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feat and dataset: scaffolding, caching, EGFR Phosphoproteomics Collection - #65

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tristan-f-r wants to merge 81 commits into

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egfr-and-infrastructure

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feat and dataset: scaffolding, caching, EGFR Phosphoproteomics Collection#65
tristan-f-r wants to merge 81 commits into
mainfrom
egfr-and-infrastructure

Commits on Mar 18, 2026
- chore: drop other datasets
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  b49439e
- Merge branch 'main' into egfr-and-infrastructure
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  committed
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- chore: re-include
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- chore: drop tools
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- chore: re-add tools
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- docs: cache
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- style: fmt
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- docs: on caching
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- docs: suggestions from review
  
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  and
  ntalluri
  authored
  4b524bc
Commits on Mar 19, 2026
- docs: more comments, refactor: mv function out of Snakefile
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- docs(datasets): mention responsenet and egfr
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- docs(datasets): add old synthetic data branch
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Commits on Mar 23, 2026
- chore: mv to scores instead of dmmm
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- docs: drop expiration docs
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- docs: clarify snakemake importing
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Commits on Mar 24, 2026
- docs: more clarification on data and files
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  85ba6e9
- refactor: move irefindex back to egfr
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- chore: revert web
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- docs: clarify on cache
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Commits on Mar 25, 2026
- chore: apply suggestions
  
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  and
  ntalluri
  authored
  bd3bcab
- docs: apply suggestions
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  committed
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- chore: apply suggestions
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  b3cf691
- drop extensions
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  193f75a
- refactor(egfr): correctly specify output dirs
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  committed
  0581bea
Commits on Mar 26, 2026
- feat(egfr): add target nodes, fmt
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  320aa87
- feat: archived biomart url
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  committed
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- docs: apply suggestion
  
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  and
  ntalluri
  authored
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- docs: apply more suggestions, fix config, unfix magic value
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  committed
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- Merge branch 'egfr-and-infrastructure' of https://github.com/Reed-CompBio/spras-benchmarking into egfr-and-infrastructure
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  committed
  c18d841
- move contributing over
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  committed
  0063ae2
- chore: mv
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  committed
  bf55684
- fix up references
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  committed
  794e8ae
- refactor: use ensp name
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Commits on Apr 7, 2026
- clean up on docs
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  6b4841a
Commits on Apr 20, 2026
- docs: update err msg
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- chore: address some comments
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  committed
  d5b295d
Commits on Apr 21, 2026
- feat: allow for version aliasing
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  committed
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- Merge branch 'egfr-and-infrastructure' of https://github.com/Reed-CompBio/spras-benchmarking into egfr-and-infrastructure
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  committed
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- docs: mention v12 in the file name
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  ef1773b
- docs: mention aliasing
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- feat: uncompressing zip files
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  c2d17db
- test: setup with directory redirects
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  66de95b
- feat: deduplicate edges of output interactome
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  d4749e7
- chore: mv directory test
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  b5e6332
- fix: add init file to cache tests
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- docs: apply suggestions
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- docs: cache
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  8a51052
- fix: designate cache & tools as modules
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  committed
  69de55b
- docs: general egfr cmts, fix: make egfr dataset work
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  committed
  df4a16e
Commits on Apr 23, 2026
- feat: actual interactome trimming
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  committed
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- style: fmt
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  committed
  5df4a13
Commits on Apr 29, 2026
- style: fmt
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  committed
  5e13705
- fix: address larger notes
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  committed
  b5ddaa4
- docs: fix outdated comments, apply some minor suggestions
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  cd41227
- chore: more minor suggestions
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  38ef456
- chore: apply suggestions
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  b6b958e
Commits on Apr 30, 2026
- refactor: change file name
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  5f6720c
- chore: apply suggestions
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  committed
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- fix: set header=False for normalized interactome
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  committed
  c7efcba
- refactor: use other prize value
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  1b60dcb
Commits on May 4, 2026
- refactor: move config to egfr
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  committed
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- ci: use EGFR for config name
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Commits on May 5, 2026
- ci: add uv environment tests
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Commits on May 14, 2026
- update the deduplicate tool function, remove normalize function and be direct
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  committed
  5276687
- remove concept of latest
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- precommit
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  3f69499
- fix tools test
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- cleanup
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  1f0ca12
- precommit
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  78c0adf
- add todo
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  committed
  e682f09
- update trim_input_nodes.py, it was an & and it needed to be an |
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- update comment and precommit
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Commits on May 21, 2026
- add in physical links
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- todo
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Commits on Jun 22, 2026
- add targets to the ensp data
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- add a TODO
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- update to actual SPRAS format
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  5fa0e59
- update weights
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- make a single trim file, add todos for trimming
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  committed
  30bb20f
- precommit
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  committed
  04ba202
- update cli trim code
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  committed
  e73403b

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