrations
-from qcelemental.util import msgpackext_dumps, msgpackext_loads
+from qcelemental.util import msgpackext_dumps
 
 # revision identifiers, used by Alembic.
 revision = "da7c6f141bcb"

diff --git a/qcfractal/qcfractal/alembic/versions/2019-08-12-e32b61e2516f_extras_msgpack_2.py b/qcfractal/qcfractal/alembic/versions/2019-08-12-e32b61e2516f_extras_msgpack_2.py
@@ -5,15 +5,12 @@
 Create Date: 2019-08-12 10:13:09.694643
 
 """
-from alembic import op
-import sqlalchemy as sa
 
 import os
 import sys
 
 sys.path.insert(1, os.path.dirname(os.path.abspath(__file__)))
 from migration_helpers import msgpack_migrations
-from qcelemental.util import msgpackext_dumps, msgpackext_loads
 
 # revision identifiers, used by Alembic.
 revision = "e32b61e2516f"

diff --git a/...actal/alembic/versions/2019-08-19-129ff3ce9247_add_collection_tables_dataset_reaction_.py b/...actal/alembic/versions/2019-08-19-129ff3ce9247_add_collection_tables_dataset_reaction_.py
@@ -5,6 +5,7 @@
 Create Date: 2019-08-19 16:35:19.100113
 
 """
+
 import sqlalchemy as sa
 from alembic import op
 from sqlalchemy.orm.session import Session

diff --git a/qcfractal/qcfractal/alembic/versions/2019-09-19-cc54842bb6ba_updates_dataset_pk.py b/qcfractal/qcfractal/alembic/versions/2019-09-19-cc54842bb6ba_updates_dataset_pk.py
@@ -5,9 +5,8 @@
 Create Date: 2019-09-19 15:10:26.146940
 
 """
-from alembic import op
-import sqlalchemy as sa
 
+from alembic import op
 
 # revision identifiers, used by Alembic.
 revision = "cc54842bb6ba"

diff --git a/qcfractal/qcfractal/alembic/versions/2019-09-30-c194a8ef6acf_protocols.py b/qcfractal/qcfractal/alembic/versions/2019-09-30-c194a8ef6acf_protocols.py
@@ -5,8 +5,9 @@
 Create Date: 2019-09-30 10:31:23.552722
 
 """
-from alembic import op
+
 import sqlalchemy as sa
+from alembic import op
 from sqlalchemy.dialects import postgresql
 
 # revision identifiers, used by Alembic.

diff --git a/...fractal/alembic/versions/2019-10-08-a2f76bb7be65_updates_collections_table_with_owner_.py b/...fractal/alembic/versions/2019-10-08-a2f76bb7be65_updates_collections_table_with_owner_.py
@@ -5,6 +5,7 @@
 Create Date: 2019-10-08 11:06:15.438742
 
 """
+
 import sqlalchemy as sa
 from alembic import op
 

diff --git a/qcfractal/qcfractal/alembic/versions/2019-10-17-1bd2f7711e68_wavefunction_table.py b/qcfractal/qcfractal/alembic/versions/2019-10-17-1bd2f7711e68_wavefunction_table.py
@@ -5,10 +5,11 @@
 Create Date: 2019-10-17 14:03:07.364322
 
 """
-from alembic import op
+
 import sqlalchemy as sa
-import qcfractal
+from alembic import op
 
+import qcfractal
 
 # revision identifiers, used by Alembic.
 import qcfractal.db_socket.column_types