T3 Migration

[alongd]

An overhaul of the T3 repo

[Copilot]

Pull request overview

This PR performs a broad “T3 Migration” overhaul focused on reducing direct RMG-Py coupling, standardizing simulation adapters around a shared Cantera base, and modernizing packaging/CI + test fixtures to match the new architecture.

Changes:

• Introduces Cantera-based simulate adapters (TP/HP/UV + PFR) with a shared CanteraBase, plus a lightweight Cantera YAML parser and an RMG SA CSV parser that avoid rmgpy at runtime.
• Refactors the RMGConstantTP adapter to run SA via an incore subprocess script and YAML output, and updates writer/schema/tests accordingly.
• Updates repo packaging/CI/devtools and refreshes test data/fixtures for the new simulate + SA workflows.

Reviewed changes

Copilot reviewed 76 out of 94 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
tests/test_utils/test_writer.py	Updates expected RMG input writing behavior (pydantic model_dump, simulator args, adapter name changes).
tests/test_utils/test_libraries.py	Adds new unit tests for library append + atomic dictionary update behavior using shim APIs.
tests/test_utils/test_generator.py	Migrates radical generation tests from rmgpy.Species to T3Species.
tests/test_utils/test_fix_cantera.py	Adds tests for Cantera file fix utilities + traceback parsing.
tests/test_utils/test_cantera_parser.py	Adds test coverage for new Cantera YAML parser (species/reactions/thermo comment parsing).
tests/test_simulate/test_cantera_constant_uv.py	Adds Cantera constant-U/V adapter simulation tests.
tests/test_simulate/test_cantera_constant_hp.py	Adds Cantera constant-H/P adapter simulation tests.
tests/test_simulate/test_cantera_base.py	Adds comprehensive tests for shared CanteraBase behavior and regression fixes.
tests/test_simulate/data/rms_simulator_test/input.yml	Adds RMS simulator test input fixture.
tests/test_simulate/data/rmg_simulator_test/iteration_0/SA/solver/simulation_1_12.csv	Adds RMG SA fixture output (simulation profile).
tests/test_simulate/data/rmg_simulator_test/iteration_0/SA/solver/sensitivity_1_SPC_4.csv	Adds RMG SA fixture output (OH observable).
tests/test_simulate/data/rmg_simulator_test/iteration_0/SA/solver/sensitivity_1_SPC_3.csv	Adds RMG SA fixture output (H observable).
tests/test_simulate/data/rmg_simulator_test/iteration_0/RMG/solver/simulation_1_12.csv	Adds RMG fixture output (simulation profile).
tests/test_simulate/data/rmg_simulator_test/iteration_0/RMG/input.py	Updates stored RMG input fixture (simulator/options changes).
tests/test_simulate/data/rmg_simulator_test/iteration_0/RMG/chemkin/species_dictionary.txt	Adds fixture species dictionary for RMG/Cantera tests.
tests/test_simulate/data/rmg_simulator_test/input.yml	Adds RMG simulator test input fixture.
tests/test_simulate/data/cantera_simulator_test/iteration_0/RMG/input.py	Adds fixture RMG input used by Cantera simulate tests.
tests/test_simulate/data/cantera_simulator_test/iteration_0/RMG/chemkin/species_dictionary.txt	Adds fixture species dictionary used by Cantera simulate tests.
tests/test_simulate/data/cantera_simulator_test/input.yml	Adds Cantera simulator test input fixture.
tests/test_simulate_adapters/test_rmg_constantTP.py	Removes legacy adapter tests (superseded by new simulate test suite).
tests/test_simulate_adapters/data/rmg_simulator_test_ranges_3c/t3.log	Removes legacy log fixture.
tests/test_schema.py	Updates schema tests for adapter defaults and termination_time typing.
tests/test_runners/test_rmg_runner.py	Updates expected submit/run commands from python-jl to python.
tests/test_libraries.py	Removes old rmgpy-dependent library tests (replaced by shim-based tests).
tests/test_functional.py	Updates functional tests/log assertions for the migrated workflow and makes backup test more isolated.
tests/test_common.py	Updates common tests to use T3Species and adds YAML key-ordering + /dH[ SA header parsing tests.
tests/data/pdep_network/iteration_1/PDep_SA/network4_2/CSE/chem.inp	Adds/updates fixture file for pdep network tests.
tests/data/models/test_species_dictionary.txt	Adds fixture RMG species dictionary for Cantera parser tests.
tests/data/models/test_cantera_parser.yaml	Adds fixture Cantera YAML for parser tests.
tests/data/functional_2_thermo/input.yml	Renames functional test project fixture.
tests/common.py	Updates test helpers (ARC Molecule import, radical checks, forces CanteraConstantTP in run_minimal).
tests/check_t3_path.py	Adds debug helper script to print import path.
t3/utils/writer.py	Refactors species object creation to T3Species, fixes tolerance fallback logic, and adds get_species_obj_from_a_species_dict.
t3/utils/rmg_sa_parser.py	Adds a lightweight RMG SA CSV parser and converter to standardized sa_dict without rmgpy.
t3/utils/generator.py	Migrates radical generation implementation to ARC molecule objects + T3Species.
t3/utils/flux.py	Updates defaults/API usage for Cantera and simplifies ROP accumulation logic + graph output writing.
t3/utils/dependencies.py	Simplifies dependency checks (ARC-only in t3_env).
t3/utils/cantera_parser.py	Adds a lightweight Cantera YAML parser that produces T3Species/T3Reaction.
t3/simulate/rmg_constantTP.py	Removes legacy in-process RMG adapter implementation.
t3/simulate/rmg_constant_tp.py	Adds new RMGConstantTP adapter that runs SA via subprocess incore script and YAML output.
t3/simulate/factory.py	Minor refactor of factory construction and docstrings.
t3/simulate/cantera_pfr.py	Adds a Cantera PFR adapter (lagrangian + chain-of-reactors modes).
t3/simulate/cantera_constant_uv.py	Adds Cantera constant UV adapter.
t3/simulate/cantera_constant_tp.py	Adds Cantera constant TP adapter.
t3/simulate/cantera_constant_hp.py	Adds Cantera constant HP adapter.
t3/simulate/init.py	Updates simulate module exports to new adapter modules/base.
t3/settings/t3_submit.py	Updates template scripts to run via python instead of python-jl.
t3/runners/rmg_runner.py	Updates incore RMG command to python and adds Arkane runner + RMG SA incore runner helper.
t3/runners/rmg_incore_script.py	Updates docs/exception list to match current RMG errors and python invocation.
t3/runners/rmg_incore_sa.py	Adds incore RMG SA runner script producing YAML output.
t3/logger.py	Migrates logger summaries to use T3Species/T3Reaction objects and adds clean_t3_status.
t3/common.py	Bumps version, adds SA (de)serialization helpers, adds YAML saving with key ordering, updates SA header parsing.
requirements.txt	Updates python dependency set (adds Cantera, bumps numpy/cython/rdkit, etc.).
pyproject.toml	Adds packaging metadata for setuptools build.
Makefile	Updates install targets (renames PyRMS to PyRDL install).
ipython/sa_coefficients_viewer.ipynb	Adds notebook for visualizing SA coefficient YAML output.
examples/minimal/input.yml	Switches minimal example SA adapter default and updates QM job_types fields.
environment.yml	Major environment modernization (Python 3.12+, Cantera 3.2+, numpy 2.1+, revised channels/deps).
devtools/install_pyrms.sh	Removes old PyRMS installer.
devtools/install_pyrdl.sh	Adds wrapper installer delegating to ARC’s PyRDL installer.
devtools/install_arc.sh	Removes old combined ARC/RMG installation script.
devtools/install_all.sh	Updates “install all” workflow and adds PyRDL installation step.
.github/workflows/cont_int.yml	Removes legacy CI workflow.
.github/workflows/ci.yml	Adds new CI workflow using micromamba + ARC + RMG-database checkout.

Comments suppressed due to low confidence (1)

t3/utils/flux.py:195

• get_profiles_from_simulation() now defaults V=100, but generate_flux() always forwards its V argument (defaulting to None). For JSR runs this still passes None into run_jsr()/set_jsr() and will raise a TypeError when computing volume=V * 1e-6. Consider treating V=None as “use default volume” (e.g., only pass V through when it’s not None, or default generate_flux(..., V=100) / handle None inside set_jsr).

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[Copilot]

Pull request overview

Copilot reviewed 89 out of 111 changed files in this pull request and generated 14 comments.

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