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v0.3.1 #197

Merged
merged 52 commits into from
May 22, 2024
Merged

v0.3.1 #197

merged 52 commits into from
May 22, 2024

Commits on May 13, 2024

  1. chore: raise R version for dev

    @jiajic
    jiajic committed May 13, 2024
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Commits on May 15, 2024

  1. adjust line lenght

    @josschavezf
    josschavezf committed May 15, 2024
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  2. replace wrap_msg -> print to avoid error printing list

    @josschavezf
    josschavezf committed May 15, 2024
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  3. Merge pull request #195 from josschavezf/dev 

    replace wrap_msg -> print to avoid error printing list
    @josschavezf
    josschavezf authored May 15, 2024
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Commits on May 17, 2024

  1. fix: allow additional param passing for setGiotto() with list inputs

    @jiajic
    jiajic committed May 17, 2024
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  2. fix: spatShift methods for spatlocs and spatnets 

    - allow NULL inputs, which are interpreted as 0 shifts
- allow z manipulations even when z values are not originally in these objects to facilitate z stacking.
- add col ordering before outputs for zstacking
    @jiajic
    jiajic committed May 17, 2024
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  3. fix: update joinGiottoObjects() 

    - update to be compatible now that @largeImages slot is gone
- object extent detection and xshift defaults no longer depend on images, but `ext()` of the `gobject`
- update xy shifts to use `spatShift()`
    @jiajic
    jiajic committed May 17, 2024
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  4. chore: fix version notation for Matrix

    @jiajic
    jiajic committed May 17, 2024
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  5. chore: drop requirements for main

    @jiajic
    jiajic committed May 17, 2024
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  6. chore: have GHA point to dev2

    @jiajic
    jiajic committed May 17, 2024
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  7. fix: typo

    @jiajic
    jiajic committed May 17, 2024
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  8. Merge branch 'dev' into dev2

    @jiajic
    jiajic committed May 17, 2024
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Commits on May 18, 2024

  1. chore: document

    @jiajic
    jiajic committed May 18, 2024
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  2. chore: document

    @jiajic
    jiajic committed May 18, 2024
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  3. chore: fix doc link

    @jiajic
    jiajic committed May 18, 2024
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Commits on May 19, 2024

  1. fix: docs and code fixes 

    - fix image slot updates when no giottoLargeImages in object
- fix a print statement in createGiottoObjectSubcellular
    @jiajic
    jiajic committed May 19, 2024
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  2. Merge branch 'dev' into dev2

    @jiajic
    jiajic committed May 19, 2024
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Commits on May 20, 2024

  1. chore: update versions and news

    @jiajic
    jiajic committed May 20, 2024
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  2. Merge branch 'dev' into dev2

    @jiajic
    jiajic committed May 20, 2024
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  3. enh: expose simplify param 

    - also fix error when `joinGiottoObjects` only has one spatLocsObj and a list input is expected
    @jiajic
    jiajic committed May 20, 2024
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  4. Merge branch 'dev' into dev2

    @jiajic
    jiajic committed May 20, 2024
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  5. fix: giotto_slot_depths()

    @jiajic
    jiajic committed May 20, 2024
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  6. chore: NSE vars

    @jiajic
    jiajic committed May 20, 2024
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  7. fix: specific image accessors 

    - fix get_giottoLargeImage() and get_giottoImage_MG
    @jiajic
    jiajic committed May 20, 2024
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  8. chore: fix typos

    @jiajic
    jiajic committed May 20, 2024
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  9. chore: document

    @jiajic
    jiajic committed May 20, 2024
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  10. chore: update examples with changes in minidatasets

    @jiajic
    jiajic committed May 20, 2024
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  11. chore: fix ext() example

    @jiajic
    jiajic committed May 20, 2024
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  12. chore: change visium image name in examples 

    - GiottoData 0.2.11.0 changes the image name of the he image from he back to 'image'. Update the examples that have already been switched back to that name.
    @jiajic
    jiajic committed May 20, 2024
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  13. enh: as() conversion of giottoLargeImage to array

    @jiajic
    jiajic committed May 20, 2024
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  14. fix: seurat interop image mapping

    @jiajic
    jiajic committed May 20, 2024
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  15. fix: seurat -> Giotto image mapping

    @jiajic
    jiajic committed May 20, 2024
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  16. fix: rescale and spatShift for giotto when no images are present

    @jiajic
    jiajic committed May 20, 2024
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  17. chore: update joinGiottoObjects() example

    @jiajic
    jiajic committed May 20, 2024
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  18. fix: joinGiottoObjects and name wrangling example

    @jiajic
    jiajic committed May 20, 2024
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  19. chore: document

    @jiajic
    jiajic committed May 20, 2024
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  20. chore: dontrun an internal example

    @jiajic
    jiajic committed May 20, 2024
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  21. Merge branch 'dev' into dev2

    @jiajic
    jiajic committed May 20, 2024
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  22. chore: try to fix GHA

    @jiajic
    jiajic committed May 20, 2024
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  23. chore: try to set up giotto env

    @jiajic
    jiajic committed May 20, 2024
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  24. fix: typo

    @jiajic
    jiajic committed May 20, 2024
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  25. chore: try different way to install giottoenv

    @jiajic
    jiajic committed May 20, 2024
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  26. chore: try moving genv install to testthat.R

    @jiajic
    jiajic committed May 20, 2024
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  27. chore: GHA add more packages for tested examples

    @jiajic
    jiajic committed May 20, 2024
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  28. try to fix install

    @jiajic
    jiajic committed May 20, 2024
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  29. fix indents

    @jiajic
    jiajic committed May 20, 2024
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  30. try again

    @jiajic
    jiajic committed May 20, 2024
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  31. try to fix by specifying py version

    @jiajic
    jiajic committed May 20, 2024
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Commits on May 21, 2024

  1. make py version less stringent

    @jiajic
    jiajic committed May 21, 2024
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  2. feat: as.matrix for spatLocsObj

    @jiajic
    jiajic committed May 21, 2024
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  3. Merge branch 'dev' into dev2

    @jiajic
    jiajic committed May 21, 2024
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  4. Merge pull request #196 from jiajic/dev2 

    Dev2 with lower requirements and remotes added back
    @jiajic
    jiajic authored May 21, 2024
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