indicium-adapters 0.6.0__tar.gz

indicium_adapters-0.6.0/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.11", "3.12", "3.13"]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          # indicium-standard resolves from PyPI (2.0.0 and later).
+          # .[asb] brings httpx + pydantic + pyyaml for the src/indicium_adapters/asb
+          # submodule that tests/asb exercises; .[dev] brings pytest, pytest-cov,
+          # pyshacl and the pinned ruff.
+          pip install -e ".[dev,asb]"
+      - name: Lint
+        run: ruff check .
+      - name: Run tests
+        run: pytest --cov=indicium_adapters --cov-report=term-missing

indicium_adapters-0.6.0/.github/workflows/release.yml

@@ -0,0 +1,97 @@
+name: Release
+
+on:
+  push:
+    tags:
+      - "v*"
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v7
+
+      - uses: astral-sh/setup-uv@v7
+
+      - name: Check tag, version and release date
+        run: uv run --no-project --python 3.12 python scripts/check_release.py --tag "$GITHUB_REF_NAME" --notes-output "$RUNNER_TEMP/release-notes.md"
+
+      - name: Require indicium-standard on PyPI
+        run: |
+          curl -sSf -o /dev/null https://pypi.org/pypi/indicium-standard/2.0.0/json || {
+            echo "::error::indicium-standard 2.0.0 is not on PyPI yet; release after it"
+            exit 1
+          }
+
+      - name: Install, lint and test
+        run: |
+          uv venv --python 3.12 .venv
+          uv pip install --python .venv/bin/python --no-sources -e ".[dev,asb]"
+          .venv/bin/ruff check .
+          .venv/bin/pytest
+
+      - name: Build and check distributions
+        run: |
+          rm -rf dist
+          uv build --no-sources
+          uvx --from twine==7.0.0 twine check --strict dist/*
+
+      - name: Check installed wheel
+        run: |
+          uv venv --python 3.11 .wheel-env
+          uv pip install --python .wheel-env/bin/python --no-sources dist/*.whl
+          uv pip check --python .wheel-env/bin/python
+          .wheel-env/bin/python -c "import sys, indicium, indicium_adapters; from importlib.metadata import version; v = version('indicium-adapters'); assert 'v' + v == sys.argv[1], v; print('indicium-adapters', v, 'indicium-standard', version('indicium-standard'))" "$GITHUB_REF_NAME"
+
+      - uses: actions/upload-artifact@v7
+        with:
+          name: release-distributions
+          path: dist/*
+          if-no-files-found: error
+
+      - uses: actions/upload-artifact@v7
+        with:
+          name: release-notes
+          path: ${{ runner.temp }}/release-notes.md
+          if-no-files-found: error
+
+  publish:
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/indicium-adapters
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v8
+        with:
+          name: release-distributions
+          path: dist
+
+      - name: Publish to PyPI with Trusted Publishing
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+  github-release:
+    needs: publish
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/download-artifact@v8
+        with:
+          name: release-distributions
+          path: dist
+
+      - uses: actions/download-artifact@v8
+        with:
+          name: release-notes
+          path: release-notes
+
+      - uses: softprops/action-gh-release@v3
+        with:
+          body_path: release-notes/release-notes.md
+          files: dist/*

indicium_adapters-0.6.0/.gitignore

@@ -0,0 +1,12 @@
+__pycache__/
+*.pyc
+*.pyo
+*.egg-info/
+.pytest_cache/
+dist/
+build/
+.coverage
+htmlcov/
+*.so
+.venv/
+.wheel-env/

indicium_adapters-0.6.0/CHANGELOG.md

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+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+---
+
+## [0.6.0] - 2026-11-02
+
+First release published to PyPI. 0.5.0 was never tagged or published, and its
+changes ship in this release; the tag before this one is `v0.4.0`.
+
+### Added
+- `ClassificationVocabularyProvider`, an opt-in protocol for an adapter that
+  declares curated classification vocabulary: `primary_domain`, `subdomains` and
+  `techniques`. `classification_vocabulary(adapter)` reads the three members into a
+  `ClassificationVocabulary` and never substitutes `domain_id` for a missing
+  `primary_domain`; an adapter that declares nothing reports `primary_domain=None`.
+  (#5)
+- Convention: `DomainAdapter.enrich_claim()` MAY set an
+  `ontology_term_justifications: dict[str, str]` companion map alongside
+  `ontology_terms`, mapping the same slot keys to SEMAPV justification CURIEs (e.g.
+  `semapv:CompositeMatching`, `semapv:LexicalMatching`). Downstream SSSOM emitters
+  (Perspicacité) use this as `mapping_justification`; absent keys default to
+  `semapv:CompositeMatching`. Documented in the `enrich_claim` docstring and the
+  README.
+- `RoundTripResult.skills_checked`, also printed by `verify-claims` and returned
+  under `skills_checked` in its JSON: the number of skills read from disk, so a pass
+  that read no skill is visible.
+- `RoundTripResult.skills_listed` and `skills_skipped`, also in the `verify-claims`
+  JSON and pretty output: the entries under `skills` in `collection.yaml`, and the
+  slug and reason of each listed skill that has no SKILL.md or fails validation.
+  The loader keeps such skills in `ASBCollection.skipped_skills` (new model
+  `ASBSkippedSkill`) instead of dropping them.
+- `ASBClaimRecord.context`, the SuperPattern context slot. The mapper writes it as
+  `asb:context`, which the indicium `asb:Claim` shape requires, when the record has
+  one. An earlier entry and the body of commit 8ebaff0 said ASB claim records carry
+  no context; ASB's own claims do, and it was this package's record that lacked the
+  field.
+- `RoundTripResult.skills_with_unlisted_claims`: skills whose frontmatter declares
+  `n_claims` above 0 but lists no claim IRI. `verify-claims` returns it in its JSON
+  and prints a warning on stderr; it does not fail the gate. `ASBSkillRecord` reads
+  `n_claims`.
+- **The round-trip gate fails on a graph that indicium's shapes would not check.**
+  `run_round_trip_check()` and `verify-claims` now fail (exit 1) when no node of the
+  indicium graph is typed with a class an indicium SHACL shape targets: validating
+  such a graph has no focus node and conforms whatever it holds. The count is
+  `RoundTripResult.shape_targeted_nodes`, returned as `shape_targeted_nodes` in the
+  `verify-claims` JSON. `shape_targeted_classes()` reads the targets from the shape
+  files indicium ships, and `count_shape_targeted_nodes()` counts a graph's nodes.
+- `tests/test_release_metadata.py`: `CITATION.cff` and `pyproject.toml` carry the
+  same version, `indicium_adapters.asb.__version__` is the installed distribution
+  version, this file has a section for that version and at most one Unreleased
+  section, and `SECURITY.md` supports the `pyproject.toml` major.minor line.
+- `.github/workflows/release.yml`: on a `v*` tag, checks the tag, the versions and
+  the changelog date (`scripts/check_release.py`), runs lint and tests, builds the
+  sdist and the wheel with `uv build`, runs `twine check --strict`, installs the
+  wheel in a clean environment and imports it, publishes to PyPI with Trusted
+  Publishing from the `pypi` environment, and creates the GitHub release with the
+  two distributions. `RELEASING.md` holds the checklist.
+
+### Changed
+- **The dependency is the renamed `indicium-standard>=2.0.0`** (was `indicium>=1.7`),
+  and the version moved to 0.6.0 in the same commit. The import name stays
+  `indicium`. The ASB mapper requires indicium main at or after 62c7f52, the first
+  commit exporting `ASB_BASE` and `INDICIUM_BASE`; earlier 2.0.0 builds satisfy the
+  floor but make `import indicium_adapters.asb` raise `ImportError`.
+- **`requires-python` lowered from `>=3.12` to `>=3.11`.** Nothing in the package
+  needed 3.12: all 24 source and test modules parse under 3.11 (no PEP 695
+  type-parameter syntax, no `type` alias statements), there is no 3.12-only stdlib
+  API in use, and the only runtime dependency, `indicium-standard`, already declares
+  `>=3.11`. At that commit the suite passed unchanged on 3.11: 73 passed, 4 skipped,
+  90.31% coverage.
+
+  The floor mattered because it made every `DomainAdapter` uninstallable in the
+  AgenticScienceBuilder environment, which runs Python 3.11 and is where the
+  classification vocabulary adapters feed is actually consumed. With the floor
+  lowered, installing `indicium-adapters` plus `indicium-adapters-astronomy` into
+  that environment takes ASB's controlled vocabulary from 17 primary domains to 18,
+  adding `astronomy` along with its 11 subdomains and its techniques; previously an
+  astronomy paper was classified as `other` no matter what.
+- Dropped the `Programming Language :: Python :: 3.10` classifier. It advertised a
+  version that could never resolve, since `indicium-standard` requires `>=3.11`.
+- **The ASB mapper takes its vocabulary bases from indicium** (`ASB_BASE`,
+  `INDICIUM_BASE`) instead of the hardcoded
+  `https://w3id.org/holobiomicslab/indicium#`. A claim is typed `asb:Claim`; its
+  subject, predicate and object fill `asb:subject`, `asb:relation` and `asb:object`,
+  the terms the indicium `asb:Claim` shape declares. A qualifier rides
+  `asb:qualifier` when it is a closed Bucur term and `asb:domainQualifier`
+  otherwise, as the `DomainAdapter.qualifiers` contract states. The other mapper
+  terms keep their local names under `INDICIUM_BASE`. No file in the current
+  collections uses the old namespace, so it is not read as an alias.
+- **Evidence spans, tools and papers are typed and described with indicium's own
+  terms, so its shapes check them.** On the metabolomics v2 collection the graph
+  typed 0 of its 22,753 typed nodes with a class an indicium shape targets, and
+  `validate_graph` conformed without checking anything. An evidence span is now an
+  Evidence, `sepio:0000002` (was `indicium:Evidence`), with `indicium:eco_code`,
+  `indicium:quote_exact`, `indicium:source_doi` and `indicium:paragraph_id`. A tool
+  is a SoftwareEntity, `fabio:ComputerProgram` (was `indicium:SoftwareEntity`), with
+  its IRI in `dct:identifier`, `indicium:canonical_url` as an IRI (a value that is
+  not an absolute IRI stays a literal, which the shape reports) and
+  `indicium:edam_operation` and `indicium:edam_topics`. A paper is a Source,
+  `fabio:Expression` (was `indicium:InformationSource`), with its DOI in
+  `dct:identifier` (was `cito:hasIdentifier`) and its title in `dct:title`. The v2
+  graph now has 16,894 nodes the shapes target, and it conforms.
+- `ASBEvidenceSpan.eco_code` defaults to `textual_quotation`, the EcoCodeAsbSubset
+  value indicium maps to `ECO:0000033`. The former default `eco:textual-quotation`
+  was written as `ECO_textual-quotation`, an ECO IRI that does not exist. Every
+  EcoCodeAsbSubset value maps to the ECO term indicium gives it, an `ECO:` CURIE to
+  its IRI, and any other value stays a literal that the indicium shape reports.
+- `indicium:bio_tools_id` is a string, written only when a bio.tools id is known;
+  an unresolved id is no longer written as `rdf:nil`, which the shape rejects.
+- `ASBAdapter` writes one paper node per DOI. When the records citing a paper give
+  it different titles it gets no `dct:title`, which the indicium shape allows once,
+  and the adapter warns with their count and the first ten DOIs: 50 of the 498
+  papers of metabolomics v2.
+- Skill and tool instance IRIs keep the `https://w3id.org/holobiomicslab/asb-skill/`
+  and `.../asb-tool/` form that ASB's release code mints, now exported as
+  `ASB_SKILL_BASE` and `ASB_TOOL_BASE`. `ASBAdapter` binds the `asb:` prefix to the
+  vocabulary and `asbskill:` to the skill instances.
+- `ASBSourcePaper.title` may be empty: current releases leave it empty when the
+  title was not resolved, and the DOI identifies the paper. The mapper writes no
+  empty title.
+- A skill or tool record that fails validation is skipped with a warning; the
+  loader no longer catches every exception, and `tools.lock.yaml` entries that fail
+  are no longer dropped silently.
+- `indicium_adapters.asb.__version__` reads the installed distribution version (it
+  was a hardcoded `0.5.0`). `CITATION.cff` moves from 0.4.0 to 0.6.0, gains the
+  author's ORCID and drops the `date-released` of 0.4.0, since 0.6.0 has no release.
+- `SECURITY.md` writes its supported-versions table in plain text and lists 0.6.x
+  as the supported line (it still listed 0.4.x).
+- CI tests Python 3.11, 3.12 and 3.13. `ruff check .` now fails the job on any
+  finding; ruff is pinned to 0.17.3 in the `dev` extra because each release widens
+  its default rule set. The extras install no longer falls back to a bare install.
+  CI installs `indicium-standard` from the public repository, pinned to commit
+  500dd82, and no longer needs the `ORG_PAT` token; the pin moves to PyPI once
+  2.0.0 is published.
+- `uv.lock` is refreshed: it still declared `requires-python = ">=3.12"`.
+- `pyproject.toml` declares `readme = "README.md"`. The built wheel's METADATA had
+  no long description, so its package index page would have been empty; it now
+  carries the README with `Description-Content-Type: text/markdown`, and
+  `twine check --strict` passes on the wheel and the sdist.
+
+### Fixed
+- **`verify-claims` raised `AttributeError: 'str' object has no attribute 'get'` on
+  every current collection.** `load_collection()` read only the earlier layout,
+  where `collection.yaml` lists skills as mappings. Current releases list skills and
+  tools as slugs, keep leaf skills in `leaves/<slug>/SKILL.md`, put the collection
+  IRI under `iri`, write evidence spans as plain strings and papers under
+  `derived_from` or `provenance.source_papers`. The loader now reads both layouts.
+- SKILL.md frontmatter was split on any `---`, so a quoted value containing it cut
+  the YAML short. Only a fence line closes the block now.
+- A tool slug containing the word `path` was indexed as a mapping and raised
+  `TypeError`.
+- The round-trip gate counted a claim as resolved only when typed with the
+  hardcoded holobiomicslab `Claim` class. It now resolves claims typed with
+  indicium's `asb:Claim`, the class ASB's indicium emitter writes.
+- The pretty `verify-claims` FAIL report printed each dangling reference as a
+  dataclass repr; it now prints `<skill slug>: <claim IRI>`.
+- **The round-trip gate failed open.** A listed skill with no SKILL.md was dropped
+  without a word, and one that failed validation was dropped with a warning, so
+  `verify-claims` exited 0 without checking the claim IRIs it listed. Both now fail
+  the gate (exit 1, `RoundTripResult.ok` false), and the claim IRIs a skipped
+  skill's frontmatter lists are still checked. `RoundTripResult.render()` now
+  returns the report `verify-claims` prints.
+- The `verify-claims --help` text named only `metadata.claims` and the
+  `skills/<slug>/SKILL.md` layout; it now names the frontmatter `claims` key and
+  `leaves/<slug>/SKILL.md`.
+
+### Known gaps
+- Claims, evidence spans, tools and papers are typed with the classes the indicium
+  shapes target. Skills, which the indicium model does not describe, a claim's
+  `super_pattern`, the `name` of skills and tools and the skill-to-evidence link
+  `hasEvidence` use this mapper's local names under `INDICIUM_BASE`.
+- Evidence spans carry `indicium:source_doi` and `indicium:paragraph_id`, which
+  indicium declares on other classes (`paragraph_id` on Source, `source_doi` on
+  Figure, Script and DataAsset). The Evidence shape is open, so no shape checks
+  them. `indicium:of_source`, the Evidence-to-Source link indicium models, is not
+  written.
+- The skill-to-claim assertion nodes use `SEPIO_Assertion`, `SEPIO_hasSubject` and
+  `SEPIO_hasObject`, which are not SEPIO terms; no shape targets them.
+- A paper whose records give different titles is written without `dct:title`, with
+  a warning naming its DOI.
+- The `verify-claims` shape-targeted count is graph-wide: one targeted node passes
+  it, and instances of subclasses of a targeted class are not counted.
+- A claims-file record without `context` maps to a claim without `asb:context`,
+  which the `asb:Claim` shape requires, and the shape reports a violation. ASB's
+  own claims carry a context; the mapper writes it when the record has one.
+- Current tool records carry `repo_url`, not `canonical_url`, so the bio.tools
+  resolver has nothing to look up for them.
+- No SKILL.md in the current collections lists a claim IRI, so `verify-claims`
+  checks none. Metabolomics v2 has 5859 skills and none lists a claim IRI.
+  Proteomics v1 and genomics v1 declare `n_claims` totalling 5454 across 558 skills
+  and 34070 across 3246 skills, but list no IRI. Each passes with 0 claims
+  resolved.
+- `uv lock` and `uv sync` need the indicium checkout beside this one:
+  `[tool.uv.sources]` points `indicium-standard` at `../indicium`.
+
+---
+
+## [0.5.0] - 2026-05-24 (never tagged)
+
+### Added
+
+- New `indicium_adapters.asb` subpackage: maps ASB-Skill collection
+  on-disk artifacts (collection.yaml, SKILL.md frontmatter,
+  tools/<slug>.yaml) onto `indicium:Evidence`, `indicium:SoftwareEntity`,
+  `indicium:Claim`, `indicium:InformationSource`, and SEPIO skill→claim
+  assertions.
+- PROV-O envelope (`prov:wasGeneratedBy`, `prov:wasDerivedFrom`,
+  `prov:atTime`) attached to every typed node.
+- `BioToolsResolver` with SQLite cache and `ASB_ADAPTER_OFFLINE` env
+  hook for CI determinism.
+- `run_round_trip_check()` CI gate that fails on any dangling
+  `metadata.claims` URI in any SKILL.md.
+- `verify-claims` console script for `asb-skill-collections` CI integration.
+
+### Notes
+
+- Subpackage requires the new optional extra: `pip install -e '.[asb]'`.
+- The reverse (indicium → ASB-Skill hints) adapter is deferred to v1.1.
+- The `SciSkill`→`ASBSkill` Python rename in ASB lands in Wave 2;
+  this subpackage works against on-disk artifacts only and is unaffected.
+
+---
+
+## [0.4.0] - 2026-05-24
+
+### Removed
+- `MetabolomicsAdapter` and its `metabolomics.shapes.ttl` and associated tests.
+  These have moved to the new `indicium-adapters-metabolomics` package, which
+  ships richer enrichment (RefMet+BridgeDb compound index) and adds two sibling
+  adapters: `MetaboKGAdapter` and `EMIAdapter`.
+  Migration: `pip install indicium-adapters-metabolomics`; the
+  `discover_adapters()["metabolomics"]` entry remains available, now sourced
+  from the new package.
+
+---
+
+## [0.3.0] - 2026-05-23
+
+### Added
+- `CompositeAdapter`: combines 2+ `DomainAdapter` instances into one that satisfies both
+  `DomainAdapter` and `SHACLProvider` protocols. Composition rules: `qualifiers` (union),
+  `ontology_prefixes` (merged dict, later adapter wins on key conflict), `extraction_context()`
+  (concatenated with double newline), `enrich_claim()` (sequential chain: each adapter
+  enriches the output of the previous), `shacl_shapes()` (merged `rdflib.Graph`; adapters
+  without `shacl_shapes()` are silently skipped; uses `isinstance(SHACLProvider)` check).
+- `compose_adapters(adapters)`: factory function: returns the single adapter unchanged
+  when `len(adapters) == 1` (no wrapping overhead); returns `CompositeAdapter` for 2+;
+  raises `ValueError` for an empty list.
+- Both `CompositeAdapter` and `compose_adapters` exported from the top-level
+  `indicium_adapters` package.
+
+---
+
+## [0.2.0] - 2026-05-23
+
+### Added
+- `SHACLProvider` Protocol mixin: adapters that implement `shacl_shapes() -> rdflib.Graph` are
+  automatically detected by `indicium.validate_graph()` and their shapes are merged into validation.
+- `api_version: int` field on `DomainAdapter` Protocol and `CURRENT_API_VERSION` constant.
+  `discover_adapters()` now skips adapters whose `api_version` does not match `CURRENT_API_VERSION`
+  and emits a `RuntimeWarning` with upgrade instructions.
+- `MetabolomicsAdapter.shacl_shapes()`: returns the bundled `metabolomics.shapes.ttl` graph
+  containing CURIE-format constraints on `asb:subject_ontology_term` / `asb:object_ontology_term`.
+
+### Fixed
+- `metabolomics.shapes.ttl` shape target corrected from the inert `sh:targetSubjectsOf CHEBI:is_a`
+  to `sh:targetClass asb:Claim` with property shapes on the `asb:{slot}_ontology_term` predicates
+  emitted by `claims_to_graph()`.
+- CURIE regex pattern in `metabolomics.shapes.ttl` broadened from `[A-Za-z0-9_]+` to
+  `[A-Za-z0-9_.+-]+` in the local part, accommodating PubChem, InChIKey, and other identifiers
+  that contain dots, hyphens, or plus signs.
+- `rdflib>=7.0` added as an explicit runtime dependency (was only transitive via `indicium`).
+- `indicium` dependency floor raised from `>=1.0` to `>=1.4`, which is the minimum version that
+  provides the `extra_shapes` kwarg required by `SHACLProvider` injection.
+
+---
+
+## [0.1.0] - 2026-05-20
+
+### Added
+- `DomainAdapter` Protocol with `domain_id`, `domain_label`, and `api_version` fields.
+- `discover_adapters()`: entry-point discovery function resolving all `indicium.adapters`
+  entry points at import time; returns a `dict[str, DomainAdapter]` keyed by `domain_id`.
+- `MetabolomicsAdapter` with:
+  - `enrich_claim()`: annotates `subject` / `object` / `qualifier` slots with CHEBI CURIEs from
+    a static compound lookup table (live network lookup planned for a future `[network]` extra).
+  - `domain_context` string injected into LLM extraction prompts for metabolomics-aware extraction.

indicium_adapters-0.6.0/CITATION.cff

@@ -0,0 +1,25 @@
+cff-version: 1.2.0
+title: indicium-adapters
+message: "If you use this software, please cite it as below."
+type: software
+version: 0.6.0
+authors:
+  - family-names: Nothias
+    given-names: Louis-Felix
+    email: louis-felix.nothias@cnrs.fr
+    orcid: "https://orcid.org/0000-0001-6711-6719"
+repository-code: "https://github.com/HolobiomicsLab/indicium-adapters"
+license: MIT
+keywords:
+  - indicium
+  - knowledge-graph
+  - rdf
+  - shacl
+  - domain-adapter
+  - protocol
+abstract: >-
+  Protocol-only core of the indicium domain-adapter ecosystem.
+  Defines DomainAdapter and SHACLProvider structural Protocols, the
+  CompositeAdapter helper, and the discover_adapters() entry-point
+  discovery function. Domain-specific bundles ship in sibling
+  indicium-adapters-<domain> packages.

indicium_adapters-0.6.0/CONTRIBUTING.md

@@ -0,0 +1,39 @@
+# Contributing to indicium-adapters
+
+Thanks for your interest!
+
+## Setup
+
+The sibling path in `[tool.uv.sources]` supports contributors who clone
+`indicium` and `indicium-adapters` side by side:
+
+```bash
+cd indicium-adapters
+uv sync --extra dev --extra asb
+```
+
+In a lone public clone, use `uv sync --no-sources --extra dev --extra asb`
+until the lock is regenerated after the `indicium-standard` 2.0.0 upload.
+Keep `--no-sources` on later `uv run` commands too.
+
+## Development workflow
+
+1. Create a feature branch from `main`.
+2. Write tests first (TDD). The suite is `pytest`.
+3. Run `uv run ruff check .` and `uv run pytest` before pushing. In a lone
+   clone, pass `--no-sources` to both `uv run` commands. CI fails on any ruff
+   finding.
+4. Open a PR.
+
+## Scope
+
+This package is the Protocol-only core. Domain-specific adapters
+(metabolomics, lipidomics, proteomics, ...) live in sibling
+`indicium-adapters-<domain>` repositories. Don't add domain enrichment
+logic here.
+
+## Bumping CURRENT_API_VERSION
+
+Bumping `CURRENT_API_VERSION` is a coordinated cross-repo release. Plan
+it with the maintainers of every `indicium-adapters-*` package; the README
+lists the ten known at 0.6.0.

indicium_adapters-0.6.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Louis-Felix Nothias
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.