RMG-Py v4.0.0

What's Changed

• Update Jupyter Notebooks to call RMS using juliacall by @mjohnson541 in #2829
• Merge 3.3.0 release from stable back into main by @rwest in #2830
• Dockerfile: use miniforge instead of miniconda to avoid defaults by @JacksonBurns in #2834
• Avoid Accidental conda Uploads by @JacksonBurns in #2839
• More helpful debugging for PDep networks, and option to always generatePESDiagrams. by @rwest in #2825
• Fix Li atom type defs by @alongd in #2845
• Explicitly Forbid Default conda Channels by @JacksonBurns in #2846
• Expanding the unit testing of ring decomposition features. by @rwest in #2852
• Load spin multiplicity into the Arkane Species Molecule if given explicitly in the main Arkane input file by @alongd in #2854
• Tweaking install_rms for Github Actions by @rwest in #2862
• Fix regression tests coming back from the dead. by @rwest in #2863
• Small fix - added missing period by @calvinp0 in #2860
• Update CI to use new macOS runner images by @jonwzheng in #2869
• Fix broken examples by @jonwzheng in #2824
• added full path to hessian search in orca adapter. by @kfir4444 in #2873
• Tests: Use np.isclose() for reaction rate coefficient tests by @rwest in #2876
• Correct constant-species index mapping in SimpleReactor by @alongd in #2867
• Add environment validation and error handling to RMS installation script by @ssun30 in #2828
• Fix E0 energy_correction in pressure dependence calculations. by @rwest in #2835
• Imports Species class locally for diffusion_limited_rate function by @calvinp0 in #2880
• Fix writing of RMG input files by rmgpy.rmg.input.save_input_file by @sevyharris in #2532
• Added completedNetworks option to prevent exploring PDep networks that are complete. by @rwest in #2853
• Replace deprecated imp.load_source call by @sevyharris in #2871
• Add comprehensive copilot instructions for RMG-Py by @rwest in #2881
• Update installation instructions for Anaconda and Conda by @rwest in #2887
• Force desired channel resolution order in binary install by @JacksonBurns in #2890
• Use rdkit for SSSR and RCs (bug fix + Python upgrade) by @JacksonBurns in #2796
• Upgrade to Cantera 3 (again?) by @rwest in #2885
• Fix pdep reaction deepcopy error by @sevyharris in #2897
• Delete unreachable code in _make_rule by @sevyharris in #2893
• Fixes to RPATH on MacOS for Cython compilation, and update Conda build recipe for CI by @rwest in #2900
• Restore incremental Cython builds in Makefile by @Copilot in #2902
• Get thermochemistry even for non-reactive species during model initialization by @alongd in #2899
• Fix extra duplicate reactions from same template being added to mechanism by @Copilot in #2898
• Fix flux diagram naming of species images by @sevyharris in #2905
• Reduce CI runtime by @JacksonBurns in #2907
• Add coordination number and lone-pair regularization dimension tracking by @mjohnson541 in #2911
• export RMS_BRANCH so var exists inside Julia by @sevyharris in #2916
• Arkane: add check for iop(2/9=2000) in Gaussian load geometry by @sevyharris in #2758
• Added a species constraint for the max number of rings fused together (revived) by @alongd in #2868
• Coverage-dependent thermochemistry for catalysis by @12Chao in #2646
• Blowers-Masel fitting: changes and refactoring by @rwest in #2917
• Cov dep example notebook by @sevyharris in #2918
• Update Jupyter notebooks and associated codebase [RMG-Py] by @jonwzheng in #2815
• Handle thermo comment with newline through group name by @sevyharris in #2927
• Added Arkane xTB ESS adapter by @alongd in #2914
• Added the auto-database feature by @alongd in #2909
• RDKit GetSSSR Non-determinism Fix by @JacksonBurns in #2920
• Uncertainty Part 1: Basic surface extension by @sevyharris in #2924
• Fix coverage dependent kinetics read/write for chemkin. by @rwest in #2937
• Miscellaneous changes, including a change to how species are named. by @rwest in #2921
• Change orthonormalization when projecting out rotors in Arkane by @rwest in #2913
• Regression test fix option 1: Create fresh and not cloned environment to avoid cache issues by @sevyharris in #2942
• Fix regression tests attempt 2: Work around failed conda activation in regression test by @sevyharris in #2944
• Miscellaneous changes, mostly quieting warnings in the unit test logs, with a change to Arkane output by @rwest in #2940
• Claude.md by @rwest in #2938
• Uncertainty Part 1.5: Adding in quadrature by @sevyharris in #2933
• Update charge for Val5, and N by @kirkbadger18 in #2929
• Improvements to Chemkin file reading/parsing by @rwest in #2919
• Yaml writer addition by @rwest in #2800
• Implement sensitivity for SurfaceReactor by @sevyharris in #2935
• Uncertainty Part 3: Export Covariance Matrices by @sevyharris in #2932
• iter_item_cap passed to make_tree_nodes even if cascade algo isn't used by @Nora-Khalil in #2941
• Uncertainty Part 2: Surface sensitivity by @sevyharris in #2928
• Add SIDT adsorption correction predictors by @mjohnson541 in #2939
• Uncertainty Part 4: Load correlations for surfaceThermoPt111 library and adsorption tree by @sevyharris in #2934
• Version 4.0.0 Release Candidate 1 by @JacksonBurns in #2931
• Fix thermo tests by @bjkreitz in #2949
• Upgrade CI actions to latest major versions (Node.js 24) by @Copilot in #2951
• Use eigh (not eig) for moment-of-inertia diagonalization by @rwest in #2954
• Fix conda env creation hang and clang build failure on macOS; improve install docs by @rwest in #2953
• Trying to diagnose and fix conda build (on intel mac) by @rwest in #2956
• Harden Conda Build workflow against broken-pipe diagnostic failure by @Copilot in #2957
• Optimizations (largely Cython) by @rwest in #2958
• Fix cython declarations and some optimizations in molecule.py by @rwest in #2960
• Fixes to Chemkin file writing and reading by @rwest in #2955
• Add unload_libraries helper function by @sevyharris in #2964
• Fixes to RMG Cantera yaml writers to better match ck2yaml by @djlucey in #2947
• Reset solvent database in liquidTest teardown by @sevyharris in #2966
• modify max_heavy_atoms constraint by @bjkreitz in #2972
• Improvements to constraints handling. by @rwest in #2974
• Fix covdep by @bjkreitz in #2975
• Surface uncertainty demo notebook by @sevyharris in #2959
• Address a couple of minor deprecations in calls to Cantera by @rwest in #2976
• Specify initial core species using external dictionary by @sevyharris in #2891
• Reduce "error" logging in regression testing (only WARN and above) by @rwest in #2978
• Add uq assign_intermediate_uncertainties tests by @sevyharris in #2968
• Vdw bonds by @bjkreitz in #2706
• Update headers to 2026 by @sevyharris in #2980
• RMG-Py v4.0.0 🎉 by @JacksonBurns in #2967
• RMG-Py v4.0.0 stable by @JacksonBurns in #2981

New Contributors

• @12Chao made their first contribution in #2646
• @djlucey made their first contribution in #2947

Full Changelog: 3.3.0...4.0.0