Package Health Score

81 / 100

security
Security review needed
popularity
Recognized
maintenance
Healthy
community
Active

Popularity

Recognized

GitHub Stars: 1.42K
Forks: 1.01K
Contributors: 270

Direct Usage Popularity

Based on project statistics from the GitHub repository for the PyPI package galaxy-tool-util, we found that it has been starred 1,416 times.

Security

Security review needed

Security and license risk for latest version

Release Date: Dec 11, 2024
Direct Vulnerabilities: 0
C
0
H
0
M
0
L
Indirect Vulnerabilities: 0
C
0
H
0
M
0
L
License Risk: 1
H
3
M
0
L

All security vulnerabilities belong to production dependencies of direct and indirect packages.

License

AFL-3.0

Security Policy

Yes

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Maintenance

Healthy

Commit Frequency

Open Issues: 2.11K
Open PR: 246
Last Release: 10 days ago
Last Commit: 25 days ago

Further analysis of the maintenance status of galaxy-tool-util based on released PyPI versions cadence, the repository activity, and other data points determined that its maintenance is Healthy.

We found that galaxy-tool-util demonstrates a positive version release cadence with at least one new version released in the past 3 months.

As a healthy sign for on-going project maintenance, we found that the GitHub repository had at least 1 pull request or issue interacted with by the community.

Community

Active

Readme: Yes
Contributing.md: Yes
Code of Conduct: Yes
Contributors: 270
Funding: No

A good and healthy external contribution signal for galaxy-tool-util project, which invites more than one hundred open source maintainers to collaborate on the repository.

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Package

Python Versions Compatibility: >=3.7

Age: 6 years
Latest Release: 10 days ago
Dependencies: 7 Direct / 29 Total
Versions: 66
Maintainers: 0
Wheels: OS Independent

Readme

Overview

The Galaxy tool utilities.

Code:

History

24.1.4 (2024-12-11)

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
Remove defaults channel for conda usage by @bernt-matthias in #18859
Don't check availability of shellescape by @nsoranzo in #18954
Backport 2 CI fixes by @nsoranzo in #18973
Disable locking when opening h5 files, add missing with by @mvdbeek in #18976
Fix extra call to test_data_path that requires an admin key by @jmchilton in #19011
flip default value for use_mamba to false by @bgruening in #19295
Linter: allow dynamic option definition by from_url by @bernt-matthias in #19300

Enhancements

Make default_panel_view a _by_host option by @natefoo in #18471

24.1.3 (2024-10-25)

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
Remove defaults channel for conda usage by @bernt-matthias in #18859
Don't check availability of shellescape by @nsoranzo in #18954
Backport 2 CI fixes by @nsoranzo in #18973
Disable locking when opening h5 files, add missing with by @mvdbeek in #18976
Fix extra call to test_data_path that requires an admin key by @jmchilton in #19011

Enhancements

Make default_panel_view a _by_host option by @natefoo in #18471

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

Make default_panel_view a _by_host option by @natefoo in #18471

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 improvements by @nsoranzo in #17601
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
SQLAlchemy 2.0 by @jdavcs in #17778
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
Add galaxy to user agent by @mvdbeek in #18003
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

Fix conditional Image imports by @mvdbeek in #17899

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
Fixes for flake8-bugbear 24.1.17 by @nsoranzo in #17340
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
Python 3.8 as minimum by @mr-c in #16954
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
Migrate models to pydantic 2 by @mvdbeek in #17262
Add element_identifier and ext to inputs config file export by @bernt-matthias in #17357
Enable warn_unreachable mypy option by @mvdbeek in #17365
Fix type annotation of code using XML etree by @nsoranzo in #17367
Update to black 2024 stable style by @nsoranzo in #17391
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
Ruff and flake8 fixes by @nsoranzo in #16884
Quote singularity env parameters by @bernt-matthias in #17055
Remove duplicates when copying sections for tool panel view by @bernt-matthias in #17117
Display application fixes and tests by @mvdbeek in #17233

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

Merge 23.1 into dev by @mvdbeek in #16534
Explicitly document default of multiple by @bernt-matthias in #16625

23.1.4 (2024-01-04)

Bug fixes

Separate collection and non-collection data element by @mvdbeek in #17236

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 up unit tests for local use by @mvdbeek in #16483
Fix multiple remote test data by @davelopez in #16542
Don't use docker run --user flag on OSX by @mvdbeek in #16573
Backport tool mem fixes by @mvdbeek in #16601
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
Merge Target class with CondaTarget by @nsoranzo in #16181
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

Restore tmp mounting by @mvdbeek in #16533

23.0.6 (2023-10-23)

Bug fixes

Fixes for extra files handling and cached object stores by @mvdbeek in #16595
Fix create/install commands for conda 23.9.0 by @nsoranzo in #16831

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

When importing tool data bundles, use the first loc file for the matching table by @natefoo in #16247

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

Fix assertion linting to not fail on byte suffixes by @bernt-matthias in #15873
Fix get_test_from_anaconda() and base_image_for_targets() functions by @nsoranzo in #16125
Fix test search for mulled container hashes by @mvdbeek in #16170

Enhancements

Allow setting auto_decompress property in staging interface by @mvdbeek in #16014

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.

galaxy-tool-util dependencies

conda-package-streaming markupsafe packaging pyyaml requests sortedcontainers typing-extensions

FAQs

What is galaxy-tool-util?

Galaxy tool and tool dependency utilities. Visit Snyk Advisor to see a full health score report for galaxy-tool-util, including popularity, security, maintenance & community analysis.

Is galaxy-tool-util popular?

The python package galaxy-tool-util receives a total of 6,881 weekly downloads. As such, galaxy-tool-util popularity was classified as a recognized. Visit the popularity section on Snyk Advisor to see the full health analysis.

Is galaxy-tool-util well maintained?

We found that galaxy-tool-util demonstrated a healthy version release cadence and project activity. It has a community of 270 open source contributors collaborating on the project. See the full package health analysis to learn more about the package maintenance status.

Is galaxy-tool-util safe to use?

While scanning the latest version of galaxy-tool-util, we found that a security review is needed. A total of 0 vulnerabilities or license issues were detected. See the full security scan results.

Last updated on 19 December-2024, at 22:50 (UTC).

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