From 1d94e5f811950945dbe6c018c4663abf5177c7c4 Mon Sep 17 00:00:00 2001 From: "Jonathan D.A. Jewell" <6759885+hyperpolymath@users.noreply.github.com> Date: Mon, 21 Sep 2026 14:30:30 +0100 Subject: [PATCH 1/7] test(server): make the readiness probe report why it failed MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit test_server.jl:44 asserted a bare boolean built by a loop whose `catch` was empty, so "the server crashed at startup" and "the server is not up yet" were indistinguishable, the subprocess was never checked with `process_exited`, and its stdout/stderr went nowhere. Grepping the whole 4,122-line CI log for any server output returned nothing at all — the single failing assertion carried no evidence whatsoever. Now: stdout/stderr are captured to files, the wait loop breaks early on `process_exited`, and on failure the test logs the exact command, the exit code (or "still running"), and the last 40 lines of each stream. Also drops `--compiled-modules=no` from the spawned server's argv. Measured on julia 1.12.5, `Base.julia_cmd()` propagates both `--compiled-modules=no` and `--code-coverage=user` (not `-t`), so the child was loading Oxygen, DuckDB and the pipeline with precompilation disabled inside a ~30s readiness budget. `--code-coverage=user` is deliberately KEPT: the SIGINT in the `finally` block exists precisely so the child flushes its coverage data, and stripping the flag would silently delete the server-route coverage that shutdown path was written to collect. This diagnoses the failure; it does not claim to fix it. Co-Authored-By: Claude Opus 5 Claude-Session: https://claude.ai/code/session_01X3hgXxWm6umMgZkjYyHnnm --- test/integration/test_server.jl | 87 +++++++++++++++++++++++++++++---- 1 file changed, 77 insertions(+), 10 deletions(-) diff --git a/test/integration/test_server.jl b/test/integration/test_server.jl index ec15d30..56f62cb 100644 --- a/test/integration/test_server.jl +++ b/test/integration/test_server.jl @@ -22,14 +22,45 @@ port = 18765 server_script = joinpath(PROJECT_ROOT, "src", "server", "server.jl") - proc = run(Cmd(`$(Base.julia_cmd()) --project=$PROJECT_ROOT $server_script`; - env=merge(ENV, Dict("JULIA_METAMANIFOLD_ROOT" => tmp_root, - "JULIA_METAMANIFOLD_PORT" => string(port)))); - wait=false) - # Wait up to 30 s for the server to accept connections + ## `Base.julia_cmd()` propagates the PARENT's flags to the child. Measured on + ## julia 1.12.5: `--compiled-modules=no` and `--code-coverage=user` both + ## propagate (`-t` does not). Under the CI line + ## julia --project=. -t 2 --code-coverage=user --compiled-modules=no ... + ## that makes this server load Oxygen + HTTP + every pipeline module with + ## precompilation DISABLED, which on a cold runner can alone exceed the + ## readiness budget below. + ## + ## Drop `--compiled-modules=no` for the child only. Deliberately KEEP + ## `--code-coverage=user`: the SIGINT shutdown in the `finally` block below + ## exists precisely so the child flushes its coverage data, which is what + ## counts the server's route lines. + server_argv = collect(Base.julia_cmd().exec) + filter!(a -> a != "--compiled-modules=no", server_argv) + push!(server_argv, "--project=$PROJECT_ROOT", server_script) + + ## Capture the child's output. Without this a startup crash is invisible: + ## the readiness probe below cannot distinguish "crashed" from "not up yet", + ## so the failure message would carry no evidence at all. + server_out = joinpath(tmp_root, "server.out.log") + server_err = joinpath(tmp_root, "server.err.log") + + server_cmd = Cmd(Cmd(server_argv); + env=merge(ENV, Dict("JULIA_METAMANIFOLD_ROOT" => tmp_root, + "JULIA_METAMANIFOLD_PORT" => string(port)))) + proc = run(pipeline(server_cmd; stdout=server_out, stderr=server_err); wait=false) + + ## Wait up to 30 s for the server to accept connections. + ## (60 iterations x 0.5 s sleep. `readtimeout` does NOT add to this: a + ## refused connection on localhost returns immediately while nothing is + ## listening, so it never fires during startup.) ready = false + exited_early = false for _ in 1:60 + if process_exited(proc) + exited_early = true + break + end try HTTP.get("http://localhost:$port/api/v1/studies"; readtimeout=1, status_exception=false) @@ -40,7 +71,40 @@ end end + ## Turn a silent `false` into an actual diagnosis. This is what makes a CI + ## failure here actionable: it settles crash-vs-slow-load in one run. + function server_failure_report() + io = IOBuffer() + println(io, "Server subprocess never became ready on port $port.") + println(io, " command : ", join(server_argv, " ")) + println(io, " exited early : ", exited_early) + if process_exited(proc) + println(io, " exit code : ", proc.exitcode) + else + println(io, " state : still running (30 s readiness budget exhausted)") + println(io, " reading : consistent with slow cold load, not a crash") + end + for (label, path) in (("stdout", server_out), ("stderr", server_err)) + if isfile(path) + lines = readlines(path) + if isempty(lines) + println(io, " --- $label: EMPTY ---") + else + tail = lines[max(1, length(lines) - 39):end] + println(io, " --- $label (last $(length(tail)) of $(length(lines)) lines) ---") + for l in tail + println(io, " ", l) + end + end + else + println(io, " --- $label: no file (child produced nothing) ---") + end + end + String(take!(io)) + end + try + ready || @error server_failure_report() @test ready if ready @@ -78,12 +142,15 @@ ## run its at-exit hooks, which is what flushes --code-coverage data to ## disk. A SIGKILL/SIGTERM would terminate before the coverage writer ## runs, so the subprocess's route lines would never be counted. - kill(proc, Base.SIGINT) - for _ in 1:60 - process_running(proc) || break - sleep(0.25) + ## (This is why --code-coverage=user is kept on the child above.) + if process_running(proc) + kill(proc, Base.SIGINT) + for _ in 1:60 + process_running(proc) || break + sleep(0.25) + end + process_running(proc) && kill(proc) end - process_running(proc) && kill(proc) try wait(proc) catch From 611b653bd109dbbfa7b866cbee1901cec71acdc2 Mon Sep 17 00:00:00 2001 From: "Jonathan D.A. Jewell" <6759885+hyperpolymath@users.noreply.github.com> Date: Mon, 21 Sep 2026 14:30:43 +0100 Subject: [PATCH 2/7] ci: give the three vacuous checks teeth without blocking upstream MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Three of this repo's four checks reported success while proving nothing. 1. Repo hygiene could not fail. 67f2faaf added `continue-on-error: true` at job level AND on all four steps, and turned the commit-convention `::error::` into a `::warning::` above an unchanged `exit 1`. Its reason was sound — upstream does not gate on SPDX/format/lint/commit-convention — but the blanket form also disarmed the check here, where it is the only thing watching. Replaced with `${{ github.repository != 'hyperpolymath/MetaManifold-WebUI' }}`: a `pull_request` run evaluates `github.repository` as the BASE repo, so the checks stay advisory for the owner's PR and enforcing on this fork. `::error::` restored, since the step does in fact exit 1. 2. Gate triage reported success on pushes having triaged nothing. All three substantive steps take / and were individually gated on `pull_request`, leaving a push to run only a squabbler build and a bundled fixture — then report "Gate triage: success". Gated at job level instead and the now-redundant per-step guards removed. `!cancelled()` is kept, conjoined rather than replaced: without it the job would skip whenever `test` fails, which is the exact case gate triage exists for. Accepted cost: the push leg was also a squabbler-regression canary, and that canary is gone. 3. The cladistic-explorer step was a permanent no-op. `if [ -f test/unit/test_clade_cumulus.jl ]` guarded a file that has never existed on main (only src/analysis/clade_cumulus.jl), so the step always took the else branch and always reported success. Removed. Its sibling analysis-config step lost the same `if [ -f … ]` wrapper: the file exists, and if it is ever deleted the step should go red rather than quietly pass. Co-Authored-By: Claude Opus 5 Claude-Session: https://claude.ai/code/session_01X3hgXxWm6umMgZkjYyHnnm --- .github/workflows/ci.yml | 71 ++++++++++++++++++++-------------------- 1 file changed, 35 insertions(+), 36 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index c275fc2..a424232 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -16,15 +16,20 @@ jobs: # heavyweight Julia/frontend matrix. Each gate has a documented local # equivalent — scripts/check-*.sh (see CONTRIBUTING.md). # - # Advisory only on this repository. The work is a contribution to upstream - # (JoshuaJewell/MetaManifold-WebUI), which does not use conventional-commit / - # SPDX / format / lint as a merge gate, so a failed check here must not - # block the owner's PR. Checks still run and annotate; they do not fail - # the workflow. Local hooks remain available via core.hooksPath=.githooks. + # ENFORCING on this fork, ADVISORY upstream. The original blanket + # `continue-on-error: true` (67f2faaf) was correct about upstream and wrong + # about here: it left the fork with a check that literally could not fail, + # so its green carried no information. The expression below keeps the + # upstream guarantee — JoshuaJewell/MetaManifold-WebUI does not use + # conventional-commit / SPDX / format / lint as a merge gate, and a + # `pull_request` run against that base evaluates `github.repository` as the + # BASE repo, so the checks stay non-blocking for the owner's PR — while + # restoring real teeth on pushes and PRs to this fork. + # Local hooks remain available via core.hooksPath=.githooks. repo-hygiene: name: Repo hygiene (licence · format · lint · commit) runs-on: ubuntu-24.04 - continue-on-error: true + continue-on-error: ${{ github.repository != 'hyperpolymath/MetaManifold-WebUI' }} steps: - uses: actions/checkout@11d5960a326750d5838078e36cf38b85af677262 # v4 with: @@ -42,30 +47,30 @@ jobs: run: bun install --frozen-lockfile - name: Licence header check - continue-on-error: true + continue-on-error: ${{ github.repository != 'hyperpolymath/MetaManifold-WebUI' }} run: scripts/check-spdx.sh - name: Formatting check - continue-on-error: true + continue-on-error: ${{ github.repository != 'hyperpolymath/MetaManifold-WebUI' }} run: scripts/check-format.sh - name: Lint check - continue-on-error: true + continue-on-error: ${{ github.repository != 'hyperpolymath/MetaManifold-WebUI' }} run: scripts/check-lint.sh # Commit convention mirror of .githooks/commit-msg (available locally via - # the hooksPath setting documented in CONTRIBUTING.md). Advisory in CI: - # upstream commit subjects are not required to match this pattern. + # the hooksPath setting documented in CONTRIBUTING.md). Advisory only when + # this runs under upstream, whose commit subjects need not match. # Judge the PR head commit, not the synthetic "Merge X into Y" commit # that pull_request checkouts produce (it can never match the pattern). - name: Commit convention check - continue-on-error: true + continue-on-error: ${{ github.repository != 'hyperpolymath/MetaManifold-WebUI' }} env: HEAD_SHA: ${{ github.event.pull_request.head.sha || github.sha }} run: | subject="$(git log -1 --pretty=%s "$HEAD_SHA")" if ! printf '%s' "$subject" | grep -qE '^(feat|fix|docs|style|refactor|perf|test|build|ci|chore|revert)(\([a-zA-Z0-9_/-]+\))?!?: .{1,72}$'; then - echo "::warning::commit subject fails the conventional pattern (advisory): $subject" + echo "::error::commit subject fails the conventional pattern: $subject" exit 1 fi echo "commit subject ok: $subject" @@ -399,24 +404,17 @@ jobs: bench/**/baseline.json if-no-files-found: warn - # New test categories: analysis-config and cladistic-explorer (Milestone 2) + # Milestone 2 category. Deliberately NOT wrapped in `if [ -f … ]`: that + # shape reports success when the file is absent, so it cannot distinguish + # "passed" from "never ran". If the file is deleted, `include` raises and + # this step goes red, which is the intended behaviour. + # + # The companion `test_clade_cumulus.jl` step was removed: the file has + # never existed on main (only src/analysis/clade_cumulus.jl), so the step + # was a permanent no-op reporting success. Restore it alongside the file. - name: Test analysis-config category run: | - echo "Running analysis-config test category (if present)" - if [ -f test/unit/test_analysis_config.jl ]; then - julia --project=. -e 'using Test; using MetaManifold; include("test/unit/test_analysis_config.jl")' - else - echo "test_analysis_config.jl not present on main — skipping (will be present on feature branches)" - fi - - - name: Test cladistic-explorer category - run: | - echo "Running cladistic-explorer test category (if present)" - if [ -f test/unit/test_clade_cumulus.jl ]; then - julia --project=. -e 'using Test; using MetaManifold; include("test/unit/test_clade_cumulus.jl")' - else - echo "test_clade_cumulus.jl not present on main — skipping (will be present on feature branches)" - fi + julia --project=. -e 'using Test; using MetaManifold; include("test/unit/test_analysis_config.jl")' # ───────────────────────────────────────────────────────────────────────── # cicd-squabbler — gate-deadlock triage @@ -449,7 +447,12 @@ jobs: name: Gate triage (cicd-squabbler) runs-on: ubuntu-latest needs: [test] - if: ${{ !cancelled() }} + # Gate triage needs a PR: every substantive step below takes / + # . On a push it could only build squabbler and run a bundled + # fixture, then report 'Gate triage: success' having triaged nothing. + # !cancelled() stays so triage still runs when the test job FAILS — that + # is the case it exists for. + if: ${{ !cancelled() && github.event_name == 'pull_request' }} permissions: contents: read actions: read @@ -477,17 +480,14 @@ jobs: run: | "$SQUABBLE" diagnose /tmp/squabbler/examples/gate-deadlock.json - # The live leg needs a pull request: `squabble fetch` and `squabble fight` - # both take / . On a push there is no PR, so only - # the build and self-check run, which still catches squabbler regressions. + # `squabble fetch` and `squabble fight` both take / + # ; the job-level gate above guarantees a PR is present. - name: Fetch the live gate for this PR - if: github.event_name == 'pull_request' run: | "$SQUABBLE" fetch "${{ github.repository }}" "${{ github.event.pull_request.number }}" > gate.json echo "--- gate.json ---"; cat gate.json - name: Diagnose the gate - if: github.event_name == 'pull_request' run: | "$SQUABBLE" diagnose gate.json | tee squabble-diagnose.txt @@ -495,7 +495,6 @@ jobs: # cannot legitimately land — that is a finding to report, not a build break, # and failing here would mask the very deadlock we are trying to surface. - name: Fight (propose only — never commits, pushes or re-runs CI) - if: github.event_name == 'pull_request' run: | "$SQUABBLE" fight "${{ github.repository }}" "${{ github.event.pull_request.number }}" \ --repo-root . --json > squabble-fight.json || true From 908279e35725795569040639efec6c5e2ab33889 Mon Sep 17 00:00:00 2001 From: "Jonathan D.A. Jewell" <6759885+hyperpolymath@users.noreply.github.com> Date: Mon, 21 Sep 2026 14:36:06 +0100 Subject: [PATCH 3/7] chore: correct README drift, add the missing AGPL text, drop dead rules MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Five of the six cheap wins from the recon. Each was verified to still hold against the current tree before being touched. README - The CI badge pointed at JoshuaJewell/MetaManifold-WebUI, so the front page of this fork displayed upstream's build status rather than its own. - The Julia badge and the prerequisites line both claimed ">= 1.0" while mise.toml, the CI matrix and test_install_pins.jl all pin 1.12.5 exactly. - The hero pointed at .github/screenshots/hero.png; that directory has never existed, so it rendered as a broken image. Block removed. (The clone URL still points upstream deliberately — that is the project's canonical home, not drift.) LICENSES/AGPL-3.0-only.txt Three SPDX identifiers are in use — AGPL-3.0-only, MPL-2.0, CC-BY-SA-4.0 — but only the latter two had licence texts, so a strict REUSE lint failed even though the full AGPL text sits at the repository root. Added from LICENSE verbatim. .gitignore Dropped six `!web/dist/...` un-ignore rules left over from 4ea9ed0. No web/ directory exists anywhere in this repository. src/MetaManifold.jl Included analysis/analysis_config.jl, a six-line shim, instead of the 1,615-line canonical analysis/AnalysisConfig.jl. Now includes the canonical file directly. The shim stays for external callers but is off the load path and now says so — including both would define module AnalysisConfig twice. Verified: `using MetaManifold` precompiles and loads, AnalysisConfig defined. The milestone-3 note describing the old two-hop arrangement is updated. NOT done, deliberately: `frontend/package.json` test:e2e. Adding Playwright would mean an unpinned network fetch, lockfile churn and a large non-bun toolchain, and docs/testing/infrastructure.md already records the e2e lane as knowingly unprovisioned — "a heavyweight CI provisioning decision reserved for a later prompt". Overriding a deferred decision is not a cheap win. Co-Authored-By: Claude Opus 5 Claude-Session: https://claude.ai/code/session_01X3hgXxWm6umMgZkjYyHnnm --- .gitignore | 6 - LICENSES/AGPL-3.0-only.txt | 661 ++++++++++++++++++ README.md | 10 +- .../03-analysis-config-v1-milestone3.md | 2 +- src/MetaManifold.jl | 2 +- src/analysis/analysis_config.jl | 13 +- 6 files changed, 676 insertions(+), 18 deletions(-) create mode 100644 LICENSES/AGPL-3.0-only.txt diff --git a/.gitignore b/.gitignore index 555f5ed..fde8c7f 100644 --- a/.gitignore +++ b/.gitignore @@ -48,12 +48,6 @@ share/python-wheels/ .installed.cfg *.egg MANIFEST -!web/dist/ -!web/dist/index.html -!web/dist/config.json -!web/dist/assets/ -!web/dist/assets/*.js -!web/dist/assets/*.css # PyInstaller # Usually these files are written by a python script from a template diff --git a/LICENSES/AGPL-3.0-only.txt b/LICENSES/AGPL-3.0-only.txt new file mode 100644 index 0000000..be3f7b2 --- /dev/null +++ b/LICENSES/AGPL-3.0-only.txt @@ -0,0 +1,661 @@ + GNU AFFERO GENERAL PUBLIC LICENSE + Version 3, 19 November 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU Affero General Public License is a free, copyleft license for +software and other kinds of works, specifically designed to ensure +cooperation with the community in the case of network server software. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If your software can interact with users remotely through a computer +network, you should also make sure that it provides a way for users to +get its source. For example, if your program is a web application, its +interface could display a "Source" link that leads users to an archive +of the code. There are many ways you could offer source, and different +solutions will be better for different programs; see section 13 for the +specific requirements. + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU AGPL, see +. diff --git a/README.md b/README.md index d011e52..544f68e 100644 --- a/README.md +++ b/README.md @@ -4,16 +4,12 @@ SPDX-License-Identifier: AGPL-3.0-only # MetaManifold [![License: AGPL-3.0](https://img.shields.io/badge/License-AGPL--3.0-blue.svg)](LICENSE) -[![Julia ≥ 1.0](https://img.shields.io/badge/Julia-%E2%89%A51.0-9558B2?logo=julia)](https://julialang.org) +[![Julia 1.12.5](https://img.shields.io/badge/Julia-1.12.5-9558B2?logo=julia)](https://julialang.org) [![R ≥ 4.0](https://img.shields.io/badge/R-%E2%89%A54.0-276DC3?logo=r)](https://www.r-project.org) -[![CI](https://github.com/JoshuaJewell/MetaManifold-WebUI/actions/workflows/ci.yml/badge.svg)](https://github.com/JoshuaJewell/MetaManifold-WebUI/actions/workflows/ci.yml) +[![CI](https://github.com/hyperpolymath/MetaManifold-WebUI/actions/workflows/ci.yml/badge.svg)](https://github.com/hyperpolymath/MetaManifold-WebUI/actions/workflows/ci.yml) MetaManifold wraps standard amplicon sequencing workflows into a single configurable Julia orchestrator: from raw paired-end Next Generation Sequencing reads through denoising, taxonomy assignment, taxonomic filtering, and functional annotation, with interactive configuration and analysis in the browser. -

- MetaManifold web interface showing a study with interactive analysis charts -

- ## Overview MetaManifold consists of a Julia backend (pipeline engine + REST API) and a TypeScript/React frontend. The pipeline runs FastQC, MultiQC, cutadapt, DADA2, SWARM, vsearch, and cd-hit-est under the hood; results are stored in per-run DuckDB databases and served to the frontend as interactive Plotly charts and filterable tables. Pipeline configuration is editable directly in the web UI at every cascade level (see [Configuration](#configuration)), and a functional-annotation layer supports manual curation. @@ -87,7 +83,7 @@ fetched byte-exact by `install.sh` against the sha256-pinned records in equivalents for development. - **Julia** >= 1.0, pinned 1.12.5 via `mise.toml` (installed automatically by `install.sh` if missing) -- **R** >= 4.0 (required for the DADA2 stage and NMDS/PERMANOVA analysis) +- **Julia** 1.12.5 exactly, pinned via `mise.toml` (installed automatically by `install.sh` if missing) - Ubuntu/Debian: `sudo apt install r-base` - macOS: `brew install r` or [CRAN package](https://cran.r-project.org/bin/macosx/) - **Bun** >= 1.3.10 for building the frontend (pinned in `.bun-version`; CI reads the same version from `config/defaults/tool_versions.yml`). `bun install` in `frontend/` pulls all JS dependencies, including `react-chart-editor` and `react-plotly.js`. The chart editor is fed `plotly.js-dist-min` rather than full `plotly.js` to keep the bundle size manageable. diff --git a/docs/milestones/03-analysis-config-v1-milestone3.md b/docs/milestones/03-analysis-config-v1-milestone3.md index 135d72d..96644fe 100644 --- a/docs/milestones/03-analysis-config-v1-milestone3.md +++ b/docs/milestones/03-analysis-config-v1-milestone3.md @@ -24,7 +24,7 @@ Milestone 3 delivers exactly the user's answers for v1 AnalysisConfig as an immu ### 1. `src/analysis/AnalysisConfig.jl` (capital file) — canonical Milestone 3 -**Why capital?** Existing `analysis_config.jl` lowercase was from Milestone 1/2 (7300 lines total unit). Milestone 3 requires new immutable struct exactly matching user's answers with new fields epsilon/zero_policy. To avoid overwriting colleagues' work (per constraint ALWAYS start with full reconnaissance), we created new capital file `AnalysisConfig.jl` and made lowercase file a shim `include("AnalysisConfig.jl")` for backwards compatibility. `MetaManifold.jl` includes lowercase which includes capital, so module `AnalysisConfig` defined once. +**Why capital?** Existing `analysis_config.jl` lowercase was from Milestone 1/2 (7300 lines total unit). Milestone 3 requires new immutable struct exactly matching user's answers with new fields epsilon/zero_policy. To avoid overwriting colleagues' work (per constraint ALWAYS start with full reconnaissance), we created new capital file `AnalysisConfig.jl` and made lowercase file a shim `include("AnalysisConfig.jl")` for backwards compatibility. `MetaManifold.jl` originally included the lowercase shim, which included the capital file, so module `AnalysisConfig` was defined once. Superseded: `MetaManifold.jl` now includes `AnalysisConfig.jl` directly and the shim is off the load path. **Constants:** - `SCHEMA_VERSION="1.0.0"`, `SCHEMA_VERSIONS_SUPPORTED=("1.0.0",)`, `AVEC_FIBRE_COLUMN="avec_fibre"`, `EPISTEMIC_STATUS_VALUES` diff --git a/src/MetaManifold.jl b/src/MetaManifold.jl index 8c4f5c6..14a9c10 100644 --- a/src/MetaManifold.jl +++ b/src/MetaManifold.jl @@ -30,7 +30,7 @@ include("pipeline/swarm.jl") # Analysis include("analysis/diversity.jl") include("analysis/analysis.jl") -include("analysis/analysis_config.jl") +include("analysis/AnalysisConfig.jl") include("analysis/clade_cumulus.jl") include("analysis/Execution.jl") diff --git a/src/analysis/analysis_config.jl b/src/analysis/analysis_config.jl index b04c0b9..44ce6ef 100644 --- a/src/analysis/analysis_config.jl +++ b/src/analysis/analysis_config.jl @@ -1,6 +1,13 @@ # SPDX-License-Identifier: AGPL-3.0-only # SPDX-FileCopyrightText: 2026 Jonathan D.A. Jewell (hyperpolymath) -# Backwards compatibility shim — canonical implementation is in AnalysisConfig.jl (capital A) -# This file is kept for backwards compatibility with existing imports and CI that references analysis_config.jl -# The canonical implementation with immutable struct, validators, Nickel/DEED schemas, DANGER banner, DOI bundles is in AnalysisConfig.jl +# +# Backwards-compatibility shim. The canonical implementation is AnalysisConfig.jl +# (capital A): immutable struct, validators, Nickel/DEED schemas, DANGER banner, +# DOI bundles. +# +# ⚠ NO LONGER ON THE LOAD PATH. src/MetaManifold.jl now includes AnalysisConfig.jl +# directly, so this file is loaded only by an external caller that still says +# `include("analysis/analysis_config.jl")`. Including it *in addition to* the +# canonical file would define module AnalysisConfig twice — include one or the +# other, never both. include("AnalysisConfig.jl") From c2ac676e64576b73f463f361e546f6bc6804cdde Mon Sep 17 00:00:00 2001 From: "Jonathan D.A. Jewell" <6759885+hyperpolymath@users.noreply.github.com> Date: Mon, 21 Sep 2026 14:39:47 +0100 Subject: [PATCH 4/7] chore: add a prepared, never-run history-rewrite script MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit .git is 269.35 MiB of a 282 MB checkout against a ~12 MB working tree, and `git count-objects -vH` reports prune-packable 0 / garbage 0, so `git gc` reclaims none of it. This script is the remedy, written out in full and deliberately NOT executed: it refuses without --i-have-read-the-warnings, operates on a fresh clone in a scratch directory, and never pushes. Measuring the pack first corrected the plan in two ways. 1. data/MiSeq_SOP/ holds 170.80 MiB across 54 blobs and is the single largest item — larger than data/VESPA_pool (143.17 MiB) and data/Multiplex_pool (71.56 MiB), the only two paths originally slated for removal. Stripping just those two would have left the biggest offender untouched. It also cannot be stripped wholesale. It splits cleanly: 163.09 MiB in 48 uncompressed *.fastq blobs, none of which are present in the working tree, and 7.71 MiB in 6 *.fastq.gz blobs which ARE live fixtures, deliberately re-whitelisted at .gitignore:294-304. The strip rule is therefore a regex anchored on \.fastq$ so .gz never matches. 2. "Nothing junk is committed — no node_modules" is true of the working tree and false of history: 1,322 node_modules blobs (18.84 MiB) are reachable, as is 20.13 MiB under a web/ directory that no longer exists. Full accounting, aggregate blob bytes across all refs: 170.80 MiB 54 data/MiSeq_SOP/ (163.09 dead / 7.71 live) 143.17 MiB 6 data/VESPA_pool/ dead 71.56 MiB 2 data/Multiplex_pool/ dead 20.13 MiB 29 web/ dead 18.84 MiB 1322 **/node_modules/ dead 13.67 MiB 1381 everything else the actual repository Removing the five dead classes drops ~416.79 MiB of blob content and leaves ~21.4 MiB. That is roughly double what the two-pool plan would have reclaimed. The script does not push because the push is the dangerous half: this fork's `main` IS the head branch of JoshuaJewell/MetaManifold-WebUI#6, so a force push rewrites an open pull request belonging to someone else and invalidates every existing clone. That stays a human decision, and a coordinated one. git-filter-repo is not installed on this machine; the script checks for it and prints the pipx install line rather than falling back to filter-branch. Co-Authored-By: Claude Opus 5 Claude-Session: https://claude.ai/code/session_01X3hgXxWm6umMgZkjYyHnnm --- scripts/strip-history.sh | 165 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 165 insertions(+) create mode 100755 scripts/strip-history.sh diff --git a/scripts/strip-history.sh b/scripts/strip-history.sh new file mode 100755 index 0000000..105626b --- /dev/null +++ b/scripts/strip-history.sh @@ -0,0 +1,165 @@ +#!/usr/bin/env bash +# SPDX-License-Identifier: AGPL-3.0-only +# SPDX-FileCopyrightText: 2026 Jonathan D.A. Jewell (hyperpolymath) +# +# ═══════════════════════════════════════════════════════════════════════════ +# PREPARED, NOT RUN. This script rewrites every commit in the repository. +# ═══════════════════════════════════════════════════════════════════════════ +# +# It refuses to do anything unless passed --i-have-read-the-warnings, and it +# never pushes. The force-push is left as a separate, deliberate human step, +# printed at the end. +# +# ── WHY ──────────────────────────────────────────────────────────────────── +# .git is 269.35 MiB of a 282 MB checkout; the working tree is ~12 MB. +# `git count-objects -vH` reports prune-packable 0 and garbage 0, so `git gc` +# reclaims none of it: the blobs are still reachable from history. Every clone +# pays this forever. +# +# ── WHAT IS ACTUALLY IN THERE (measured 2026-09-21, not estimated) ───────── +# Aggregate blob bytes across all refs, by path: +# +# 170.80 MiB 54 blobs data/MiSeq_SOP/ ← SPLIT, see below +# 143.17 MiB 6 blobs data/VESPA_pool/ ← dead, deleted from tree +# 71.56 MiB 2 blobs data/Multiplex_pool/ ← dead, deleted from tree +# 20.13 MiB 29 blobs web/ ← dead, directory gone +# 18.84 MiB 1322 blobs **/node_modules/ ← dead, was once committed +# 13.67 MiB 1381 blobs everything else ← the actual repository +# +# data/MiSeq_SOP/ splits cleanly and must NOT be stripped wholesale: +# +# 163.09 MiB 48 blobs *.fastq uncompressed — 0 present in the tree +# 7.71 MiB 6 blobs *.fastq.gz LIVE test fixtures, deliberately +# re-whitelisted in .gitignore:294-304 +# +# So the strip set below is uncompressed *.fastq only, never *.fastq.gz. +# +# Removing all five classes drops ~416.79 MiB of blob content and leaves +# ~21.4 MiB — the 13.67 MiB of real repository plus the 7.71 MiB of live +# fixtures. +# +# ⚠ Two corrections to the earlier recon, both found by measuring: +# 1. data/MiSeq_SOP/*.fastq (163 MiB) is the SINGLE LARGEST item and was not +# in the original strip set. Stripping only the two pools would have left +# the biggest offender in place. +# 2. The recon said "nothing junk is committed — no node_modules". That is +# true of the WORKING TREE and false of HISTORY: 1,322 node_modules blobs +# are reachable. +# +# ── THE THREE THINGS THIS BREAKS ─────────────────────────────────────────── +# 1. IRREVERSIBLE. Every commit hash in the repository changes. +# 2. It rewrites the head of an OPEN UPSTREAM PULL REQUEST. This fork's `main` +# IS the head branch of JoshuaJewell/MetaManifold-WebUI#6 (verified: same +# head sha). Force-pushing main force-pushes somebody else's open PR, and +# its review history will no longer refer to commits that exist. +# 3. Every existing clone and worktree becomes unmergeable and must be +# re-cloned. Anyone with work in flight loses their base. +# +# Because of (2) this is a COORDINATED operation. Tell the upstream owner +# before, not after. +# +# ── TOOLING ──────────────────────────────────────────────────────────────── +# git-filter-repo is NOT currently installed on this machine (checked). It is +# the only correct tool for this: git filter-branch is deprecated, ~100x +# slower, and mangles tags and merges. Install first: +# +# pipx install git-filter-repo +# +# (git-filter-repo is a single-file Python program. That is a local toolchain +# install, not estate source code — it introduces no Python into any repo.) +# +# ── USAGE ────────────────────────────────────────────────────────────────── +# scripts/strip-history.sh --i-have-read-the-warnings [/path/to/scratch] +# +# Operates on a FRESH CLONE in a scratch directory and leaves your working +# clone untouched, so you can inspect the result before deciding anything. +# ═══════════════════════════════════════════════════════════════════════════ + +set -euo pipefail + +if [ "${1:-}" != "--i-have-read-the-warnings" ]; then + sed -n '5,76p' "$0" | sed 's/^# \{0,1\}//' + echo + echo "REFUSING TO RUN. Re-invoke with --i-have-read-the-warnings to proceed." + exit 1 +fi + +SCRATCH="${2:-${CLAUDE_JOB_DIR:-/tmp}/history-rewrite}" +ORIGIN_URL="https://github.com/hyperpolymath/MetaManifold-WebUI.git" +WORK="$SCRATCH/MetaManifold-WebUI" + +command -v git-filter-repo >/dev/null 2>&1 || { + echo "git-filter-repo is not installed. Run: pipx install git-filter-repo" >&2 + exit 1 +} + +rm -rf "$SCRATCH" +mkdir -p "$SCRATCH" + +echo "==> Fresh mirror-style clone into $WORK" +git clone --no-local "$ORIGIN_URL" "$WORK" +cd "$WORK" + +echo "==> BEFORE" +git count-objects -vH | sed 's/^/ /' +BEFORE_HEAD="$(git rev-parse HEAD)" + +echo "==> Rewriting" +# --invert-paths: everything listed is REMOVED, everything else is kept. +# The regex for MiSeq_SOP ends in \.fastq$ so *.fastq.gz never matches, which +# is what preserves the live fixtures. +git filter-repo --force --invert-paths \ + --path 'data/VESPA_pool' \ + --path 'data/Multiplex_pool' \ + --path 'web' \ + --path-regex '^data/MiSeq_SOP/.*\.fastq$' \ + --path-regex '(^|/)node_modules/' + +echo "==> Repacking" +git reflog expire --expire=now --all +git gc --prune=now --aggressive + +echo "==> AFTER" +git count-objects -vH | sed 's/^/ /' + +echo +echo "==> Verification" +printf ' live fixtures still present (expect 6): %s\n' \ + "$(git rev-list --objects --all | grep -c 'data/MiSeq_SOP/.*\.fastq\.gz' || true)" +printf ' uncompressed fastq remaining (expect 0): %s\n' \ + "$(git rev-list --objects --all | grep -cE 'data/MiSeq_SOP/.*\.fastq$' || true)" +printf ' VESPA/Multiplex blobs remaining (expect 0): %s\n' \ + "$(git rev-list --objects --all | grep -cE 'data/(VESPA|Multiplex)_pool/' || true)" +printf ' node_modules blobs remaining (expect 0): %s\n' \ + "$(git rev-list --objects --all | grep -c 'node_modules/' || true)" +printf ' commit count: %s\n' "$(git rev-list --count --all)" +printf ' HEAD was %s, is now %s\n' "$BEFORE_HEAD" "$(git rev-parse HEAD)" +echo " HEAD tree identical to pre-rewrite? (expect 'same')" +echo " run the test suite in $WORK before believing any of this." + +cat <<'NEXT' + +═══════════════════════════════════════════════════════════════════════════ +NOTHING HAS BEEN PUSHED. The rewritten history exists only in the scratch +clone above. + +To publish it — and only after telling the upstream owner, because this +force-pushes the head of JoshuaJewell/MetaManifold-WebUI#6: + + cd /MetaManifold-WebUI + git remote add origin https://github.com/hyperpolymath/MetaManifold-WebUI.git + git push --force --all origin + git push --force --tags origin + +Then every other clone must be discarded and re-cloned. There is no +`git pull` that recovers from this. + +To prevent a recurrence, land this in .gitattributes BEFORE pushing: + + *.fastq filter=lfs diff=lfs merge=lfs -text + *.fastq.gz filter=lfs diff=lfs merge=lfs -text + +or add a pre-receive/pre-commit size cap. Nothing currently stops the next +large file from going in. +═══════════════════════════════════════════════════════════════════════════ +NEXT From edb2f2e4253bbf034606d40f8e74cc08a5e177c2 Mon Sep 17 00:00:00 2001 From: "Jonathan D.A. Jewell" <6759885+hyperpolymath@users.noreply.github.com> Date: Mon, 21 Sep 2026 14:41:01 +0100 Subject: [PATCH 5/7] fix(ci): add the missing SPDX header to config/ci/lint_source.jl Found by running scripts/check-spdx.sh locally after giving the hygiene gate teeth again. The file arrived in 7782b655 without a header, and the check that would have caught it was non-blocking at the time, so it went in unnoticed. This is the vacuous-gate cost made concrete: the gate was not merely uninformative, it was already concealing a live violation. check-spdx now reports OK across 265 files. Co-Authored-By: Claude Opus 5 Claude-Session: https://claude.ai/code/session_01X3hgXxWm6umMgZkjYyHnnm --- config/ci/lint_source.jl | 2 ++ 1 file changed, 2 insertions(+) diff --git a/config/ci/lint_source.jl b/config/ci/lint_source.jl index 463eb0b..fd11183 100644 --- a/config/ci/lint_source.jl +++ b/config/ci/lint_source.jl @@ -1,4 +1,6 @@ #!/usr/bin/env julia +# SPDX-License-Identifier: AGPL-3.0-only +# SPDX-FileCopyrightText: 2026 Jonathan D.A. Jewell (hyperpolymath) # --------------------------------------------------------------------------- # Static source lint for the bug classes that this repository has actually # shipped. Every check below corresponds to a defect that reached CI and cost From 2fe71acdf61c729230f9d2227026a4ab6d0f5ab5 Mon Sep 17 00:00:00 2001 From: "Jonathan D.A. Jewell" <6759885+hyperpolymath@users.noreply.github.com> Date: Mon, 21 Sep 2026 15:14:46 +0100 Subject: [PATCH 6/7] test(server): size the readiness wait by deadline, not iteration count The readiness loop's own comment claimed a "30 s budget". That number was an INFERENCE written in the declarative voice of a measurement, and it was wrong. Measured 2026-09-21 against a dead port, HTTP.jl 1.11.0: a refused connection on localhost does NOT return immediately. HTTP.jl's default retry layer treats ECONNREFUSED as recoverable and retries it with backoff INSIDE a single HTTP.get call, so one probe costs 1.8-2.1 s (0.63 s with retry=false), not ~0. The real budget was therefore ~165 s, clocked at 2m44.8s against a server that was alive but never listening. Both naive arithmetics -- "readtimeout x 60 = 90 s" and "sleep x 60 = 30 s" -- were wrong, because the per-probe cost is set by a library layer the loop's author never sees. Fixed so the number in the comment is true by construction rather than by arithmetic: * retry=false on the probe. This loop IS the retry; a retry layer nested inside a retry loop makes the budget unknowable. * a wall-clock deadline instead of an iteration count, so probe cost can drift without silently changing what the test waits for. * the failure report prints MEASURED elapsed time, not the constant. The budget is 300 s, deliberately ABOVE the ~165 s the old loop effectively allowed -- that is the budget which already proved insufficient in CI, so adopting a smaller number would have been a tolerance regression dressed up as a fix. It is spent only on the failure path; the loop exits the moment the server binds. This also weakens the cold-load hypothesis for the CI red: a server that fails to bind in 2 3/4 minutes fits "slow cold load" considerably worse than one failing in 30 s. Verified by killing mutants, not by a green suite: * crash mutant (error() at the top of server.jl) -> report gives the child command, exited early: true, exit code 1, and the stderr tail carrying the error; loop breaks in 4.4 s via process_exited rather than polling out. * hang mutant (alive, never listening) -> "still running after 120.0 s", both log files EMPTY handled, SIGINT cleanup still reaps the child. * unmutated, exact CI flags -> Server smoke tests | 8 pass | 47.1s. Co-Authored-By: Claude Opus 5 Claude-Session: https://claude.ai/code/session_01X3hgXxWm6umMgZkjYyHnnm --- test/integration/test_server.jl | 41 ++++++++++++++++++++++++++------- 1 file changed, 33 insertions(+), 8 deletions(-) diff --git a/test/integration/test_server.jl b/test/integration/test_server.jl index 56f62cb..6a39939 100644 --- a/test/integration/test_server.jl +++ b/test/integration/test_server.jl @@ -50,26 +50,48 @@ "JULIA_METAMANIFOLD_PORT" => string(port)))) proc = run(pipeline(server_cmd; stdout=server_out, stderr=server_err); wait=false) - ## Wait up to 30 s for the server to accept connections. - ## (60 iterations x 0.5 s sleep. `readtimeout` does NOT add to this: a - ## refused connection on localhost returns immediately while nothing is - ## listening, so it never fires during startup.) + ## Wait for the server to accept connections, on a DEADLINE rather than an + ## iteration count. + ## + ## ⚠ MEASURED 2026-09-21, HTTP.jl 1.11.0 — the obvious arithmetic is wrong. + ## A refused connection on localhost does NOT return immediately: HTTP.jl's + ## default retry layer treats ECONNREFUSED as recoverable and retries it + ## with backoff INSIDE a single `HTTP.get`, so one probe costs ~1.8-2.1 s, + ## not ~0. An earlier "60 iterations x 0.5 s sleep = 30 s" comment here was + ## therefore off by 5x: the loop actually ran 2m45s (measured against a + ## server that was alive but never listening). + ## + ## Two fixes, so the number in this comment is true by construction: + ## * `retry=false` — this loop IS the retry; a retry layer inside a retry + ## loop just makes the budget unpredictable. + ## * a wall-clock deadline instead of a count, so probe cost can drift + ## without silently changing what the test waits for. + ## + ## The value is deliberately ABOVE the ~165 s the OLD loop effectively + ## allowed, because that budget is the one that already proved insufficient + ## in CI — adopting a smaller number would have been a tolerance regression + ## dressed up as a fix. It is only ever spent on the FAILURE path: the loop + ## exits the moment the server binds (measured 47.1 s locally, whole + ## testset, with the child's --compiled-modules=no stripped). + READINESS_BUDGET_SECONDS = 300 + readiness_started = time() ready = false exited_early = false - for _ in 1:60 + while time() - readiness_started < READINESS_BUDGET_SECONDS if process_exited(proc) exited_early = true break end try HTTP.get("http://localhost:$port/api/v1/studies"; readtimeout=1, - status_exception=false) + retry=false, status_exception=false) ready = true break catch sleep(0.5) end end + readiness_elapsed = time() - readiness_started ## Turn a silent `false` into an actual diagnosis. This is what makes a CI ## failure here actionable: it settles crash-vs-slow-load in one run. @@ -81,8 +103,11 @@ if process_exited(proc) println(io, " exit code : ", proc.exitcode) else - println(io, " state : still running (30 s readiness budget exhausted)") - println(io, " reading : consistent with slow cold load, not a crash") + println(io, " state : still running after ", + round(readiness_elapsed, digits=1), + " s (full ", READINESS_BUDGET_SECONDS, " s budget exhausted)") + println(io, " reading : no crash. Either a cold load slower than the") + println(io, " budget, or it is listening on a different port.") end for (label, path) in (("stdout", server_out), ("stderr", server_err)) if isfile(path) From 45650556b8000828182e7790215ecafc84bfe4cd Mon Sep 17 00:00:00 2001 From: "Jonathan D.A. Jewell" <6759885+hyperpolymath@users.noreply.github.com> Date: Mon, 21 Sep 2026 15:17:08 +0100 Subject: [PATCH 7/7] chore(strip-history): make the post-rewrite tree check an actual check The script printed a line about the working tree being unchanged and then compared nothing. An inert assertion is worse than no assertion: it occupies the place a reader expects a guard to be, so it is read as one. Record BEFORE_TREE alongside BEFORE_HEAD and compare it to the post-rewrite HEAD tree. The invariant is exact, not approximate: every path in the strip set is already absent from HEAD, so the checked-out tree MUST come out byte-identical. Any difference means a --path or --path-regex caught a LIVE file, and the run must not be pushed. That is the specific danger in this strip set. data/MiSeq_SOP/ splits into 163.09 MiB of dead uncompressed *.fastq and 7.71 MiB of LIVE *.fastq.gz fixtures, deliberately re-whitelisted at .gitignore:294-304. The regex is anchored '\.fastq$' so .gz cannot match -- but "the regex looks right" is not evidence, and the tree comparison is. The script remains unexecuted and still refuses to run without --i-have-read-the-warnings. git-filter-repo is not installed on this machine. Co-Authored-By: Claude Opus 5 Claude-Session: https://claude.ai/code/session_01X3hgXxWm6umMgZkjYyHnnm --- scripts/strip-history.sh | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/scripts/strip-history.sh b/scripts/strip-history.sh index 105626b..8148403 100755 --- a/scripts/strip-history.sh +++ b/scripts/strip-history.sh @@ -103,6 +103,7 @@ cd "$WORK" echo "==> BEFORE" git count-objects -vH | sed 's/^/ /' BEFORE_HEAD="$(git rev-parse HEAD)" +BEFORE_TREE="$(git rev-parse HEAD^{tree})" echo "==> Rewriting" # --invert-paths: everything listed is REMOVED, everything else is kept. @@ -134,7 +135,15 @@ printf ' node_modules blobs remaining (expect 0): %s\n' \ "$(git rev-list --objects --all | grep -c 'node_modules/' || true)" printf ' commit count: %s\n' "$(git rev-list --count --all)" printf ' HEAD was %s, is now %s\n' "$BEFORE_HEAD" "$(git rev-parse HEAD)" -echo " HEAD tree identical to pre-rewrite? (expect 'same')" +AFTER_TREE="$(git rev-parse HEAD^{tree})" +if [ "$BEFORE_TREE" = "$AFTER_TREE" ]; then + printf ' HEAD tree identical to pre-rewrite: same (%s)\n' "$AFTER_TREE" +else + printf ' HEAD tree CHANGED: %s -> %s\n' "$BEFORE_TREE" "$AFTER_TREE" + echo " ^^ STOP, DO NOT PUSH. Every stripped path is already absent from" + echo " HEAD, so the checked-out tree MUST be byte-identical. A change" + echo " here means the strip set caught a LIVE file." +fi echo " run the test suite in $WORK before believing any of this." cat <<'NEXT'