Upgrade to Python 3.14 by alongd · Pull Request #171 · ReactionMechanismGenerator/T3

alongd · 2026-06-06T11:25:07Z

Bumps T3 to Python 3.14.

Changes

Runtime → 3.14: environment.yml + pyproject.toml (cython ≥3.1, rdkit ≥2026.03, ruff target-version = py314). Added the danagroup channel for openbabel and py-rdl, which have no py314
builds on conda-forge.
cantera/numpy-2.x fix: the simulate adapters indexed thermo[species_names_list].X, which triggers numpy 2.x's stricter ndarray.resize check and breaks every cantera run on 3.14.
Switched to indexing the full mole-fraction array (batch + both PFR adapters).
Type hints modernized to PEP 585/604 (List→list, Optional[X]→X | None, …); ruff check . passes.
CI: dropped the redundant PyRDL step (now in environment.yml) and pointed RMG-Py at main (xTB is merged upstream).
Docs: Python badge + prerequisites → 3.14+.

Bump the runtime to Python 3.14, mirroring ARC: - environment.yml: python =3.14, cython >=3.1, rdkit >=2026.03 - pyproject.toml: requires-python >=3.14, ruff target-version py314 Add the danagroup channel for openbabel and py-rdl, which have no py314 builds on conda-forge (the same builds ARC uses). cantera stays a loose >=3.2.0 core dep (conda-forge has a py314 build). CI: drop the now-redundant install_pyrdl.sh step (py-rdl is provided by environment.yml) and check out RMG-Py main for rmg_env (the xTB feature is merged upstream). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

cantera's Solution.__getitem__ with a list of species names sets selected_species, which calls ndarray.resize(); numpy 2.x rejects this with "cannot resize an array that may be referenced by another object", breaking every cantera simulation (batch + PFR) on the Python 3.14 stack. Index the full mole-fraction array via species_index instead, which is equivalent (species_names_list is the full model species set) and avoids the resize path. Applied to the batch base adapter and both PFR adapters. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

List/Dict/Tuple -> list/dict/tuple, Optional[X] -> X | None, Union[X, Y] -> X | Y, and drop the now-unused typing imports (ruff UP006/UP007/UP035/UP045 + F401). ~500 annotation rewrites. `ruff check .` passes under target-version py314. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Update the Python badge and the Prerequisites line from 3.12+ to 3.14+. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

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Pull request overview

Upgrades T3’s supported runtime to Python 3.14, modernizes type annotations to PEP 585/604, and includes a Cantera/Numpy 2.x compatibility fix in the simulation adapters, along with corresponding environment/CI/docs updates.

Changes:

Bump declared Python support to 3.14 (packaging + conda env + docs + ruff target version).
Update many type hints to built-in generics and X | None unions.
Fix Cantera adapter species mole-fraction collection to avoid Numpy 2.x resize() refcheck failures.

Reviewed changes

Copilot reviewed 25 out of 25 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
tests/test_utils/test_libraries.py	Update typing annotations to built-in generics.
tests/test_logger.py	Replace `Optional[...]` hints with `X
tests/common.py	Modernize optional type hints.
t3/utils/rmg_shim.py	Remove legacy typing imports; modernize hints across shim dataclasses/APIs.
t3/utils/rmg_sa_parser.py	Modernize return/variable annotations to built-in generics.
t3/utils/libraries.py	Modernize typing and dict/list annotations; lock/util signatures updated.
t3/utils/flux.py	Update function signatures and typing to built-in generics/PEP 604.
t3/utils/fix_cantera.py	Modernize typing for traceback/duplicate-reaction helpers.
t3/utils/cantera_parser.py	Modernize typing for YAML parsing helpers.
t3/simulate/rmg_constant_tp.py	Update adapter typing annotations (observables, SA return types).
t3/simulate/factory.py	Update adapter registration/factory typing (`type[...]`, `X
t3/simulate/cantera_pfr.py	Change species mole-fraction indexing to avoid Cantera `__getitem__` path.
t3/simulate/cantera_pfr_t_profile.py	Same Cantera mole-fraction indexing adjustment as other adapters.
t3/simulate/cantera_base.py	Apply the Cantera/Numpy 2.x-safe mole-fraction indexing in base simulate loop.
t3/schema.py	Modernize Pydantic model field type annotations to PEP 604/built-in generics.
t3/runners/rmg_runner.py	Modernize runner function annotations and return types.
t3/runners/rmg_incore_sa.py	Update return typing to built-in generics.
t3/main.py	Modernize optional and collection type hints.
t3/logger.py	Update typed container annotations for log helpers.
t3/common.py	Modernize typing; update helper signatures/return types.
t3/chem.py	Modernize typing in core Species/Reaction wrappers.
README.md	Update Python version badge and prerequisites to 3.14+.
pyproject.toml	Set `requires-python >=3.14` and ruff `target-version = py314`.
environment.yml	Pin python to 3.14, bump deps, add `danagroup` channel and packages.
.github/workflows/ci.yml	Point RMG-Py checkout to `main` and remove redundant PyRDL install step.

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-def check_race_condition(race_path: str, logger: Optional["Logger"] = None) -> bool:
+def check_race_condition(race_path: str, logger: "Logger" | None = None) -> bool:


 def load_rmg_species_dictionary_file(
    dict_path: str,
-    logger: Optional["Logger"] = None,
+    logger: "Logger" | None = None,
    *,


 def get_species_by_label(label: str,
                         species_list: list['T3Species'],
-                         ) -> Optional['T3Species']:
+                         ) -> 'T3Species' | None:
    """


 def run_arkane_job(input_file: str,
                   output_directory: str,
                   plot: bool = False,
-                   logger: Optional['Logger'] = None,
+                   logger: 'Logger' | None = None,
                   ) -> bool:


The ruff UP045 sweep turned Optional["Logger"] into the partially-quoted union "Logger" | None, which evaluates str.__or__(None) -> TypeError if the annotation is ever introspected (get_type_hints / pydantic / inspect). Python 3.14 defers annotation evaluation so import doesn't crash, but the form is still invalid. Quote the entire union ("Logger | None", 'T3Species | None') so it resolves correctly for TYPE_CHECKING forward refs. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

RMG main now writes the chemkin-translated model to RMG/cantera_from_ck/chem_annotated.yaml instead of RMG/cantera/. Point set_paths at the new location and migrate the committed test fixtures to match. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

codecov-commenter · 2026-06-06T21:29:35Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 72.08%. Comparing base (4b53415) to head (9aa5fb0).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #171      +/-   ##
==========================================
- Coverage   72.37%   72.08%   -0.29%     
==========================================
  Files          35       35              
  Lines        4727     4678      -49     
  Branches      998      998              
==========================================
- Hits         3421     3372      -49     
  Misses        968      968              
  Partials      338      338

Flag	Coverage Δ
unittests	`72.08% <ø> (-0.29%)`	⬇️

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Rebased idt onto main (post py314 merge, PR #171). Integration fixes: - rmg_runner.fix_cantera_model_files: read RMG cantera output from 'cantera_from_ck/' instead of 'cantera/' (main moved it in 9aa5fb0) - migrate IDT test fixtures iteration_{0..4}/RMG/cantera -> cantera_from_ck to match the new layout - modernize idt type hints to PEP 585/604 (main removed the typing imports the idt code relied on, surfacing F821) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

alongd and others added 4 commits June 6, 2026 14:20

docs: bump Python requirement to 3.14 in README

ab26dcc

Update the Python badge and the Prerequisites line from 3.12+ to 3.14+. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

alongd requested a review from Copilot June 6, 2026 11:25

Copilot started reviewing on behalf of alongd June 6, 2026 11:25 View session

Copilot AI reviewed Jun 6, 2026

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alongd and others added 2 commits June 6, 2026 14:31

alongd force-pushed the py314 branch from 433e8e6 to 9aa5fb0 Compare June 6, 2026 20:36

alongd merged commit 25e1636 into main Jun 6, 2026
4 checks passed

alongd deleted the py314 branch June 6, 2026 21:34

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Upgrade to Python 3.14#171

Upgrade to Python 3.14#171
alongd merged 6 commits into
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		def check_race_condition(race_path: str, logger: Optional["Logger"] = None) -> bool:
		def check_race_condition(race_path: str, logger: "Logger" \| None = None) -> bool:

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