John ChiltonandClaude Opus 4.6 74fefc89d8 Add structured YAML then expressions with bug fix and polish ...

Convert 32 free-form then string expressions in collection_semantics.yml
to structured typed YAML with 14 Pydantic models and as_latex() methods.

Bug fix: NestedElements.elements typed as dict[str, "OutputBinding"]
with model_rebuild() to resolve forward ref (was dict[str, Any]).

Polish: discriminated unions via Annotated[..., Field(discriminator="type")]
on all 4 union type aliases, rename elements_to_latex to
_assumption_elements_to_latex.

61 tests (was 40): smoke tests for all as_latex() and generate_docs(),
unit tests for EllipsisMarker, DatasetListInput, NestedElements,
CollectionOutput with ellipsis, compound sub_collection_type,
MapOverThen producing DatasetOutput.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

2026-03-17 15:15:27 -04:00

..

api_guidelines.rst

Apply suggestions from code review

2021-01-13 18:19:29 -05:00

build_a_job_runner.rst

Update doc/source/dev/build_a_job_runner.rst

2023-09-25 16:41:24 -04:00

collection_semantics.md

Add structured YAML then expressions with bug fix and polish

2026-03-17 15:15:27 -04:00

create_release.rst

Update doc/source/dev/create_release.rst

2024-06-28 11:42:01 +02:00

data_managers_schematic_overview.png

Add remove operation to data managers and document data managers in regular Galaxy docs.

2019-06-28 20:02:37 +02:00

data_managers.rst

deprecate data manager version

2021-07-14 15:24:38 +02:00

data_source.rst

add doc for data source

2024-01-18 18:36:14 +01:00

data_types.md

Apply suggestions from code review

2025-08-13 14:43:31 -04:00

database_session_management.md

Fix typo

2024-01-18 16:31:26 +01:00

debugging_galaxy_slurm.md

Doc fixes

2022-08-15 19:15:02 +01:00

debugging_galaxy.md

Migrate to MyST-Parser for Markdown docs

2023-03-27 15:01:27 +01:00

debugging_tests.md

Update docs on debugging tests within GitHub actions

2025-08-27 16:33:43 +01:00

faq.rst

Update descriptions to indicate these are UI-options only

2025-03-07 11:11:00 -05:00

finding_and_improving_slow_code.rst

Fix documentation more, spread data managers documentation over multiple lines so it's easier to read when editing.

2019-08-24 11:56:47 +02:00

image.Makefile

Input parameter schema.

2024-07-15 09:46:13 -04:00

index.rst

Implement paired_or_unpaired collections, list wizards.

2025-05-09 17:39:38 -04:00

inherit.png

Add and use local images for build runner doc

2016-10-24 19:40:42 +01:00

interactive_environments.rst

Doc fixes

2022-08-15 19:15:02 +01:00

plantuml_options.txt

Input parameter schema.

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plantuml_style.txt

Input parameter schema.

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queue_b.png

Add and use local images for build runner doc

2016-10-24 19:40:42 +01:00

queue.png

Add and use local images for build runner doc

2016-10-24 19:40:42 +01:00

run_tests_help.txt

Clean up stale yarn references after pnpm migration

2026-02-08 12:27:02 -05:00

runner_diag.png

Add and use local images for build runner doc

2016-10-24 19:40:42 +01:00

select_python_interpreter.png

Add a note to get Python extension and set interpreter

2021-07-06 14:07:05 +02:00

tests.png

Added doc pages for debugging tests and Galaxy.

2020-04-24 16:27:43 -04:00

tool_state_api.plantuml.svg

Update tool state docs for relaxed requests.

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tool_state_api.plantuml.txt

Update tool state docs for relaxed requests.

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tool_state_state_classes.plantuml.svg

Update tool state docs for relaxed requests.

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tool_state_state_classes.plantuml.txt

Update tool state docs for relaxed requests.

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tool_state_task.plantuml.svg

Tool Request models.

2024-09-30 13:25:02 -04:00

tool_state_task.plantuml.txt

Tool Request models.

2024-09-30 13:25:02 -04:00

translating.rst

Doc fixes

2022-08-15 19:15:02 +01:00

writing_tests.md

Add docs section on using base64 URLs to avoid external test dependencies

2026-03-07 16:26:19 -05:00