ontometer 0.1.0__tar.gz

ontometer-0.1.0/.gitignore

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+# .idea/
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+# Abstra
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+# Visual Studio Code
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+#   you could uncomment the following to ignore the entire vscode folder
+# .vscode/
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+data/backup/

ontometer-0.1.0/CHANGELOG.md

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+# Changelog
+
+All notable changes to this project are documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+**This release turns a corpus pipeline into a package someone can install.**
+Until now the repository held a multi-registry ontology corpus and a parse
+pipeline, with every derived metric living in a notebook — nothing in it took an
+ontology file and returned an assessment. The evaluator is new, the research half
+moved under `ontometer.corpus`, and the distribution metadata now says what the
+license is.
+
+### Added
+
+- **`ontometer eval <file>` — the single-ontology evaluator.** Loads an ontology,
+  computes the sixteen OQuaRE metrics, scales each to 1–5, rolls them up through
+  the quality model, and renders Markdown or JSON. `--fail-under` exits non-zero
+  below a threshold, for CI use.
+- **The quality model ships as configuration, not code.** `model/scales.yaml`
+  holds the threshold families; `model/quality_model.yaml` holds the
+  characteristic → sub-characteristic → metric map and names the aggregation
+  rule. Both are read at runtime, so thresholds can be retuned for a domain
+  without forking. `ontometer model --what scales|characteristics|unsupported`
+  prints what the current build uses.
+- **Every metric carries the formula it computes.** The published OQuaRE sources
+  disagree with each other on several metrics, so each one reports its own
+  definition in the metric table rather than leaving a reader to guess which
+  rendering was implemented.
+- **An LLM review, grounded on the metrics.** The five weakest metrics and the
+  specific entities driving them are passed to the model, which explains and
+  recommends but never emits a number the report presents as a measurement.
+  Findings are ranked `defect` / `weakness` / `suggestion`, where `defect` means
+  a reasoner would draw a different conclusion.
+- **Ollama and OpenAI providers**, selected by `LLM_PROVIDER`. Configuration is
+  read from the process environment under the `LLM_` prefix.
+- **Seed-term heuristics** mapping a weak metric back to the entities responsible
+  for it — classes with no individuals, properties with no declared domain,
+  undocumented classes, tangled classes, the deepest and widest parts of the
+  hierarchy.
+- **Subsumption-cycle detection.** Classes trapped in a cycle are reported
+  explicitly, independently of any metric.
+- **A test suite.** There were none; `test/` now covers metric values against
+  hand-checked fixtures, scale boundaries, model/registry agreement, and the full
+  review path against a fake chat model with no network.
+
+### Changed
+
+- **The research half moved to `ontometer.corpus`** (`fetchers`, `pipeline`,
+  `network`) and sits behind the `corpus` extra, so the base install no longer
+  pulls a scraping, dataframe and plotting stack onto users of the evaluator.
+  Importing it without the extra raises a directive message naming what to
+  install.
+- **Namespace helpers are public and shared.** `iri_namespace` and the
+  generic-namespace set were private to the corpus parser and reached across a
+  `sys.path` insertion by the coupling script. They now live in
+  `ontometer.onto.namespaces`, and the parser reads them from there — one
+  definition, not two, because a duplicated generic-namespace set drifts and
+  makes coupling numbers from the two halves incomparable. The evaluator gains
+  the parser's OBO handling as a result: OBO terms split by their `PREFIX_`
+  rather than collapsing onto the shared `purl.obolibrary.org/obo/` path.
+- **The corpus artifacts in `data/` are compact rather than untracked.** They
+  stay in git — they cannot be re-fetched into existence, since the registries
+  they came from change underneath you and the object store they were parsed
+  from lives on the machine that ran the crawl. What changed is their size:
+  `corpus.db` 98.0 MiB → 34.3 MiB, `manifest.jsonl` 67.5 MiB → 13.3 MiB, the
+  network 8.3 MiB → 1.3 MiB, `data/` overall ~175 MiB → ~49 MiB. This was not
+  optional housekeeping: `corpus.db` had reached 97.97 MiB against GitHub's hard
+  100 MiB push limit, growing 3.4 MiB in a single refresh.
+- **Registry metadata is projected to a field allowlist before storage**
+  (`ontometer/corpus/metadata.py`). The verbatim API response was 58 MiB, 72% of
+  the database, written a second time into `manifest.jsonl` — which was 92% this
+  one field — and read by nothing. Kept: `description`, `name`, `acronym`,
+  `hasDomain`, `group`, `hasOntologyLanguage`, `hasLicense`, `homepage`,
+  `publication`, `version`, `status`. Dropped: the JSON-LD `links` and
+  `@context` boilerplate (24 MiB of templated URLs), and `contact`,
+  `administeredBy`, `reviews` and `projects` — which carried several hundred
+  ontology maintainers' names and email addresses. Addresses are redacted from
+  retained free text as well. The projection runs at fetch time, so a new crawl
+  never materialises the bulk.
+- **`parse_error` is bounded at 2,000 characters.** Two rows held 7.28 of the
+  7.31 MiB the column occupied, because an rdflib error echoed an entire
+  unparseable file back into its own message.
+- **`retrieved_file` is stored relative to the object-store root.** It held
+  absolute paths into the home directory of the machine that ran the crawl,
+  which resolve nowhere else.
+- **The dependency network is two Parquet tables, not a pickle.** Loading a
+  pickle executes arbitrary code, which is not acceptable for an artifact
+  intended to be published and downloaded; the pair is also a sixth of the size
+  and round-trips the graph exactly.
+- **Every filesystem location is a parameter.** `ontometer/corpus/paths.py`
+  resolves exactly two inputs — `--data-dir` / `ONTOMETER_DATA_DIR` for tracked
+  artifacts and `--ontology-dir` / `ONTOLOGY_DIR` for the object store — and
+  derives everything else. Each stage previously computed its own: some from
+  `__file__` (the repository root from a checkout, `site-packages` once
+  installed), one with a hardcoded fallback into a specific user's home
+  directory, and the object-store root was read from the environment deep inside
+  a parse worker. Every `run/` script and the network builder now take both
+  flags, so a run can be pointed at a scratch directory.
+- **`retrieved_file` resolves on any machine.** Paths are stored relative to the
+  object-store root and resolved in the parent process before a worker sees
+  them; `CorpusPaths.resolve_object` still accepts the absolute paths older
+  databases hold, re-anchoring them on the configured store.
+- **The metadata projection is applied at the seed boundary too**, not only at
+  fetch time — a manifest captured before the projection existed still holds the
+  full registry response, and seeding from one must not put it back into the
+  database.
+- **The retired `graph_hash` and `fuseki_*` columns are gone**, along with the
+  `update_fuseki` writer that no longer had callers, and `okg_metadata.json`,
+  a 1 MiB registry cache nothing read.
+
+### Fixed
+
+- **The distribution declared no license.** `LICENSE` was already Apache-2.0 but
+  neither `pyproject.toml` nor the copyright appendix said so, so PyPI would have
+  rendered the package as unlicensed.
+- **Network construction resolved paths relative to the repository root**, which
+  in an installed wheel pointed inside `site-packages`.
+- **`dotenv` was declared as a dependency alongside `python-dotenv`.** They are
+  different packages; the code imports the latter. `pip` was also declared as a
+  runtime dependency.
+- **Vocabularies without an `owl:Ontology` declaration entered the network as
+  anonymous `row:<id>` nodes** that nothing could reference, zeroing their
+  in-degree. Where the registry's `source_id` carries the IRI (LOV's does), it
+  is now used as a fallback, and the new `iri_source` column records `declared`
+  vs `registry`. (@dahrb)
+- **`rdf:Property` terms were not counted as properties**, so pre-OWL
+  vocabularies reported none. `property_count` and `compute_content_hash` now
+  share one type list, and dedup Pass B rejects the empty content hash directly
+  instead of trusting the counters as a proxy for it. (@dahrb)
+- **Usage edges to generic namespaces (FOAF, SKOS, RDF, …) always became external
+  placeholders**, even when the vocabulary itself was in the corpus, splitting
+  one vocabulary across two nodes. They now resolve to the owning row when that
+  row comes from LOV, the curated registry of such vocabularies; otherwise they
+  stay external. A namespace with a trailing `#` or `/` now also matches its
+  ontology's bare IRI, and a row referencing its own generic namespace no longer
+  gets a self-loop. The network build prints which generic namespaces merged.
+  (@dahrb)
+- **A failed structural-sidecar write was silently swallowed**, which made an
+  ontology indistinguishable from one without a hierarchy in the structural
+  metrics. It now prints a warning. (@dahrb)

ontometer-0.1.0/CITATION.cff

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+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+title: "OntoMeter: ontology quality assessment"
+abstract: >-
+  OntoMeter evaluates a single ontology against the OQuaRE quality model and
+  adds a language-model review of the quality dimensions that structural metrics
+  cannot cover. It also carries a corpus-scale research half that builds a
+  multi-registry ontology corpus and its dependency network.
+type: software
+authors:
+  - family-names: Belikov
+    given-names: Alexander
+    email: alexander@growgraph.dev
+  - family-names: Bareham
+    given-names: David
+    email: d.bareham@liverpool.ac.uk
+repository-code: "https://github.com/growgraph/OntoMeter"
+license: Apache-2.0
+version: 0.1.0
+keywords:
+  - ontology
+  - ontology evaluation
+  - OQuaRE
+  - knowledge graphs
+  - semantic web

ontometer-0.1.0/LICENSE

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ontometer-0.1.0/NOTICE

@@ -0,0 +1,15 @@
+OntoMeter — ontology quality assessment
+Copyright 2025-2026 Growgraph SAS
+
+Licensed under the Apache License, Version 2.0 (the "License"); you may not
+use this software except in compliance with the License. You may obtain a
+copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
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+
+This product implements metrics from the OQuaRE ontology quality framework
+(Duque-Ramos et al.), an independent work not affiliated with this project.