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Chore/record upstream bcf52af - #135

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hyperpolymath wants to merge 27 commits into

mainfrom

chore/record-upstream-bcf52af

Closed

Chore/record upstream bcf52af#135
hyperpolymath wants to merge 27 commits into
mainfrom
chore/record-upstream-bcf52af

Commits on Oct 7, 2026
- Add a CLR linear-model method for differential abundance
  
  authored and
  JoshuaJewell
  committed
  b21d005
- clr_lm: filter by prevalence before cmultRepl, and test with Welch
  
  authored and
  JoshuaJewell
  committed
  3acf607
- Rename the clr_lm method to clr_welch
  
  authored and
  JoshuaJewell
  committed
  c548451
- Test clr_welch when zCompositions is missing
  
  authored and
  JoshuaJewell
  committed
  657120c
- Run the zCompositions-absent test in CI instead of skipping it
  
  authored and
  JoshuaJewell
  committed
  b86d59f
- Test the cmultRepl output check directly
  
  authored and
  JoshuaJewell
  committed
  7799de8
- proofs(agda): Benjamini-Hochberg adjustment over exact rationals
  
  authored and
  JoshuaJewell
  committed
  3f9a5bc
- proofs(agda): TSS proportions and RLE median positivity over exact rationals
  
  authored and
  JoshuaJewell
  committed
  1d8572f
- proofs: axiom audit for the Agda tree; align headers with D1's Julia
  
  authored and
  JoshuaJewell
  committed
  b3e871d
- proofs: ignore Agda interface files
  
  authored and
  JoshuaJewell
  committed
  a3ccd2e
- ci: type-check the Agda proofs; docs: map each theorem to its Julia code
  
  authored and
  JoshuaJewell
  committed
  6df0e56
- docs: keep the theorem-to-code map with the proofs
  
  authored and
  JoshuaJewell
  committed
  aacf5d1
- fix(differential): refuse complete separation instead of reporting p≈1
  
  authored and
  JoshuaJewell
  committed
  af75c8c
- fix: separate a significance test that did not run from a null result
  
  authored and
  JoshuaJewell
  committed
  c860980
- Test that an omnibus statistic R cannot compute is a failed test
  
  authored and
  JoshuaJewell
  committed
  f71fa03
Commits on Oct 9, 2026
- fix(server): log an unreadable config at warn, not error
  
  authored and
  JoshuaJewell
  committed
  c4b2efc
- Test that an unreadable primers.yml is logged as a warning
  
  authored and
  JoshuaJewell
  committed
  144d0c1
Commits on Oct 14, 2026
- fix(ci): give the required status check a version-stable name
  
  authored and
  JoshuaJewell
  committed
  d0b31f4
- fix(ci): drop the 1x1 matrix so the check name is actually stable
  
  authored and
  JoshuaJewell
  committed
  5b45d09
- docs(ci): name the fork PR that measured the matrix-suffixed check name
  
  authored and
  JoshuaJewell
  committed
  f9cf729
- docs: the Julia pin is repeated in the CI workflow, which has no matrix
  
  authored and
  JoshuaJewell
  committed
  9d888f1
- Gate file-name config values and remote keys; guard pipeline tables on delete
  
  authored and
  JoshuaJewell
  committed
  a37a642
- Test that a remote host without a staging_dir is refused
  
  authored and
  JoshuaJewell
  committed
  578915c
- fix(permanova): test each term, report permutations, refuse untestable terms (#35)
  
  authored
  592ddd7
- Clear stale analysis results and surface request failures in the UI
  
  authored and
  JoshuaJewell
  committed
  bcf52af
- chore(sync): record upstream bcf52af as merged (history only, no file changes)
  hyperpolymath
  committed
  3301dcf
Commits on Oct 15, 2026
- Merge branch 'main' into chore/record-upstream-bcf52af
  hyperpolymath
  authored
  9a2c6b5

Commits

Commits on Oct 7, 2026

Commits on Oct 9, 2026

Commits on Oct 14, 2026

Commits on Oct 15, 2026