Various YAML Tool Hardening and Progress toward Tool State Goals#21828

Merged

mvdbeek merged 45 commits intogalaxyproject:devfrom

jmchilton:yaml_tool_harden_1

Feb 13, 2026

Commits on Feb 12, 2026

Another pass at fixing redundant work during tool loading.

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claude
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Test serialization roundtrip (discovered bugs in YAML parsing).
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Modeling and validation of YAML tool test cases.
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fix: don't let yaml tool source parsing change yaml tool source serialization
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Refactor path for loading user defined tools for consistency.
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Small tweaks to tool loading in celery task for downstream.
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[WIP] track abstract inputs type in tool source interface.
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Migration for job.tool_state.
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Persist validated job tool state.
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Add a function tests for multiple selects from user tools.
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Does this change make sense in light of select handling changes that seem to be working?
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Failing gx_boolean_user.yml tool to develop against.
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claude infrastructure for managing test tools.
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Do not allow the legacy tool submission with user tools from tests.
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YAML test for collection WIP.
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Allow YAML-based tools to produce output collections.
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YAML tools specify a minimum profile of 24.2 so test requests load.
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WIP: allow collection inputs to YAML tools.
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Improved error handling for tool tests when requests are unavailable.
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Linting fixes...
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Implement collection input runtimeify for YAML tools.

jmchilton
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claude
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Remove dead collection runtime models.

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Wire job_runtime validation into parameter specification tests.

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Typed Models for collection_to_runtime
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Add explicit job_runtime specs for scalar parameter types.

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Harmonize py_type_internal_json with runtime validation.

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Add cross-type discrimination tests for collection runtime.

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Harden collection runtime models with discriminated unions.

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Dynamic model factory for recursive collection type validation.

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Polish dynamic model factory: fix return types, consolidate routing.

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Add 8 collection type functional tool definitions.

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Comma-separated collection type specs, deeper E2E tests.

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Linting fixes: unused imports, deprecated typing, loop variable.

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Fix linter test for YAML tool minimum profile 24.2.

jmchilton
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Fix linting.
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Fix mypy errors in evaluation, runtime, and test_runtime.

jmchilton
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claude
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Fix mypy errors in parameters, yaml parser, interactor, runtime.

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Normalize YAML tool naming scheme in test tools.

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Add any-collection-type YAML tool with comprehensive job_runtime specs.

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Move galaxy.model-dependent runtime tests to test/unit/app/tools/.

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Fix Python 3.8 compat: use List[] instead of list[] in tool_util.

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Make adapt_collection a required param of runtimeify().

jmchilton
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Fail fast on unknown collection_type instead of silent fallbacks.

jmchilton
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claude
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Commits on Feb 13, 2026