…ssable (#28) ## Why The Julia job (`Julia 1.12.5 / ubuntu-24.04`) is the only gate on this repo carrying no `continue-on-error` at job or step level — verified by `awk 'NR>=78 && NR<=445 && /continue-on-error/'` returning nothing. It is also the gate blocking upstream `JoshuaJewell#6`. The original blocker (`test/integration/test_server.jl:44`) is **fixed and verified**: run `35614055917` shows `Server smoke tests` by name and `1727 passed` with no Fail column. What that fix uncovered was a second wall of failures sitting behind it, in the bench scripts. ## The trap: serial unmasking The `test` job runs seven bench scripts sequentially. The first one to fail aborts the step and **hides every later one**. `bench/duckdb_aggregation` alone held six broken calls, each visible only once the previous was fixed — so CI could surface at most one defect per ~21-minute cycle. Running the suite locally exposed all of them in a single sitting. Every one of these calls failed *the first time it ever ran*. The bench scripts were only recently wired into CI, and code that is never executed cannot drift-check itself. The unit tests have been calling the same functions correctly the whole time. ## The eight fixes Corrected against the definitions in `src/analysis/analysis.jl` and against the unit tests, which call every one of these functions correctly. | script | function | defect | |---|---|---| | `table_loading` | `filtered_df` | 7 args → 4 (`:130`) | | `duckdb_aggregation` | `aggregate_by_taxon` | 4 args → 6 (`:141`) | | `duckdb_aggregation` | `venn_taxa_present` | invented a `[g1, g2]` group-list parameter no method has ever taken; a Venn is assembled by calling it once per group (`:161`) | | `duckdb_aggregation` | `bar_chart` | passed `(labels, counts, names)`; counts belongs third, and the matrix is (segments × samples) per `:403` and `test_analysis.jl:35` | | `duckdb_aggregation` | `taxa_bar_chart` | arguments 2 and 3 transposed (`:475`) | | `duckdb_aggregation` | `alpha_chart` | passed a 5th `groups` argument no method accepts (`:312`) | | `permanova_nmds` | `alpha_boxplot` | `Vector{Any}` matched neither concrete method, and `metric=` is not a keyword of either (`:734`, `:840`) | | `analysis_config` | — | built on BenchmarkTools, which was in neither `Project.toml` nor `Manifest.toml` | `bench/analysis_config/benchmark.jl` is structurally built on BenchmarkTools (`@benchmarkable`, `BenchmarkGroup`, save/load/median) and CI never installs it, so **that step has never once succeeded since it was wired in**. Pinned rather than fetched at CI time, because an unpinned network fetch would defeat the committed Manifest. The resolve is purely additive: BenchmarkTools 1.8.0 plus the Profile stdlib, **no existing package version changed** (`git diff -U0 Manifest.toml | grep '^-version'` → 0 lines). ### One trap the resolve set, caught by mutation `Pkg.resolve` also rewrote the Manifest's `julia_version` from 1.12.5 to **1.12.6** — the julia this laptop runs, despite `mise.toml` pinning 1.12.5. That line is asserted by `test/unit/test_install_pins.jl:112` against `config/defaults/tool_versions.yml`, so shipping it would have turned a *second* gate red. Restored by hand (Pkg only warns on that field; it does not gate) and verified by mutation: with 1.12.6 the suite reports 94 pass / 1 fail at `:112` (`"1.12.5" == "1.12.6"`); with 1.12.5, 95/95. ## Concurrency (second commit) `cancel-in-progress: true` applied to every event. `main` was merged to at 14:25, 14:28 and 14:43 on 2026-09-21; each run was cancelled 17–18 min into a ~31 min job by the next push, so **three consecutive commits produced no test verdict of any kind**. The red everyone was reading as "CI is broken" was, for those commits, no result at all. Cancelling stays correct for a `pull_request` — a verdict on a superseded head is worthless — so the flag is conditioned on the event rather than removed. ⚠ This does **not** rescue upstream #6, whose head *is* this fork's `main`: its runs are cancelled by the head update itself, not by this setting. Only letting `main` settle for ~31 min does that. ## Verification - All seven bench scripts run clean locally, **twice each** — once creating a baseline, once comparing against it, which is the path CI takes. - Tracked baselines for the five original categories were **not** modified by any run. - `bench/analysis_config/baseline.json` is deliberately **not** committed: the other five came from whichever host produced them, and adding a sixth from a laptop would make this machine's timings the estate reference. CI regenerates it per run and exits 0, matching the workflow's own statement that the deltas are informational. - Repo hygiene is **enforcing** on this PR (a `pull_request` reads `github.repository` as the BASE repo, which is this fork). All three scripts run clean locally: `check-spdx` OK 265 files, `check-format` OK 311 files, `check-lint` OK. Both commit subjects pass the conventional-commit regex. - `test_install_pins.jl`: 95 passed / 95 total. 🤖 Generated with [Claude Code](https://claude.com/claude-code) https://claude.ai/code/session_01X3hgXxWm6umMgZkjYyHnnm

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feat(cladistics): CladeCumulus phylogenetic integration #6

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