Major List Update 2024-08

[Irratzo]

Major list update 2024-08. Postponed from 2024-01, 2024-03, 2024-06.

Previous major updates in issues #181, #94.

For the procedure, reusing the Major List Update How-To from issue #94 comments.

Subtasks.

• Fix Actions error create-update-branch #303
• close external issues
  • Add project: GPUMD (with the NEP MLP) #233, Add project: apax: Atomistic learned Potentials in JAX! #268, Add project: LLaMP #295, Add project: IPSuite - Python toolkit for FAIR development and deployment of MLPs #298
• add new authors from external issues
  • 3389d34
• close "update project" issues
  • Update project: JAX-DFT #254
• close "change config" issues
  • Add category Universal Potentials #279, Add new labels #299,
  • Address Clean up categorization I #301 in a future major update.
• Split off stale projects acc. to Split list at cap of 500+ projects #302?
  • No need. Still well away from the 500+ projects cap.
• add new projects from feeds
  • twitter, linkedin, mastodon, bluesky
  • skip for now, backlog too large. do in next update.
• separate open issues into batch-processable yes / no
• collect open issues into buckets batch-processable yes / no
  • batch-processable 'yes' issues
    • Add project: tmQM_wB97MV Dataset #207, Add project: ML for catalysis tutorials #209, Add project: GDB-9-Ex9 and ORNL_AISD-Ex #216, Add project: HydraGNN #217, Add project: OpenML #218, Add project: MatterGen #219, Add project: ACEpsi.jl #221, Add project: The Perovskite Database Project #226, Add project: MADICES Awesome Interoperability #227, Add project: MAGUS #230, Add project: HamGNN #232, Add project: Awesome Neural SBI #236, Add project: Geometric-GNNs #239, Add project: MACE-MP #242, Add project: GAP-ML.org homepage #245, Add project: load-atoms #247, Add project: QMLearn #250, Add project: rho_learn #251, Add project: Q-stack #252, Add project: KSR-DFT #255, Add project: Awesome-Graph-Generation #260, Add project: AI for Science 101 #261, , Add project: Allegro-Legato #265, Add project: mag-ace #270, Add project: AIS Square / OpenLAM #273, Add project: crystal-text-llm #274, Add project: Neural-Network-Models-for-Chemistry #276, Add project: EGraFFBench #277, Add project: automl-materials #280, Add project: ML-atomate #283, Add project: ChargE3Net #284, Add project: InfGCN for Electron Density Estimation #285, Add project: MXenes4HER  #286, Add project: Mapping out phase diagrams with generative classifiers #288, Add project: ChatMOF #289, Add project: PMTransformer #290, Add project: PyFLAME #292, Add project: IKS-PIML #293, Add project: AI4Chemistry course #294, Add project: Graphormer #296, Add project: Joint Multi-domain Pre-Training (JMP) #300, Add project: AisNet #306, Add project: DPA-2 #308, Add project: nnp-pre-training #310, Add project: SiMGen #312, Add project: TeaNet #313, Add project: PreFerred Potential (PFP) #314, Add project: HME21 Dataset #315, Add project: GN-MM #316, Add project: apax #317, Add project: ALEBREW #318, Add project: Materials Project Trajectory (MPtrj) Dataset #319, Add project: MPF.2021.2.8 #320, Add project: Graphs of Materials Project 20190401 #321, Add project: Cephalo #325, Add project: Alexandria Materials Database #331, Add project: SevenNet #332, Add project: MatterSim #339, Add project: AI for Science paper collection #341, Add project: AI4ChemMat Hands-On Series #342, Add project: Awesome-Crystal-GNNs #343
  • batch-processable 'no' issues
    • from quarterly update 2023-11. Add project: paperswithcode #20, Add project: All from Wasmer's research library #22, Add project: WMDGroup's projects #26, Add project: Materials repositories popular in AML research #34, Add project: Materials Intelligence's projects #46, Add project: DIVE Lab's projects #50 (DIVE), Add publication metrics #51, Add project: Add all LAMMPS ML potentials #79, Add project: Projects from TsudaLab #85, Add project: Projects of Ramprasad-Group #113, Sharpen the list's thematic focus #125, Add project: Projects from MolecularAI #126, Add project: atomisticnet projects #132, Add project: kjappelbaum's projects #164, Add project: Matrix Function Neural Networks #171, Add project: Projects of cesmix-mit group #185
    • New. Add project: Graph ACE #220, Add project: Projects from LLM Hackathon 2023 #234, Add project: Add models and datasets from Geometric-GNNs #240, Add project: Add new projects from GitHub topic ai4science #241, Add project: MaRDA projects #244, Add project: Add missing DeepModeling projects #307
• batch-process bp 'yes' issues.
• add citation instructions to header
• clean up releases
  • manually merge release drafts into regular releases. Collect all "added projects" of intermediate releases, delete these, and paste into the next minor or major release to be published. minor releases should ensure that there is a regular release update every 1-2 months. major release updates correspond to "Major List Update" issues with lots of project additions.
• create new release for Zenodo
  • since Zenodo auto-update from GitHub releases is activated, this is done automatically by publishing release on GitHub. It may take some time (hours) for Zenodo to update to the latest release, but eventually it will show up there.
• announce new release on feeds
  • twitter, linkedin, mastodon, bluesky, facebook, other sites

[Irratzo]

Closed batch-processable 'yes' issues in commit c21de8e.

Subsequent Actions run of workflow update-best-of-list failed with error

Traceback (most recent call last):
  File "/usr/local/lib/python3.8/site-packages/best_of/generator.py", line 107, in generate_markdown
    projects = projects_collection.collect_projects_info(
  File "/usr/local/lib/python3.8/site-packages/best_of/projects_collection.py", line 622, in collect_projects_info
    if project_info.name.lower() in unique_projects:
TypeError: 'Dict' object is not callable

As this error seemed unrelated to this List Update, I split it off into issue #345.

[Irratzo]

Side note. Here on reddit is some activity by the orignal best-of authors. Some good insights into, and criticisms, of the best-of project ranking design. Sadly, they are not active there anymore, either.

• https://www.reddit.com/r/Python/comments/kx94kc/bestofpython_a_ranked_list_of_awesome_python/
• https://www.reddit.com/user/mltooling/

[Irratzo]

Side note. While examining the failed runs, I noticed that I was not using libraries.io information for the project ranking. Outsourced to issue #344.

[Irratzo]

subtask "add citation instructions to header" , done in commit baf90d2.

[Irratzo]

Social media announcements

• Twitter https://x.com/JohannesWasmer/status/1825531240616739294
• LinkedIn URL
• BluSky URL
• Mastodon https://chaos.social/@irratzo/112989268401046973
• Facebook see below

Note. The '@' handles below are the respective social media site's profile handles, not GitHub profile handles.

Message template

Message template.

Best of atomistic machine learning list, major update. 60 new projects added. Seven universal potentials enter the list, along with an equal share of new generative, active learning, and electronic structure models, datasets and community resources. go.fzj.de/baml

Tagging some new project contributors & others.

Facebook

Searched MD and DFT and computational chemistry and materials groups, sorted by membership count and suitability, cut-off at ~5k members.

• https://www.facebook.com/groups/654236308757812/
  • admin approval pending
• https://www.facebook.com/groups/1538107966433119/
  • admin approval pending
• https://www.facebook.com/groups/184031292131597/
  • admin approval pending
• https://www.facebook.com/groups/822220618558665/
  • https://www.facebook.com/groups/822220618558665/posts/1633358027444916/
• https://www.facebook.com/groups/719389768429753/
  • https://www.facebook.com/groups/719389768429753/posts/2262214980813883/
• https://www.facebook.com/groups/compscieng/
  • admin approval pending
• https://www.facebook.com/groups/665767233454007/
  • admin approval pending
• https://www.facebook.com/groups/mlchem/
  • https://www.facebook.com/groups/mlchem/posts/1172355960716234/
• https://www.facebook.com/groups/vasptools.marjaouiadil/
  • admin approval pending
• https://www.facebook.com/groups/747922102856346/
  • https://www.facebook.com/groups/747922102856346/posts/1292547661727118/
• https://www.facebook.com/groups/wien2k.Algeria/
  • admin approval pending
• https://www.facebook.com/groups/MaterialsModelingStackExchange/
  • admin approval pending

[Irratzo]

Done.