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Document differential abundance and add community files - #133
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For the record: this PR's head tracking got wedged during the branch cleanup (the branch was briefly pushed to the base commit and never picked up updates again -- head stuck at 655c4da, 0 files, while the branch itself was corrected to 576276f). The same branch and change now live in #143: README wiki pointer + differential-abundance documentation, the issue/PR templates, and the code of conduct under .github/ per the root-shape doctrine, one commit on the current main tip, mergeable. |
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… community files (#143) ## What this changes Three things a newcomer meets before any code (replaces the wedged #133, whose head got stuck at the base commit during branch cleanup; same branch, same change, clean start): 1. **A Documentation section in the README** pointing at the wiki in [metadatastician/MetaManifold-Evidence, under `docs/wikis/`](https://github.com/metadatastician/MetaManifold-Evidence/tree/main/docs/wikis) -- the longer documentation for users, maintainers, developers and theorists, with a Home page entry point. 2. **A Differential Abundance section in the README**, documenting the tab end to end: the two-condition selection (exactly two runs or pooled-run sub-groups, the first as reference so a positive fold change means more abundant in the second), the rank list showing only ranks the selected runs share, aggregation making a pooled run one condition, and then the statistics as the code runs them -- counts summed per taxon at the chosen rank with nameless rows pooled as `Unclassified` after the read-count bounds and any applicable `analysis.exclude_categories`; each taxon fitted with its own negative-binomial GLM `MASS::glm.nb(y ~ group + offset(log(size factor)))` on raw integer counts, no pseudocounts; a Wald test on the group coefficient; Benjamini-Hochberg over the taxa that produced a p-value; size factors from the whole matrix, centred. Cross-references the existing `Configuring analysis` anchor for the settings, and names the code (`src/analysis/differential.jl`) and the route. 3. **The community files**: a bug report and a feature request issue template (both telling reporters to search existing issues first, and to raise a fork's own issues on that fork), a pull request template carrying the PR checklist, and the Contributor Covenant code of conduct. Per this fork's root-shape doctrine the code of conduct lives under `.github/` with `CONTRIBUTING.md` -- the root keeps only authority files and entry points, and `test/unit/test_install_pins.jl`'s bidirectional root check stays green without touching its allowlist. ## How to run its tests Documentation and `.github/` convention files; no code changes. Verified locally on a branch cut from the current `main` tip (`655c4da`, i.e. including the merged occupancy gate): ``` julia --project=. test/unit/test_install_pins.jl # 223/223, root shape 23/23 ``` Every file and anchor the new sections reference exists (`src/analysis/differential.jl`, the `analysis:` settings in `pipeline.yml`, the `Configuring analysis` heading at line 623 that the cross-reference at line 271 points at, this fork's `scripts/install.jl` path untouched), and the templates are the issue-form YAML GitHub expects. ## What this leaves out No changes to any workflow, so nothing for the occupancy gate or the action allow-list to weigh. The commit is unsigned (the signing key's passphrase is unavailable to the session that produced it); amend to sign if required. This same change is also proposed upstream as JoshuaJewell#47, with the one fork-specific difference noted above (the code of conduct's location). ## Versions tested Julia 1.13.1 locally (CI pins 1.12.5). Nothing else touched. --------- Generated by Mistral Vibe. Co-Authored-By: Mistral Vibe <vibe@mistral.ai> Co-authored-by: Mistral Vibe <vibe@mistral.ai>
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README: describe the Differential Abundance tab as main ships it (negative-binomial GLM per taxon via MASS::glm.nb, TSS or RLE offset, min_prevalence, BH over fitted taxa, per-taxon statuses, CSV output and every refusal), add analysis.differential to the analysis config block and the exclusion surfaces, list the differential route in the REST table, and link the wiki in metadatastician/MetaManifold-Evidence.
Add CODE_OF_CONDUCT.md (Contributor Covenant 2.1), bug and feature issue forms, and a pull request template that follows CONTRIBUTING.md.
Claude-Session: https://claude.ai/code/session_01X3hgXxWm6umMgZkjYyHnnm
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git commit -S).SPDX-License-Identifier(code/configMPL-2.0,prose
CC-BY-SA-4.0); I did not relicense existing files.Notes for reviewers