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Parallelisation with Future - #634

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janaobsteter wants to merge 124 commits into

HighlanderLab:develfrom

janaobsteter:Future

Open

Parallelisation with Future#634
janaobsteter wants to merge 124 commits into
HighlanderLab:develfrom
janaobsteter:Future

Commits on Aug 29, 2024
- Merge pull request #583 from HighlanderLab/devel
  janaobsteter
  authored
  c018375
Commits on Sep 19, 2024
- Merge pull request #587 from HighlanderLab/devel
  janaobsteter
  authored
  01a56ee
Commits on Apr 8, 2025
- Parallelising functions, keeping both options
  janaobsteter
  committed
  d1939bf
Commits on Apr 9, 2025
- Parallelisation
  janaobsteter
  committed
  004065f
- Adding export to cross_parallel
  janaobsteter
  committed
  d0c561c
Commits on Apr 11, 2025
- renaming to enable switching from parallel (p) to non-parallel (np)
  janaobsteter
  committed
  da5b0de
- renaming to enable switching from parallel (p) to non-parallel (np)
  janaobsteter
  committed
  377f499
- Merge branch 'Parallelisation' into Parallelisation
  janaobsteter
  authored
  24a3ea0
- Merge pull request #599 from janaobsteter/Parallelisation
  janaobsteter
  authored
  647aa3f
- Adding correct NAMESPACE
  janaobsteter
  committed
  04d4d0d
- Correcting namesapce
  janaobsteter
  committed
  24453c7
- Correcting L2
  janaobsteter
  committed
  5c668a3
- Correcting L2
  janaobsteter
  committed
  6403cd0
- Merge pull request #600 from janaobsteter/Parallelisation
  janaobsteter
  authored
  d7dc74f
- Correcting L2
  janaobsteter
  committed
  7176b74
- Merge pull request #601 from janaobsteter/Parallelisation
  janaobsteter
  authored
  fabda90
Commits on Apr 14, 2025
- Changing removeQueen to not include nTHreads
  janaobsteter
  committed
  842d98d
- Merge pull request #602 from janaobsteter/Parallelisation
  janaobsteter
  authored
  cdeacf8
Commits on Apr 15, 2025
- Removing non-parallel versions
  janaobsteter
  committed
  aa2fc6b
- Merge pull request #603 from janaobsteter/Parallelisation
  janaobsteter
  authored
  c3574aa
- Addding nThreads
  janaobsteter
  committed
  b501b19
- Merge pull request #604 from janaobsteter/Parallelisation
  janaobsteter
  authored
  2ba4ae8
- Solving nThreads inconsistencies
  janaobsteter
  committed
  997449f
- Merge pull request #605 from janaobsteter/Parallelisation
  janaobsteter
  authored
  eacb499
Commits on Apr 22, 2025
- Setting nThreads = 1 before creating individuals
  janaobsteter
  committed
  510b7ca
- Merge pull request #606 from janaobsteter/Parallelisation
  janaobsteter
  authored
  851d007
- Removing print statements
  janaobsteter
  committed
  1830879
- Merge pull request #607 from janaobsteter/Parallelisation
  janaobsteter
  authored
  79641ff
Commits on Apr 25, 2025
- Solving the issue of spatial mating in cross
  janaobsteter
  committed
  f35401a
Commits on May 28, 2025
- Addded collecting recHist and fixed isCsdHeterozygous
  janaobsteter
  committed
  cfe9d38
- Merge pull request #610 from janaobsteter/Parallelisation
  janaobsteter
  authored
  e863ff9
- Minor edits for my OCD
  gregorgorjanc
  committed
  4f69148
- Adding docs
  janaobsteter
  committed
  8b0a130
- Merge branch 'Parallelisation' of https://github.com/janaobsteter/SIMplyBee_fork into Parallelisation
  janaobsteter
  committed
  108b651
- Merge pull request #612 from janaobsteter/Parallelisation
  janaobsteter
  authored
  d6b0637
- Polishing code
  gregorgorjanc
  committed
  691017b
Commits on May 29, 2025
- Adding docs and correcting the cross
  janaobsteter
  committed
  42be86b
- Merge conflicts
  janaobsteter
  committed
  322e1fa
- Amending previous push
  janaobsteter
  committed
  5968402
- Merge pull request #613 from janaobsteter/Parallelisation
  janaobsteter
  authored
  ffd4106
- Rd files update
  gregorgorjanc
  committed
  e566f55
- Add imports
  gregorgorjanc
  committed
  e3cf5d6
- .gitignore change
  gregorgorjanc
  committed
  a069ddd
Commits on May 30, 2025
Commits on Jun 3, 2025
- Fixing error to make examples and tests run
  janaobsteter
  committed
  481377a
- Resolving conflicts
  janaobsteter
  committed
  fea7113
- Merge branch 'HighlanderLab:Parallelisation' into Parallelisation
  janaobsteter
  authored
  0cbac1f
Commits on Jun 8, 2025
- Fixing errors in the cross function
  janaobsteter
  committed
  b51c879
- Merge branch 'Parallelisation' of https://github.com/janaobsteter/SIMplyBee_fork into Parallelisation
  janaobsteter
  committed
  73f004f
Commits on Jun 23, 2025
- Fixing errors in cross()
  janaobsteter
  committed
  6fc7d0d
Commits on Jun 26, 2025
- Adding print message into cross
  janaobsteter
  committed
  03b17c9
Commits on Oct 20, 2025
Commits on Oct 21, 2025
- Update NEWS.md
  gregorgorjanc
  authored
  4a4764f
Commits on Nov 19, 2025
- Removed "year" argument from functions (that is year of queen birth), resolved issues in the split function
  janaobsteter
  committed
  bf1384f
- Merge branch 'Parallelisation' of https://github.com/janaobsteter/SIMplyBee_fork into Parallelisation
  janaobsteter
  committed
  a744340
Commits on Nov 20, 2025
Commits on Nov 26, 2025
- Implementing PSOCK parallelisation, instead of forking (mcapply). Since it's slower, we keep the older version for then nThread = 1
  janaobsteter
  committed
  6ba1ec6
Commits on Nov 27, 2025
- Reversing back to the original foreach loop in cross
  janaobsteter
  committed
  1bb0363
- Resolving merge conflicts
  janaobsteter
  committed
  87ed4ba
- Resolving merge conflicts
  janaobsteter
  committed
  3834a4e
- Merge branch 'Parallelisation' of https://github.com/janaobsteter/SIMplyBee_fork into Parallelisation
  janaobsteter
  committed
  7c677c2
Commits on Nov 28, 2025
- Removing the creation of the clusters from within the functions
  janaobsteter
  committed
  224dfb4
Commits on Dec 8, 2025
- Resolving high-priority issues, adding a parallelisation vignette, and preparing the package for a new stable version
  janaobsteter
  committed
  efbf77a
Commits on Dec 17, 2025
- Last edits regarding sampling functions --> I've squished them all into nCaste
  janaobsteter
  committed
  f567df9
Commits on Dec 18, 2025
- Switching to future_lapply from foreach
  janaobsteter
  committed
  ed15b9a
Commits on May 12, 2026
- Updating variance calculation scripts on Gregor's visit to SLO
  janaobsteter
  committed
  5d68ec2
- Add AGENT plan
  gregorgorjanc
  committed
  67c6e81
Commits on May 13, 2026
- Adding AGENTS.md
  gregorgorjanc
  committed
  6b43d92
- Adding document.yaml GitHub Action
  gregorgorjanc
  committed
  393b398
- Adding test-coverage.yaml GitHub Action
  gregorgorjanc
  committed
  43872ff
- Updating R CMD check GitHub Action
  gregorgorjanc
  committed
  a470e85
- air and jarl specs
  gregorgorjanc
  committed
  ff15974
Commits on May 15, 2026
- Mapping individual to colony variances
  janaobsteter
  committed
  d557e6c
- Merge branch 'Future' of https://github.com/janaobsteter/SIMplyBee_fork into Future
  janaobsteter
  committed
  ce3fe67
- Update documentation
  janaobsteter
  committed
  0fad5da
- Resolving
  janaobsteter
  committed
  d342130
- Sup files changed
  janaobsteter
  committed
  69739a5
- Merge branch 'Future' of https://github.com/janaobsteter/SIMplyBee_fork into Future
  janaobsteter
  committed
  3471d59
- Adding back the F2 vignetet
  janaobsteter
  committed
  7d6a3a4
- Cleaning up variance vignetets
  janaobsteter
  committed
  1a49e17
Commits on Aug 31, 2026
- Adding variance component calculations functions and vignette
  janaobsteter
  committed
  cdbc58b
- Update documentation
  janaobsteter
  committed
  24e9676
Commits on Sep 29, 2026
- Filename changes
  gregorgorjanc
  committed
  c97c73a
- Merge pull request #1 from gregorgorjanc/review/pr-634
  janaobsteter
  authored
  30bf6eb
- Correcting errors from Gregor's agent check
  janaobsteter
  committed
  bd08866
- Adding docs to pull
  janaobsteter
  committed
  1be1b39
- Resolving conflicts
  janaobsteter
  committed
  5a0fe7f
- Update documentation
  janaobsteter
  committed
  49d5c5e
- Merge branch 'devel' into Future
  janaobsteter
  authored
  4b73960
- Update documentation
  janaobsteter
  committed
  6ab9367
- Updating NEWS.md
  janaobsteter
  committed
  cbe04aa
- Adding .gitignore
  janaobsteter
  committed
  b4d8646
- Recolving issues in gitignore
  janaobsteter
  committed
  6451940
- Recolving issues in gitignore
  janaobsteter
  committed
  159cb0e
- Merge branch 'Future' of github.com:janaobsteter/SIMplyBee_fork into Future
  janaobsteter
  committed
  d13898e
Commits on Sep 30, 2026
- WIP
  gregorgorjanc
  committed
  c1a9b82
- Update documentation
  gregorgorjanc
  committed
  662047d
- Exclude AGENTS.md from R package builds
  gregorgorjanc
  committed
  c7ba958
- Added h2 to mapping output
  gregorgorjanc
  committed
  6c4d9df
- Docs
  gregorgorjanc
  committed
  946a8f0
- Document heritability outputs in release notes
  gregorgorjanc
  committed
  8d83dd5
- Update documentation
  gregorgorjanc
  committed
  69aa910
- Polish of various things (pHomBrood, etc.)
  gregorgorjanc
  committed
  605301d
- Update documentation
  gregorgorjanc
  committed
  ebb8e8a
- Ignore local IDE state and generated build artifacts
  gregorgorjanc
  committed
  72b4311
- Fortifying the pHomBrood test
  gregorgorjanc
  committed
  dd323de
Commits on Oct 1, 2026
- more testing
  gregorgorjanc
  committed
  1d6010b
Commits on Oct 3, 2026
- Polish indexing, character IDs, colony vs queen ID, and AGENTS.md
  gregorgorjanc
  committed
  348249d
- Merging different worktrees
  gregorgorjanc
  committed
  59a15c4
- Update documentation
  gregorgorjanc
  committed
  90873c1
Commits on Oct 6, 2026
- Apply suggestion from @gregorgorjanc
  gregorgorjanc
  authored
  25f3b38
- Update documentation
  gregorgorjanc
  committed
  ecc27d2
- Fix empty else block in Functions_L3_Colonies.R
  gregorgorjanc
  authored
  5cfaa2c
- Apply batched suggestions from code review
  gregorgorjanc
  authored
  98aaa9b
Commits on Oct 7, 2026
- Fix colony callback dispatch and clarify parallelisation
  gregorgorjanc
  committed
  e00f9d3
- Update documentation
  gregorgorjanc
  committed
  ab45fc8
Commits on Oct 26, 2026
- Merge pull request #2 from gregorgorjanc/review/jana-variance-updates
  janaobsteter
  authored
  299b231
- Update documentation
  janaobsteter
  committed
  5013370

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