Major List Update 2023-08

[Irratzo]

Issue corresponding to 1) commit c850b31 and its corresponding README update f99194f ...

closing add project issues #21, #23, #28, #29, #30, #31, #35, #36, #37, #39, #44, #45, #49, #54, #66, #67, #68, #69, #70, #71, #73, #74, #75, #76, #77, #78, #80, #86, #87, #88

Note: Closing multiple issues with commit message.. The correct syntax is git commit -m "closes #1, closes #2, closes #3; YOUR COMMIT MESSAGE".

and 2) commit series b666491 ... ba49089, adding some distnguishing graphical deco to the header, in this case, an emoji-tuple as list "logo". Started with the idea of having combining the Atom emoji with a self-made, same-style neural network emoji. Didn't like that in the end. Found no emoji that really works for signifying ML, so just stuck with the emoji triple Atom, DNA, Gem Stone / Snowflake, to signify atomistic molecules & materials.

The following is about the 1), the batch processing of a long list of add project issues. I document here how I did it for the next quarterly update around October.

[Irratzo]

Major List Update How-To.

The following is about the batch processing of a long list of accumulated add-project issues. I document here how I did it this time, as reference for the next quarterly update around October.

[Irratzo]

1. Copy-paste all issues' project lists into a text file. We want to turn those into the format required by projects.yaml, so that we can just paste it there and run the Action update-best-of-list to incorporate them in the README.

Note:

• In the following replacements, some replacements depend on earlier ones, so order matters.
• Applied hand-made corrections (some issues don't conform to the format) are not explicitly mentioned here.

2. Apply replacements to property keys.

Issue format	projects.yaml format
- Project Name:	- name:
- Gitbub URL: https://github.com/	github_id:
- Category:	category:
- Labels:	labels:
- Description:	description:
- License:	license:
pypi:	^J pypi_id:
conda:	^J conda_id:
maven:	^J maven_id:
- Package Managers: ^J	EMPTY
- Resource:	resource:
^J-----^J	^J
- Package Managers: None	# package managers: none
- URL:	# homepage:
license: None	# license: # none found

Legend:

• ^J = newline character (Emacs)
• ----- lines were used to visually separate projects

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3. Convert labels values, list of comma-separated strings into bracket-encased list of comma-separated double-quoted strings.

Did not find a single regex command that manages to do this in one operation. Seems to required nested grouping, and couldn't get it to work. Instead, here did it like this.

# regex: single-item labels.
# description: in each line beginning with "labels: " and ending with single string, quote string, encase in brackets.
# example: labels: ab-c --> labels: ["ab-c"].
# reference: chatpgt.
sed -E '/^  labels: [^,]+$/ s/(labels: )(.+)/\1["\2"]/; /^labels: [^,]+$/! s/, /, /' in.file > out.file

# regex: multi-item labels bracketing.
# description: in each line beginning with "labels: " and ending with comma-separated list of strings, encase list in brackets.
# example: labels: ab-c, def --> labels: [ab-c, def].
# reference: chatgpt.
sed -E '/^  labels: .*[ ,].*$/ s/([^:]+: )(.+)/\1[\2]/; /^labels: .*[ ,].*$/! s/, */, /' in.file > out.file

Note that order of replacement matters here.

• Apply regex: multi-item labels bracketing.
• Manually insert quotes to multi-item labels ([ab-c, def] --> ["ab-c", "def"]).
  • Back up all non-label lines containing commas somehwere. (In case, same for brackets).
  • Replace [ --> [", and , --> ", ", and ] --> "].
• Apply regex: single-item labels.

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4. Go over list again, correct by hand, incorrect categories, labels, links, missing descriptions, etc. In case new categories or labels had to be added, also add them in projects.yaml.

5. sort some of the projects into sections as done in current projects.yaml. Some of the categories, such as community, datasets, educational, have some resource: true projects. Those don't get sorted by CI/CD project-score rank in the final README, but appear in order of appearance as in projects.yaml. So, separate them out and sort them alphabetically.

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6. Copy-paste the processed list over into projects.yaml. Don't just append, but merge with the existing sections. That means, for the resource: true sections, resort merger alphabetically.

7. Normal update process: Push. Use commit syntax git commit -m "quarterly update YYYY-MM. closes #1, closes #2, closes #3.". On GitHub, run action update-best-of-list. Merge & rebase resulting pull request. Done.

8. Clean up releases list. TODO

9. Publish Zenodo release, update DOI. TODO

10. Social media announcements. See below.

[Irratzo]

Closed with commit c069f2a.

[Irratzo]

Social media announcements

• Twitter https://x.com/JohannesWasmer/status/1695966269080518718
• LinkedIn https://www.linkedin.com/posts/johannes-wasmer-359749126_github-judftteambest-of-atomistic-machine-learning-activity-7137379626145701888-ttc3
• BluSkey NA
• Mastodon https://chaos.social/@irratzo/110967047468096843

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

Twitter

Main message.

"Best of Atomistic Machine Learning" is a new, comprehensive list of 300+ popular AML projects, auto-ranked by quality score. Interatomic potentials, electronic structure, datasets, community resources. Courtesy http://judft.de team. https://go.fzj.de/best-of-aml #AI4Science

Response messages.

Updated quarterly. Current focus rather more on materials than drug design. Write me if you'd like to maintain & expand it together.

Tagging some project authors & others. @shuiwangji, @ruben_laplaza, @stefabat, @pavlodral, @JWestermayr, @LabOfScience, @lab_COSMO, @vl_deringer, @bfocassio, @Patilurvesh, @xie_tian, @tesssmidt, @marceldotsci, @niklasschmitz_, @RGBLabMIT, @AttilaCangi, @IlyesBatatia, @gncsimm,

@MichelangeloDo9, @MatteoCobelli1, @_RossiKevin, @davkovacs10, @lopanits, @DrugTorch, @ja_kirkpatrick, @RosyCers, @gasteigerjo, @chrsmrrs, @gdefabritiis, @MScherbela, @UllahArif_Hkt, @bm_chiheb, @tk_rusch, @j0hnparkhill, @1stBZ, @AlexLavin_C137, @mniepert, @ai4sciencetalks,

@Matgenix, @GerCanMAC, @andrrizzi, @andrea_anelli, @jigyasa_nigam, @andrewwhite01, @JoshRackers, @isomorphiclabs, @wenzel_susanne, @s_the_kessel, @luthaf, @RhysGoodall, @AleLunghi, @zany_cloud, @Smlqc1Smlqc, @albertfabriz, @ZakJost, @ssanvito, @GrohsPhilipp, @TobiasMorawietz,

@HannesStaerk, @CASUSscience, @simonbatzner, @openmsf, @hongbin_zhang, @wim_tuerger, @rbhar90, @deep_chem, @LuigiSbailo, @acceleration_c, @SandipDeScience, @NArtrith, @Ms_VS_voice, @jtmargraf, @_MatthiasRupp, @venkvis, @ktschuett, @JasonUnkcpz, @gerhardgoldbeck, @EMMC_ASBL,

@aytwang, @MaterialismPod, @ChengBingqing, @GroupTuckerman, @cedergroup, @persson_group, @bkoz37, @Materials_Intel, @nc_frey, @mat_mol_ml, @AENET_Network, @KPatBerkeley, @materialsvrlab, @MolecularXtal, @FelixMusil, @zackulissi, @P_Friederich, @Bjork_Hammer, @MicheleCeriotti,

@Evert_v_N, @MPBircher, @leeley18, @ArghyaBhowmik5, @EliskaGreplova, @EntosAI, @helmholtz_ai, @jhrmnn, @itamblyn, @olexandr, @FrankNoeBerlin, @MLSTjournal, @toniobuonassisi, @keeeto2000, @AndersSChristen, @janhjensen, @ProfvLilienfeld, @MolSSI_NSF, @KulikGroup, @Psik_Network

LinkedIn

Message text.

"Best of Atomistic Machine Learning" is a new, comprehensive list of 350+ popular AML projects, auto-ranked by quality score. Interatomic potentials, electronic structure, datasets, language models, community resources. https://lnkd.in/efgkYs_y. Courtesy http://judft.de/. hashtag#AI4Science

BlueSky

None.

Mastodon

Main message.

"Best of Atomistic Machine Learning" https://go.fzj.de/best-of-aml is a new, comprehensive list of 300+ popular AML projects, auto-ranked by quality score. Interatomic potentials, electronic structure, datasets, community resources. Courtesy http://judft.de/ team.

Response messages.

Updated quarterly. Current focus rather more on materials than drug design. Write me if you’d like to maintain & expand it together 🙏 .

Tagging some project authors & others. @ncfrey, @carrasqu, @jonkhler, @rbhar90, @janhjensen, @MolecularXtal, @volkerblum, @pfau, @marcel, @margraf, @physics_ange, @grynova_CCC, @JuliaWestermayr, @FMarquardtGroup, @mpifkf, @vl_deringer, @jhrmnn, @andrewwhite01, @luthaf, @simonbatzner, @michele_ceriotti, @lab_COSMO.

Facebook

• https://www.facebook.com/groups/mlchem/
  • https://www.facebook.com/groups/mlchem/posts/975260703759095/
• https://www.facebook.com/groups/719389768429753/
  • https://www.facebook.com/groups/719389768429753/posts/2026154934419890/
• https://www.facebook.com/groups/compscieng/
  • https://www.facebook.com/groups/compscieng/posts/2493475387501570/
• https://www.facebook.com/groups/vasptools.marjaouiadil/
  • https://www.facebook.com/groups/vasptools.marjaouiadil/posts/1329484534333722/
• https://www.facebook.com/groups/Quantum.Espresso/
  • https://www.facebook.com/groups/Quantum.Espresso/posts/6485313858213756/