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 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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It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. 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/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 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/scripts/strip-history.sh b/scripts/strip-history.sh new file mode 100755 index 0000000..8148403 --- /dev/null +++ b/scripts/strip-history.sh @@ -0,0 +1,174 @@ +#!/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="$(git rev-parse HEAD)" +BEFORE_TREE="$(git rev-parse HEAD^{tree})" + +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" "$(git rev-parse HEAD)" +AFTER_TREE="$(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' + +═══════════════════════════════════════════════════════════════════════════ +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 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") diff --git a/test/integration/test_server.jl b/test/integration/test_server.jl index ec15d30..6a39939 100644 --- a/test/integration/test_server.jl +++ b/test/integration/test_server.jl @@ -22,25 +22,114 @@ 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 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 - for _ in 1:60 + exited_early = false + 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. + 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 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) + 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 +167,15 @@ ## 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