Fix NameError from TYPE_CHECKING annotations evaluated at runtime

arc/checks/nmd.py

@@ -2,6 +2,8 @@
 A module for checking the normal mode displacement of a TS.
 """
 
+from __future__ import annotations
+
 import numpy as np
 from collections import Counter
 from itertools import product

arc/checks/ts.py

@@ -2,6 +2,8 @@
 A module for checking the quality of TS-related calculations, contains helper functions for Scheduler.
 """
 
+from __future__ import annotations
+
 from itertools import product
 import os
 

arc/common.py

@@ -6,6 +6,8 @@
 VERSION is the full ARC version, using `semantic versioning <https://semver.org/>`_.
 """
 
+from __future__ import annotations
+
 import ast
 import datetime
 import logging

arc/family/family.py

@@ -2,6 +2,8 @@
 A module for working with RMG reaction families.
 """
 
+from __future__ import annotations
+
 from typing import TYPE_CHECKING
 import ast
 import functools

arc/job/adapters/cfour.py

@@ -7,6 +7,8 @@
 http://slater.chemie.uni-mainz.de/cfour/index.php?n=Main.ListOfKeywordsInAlphabeticalOrder
 """
 
+from __future__ import annotations
+
 import datetime
 import math
 import os

arc/job/adapters/common.py

@@ -3,6 +3,8 @@
 As such, it should not import any other ARC modules to avoid circular imports.
 """
 
+from __future__ import annotations
+
 import datetime
 import os
 import shutil

arc/job/adapters/gaussian.py

@@ -4,6 +4,8 @@
 https://gaussian.com/
 """
 
+from __future__ import annotations
+
 import datetime
 import math
 import os

arc/job/adapters/mockter.py

@@ -2,6 +2,8 @@
 An adapter for dummy jobs, meant for testing and debugging only.
 """
 
+from __future__ import annotations
+
 import datetime
 import os
 from typing import TYPE_CHECKING

arc/job/adapters/molpro.py

@@ -4,6 +4,8 @@
 https://www.molpro.net/
 """
 
+from __future__ import annotations
+
 import datetime
 import math
 import os

arc/job/adapters/obabel.py

@@ -3,6 +3,8 @@
 http://openbabel.org/docs/current/
 """
 
+from __future__ import annotations
+
 import datetime
 import os
 import subprocess

arc/job/adapters/orca.py

@@ -4,6 +4,8 @@
 https://orcaforum.kofo.mpg.de/app.php/portal
 """
 
+from __future__ import annotations
+
 import datetime
 import math
 import os

arc/job/adapters/psi_4.py

@@ -4,6 +4,8 @@
 https://www.psicode.org/
 """
 
+from __future__ import annotations
+
 import datetime
 import math
 import os

arc/job/adapters/qchem.py

@@ -4,6 +4,8 @@
 https://www.q-chem.com/
 """
 
+from __future__ import annotations
+
 import datetime
 import os
 from typing import TYPE_CHECKING

arc/job/adapters/terachem.py

@@ -4,6 +4,8 @@
 http://www.petachem.com/products.html
 """
 
+from __future__ import annotations
+
 import datetime
 import math
 import os

arc/job/adapters/torch_ani.py

@@ -6,6 +6,8 @@
 ASE: https://wiki.fysik.dtu.dk/ase/index.html, https://core.ac.uk/download/84004505.pdf
 """
 
+from __future__ import annotations
+
 import datetime
 import os
 from typing import TYPE_CHECKING

arc/job/adapters/ts/autotst_ts.py

@@ -4,6 +4,8 @@
 https://github.com/ReactionMechanismGenerator/AutoTST
 """
 
+from __future__ import annotations
+
 import datetime
 import os
 from typing import TYPE_CHECKING

arc/job/adapters/ts/gcn_ts.py

@@ -7,6 +7,8 @@
 https://chemrxiv.org/articles/Genereting_Transition_States_of_Isomerization_Reactions_with_Deep_Learning/12302084
 """
 
+from __future__ import annotations
+
 import datetime
 import os
 from typing import TYPE_CHECKING

arc/job/adapters/ts/heuristics.py

@@ -15,6 +15,8 @@
       Can/should we try both?
 """
 
+from __future__ import annotations
+
 import copy
 import datetime
 import itertools

arc/job/adapters/ts/kinbot_ts.py

@@ -4,6 +4,8 @@
 https://github.com/zadorlab/KinBot
 """
 
+from __future__ import annotations
+
 import datetime
 from typing import TYPE_CHECKING
 

arc/job/adapters/ts/linear.py

@@ -132,6 +132,8 @@
 degraded-mode smoke test).
 """
 
+from __future__ import annotations
+
 import copy
 import datetime
 import math

arc/job/adapters/ts/linear_utils/addition.py

@@ -2,6 +2,8 @@
 Fragment-based addition / dissociation TS geometry builders
 """
 
+from __future__ import annotations
+
 from collections import deque
 from functools import partial
 from itertools import permutations, product

arc/job/adapters/ts/linear_utils/families.py

@@ -22,6 +22,8 @@
 unambiguously or the resulting geometry collides.
 """
 
+from __future__ import annotations
+
 import logging
 from collections import deque
 from typing import TYPE_CHECKING

arc/job/adapters/ts/linear_utils/geom_utils.py

@@ -13,6 +13,8 @@
 * :func:`split_mol_at_bonds`: split a molecule into connected components after removing specified bonds.
 """
 
+from __future__ import annotations
+
 from collections import deque
 from typing import TYPE_CHECKING
 from collections.abc import Sequence

arc/job/adapters/ts/linear_utils/isomerization.py

@@ -4,6 +4,8 @@
 extracted from ``arc.job.adapters.ts.linear``.
 """
 
+from __future__ import annotations
+
 from collections import defaultdict, deque
 from typing import TYPE_CHECKING
 

arc/job/adapters/ts/linear_utils/local_geometry.py

@@ -58,6 +58,8 @@
 :mod:`arc.job.adapters.ts.linear_utils.migration_inference`.
 """
 
+from __future__ import annotations
+
 from typing import TYPE_CHECKING
 from collections.abc import Sequence
 

arc/job/adapters/ts/linear_utils/math_zmat.py

@@ -3,6 +3,8 @@
 extracted from ``arc.job.adapters.ts.linear``.
 """
 
+from __future__ import annotations
+
 import copy
 from typing import TYPE_CHECKING
 

arc/job/adapters/ts/linear_utils/migration_inference.py

@@ -32,6 +32,8 @@
 or ``None``; they never mutate inputs.
 """
 
+from __future__ import annotations
+
 from typing import TYPE_CHECKING
 from collections.abc import Sequence
 

arc/job/adapters/ts/linear_utils/path_spec.py

@@ -60,6 +60,8 @@
 change generation policies.
 """
 
+from __future__ import annotations
+
 from collections import deque
 from dataclasses import dataclass, field
 from enum import Enum

arc/job/adapters/ts/linear_utils/postprocess.py

@@ -24,6 +24,8 @@
     based on the ``FAMILY_POSTPROCESSORS`` registry.
 """
 
+from __future__ import annotations
+
 from typing import TYPE_CHECKING
 from collections.abc import Callable, Sequence
 

arc/job/adapters/ts/orca_neb.py

@@ -5,6 +5,8 @@
 https://www.faccts.de/docs/orca/6.1/manual/contents/structurereactivity/neb.html
 """
 
+from __future__ import annotations
+
 import datetime
 import os
 from typing import TYPE_CHECKING

arc/job/adapters/ts/xtb_gsm.py

@@ -12,6 +12,8 @@
 Advanced GSM settings: https://github.com/ZimmermanGroup/molecularGSM/wiki#items-of-note-and-advanced-options
 """
 
+from __future__ import annotations
+
 import datetime
 import os
 import shutil

arc/job/adapters/xtb_adapter.py

@@ -6,6 +6,8 @@
 run types: https://xtb-docs.readthedocs.io/en/latest/commandline.html?highlight=--grad#runtypes
 """
 
+from __future__ import annotations
+
 import datetime
 import os
 from typing import TYPE_CHECKING

arc/job/factory.py

@@ -2,6 +2,8 @@
 A module for generating job adapters.
 """
 
+from __future__ import annotations
+
 from typing import TYPE_CHECKING
 
 from arc.exceptions import JobError

arc/job/pipe/pipe_planner.py

@@ -24,6 +24,8 @@
   hitting ``min_tasks``.  Wire when workload stats justify it.
 """
 
+from __future__ import annotations
+
 from collections import Counter
 from typing import TYPE_CHECKING
 from collections.abc import Callable

arc/job/pipe/pipe_run.py

@@ -12,6 +12,8 @@
 All QA, troubleshooting, and downstream branching remain in mother ARC.
 """
 
+from __future__ import annotations
+
 import json
 import os
 import stat

arc/job/pipe/pipe_state.py

@@ -22,6 +22,8 @@
                         worker.log     # per-attempt log
 """
 
+from __future__ import annotations
+
 import fcntl
 import json
 import os

arc/job/ssh.py

@@ -6,6 +6,8 @@
     * delete scratch files of a failed job: ssh nodeXX; rm scratch/dhdhdhd/job_number
 """
 
+from __future__ import annotations
+
 import datetime
 import logging
 import os

arc/level.py

@@ -2,6 +2,8 @@
 A module for working with levels of theory.
 """
 
+from __future__ import annotations
+
 import os
 from collections.abc import Iterable
 

arc/mapping/driver.py

@@ -7,6 +7,8 @@
     3) If the reaction is supported by RMG, it is sent to the driver. Else, it is mapped with map_general_rxn.
 """
 
+from __future__ import annotations
+
 from typing import TYPE_CHECKING
 
 from arc.common import logger

arc/mapping/engine.py

@@ -7,6 +7,8 @@
     3) The atom map is returned to the driver.
 """
 
+from __future__ import annotations
+
 import numpy as np
 from collections import deque
 from itertools import product

arc/parser/adapter.py

@@ -2,6 +2,8 @@
 A module for the abstract ESSAdapter class
 """
 
+from __future__ import annotations
+
 import os
 import time
 from abc import ABC, abstractmethod

arc/parser/adapters/qchem.py

@@ -2,6 +2,8 @@
 An adapter for parsing Q-Chem log files.
 """
 
+from __future__ import annotations
+
 from abc import ABC
 
 import numpy as np

arc/parser/adapters/terachem.py

@@ -2,6 +2,8 @@
 An adapter for parsing CFOUR log files.
 """
 
+from __future__ import annotations
+
 from abc import ABC
 
 import numpy as np

arc/parser/adapters/yaml.py

@@ -2,6 +2,8 @@
 An adapter for parsing YAML log files created by ARC for other packages.
 """
 
+from __future__ import annotations
+
 from abc import ABC
 
 import numpy as np