sort imports

src/kimmdy/analysis.py

@@ -2,24 +2,25 @@
 For command line usage, run `kimmdy-analysis -h`.
 """
 
-from typing import Optional, Union
-from pathlib import Path
-import MDAnalysis as mda
+import argparse
+import json
 import subprocess as sp
-import matplotlib.pyplot as plt
-import matplotlib.patches as mpatches
+from datetime import datetime
+from pathlib import Path
+from typing import Optional, Union
+
 import matplotlib as mpl
-import seaborn.objects as so
+import matplotlib.patches as mpatches
+import matplotlib.pyplot as plt
+import MDAnalysis as mda
+import pandas as pd
 import seaborn as sns
-import argparse
+import seaborn.objects as so
 from seaborn import axes_style
-import pandas as pd
-from datetime import datetime
-import json
 
-from kimmdy.utils import run_shell_cmd
 from kimmdy.parsing import read_json, write_json
-from kimmdy.recipe import RecipeCollection, Break, Bind, Place, Relax
+from kimmdy.recipe import Bind, Break, Place, RecipeCollection
+from kimmdy.utils import run_shell_cmd
 
 
 def get_analysis_dir(dir: Path) -> Path:

src/kimmdy/cmd.py

@@ -4,27 +4,28 @@
 """
 
 import argparse
+import logging
+import logging.config
+import os
+import sys
+import textwrap
 from os import chmod
 from pathlib import Path
-import textwrap
 from typing import Optional
+
 import dill
-import logging
-import logging.config
-from kimmdy.config import Config
-from kimmdy.runmanager import RunManager
+
 from kimmdy.assets.templates import jobscript
-from kimmdy.utils import longFormatter
-from kimmdy.plugins import discover_plugins
+from kimmdy.config import Config
 from kimmdy.plugins import (
-    reaction_plugins,
+    broken_parameterization_plugins,
     broken_reaction_plugins,
+    discover_plugins,
     parameterization_plugins,
-    broken_parameterization_plugins,
+    reaction_plugins,
 )
-import importlib.resources as pkg_resources
-import sys
-import os
+from kimmdy.runmanager import RunManager
+from kimmdy.utils import longFormatter
 
 if sys.version_info > (3, 10):
     from importlib_metadata import version
@@ -258,9 +259,9 @@ def _run(args: argparse.Namespace):
             if args.callgraph:
                 try:
                     from pycallgraph2 import PyCallGraph
-                    from pycallgraph2.output import GraphvizOutput
                     from pycallgraph2.config import Config as Vis_conf
                     from pycallgraph2.globbing_filter import GlobbingFilter
+                    from pycallgraph2.output import GraphvizOutput
                 except ImportError as e:
                     logger.error(
                         "pycallgraph2 needed for call visualization. Get it with `pip install pycallgraph2`"

src/kimmdy/config.py

@@ -4,19 +4,22 @@
 """
 
 from __future__ import annotations
+
 import shutil
-from pprint import pformat, pprint
+from pathlib import Path
+from pprint import pformat
 from typing import Any, Optional
+
 import yaml
-from pathlib import Path
+
 from kimmdy.plugins import (
-    reaction_plugins,
+    broken_parameterization_plugins,
     broken_reaction_plugins,
     parameterization_plugins,
-    broken_parameterization_plugins,
+    reaction_plugins,
 )
-from kimmdy.schema import Sequence, get_combined_scheme
-from kimmdy.utils import get_gmx_dir, check_file_exists, check_gmx_version
+from kimmdy.schema import get_combined_scheme
+from kimmdy.utils import check_file_exists, check_gmx_version, get_gmx_dir
 
 
 class Config:

src/kimmdy/coordinates.py

@@ -1,31 +1,32 @@
 """coordinate, topology and plumed modification functions"""
 
 import logging
-from typing import Optional, Union
 from copy import deepcopy
-import MDAnalysis as mda
 from pathlib import Path
+from typing import Optional, Union
+
+import MDAnalysis as mda
 import numpy as np
 
-from kimmdy.tasks import TaskFiles
-from kimmdy.parsing import read_plumed, write_plumed
 from kimmdy.constants import REACTIVE_MOLECULEYPE
+from kimmdy.parsing import read_plumed, write_plumed
 from kimmdy.recipe import Place
-from kimmdy.topology.topology import MoleculeType, Topology
-from kimmdy.topology.ff import FF
+from kimmdy.tasks import TaskFiles
 from kimmdy.topology.atomic import (
-    Bond,
     Angle,
+    Bond,
     Dihedral,
     DihedralType,
-    ProperDihedralId,
+    Exclusion,
     ImproperDihedralId,
-    MultipleDihedrals,
     Interaction,
     InteractionType,
     InteractionTypes,
-    Exclusion,
+    MultipleDihedrals,
+    ProperDihedralId,
 )
+from kimmdy.topology.ff import FF
+from kimmdy.topology.topology import MoleculeType, Topology
 from kimmdy.topology.utils import match_atomic_item_to_atomic_type
 
 logger = logging.getLogger(__name__)

src/kimmdy/kmc.py

@@ -8,13 +8,15 @@
 and because we have one reactant molecule
 """
 
-from typing import Optional
 import logging
-import numpy as np
-from itertools import pairwise
 from dataclasses import dataclass, field
+from itertools import pairwise
+from typing import Optional
+
+import numpy as np
 from numpy.random import default_rng
-from kimmdy.recipe import RecipeCollection, Recipe
+
+from kimmdy.recipe import Recipe, RecipeCollection
 
 
 @dataclass

src/kimmdy/parsing.py

@@ -2,14 +2,14 @@
 All read_<...> and write_<...> functions.
 """
 
-import os
-import logging
 import json
-import numpy as np
-from pathlib import Path
-from typing import Optional, Union
+import logging
+import os
 from itertools import takewhile
-from typing import TypedDict
+from pathlib import Path
+from typing import Optional, TypedDict, Union
+
+import numpy as np
 
 from kimmdy.utils import get_gmx_dir
 

src/kimmdy/plugins.py

@@ -4,15 +4,16 @@
 """
 
 from __future__ import annotations
-from typing import TYPE_CHECKING
-from abc import ABC, abstractmethod
+
 import logging
 import sys
+from abc import ABC, abstractmethod
+from typing import TYPE_CHECKING
 
 if TYPE_CHECKING:
-    from kimmdy.runmanager import RunManager
     from kimmdy.config import Config
     from kimmdy.recipe import RecipeCollection
+    from kimmdy.runmanager import RunManager
     from kimmdy.tasks import TaskFiles
     from kimmdy.topology.topology import Topology
 

src/kimmdy/recipe.py

@@ -2,15 +2,16 @@
 """
 
 from __future__ import annotations
-from typing import TYPE_CHECKING, Callable, Optional
 
+import csv
+import logging
 from abc import ABC
+from copy import copy
 from dataclasses import dataclass, field
 from pathlib import Path
-import logging
-from copy import copy
+from typing import TYPE_CHECKING, Callable, Optional
+
 import dill
-import csv
 import numpy as np
 
 logger = logging.getLogger(__name__)
@@ -527,8 +528,8 @@ def plot(self, outfile, highlight_r=None, highlight_t=None):
         """
 
         import matplotlib.pyplot as plt
-        import seaborn as sns
         import numpy as np
+        import seaborn as sns
 
         self.aggregate_reactions()
         cumprob = self.calc_cumprob()

src/kimmdy/runmanager.py

@@ -6,32 +6,35 @@
 """
 
 from __future__ import annotations
+
 import logging
-from pathlib import Path
-from copy import copy, deepcopy
-import dill
 import queue
+import time
+from copy import copy, deepcopy
+from datetime import timedelta
 from enum import Enum, auto
 from functools import partial
-from datetime import timedelta
+from pathlib import Path
+from pprint import pformat
 from typing import Optional
+
+import dill
+
 from kimmdy.config import Config
+from kimmdy.coordinates import break_bond_plumed, merge_top_slow_growth, place_atom
+from kimmdy.kmc import KMCResult, extrande, extrande_mod, frm, rf_kmc
 from kimmdy.parsing import read_top, write_json, write_top
 from kimmdy.plugins import (
     BasicParameterizer,
+    ReactionPlugin,
     parameterization_plugins,
     reaction_plugins,
-    ReactionPlugin,
 )
-from kimmdy.recipe import CustomTopMod, RecipeCollection, Break, Bind, Place, Relax
-from kimmdy.utils import run_gmx, truncate_sim_files
-from kimmdy.coordinates import place_atom, break_bond_plumed, merge_top_slow_growth
+from kimmdy.recipe import Bind, Break, CustomTopMod, Place, RecipeCollection, Relax
 from kimmdy.tasks import Task, TaskFiles, get_plumed_out
-from pprint import pformat
 from kimmdy.topology.topology import Topology
 from kimmdy.topology.utils import get_is_reactive_predicate_f
-import time
-from kimmdy.kmc import KMCResult, rf_kmc, extrande, frm, extrande_mod
+from kimmdy.utils import run_gmx, truncate_sim_files
 
 logger = logging.getLogger(__name__)
 

src/kimmdy/schema.py

@@ -11,17 +11,18 @@
     - required
 """
 
-import json
 import importlib.resources as pkg_resources
+import json
 import logging
-from kimmdy.plugins import reaction_plugins
 
 # needed for eval of type_scheme from schema
 # don't remove even if lsp says it's unused
-import kimmdy
 import pathlib
 from pathlib import Path
 
+import kimmdy
+from kimmdy.plugins import reaction_plugins
+
 logger = logging.getLogger(__name__)
 
 

src/kimmdy/tasks.py

@@ -3,11 +3,12 @@
 output paths and the Task class for steps in the runmanager.
 """
 
+import logging
+import shutil
 from dataclasses import dataclass, field
 from pathlib import Path
-import shutil
 from typing import Any, Callable, Optional
-import logging
+
 from kimmdy.parsing import read_plumed
 from kimmdy.utils import longFormatter
 
@@ -144,7 +145,7 @@ def __init__(
 
         logger.debug(f"Init task {self.name}\tkwargs: {self.kwargs}\tOut: {self.out}")
 
-    def __call__(self) -> TaskFiles:
+    def __call__(self) -> Optional[TaskFiles]:
         if self.out is not None:
             self.kwargs.update({"files": create_task_directory(self.runmng, self.out)})
 

src/kimmdy/tools.py

@@ -2,16 +2,15 @@
 Standalone tools that are complementary to KIMMDY.
 """
 
-from pathlib import Path
-import shutil
 import argparse
-from typing import Optional
 import json
+import shutil
+from pathlib import Path
+from typing import Optional
 
-from kimmdy.topology.topology import Topology
 from kimmdy.parsing import read_top, write_top
-from kimmdy.plugins import parameterization_plugins
-from kimmdy.plugins import discover_plugins
+from kimmdy.plugins import discover_plugins, parameterization_plugins
+from kimmdy.topology.topology import Topology
 
 
 def build_examples(restore: str):