Galaxy tool and tool dependency utilities
Project description
Overview
The Galaxy tool utilities.
History
24.1.2 (2024-09-25)
Bug fixes
Handle all requests error in ApiBiotoolsMetadataSource._raw_get_metadata by @nsoranzo in #18510
xsd: allow change_format and actions also in statically defined collection elements, and break recursion by @bernt-matthias in #18605
Enhancements
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.
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
File details
Details for the file galaxy_tool_util-24.1.2.tar.gz.
File metadata
- Download URL: galaxy_tool_util-24.1.2.tar.gz
- Upload date:
- Size: 378.5 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/5.1.1 CPython/3.8.18
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 1b6b93727a83fb36e08f1e952f28ff8ea54c1b4ae51a08469f48ad12a3a5bb0c |
|
| MD5 | 2aec59e460fbb482651b4affa857a857 |
|
| BLAKE2b-256 | dac73ea0fd5c014e0f01e36db724443b7c23557c662b9f0a519927b2b3d2957b |
File details
Details for the file galaxy_tool_util-24.1.2-py3-none-any.whl.
File metadata
- Download URL: galaxy_tool_util-24.1.2-py3-none-any.whl
- Upload date:
- Size: 424.5 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/5.1.1 CPython/3.8.18
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 16cea48774e1a3f57ad683054de1d9047740147b6b424e9f6945b8a34dfcf131 |
|
| MD5 | 66b532dae3de8260351c23efead6ad09 |
|
| BLAKE2b-256 | 147bf58a11282771b73fe105bb8ec20f023cb433aebe1f7fbae76e4b3b09817e |
