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feat(meta.analysis): in-memory trait_data/prior_distns for run.meta.analysis.pft (Modularity Part 2)#4010

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feat(meta.analysis): in-memory trait_data/prior_distns for run.meta.analysis.pft (Modularity Part 2)#4010
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@omkarrr2533 omkarrr2533 commented May 24, 2026

Follows #3978. Cuts the second disk hop in the chain — right now run.meta.analysis.pft() reloads trait.data.Rdata/prior.distns.Rdata that get.trait.data.pft() just wrote seconds earlier.

  • Added optional trait_data + prior_distns. Pass both and the load() from pft$outdir is skipped. Pass only one and it errors instead of doing a half-disk/half-memory load.
  • Added return_data (default FALSE). On TRUE the MA outputs get attached to the returned pft; on FALSE you get the bare pft like before. Did it this way because of your feat(db): extract get_trait_data_pft() as standalone file-I/O-free function #3978 point — attaching these to a pft that goes back into settings breaks serialization, so default stays legacy-safe.
  • runModule.run.meta.analysis() left on default FALSE since that's the one writing into settings.
  • Provenance saves / dbfile.insert() unchanged.
  • Also fixed a broken roxygen title on run.meta.analysis.pft.

Format-agnostic on purpose — doesn't touch file formats, that's the separate saveRDS/CSV track. Independent of #3810.
Tests green: FAIL 0 | WARN 0 | SKIP 1 | PASS 116.
GSoC 2026 Week 2.

@omkarrr2533 omkarrr2533 marked this pull request as ready for review May 24, 2026 13:16
@mdietze mdietze added this pull request to the merge queue May 26, 2026
@github-merge-queue github-merge-queue Bot removed this pull request from the merge queue due to failed status checks May 26, 2026
@omkarrr2533 omkarrr2533 mentioned this pull request May 30, 2026
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omkarrr2533 added a commit to omkarrr2533/pecan that referenced this pull request Jun 3, 2026
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fix(db): migrate zero-rows PFT check to get_trait_data_pft
9ee4888 
query_pfts(strict = TRUE) only catches missing PFTs via setequal(),
not multi-row results (duplicates are equal under set semantics).
Drop strict and do both nrow == 0L and nrow > 1L checks explicitly,
matching the wrapper's canonical error wording so existing test
patterns continue to match.

Addresses review feedback on PecanProject#4010.
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@mdietze mdietze mdietze approved these changes

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