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feat: seeds#335

Merged
71 commits merged intoReed-CompBio:mainfrom
tristan-f-r:config-args-seed
Jan 9, 2026
Merged

feat: seeds#335
71 commits merged intoReed-CompBio:mainfrom
tristan-f-r:config-args-seed

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@tristan-f-r tristan-f-r commented Jul 17, 2025 •
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Do not review this. The actual changes this PR makes are hard to see. See the two PRs below.

Closes #323. Closes #174.

tristan-f-r and others added 30 commits June 23, 2025 20:31
@tristan-f-r
chore: re-refactor PRM properties
13824a6
@tristan-f-r
fix: correct prop names
543915f
@tristan-f-r
style: fmt
352ba56
@tristan-f-r
chore: add second doi in pl
2fdb13c
@tristan-f-r
refactor: don't use globals in runner
49fd4be 
makes 'unused variable' warnings in runner.py meaningful - this bit @AMINOexe when running into an 'algorithm is not supported' error despite having the class prepared.
@tristan-f-r
feat: begin config refactor
c2e64f7
@tristan-f-r
feat: mostly structured config
4d1a19c
@tristan-f-r
feat: add enum variants on ml
b56ecde
@tristan-f-r
fix: some defaults
bf95888
@tristan-f-r
feat: fully finish config parsing
51d6a7b
@tristan-f-r
style: fmt
a27d38d
@tristan-f-r
fix: remove dep mark, use strict is None
dd4674a
@tristan-f-r
chore: correct config loc
5a8826d
@tristan-f-r
fix: specify hac params
a47b0df
@tristan-f-r
Merge branch 'umain' into config-pydantic
d721656
@tristan-f-r
fix: expand class params
8d75604
@tristan-f-r
fix: expand on pca_params
afa1de5
@tristan-f-r
fix: drop include dict
5eefc51
@tristan-f-r
fix: call items
5243186
@tristan-f-r
fix: better typing and deafults
3b20c48
@tristan-f-r
Merge branch 'umain' into config-pydantic
4c1fcb6
@tristan-f-r
style: fmt
2d4a90f
@tristan-f-r
docs: mention oi2 paper link
31ba9d8
@tristan-f-r
Merge branch 'umain' into property-expe
a296a9b
@tristan-f-r
chore: add nodoi to rwr
fcbf673
@tristan-f-r
Merge branch 'umain' into no-globals
ec7e19a
@tristan-f-r
fix: use correct naming convention for strwr
b9352e8
@tristan-f-r
Merge branch 'umain' into config-pydantic
1c55925
@tristan-f-r
refactor: add config forbid
2a4fb2e
@tristan-f-r
refactor: update config imports
4ded57e
@tristan-f-r tristan-f-r mentioned this pull request Jul 17, 2025
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@tristan-f-r tristan-f-r marked this pull request as draft July 17, 2025 22:04
@tristan-f-r tristan-f-r added enhancement New feature or request needed for benchmarking Priority PRs needed for the benchmarking paper labels Jul 18, 2025
This was referenced Jul 18, 2025
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@tristan-f-r tristan-f-r mentioned this pull request Jul 14, 2025
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@tristan-f-r tristan-f-r mentioned this pull request Sep 24, 2025
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2 tasks
@tristan-f-r tristan-f-r added the awaiting-author Author of the PR needs to fix something from a review / etc. label Sep 25, 2025
@github-actions github-actions bot added the merge-conflict This PR has merge conflicts. label Oct 3, 2025
@agitter agitter closed this pull request by merging all changes into Reed-CompBio:main in 90ee7a3 Jan 9, 2026
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tristan-f-r commented Jan 9, 2026

[Fascinating behavior - I split #335 into #321 and removed all of the seeding changes, but this behavior causes a PR to be automatically closed? I do probably have to rebuild some of it anyways.]

@tristan-f-r tristan-f-r deleted the config-args-seed branch January 9, 2026 22:41
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agitter commented Jan 17, 2026

Why was it automatically closed? All the commits from this branch also belonged to the branch of the merged PR? I don't recall seeing that behavior before.

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tristan-f-r commented Jan 17, 2026 •
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Why was it automatically closed? All the commits from this branch also belonged to the branch of the merged PR?

They did: I designed this PR and split it up into the other PRs (e.g. in #329 you can find commits where I undo algorithm seeding.)

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Guaranteed immutable output Support running an algorithm multiple times with the same parameter combination

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