Galaxy tool and tool dependency utilities
Project description
Overview
The Galaxy tool utilities.
History
24.1.1 (2024-07-02)
Bug fixes
Fix bug in galaxy.xsd by @kostrykin in #17752
Fix bug in assert_has_image_n_labels by @kostrykin in #17754
Remove linter for unstripped text content for tool xml leaves by @bernt-matthias in #18252
Enhancements
Add test and doc showing how dynamic selects are used by @bernt-matthias in #16885
Add content assertion XML tags for test output verification using images by @kostrykin in #17581
Set minimal metadata also for empty bed datasets by @wm75 in #17586
Automatically bind galaxy_data_manager_data_path in containers by @bernt-matthias in #17596
Type annotation and CWL-related improvements by @nsoranzo in #17630
Update Python dependencies by @galaxybot in #17653
Code cleanups from ruff and pyupgrade by @nsoranzo in #17654
Tool linter: check for valid bio.tools entries by @bernt-matthias in #17655
Tool linter: check for leaf nodes with unstripped text content by @bernt-matthias in #17656
Issue #17631: Make it possible to use custom invfile.lua if needed by @martin-g in #17693
Add support for floating point TIFF files in verification of image-based tool outputs by @kostrykin in #17797
Add tool linting for valid EDAM terms by @bernt-matthias in #17839
Add pin_labels attribute for image_diff comparison method by @kostrykin in #17866
Enable warn_unused_ignores mypy option by @nsoranzo in #17991
Document syntax for accessing nested parameters in change_format - when tags by @bernt-matthias in #18018
Update Python dependencies by @galaxybot in #18063
Enable flake8-implicit-str-concat ruff rules by @nsoranzo in #18067
24.0.3 (2024-06-28)
Bug fixes
Allow purge query param, deprecate purge body param by @mvdbeek in #18105
Make sure that all Linter subclasses are imported for listing them by @bernt-matthias in #18339
Assign default data extension on discovered collection output by @mvdbeek in #18389
Allow in_range validator for selects by @bernt-matthias in #18403
24.0.2 (2024-05-07)
Bug fixes
Tool linters: allow to skip by old linter names (by allowing to skip linter modules) by @bernt-matthias in #18091
tool linters: output filters should only consider child filter nodes by @bernt-matthias in #18096
24.0.1 (2024-05-02)
Bug fixes
24.0.0 (2024-04-02)
Bug fixes
xsd: reorder choices for permissive boolean by @bernt-matthias in #17187
Allow for upper case container tags by @bernt-matthias in #17254
Escape pipe character in tool XSD docs by @neoformit in #17359
XSD schema doc building: quote pipe characters in attribute tables by @bernt-matthias in #17364
Fix IUC best practices links, mention data_source_async in XSD by @wm75 in #17409
Fix data_source and data_source_async bugs by @wm75 in #17422
Add tool XML schema documention for outputs - collection - data by @bernt-matthias in #17465
has_size assertion: implement size (as synonym for value) by @bernt-matthias in #17490
Yaml nested assertions: fix parsing by @bernt-matthias in #17641
Enhancements
build_mulled: also use namespace for building singularity images by @bernt-matthias in #15657
Extend regex groups in stdio regex matches by @bernt-matthias in #17016
Split linters in separate classes by @bernt-matthias in #17081
Add select parameter with options from remote resources by @mvdbeek in #17087
Replace discouraged Mambaforge with Miniforge3 by @nsoranzo in #17177
Clarify the meaning of lexical sorting of discovered datasets by @bernt-matthias in #17190
Add element_identifier and ext to inputs config file export by @bernt-matthias in #17357
Fix type annotation of code using XML etree by @nsoranzo in #17367
Some additional typing for test interactor stuff. by @jmchilton in #17398
Allow using tool data bundles as inputs to reference data select parameters by @mvdbeek in #17435
data_column parameter: use column_names metadata if present by @bernt-matthias in #17478
Fixing data_source tools and incrementing tool profile by @wm75 in #17515
Add image_diff comparison method for test output verification using images by @kostrykin in #17556
add shm_size based on ShmSize by @richard-burhans in #17565
Record missing outputs as test errors by @bernt-matthias in #17874
Other changes
consistently compare profile versions by @bernt-matthias in #16492
23.2.1 (2024-02-21)
Bug fixes
Never consider _galaxy_ conda env as unused by @bernt-matthias in #16460
chore: fix typos by @afuetterer in #16851
Quote singularity env parameters by @bernt-matthias in #17055
Remove duplicates when copying sections for tool panel view by @bernt-matthias in #17117
Enhancements
Implement default locations for data and collection parameters. by @jmchilton in #14955
Add framework test for profile behavior of format=”input” by @bernt-matthias in #15482
Tool Shed 2.0 by @jmchilton in #15639
Add ability to assert metadata properties on input dataset parameters by @bernt-matthias in #15825
Migrate a part of the users API to Fast API by @heisner-tillman in #16341
Update Python dependencies by @galaxybot in #16436
Tweak tool memory use and optimize shared memory when using preload by @mvdbeek in #16536
Document that required text parameters need a validator by @bernt-matthias in #16538
Include regex when linting validators by @davelopez in #16684
Refactor Tool Panel views structures and combine ToolBox and ToolBoxWorkflow into one component by @ahmedhamidawan in #16739
Replace file_name property with get_file_name function by @SergeyYakubov in #16783
Updated path-based interactive tools with entry point path injection, support for ITs with relative links, shortened URLs, doc and config updates including Podman job_conf by @sveinugu in #16795
Remove remaining legacy backbone form input elements by @guerler in #16834
Change api/tool_panel to api/tool_panels/… by @ahmedhamidawan in #16928
optimize object store cache operations by @SergeyYakubov in #17025
Enhance xsd schema and allow simpler assertion lists by @mvdbeek in #17134
Other changes
Explicitly document default of multiple by @bernt-matthias in #16625
23.1.4 (2024-01-04)
Bug fixes
23.1.3 (2023-12-01)
No recorded changes since last release
23.1.2 (2023-11-29)
Bug fixes
Change log level for duplicate data table entries to warning by @mvdbeek in #16988
Upgrade minimum conda to be compatible with latest conda-build by @bernt-matthias in #17013
Fix duplicated tools in tool panel view section copying by @jmchilton in #17036
Enhancements
Adds biii as supported xref reference type by @kostrykin in #16952
23.1.1 (2023-10-23)
Bug fixes
Fixes for two framework test tools by @bernt-matthias in #15483
add missing f for f-string by @bernt-matthias in #15584
Fix call to docker_cached_container_description by @bernt-matthias in #15598
Fix log message by @bernt-matthias in #15838
add required_files to the tag list for linting by @bernt-matthias in #16129
Handle appending to a results file that does not exists. by @ksuderman in #16233
Improve container resolver documentation by @mvdbeek in #16280
Add missing singularity_no_mount prop parsing by @mvdbeek in #16367
Restore resolution of Conda environments generated from non-lowercase package names by @nsoranzo in #16474
Fix multiple remote test data by @davelopez in #16542
Don’t use docker run –user flag on OSX by @mvdbeek in #16573
xsd: allow name attribute of test collections by @bernt-matthias in #16663
Fix short ids in tool panel views. by @jmchilton in #16800
Fix tool panel views for versionless tool ids by @mvdbeek in #16809
Enhancements
Decompress history data for testing assertions by @bernt-matthias in #15085
OIDC tokens by @SergeyYakubov in #15300
Fix for new style conda packages by @bernt-matthias in #15446
Move database access code out of tool_util by @jdavcs in #15467
Protection against problematic boolean parameters. by @jmchilton in #15493
Implement initial tool/wf test assertions module for JSON data. by @jmchilton in #15494
Explore tool remote test data by @davelopez in #15510
xsd: add multiple to the list of attributes for all parameter types deriving from select by @bernt-matthias in #15534
Update Python dependencies by @galaxybot in #15564
Container resolvers: add docs, typing and tests by @bernt-matthias in #15614
Migrate to MyST-Parser for Markdown docs by @nsoranzo in #15844
Enable per-destination container_resolver_config_file by @bernt-matthias in #15884
Updated doc and tests for attribute value filter by @tuncK in #15929
Make container builders use mamba by @bernt-matthias in #15953
Code cleanups from ruff and pyupgrade by @nsoranzo in #16035
Vendorise packaging.versions.LegacyVersion by @nsoranzo in #16058
Small test decorator improvements. by @jmchilton in #16220
tool_util: switch to mambaforge on non-32bit; add arm64 support by @mr-c in #16223
Fix tool remote test data by @davelopez in #16311
Other changes
23.0.6 (2023-10-23)
Bug fixes
23.0.5 (2023-07-29)
Bug fixes
Allow duplicate labels in linter if outputs contain filters by @bernt-matthias in #15933
Fix parsing tool metadata from bio.tools by @kysrpex in #16449
Linter: fix regex for profile version by @bernt-matthias in #16480
Adjust test_data_download method in GalaxyInteractorApi so an admin user is not required by @simonbray in #16482
23.0.4 (2023-06-30)
No recorded changes since last release
23.0.3 (2023-06-26)
Bug fixes
xsd: add missing sep attribute for has_n_columns by @bernt-matthias in #16262
Missing init prevents models.py being bundled into tool_util by @nuwang in #16308
Enhancements
23.0.2 (2023-06-13)
Bug fixes
Don’t fail CWL tool parsing when Cheetah not installed by @mvdbeek in #16219
Allow skipping expect_num_outputs when expect_failure is set in tool test by @bernt-matthias in #16237
23.0.1 (2023-06-08)
Bug fixes
Enhancements
22.1.5 (2022-11-14)
Set test status to success on expected failure
22.1.4 (2022-10-28)
Add missing unittest_utils package to galaxy-tool-util
22.1.3 (2022-10-27)
Pin minimum pyopenssl version when installing Conda
Add --strict-channel-priority to conda create/install commands if using conda >=4.7.5
22.1.2 (2022-08-29)
Fix lint context error level
Pin galaxy-util to >= 22.1
Fix biocontainer resolution without beaker cache
22.1.1 (2022-08-22)
First release from the 22.01 branch of Galaxy
21.9.2 (2021-11-23)
Fix linting of multiple="true" select inputs.
21.9.1 (2021-11-03)
Fix tool linting.
21.9.0 (2021-11-03)
First release from the 21.09 branch of Galaxy.
21.1.2 (2021-06-23)
21.1.1 (2021-05-21)
21.1.0 (2021-03-19)
First release from the 21.01 branch of Galaxy.
20.9.1 (2020-10-28)
Bugfixes to work around & annotate expected tool test failures.
20.9.0 (2020-10-28)
First release from the 20.09 branch of Galaxy.
20.9.0.dev2 (2020-08-02)
First release from the 20.09 branch of Galaxy.
20.5.0 (2020-07-04)
First release from the 20.05 branch of Galaxy.
20.1.0 (2020-07-04)
First release from the 20.01 branch of Galaxy.
19.9.1 (2019-12-28)
Fix declared dependency problem with package.
19.9.0 (2019-12-16)
Initial import from dev branch of Galaxy during 19.09 development cycle.
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