Code

JOSS paper#328

Code

Closed

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

+575

Commits

Commits on Jul 8, 2023

• first draft

  xiki-tempula

  committed
  d9a153b

Commits on Aug 21, 2023

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

  dotsdl

  authored
  7816c2f

Commits on Dec 29, 2023

• Test render

  xiki-tempula

  committed
  7d69775

• fix end

  xiki-tempula

  committed
  1192a1d

• update action

  xiki-tempula

  committed
  0fc12b4

• fix citation

  xiki-tempula

  committed
  e8976be

• edit

  xiki-tempula

  committed
  7816081

Commits on Dec 30, 2023

• MRS comments (#339)

  Show description for 557d13d
  

  mrshirts

  and

  xiki-tempula

  authored
  557d13d

• first fix

  xiki-tempula

  committed
  2057c41

• update the content

  xiki-tempula

  committed
  aa2e189

• update

  xiki-tempula

  committed
  87153a0

• Correct the figure

  xiki-tempula

  committed
  edb9429

Commits on Jan 3, 2024

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

  xiki-tempula

  authored
  966e386

Commits on Apr 6, 2024

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

  orbeckst

  authored
  d040546

Commits on Apr 7, 2024

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

  xiki-tempula

  authored
  1ab91ab

Commits on Apr 9, 2024

• Small edits, clauses set as newlines for easier diffs

  dotsdl

  committed
  081e90c

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

  dotsdl

  committed
  b5c3d1d

• Small rearrangement of metadata items

  dotsdl

  committed
  ed01447

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

  dotsdl

  committed
  0559c9f

Commits on Apr 25, 2024

• added Oliver as author

  orbeckst

  committed
  13b13c7

• consistent line breaking in markdown

  Show description for 850ec5a
  orbeckst

  committed
  850ec5a

• updated Acknowledgements/Contributions

  Show description for 6e7fdb6
  orbeckst

  committed
  6e7fdb6

• edited summary

  orbeckst

  committed
  1c2ec9d

• WIP: editing statement of need

  orbeckst

  committed
  0b14e7c

• removed download stats

  Show description for 6b202b2
  orbeckst

  committed
  6b202b2

• completed editing of Statement of need section

  orbeckst

  committed
  5002923

• Ack/Author contrib update

  Show description for 0ca06f6
  orbeckst

  committed
  0ca06f6

Commits on Apr 27, 2024

• Update paper.md with some comments.

  Show description for e8d57e9
  mrshirts

  authored
  e8d57e9

• Update paper.bib

  Show description for eca0066
  mrshirts

  authored
  eca0066

Commits on May 15, 2024

• add MDPOW

  orbeckst

  committed
  ae955d8

• add fractional equilibration time

  orbeckst

  committed
  e08a52e

• edited Implementation section

  Show description for 64de66d
  orbeckst

  committed
  64de66d

Commits on May 16, 2024

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

  Show description for bfda924
  orbeckst

  committed
  bfda924

• spell checked

  orbeckst

  committed
  cb5e5dc

• added David Mobley to authors

  Show description for e6c6023
  orbeckst

  committed
  e6c6023

• minor abstract edits

  orbeckst

  committed
  ea900ca

• updated author contribs

  Show description for 98b829e
  orbeckst

  committed
  98b829e

• fix citation syntax

  Show description for 7541d71
  orbeckst

  committed
  7541d71

• minor edits

  orbeckst

  committed
  dc99971

• added all other authors to acknowledgements

  Show description for 82d45a0
  orbeckst

  committed
  82d45a0

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

  orbeckst

  authored
  791c03a

• changed Author contributions: maintenance

  Show description for cf04861
  orbeckst

  committed
  cf04861

• funding ack

  Show description for 3f39574
  orbeckst

  committed
  3f39574

• minor edit (use MD after first definition)

  orbeckst

  committed
  834ed86

• add ASU to @dotsdl affiliation

  orbeckst

  committed
  7d56536

• use referencing for figure

  orbeckst

  committed
  3dad66f

• add ASU to @dotsdl 's affiliation

  orbeckst

  committed
  950b1d8

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

  orbeckst

  committed
  bf9c515

• reference update/cleanup

  Show description for e3ee72c
  orbeckst

  committed
  e3ee72c

• use hyperlinks instead of bare URLs

  Show description for 1ae8464
  orbeckst

  committed
  1ae8464

• update artifact upload action

  orbeckst

  committed
  a9809d2

Commits on May 21, 2024

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

  orbeckst

  authored
  f21f170

• add PDF for author review

  orbeckst

  committed
  4d79965

• used DLD instead of DD for @dotsdl

  orbeckst

  committed
  1bde8d1

Commits on May 22, 2024

• added my name (#361)

  DrDomenicoMarson

  authored
  6344006

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

  Show description for 4fc3ee5
  ttjoseph

  authored
  4fc3ee5

Commits on May 23, 2024

• add name and minor change (#363)

  hl2500

  authored
  adf5a26

Commits on May 25, 2024

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

  xiki-tempula

  authored
  414320d

Commits on May 27, 2024

• edits by Alexander Schlaich

  Show description for f663f50
  

  orbeckst

  and

  schlaicha

  authored
  f663f50

• additional edis suggested by @schlaicha

  Show description for 4a0d892
  orbeckst

  committed
  4a0d892

• add @schlaicha to paper writers

  orbeckst

  committed
  0a4291b

• name the JOSS paper build workflow

  orbeckst

  committed
  bc3b7fb

Commits on May 28, 2024

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

  Show description for 1f01ec7
  

  jhenin

  and

  ttjoseph

  authored
  1f01ec7

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

  Show description for b7b15cb
  lee212

  authored
  b7b15cb

• Add Ian Kenney to author list (#367)

  Show description for 1161e03
  ianmkenney

  authored
  1161e03

• Move JH from Acknowledgments to Contributions (#368)

  jhenin

  authored
  6260d21

• fixed typo LAMPPS -> LAMMPS

  

  jhenin

  authored and

  orbeckst

  committed
  29aee32

• fiddle with bib to make JC Chodera citations appear unformly

  orbeckst

  committed
  ae2bd7c

• software engineering details and minor touch-ups

  Show description for 1c1bc71
  orbeckst

  committed
  1c1bc71

• update @orbeckst's affiliation

  orbeckst

  committed
  be4c2e7

Commits on May 29, 2024

• using SPEC 0 (updated from NEP29)

  Show description for 9b2657e
  orbeckst

  committed
  9b2657e

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

  orbeckst

  authored
  d0be813

Commits on May 30, 2024

• Add Irfan Alibay to paper.md (#372)

  IAlibay

  authored
  00e4f10

• PDF draft of paper as of 2024-05-30

  Show description for d9df3e4
  orbeckst

  committed
  d9df3e4

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

  orbeckst

  committed
  4c7a82f

• update information for David Mobley

  Show description for 4bcf959
  

  davidlmobley

  authored and

  orbeckst

  committed
  4bcf959

Commits on May 31, 2024

• fix DM affiliation

  Show description for 19c963c
  

  orbeckst

  and

  ianmkenney

  authored
  19c963c

• add @vtlim to Author list

  

  vtlim

  authored and

  orbeckst

  committed
  767e89f

Commits on Jun 3, 2024

• Update joss_paper/paper.md

  Show description for 5fe9ec9
  

  xiki-tempula

  and

  ptmerz

  authored
  5fe9ec9

Commits on Jun 4, 2024

• Add affiliation (#374)

  Show description for 41285c3
  

  brycestx

  and

  xiki-tempula

  authored
  41285c3

• Update paper.md (#373)

  Show description for bc46b48
  

  ptmerz

  and

  xiki-tempula

  authored
  bc46b48

• Update paper.md for authorship (#375)

  Show description for 74d164a
  

  msoroush

  and

  xiki-tempula

  authored
  74d164a

• finalized author information and date

  Show description for 388dc54
  orbeckst

  committed
  388dc54

• introduce alchemical free energy calcs outside Implementation section

  Show description for 9215695
  

  ptmerz

  authored and

  orbeckst

  committed
  9215695

Commits on Jun 5, 2024

• edited paragraph on solvation free energy calc to improve clarity

  Show description for f9f5429
  

  ptmerz

  authored and

  orbeckst

  committed
  f9f5429

• fixed front matter

  orbeckst

  committed
  85226d5

• add PTM to "wrote manuscript"

  orbeckst

  committed
  1902b70

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

  orbeckst

  committed
  463ce35

• Fix Shuai Liu’s name (sorry)

  orbeckst

  authored
  9706f56

• Updated author order and contributions

  orbeckst

  authored
  3926c0c

• full author list for NAMD paper

  orbeckst

  committed
  9fa2352

• re-numbered affiliations

  orbeckst

  committed
  a61bddc

• finalized acknowledgements

  Show description for d124059
  orbeckst

  committed
  d124059

• clean up: removed PDF versions

  orbeckst

  committed
  df864a7

• fixed name of Wei-Tse Hu in Ack

  orbeckst

  committed
  cd991d9

• add missing DOIs

  Show description for e85a327
  orbeckst

  committed
  e85a327

• add DOI for Kirkwood 1935

  orbeckst

  committed
  4cbea4c

Commits on Jun 6, 2024

• Fix name Hu -> Hsu in Ack

  Show description for 4f01ac8
  

  orbeckst

  and

  ptmerz

  authored
  4f01ac8

Commits on Jun 26, 2024

• Update affiliation

  xiki-tempula

  authored
  7a2b140

Commits on Jul 18, 2024

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

  orbeckst

  authored
  2fca23e

Commits on Jul 27, 2024

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

  orbeckst

  authored
  0fcae51

Commits on Aug 15, 2024

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

  orbeckst

  authored
  42f3c46

Commits on Aug 17, 2024

• Minor changes to the paper (#387)

  Show description for 1f32e88
  xiki-tempula

  authored
  1f32e88

Commits on Sep 5, 2024

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

  orbeckst

  authored
  464c2cf

Commits on Sep 17, 2024

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

  orbeckst

  authored
  dd117d8

Commits on Sep 19, 2024

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

  orbeckst

  authored
  acac89d

• add @jaclark5 to acknowledgements

  Show description for 4f7e2db
  orbeckst

  authored
  4f7e2db

Commits on Sep 24, 2024

• paper affiliations: spell out USA

  Show description for 27caba8
  orbeckst

  committed
  27caba8