Fix stuff that failed in full run - #99

Merged

ghar1821 merged 48 commits into

mainfrom

fix_failed_stuff

Oct 1, 2025

Commits on Aug 12, 2025

Update emd vertical when it cannot be calculated
ghar1821
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e40a104
Added accessory function for subsetting (R)
LuLeom
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53a8ae5
CMS computed on subsets
LuLeom
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1d08ddf
disabling seurat rpca for now
ghar1821
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d947650

Commits on Aug 13, 2025

subsetting now is stratified -per cell -per sample.
LuLeom
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b80affe
Merge branch 'fix_failed_stuff' of https://github.com/openproblems-bio/task_cyto_batch_integration into fix_failed_stuff
LuLeom
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076fa18
CMS is now computed on 60% of the data.
LuLeom
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6d3e669

Commits on Aug 14, 2025

Commits on Aug 15, 2025

update emd scripts
ghar1821
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5a20459

Commits on Aug 18, 2025

Merge branch 'main' into fix_failed_stuff
ghar1821
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1454fb3
re-enabling rpca and n peaks
ghar1821
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69c61c3

Commits on Aug 19, 2025

increase resourhces to mnn
ghar1821
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7e7a7d1
patch batchadjust
ghar1821
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e15b897
increase global size limit
ghar1821
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a46b43d
update batchadjust again
ghar1821
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25dd675
increase ram max size for rpca
ghar1821
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6d5550f

Commits on Aug 20, 2025

patch bug to remove Original_ID if it wasn't there in the first place
ghar1821
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8af2119
increase rpca global maxsize again
ghar1821
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b2de53e
update rpca to hightime
ghar1821
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5ea510a

Commits on Aug 26, 2025

fix bug in perfect integration get obs
ghar1821
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a584eef

Commits on Aug 28, 2025

increase mnn and rpca goal to very high
ghar1821
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9fbefbb

Commits on Aug 29, 2025

update cycombine
ghar1821
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18a7440

Commits on Aug 30, 2025

add pbmcapply as dependency
ghar1821
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d715b27

Commits on Sep 11, 2025

update bras metric
ghar1821
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6ed68c4

Commits on Sep 23, 2025

adding cytovi
ghar1821
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18ebe83
use gpu image for cytovi
ghar1821
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d05262b
cannot use gpu
ghar1821
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1bac1fd
used gpu for cytovi
ghar1821
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be5f1c6
add mnnpy
ghar1821
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def6ad6
try cytovi again
ghar1821
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0431d13
Implemented lisi
LuLeom
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97ebe0c

Commits on Sep 24, 2025

test cytovi setup again
ghar1821
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fdc33df
testing different dependencies
ghar1821
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7c2b1ea
remove package versioining for now
ghar1821
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408f245
revert to cpu fior cytovi and update mnnpy settings
ghar1821
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4547726
testing gpu again
ghar1821
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e18afe3
increase memory allocation for mnnpy
ghar1821
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d5fcc03
Removed CMS, changed cms with lisi in `workflows/run_benchmark/` files
LuLeom
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7c94058

Commits on Sep 25, 2025

Removed mnn.
LuLeom
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1387ec8

Commits on Sep 29, 2025

Re-implemented control methods `shuffle_integration_by_batch` and `shuffle_integration_by_cell_type`
LuLeom
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6810ed0

Commits on Sep 30, 2025

test cytovi
ghar1821
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381a140
removed global emd
ghar1821
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6b1d40a
simplify emd vertical output
ghar1821
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98f26a9

Commits on Oct 1, 2025

remove mnnpy
ghar1821
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62d8863