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JOSS paper#328

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xiki-tempula wants to merge 108 commits intomasteralchemistry/alchemlyb:masterfrom 71-joss-paperalchemistry/alchemlyb:71-joss-paperCopy head branch name to clipboard

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Commits on Jul 8, 2023

• first draft

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Commits on Aug 21, 2023

• Merge branch 'master' into 71-joss-paper

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Commits on Dec 29, 2023

• Test render

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• fix end

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• fix citation

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• edit

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Commits on Dec 30, 2023

• MRS comments (#339)

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• first fix

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• update the content

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• update

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• Correct the figure

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Commits on Jan 3, 2024

• Merge branch 'master' into 71-joss-paper

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Commits on Apr 6, 2024

• Merge branch 'master' into 71-joss-paper

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Commits on Apr 7, 2024

• Merge branch 'master' into 71-joss-paper

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Commits on Apr 9, 2024

• Small edits, clauses set as newlines for easier diffs

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• Some additional minor edits for internal consistency around estimators, standard data forms

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• Small rearrangement of metadata items

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• Set alchemlyb to lowercase throughout (stylistic choice); small rearrangement of paper metadata items

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Commits on Apr 25, 2024

• added Oliver as author

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• consistent line breaking in markdown

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• updated Acknowledgements/Contributions

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• edited summary

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• WIP: editing statement of need

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• completed editing of Statement of need section

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• Ack/Author contrib update

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Commits on Apr 27, 2024

• Update paper.md with some comments.

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• Update paper.bib

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Commits on May 15, 2024

• add MDPOW

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• add fractional equilibration time

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• edited Implementation section

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Commits on May 16, 2024

• Merge branch '71-joss-paper' of github.com:alchemistry/alchemlyb into 71-joss-paper

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• spell checked

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• added David Mobley to authors

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• minor abstract edits

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• fix citation syntax

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• minor edits

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• added all other authors to acknowledgements

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• Merge branch 'master' into 71-joss-paper

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• changed Author contributions: maintenance

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• funding ack

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• minor edit (use MD after first definition)

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• add ASU to @dotsdl affiliation

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• use referencing for figure

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• add @dotsdl to "wrote paper" in contributions as he was missing from there

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• reference update/cleanup

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• update artifact upload action

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Commits on May 21, 2024

• Merge branch 'master' into 71-joss-paper

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• add PDF for author review

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• used DLD instead of DD for @dotsdl

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Commits on May 22, 2024

• added my name (#361)

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• JOSS paper: Add T. Joseph to authors and grant to acknowledgements (#362)

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Commits on May 23, 2024

• add name and minor change (#363)

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Commits on May 25, 2024

• Merge branch 'master' into 71-joss-paper

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Commits on May 27, 2024

• edits by Alexander Schlaich

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• additional edis suggested by @schlaicha

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• add @schlaicha to paper writers

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• name the JOSS paper build workflow

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Commits on May 28, 2024

• Add JH to author lists, extra reference (#365)

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• Add HL to author list with affiliation (#366)

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• Add Ian Kenney to author list (#367)

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• Move JH from Acknowledgments to Contributions (#368)

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• fixed typo LAMPPS -> LAMMPS

  

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• fiddle with bib to make JC Chodera citations appear unformly

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• software engineering details and minor touch-ups

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• update @orbeckst's affiliation

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Commits on May 29, 2024

• using SPEC 0 (updated from NEP29)

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• Merge branch 'master' into 71-joss-paper

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Commits on May 30, 2024

• Add Irfan Alibay to paper.md (#372)

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• PDF draft of paper as of 2024-05-30

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• Merge branch '71-joss-paper' of github.com:alchemistry/alchemlyb into 71-joss-paper

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Commits on May 31, 2024

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• add @vtlim to Author list

  

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Commits on Jun 3, 2024

• Update joss_paper/paper.md

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Commits on Jun 4, 2024

• Add affiliation (#374)

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• Update paper.md (#373)

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• Update paper.md for authorship (#375)

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• finalized author information and date

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• introduce alchemical free energy calcs outside Implementation section

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Commits on Jun 5, 2024

• edited paragraph on solvation free energy calc to improve clarity

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• fixed front matter

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• add PTM to "wrote manuscript"

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• add Shuai Li to authors (but need to renumber affiliations)

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• Fix Shuai Liu’s name (sorry)

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• Updated author order and contributions

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• full author list for NAMD paper

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• re-numbered affiliations

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• finalized acknowledgements

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• clean up: removed PDF versions

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• fixed name of Wei-Tse Hu in Ack

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• add DOI for Kirkwood 1935

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Commits on Jun 6, 2024

• Fix name Hu -> Hsu in Ack

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Commits on Jun 26, 2024

• Update affiliation

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Commits on Jul 18, 2024

• Merge branch 'master' into 71-joss-paper

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Commits on Jul 27, 2024

• Merge branch 'master' into 71-joss-paper

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Commits on Aug 15, 2024

• Merge branch 'master' into 71-joss-paper

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Commits on Aug 17, 2024

• Minor changes to the paper (#387)

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Commits on Sep 5, 2024

• Merge branch 'master' into 71-joss-paper

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Commits on Sep 17, 2024

• Merge branch 'master' into 71-joss-paper

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Commits on Sep 19, 2024

• Merge branch 'master' into 71-joss-paper

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• add @jaclark5 to acknowledgements

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Commits on Sep 24, 2024

• paper affiliations: spell out USA

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