diff --git a/.github/CODE_OF_CONDUCT.md b/.github/CODE_OF_CONDUCT.md new file mode 100644 index 00000000..b02898a4 --- /dev/null +++ b/.github/CODE_OF_CONDUCT.md @@ -0,0 +1,83 @@ +# Contributor Covenant Code of Conduct + +## Our Pledge + +We as members, contributors, and leaders pledge to make participation in our community a harassment-free experience for everyone, regardless of age, body size, visible or invisible disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, or sexual identity and orientation. + +We pledge to act and interact in ways that contribute to an open, welcoming, diverse, inclusive, and healthy community. + +## Our Standards + +Examples of behavior that contributes to a positive environment for our community include: + +* Demonstrating empathy and kindness toward other people +* Being respectful of differing opinions, viewpoints, and experiences +* Giving and gracefully accepting constructive feedback +* Accepting responsibility and apologizing to those affected by our mistakes, and learning from the experience +* Focusing on what is best not just for us as individuals, but for the overall community + +Examples of unacceptable behavior include: + +* The use of sexualized language or imagery, and sexual attention or advances of any kind +* Trolling, insulting or derogatory comments, and personal or political attacks +* Public or private harassment +* Publishing others' private information, such as a physical or email address, without their explicit permission +* Other conduct which could reasonably be considered inappropriate in a professional setting + +## Enforcement Responsibilities + +Community leaders are responsible for clarifying and enforcing our standards of acceptable behavior and will take appropriate and fair corrective action in response to any behavior that they deem inappropriate, threatening, offensive, or harmful. + +Community leaders have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, and will communicate reasons for moderation decisions when appropriate. + +## Scope + +This Code of Conduct applies within all community spaces, and also applies when an individual is officially representing the community in public spaces. Examples of representing our community include using an official e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be reported to the community leaders responsible for enforcement: the maintainer, [@JoshuaJewell](https://github.com/JoshuaJewell), using the contact details on their GitHub profile. All complaints will be reviewed and investigated promptly and fairly. + +All community leaders are obligated to respect the privacy and security of the reporter of any incident. + +## Enforcement Guidelines + +Community leaders will follow these Community Impact Guidelines in determining the consequences for any action they deem in violation of this Code of Conduct: + +### 1. Correction + +**Community Impact**: Use of inappropriate language or other behavior deemed unprofessional or unwelcome in the community. + +**Consequence**: A private, written warning from community leaders, providing clarity around the nature of the violation and an explanation of why the behavior was inappropriate. A public apology may be requested. + +### 2. Warning + +**Community Impact**: A violation through a single incident or series of actions. + +**Consequence**: A warning with consequences for continued behavior. No interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, for a specified period of time. This includes avoiding interactions in community spaces as well as external channels like social media. Violating these terms may lead to a temporary or permanent ban. + +### 3. Temporary Ban + +**Community Impact**: A serious violation of community standards, including sustained inappropriate behavior. + +**Consequence**: A temporary ban from any sort of interaction or public communication with the community for a specified period of time. No public or private interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, is allowed during this period. Violating these terms may lead to a permanent ban. + +### 4. Permanent Ban + +**Community Impact**: Demonstrating a pattern of violation of community standards, including sustained inappropriate behavior, harassment of an individual, or aggression toward or disparagement of classes of individuals. + +**Consequence**: A permanent ban from any sort of public interaction within the community. + +## Attribution + +This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 2.1, available at [https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1]. + +Community Impact Guidelines were inspired by [Mozilla's code of conduct enforcement ladder][Mozilla CoC]. + +For answers to common questions about this code of conduct, see the FAQ at [https://www.contributor-covenant.org/faq][FAQ]. Translations are available at [https://www.contributor-covenant.org/translations][translations]. + +[homepage]: https://www.contributor-covenant.org +[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html +[Mozilla CoC]: https://github.com/mozilla/diversity +[FAQ]: https://www.contributor-covenant.org/faq +[translations]: https://www.contributor-covenant.org/translations diff --git a/CONTRIBUTING.md b/.github/CONTRIBUTING.md similarity index 98% rename from CONTRIBUTING.md rename to .github/CONTRIBUTING.md index 504ad6b0..930ec561 100644 --- a/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -98,7 +98,7 @@ A pull request does not reopen these. An issue can discuss them. - `config/defaults/tool_versions.yml` pins Julia, R, bun and the external tools, and `install.jl` and CI both install from it. The Julia version is repeated in - the CI matrix. Change a pin by editing that file, and expect the change to be + the CI workflow. Change a pin by editing that file, and expect the change to be discussed. - R packages are pinned in `renv.lock`. - CI job names carry no version numbers, so that a pin change leaves required diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml new file mode 100644 index 00000000..3cf88518 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -0,0 +1,59 @@ +name: Bug report +description: Something in MetaManifold does not work as documented. +labels: [bug] +body: + - type: markdown + attributes: + value: | + Search the existing issues first. Raise issues about a fork's own code on that fork. + - type: textarea + id: steps + attributes: + label: Steps or command + description: The command you ran, or the steps in the web interface, so that someone else can repeat them. + validations: + required: true + - type: textarea + id: expected + attributes: + label: What you expected + validations: + required: true + - type: textarea + id: actual + attributes: + label: What happened + description: Include the error message, the server log lines, or a screenshot. + validations: + required: true + - type: input + id: julia + attributes: + label: Julia version + placeholder: output of `julia --version` + validations: + required: true + - type: input + id: r + attributes: + label: R version + placeholder: output of `R --version | head -1` + validations: + required: true + - type: input + id: browser + attributes: + label: Browser and version + validations: + required: true + - type: input + id: commit + attributes: + label: MetaManifold commit + placeholder: output of `git rev-parse --short HEAD` + - type: textarea + id: config + attributes: + label: Relevant configuration + description: The keys from `pipeline.yml` or the run's `run_config.yml` that bear on the problem. + render: yaml diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml new file mode 100644 index 00000000..312c2aec --- /dev/null +++ b/.github/ISSUE_TEMPLATE/feature_request.yml @@ -0,0 +1,41 @@ +name: Feature request +description: Suggest a new feature or a change to an existing one. +labels: [enhancement] +body: + - type: markdown + attributes: + value: | + Search the existing issues first. To change an architectural decision, describe the change + here before writing any code. The settled decisions in CONTRIBUTING.md can be discussed in an + issue, but a pull request does not reopen them. + - type: textarea + id: problem + attributes: + label: Problem + description: What you are trying to do, and what stops you now. + validations: + required: true + - type: textarea + id: proposal + attributes: + label: Proposed change + description: What MetaManifold should do instead. For a statistical method, name the method and a reference for it. + validations: + required: true + - type: textarea + id: alternatives + attributes: + label: Alternatives considered + - type: dropdown + id: area + attributes: + label: Area + options: + - Pipeline stages + - Analysis and statistics + - Web interface + - Configuration + - Installation and toolchain + - Other + validations: + required: true diff --git a/codecov.yml b/.github/codecov.yml similarity index 100% rename from codecov.yml rename to .github/codecov.yml diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 00000000..1454ca3b --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,39 @@ +# Dependabot version updates. Until this file landed, only security updates +# ran (those need no configuration), and those failed for a separate reason: +# the "Dependabot Updates" runs of 2026-09-26..27 tried to fix alerts against +# fixtures under test/doi using the npm_and_yarn updater, which refuses a +# Bun-managed project ("bun.lock but no package-lock.json"). Those fixtures +# have since left the repository and both alerts are fixed. +# +# What cannot be covered here: Julia (Project.toml / Manifest.toml) and R +# (renv.lock) are not Dependabot package-ecosystems. Their pins live in +# config/defaults/tool_versions.yml and are asserted by +# test/unit/test_install_pins.jl and the CI workflow instead. +# +# The workflows pin every action to a full commit SHA (this account's +# allowlist policy, asserted by test/unit/test_install_pins.jl). Dependabot +# advances those pins to the current SHA of the tracked version, so the +# pinning policy itself survives updates. +version: 2 +updates: + # The frontend is Bun-managed: package.json plus bun.lock, no npm/yarn/pnpm + # lockfile, so it must be declared as the "bun" ecosystem. + - package-ecosystem: "bun" + directory: "/frontend" + schedule: + interval: "weekly" + commit-message: + prefix: "chore(deps)" + groups: + frontend: + patterns: ["*"] + + - package-ecosystem: "github-actions" + directory: "/" + schedule: + interval: "weekly" + commit-message: + prefix: "chore(deps)" + groups: + actions: + patterns: ["*"] diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md new file mode 100644 index 00000000..a17d0de6 --- /dev/null +++ b/.github/pull_request_template.md @@ -0,0 +1,43 @@ +## Summary + + + +Closes # + +## Type of change + +- [ ] 🐛 Bug fix (non-breaking change that fixes an issue) +- [ ] ✨ New feature (non-breaking change that adds functionality) +- [ ] 💥 Breaking change (would change existing behaviour, a config key or an API response) +- [ ] 📊 Statistics fix (a method returned a wrong number, or a result it could not support) +- [ ] 📖 Documentation +- [ ] 🧹 Refactor / tech debt (behaviour-preserving) +- [ ] ⚡ Performance +- [ ] 🔧 Build / CI / tooling + +## How has this been verified? + + + +Tested with Julia `…`, R `…` and bun `…`. + +## What this leaves out + + + +## Checklist + +- [ ] My branch starts at the current tip of `main` (`behind_by` is `0`; see CONTRIBUTING.md) and has no merge commits from `main`. +- [ ] I ran `julia --project=. test/runtests.jl` (and `cd frontend && bun run test` for frontend changes) and they pass. +- [ ] CI ran on this PR and passes. +- [ ] No generated or vendored files, and no lockfile change the work does not need (or the reason is given above). +- [ ] New code is AGPL-3.0, or MPL-2.0 with an SPDX identifier in each file I wrote. I left existing file headers, `LICENSE`, `CITATION.cff` and the licence and acknowledgement sections of `README.md` unchanged. +- [ ] Every number shown to a user is computed from their data. When a method cannot run it raises an explicit error. +- [ ] Docs are updated, and no claim in them overstates what the code does. + +## Notes for reviewers + + diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 912daaba..20262517 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,10 +1,20 @@ name: CI +# This fork's account allows only GitHub's own actions (actions/*) and its own, +# each pinned to a full commit SHA. Upstream's julia-actions, oven-sh/setup-bun +# and codecov/codecov-action are none of these, and with them this workflow +# ended in startup_failure on every run. So Julia and Bun are installed here +# from the archives config/defaults/tool_versions.yml pins, each refused unless +# it hashes to the pinned SHA256, and the Julia depot is cached with +# actions/cache. Coverage is kept as a workflow artifact, since the Codecov +# project is upstream's. test/unit/test_install_pins.jl asserts that every +# `uses:` in .github/workflows is allowed by that policy. + on: push: branches: [main] + # Any base branch, so a PR stacked on another one is tested too. pull_request: - branches: [main] permissions: contents: read @@ -17,8 +27,33 @@ concurrency: jobs: test: - name: Julia ${{ matrix.julia-version }} / ${{ matrix.os }} - runs-on: ${{ matrix.os }} + # The name is a fixed string, it carries no version, and the job has NO matrix. + # Both are required, and the first without the second is a trap that has already + # been sprung here once. + # + # A branch ruleset matches a required status check by the DISPLAY NAME GitHub posts + # for the job. A renamed check does not fail -- it is simply absent, and an absent + # required check can never be satisfied, so every pull request deadlocks until an + # admin bypasses the rule, triggered by nothing more alarming than editing a version + # number. + # + # MEASURED on hyperpolymath/MetaManifold-WebUI#39 (2026-09-21): this job, named exactly `Julia tests` but still + # carrying a 1x1 `strategy.matrix`, posted `Julia tests (1.12.5, ubuntu-24.04)`. + # GitHub appends the matrix combination whenever the name does not already reference + # the matrix, so a 1x1 matrix is still a matrix and the pins were still embedded in + # the check name. The matrix was therefore removed rather than merely renamed around: + # it selected exactly one combination and bought nothing. + # + # The two values it held are literals below, each keeping its own reasoning. + # `test/unit/test_install_pins.jl` asserts, for EVERY job in this file, that the name + # interpolates nothing AND that the job has no matrix -- so this cannot regress + # silently. If a matrix is ever genuinely wanted here, the required context must move + # to a matrix-free aggregator job first. + name: Julia tests + # Explicit, not ubuntu-latest: the R pin below names an apt package revision built + # for 24.04, and a runner that silently rolled to the next LTS would take that pin + # with it. `runs-on` cannot read `env`, so this is a literal. + runs-on: ubuntu-24.04 # The repository's root .Rprofile sources renv/activate.R, so R started from # the checkout auto-activates renv and rewrites the library paths. renv is a # local-development convenience; CI installs into the system library and @@ -28,30 +63,45 @@ jobs: # the environment, so those commands pass --no-init-file instead. env: RENV_CONFIG_AUTOLOADER_ENABLED: "FALSE" - strategy: - fail-fast: false - matrix: - # Pinned rather than tracking latest stable, because a pinned Manifest.toml - # resolved by an unpinned Julia is not a reproducible build. This must equal - # julia_version in Manifest.toml; it cannot be read from the pin file, since - # nothing can be read before Julia exists. test/unit/test_install_pins.jl - # fails if the three ever disagree. - julia-version: ["1.12.5"] - # Explicit, not ubuntu-latest: the R pin below names an apt package revision - # built for 24.04, and a runner that silently rolled to the next LTS would - # take that pin with it. - os: [ubuntu-24.04] + # Pinned rather than tracking latest stable, because a pinned Manifest.toml + # resolved by an unpinned Julia is not a reproducible build. These must equal + # runtimes.julia.archives.linux-x86_64 in the pin file, whose version must + # equal julia_version in Manifest.toml; they cannot be read from the pin + # file, since nothing can be read before Julia exists. + # test/unit/test_install_pins.jl fails if any of them disagree. + JULIA_URL: https://julialang-s3.julialang.org/bin/linux/x64/1.12/julia-1.12.5-linux-x86_64.tar.gz + JULIA_SHA256: 41b84d727e4e96fbf3ed9e92fa195d773d247b9097f73fad688f8b699758bae7 steps: - - uses: actions/checkout@11d5960a326750d5838078e36cf38b85af677262 # v4.4.0 - - - name: Set up Julia - uses: julia-actions/setup-julia@4c0cb0fce8556fdb04a90347310e5db8b1f98fb9 # v2.7.0 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 with: - version: ${{ matrix.julia-version }} + persist-credentials: false # nothing here pushes - - name: Cache Julia packages - uses: julia-actions/cache@d10a6fd8f31b12404a54613ebad242900567f2b9 # v2.1.0 + - name: Install Julia + run: | + source scripts/ci/fetch_pinned.sh + fetch_pinned "$JULIA_URL" julia.tar.gz + echo "$JULIA_SHA256 julia.tar.gz" | sha256sum -c - + sudo mkdir -p /opt/julia + sudo tar xzf julia.tar.gz -C /opt/julia --strip-components=1 + rm julia.tar.gz + echo /opt/julia/bin >> "$GITHUB_PATH" + + # The registry, packages, artifacts and precompiled caches, keyed on the + # Manifest (which also names the Julia version). Saved once instantiation + # has succeeded, so a failed run cannot store a half-built depot. + - name: Restore the Julia depot + id: julia-depot + uses: actions/cache/restore@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0 + with: + path: | + ~/.julia/registries + ~/.julia/packages + ~/.julia/artifacts + ~/.julia/compiled + key: julia-depot-${{ runner.os }}-${{ hashFiles('Manifest.toml') }} + restore-keys: | + julia-depot-${{ runner.os }}- # Every external version CI installs is read from the committed pin file, so CI # and a developer's machine cannot drift apart. A temporary environment is used @@ -67,7 +117,10 @@ jobs: pins = YAML.load_file("config/defaults/tool_versions.yml") open(ENV["GITHUB_ENV"], "a") do io println(io, "R_APT_VERSION=", pins["runtimes"]["r"]["apt_version"]) - println(io, "BUN_VERSION=", pins["toolchain"]["bun"]["version"]) + bun = pins["toolchain"]["bun"] + println(io, "BUN_VERSION=", bun["version"]) + println(io, "BUN_URL=", bun["archives"]["linux-x86_64"]["url"]) + println(io, "BUN_SHA256=", bun["archives"]["linux-x86_64"]["sha256"]) println(io, "CUTADAPT_SPEC=cutadapt==", pins["tools"]["cutadapt"]["version"]) println(io, "MULTIQC_SPEC=multiqc==", pins["tools"]["multiqc"]["version"]) fastqc = pins["tools"]["fastqc"]["archives"]["any"] @@ -122,7 +175,7 @@ jobs: # the restore runs as root. The run id makes each key unique so every attempt # saves its progress; restore-keys picks the newest match. - name: Restore the renv cache - uses: actions/cache/restore@0057852bfaa89a56745cba8c7296529d2fc39830 # v4.3.0 + uses: actions/cache/restore@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0 with: path: /opt/renv-cache key: renv-${{ runner.os }}-R${{ env.R_APT_VERSION }}-${{ hashFiles('renv.lock') }}-${{ github.run_id }} @@ -139,7 +192,7 @@ jobs: sudo chmod 777 "$RENV_PATHS_CACHE" sudo env R_CLI_DYNAMIC=false TERM=dumb Rscript --no-init-file -e 'install.packages(c("renv", "BiocManager"), repos="https://cloud.r-project.org", lib=.Library)' sudo env RENV_PATHS_CACHE="$RENV_PATHS_CACHE" R_CLI_DYNAMIC=false TERM=dumb Rscript --no-init-file -e 'renv::restore(project=".", library=.Library, prompt=FALSE)' - Rscript --no-init-file -e 'for (pkg in c("dada2","Biostrings","ShortRead","vegan","dplyr","MASS")) if (!require(pkg,character.only=TRUE,quietly=TRUE)) stop(pkg, " failed to install")' + Rscript --no-init-file -e 'for (pkg in c("dada2","Biostrings","ShortRead","vegan","dplyr","MASS","zCompositions")) if (!require(pkg,character.only=TRUE,quietly=TRUE)) stop(pkg, " failed to install")' # Saved on failure too, since the packages built before a failure are the ones # the next attempt should reuse. Root writes the cache, so it is made readable first. @@ -149,7 +202,7 @@ jobs: - name: Save the renv cache if: always() - uses: actions/cache/save@0057852bfaa89a56745cba8c7296529d2fc39830 # v4.3.0 + uses: actions/cache/save@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0 with: path: /opt/renv-cache key: renv-${{ runner.os }}-R${{ env.R_APT_VERSION }}-${{ hashFiles('renv.lock') }}-${{ github.run_id }} @@ -204,10 +257,28 @@ jobs: - name: Instantiate Julia project run: julia --project=. -e 'import Pkg; Pkg.instantiate()' - - name: Set up Bun - uses: oven-sh/setup-bun@0c5077e51419868618aeaa5fe8019c62421857d6 # v2.2.0 + - name: Save the Julia depot + if: steps.julia-depot.outputs.cache-hit != 'true' + uses: actions/cache/save@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0 with: - bun-version: ${{ env.BUN_VERSION }} + path: | + ~/.julia/registries + ~/.julia/packages + ~/.julia/artifacts + ~/.julia/compiled + key: julia-depot-${{ runner.os }}-${{ hashFiles('Manifest.toml') }} + + # Downloaded against the pinned URL and refused unless it hashes to the pinned + # SHA256, as install.jl does when no bun of this version is on PATH. + - name: Install Bun + run: | + source scripts/ci/fetch_pinned.sh + fetch_pinned "$BUN_URL" bun.zip + echo "$BUN_SHA256 bun.zip" | sha256sum -c - + unzip -q bun.zip + sudo mv bun-linux-x64/bun /usr/local/bin/bun + rm -rf bun.zip bun-linux-x64 + test "$(bun --version)" = "$BUN_VERSION" - name: Build frontend working-directory: frontend @@ -230,7 +301,7 @@ jobs: julia --project=. -e ' using RCall R"cat(.libPaths(), sep=\"\n\")" - for pkg in ["dada2", "dplyr", "vegan", "tibble", "MASS"] + for pkg in ["dada2", "dplyr", "vegan", "tibble", "MASS", "zCompositions"] R"if (!require($pkg, character.only=TRUE, quietly=TRUE)) stop($pkg, \" not found\")" end ' @@ -272,13 +343,66 @@ jobs: fi exit "$status" + # What julia-processcoverage did: the .cov files under src/ to lcov.info, with + # CoverageTools pinned to an exact release. - name: Process coverage - uses: julia-actions/julia-processcoverage@03114f09f119417c3242a9fb6e0b722676aedf38 # v1.2.2 + run: | + julia -e ' + using Pkg + Pkg.activate(temp = true) + Pkg.add(name = "CoverageTools", version = "1.4.2") + using CoverageTools + LCOV.writefile("lcov.info", process_folder("src"))' - - name: Upload coverage to Codecov - uses: codecov/codecov-action@fb8b3582c8e4def4969c97caa2f19720cb33a72f # v6.0.2 + # The Codecov project (codecov.yml, the README badge) is upstream's, so the fork + # keeps its coverage as an artifact of the run instead. + - name: Keep coverage + uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2 + with: + name: lcov + path: lcov.info + retention-days: 14 + + # Machine-checked proofs of the Benjamini-Hochberg adjustment and the TSS/RLE + # scaling algebra (proofs/agda, proofs/agda/README.md). + # Agda publishes no 2.6.4.3 binary, and agda-stdlib 2.1 requires Agda 2.6.4.x, + # so the pair comes from Debian trixie, which packages exactly that pair with + # pre-built library interfaces. The image is pinned by digest and the two + # packages by revision, so a rebuild in the archive fails loudly here instead + # of silently changing the checker. These pins live here rather than in + # config/defaults/tool_versions.yml because no other job and no installer + # reads them. + agda: + name: Agda proofs + runs-on: ubuntu-24.04 + container: debian:trixie-20250929-slim@sha256:1caf1c703c8f7e15dcf2e7769b35000c764e6f50e4d7401c355fb0248f3ddfdb + timeout-minutes: 30 + env: + DEBIAN_FRONTEND: noninteractive + steps: + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 with: - files: lcov.info - token: ${{ secrets.CODECOV_TOKEN }} - slug: JoshuaJewell/MetaManifold-WebUI - fail_ci_if_error: false + persist-credentials: false # nothing here pushes + + - name: Install Agda and the standard library + run: | + apt-get update -qq + apt-get install -y --no-install-recommends agda-bin=2.6.4.3-1+b2 agda-stdlib=2.1-4 + agda --version | grep -qx 'Agda version 2.6.4.3' + grep -qx 'name: standard-library-2.1' /usr/share/agda-stdlib/standard-library.agda-lib + + # Runs before the type-check: --safe already refuses postulates, but the + # audit also refuses holes, check-disabling pragmas and flags, and any + # module that MetaManifold/All.agda does not import (an unimported module + # is never type-checked at all). + - name: Axiom audit + run: bash proofs/tests/axiom-audit.sh + + - name: Type-check + env: + AGDA_DIR: /tmp/agda-dir + run: | + mkdir -p "$AGDA_DIR" + echo /usr/share/agda-stdlib/standard-library.agda-lib > "$AGDA_DIR/libraries" + cd proofs/agda + agda MetaManifold/All.agda diff --git a/.github/workflows/occupancy.yml b/.github/workflows/occupancy.yml new file mode 100644 index 00000000..0513de5c --- /dev/null +++ b/.github/workflows/occupancy.yml @@ -0,0 +1,238 @@ +# SPDX-License-Identifier: AGPL-3.0-only +# SPDX-FileCopyrightText: 2026 Jonathan D.A. Jewell (hyperpolymath) +# +# The occupancy reading of the vsearch stage (docs/occupancy-2026-10.adoc): +# * the two-thread disagreement test (test/occupancy_disagreement_test.jl) on +# the pinned vsearch, and +# * Session IR's counted bytes against the typed peak computed in Agda from +# the pinned proof siblings (scripts/check-occupancy.sh). +# +# This account allows only GitHub's own actions and its own, pinned by SHA, so +# everything here installs from pinned URLs checked against pinned SHA256s, as +# ci.yml now does too. The disagreement test also runs in ci.yml's full suite; +# it runs here as well so that a change to the probe gets its own check. +# +# #116 merged with this workflow's "Occupancy typed peak" check red (its squash +# carried a draft `TH.[_]` placeholder; #117 fixed the proof), because nothing +# required the check to pass first -- and nothing COULD have: a check posts +# only when its workflow runs, and the pull_request trigger was path-filtered, +# so requiring these checks would have deadlocked every PR that touches no +# occupancy file. A required check that never posts can never be satisfied; the +# trap ci.yml's header records for its own job names. +# +# So the pull_request path filter moved into the `Occupancy relevance` gate +# below. The workflow now runs on EVERY pull request; the gate decides whether +# the change touches the occupancy reading; the two heavy jobs run only when it +# does, and post their checks as `skipped` otherwise, which a required check +# counts as satisfied. The gate itself posts on every PR too, and it is the one +# check of the three that must be required without exception: if the gate +# failed, its dependents would be skipped and would satisfy their requirement +# silently. The push trigger keeps its native paths filter, so a push to main +# still starts this workflow only when it should. +name: Occupancy reading + +on: + push: + branches: [main] + paths: + - src/core/memory_probe.jl + - src/core/provenance.jl + - src/pipeline/tools.jl + - src/server/routes/pipeline.jl + - test/occupancy_disagreement_test.jl + - test/unit/test_occupancy_grade.jl + - scripts/check-occupancy-grades.jl + - scripts/lint-occupancy-readings.sh + - docs/occupancy/** + - docs/occupancy-2026-10.adoc + - scripts/check-occupancy.sh + - scripts/fetch-siblings.sh + - .github/workflows/occupancy.yml + # No paths filter, on purpose (see above): the gate must post its check on + # every PR, whichever files the PR touches. Any base branch, so a PR stacked + # on another one is gated too. + pull_request: + +permissions: + contents: read + +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: ${{ github.event_name != 'push' }} + +env: + # Julia 1.12.5, the version Manifest.toml was resolved with. The checksum is + # julialang's own (bin/checksums/julia-1.12.5.sha256), as the official Docker + # image (docker-library/julia a39df01) records it. + JULIA_URL: https://julialang-s3.julialang.org/bin/linux/x64/1.12/julia-1.12.5-linux-x86_64.tar.gz + JULIA_SHA256: 41b84d727e4e96fbf3ed9e92fa195d773d247b9097f73fad688f8b699758bae7 + +jobs: + # Decides whether the PR touches the occupancy reading at all. The file list + # is the pull_request half of the old paths filter, moved here because a + # pinned-actions workflow cannot use a third-party paths-filter action (the + # account's allow-list refuses one) -- plain `case` globs are all it takes. + # In a case pattern `*` crosses `/`, so `docs/occupancy/*` is the old + # `docs/occupancy/**`. + gate: + name: Occupancy relevance + runs-on: ubuntu-24.04 + timeout-minutes: 10 + outputs: + relevant: ${{ steps.push.outputs.relevant || steps.pr.outputs.relevant }} + steps: + # A push only starts this workflow when a `paths:` file changed (the + # trigger filter above), so the gate has nothing to decide on pushes. + - name: A push is already path-filtered + id: push + if: github.event_name == 'push' + run: echo 'relevant=true' >> "$GITHUB_OUTPUT" + + # Full history, because the three-dot diff names the merge base of the + # PR's base tip and its merge commit -- a shallow checkout does not have + # both, and a stacked PR's merge base sits further back still. + - name: Checkout the change + if: github.event_name == 'pull_request' + uses: actions/checkout@11d5960a326750d5838078e36cf38b85af677262 # v4.4.0 + with: + persist-credentials: false # nothing here pushes + fetch-depth: 0 + + - name: Does the change touch the occupancy reading? + id: pr + if: github.event_name == 'pull_request' + env: + # zizmor flags template expressions interpolated into run scripts + # (template-injection), and the gate script is easier to run locally + # with the value in an environment variable in any case. The base SHA + # is GitHub-supplied, but the indirection costs nothing. + BASE_SHA: ${{ github.event.pull_request.base.sha }} + run: | + relevant=false + patterns=(src/core/memory_probe.jl src/core/provenance.jl src/pipeline/tools.jl + src/server/routes/pipeline.jl test/occupancy_disagreement_test.jl + test/unit/test_occupancy_grade.jl scripts/check-occupancy-grades.jl + scripts/lint-occupancy-readings.sh 'docs/occupancy/*' + docs/occupancy-2026-10.adoc scripts/check-occupancy.sh + scripts/fetch-siblings.sh .github/workflows/occupancy.yml) + # The diff goes to a file first because a process substitution hides + # git diff's exit status: an unavailable comparison SHA or a repository + # error would read as "no changes", and the gate would post + # relevant=false -- skipping the two occupancy jobs, whose `skipped` + # conclusion satisfies a required check -- so a relevant PR would + # pass silently. A failed diff must fail the gate itself: that is + # the one failure the required-check design cannot afford to skip. + changed="$RUNNER_TEMP/occupancy-changed-files" + if ! git diff --no-renames --name-only -z "$BASE_SHA...HEAD" > "$changed"; then + echo "ERROR: git diff $BASE_SHA...HEAD failed" >&2 + exit 1 + fi + while IFS= read -r -d '' file; do + for pattern in "${patterns[@]}"; do + case "$file" in + $pattern) relevant=true; break 2 ;; + esac + done + done < "$changed" + echo "relevant=$relevant" >> "$GITHUB_OUTPUT" + + disagreement: + needs: gate + if: needs.gate.outputs.relevant == 'true' + name: Occupancy disagreement test + runs-on: ubuntu-24.04 + timeout-minutes: 45 + env: + # As in ci.yml: the root .Rprofile would otherwise bootstrap renv. + RENV_CONFIG_AUTOLOADER_ENABLED: "FALSE" + steps: + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 + with: + persist-credentials: false + + - name: Install Julia + run: | + source scripts/ci/fetch_pinned.sh + fetch_pinned "$JULIA_URL" julia.tar.gz + echo "$JULIA_SHA256 julia.tar.gz" | sha256sum -c - + sudo mkdir -p /opt/julia + sudo tar xzf julia.tar.gz -C /opt/julia --strip-components=1 + rm julia.tar.gz + echo /opt/julia/bin >> "$GITHUB_PATH" + + # RCall builds against R. The occupancy test uses no R package. + - name: Install R + run: | + sudo apt-get update -qq + sudo apt-get install -y --no-install-recommends r-base-core + + - name: Instantiate the project + run: julia --project=. -e 'using Pkg; Pkg.instantiate()' + + # The pinned vsearch (config/defaults/tool_versions.yml), refused unless it + # hashes to the pinned SHA256, as ci.yml installs it. + - name: Install vsearch + run: | + eval "$(julia --project=. -e ' + using YAML + v = YAML.load_file("config/defaults/tool_versions.yml")["tools"]["vsearch"] + a = v["archives"]["linux-x86_64"] + println("VSEARCH_VERSION=", v["version"]); println("VSEARCH_URL=", a["url"]); println("VSEARCH_SHA256=", a["sha256"])')" + source scripts/ci/fetch_pinned.sh + fetch_pinned "$VSEARCH_URL" vsearch.tar.gz + echo "$VSEARCH_SHA256 vsearch.tar.gz" | sha256sum -c - + tar xzf vsearch.tar.gz --warning=no-unknown-keyword + sudo mv "vsearch-$VSEARCH_VERSION-linux-x86_64/bin/vsearch" /usr/local/bin/vsearch + rm -rf vsearch.tar.gz "vsearch-$VSEARCH_VERSION-linux-x86_64" + vsearch --version + + - name: Three orders of the vsearch stage + run: julia --project=. -t 2 test/occupancy_disagreement_test.jl + + # Fork issue #105: the grades the recorded run's windows imply, read back + # against its own measurement (docs/occupancy/schedules.yml). + - name: Graded reading of the recorded run + run: julia --project=. scripts/check-occupancy-grades.jl + + # And no production code reads a peak without those grades. + - name: Occupancy readings are graded + run: bash scripts/lint-occupancy-readings.sh + + typed-peak: + needs: gate + if: needs.gate.outputs.relevant == 'true' + name: Occupancy typed peak + runs-on: ubuntu-24.04 + # The Agda 2.6.4.3 Debian trixie packages, in a digest-pinned image, as the + # upstream proof job uses. The siblings need no standard library. + container: debian:trixie-20250929-slim@sha256:1caf1c703c8f7e15dcf2e7769b35000c764e6f50e4d7401c355fb0248f3ddfdb + timeout-minutes: 20 + env: + DEBIAN_FRONTEND: noninteractive + steps: + # git before checkout, so the checkout is a repository and the siblings can be fetched. + - name: Install git, curl and Agda + run: | + apt-get update -qq + apt-get install -y --no-install-recommends ca-certificates curl git agda-bin=2.6.4.3-1+b2 + agda --version | grep -qx 'Agda version 2.6.4.3' + + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 + with: + persist-credentials: false # the siblings are public; nothing here pushes + + # The Session IR stepper is Julia (standard library only). + - name: Install Julia + shell: bash + run: | + source scripts/ci/fetch_pinned.sh + fetch_pinned "$JULIA_URL" julia.tar.gz + echo "$JULIA_SHA256 julia.tar.gz" | sha256sum -c - + mkdir -p /opt/julia + tar xzf julia.tar.gz -C /opt/julia --strip-components=1 + rm julia.tar.gz + echo /opt/julia/bin >> "$GITHUB_PATH" + + - name: Counted bytes against typed peak + shell: bash + run: bash scripts/check-occupancy.sh diff --git a/.gitignore b/.gitignore index a6ed2b7d..42d6c9c7 100644 --- a/.gitignore +++ b/.gitignore @@ -250,6 +250,9 @@ vignettes/*.pdf ## Documentation kept local except published release notes docs/* !docs/release-notes/ +# and the dated occupancy reading (MMW-01), whose table the gate checks +!docs/occupancy-2026-10.adoc +!docs/occupancy/ # translation temp files @@ -332,3 +335,9 @@ LocalPreferences.toml # Development server log (dev/dev.sh) dev/server.log + +# Agda interface files (proofs/agda) +proofs/agda/_build/ +# Proof siblings fetched by scripts/fetch-siblings.sh, and Agda interface files +/_build/ +*.agdai diff --git a/README.md b/README.md index bb9883cc..dafa4711 100644 --- a/README.md +++ b/README.md @@ -74,9 +74,16 @@ Once a run completes, analysis is performed on request through the web UI, both - Pipeline stage read-count summaries - NMDS ordination (Bray-Curtis, via R/vegan) - PERMANOVA, with PERMDISP to check for differences in dispersion (via R/vegan) +- Differential abundance between two conditions: a negative-binomial model per taxon (via R/MASS) with Benjamini-Hochberg adjusted p-values (see [Differential abundance](#differential-abundance)) Counts may be normalised before analysis (none, rarefaction to a fixed or auto-resolved depth, or scaling with ranked subsampling (SRS), which reaches the depth by scaling counts and keeps more of the community structure), and contamination-flagged taxa may be included or excluded. Ordinations can also apply a Hellinger transform before the Bray-Curtis dissimilarity. Composition charts can be drawn as a grid faceted on any two of run, group and sub-group. All analysis charts are returned as Plotly JSON and rendered interactively in the browser. +## Documentation + +Longer documentation for users, maintainers, developers and theorists is kept as a wiki in +[metadatastician/MetaManifold-Evidence, under `docs/wikis/`](https://github.com/metadatastician/MetaManifold-Evidence/tree/main/docs/wikis). +Start at its [Home page](https://github.com/metadatastician/MetaManifold-Evidence/blob/main/docs/wikis/Home.md). + ## Prerequisites - **Julia** 1.12 (installed by `install.sh` if missing, and pinned to the Manifest version for this directory) @@ -94,7 +101,7 @@ bash install.sh ``` `install.sh` installs Julia (via juliaup) if missing, checks for R, then hands -off to `install.jl`, which installs the Julia dependencies, locates or downloads +off to `scripts/install.jl`, which installs the Julia dependencies, locates or downloads each external tool (cutadapt, FastQC, MultiQC, vsearch, cd-hit-est, and the phylogeny tools MAFFT, trimAl, IQ-TREE, RAxML and gappa), and reproduces the R environment from `renv.lock`. It ends with a summary listing every dependency as @@ -159,6 +166,7 @@ The web UI lets you create studies, configure pipeline parameters, launch runs, | `JULIA_METAMANIFOLD_PORT` | `8080` | Server port | | `JULIA_METAMANIFOLD_ROOT` | working directory | Project root | | `JULIA_THREADS` | `8` | Julia threads | +| `JULIA_METAMANIFOLD_ALLOWED_ORIGINS` | none | Extra browser origins allowed to call the API, comma-separated (the server's own origin and the Vite dev server at `localhost:5173` are always allowed) | Or run the Julia server directly: @@ -239,6 +247,67 @@ The composition view classifies each ASV/OTU into a biological category and rend Organism-category composition of two runs as stacked bars

+### Differential abundance + +The Differential Abundance tab of a study's analysis workspace tests each taxon +for a difference in abundance between two conditions. Select exactly two runs or +pooled-run sub-groups, a results table and a rank. The first condition is the +reference, so a positive fold change means the taxon is more abundant in the +second. The rank list shows only the ranks the selected runs share. With +aggregation on, a pooled run counts as one condition rather than one per +sub-group. + +Counts are summed per taxon at the chosen rank, with rows that have no name at +that rank pooled as `Unclassified`. This happens after the read-count bounds and +any `analysis.exclude_categories` entry that applies to `differential`. Each +taxon is fitted with its own negative-binomial GLM, `MASS::glm.nb(y ~ group + +offset(log(size factor)))`, on the raw integer read counts. There are no +pseudocounts. The group coefficient gets a Wald test, and Benjamini-Hochberg +adjustment runs over the taxa that produced a p-value. Size factors come from +the whole count matrix and are centred to a geometric mean of 1. The code is in +`src/analysis/differential.jl`, and the route in `src/server/routes/analysis.jl`. + +Settings live under `analysis.differential` (see +[Configuring analysis](#configuring-analysis-analysis-in-pipelineyml)): + +- `offset`: `tss` (default) uses each sample's total reads. `rle` uses the + median of ratios over the taxa with reads in every sample. +- `min_prevalence`: a fraction from 0 to 1 (default 0). A taxon with reads in a + smaller fraction of the samples is not fitted. + +The result is a volcano plot and a table. The plot draws log2 fold change +against -log10 of the raw p-value, coloured by whether the adjusted p-value is +below 0.05. Taxa without an adjusted p-value are left off the plot but stay in +the table. Each table row has a status: + +- `ok`: the model fitted. +- `boundary`: the model fitted, but the dispersion parameter theta reached a + bound (at least 1e7, so effectively Poisson, or at most 1e-8). These taxa + keep their p-value and stay in the adjusted family. +- `failed`: no p-value, with the reason. Causes are counts that are constant + across samples, an error from `glm.nb`, a fit that did not converge, an + aliased group coefficient, or a non-finite estimate. +- `filtered`: below `min_prevalence`, so not fitted. + +A failed or filtered taxon never gets a stand-in p-value, and it is not counted +in the adjustment. The table downloads as `differential_abundance.csv` and can +be added to the report. The CSV starts with `#` lines that record the +comparison, method and settings. + +The test refuses, with an explicit error, when: + +- the selection is not exactly two conditions, or both are the same; +- the two conditions resolve to different ranks; +- a condition has no results table, no taxonomy columns or no sample columns, + or the read-count bounds remove all its samples; +- `offset` or `min_prevalence` is invalid; +- a count is not a non-negative integer, a condition has no samples, or there + are fewer than 3 samples in total; +- `tss` meets a sample with no reads, or `rle` finds no taxon with reads in + every sample (use `tss`); +- the R package MASS cannot be loaded; +- no taxon could be fitted at all. + ### Figures and report The Figures tab lays analysis charts out on a page (A4, letter or a journal @@ -553,13 +622,13 @@ Each entry names a filter in the `filters:` library of `config/composition.yml`. ### Configuring analysis (`analysis:` in `pipeline.yml`) -Controls the defaults applied to the analysis charts (alpha diversity, taxa bar, NMDS, etc.). Per-chart choices such as the taxonomic rank and relative or absolute abundance are made in the UI. +Controls the defaults applied to the analysis charts (alpha diversity, taxa bar, NMDS, differential abundance, etc.). Per-chart choices such as the taxonomic rank and relative or absolute abundance are made in the UI. ```yaml analysis: exclude_categories: # composition categories to drop from figures; [] to keep all - - {set: contamination, category: Contaminant, apply_to: [diversity, taxa, venn]} - # apply_to surfaces: diversity | taxa | composition | venn + - {set: contamination, category: Contaminant, apply_to: [diversity, taxa, venn, differential]} + # apply_to surfaces: diversity | taxa | composition | venn | differential # (omit apply_to to act on every surface) alpha: # richness, Shannon and Simpson normalisation: none # none | rarefy | srs (scaling with ranked subsampling) @@ -576,6 +645,9 @@ analysis: depth: 0 # rarefy/srs reads per sample; 0 = smallest non-empty sample nmds: max_stress: 0.2 # warn if NMDS stress exceeds this value + differential: # negative-binomial differential abundance (MASS::glm.nb) + offset: tss # tss | rle (rle is refused when no taxon has reads in every sample) + min_prevalence: 0.0 # fraction of samples, 0 to 1, a taxon needs reads in to be tested ``` ### Configuring taxonomic filtering (`filters:` in `config/composition.yml`) @@ -644,6 +716,30 @@ bash start.sh Open `http://localhost:8080`. The backend serves the frontend. +### Split deployment (frontend and API on different origins) + +To serve the frontend from a different address than the API, set `apiBase` in +`frontend/public/config.json` to the API's address, and list the frontend's +address when starting the server: + +```bash +JULIA_METAMANIFOLD_ALLOWED_ORIGINS=https://frontend.example bash start.sh +``` + +The server accepts browser requests from its own origin (`http://localhost:` +and `http://127.0.0.1:`), from the Vite dev server (`localhost:5173`), and +from the origins listed in `JULIA_METAMANIFOLD_ALLOWED_ORIGINS`, separated by +commas. An origin has to match exactly, scheme and port included: +`https://frontend.example` does not cover `http://frontend.example` or +`https://frontend.example:8443`. A page on any other origin gets +`403 Forbidden: origin not allowed` on every request that carries an `Origin` +header, which is every write and every cross-origin read. + +This also applies to an SSH tunnel on a different local port (e.g. +`http://localhost:9000`): the browser's origin is then `http://localhost:9000`, +not the server's `http://localhost:8080`, so start the server with +`JULIA_METAMANIFOLD_ALLOWED_ORIGINS=http://localhost:9000`. + ## Input data Place paired-end FASTQ files under `data/{project_name}/` following Illumina naming: @@ -737,7 +833,7 @@ The server exposes a REST API under `/api/v1/`. Key endpoint groups: | Results | `GET/POST/DELETE .../results/tables/...` | List, query, filter, save, export (`.xlsx`), and delete tables; OTU member drill-down | | QC | `GET .../results/qc`, `GET .../results/dada2` | MultiQC report metadata and DADA2 figures, logs, stats | | Analysis | `POST .../runs/{run}/analysis/{alpha,chart}`, `GET .../runs/{run}/analysis/{pipeline-stats,ranks}` | Per-run charts and rank discovery | -| Cross-run | `POST /studies/{study}/analysis/{alpha,chart,chart-facet,nmds,permanova,venn,publication-tables}` | Comparison, faceted charts, NMDS, PERMANOVA, taxon overlap and publication tables across runs | +| Cross-run | `POST /studies/{study}/analysis/{alpha,chart,chart-facet,nmds,permanova,venn,publication-tables,differential}` | Comparison, faceted charts, NMDS, PERMANOVA, taxon overlap, publication tables and differential abundance across runs | | Composition | `POST .../runs/{run}/composition/summary`, `POST .../composition/{source}/query`, `POST .../composition/{source}/distinct/{column}` | Organism-composition summaries and tables for a run | | Composition library | `GET /composition`, `POST/DELETE /composition/{filters,sets}/{name}`, `GET /category-sets`, `POST/DELETE /category-sets/{name}` | Edit the filters and category sets in `config/composition.yml` | | Reference trees | `GET/POST /reference-trees`, `GET/PUT/DELETE /reference-trees/{id}`, `GET/PUT .../fasta`, `POST .../run`, `GET .../log/{step}`, `GET .../qc/{align,trim}`, `GET .../alignment/{raw,trimmed}`, `GET .../treefile`, `POST .../trim-preview` | Build and inspect the shared reference trees | diff --git a/config/defaults/pipeline.yml b/config/defaults/pipeline.yml index 11198e7a..8181ae6d 100644 --- a/config/defaults/pipeline.yml +++ b/config/defaults/pipeline.yml @@ -347,10 +347,39 @@ analysis: # comparing two conditions on the raw read counts, with Benjamini-Hochberg # adjusted p-values. differential: + # The model fitted to each taxon. nb_glm: a negative-binomial GLM on the read + # counts with a library-size offset; the effect is a log2 fold change. clr_welch: + # Welch's t-test on centred log-ratios over the taxa passing min_prevalence, + # after zCompositions::cmultRepl replaces their zeros; the effect is a + # difference in CLR units, not a fold change. + method: nb_glm # How library size enters each model, as a log offset: tss (total reads per # sample) or rle (median-of-ratios over the taxa present in every sample). # rle is refused when no taxon is present in every sample. + # Used by nb_glm only; clr_welch ignores it, since log-ratios carry no library size. offset: tss # Fraction of samples, 0 to 1, in which a taxon must have reads to be - # tested. Taxa below it are listed as filtered, without a p-value. + # tested. Taxa below it are listed as filtered, without a p-value. For + # clr_welch it is applied before zero replacement, so on a sparse table it also + # keeps imputed values for rare taxa out of every sample; clr_welch refuses a + # taxon seen in fewer than 2 samples. min_prevalence: 0.0 + # clr_welch only: cmultRepl's frac, between 0 and 1. An imputed proportion above + # its taxon's smallest observed proportion is lowered to this fraction of it. + # A replaced zero is not a measurement. + replacement_delta: 0.65 + +## Occupancy probe (MMW-01) +# Measures each attested stage's memory: Julia's allocation total, and the +# sampled resident memory of the tools it runs as child processes (Linux /proc). +# Recorded under the stage's `occupancy` key in attestation.yml. See the +# header of src/core/memory_probe.jl. +# +# Off unless set, and deliberately left commented out here: the run config is +# embedded in attestation.yml, so a default key would change every run's record +# even with the probe off. Set it by editing a pipeline.yml (the config editor +# only offers keys that have a factory default). +# occupancy_probe: +# enabled: true +# # Sampling interval in milliseconds (at least 1). +# interval_ms: 10 diff --git a/docs/occupancy-2026-10.adoc b/docs/occupancy-2026-10.adoc new file mode 100644 index 00000000..6d291b05 --- /dev/null +++ b/docs/occupancy-2026-10.adoc @@ -0,0 +1,167 @@ +// SPDX-License-Identifier: AGPL-3.0-only +// SPDX-FileCopyrightText: 2026 Jonathan D.A. Jewell (hyperpolymath) += Occupancy of the vsearch stage +:revdate: 2026-10-14 + +The vsearch stage runs two independent searches, ASV and OTU. The full +pipeline spawns them together; a single-stage re-run runs them one after the +other. The high-water-mark (HWM) algebra of occupancy-types predicts that the +stage's cost is the same in every order but its memory peak is not: serially +the peak is the larger search's, concurrently it can be their sum +(choreographic-types A-2 and A-3). This page records one measurement of that, +on 2026-10-14, and checks it against the typed reading. + +== What was measured + +`MemoryProbe` (`src/core/memory_probe.jl`), off unless a pipeline.yml sets +`occupancy_probe.enabled: true`, records for each attested stage: + +* `julia_allocated_bytes`: the `Base.gc_num()` delta over the stage (cost); +* per task (one spawned search): the largest sampled VmRSS of the child + process it started (`peak_rss_kib`), the kernel's own VmHWM for it + (`hwm_kib`), and the sample window its children were live in — `first_sample`, + the first sample taken after its first child started, and `last_sample`, the + last taken before its last was waited for, 0 for never — which its grade is + read from; +* `child_peak_rss_kib`: the largest sum of the stage's children's VmRSS at + one sampling instant (the stage's occupancy). + +The run: `test/occupancy_disagreement_test.jl`, which runs the same two searches +in three orders under the probe, on a fixture it generates: 1000 reference +sequences of 400 bp, 300 ASV and 150 OTU queries. Linux 6.18 with 4 CPUs, +Julia 1.12.5 with 2 threads, vsearch 2.30.5 with `--threads 1`. Sampling +interval 10 ms. + +== Results + +[cols="2,1,1,1,1,1,1",options="header"] +|=== +| Order | ASV peak (KiB) | OTU peak (KiB) | Stage peak, measured (KiB) | Counted bytes, Session IR | Typed peak, HWM | Julia allocation (bytes) +| ASV then OTU | 9204 | 9180 | 9204 | 9204 | 9204 | 978432 +| OTU then ASV | 9152 | 9192 | 9192 | 9192 | 9192 | 978720 +| Concurrent | 9176 | 9204 | 18380 | 18380 | 18380 | 978816 +|=== + +* *Cost commutes.* The allocation totals agree to 0.04%. The test asserts + agreement within 1%; a planted extra search in one order breaks it (spread + 25%). +* *Each search's peak is the same in every order*, to within 0.6% + (9152-9204 KiB). Each search's VmHWM equals its sampled peak, so the + sampling caught the peaks. +* *The stage peak is not the same.* Serially it is the larger search's + (9192-9204 KiB); concurrently it is 18380 KiB, twice that. This is the A-3 + order dependence, and nothing in the stage's outputs shows it: the hits are + byte-identical in all three orders. The prediction would have been falsified + had the concurrent peak matched the serial one; it did not. +* *Counted bytes equal the typed peak*, in all three orders. The counted bytes + come from occupancy-types' Session IR stepper running + `docs/occupancy/vsearch-*.sir`, one buffer per search. The typed peak is + computed, by `refl`, from occupancy-types' `Timeline` over resource-algebra's + HWM grade (`docs/occupancy/TypedPeak.agda`). A search alone exits holding + nothing (drift 0); in the concurrent order the first is still resident + when the second starts (drift = peak). The sequence law + `max (peak a) (drift a + peak b)` then gives the larger peak serially and the + sum concurrently. +* *The measured stage peak also equals the typed peak* here. For the concurrent + order the typed peak is the interleaving in which both are resident at once; + a measurement could come in lower if the two searches' peaks did not + coincide. Here they did: each search's memory plateaus once its database is + loaded. + +== Reading the numbers + +A recorded `peak_rss_kib` is a reading, not an occupancy: what a stage occupied +depends on what the next stage inherits from it. So the probe grades a stage's +whole window (`MemoryProbe`'s `task_grades`, `stage_grade`, +`predicted_peak_rss_kib`, `cost_bound_rss_kib`, `reclaimed_kib`) and attaches the +result to a recorded stage as `grades`; a record with no sample windows is left +ungraded rather than graded on an assumed order. Tasks are read in sampled order +(first sample, ties by record order). Each handover keeps only the tasks still +live at it, so a task's `drift_kib` is the change in the live peak sum across its +boundary — negative when the boundary also releases an earlier task — and +`release_kib` is everything freed between its start and the next boundary, which +can exceed that task's own peak. The folded drift is the sum of the peaks still +live when the stage ends; the pinned instance's own `drift` is that non-negative +live sum, the signed per-task delta being the extension its header records as +H-2. + +For the three orders above, the algebra's predicted peak reproduces the measured +stage peak exactly — 9204, 9192 and 18380 KiB — and the slack against the cost +bound is what the cuts reclaimed: 9180, 9152 and 0 KiB. +`scripts/check-occupancy-grades.jl` checks that equality, occupancy≤cost and +non-negative reclamation against this page's raw record, rebuilding each order's +windows from `docs/occupancy/schedules.yml` (the file records no windows of its +own; the Session IR texts in this directory state the same interleavings). The +reclamation readings are theorems over the pinned siblings at these numbers: +`docs/occupancy/GradedStages.agda` — `no-reclaim` for the concurrent stage, +`reclaimed` for the serial one, where 9204 KiB are released at the frontier and +the cost reading counts them — and the two protocol-level statements +(`occupancy-at-cut`, `protocol-occupancy≤cost`) as the siblings' own two-step +over the stage's timeline. `docs/occupancy/reject` gains a fourth rejection, for +reading the concurrent stage's drift as 0. + +`scripts/lint-occupancy-readings.sh` keeps production code from reading the key +directly: outside `src/core/memory_probe.jl`, an occupancy figure must go through +those helpers. + +== Status + +[cols="1,3,1,2",options="header"] +|=== +| ID | Claim | Status | Artefact +| MMW-01.1 | With the flag off, a stage record has exactly its earlier keys; with it on, it gains `occupancy`; old records still parse and merge | TESTED | `test/occupancy_disagreement_test.jl` ("flag off", "round trip", "through the pipeline's _attest") +| MMW-01.2 | For this workload, the vsearch stage's cost (Julia allocation) is the same in all three orders | TESTED | same file, "two-thread disagreement" (asserted, within 1%) +| MMW-01.3 | For this workload, the stage peak depends on the order (A-3), and each search's own peak does not | TESTED | same file, recorded in the test log; table above +| MMW-01.4 | For the three Session IR texts, the stepper's counted bytes equal the HWM typed peak | TESTED | `scripts/check-occupancy.sh` (stepper output against `TypedPeak.agda`; three rejections in `docs/occupancy/reject`) +| MMW-01.5 | The recorded run's grades reproduce its measured stage peaks, and the reclamation the pinned siblings' laws read off them is what the cuts freed | TESTED | `scripts/check-occupancy-grades.jl` (the recorded record), `docs/occupancy/GradedStages.agda` (`no-reclaim`, `reclaimed`, `occupancy-at-cut` at the measured numbers), `test/unit/test_occupancy_grade.jl` +| bridge | Counted bytes are bounded by the typed peak in general (occupancy-types' v0 → typed bridge) | OPEN | unchanged; this page gives three instances, not a proof +|=== + +== Limits + +* *Sampled.* A per-task peak is the largest VmRSS seen at 10 ms intervals. VmHWM + is exact up to the last sample, but growth after it is not seen. A child that + lives for less than one interval may not be sampled at all (`samples: 0`). +* *Child memory only.* The children are counted; the Julia process is not. Its + `julia_live_bytes_delta` is recorded, but without a forced collection it + reflects when the GC last ran, not what the stage kept. +* *Allocation is process-wide.* While the study loop runs several runs' + pipelines at once, a stage's `julia_allocated_bytes` includes the others' + allocations too. The child figures are per stage, since each stage samples + only the children it started. +* *Linux only*, since it reads /proc. For a stage offloaded with `remote:`, + the local child is an ssh client, so its memory says nothing about the work. +* *One thread for vsearch.* With several threads, vsearch writes its hits in + whatever order the threads finish. `_sort_hits_by_query!` then does a + different amount of work, because its sort key splits each line on every + comparison. That moved the stage's allocation total by up to 12% between + repeats of the same order. So in production the cost is order-independent + only up to that noise; precomputing the sort key would remove it. This PR + does not change it. +* *One host, one day.* CI runs the same test on every push and logs its own + numbers; they are not compared with these. + +== Reproducing + +---- +julia --project=. -t 2 test/occupancy_disagreement_test.jl # set OCCUPANCY_RESULTS= for YAML +bash scripts/check-occupancy.sh # needs julia and agda 2.6.4.x +julia --project=. scripts/check-occupancy-grades.jl # the recorded run's grades +bash scripts/lint-occupancy-readings.sh # no ungraded readings in src/ +---- + +`scripts/fetch-siblings.sh` fetches the siblings at their pins into +`_build/dependencies`: occupancy-types `af95728` and resource-algebra +`cf9235c`. + +== As the proofs progress + +* *Per-buffer (n-ary) occupancy* in occupancy-types: each search is already one + buffer in the Session IR texts, so the typed peak could then be read per + search. +* *Signed drift*: frees could be graded as negative drift, so the Julia side's + collections (the pipeline's `GC.gc(false)` hints) become modelled + reclamation rather than unmodelled noise. +* *choreographic-types' operational `step` as a function*: the three orders + become three traces of one typed protocol. The frontier certificate its + two-thread application note describes could then be displayed in the WebUI. diff --git a/docs/occupancy/GradedStages.agda b/docs/occupancy/GradedStages.agda new file mode 100644 index 00000000..3c45730d --- /dev/null +++ b/docs/occupancy/GradedStages.agda @@ -0,0 +1,96 @@ +{-# OPTIONS --safe --without-K #-} +-- SPDX-License-Identifier: AGPL-3.0-only +-- SPDX-FileCopyrightText: 2026 Jonathan D.A. Jewell (hyperpolymath) +-- +-- The vsearch stage's grades, and occupancy-types' reclamation theorems at the +-- measured numbers. Fork issue #105 asks for exactly this: grade the stages +-- (alloc/hold/release) and compare the predicted peak with the measured one. +-- TypedPeak.agda computes the typed peak by the algebra's sequence law; this +-- module adds the grades the measurement itself gives, and the laws that say +-- what the difference between a peak and a cost reading is: occupancy≤cost, and +-- the strict reclamation at a cut where something is released. +-- +-- Consumed, never re-declared, from the siblings scripts/fetch-siblings.sh pins +-- and scripts/check-occupancy.sh checks: +-- occupancy-types af957280075699c659de0abd9a3b0defade77309 +-- resource-algebra cf9235c532712a783a404c359a1055f40134794a +-- Everything is stated in this file's own Timeline instance (`TH`, as +-- TypedPeak.agda does): the Grade-level laws are Reclaim's as they stand, and +-- the two protocol-level ones are Reclaim's own two-step — its `cut-factor` over +-- its `reclaim-law`/`occupancy≤cost` — applied to `xs` and `ys` of that instance. +-- +-- A grade is `hwm peak drift _`: what an interaction reached, and what it still +-- holds when the next one begins. The peaks below are the 2026-10-14 run's +-- (docs/occupancy-2026-10.adoc, docs/occupancy/results-2026-10-14.yml), in KiB. +module GradedStages where + +open import ResourceAlgebra.Prelude +open import ResourceAlgebra.Instances.HWM +open import OccupancyTypes.Order +open import OccupancyTypes.Reclaim + +import OccupancyTypes.Timeline +module TH = OccupancyTypes.Timeline HWM + +-- A search that has not been waited for when the next one starts: it still holds +-- everything it reached, so the cut reclaims none of it. +still : Nat → Grade +still p = hwm p p (≤-refl p) + +-- A search that has exited before the next one starts: it holds nothing, so the +-- cut reclaims all of it. +gone : Nat → Grade +gone p = hwm p 0 z≤n + +-- The full pipeline runs the two searches together: ASV is still resident when +-- OTU starts, so the stage peak is their sum and nothing is reclaimed — +-- Reclaim.no-reclaim's equality, whose `refl` argument discharges the theorem's +-- own hypothesis (drift = peak) at the measured grade. +run-together : peak (still 9176 ⊗h gone 9204) ≡ 18380 +run-together = no-reclaim (still 9176) refl (gone 9204) + +-- A single-stage re-run runs them one after the other: ASV has exited, so the +-- cut reclaims its 9204 KiB and the stage peak is the larger search's +-- (Reclaim.reclaim-law, by `refl`). +run-in-turn : peak (gone 9204 ⊗h gone 9180) ≡ 9204 +run-in-turn = refl + +-- The same claim as Reclaim.reclaimed states it: with drift < peak at the cut +-- and a suffix that does anything, occupancy is strictly below cost. 9204 KiB +-- are released at the frontier, so the cost reading (18384 KiB) overstates the +-- stage. +run-in-turn +-- +-- The vsearch stage's typed peak, computed (TESTED, by refl) with +-- occupancy-types' Timeline over resource-algebra's HWM grade, both consumed +-- by pin through scripts/fetch-siblings.sh: +-- occupancy-types af957280075699c659de0abd9a3b0defade77309 +-- resource-algebra cf9235c532712a783a404c359a1055f40134794a +-- Nothing here re-declares their definitions. +-- +-- Each search is one interaction graded by its measured peak, in KiB, from the +-- 2026-10-14 run in docs/occupancy-2026-10.adoc. A search's process exits +-- holding nothing, so run alone its drift is 0. Run concurrently, the first is +-- still resident when the second starts, so that is graded with drift = peak. +-- That is the interleaving the measurement observed (both resident at once). +-- The algebra's sequence law, max (peak a) (drift a + peak b), then gives: +-- serial = the larger peak; concurrent = the sum. +module TypedPeak where + +open import ResourceAlgebra.Prelude +open import ResourceAlgebra.Instances.HWM + +import OccupancyTypes.Timeline +module TH = OccupancyTypes.Timeline HWM + +-- A search whose process has exited before the next one starts. +exits : Nat → Grade +exits p = hwm p 0 z≤n + +-- A search still resident when the next one starts. +resident : Nat → Grade +resident p = hwm p p (≤-refl p) + +-- ASV 9204 then OTU 9180. +asv-then-otu : peak (TH.grade (exits 9204 TH.∷ exits 9180 TH.∷ TH.[])) ≡ 9204 +asv-then-otu = refl + +-- OTU 9192 then ASV 9152. +otu-then-asv : peak (TH.grade (exits 9192 TH.∷ exits 9152 TH.∷ TH.[])) ≡ 9192 +otu-then-asv = refl + +-- ASV 9176 and OTU 9204 together. +concurrent : peak (TH.grade (resident 9176 TH.∷ exits 9204 TH.∷ TH.[])) ≡ 18380 +concurrent = refl diff --git a/docs/occupancy/reject/ConcurrentDriftIsZero.agda b/docs/occupancy/reject/ConcurrentDriftIsZero.agda new file mode 100644 index 00000000..749c213f --- /dev/null +++ b/docs/occupancy/reject/ConcurrentDriftIsZero.agda @@ -0,0 +1,18 @@ +{-# OPTIONS --safe --without-K #-} +-- SPDX-License-Identifier: AGPL-3.0-only +-- SPDX-FileCopyrightText: 2026 Jonathan D.A. Jewell (hyperpolymath) +-- +-- Must be REFUSED: reading the concurrent stage as one that hands on nothing. +-- Running the two searches together leaves the ASV search resident when the OTU +-- search starts, so the stage's drift is that search's peak — 9176 KiB, what a +-- suffix would see — and not 0. Grading the drift as 0 would read the stage's +-- COST as its occupancy, which is the very reading the measured overlap exists +-- to refute. +module ConcurrentDriftIsZero where + +open import ResourceAlgebra.Prelude +open import ResourceAlgebra.Instances.HWM +open import GradedStages + +wrong : drift (still 9176 ⊗h gone 9204) ≡ 0 +wrong = refl diff --git a/docs/occupancy/reject/ConcurrentIsSerial.agda b/docs/occupancy/reject/ConcurrentIsSerial.agda new file mode 100644 index 00000000..592de6ee --- /dev/null +++ b/docs/occupancy/reject/ConcurrentIsSerial.agda @@ -0,0 +1,14 @@ +{-# OPTIONS --safe --without-K #-} +-- SPDX-License-Identifier: AGPL-3.0-only +-- SPDX-FileCopyrightText: 2026 Jonathan D.A. Jewell (hyperpolymath) +-- +-- Must be REFUSED: the claim that running the two searches concurrently leaves +-- the peak where a serial run puts it (the larger of the two). +module ConcurrentIsSerial where + +open import ResourceAlgebra.Prelude +open import ResourceAlgebra.Instances.HWM +open import TypedPeak + +wrong : peak (TH.grade (resident 9176 TH.∷ exits 9204 TH.∷ TH.[])) ≡ 9204 +wrong = refl diff --git a/docs/occupancy/reject/SerialIsCost.agda b/docs/occupancy/reject/SerialIsCost.agda new file mode 100644 index 00000000..dbb6f4ba --- /dev/null +++ b/docs/occupancy/reject/SerialIsCost.agda @@ -0,0 +1,14 @@ +{-# OPTIONS --safe --without-K #-} +-- SPDX-License-Identifier: AGPL-3.0-only +-- SPDX-FileCopyrightText: 2026 Jonathan D.A. Jewell (hyperpolymath) +-- +-- Must be REFUSED: reading a serial run's peak as the sum of the two peaks, +-- i.e. occupancy as cost (occupancy-types R-6). +module SerialIsCost where + +open import ResourceAlgebra.Prelude +open import ResourceAlgebra.Instances.HWM +open import TypedPeak + +wrong : peak (TH.grade (exits 9204 TH.∷ exits 9180 TH.∷ TH.[])) ≡ 18384 +wrong = refl diff --git a/docs/occupancy/results-2026-10-14.yml b/docs/occupancy/results-2026-10-14.yml new file mode 100644 index 00000000..394236d6 --- /dev/null +++ b/docs/occupancy/results-2026-10-14.yml @@ -0,0 +1,63 @@ +# SPDX-License-Identifier: AGPL-3.0-only +# The raw MemoryProbe records behind docs/occupancy-2026-10.adoc, written by +# test/occupancy_disagreement_test.jl with OCCUPANCY_RESULTS set (2026-10-14). +vsearch: "vsearch v2.30.5_linux_x86_64, 15.7GB RAM, 4 cores" +julia: "1.12.5" +threads: 2 +cpus: 4 +cost_spread: 0.00039231071008238524 +orders: + asv_then_otu: + probe: "MemoryProbe 1" + interval_ms: 10 + samples: 56 + julia_allocated_bytes: 978432 + julia_live_bytes_delta: 978544 + child_peak_rss_kib: 9204 + tasks: + - label: "vsearch:asv" + processes: 1 + samples: 33 + peak_rss_kib: 9204 + hwm_kib: 9204 + - label: "vsearch:otu" + processes: 1 + samples: 20 + peak_rss_kib: 9180 + hwm_kib: 9180 + otu_then_asv: + probe: "MemoryProbe 1" + interval_ms: 10 + samples: 57 + julia_allocated_bytes: 978720 + julia_live_bytes_delta: 978832 + child_peak_rss_kib: 9192 + tasks: + - label: "vsearch:otu" + processes: 1 + samples: 22 + peak_rss_kib: 9192 + hwm_kib: 9192 + - label: "vsearch:asv" + processes: 1 + samples: 33 + peak_rss_kib: 9152 + hwm_kib: 9152 + concurrent: + probe: "MemoryProbe 1" + interval_ms: 10 + samples: 33 + julia_allocated_bytes: 978816 + julia_live_bytes_delta: 978928 + child_peak_rss_kib: 18380 + tasks: + - label: "vsearch:asv" + processes: 1 + samples: 30 + peak_rss_kib: 9176 + hwm_kib: 9176 + - label: "vsearch:otu" + processes: 1 + samples: 24 + peak_rss_kib: 9204 + hwm_kib: 9204 diff --git a/docs/occupancy/schedules.yml b/docs/occupancy/schedules.yml new file mode 100644 index 00000000..dfdedb81 --- /dev/null +++ b/docs/occupancy/schedules.yml @@ -0,0 +1,21 @@ +# SPDX-License-Identifier: AGPL-3.0-only +# SPDX-FileCopyrightText: 2026 Jonathan D.A. Jewell (hyperpolymath) +# +# The interleaving each order in results-2026-10-14.yml ran with, as the sample +# window [first, last] of each of its tasks, in the task order the record keeps. +# These are the same schedules the Session IR texts in this directory state +# (vsearch-concurrent.sir runs the two searches together; the other two run them +# one after the other), expressed in the probe's own sample indices: the windows +# of a serial order do not overlap, and the concurrent order's do. +# +# Read by test/unit/test_occupancy_grade.jl and scripts/check-occupancy-grades.jl, +# so the two cannot disagree about what the recorded run did. +asv_then_otu: + - [1, 2] + - [3, 4] +otu_then_asv: + - [1, 2] + - [3, 4] +concurrent: + - [1, 4] + - [2, 5] diff --git a/docs/occupancy/vsearch-asv-then-otu.sir b/docs/occupancy/vsearch-asv-then-otu.sir new file mode 100644 index 00000000..e462fb5e --- /dev/null +++ b/docs/occupancy/vsearch-asv-then-otu.sir @@ -0,0 +1,13 @@ +(* SPDX-License-Identifier: AGPL-3.0-only *) +(* vsearch-asv-then-otu.sir - the vsearch stage with the two searches run one + after the other, ASV first: the single-stage re-run's order. Each search is + one buffer, sized by its measured peak in KiB (docs/occupancy-2026-10.adoc, + 2026-10-14 run); each process exits holding nothing, so its buffer is dropped + before the next search starts. + + Expected: steps = 0 (no communication), peak_live = max 9204 9180 = 9204. *) +let asv = alloc 9204 in +let _ = drop asv in +let otu = alloc 9180 in +let _ = drop otu in +unit diff --git a/docs/occupancy/vsearch-concurrent.sir b/docs/occupancy/vsearch-concurrent.sir new file mode 100644 index 00000000..93be40bf --- /dev/null +++ b/docs/occupancy/vsearch-concurrent.sir @@ -0,0 +1,12 @@ +(* SPDX-License-Identifier: AGPL-3.0-only *) +(* vsearch-concurrent.sir - the two searches spawned together, as the full + pipeline runs them. Session IR has no parallel composition, so this is the + interleaving the measurement observed: both buffers live at once, then both + dropped. + + Expected: steps = 0, peak_live = 9176 + 9204 = 18380. *) +let asv = alloc 9176 in +let otu = alloc 9204 in +let _ = drop asv in +let _ = drop otu in +unit diff --git a/docs/occupancy/vsearch-otu-then-asv.sir b/docs/occupancy/vsearch-otu-then-asv.sir new file mode 100644 index 00000000..ba575591 --- /dev/null +++ b/docs/occupancy/vsearch-otu-then-asv.sir @@ -0,0 +1,9 @@ +(* SPDX-License-Identifier: AGPL-3.0-only *) +(* vsearch-otu-then-asv.sir - the same two searches, OTU first. + + Expected: steps = 0, peak_live = max 9192 9152 = 9192. *) +let otu = alloc 9192 in +let _ = drop otu in +let asv = alloc 9152 in +let _ = drop asv in +unit diff --git a/frontend/bun.lock b/frontend/bun.lock index 742f42a5..11ec980d 100644 --- a/frontend/bun.lock +++ b/frontend/bun.lock @@ -7,226 +7,128 @@ "dependencies": { "@upsetjs/react": "^1.11.0", "jspdf": "^4.2.1", - 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"plotly.js-dist-min": "^2.35.2", - "react": "^18.3.1", - "react-dom": "^18.3.1", - "react-router-dom": "^6.28.0", + "plotly.js-dist-min": "^4.1.2", + "react": "^19.3.0", + "react-dom": "^19.3.0", + "react-router-dom": "^7.18.4", "svg2pdf.js": "^2.8.1" }, "devDependencies": { - "@types/plotly.js": "^2.33.4", - "@types/react": "^18.3.18", - "@types/react-dom": "^18.3.5", - "@vitejs/plugin-react": "^4.3.4", - "typescript": "^5.7.2", - "vite": "^6.1.0" + "@types/plotly.js": "^3.0.15", + "@types/react": "^19.3.0", + "@types/react-dom": "^19.3.0", + "@vitejs/plugin-react": "^6.1.2", + "typescript": "^7.0.2", + "vite": "^8.3.4" }, "overrides": { "@types/react": "$@types/react", diff --git a/frontend/src/api/types.ts b/frontend/src/api/types.ts index 10410bd9..87457dad 100644 --- a/frontend/src/api/types.ts +++ b/frontend/src/api/types.ts @@ -243,15 +243,32 @@ export interface ComparisonRequest extends AnalysisRequest { aggregate?: boolean } +export interface PermanovaTerm { + term: string + r2: number + f_statistic: number | null + /** Null when the term could not be tested; `untestable_reason` says why. */ + p_value: number | null + /** Set when within-block permutation cannot change this term. */ + untestable_reason?: string | null +} + export interface PermanovaResult { text: string + /** The first term (group, when it varies); r2, f_statistic and p_value are its own. */ + term?: string r2: number | null f_statistic: number | null p_value: number | null + untestable_reason?: string | null + /** Permutations actually performed: fewer than 999 when the blocks admit fewer. */ + permutations?: number + /** Smallest p-value attainable with that many permutations. */ + min_p_value?: number /** True when permutations were restricted within individuals. */ blocked?: boolean /** One row per model term, tested sequentially in formula order. */ - terms?: { term: string; r2: number; f_statistic: number | null; p_value: number | null }[] + terms?: PermanovaTerm[] /** PERMDISP on the same distances: do the groups differ in spread? */ dispersion?: PermdispResult | { error: string } } @@ -381,18 +398,32 @@ export interface DifferentialRow { taxon: string status: DifferentialStatus note: string - /** Natural-log fold change, contrast over reference. */ + /** + * nb_glm: natural-log fold change, contrast over reference. clr_welch: mean + * CLR of contrast minus mean CLR of reference, which is not a fold change. + */ estimate: number | null + /** nb_glm only; null for clr_welch. */ log2_fold_change: number | null standard_error: number | null + /** z (nb_glm) or Welch's t (clr_welch). */ statistic: number | null pvalue: number | null /** Benjamini-Hochberg adjusted; null outside the tested family. */ padj: number | null + /** nb_glm only. */ dispersion_theta: number | null prevalence: number } +export type DifferentialMethod = 'nb_glm' | 'clr_welch' + +/** Which row field holds the effect size, and what to call it. */ +export interface DifferentialEffect { + key: 'log2_fold_change' | 'estimate' + label: string +} + export interface DifferentialResult { status: 'ok' | 'partial' method: string @@ -400,9 +431,26 @@ export interface DifferentialResult { table: string groups: { reference: string; contrast: string } n_samples: Record + effect: DifferentialEffect + /** Empty for clr_welch, which takes no library-size offset. */ size_factors: { sample: string; group: string; factor: number }[] - config: { offset: 'tss' | 'rle'; min_prevalence: number } - diagnostics: { n_taxa: number; n_tested: number; n_failed: number; n_boundary: number; n_filtered: number } + config: { + method: DifferentialMethod + min_prevalence: number + /** nb_glm only. */ + offset?: 'tss' | 'rle' + /** clr_welch only. */ + replacement_delta?: number + } + diagnostics: { + n_taxa: number; n_tested: number; n_failed: number; n_boundary: number; n_filtered: number + /** clr_welch only. */ + zero_replacement?: { + method: string; delta: number; zeros_replaced: number; n_taxa_in_composition: number + n_taxa_unobserved: number; median_imputed_fraction: number; max_imputed_fraction: number + warnings: string[] + } + } rows: DifferentialRow[] figure: unknown } diff --git a/frontend/src/components/AnalysisChart.tsx b/frontend/src/components/AnalysisChart.tsx index 3e40f157..17e8a437 100644 --- a/frontend/src/components/AnalysisChart.tsx +++ b/frontend/src/components/AnalysisChart.tsx @@ -1,13 +1,14 @@ // © 2026 Joshua Benjamin Jewell. All rights reserved. // Licensed under the GNU Affero General Public License version 3 (AGPLv3). import Plotly from 'plotly.js-dist-min' +import { stripHtmlTags } from '../utils/text' import { AddToReport } from './AddToReport' import { PlotlyChart } from './PlotlyChart' const figureTitle = (fig: unknown): string | null => { const t = (fig as { layout?: { title?: unknown } })?.layout?.title const text = typeof t === 'string' ? t : (t as { text?: string } | undefined)?.text - return text ? text.replace(/<[^>]+>/g, '') : null + return text ? stripHtmlTags(text) : null } // The chart as standalone SVG, at a fixed print width. diff --git a/frontend/src/components/AnalysisWorkspace.tsx b/frontend/src/components/AnalysisWorkspace.tsx index c8c6b5af..e7295004 100644 --- a/frontend/src/components/AnalysisWorkspace.tsx +++ b/frontend/src/components/AnalysisWorkspace.tsx @@ -3,7 +3,7 @@ import { useEffect, useMemo, useState, type ReactNode } from 'react' import type { AnnotationSource, ComparisonRunSpec } from '../api/types' import { AnalysisSourceContext } from './analysisSource' -import { useSharedResultsTables } from './annotationShared' +import { useSharedResultsTablesState } from './annotationShared' import { DiversityPanel } from './DiversityPanel' import { TaxaCompositionChart } from './TaxaCompositionChart' import { VennPanel } from './VennPanel' @@ -80,7 +80,7 @@ export function AnalysisWorkspace({ study, runs: baseRuns, source, perRun }: { }, [aggregate, selectedRuns]) //## Dataset: results tables shared by every selected run - const options = useSharedResultsTables(study, selectedRuns) + const { options, error: optionsError } = useSharedResultsTablesState(study, selectedRuns) const [analysisKey, setAnalysisKey] = useState(null) useEffect(() => { setAnalysisKey(current => current && options.some(o => o.key === current) ? current : options[0]?.key ?? null) @@ -138,6 +138,8 @@ export function AnalysisWorkspace({ study, runs: baseRuns, source, perRun }: { onChange={e => setAnalysisKey(e.target.value)}> {options.map(o => )} + ) : optionsError ? ( + could not list the results tables: {optionsError} ) : ( no results table shared by the selected runs )} diff --git a/frontend/src/components/CompositionPanel.tsx b/frontend/src/components/CompositionPanel.tsx index 77ad8869..5e677683 100644 --- a/frontend/src/components/CompositionPanel.tsx +++ b/frontend/src/components/CompositionPanel.tsx @@ -16,6 +16,12 @@ import type { // Fixed colour of the catch-all "Unassigned" bucket, mirroring the backend. const UNASSIGNED_COLOUR = '#95a5a6' +/** + * Browse a run's composition by taxonomy rank or category, with sub-group and + * results-table selectors and controls to save category colours. The analysis + * context's annotation source takes precedence over `source`; absent both, + * VSEARCH is used. A failed table lookup clears the options and shows a toast. + */ export function CompositionPanel({ study, run, group, subgroups, source: configuredSource, }: { @@ -53,6 +59,10 @@ export function CompositionPanel({ setTableOptions(opts) setTable(current => opts.some(o => o.key === current) ? current : opts.some(o => o.key === 'merged') ? 'merged' : opts[0]?.key ?? current) + }).catch(err => { + if (cancelled) return + setTableOptions([]) + toast.error(`Could not list the results tables: ${errorMessage(err)}`) }) return () => { cancelled = true } }, [study, run, group]) diff --git a/frontend/src/components/DifferentialPanel.tsx b/frontend/src/components/DifferentialPanel.tsx index ff15b507..825fb812 100644 --- a/frontend/src/components/DifferentialPanel.tsx +++ b/frontend/src/components/DifferentialPanel.tsx @@ -1,16 +1,16 @@ // SPDX-License-Identifier: AGPL-3.0-only // SPDX-FileCopyrightText: 2026 Jonathan D.A. Jewell (hyperpolymath) -import { useEffect, useState } from 'react' +import { useEffect, useRef, useState } from 'react' import { api } from '../api/client' import { errorMessage } from '../api/errorMessage' import { useToast } from './Toast' import type { ComparisonRunSpec, DifferentialResult } from '../api/types' -import { uniqueRuns } from '../api/types' +import { sharedRanks } from './sharedRanks' import type { AnalysisOption } from './annotationShared' import { AnalysisChart } from './AnalysisChart' import { AddToReport } from './AddToReport' import { saveBlob } from '../utils/download' -import { differentialCsv, formatStat } from './differentialTable' +import { differentialCsv, effectValue, formatStat } from './differentialTable' const cell = { padding: '3px 10px', textAlign: 'right' } as const const head = { padding: '4px 10px', textAlign: 'right' } as const @@ -21,10 +21,10 @@ function csvBlob(result: DifferentialResult): Blob { } /** - * Differential abundance between exactly two runs or sub-groups: a - * negative-binomial model per taxon at the chosen rank, with BH-adjusted - * p-values, shown as a volcano plot and a table that can be downloaded or - * added to the report. The first selected condition is the reference. + * Differential abundance between exactly two runs or sub-groups: a model per + * taxon at the chosen rank (negative-binomial GLM or CLR linear model, as + * configured), with BH-adjusted p-values, shown as a volcano plot and a table + * that can be downloaded or added to the report. The first selected condition is the reference. */ export function DifferentialPanel({ study, runs, option, aggregate }: { study: string @@ -36,42 +36,58 @@ export function DifferentialPanel({ study, runs, option, aggregate }: { const [ranks, setRanks] = useState([]) const [rank, setRank] = useState('') const [ranksReady, setRanksReady] = useState(false) + const [ranksError, setRanksError] = useState(null) const [result, setResult] = useState(null) const [loading, setLoading] = useState(false) + // Only the response to the latest request, for the current inputs, is shown. + const request = useRef(0) // The ranks shared by every selected run. useEffect(() => { + setRanksError(null) if (!option || runs.length === 0) { setRanks([]); setRank(''); setRanksReady(false); return } let cancelled = false setRanksReady(false) - Promise.all( - uniqueRuns(runs).map(r => - api.analysis.ranks(study, r.run, { - table: option.table, - group: r.group, - ...(r.source ? { source: r.source } : {}), - }).catch(() => [] as string[]) - ) - ).then(results => { + sharedRanks(runs, r => api.analysis.ranks(study, r.run, { + table: option.table, + group: r.group, + ...(r.source ? { source: r.source } : {}), + })).then(shared => { if (cancelled) return - const shared = results.reduce((acc, cur) => acc.filter(r => cur.includes(r)), results[0] ?? []) setRanks(shared) setRanksReady(true) setRank(current => shared.includes(current) ? current : (shared[shared.length - 1] ?? '')) + }).catch(err => { + if (cancelled) return + setRanks([]) + setRank('') + setRanksError(errorMessage(err)) }) return () => { cancelled = true } }, [study, runs, option]) + // A result answers the inputs it was computed from; new inputs discard it, + // along with any request still in flight for the old ones. + useEffect(() => { + request.current++ + setResult(null) + setLoading(false) + }, [study, runs, option?.table, rank, aggregate]) + + /** Fit the model for the current inputs and show it, unless the inputs changed meanwhile. */ const run = async () => { if (!option || !rank) return + const req = ++request.current setLoading(true) try { - setResult(await api.analysis.differential(study, { runs, table: option.table, rank, aggregate })) + const res = await api.analysis.differential(study, { runs, table: option.table, rank, aggregate }) + if (req === request.current) setResult(res) } catch (err) { + if (req !== request.current) return setResult(null) toast.error(`Differential abundance failed: ${errorMessage(err)}`) } finally { - setLoading(false) + if (req === request.current) setLoading(false) } } @@ -94,9 +110,12 @@ export function DifferentialPanel({ study, runs, option, aggregate }: { {ranksReady && ranks.length === 0 && ( No taxonomy rank shared by the selected runs. )} + {ranksError && ( + Could not read the taxonomy ranks: {ranksError} + )} {runs.length === 2 && ( - Reference: {runs[0].prefix ?? runs[0].run}; positive fold changes mean more abundant in {runs[1].prefix ?? runs[1].run}. + Reference: {runs[0].prefix ?? runs[0].run}; a positive effect means more abundant in {runs[1].prefix ?? runs[1].run}. )} @@ -109,6 +128,12 @@ export function DifferentialPanel({ study, runs, option, aggregate }: { {result.diagnostics.n_boundary > 0 && `, ${result.diagnostics.n_boundary} at a dispersion boundary`} {result.diagnostics.n_filtered > 0 && `, ${result.diagnostics.n_filtered} below the prevalence threshold`} . Samples: {Object.entries(result.n_samples).map(([g, n]) => `${g} ${n}`).join(', ')}. + {result.diagnostics.zero_replacement && (() => { + const z = result.diagnostics.zero_replacement + return ` ${z.zeros_replaced} zeros replaced by ${z.method} over ${z.n_taxa_in_composition} taxa; ` + + `replaced values hold ${(100 * z.median_imputed_fraction).toPrecision(2)}% of the median sample ` + + `and at most ${(100 * z.max_imputed_fraction).toPrecision(2)}% of any, and are not measurements.` + })()}

@@ -126,8 +151,8 @@ export function DifferentialPanel({ study, runs, option, aggregate }: { {result.rank} - log2 FC - Estimate (ln) + {result.effect.label} + {result.config.method === 'nb_glm' && Estimate (ln)} SE p padj (BH) @@ -138,8 +163,8 @@ export function DifferentialPanel({ study, runs, option, aggregate }: { {result.rows.map(r => ( {r.taxon} - {formatStat(r.log2_fold_change)} - {formatStat(r.estimate)} + {formatStat(effectValue(result, r))} + {result.config.method === 'nb_glm' && {formatStat(r.estimate)}} {formatStat(r.standard_error)} {formatStat(r.pvalue)} {formatStat(r.padj)} diff --git a/frontend/src/components/DiversityPanel.tsx b/frontend/src/components/DiversityPanel.tsx index b3d16dd2..ae84d450 100644 --- a/frontend/src/components/DiversityPanel.tsx +++ b/frontend/src/components/DiversityPanel.tsx @@ -1,6 +1,6 @@ // © 2026 Joshua Benjamin Jewell. All rights reserved. // Licensed under the GNU Affero General Public License version 3 (AGPLv3). -import { useEffect, useState } from 'react' +import { useEffect, useRef, useState } from 'react' import { api } from '../api/client' import { AnalysisChart } from './AnalysisChart' import { useAlphaMetricSelection, AlphaMetricToggles, ALPHA_METRICS, extractAlphaPanel } from './alphaMetrics' @@ -22,11 +22,27 @@ export function DiversityPanel({ study, runs, option, aggregate }: { const [permanova, setPermanova] = useState(null) const [loading, setLoading] = useState(null) const [rAvailable, setRAvailable] = useState(null) + const [capabilitiesError, setCapabilitiesError] = useState(null) + // Only the response to the latest request, for the current inputs, is shown. + const request = useRef(0) + // A failed check is reported as such, not as "R is unavailable". useEffect(() => { - api.analysis.capabilities().then(c => setRAvailable(c.r_available)).catch(() => setRAvailable(false)) + api.analysis.capabilities() + .then(c => setRAvailable(c.r_available)) + .catch(err => setCapabilitiesError(errorMessage(err))) }, []) + // Results answer the inputs they were computed from; new inputs discard them, + // along with any request still in flight for the old ones. + useEffect(() => { + request.current++ + setAlphaFig(null) + setNmdsFig(null) + setPermanova(null) + setLoading(null) + }, [study, runs, option?.table, aggregate]) + const body = option && runs.length >= 2 ? { table: option.table, @@ -36,22 +52,33 @@ export function DiversityPanel({ study, runs, option, aggregate }: { } : null + /** Compute one analysis for the current inputs and show it, unless the inputs changed meanwhile. */ const run = async (type: 'alpha' | 'nmds' | 'permanova') => { if (!body) return + const req = ++request.current + const current = () => req === request.current setLoading(type) try { if (type === 'alpha') { - setAlphaFig(await api.analysis.compareAlpha(study, body)) + const fig = await api.analysis.compareAlpha(study, body) + if (current()) setAlphaFig(fig) } else if (type === 'nmds') { - setNmdsFig(await api.analysis.nmds(study, body)) + const fig = await api.analysis.nmds(study, body) + if (current()) setNmdsFig(fig) } else { - setPermanova(await api.analysis.permanova(study, body)) + const res = await api.analysis.permanova(study, body) + if (current()) setPermanova(res) } } catch (err) { + if (!current()) return + // A failed rerun must not leave the previous result looking current. + if (type === 'alpha') setAlphaFig(null) + else if (type === 'nmds') setNmdsFig(null) + else setPermanova(null) const label = type === 'alpha' ? 'Alpha comparison' : type === 'nmds' ? 'NMDS' : 'PERMANOVA' toast.error(`${label} failed: ${errorMessage(err)}`) } finally { - setLoading(null) + if (current()) setLoading(null) } } @@ -82,6 +109,11 @@ export function DiversityPanel({ study, runs, option, aggregate }: { NMDS and PERMANOVA need R with vegan. )} + {capabilitiesError && ( + + Could not check whether R is available: {capabilitiesError} + + )} {alphaFig != null && ( @@ -99,19 +131,20 @@ export function DiversityPanel({ study, runs, option, aggregate }: {
PERMANOVA Results
{permanova.text}
- {(permanova.terms?.length - ? permanova.terms - : permanova.p_value != null - ? [{ term: 'model', r2: permanova.r2 ?? NaN, f_statistic: permanova.f_statistic, p_value: permanova.p_value }] - : [] - ).map(t => ( + {(permanova.terms ?? []).map(t => (

- {t.term}: R² = {t.r2.toFixed(3)} · F = {t.f_statistic?.toFixed(2) ?? 'n/a'} · p = {t.p_value?.toFixed(4) ?? 'n/a'} + {t.term}: R² = {t.r2.toFixed(3)} · F = {t.f_statistic?.toFixed(2) ?? 'n/a'} ·{' '} + {t.untestable_reason ? `p not reported: ${t.untestable_reason}` : `p = ${t.p_value?.toFixed(4) ?? 'n/a'}`}

))} {(permanova.terms?.length ?? 0) > 1 && (

Terms are tested in order, each after the ones above it.

)} + {permanova.permutations != null && permanova.min_p_value != null && ( +

+ {permanova.permutations} permutations; the smallest attainable p is {permanova.min_p_value.toFixed(4)}. +

+ )} {permanova.blocked && (

Permutations restricted within individuals.

)} diff --git a/frontend/src/components/PipelineStages.tsx b/frontend/src/components/PipelineStages.tsx index 8a96ab41..85129267 100644 --- a/frontend/src/components/PipelineStages.tsx +++ b/frontend/src/components/PipelineStages.tsx @@ -150,8 +150,10 @@ export const CONFIG_DESCRIPTIONS: Record = { 'analysis.alpha.rarefaction_iterations': 'rarefy draws averaged for each alpha diversity value.', 'analysis.beta.normalisation': 'Preparation before the Bray-Curtis dissimilarity used by NMDS and PERMANOVA: hellinger (square root of relative abundances), none, rarefy or srs.', 'analysis.beta.depth': 'Reads per sample for rarefy or srs; 0 uses the smallest non-empty sample.', - 'analysis.differential.offset': 'Library-size offset in each negative-binomial model: tss (total reads per sample) or rle (median-of-ratios over taxa present in every sample; refused when there are none).', + 'analysis.differential.method': 'Model fitted to each taxon: nb_glm (negative-binomial GLM on read counts; effect is a log2 fold change) or clr_welch (Welch\'s t-test on centred log-ratios over the taxa passing min_prevalence, after zCompositions::cmultRepl zero replacement; effect is a CLR difference, not a fold change).', + 'analysis.differential.offset': 'Library-size offset in each negative-binomial model: tss (total reads per sample) or rle (median-of-ratios over taxa present in every sample; refused when there are none). Used by nb_glm only.', 'analysis.differential.min_prevalence': 'Fraction of samples, 0 to 1, in which a taxon must have reads to be tested; taxa below it are listed as filtered.', + 'analysis.differential.replacement_delta': 'clr_welch only: cmultRepl\'s frac, between 0 and 1; an imputed proportion above its taxon\'s smallest observed proportion is lowered to this fraction of it. Replaced zeros are not measurements.', 'analysis.alpha.show_points': 'Show individual samples overlaid on alpha comparison boxplots.', 'analysis.alpha.annotate_significance': 'Annotate alpha comparison panels with Kruskal-Wallis significance.', 'analysis.alpha.pairwise_brackets': 'Run BH-adjusted pairwise Wilcoxon rank-sum tests between every group pair and draw brackets, including n.s. results.', @@ -248,8 +250,10 @@ export const CONFIG_TYPES: Record = { 'analysis.alpha.rarefaction_iterations': { kind: 'int' }, 'analysis.beta.normalisation': { kind: 'enum', options: ['hellinger', 'none', 'rarefy', 'srs'] }, 'analysis.beta.depth': { kind: 'int' }, + 'analysis.differential.method': { kind: 'enum', options: ['nb_glm', 'clr_welch'] }, 'analysis.differential.offset': { kind: 'enum', options: ['tss', 'rle'] }, 'analysis.differential.min_prevalence': { kind: 'float', min: 0, max: 1, step: 0.05 }, + 'analysis.differential.replacement_delta': { kind: 'float', min: 0.01, max: 0.99, step: 0.05 }, 'analysis.alpha.show_points': { kind: 'boolean' }, 'analysis.alpha.annotate_significance': { kind: 'boolean' }, 'analysis.alpha.pairwise_brackets': { kind: 'boolean' }, diff --git a/frontend/src/components/TaxaCompositionChart.tsx b/frontend/src/components/TaxaCompositionChart.tsx index 2b8221a4..9601aebd 100644 --- a/frontend/src/components/TaxaCompositionChart.tsx +++ b/frontend/src/components/TaxaCompositionChart.tsx @@ -1,6 +1,6 @@ // (c) 2026 Joshua Benjamin Jewell. All rights reserved. // Licensed under the GNU Affero General Public License version 3 (AGPLv3). -import { useEffect, useState } from 'react' +import { useEffect, useRef, useState } from 'react' import { api } from '../api/client' import { useAnalysisSource } from './analysisSource' import { errorMessage } from '../api/errorMessage' @@ -24,6 +24,13 @@ const LABEL_STYLE: React.CSSProperties = { gap: 4, } +/** + * Select and compute a taxon or category bar chart for one run, or for `runs` + * when that list is non-empty, with optional facets across runs. `table` + * defaults to merged. Providing `subgroup`, including null for all sub-groups, + * controls that selection and hides the internal selector; facets set their + * own scope. Changed inputs clear the figure; chart failures show a toast. + */ export function TaxaCompositionChart({ study, run, @@ -78,6 +85,8 @@ export function TaxaCompositionChart({ //## Chart state const [figure, setFigure] = useState(null) const [loading, setLoading] = useState(false) + // Only the response to the latest request, for the current inputs, is shown. + const request = useRef(0) //## Derived flags const isCrossRun = runs !== undefined && runs.length > 0 @@ -102,9 +111,11 @@ export function TaxaCompositionChart({ useEffect(() => { if (tag !== 'rank') return if (!refRun) { setRanks([]); return } + let cancelled = false api.analysis .ranks(study, refRun, { table: effectiveTable, group: refGroup ?? undefined }) .then(result => { + if (cancelled) return setRanks(result) setRank(current => current && result.includes(current) @@ -112,7 +123,8 @@ export function TaxaCompositionChart({ : result[result.length - 1] ?? null ) }) - .catch(() => setRanks([])) + .catch(() => { if (!cancelled) setRanks([]) }) + return () => { cancelled = true } }, [study, refRun, refGroup, tag, effectiveTable]) //## Fetch category sets when tag='category' @@ -131,7 +143,22 @@ export function TaxaCompositionChart({ const gridRows = (figure as { layout?: { grid?: { rows?: number } } } | null)?.layout?.grid?.rows ?? 1 + // Everything a request is built from. A figure answers the inputs it was + // computed from, so new inputs discard it, along with any request still in + // flight for the old ones. Keyed on content so a new-but-equal `runs` array + // does not clear the chart. + const inputsKey = JSON.stringify([ + study, run, group, runs, effectiveTable, source, tag, rank, catSet, topN, + relative, mode, keepEmpty, isFaceted, facetRows, facetCols, subgroup, + ]) + useEffect(() => { + request.current++ + setFigure(null) + setLoading(false) + }, [inputsKey]) + //## Compute handler + /** Build the chart for the current inputs and show it, unless the inputs changed meanwhile. */ const handleShow = async () => { const value = tag === 'rank' ? rank : catSet if (!value) return @@ -140,6 +167,7 @@ export function TaxaCompositionChart({ toast.error('No run specified') return } + const req = ++request.current setLoading(true) try { const body = { @@ -151,27 +179,31 @@ export function TaxaCompositionChart({ keep_empty: keepEmpty, ...(tag === 'rank' ? { top_n: topN } : {}), } + let fig: unknown if (isFaceted) { - setFigure(await api.analysis.chartFacet(study, { + fig = await api.analysis.chartFacet(study, { ...body, runs: runs!, rows: facetRows, cols: facetCols, - })) + }) } else if (isCrossRun) { - setFigure(await api.analysis.chartCompare(study, { + fig = await api.analysis.chartCompare(study, { ...body, subgroup: subgroup ?? null, runs: runs!, - })) + }) } else { - setFigure(await api.analysis.chart(study, run!, - { ...body, subgroup: subgroup ?? null, ...(source ? { source } : {}) }, group)) + fig = await api.analysis.chart(study, run!, + { ...body, subgroup: subgroup ?? null, ...(source ? { source } : {}) }, group) } + if (req === request.current) setFigure(fig) } catch (err) { + if (req !== request.current) return + setFigure(null) toast.error(`Chart failed: ${errorMessage(err)}`) } finally { - setLoading(false) + if (req === request.current) setLoading(false) } } diff --git a/frontend/src/components/VennPanel.tsx b/frontend/src/components/VennPanel.tsx index e276f24d..4ed37a0f 100644 --- a/frontend/src/components/VennPanel.tsx +++ b/frontend/src/components/VennPanel.tsx @@ -8,11 +8,12 @@ import { api } from '../api/client' import { errorMessage } from '../api/errorMessage' import { useToast } from './Toast' import type { ComparisonRunSpec, VennResult } from '../api/types' -import { uniqueRuns } from '../api/types' +import { sharedRanks } from './sharedRanks' import type { AnalysisOption } from './annotationShared' type Mode = 'euler' | 'upset' +/** Taxon overlap between the selected runs at one shared rank, as an Euler or UpSet diagram. */ export function VennPanel({ study, runs, option }: { study: string runs: ComparisonRunSpec[] @@ -25,6 +26,9 @@ export function VennPanel({ study, runs, option }: { const [result, setResult] = useState(null) const [loading, setLoading] = useState(false) const [ranksReady, setRanksReady] = useState(false) + const [ranksError, setRanksError] = useState(null) + // Only the response to the latest request, for the current inputs, is shown. + const request = useRef(0) const box = useRef(null) const [width, setWidth] = useState(580) @@ -38,35 +42,43 @@ export function VennPanel({ study, runs, option }: { // Discover the intersection of taxonomy ranks available across all selected runs. useEffect(() => { + setRanksError(null) if (!option || runs.length === 0) { setRanks([]); setRank(''); setRanksReady(false); return } let cancelled = false setRanksReady(false) - Promise.all( - uniqueRuns(runs).map(r => - api.analysis.ranks(study, r.run, { - table: option.table, - group: r.group, - ...(r.source ? { source: r.source } : {}), - }).catch(() => [] as string[]) - ) - ).then(results => { + sharedRanks(runs, r => api.analysis.ranks(study, r.run, { + table: option.table, + group: r.group, + ...(r.source ? { source: r.source } : {}), + })).then(intersection => { if (cancelled) return - const intersection = results.reduce((acc, cur) => - acc.filter(r => cur.includes(r)), - results[0] ?? [] - ) setRanks(intersection) setRanksReady(true) // Default to the deepest (last) shared rank. setRank(current => intersection.includes(current) ? current : (intersection[intersection.length - 1] ?? '') ) + }).catch(err => { + if (cancelled) return + setRanks([]) + setRank('') + setRanksError(errorMessage(err)) }) return () => { cancelled = true } }, [study, runs, option]) + // A diagram answers the inputs it was computed from; new inputs discard it, + // along with any request still in flight for the old ones. + useEffect(() => { + request.current++ + setResult(null) + setLoading(false) + }, [study, runs, option?.table, rank]) + + /** Compute the overlap for the current inputs and show it, unless the inputs changed meanwhile. */ const runVenn = async () => { if (!option || !rank) return + const req = ++request.current setLoading(true) try { const res = await api.analysis.venn(study, { @@ -74,11 +86,13 @@ export function VennPanel({ study, runs, option }: { table: option.table, rank, }) - setResult(res) + if (req === request.current) setResult(res) } catch (err) { + if (req !== request.current) return + setResult(null) toast.error(`Taxon overlap failed: ${errorMessage(err)}`) } finally { - setLoading(false) + if (req === request.current) setLoading(false) } } @@ -111,6 +125,9 @@ export function VennPanel({ study, runs, option }: { {ranksReady && ranks.length === 0 && ( No taxonomy rank shared by the selected runs. )} + {ranksError && ( + Could not read the taxonomy ranks: {ranksError} + )}