RMG-Py v3.3.0

Releases:

• Source code on GitHub. git clone --branch v3.3.0 --depth 1 https://github.com/ReactionMechanismGenerator/RMG-Py.git
• Conda binaries on CondaForge. conda create --name rmg_330 'rmg::rmg==3.3.0'
• Docker on DockerHub docker pull reactionmechanismgenerator/rmg:3.3.0

What's Changed

Software Improvements

RMG-Py Itself

• Python 3.9 by @JacksonBurns in #2741
• Removing the excessive debug comment by @MichaelGeuking in #2102
• Conversion from nose to pytest by @rwest in #2516
• Modified main.py script to include TROE reactions in the violators log by @PoojaNem in #2614
• Replace a few packages maintained by us to their conda-forge version by @xiaoruiDong in #2624
• Switch muq, lpsolve55, and RingDecomposerLib from rmg to conda-forge by @jonwzheng in #2671
• environment.yml Unblocking Python 3.11 - rdkit to conda-forge channel, remove chemprop for now by @JacksonBurns in #2553
• Make chemkin read of transport and thermo files more robust by @sevyharris in #2643
• Add documentation about speciesCuttingThreshold by @donerancl in #2601
• Fix Failing Joback Method Unit Test by @JacksonBurns in #2682
• Load a kinetic library not in the RMG database by @alongd in #2663
• Draw reversible arrow if reaction is reversible by @sevyharris in #2693
• Ignore more example output files in git. by @rwest in #2822
• Make RMG-Py conda Work Again 🎉 by @JacksonBurns in #2820
• fix typos by @KnathanM in #2670
• update user and developer installation instructions to point towards miniforge by @JacksonBurns in #2719
• Add and improve to_cantera methods for conversion to in-memory Cantera objects by @rwest in #2700
• Add details to thermo comments. by @rwest in #2788
• A note about installing developer version from Docker. by @rwest in #2806

Bug Fixes

• When loading all reaction libraries, only process "reactions.py" files. by @rwest in #2513
• Fix pytest Discovery Bug (FooTest vs. TestFoo), Add Missing Tests, Fix Generator Tests by @rwest in #2525
• Minor: Added quotation marks to Pt111 in the docs by @alongd in #2529
• Fix Failing CI because of cclib by @JacksonBurns in #2535
• Update RMSE/MAE average formula for BAC cross validation by @hwpang in #2538
• Fix a logical short circuit in a test expression by @munahaf in #2542
• FIX: Updated logical expression to remove short circuit by @fazledyn-or in #2555
• Fix CC smiles by @xiaoruiDong in #2545
• changing forbidden groups documentation by @Nora-Khalil in #2561
• exempt announcements from being closed as stale by @JacksonBurns in #2565
• Update uncertainty SI when averaging ThermoData by @hwpang in #2589
• Julia restriction by @calvinp0 in #2609
• changed typo from pydas.daspk to pydas.dassl #2070 by @Julian-Ufert in #2615
• restrict newer versions of cclib by @ChrisBNEU in #2638
• Remove duplicated test data directory by @rwest in #2644
• FIx Handling of Initial Species with Seed Mechanisms by @mjohnson541 in #2653
• add check for all zeros in thermo comparison by @sevyharris in #2658
• Better debugging messages for database errors. by @rwest in #2661
• Send P in SI units to Chebyshev.fit_to_data() when reversing a rate by @alongd in #2662
• Draw Hydrogen bonds (again) by @rwest in #2734
• Fix library reaction barrier heights for linear scaling by @sevyharris in #2729
• Fix database issues with loading new kinetic libraries by @jonwzheng in #2753
• Update comment parser for autogen trees by @sevyharris in #2787

New Features (and their fixes)

Electrochemistry 🎉

• Electrochemistry! (finally) a.k.a. RMG-electrocat by @JacksonBurns in #2598
• Fix bug in electrons initialization for depository reaction data by @jonwzheng in #2775

Automated Fragment Modeling

• Remove label in adjlist before detecting cutting label by @hwpang in #2519
• Add regression input file for fragment + simple reactor and regression test for fragment + RMS reactor by @hwpang in #2571
• Compatibility of regression.py with fragment by @hwpang in #2574
• fragment.py: refactoring, patches, and compatibility with RMS by @JacksonBurns in #2413
• Add Fragment Reattachment Example Notebook by @donerancl in #2585
• Fix Fragment Resonance Structure Bug by @donerancl in #2647
• Fix AFM fragment crash in LiquidReactor by @Kyamaguchi16 in #2813

Surface Catalysis

• Doc surf rxns by @ChrisBNEU in #2497
• correcting bidentate adsorption rate constant by @bjkreitz in #2533
• fix Kc for bidentate rxns by @bjkreitz in #2554
• Group Structures for Complex Surface Representations by @mjohnson541 in #2618
• Patch for surface regression diffmodels by @sevyharris in #2656
• Add surface combustion example for regression testing by @sevyharris in #2514
• adding resonance for adsorbates by @bjkreitz in #2511

AECs and BACs

• Allow user to plot correlation matrix for AECs by @hwpang in #2550

Arkane

• Add keyword "HF=" to parse electronic energy by @JintaoWu98 in #2586
• resolved issue #2266 by @Julian-Ufert in #2651
• Allow scratch dir as input for arkane symmetry calculation by @hwpang in #2691
• Change method for loading energies from Gaussian log files to regex search to avoid errors by @donerancl in #2595
• updating 'rotconsts' ref to be compatible with cclib v1.8+ by @ChrisBNEU in #2639
• Process monoatomic molecules in Arkane's Orca ESS adapter by @alongd in #2709
• Parse RS2C (CASPT2) energy in Molpro by @alongd in #2711
• Fxi UnboundLocalError: local variable 'e_electronic_with_corrections' referenced before assignment by @alongd in #2756
• Fix rotational constants in Gaussian files listing ****s by @sevyharris in #2761
• Orca parser fixup by @kfir4444 in #2739
• Molpro f12a by @alongd in #2771
• Fix CCSD(T)-F12 energy parsing by @shihchengli in #2816

Deprecations

• Remove kinetic group additivity methods from code and documentation by @jonwzheng in #2612
• Clean up some code for calculating degeneracy in kinetics codebase by @jonwzheng in #2632
• Remove Wiki and gitter from README by @jonwzheng in #2762
• [Docs] Update outdated docs, wiki, and contributor guidelines by @jonwzheng in #2703

Continuous Integration

• Fix CI workflow to function on forked pushes. by @rwest in #2515
• Tweak annotation workflow name. by @rwest in #2517
• Instruct Docker, Github Actions, and users to use 'for_rmg' branch of RMS by @rwest in #2523
• update docker usage instructions to point to v3.2.0 by @JacksonBurns in #2522
• Switch back to RMS main in CI by @mjohnson541 in #2552
• Change Documentation Build Action to use github-actions bot instead of RMG_dev by @JacksonBurns in #2599
• fix checkout command for docs building action by @JacksonBurns in #2602
• Continuous Integration, Documentation Build, and Dockerfile Fixes by @JacksonBurns in #2608
• Continued docs build fixes by @JacksonBurns in #2610
• documentation builder bug fixes and general overhaul by @JacksonBurns in #2621
• GitHub Actions Maintenance by @JacksonBurns in #2628
• github actions CI maintainence by @JacksonBurns in #2669
• Remove default Channel from environment.yml by @mjohnson541 in #2712
• Patch minimal_surface Regression Test by @JacksonBurns in #2674
• Change CI to use Miniforge3 instead of Mambaforge by @ssun30 in https://github.com/
• Deprecate the nomkl mutex metapackage by @ssun30 in #2723
• Changed Dockerfile to use Miniforge3 by @ssun30 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2724ReactionMechanismGenerator/RMG-Py/pull/2718
• Update CI artifact actions to v4 and fix runner glitch by @jonwzheng in #2748
• require a more recent version of mkl for Cantera by @sevyharris in #2766
• Fix the CI regression logging; make Julia optional via environment and module variables. by @rwest in #2802
• Lazy loading of Julia things by @rwest in #2804
• Docker build updates by @rwest in #2808

New Contributors

• @munahaf made their first contribution in #2542
• @MichaelGeuking made their first contribution in #2102
• @fazledyn-or made their first contribution in #2555
• @bjkreitz made their first contribution in #2554
• @JintaoWu98 made their first contribution in #2586
• @donerancl made their first contribution in #2585
• @PoojaNem made their first contribution in #2614
• @Julian-Ufert made their first contribution in #2615
• @KnathanM made their first contribution in #2670
• @ssun30 made their first contribution in #2718
• @Kyamaguchi16 made their first contribution in #2813
• @shihchengli made their first contribution in #2816

Full Changelog: 3.2.0...3.3.0