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Merged
tristan-f-r merged 73 commits into from
Jul 2, 2025
Merged

feat: BTB #250

tristan-f-r merged 73 commits into from
Jul 2, 2025

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@tristan-f-r tristan-f-r commented Jun 3, 2025 •
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supersedes #150, #168, and #204 - link to algorithm

ctrlaltaf and others added 30 commits February 20, 2024 10:32
@ctrlaltaf
added placeholder files
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@ctrlaltaf
Draft: btb
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@ctrlaltaf
goes through snakemake process without any errors
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@ctrlaltaf
Added new test files
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@gabeah
LN testing complete
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finished testing the LocalNeighborhood. Moving to make the dockerfile
@gabeah
dockerfile is made!
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@gabeah
working on LN implementation
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@gabeah
dealing with some errors
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Step 4 completed
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@gabeah
stuck on modifying generate inputs and parse outputs
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finished?
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finished changes as defined in code review
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added files for BTB PR
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@gabeah
working on btb pr
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@gabeah
continual testing for btb
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@gabeah
continual testing for btb
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@gabeah
prepping for PR
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@gabeah
conflicts fixed?
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@gabeah
Merge branch 'ctrlaltaf-btb' into btb
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@gabeah
passing two tests, need to pass two more
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@gabeah
losing me mind over pytest :)
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three tests passinggit add .
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continuing finishing test functions for PR
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@gabeah
oops, forgot some extra files
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wrapping finished?
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wrapping finished
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updated dockerfile/config to reflect new repo/dockerhub images
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beginning PR fixes
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PR changes finished/comments have been made
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small fixes, preparing to merge main and resolve conflicts
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@tristan-f-r tristan-f-r added the algorithm Pathway reconstruction algorithm to add to SPRAS label Jun 3, 2025
This was referenced Jun 3, 2025
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annaritz
annaritz reviewed Jun 4, 2025
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Some minor things to check; a few larger issues raised but we'll make new PRs/Issues for them.

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annaritz commented Jun 22, 2025

This looks good (Except for my one question about the BTB index check above). This PR will change a big once the RWR PR is in (since a snakemake rule changes). My suggestion is to wait until RWR is merged in and then make the required changes here and merge it.

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annaritz commented Jul 1, 2025 •
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RWR (#261) is now merged, we can make the modifications here and wrap this up soon.

@tristan-f-r tristan-f-r mentioned this pull request Jul 1, 2025
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@tristan-f-r tristan-f-r merged commit 00cc881 into Reed-CompBio:main Jul 2, 2025
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@tristan-f-r tristan-f-r mentioned this pull request Aug 28, 2025
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@tristan-f-r tristan-f-r mentioned this pull request Oct 14, 2025
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@tristan-f-r tristan-f-r deleted the tr-btb branch October 16, 2025 20:07
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@tristan-f-r @annaritz @ctrlaltaf @gabeah @oliverfanderson