Migrating ARC to Python 14 by alongd · Pull Request #867 · ReactionMechanismGenerator/ARC

alongd · 2026-04-11T10:26:25Z

Bump the target runtime from 3.12 to 3.14 and modernize the codebase accordingly.

Update Python, Cython (≥3.1), and RDKit (≥2026.03) pins across environment.yml, requirements.txt, Dockerfile, and pyproject.toml
Fix stale check_python() gate that still referenced Python 3.7 / RMG-Py
Remove dead from future import print_function and deprecated assertDictEqual
Replace deprecated typing generics with built-in equivalents (list, dict, X | None, X | Y, collections.abc) across 70 files (−828 lines net)

RMG's separate Python 3.9 environment is unchanged.

arc/common.py


-
-def get_git_branch(path: Optional[str] = None) -> str:
+def get_git_branch(path: str | None = None) -> str:


arc/common.py

+def is_same_pivot(torsion1: list | str,
+                  torsion2: list | str,
+                  ) -> bool | None:


Copilot

Pull request overview

This PR migrates ARC’s runtime baseline to Python 3.14 and modernizes the codebase accordingly (dependency pins, version gating, and widespread typing updates).

Changes:

Bump Python target/runtime metadata (3.12 → 3.14) and update dependency minimums (e.g., Cython/RDKit) across env/packaging artifacts.
Update Python-version gate logic and remove deprecated/legacy Python constructs.
Replace deprecated typing generics with built-in generics / X | None annotations across many modules.

Reviewed changes

Copilot reviewed 76 out of 77 changed files in this pull request and generated 15 comments.

Show a summary per file

File	Description
utilities.py	Updates runtime Python version gate messaging/threshold.
requirements.txt	Raises minimum Python/RDKit/Cython versions (but see review comments).
pyproject.toml	Adds Python version metadata for packaging.
environment.yml	Pins conda env to Python 3.14 and updates Cython/RDKit pins.
Dockerfile	Builds ARC micromamba env with Python 3.14.
arc/utils/scale.py	Modernizes typing annotations and removes legacy `typing` imports.
arc/statmech/factory.py	Modernizes typing annotations for factory registration and adapter creation.
arc/species/vectors.py	Modernizes typing annotations for vector utilities.
arc/scripts/rmg_thermo.py	Updates typing annotations in the RMG thermo helper script.
arc/scripts/rmg_kinetics.py	Updates typing annotations in the RMG kinetics helper script.
arc/scripts/pipe_worker.py	Updates typing annotations in the pipe-mode worker script.
arc/scripts/common.py	Updates typing annotations for YAML I/O helpers.
arc/processor.py	Updates typing annotations around postprocessing helpers.
arc/parser/factory.py	Modernizes adapter registration typing.
arc/parser/adapters/yaml.py	Modernizes typing annotations for YAML parsing adapter.
arc/parser/adapters/xtb.py	Modernizes typing annotations for xTB parsing adapter.
arc/parser/adapters/terachem.py	Modernizes typing annotations for TeraChem parsing adapter.
arc/parser/adapters/qchem.py	Modernizes typing annotations for Q-Chem parsing adapter.
arc/parser/adapters/psi_4.py	Modernizes typing annotations for Psi4 parsing adapter.
arc/parser/adapters/orca.py	Modernizes typing annotations for ORCA parsing adapter.
arc/parser/adapters/molpro.py	Modernizes typing annotations for Molpro parsing adapter.
arc/parser/adapters/cfour.py	Modernizes typing annotations for CFOUR parsing adapter.
arc/parser/adapter.py	Modernizes abstract adapter typing for ESS parsers.
arc/output.py	Modernizes typing annotations while writing consolidated `output.yml`.
arc/molecule/resonance.py	Updates typing annotations for resonance utilities.
arc/molecule/molecule_test.py	Replaces deprecated `assertDictEqual` usage.
arc/molecule/draw.py	Updates typing annotations for drawing utilities.
arc/mapping/driver.py	Updates typing annotations for reaction mapping utilities.
arc/main.py	Modernizes typing annotations in ARC main class and helpers.
arc/level.py	Updates typing annotations and switches to `collections.abc.Iterable`.
arc/job/ssh.py	Modernizes typing annotations for SSH client utilities.
arc/job/pipe/pipe_state.py	Modernizes typing annotations for pipe state/records.
arc/job/pipe/pipe_planner.py	Modernizes typing annotations for pipe task planning.
arc/job/pipe/pipe_coordinator.py	Modernizes typing annotations for coordinating pipe runs.
arc/job/local.py	Modernizes typing annotations for local execution helpers.
arc/job/factory.py	Modernizes typing annotations for job adapter factory/registration.
arc/job/adapters/xtb_adapter.py	Modernizes typing annotations for xTB job adapter.
arc/job/adapters/ts/xtb_gsm.py	Modernizes typing annotations for xTB-GSM TS adapter.
arc/job/adapters/ts/orca_neb.py	Modernizes typing annotations for ORCA NEB TS adapter.
arc/job/adapters/ts/kinbot_ts.py	Modernizes typing annotations for KinBot TS adapter.
arc/job/adapters/ts/gcn_ts.py	Modernizes typing annotations for GCN TS adapter.
arc/job/adapters/ts/autotst_ts.py	Modernizes typing annotations for AutoTST TS adapter.
arc/job/adapters/torch_ani.py	Modernizes typing annotations for TorchANI adapter/scripts.
arc/job/adapters/terachem.py	Modernizes typing annotations for TeraChem job adapter.
arc/job/adapters/scripts/xtb_gsm/tm2orca.py	Removes dead `__future__` import usage.
arc/job/adapters/scripts/tani_script.py	Modernizes typing annotations in helper script.
arc/job/adapters/scripts/autotst_script.py	Modernizes typing annotations in helper script.
arc/job/adapters/qchem.py	Modernizes typing annotations for Q-Chem job adapter.
arc/job/adapters/psi_4.py	Modernizes typing annotations for Psi4 job adapter.
arc/job/adapters/orca.py	Modernizes typing annotations for ORCA job adapter.
arc/job/adapters/obabel.py	Modernizes typing annotations for OpenBabel job adapter.
arc/job/adapters/molpro.py	Modernizes typing annotations for Molpro job adapter.
arc/job/adapters/mockter.py	Modernizes typing annotations for mock adapter.
arc/job/adapters/gaussian.py	Modernizes typing annotations for Gaussian job adapter.
arc/job/adapters/common.py	Modernizes typing annotations for shared job-adapter helpers.
arc/job/adapters/cfour.py	Modernizes typing annotations for CFOUR job adapter.
arc/job/adapter.py	Modernizes typing annotations for the base JobAdapter API.
arc/checks/common.py	Modernizes typing annotations for common checks helpers.

Comments suppressed due to low confidence (1)

arc/output.py:37

write_output_yml() still annotates parameters as Dict/List, but those names are no longer imported (and there is no postponed annotation evaluation). This will raise NameError when importing arc.output. Replace these with built-in generics (dict[...], list[...]) or re-import the typing aliases, and apply the same fix to other Dict/List annotations in this file.

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Copilot · 2026-04-11T10:33:30Z

arc/job/local.py

+def _output_command_error_message(command: list[str],
                                  error: subprocess.CalledProcessError,
-                                  logging_func: Union[logger.warning, logger.error],
+                                  logging_func: logger.warning | logger.error,
                                  ) -> None:


_output_command_error_message() uses logging_func: logger.warning | logger.error as a type annotation. Since this module does not use postponed annotation evaluation, this expression is evaluated at import time and will raise TypeError (bitwise-or between bound methods). Use a Callable[[object], object]/Callable[..., Any] annotation instead (or stringize via from __future__ import annotations).

Copilot · 2026-04-11T10:33:30Z

arc/job/adapters/common.py


-
-def combine_parameters(input_dict: dict, terms: list) -> Tuple[dict, List]:
+def combine_parameters(input_dict: dict, terms: list) -> tuple[dict, List]:


combine_parameters() annotates its return type as tuple[dict, List], but List is no longer imported in this module. Because annotations are evaluated at function definition time here, importing this module will raise NameError: name 'List' is not defined. Replace List with a built-in list[...] type (or re-import List).

Suggested change

def combine_parameters(input_dict: dict, terms: list) -> tuple[dict, List]:

def combine_parameters(input_dict: dict, terms: list) -> tuple[dict, list]:

Copilot · 2026-04-11T10:33:31Z

arc/parser/adapter.py

    @abstractmethod
-    def parse_frequencies(self) -> Optional['np.ndarray']:
+    def parse_frequencies(self) -> 'np.ndarray' | None:
        """


This module now uses return annotations like 'np.ndarray' | None (e.g. parse_frequencies). Without postponed annotation evaluation (from __future__ import annotations), this is evaluated at import time and raises TypeError because it's a str | None expression. Use np.ndarray | None (and import numpy at runtime) or use a single quoted forward reference like 'np.ndarray | None' / enable postponed evaluation.

Copilot · 2026-04-11T10:33:31Z

arc/parser/adapters/yaml.py

+    def parse_frequencies(self) -> 'np.ndarray' | None:
        """
        Parse the frequencies from a freq job output file.

-        Returns: Optional[np.ndarray]
+        Returns: np.ndarray | None
            The parsed frequencies (in cm^-1).
        """
        freqs = self.data.get('freqs')
        return np.array(freqs, dtype=np.float64) if freqs else None

-    def parse_normal_mode_displacement(self) -> Tuple[Optional['np.ndarray'], Optional['np.ndarray']]:
+    def parse_normal_mode_displacement(self) -> tuple['np.ndarray' | None, 'np.ndarray' | None]:
        """


This file uses return annotations like 'np.ndarray' | None / tuple['np.ndarray' | None, ...] (see parse_frequencies / parse_normal_mode_displacement). Since annotations are evaluated immediately here, this will raise TypeError at import time. Prefer np.ndarray | None (no quotes) or enable postponed evaluation of annotations, and make sure np is available if using it directly.

Copilot · 2026-04-11T10:33:31Z

arc/parser/adapters/yaml.py

        return None

-    def parse_nd_scan_energies(self) -> Optional[Dict]:
+    def parse_nd_scan_energies(self) -> Dict | None:


parse_nd_scan_energies() is annotated as -> Dict | None, but Dict is no longer imported. With eager annotation evaluation, importing this module will raise NameError: name 'Dict' is not defined. Change this to dict | None (or re-import Dict).

Copilot · 2026-04-11T10:33:33Z

arc/parser/adapters/psi_4.py

        return None

-    def parse_nd_scan_energies(self) -> Optional[Dict]:
+    def parse_nd_scan_energies(self) -> Dict | None:


parse_nd_scan_energies() is annotated as -> Dict | None but Dict is not imported in this module. With eager annotation evaluation, importing the module will raise NameError. Use dict | None (or re-import Dict).

Copilot · 2026-04-11T10:33:33Z

arc/parser/adapters/terachem.py

        return None

-    def parse_nd_scan_energies(self) -> Optional[Dict]:
+    def parse_nd_scan_energies(self) -> Dict | None:


parse_nd_scan_energies() is annotated as -> Dict | None but Dict is not imported in this module anymore. This causes a NameError during import unless annotations are postponed. Replace Dict with dict (or re-import Dict).

Copilot · 2026-04-11T10:33:33Z

arc/parser/adapters/molpro.py

        return None

-    def parse_nd_scan_energies(self) -> Optional[Dict]:
+    def parse_nd_scan_energies(self) -> Dict | None:


parse_nd_scan_energies() is annotated as -> Dict | None but Dict is no longer imported in this module. This will raise NameError when importing the module. Use dict | None (or re-import Dict).

Copilot · 2026-04-11T10:33:33Z

arc/parser/adapters/cfour.py

        return None

-    def parse_nd_scan_energies(self) -> Optional[Dict]:
+    def parse_nd_scan_energies(self) -> Dict | None:


parse_nd_scan_energies() is annotated as -> Dict | None but Dict is not imported in this module. This will raise NameError at import time. Replace with dict | None (or re-import Dict).

Copilot · 2026-04-11T10:33:34Z

arc/job/adapters/torch_ani.py

                            )

-
    def write_input_file(self, settings : dict()) -> None:


write_input_file() annotates settings as dict(), which is a value expression evaluated at function definition time, not a type. This creates an empty dict object in __annotations__ and defeats type checking/introspection. Use dict or a parameterized type like dict[str, Any] instead.

Suggested change

def write_input_file(self, settings : dict()) -> None:

def write_input_file(self, settings: dict) -> None:

calvinp0 · 2026-04-11T10:48:09Z

I can't seem to properly comment on the line, and I know this has gone back to draft and I was not requested to review but I did see that the output.py still has Dict in it without either being imported or changed over

arc/molecule/translator.py

 from arc.common import get_logger
-from arc.exceptions import DependencyError
-from arc.molecule.converter import to_rdkit_mol, from_rdkit_mol, to_ob_mol, from_ob_mol
+from arc.molecule.converter import to_rdkit_mol, from_rdkit_mol


arc/molecule/translator.py

 from arc.common import get_logger
-from arc.exceptions import DependencyError
-from arc.molecule.converter import to_rdkit_mol, from_rdkit_mol, to_ob_mol, from_ob_mol
+from arc.molecule.converter import to_rdkit_mol, from_rdkit_mol


arc/job/adapters/torch_ani.py


-
-    def write_input_file(self, settings : dict()) -> None:
+    def write_input_file(self, settings: dict) -> None:


Update all version pins across environment.yml, requirements.txt, Dockerfile, and pyproject.toml for the Python 3.12 → 3.14 transition. Bump Cython (≥3.1 for 3.14 Limited API) and RDKit (≥2026.03 for 3.14 wheels). Fix the stale check_python() gate in utilities.py that still referenced Python 3.7. Remove dead `from __future__ import print_function` in tm2orca.py and deprecated assertDictEqual in molecule_test.py. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Replace deprecated typing generics with built-in equivalents across 70+ files: - List/Dict/Tuple/Set/Type → list/dict/tuple/set/type - Optional[X] → X | None - Union[X, Y] → X | Y - Sequence/Iterable/Callable → from collections.abc - typing.Match → re.Match Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

OpenBabel is effectively unmaintained (no Python 3.13+ build on conda-forge, stalled upstream PR since July 2025). RDKit already handles every critical path as the primary backend. Deleted: - obabel.py adapter, ob_script.py, and their tests - to_ob_mol/from_ob_mol, xyz_to_pybel_mol, pybel_to_inchi - openbabel_force_field, openbabel_force_field_on_rdkit_conformers, mix_rdkit_and_openbabel_force_field - OB perception fallback in alternative_perception() - _openbabel_translator backend (RDKit is now sole backend) - ob_environment.yml, install_ob.sh, install-ob Make target - All settings, enums, and data references The only loss is GAFF force field support (RDKit has MMFF94s/UFF). Accepts 'openbabel-first' backend kwarg for backwards compat. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Use explicit micromamba run -n arc_env for the docs build step (micromamba-shell defaulted to rmg_env). Add custom cache key to bust stale Python 3.12 environment cache. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

The typing modernization script replaced np.array with np.ndarray in function CALLS as well as annotations. Restore np.array() calls while keeping np.ndarray in type annotations. Also fix OB-specific SMILES 'C(1)CC(1)' → 'C1CC1' in test_scissors. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

alongd requested a review from Copilot April 11, 2026 10:26

github-actions bot added Module: Scheduler Module: Plotter Module: Species Module: Main Module: Processor Module: Conformers Module: SSH Module: Converter Module: Local Module: trsh Troubleshooting Module: Mapping labels Apr 11, 2026

Copilot started reviewing on behalf of alongd April 11, 2026 10:27 View session

github-advanced-security bot found potential problems Apr 11, 2026

View reviewed changes

arc/common.py

def get_git_branch(path: Optional[str] = None) -> str:

def get_git_branch(path: str | None = None) -> str:

arc/common.py

Comment on lines +1307 to +1309

def is_same_pivot(torsion1: list | str,

torsion2: list | str,

) -> bool | None:

alongd marked this pull request as draft April 11, 2026 10:32

Copilot AI reviewed Apr 11, 2026

View reviewed changes

github-advanced-security bot found potential problems Apr 11, 2026

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arc/job/adapters/torch_ani.py

def write_input_file(self, settings : dict()) -> None:

def write_input_file(self, settings: dict) -> None:

alongd and others added 4 commits April 12, 2026 08:01

Fix gh-pages workflow for Python 3.14

bfaad35

Use explicit micromamba run -n arc_env for the docs build step (micromamba-shell defaulted to rmg_env). Add custom cache key to bust stale Python 3.12 environment cache. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

alongd force-pushed the py14 branch from d56fb66 to bfaad35 Compare April 12, 2026 05:42

alongd force-pushed the py14 branch from 1071577 to c500ade Compare April 12, 2026 12:33

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Migrating ARC to Python 14#867

Migrating ARC to Python 14#867
alongd wants to merge 5 commits intomainfrom
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calvinp0 commented Apr 11, 2026 •

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		def get_git_branch(path: Optional[str] = None) -> str:
		def get_git_branch(path: str \| None = None) -> str:



		def combine_parameters(input_dict: dict, terms: list) -> Tuple[dict, List]:
		def combine_parameters(input_dict: dict, terms: list) -> tuple[dict, List]:

	def write_input_file(self, settings : dict()) -> None:
	def write_input_file(self, settings: dict) -> None:

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calvinp0 commented Apr 11, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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calvinp0 commented Apr 11, 2026 •

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