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b21d005
Add a CLR linear-model method for differential abundance
hyperpolymath Oct 2, 2026
3acf607
clr_lm: filter by prevalence before cmultRepl, and test with Welch
hyperpolymath Oct 5, 2026
c548451
Rename the clr_lm method to clr_welch
hyperpolymath Oct 5, 2026
657120c
Test clr_welch when zCompositions is missing
hyperpolymath Oct 6, 2026
b86d59f
Run the zCompositions-absent test in CI instead of skipping it
hyperpolymath Oct 6, 2026
7799de8
Test the cmultRepl output check directly
hyperpolymath Oct 7, 2026
3f9a5bc
proofs(agda): Benjamini-Hochberg adjustment over exact rationals
hyperpolymath Oct 2, 2026
1d8572f
proofs(agda): TSS proportions and RLE median positivity over exact ra…
hyperpolymath Oct 2, 2026
b3e871d
proofs: axiom audit for the Agda tree; align headers with D1's Julia
hyperpolymath Oct 2, 2026
a3ccd2e
proofs: ignore Agda interface files
hyperpolymath Oct 2, 2026
6df0e56
ci: type-check the Agda proofs; docs: map each theorem to its Julia code
hyperpolymath Oct 2, 2026
aacf5d1
docs: keep the theorem-to-code map with the proofs
hyperpolymath Oct 2, 2026
af75c8c
fix(differential): refuse complete separation instead of reporting p≈1
hyperpolymath Oct 5, 2026
c860980
fix: separate a significance test that did not run from a null result
hyperpolymath Sep 22, 2026
f71fa03
Test that an omnibus statistic R cannot compute is a failed test
hyperpolymath Oct 6, 2026
c4b2efc
fix(server): log an unreadable config at warn, not error
hyperpolymath Sep 21, 2026
144d0c1
Test that an unreadable primers.yml is logged as a warning
hyperpolymath Oct 6, 2026
d0b31f4
fix(ci): give the required status check a version-stable name
hyperpolymath Sep 21, 2026
5b45d09
fix(ci): drop the 1x1 matrix so the check name is actually stable
hyperpolymath Sep 21, 2026
f9cf729
docs(ci): name the fork PR that measured the matrix-suffixed check name
hyperpolymath Oct 1, 2026
9d888f1
docs: the Julia pin is repeated in the CI workflow, which has no matrix
hyperpolymath Oct 5, 2026
a37a642
Gate file-name config values and remote keys; guard pipeline tables o…
hyperpolymath Oct 6, 2026
578915c
Test that a remote host without a staging_dir is refused
hyperpolymath Oct 6, 2026
592ddd7
fix(permanova): test each term, report permutations, refuse untestabl…
hyperpolymath Oct 14, 2026
bcf52af
Clear stale analysis results and surface request failures in the UI
hyperpolymath Oct 5, 2026
8dda16d
Harden server origin checks, disable Oxygen docs, serve uploads inert
hyperpolymath Oct 5, 2026
e877e13
Accept the SPA index for /docs paths when a frontend build is present
hyperpolymath Oct 8, 2026
2775faf
docs: describe split deployments and the origins the server must be t…
hyperpolymath Oct 14, 2026
ef80481
feat(pipeline): record stage memory under a config flag, and test tha…
hyperpolymath Oct 14, 2026
5f73b70
refactor(pipeline): run the vsearch stage's two searches through one …
hyperpolymath Oct 14, 2026
52feb60
test(pipeline): run the vsearch stage through the server's entry poin…
hyperpolymath Oct 14, 2026
e9bb4e2
proofs(agda): PERMANOVA's p-value floor and which terms are withheld …
hyperpolymath Oct 15, 2026
5427ba3
Merge origin/main into PR #165: keep fork's side
hyperpolymath Oct 15, 2026
a5ea614
Merge branch 'main' into upstream/permanova-proofs
hyperpolymath Oct 15, 2026
c1ee583
Merge branch 'main' into upstream/permanova-proofs
hyperpolymath Oct 15, 2026
cefa8a8
Merge branch 'main' into upstream/permanova-proofs
hyperpolymath Oct 15, 2026
33d5c00
Merge branch 'main' into upstream/permanova-proofs
hyperpolymath Oct 15, 2026
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