Updates from upstream repository.

[douglowe]

This is a merge in of developments made upstream. Copilot summary below.

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This pull request introduces several new features and improvements, primarily focused on enhancing HTTP cache configurability, improving JSON-LD context retrieval and validation, and updating dependencies and metadata. The most significant changes include new command-line options for HTTP cache control, more robust handling of JSON-LD contexts (including alternate links), and various codebase and workflow updates.

HTTP Cache Configuration Enhancements:

• Added new command-line options (--cache-max-age, --cache-path, --no-cache) to the validate CLI command, allowing users to control HTTP cache behavior for remote resource fetching. These options are wired through to the validation settings and used to initialize the cache. [1] [2] [3] [4]
• Updated the default HTTP cache max age to 300 seconds and improved how cache settings are handled and logged throughout the codebase. [1] [2]

JSON-LD Context Retrieval & Validation:

• Refactored JSON-LD context retrieval in FileDescriptorJsonLdFormat to handle alternate links via HTTP Link headers, ensure correct content types, and robustly resolve relative URLs when necessary. This improves compatibility with various JSON-LD context hosting setups. [1] [2]
• Enhanced the logic for checking unexpected keys in JSON-LD entities, properly handling reserved keywords and compact IRIs, and improved debug logging for these checks.
• Fixed minor issues and improved error messages in JSON-LD key compaction checks.

Dependency and Workflow Updates:

• Updated GitHub Actions to use the latest versions of actions/checkout and actions/setup-python for improved reliability and security. [1] [2] [3]
• Bumped the project version to 0.9.0 in pyproject.toml.

Validation and Model Improvements:

• Improved logging and error handling in the validation models and context, including better reporting of unmatched profiles and more robust statistics output. [1] [2] [3]

RO-Crate Profile Updates:

• Added a new SHACL constraint to the RO-Crate profile to ensure the existence of a metadata file descriptor entity, strengthening conformance checks.

[Copilot]

Pull request overview

Syncs in upstream updates focused on improving SHACL validation robustness (especially for SPARQL constraints), expanding RO-Crate test coverage/data, and adding configurable HTTP caching for remote context retrieval.

Changes:

• Add HTTP caching configuration (CLI + settings) and improve remote JSON-LD @context retrieval logic (content-type handling + Link rel=alternate fallback).
• Improve SHACL validation handling for violations where sourceShape is a BNode (e.g., SPARQL constraints) and align ontology parsing publicID using JSON-LD @base.
• Add/extend unit + integration tests and new test profiles/crates (including @base use and cyclic/unlinked datasets).

Reviewed changes

Copilot reviewed 29 out of 32 changed files in this pull request and generated 7 comments.

Show a summary per file

File	Description
tests/unit/test_remote_context_retrieval.py	New unit tests for remote context retrieval logic.
tests/unit/requirements/test_shacl_checks.py	New unit tests covering SHACL check description fallbacks + parent-shape resolution.
tests/ro_crates.py	Adds new test crate path helpers.
tests/integration/test_sparql_constraints.py	New integration coverage for SPARQL constraint violations and BNode sourceShape.
tests/integration/profiles/test_metadata_only.py	Excludes the new @base crate from generic metadata-only test set.
tests/integration/profiles/ro-crate/test_valid_ro-crate.py	Adds integration test for a valid crate with @base set (with skip).
tests/integration/profiles/ro-crate/test_data_entity_metadata.py	Adds integration test for datasets not linked to the root.
tests/data/profiles/sparql_test/profile.ttl	Adds a dedicated test profile for SPARQL constraint handling.
tests/data/profiles/sparql_test/must/agent_project_intersection.ttl	Adds a shape with an always-failing SPARQL constraint to trigger violations.
tests/data/crates/valid/rocrate-with-custom-terms/ro-crate-metadata.json	Extends custom-terms crate with rdfs prefix usage.
tests/data/crates/valid/rocrate-with-at-base-set/ro-crate-metadata.json	Adds a large “valid” crate using JSON-LD @base.
tests/data/crates/valid/rocrate-with-at-base-set/index.html	Adds accompanying file for the @base crate.
tests/data/crates/valid/rocrate-with-at-base-set/example1/.gitkeep	Keeps an empty example directory tracked.
tests/data/crates/invalid/4_data_entity_metadata/cyclic_datasets/ro-crate-metadata.json	Adds an invalid crate with cyclic/unlinked datasets for negative testing.
rocrate_validator/utils/rdf.py	Adds helper to extract JSON-LD @base from metadata.
rocrate_validator/utils/io_helpers/output/text/formatters.py	Adjusts Rich padding for text output formatting.
rocrate_validator/utils/http.py	Enhances HttpRequester singleton with cache configuration and cleanup.
rocrate_validator/requirements/shacl/validator.py	Uses @base as ontology parse publicID when available.
rocrate_validator/requirements/shacl/utils.py	Adds resolve_parent_shape helper to map BNode constraint nodes to owning shapes.
rocrate_validator/requirements/shacl/models.py	Removes debug serialization side-effect when processing groups.
rocrate_validator/requirements/shacl/checks.py	Handles SHACL violations with BNode sourceShape via resolve_parent_shape; improves description fallback.
rocrate_validator/profiles/ro-crate/ontology.ttl	Adds ROCrateMetadataFileDescriptor class and an individual for ro-crate-metadata.json.
rocrate_validator/profiles/ro-crate/must/4_data_entity_metadata.ttl	Updates “linked to root” constraint to allow indirect linking via path expressions.
rocrate_validator/profiles/ro-crate/must/1_file-descriptor_metadata.ttl	Adds SPARQL-based existence check + adjusts descriptor identification and targeting.
rocrate_validator/profiles/ro-crate/must/0_file_descriptor_format.py	Improves remote context retrieval and compaction key checking (compact IRI prefixes).
rocrate_validator/models.py	Adds cache settings to ValidationSettings and initializes HttpRequester cache.
rocrate_validator/constants.py	Renames/adjusts default HTTP cache setting constant.
rocrate_validator/cli/commands/validate.py	Adds CLI options for cache configuration and wires them into ValidationSettings.
pyproject.toml	Bumps package version to 0.9.0.
.github/workflows/testing.yaml	Updates GitHub Actions versions for checkout/setup-python.
.github/workflows/release.yaml	Updates GitHub Actions versions for checkout/setup-python in release pipeline.

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