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Wip/pr62 theta - #269

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hyperpolymath wants to merge 45 commits into

mainfrom

wip/pr62-theta

Closed

Wip/pr62 theta#269
hyperpolymath wants to merge 45 commits into
mainfrom
wip/pr62-theta

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
- Harden server origin checks, disable Oxygen docs, serve uploads inert
  
  authored and
  JoshuaJewell
  committed
  8dda16d
- Accept the SPA index for /docs paths when a frontend build is present
  
  authored and
  JoshuaJewell
  committed
  e877e13
- docs: describe split deployments and the origins the server must be told about
  
  authored and
  JoshuaJewell
  committed
  2775faf
- feat(pipeline): record stage memory under a config flag, and test that the vsearch stage's peak depends on order
  
  authored and
  JoshuaJewell
  committed
  ef80481
- refactor(pipeline): run the vsearch stage's two searches through one tested helper
  
  authored and
  JoshuaJewell
  committed
  5f73b70
- test(pipeline): run the vsearch stage through the server's entry points (#113)
  
  authored and
  JoshuaJewell
  committed
  52feb60
Commits on Oct 17, 2026
- proofs(agda): isolate PERMANOVA permutation bookkeeping
  
  hyperpolymath
  authored and
  JoshuaJewell
  committed
  f2227ff
- docs: explain differential methods and streamline contribution forms
  
  hyperpolymath
  authored and
  JoshuaJewell
  committed
  89230b9
- docs: clarify that workspace does not apply sample read bounds
  
  hyperpolymath
  authored and
  JoshuaJewell
  committed
  43a7efb
- docs: clarify study-scoped differential options and fix contribution link
  
  hyperpolymath
  authored and
  JoshuaJewell
  committed
  9702084
- refactor(dada2): assemble CSV tables with base R
  
  hyperpolymath
  authored and
  JoshuaJewell
  committed
  e7907e0
- fix(install): stop requiring the removed dplyr package
  
  hyperpolymath
  authored and
  JoshuaJewell
  committed
  13658b2
- fix(dada2): preserve counts through suffix collisions and retain tibble discovery
  
  hyperpolymath
  authored and
  JoshuaJewell
  committed
  0e2fa65
- Require signed commits and fast-forward merges.
  JoshuaJewell
  committed
  bf1d3ef
- Changes to lockfile and startup package checks.
  JoshuaJewell
  committed
  17404ec
- Fixes to table renames and logging.
  JoshuaJewell
  committed
  029fa61
Commits on Oct 19, 2026
- Preparations for release.
  JoshuaJewell
  committed
  78ffc2f
- Add glmGamPoi to the pinned R dependencies
  hyperpolymath
  committed
  444535b
- Add glmGamPoi dispersion option to nb_glm differential abundance
  hyperpolymath
  committed
  3d2f859
- Report glm_gp's negative-binomial overdispersion as theta
  hyperpolymath
  committed
  258a295

Commits

Commits on Oct 7, 2026

Commits on Oct 9, 2026

Commits on Oct 14, 2026

Commits on Oct 17, 2026

Commits on Oct 19, 2026