FUZZ-7412: Updates nf-fuzzball for Fuzzball 4 compatibility

[wresch]

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[ciq-it-service-account]

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[Copilot]

Pull request overview

Updates the Nextflow nf-fuzzball plugin and the nf-fuzzball-submit helper to be compatible with Fuzzball 4 by switching to the v4 SDK/models, emitting version: v4 workflow definitions, and adopting v4’s path-keyed mount + v4 volume semantics.

Changes:

• Migrate Groovy plugin code to Fuzzball v4 models and submit version: v4 workflow definitions.
• Replace storage-class-based ephemeral filtering with v4 “persistent iff use: persistent or explicit name” filtering; filter mounts by referenced persistent volume.
• Update nf-fuzzball-submit to require a named persistent --data-volume, translate volume:// references into v4 volume blocks, and add/adjust tests + docs.

Reviewed changes

Copilot reviewed 19 out of 21 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
src/test/groovy/com/ciq/fuzzball/FuzzballExecutorSpec.groovy	Adds unit tests for v4 persistent volume + mount filtering.
src/main/groovy/com/ciq/fuzzball/FuzzballWorkflowDefinitionJobFactory.groovy	Switches job factory imports to v4 SDK model types.
src/main/groovy/com/ciq/fuzzball/FuzzballTaskHandler.groovy	Submits version: v4 per-task workflow definitions using v4 models.
src/main/groovy/com/ciq/fuzzball/FuzzballPluginConfig.groovy	Updates config schema types to v4 volume model.
src/main/groovy/com/ciq/fuzzball/FuzzballExecutor.groovy	Implements v4 persistent volume filtering and path-keyed mount filtering; removes v3 storage-class API usage.
README.md	Updates example invocation to include required --data-volume.
nf-fuzzball-submit/tests/test_workflow_definition.py	Adds coverage for v4 mounts, v4 volumes, and volume_from_reference.
nf-fuzzball-submit/tests/test_client_integration.py	Adds test that rejects pre-v4 servers.
nf-fuzzball-submit/tests/test_cli.py	Updates CLI tests for required --data-volume and new validation behavior.
nf-fuzzball-submit/tests/conftest.py	Updates default test args to include a named persistent data volume.
nf-fuzzball-submit/src/nf_fuzzball_submit/client.py	Enforces Fuzzball v4 minimum, adds volume_from_reference, updates mounts/definition version to v4.
nf-fuzzball-submit/src/nf_fuzzball_submit/cli.py	Makes --data-volume required and validates it must be named + non-ephemeral.
nf-fuzzball-submit/README.md	Updates usage examples and options table for v4 + required --data-volume.
nf-fuzzball-submit/pyproject.toml	Bumps nf-fuzzball-submit version to 0.4.0.
Makefile	Updates default OpenAPI schema URL to /v4/schema and threads spec properties through make test.
code-generation/groovy-okhttp-sync/modelClass.mustache	Adds @JsonIgnoreProperties(ignoreUnknown = true) to generated models.
code-generation/groovy-okhttp-sync/model.mustache	Adds required Jackson import for @JsonIgnoreProperties.
code-generation/generate	Updates default OpenAPI schema URL to /v4/schema.
CHANGELOG.md	Adds 0.4.0 unreleased notes describing v4 support and breaking CLI change.
build.gradle	Bumps plugin version to 0.4.0.

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