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Recent Releases of boutiques

boutiques - 0.5.30

What's Changed

  • Update --container-opts by @ngeorges-cnrs in https://github.com/boutiques/boutiques/pull/710

New Contributors

  • @ngeorges-cnrs made their first contribution in https://github.com/boutiques/boutiques/pull/710

Full Changelog: https://github.com/boutiques/boutiques/compare/0.5.29...0.5.30

What's Changed

  • Update --container-opts by @ngeorges-cnrs in https://github.com/boutiques/boutiques/pull/710
  • bump version for release by @mathdugre in https://github.com/boutiques/boutiques/pull/711

New Contributors

  • @ngeorges-cnrs made their first contribution in https://github.com/boutiques/boutiques/pull/710

Full Changelog: https://github.com/boutiques/boutiques/compare/0.5.29...0.5.30

- Python
Published by mathdugre 10 months ago

boutiques - Release 0.5.29

What's Changed

  • [ADD] alias execute to bosh exec. [FIX] invalid documentation. by @mathdugre in https://github.com/boutiques/boutiques/pull/672
  • [BUG] error message when no output-files exist in descriptor. by @mathdugre in https://github.com/boutiques/boutiques/pull/673
  • [MAINT] XFAIL Nexus token validation, sandbox server is down. by @mathdugre in https://github.com/boutiques/boutiques/pull/704
  • [ENH] Allow overwrite of the container options from command line. by @mathdugre in https://github.com/boutiques/boutiques/pull/705
  • [BUG] fix upload command by @mathdugre in https://github.com/boutiques/boutiques/pull/708

Full Changelog: https://github.com/boutiques/boutiques/compare/0.5.28...0.5.29

- Python
Published by mathdugre 11 months ago

boutiques - Release 0.5.28

New features

  • Package refactoring
  • Tests now use GitHub actions
  • Dropped Python 3.8 and added Python 3.13

Bug fixes

  • Fixed Zenodo descriptor update (#681)

- Python
Published by glatard over 1 year ago

boutiques - Release 0.5.27

New features

  • Added command-line option to display latest provenance file (#662)

Bug fixes

  • Fixed Zenodo authentication header (#660)
  • Fixed encoding issue in setup.py (#665)

- Python
Published by glatard over 1 year ago

boutiques - Release 0.5.26

New features

  • Unless disabled, bosh exec launch now mounts all the files in the invocation (#613)
  • bosh import now support configuration files (#611)
  • default install is now minimal install (#645)

Bug fixes

610, #617 #629 #630 #644 #655 #658 + various spelling mistakes

Code refactoring

621 #623 #627 #632 #633

- Python
Published by glatard over 2 years ago

boutiques - Release 0.5.25

  • New features
    • search now returns upload dates (#604)
    • Container image names can now contain an index (#588)
    • Improved documentation (#599)
    • create can now generate parameter names using CamelCase (#503)
  • Bug fixes: #577, #605, #463

- Python
Published by glatard almost 6 years ago

boutiques - Release 0.5.24

  • New command, bosh deprecate, deprecates a published tool. The tool will still be published and usable, but it won't show in search results (#593).
  • Environment variables can now be parametrized by input values (#587)
  • No-container (baremetal) executions are now supported in bosh exec launch (#582)
  • Partial Windows support (#561)
  • Tests now use Singularity v3.4 (#573)
  • Dropped support for Python < 3.5 (#581)
  • Improvements in descriptor caching (#589)
  • Improvements in descriptor formatting (#586)
  • Bug fixes: #547, #590, #591, #594, #595

- Python
Published by glatard about 6 years ago

boutiques - Release 0.5.23

  • Support for conditional outputs (#303)
  • Sphinx documentation (#280)
  • Bug fixes: #518, #559, #562

- Python
Published by glatard over 6 years ago

boutiques - Release 0.5.22

  • Schema now supports group ids in requires-inpust #524
  • Bug fixes: #548 #516 #522 #553

- Python
Published by glatard over 6 years ago

boutiques - Release 0.5.21

  • New features

    • Extended provenance publication, including support for Nexus (#521)
    • Descriptor creation from docopt (#392)

  • Bug fixes

    • #542, #535, #529, #523, #510, #509, #504, #491, #418

- Python
Published by glatard over 6 years ago

boutiques - Release 0.5.20

  • New features:
    • bosh can now track and publish anonymized executions #344
    • Python functions can now be generated from descriptors #390
    • Added issue and PR templates #479
    • Schema now supports value-only tags #385
  • Other enhancements: #298 #373 #435 #450
  • Bug fixes: #386 #423 #442 #449 #452 #453 #454 #456 #457 #458 #477 #481 #483

- Python
Published by glatard almost 7 years ago

boutiques - Release 0.5.19

  • Improved search (now uses wildcard in Zenodo API).
  • New options in publish to explicitly create a new version.
  • Bug fixes in prepare.
  • New getting started guide for developers.
  • New schema property: online-platforms.
  • Updates in the handling of default values: missing optional inputs are now substituted with their default values.
  • Various Bug fixes and code improvements.

- Python
Published by glatard about 7 years ago

boutiques - Release 0.5.18

  • Added keywords to Zenodo metadata
  • Improvements in search output display
  • All commands will now use cached descriptors if available
  • New command: bosh example
  • Zenodo tests are now mocked
  • Bug fixes

- Python
Published by glatard about 7 years ago

boutiques - Release 0.5.17

  • New command: pprint
  • Fixes in prepare (lockfile replaced by lockdir)
  • Fixes in BIDS importer
  • List separator can now be customized
  • Printed messages now use logger uniformly

- Python
Published by glatard over 7 years ago

boutiques - Release 0.5.16

  • New command: bosh prepare
  • Minor improvements and bug fixes in bosh search
  • Updates in tests

- Python
Published by glatard over 7 years ago

boutiques - Release 0.5.15

  • New commands: bosh search, bosh pull.
  • Commands, e.g. bosh exec launch and bosh validate, can now run directly from Zenodo ids return by bosh search.
  • Descriptor versions can now appear under the same tool in Zenodo (#299).
  • Inputs can now belong to multiple groups, with conditions (#304).
  • Invocations can now be created from argparse parsers.
  • Bug fixes.

- Python
Published by glatard over 7 years ago

boutiques - Release 0.5.14

  • Containers can now have runtime properties #281.
  • Execution now supports JSON objects passed on the CLI instead of just files #277.
  • Dropped support for Python 2.6.
  • stdout/stderr can now be printed on the fly during execution #263.
  • Schema can now have a descriptor-url.
  • Bug fix in simulator, creator, publisher, and argparse parser.

- Python
Published by glatard over 7 years ago

boutiques - Release 0.5.13

  • bosh import now supports CWL
  • Docker support now uses -u flag instead of adding a user to container image
  • Improved error messages and tests for Singularity
  • Bug fixes

- Python
Published by glatard over 7 years ago

boutiques - Release 0.5.12

Bug fixes!

- Python
Published by glatard almost 8 years ago

boutiques - Release 0.5.10

  • Improved tests, in particular for Singularity.
  • Updated bosh exec to return an object instead of a tuple.
  • Improved console output of bosh exec.
  • Added support for custom shells in containers.
  • Added special char escapes in command line.
  • Updates in CARMIN exporter.
  • Bug fixes

- Python
Published by glatard almost 8 years ago

boutiques - Release 0.5.8

  • bosh publish now uses Zenodo
  • Linted the code entirely
  • Added support for Python 2.6
  • Raised test coverage above 90%
  • Bug fixes

- Python
Published by glatard almost 8 years ago

boutiques - Release 0.5.7

  • New command: bosh test.
  • Fixes in Singularity support.

- Python
Published by glatard about 8 years ago

boutiques - Release 0.5.6

  • Fixed package imports within MANIFESET.in
  • Added exporter functionality * Takes Boutiques descriptor and write it out in alternative format. Formats currently supported ['carmin']
  • Made validation/invocation schema validation less verbose by default
  • Fixed parsing of stdout from bosh exec run
  • Fixed bug with lists of numbers

- Python
Published by glatard about 8 years ago

boutiques - Release 0.5.5

Schema

  • Added tool tags (list of key-value pairs).
  • Added error codes and messages associated with the tool.

Tools

  • New command: bosh evaluate: Evaluates parameter values for a descriptor and invocation.
  • Documentation updates.
  • stderr is now accessible in the API when execution fails.
  • Bug fixes.

- Python
Published by glatard about 8 years ago

boutiques - Release 0.5.4

  • New, consistent Python and CLI APIs
  • Updated documentation
  • Added contributors guide
  • Tested Singularity
  • Various bug fixes

- Python
Published by glatard over 8 years ago

boutiques - Release 0.5.3

  • Created bosh-publish to publish Boutiques descriptors to Neurolinks
  • bosh now supports JSON invocations that comply to the tool invocation schema.
  • bosh can now mount any directory to the container with -v.
  • Increased test coverage to > 80%.
  • Bug fixes

- Python
Published by glatard over 8 years ago

boutiques - Release 0.5.2.1

  • Adding importer for 0.4 and 0.4.5 schema versions to 0.5

- Python
Published by gkiar over 8 years ago

boutiques - Release 0.5.1

Bug fixes, see notes in Release 0.5 for relevant information.

- Python
Published by glatard over 8 years ago

boutiques - Release 0.5

Use with care: non-backward compatible updates are likely to occur until release 1.0.

Schema

Modifications

The following modifications break backward compatibility with version 0.4: - Singularity containers are now declared the same way as Docker images. - Moved walltime-estimate to suggested-requirements.

Additions

  • Added entry points for containers.
  • Added new suggested-requirements section.
  • New group property: all-or-none.

See detailed documentation in README.md.

Tools

  • All tools are now on pip (pip install boutiques).
  • Added new tool to import BIDS apps (bosh-import).
  • Introduced tests for all tools.
  • Validator was ported to Python.
  • ... and fixed plenty of bugs!

- Python
Published by glatard over 8 years ago

boutiques - Release 0.4

Use with care: non-backward compatible updates are likely to occur until release 1.0.

Schema

See detailed documentation in README.md.

Modifications

The following modifications break backward compatibility with version 0.3: - Input property command-line-key was renamed to value-key. - Output file property command-line-key was renamed to value-key. - Type Enum was removed. Instead, the other types must be used in conjunction with property value-choices. - enum-value-choices was renamed to value-choices. - Custom properties must now be corralled in property custom. Additional properties are now forbidden. - docker-image and docker-index were removed. Information about containers is now corralled in object container-image.

Additions

  • Container support was extended:
    • Singularity and rootfs are now supported.
    • Properties working-directory and container-hash were added.
  • Configuration files are now supported (file-template).
  • An invocation schema may now be specified to validate input values (invocation-schema).
  • Environment variables can now be defined (environment-variables).
  • It can now be specified that absolute path files have to be used on the command line (uses-absolute-path).
  • Output files now have a command-line-flag-separator.

Tools

  • Validator and local executor support schema additions.
  • Added invocation schema handler

- Python
Published by glatard over 9 years ago

boutiques - Release 0.3

Schema

See detailed documentation in README.md.

Modifications

The following modifications break backward compatibility with version 0.2: - Input properties required-inputs and disabled-by-inputs where renamed requires-inputs and disables-inputs. Meaning has changed accordingly. - tool-version is now a required property.

Additions

  • New tool properties: walltime-estimate, groups.
  • New input properties: command-line-flag-separator, enum-value-choices, integer, minimum, maximum, exclusive-minimum, exclusive-maximum, min-list-entries, max-list-entries.
  • New input type: Enum.
  • Added anyOf properties and dependencies to improve validation.
  • Allowed for additional (platform-specific) properties.

Tools

  • Improved validator.
  • Added local executor.

- Python
Published by glatard over 9 years ago