Planemo

Latest version: v0.75.26

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0.41.0

---------------------

* Fix ``shed_update`` not fail if there is nothing to update
(thanks to `nsoranzo`_). `Issue 494`_, `Pull Request 680`_
* Conda documentation and option naming improvements.
`Pull Request 683`_
* Implement ``container_register`` for tool repositories.
`Pull Request 675`_
* Fix ``hub`` binary installation for Mac OS X.
`Pull Request 682`_

---------------------

0.40.1

---------------------

* Fix data manager configuration to not conflict with original Galaxy at
``galaxy_root`` (thanks to `nsoranzo`_). `Pull Request 662`_
* Fix ``filter_paths()`` to not partial match paths when filtering shed repositories
(thanks to `nsoranzo`_). `Pull Request 665`_
* Fix description when creating ``.shed.yml`` files (thanks to `RJMW`_).
`Pull Request 664`_

---------------------

0.40.0

---------------------

* Implement instructions and project template for GA4GH Tool Execution
Challenge Phase 1. 84c4a73_
* Eliminate Conda hack forcing ``/tmp`` as temp directory. b4ae44d_
* Run dependency script tests in isolated directories. 32f41c9_
* Fix OS X bug in ``planemo run`` by reworking it to wait using urllib instead of sockets.
3129216_

---------------------

0.39.0

---------------------

* Implement documentation and examples for Conda-based dependency development (under
"Advanced" topics).
`Pull Request 642`_, `Pull Request 643`_
* Implement documentation and examples for container-based dependency development (under
"Advanced" topics).
0a1abfe_
* Implement a ``planemo conda_search`` command for searching best practice channels
from the command line.
`Pull Request 642`_
* Allow Planemo to work with locally built Conda packages using the ``--conda_use_local``
command.
`Pull Request 643`_, `Issue 620`_
* Implement an ``open`` (or just ``o``) command to quickly open the last test results
(or any file if supplied). `Pull Request 641`_
* Linting improvements and fixes due to `galaxy-lib`_ update.
* WARN on test output names not found or not matching.
* INFO correct information about stdio if profile version is found.
* WARN if profile version is incorrect.
* INFO profile version
* Fix ``assert_command`` not detected as a valid test (fixes `Issue 260`_).
* Have ``lint --conda_requirements`` check that at least one actual requirement is found.
6638caa_
* Allow ``conda_install`` to work with packages as well as just tools.
8faf661_
* Add ``--global`` option to conda_install to install requirements into global Conda setup
instead of using an environment.
8faf661_
* Implement ``planemo lint --biocontainer`` that checks that a tool has an available BioContainer
registered.
0a1abfe_
* Add more options and more documentation to the ``planemo mull`` command.
0a1abfe_
* Hack around a bug in Conda 4.2 that makes it so ``planemo mull`` doesn't work out of the box on
Mac OS X.
0a1abfe_
* Allow URIs to be used instead of paths for a couple operations. ce0dc4e_
* Implement non-strict CWL parsing option. 4c0f100_
* Fixes for changes to cwltool_ and general CWL-relate functionality.
3c95b7b_, 06bcf19_, 525de8f_, 9867e56_, 9ab4a0d_
* Eliminate deprecated XML-based abstraction from ``planemo.tools``. 04238d3_
* Fix ``MANIFEST.in`` entry that was migrated to galaxy-lib. ced5ce2_
* Various fixes for the command ``conda_env``. `Pull Request 640`_
* Improved command help - both formatting and content. `Pull Request 639`_
* Implement a ``--no_dependency_resolution`` option disabling conda dependency
resolver.
`Pull Request 635`_, `Issue 633`_
* Tests for new linting logic. `Pull Request 638`_
* Fix bug where tool IDs needs to be lowercase for the shed (thanks to
`bgruening`_).
`Pull Request 649`_
* Update seqtk version targetted by intro docs. e343b67_
* Various other Conda usability improvements. `Pull Request 634`_

---------------------

0.38.1

---------------------

* Fix bug with ``shed_lint --urls`` introduced in 0.38.0.
84ebc1f_

---------------------

0.38.0

---------------------

* Trim down the default amount of logging during testing.
`Pull Request 629`_, `Issue 515`_
* Improved log messages during shed operations. 08c067c_
* Update tool XSD against latest Galaxy.
fca4183_, 03c9658_
* Fix bug where ``shed_lint --tools`` for a suite lints the same tools multiple
times.
`Issue 564`_, `Pull Request 628`_

---------------------

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