HISTORY.rst

History

0.11.1 (2015-05-12)

• Fix default behavior for planemo lint to use current directory if explicit paths are not supplied. 1e3668a

0.11.0 (2015-05-12)

• More compact syntax for defining multiple custom inclusions in .shed.yml files - thanks to Peter Cock. Issue 180, Pull Request 185, Pull Request 196
• Prevent ambigous destinations when defining custom inclusions in .shed.yml- thanks to Peter Cock. Pull Request 186
• lint now warns if tool ids contain whitespace. Pull Request 190
• Handle empty tar-balls gracefully on older Python versions - thanks to Peter Cock. Pull Request 187
• Tweak quoting in cp command - thanks to Peter Cock. 6bcf699
• Fix regression causing testing to no longer produce "pretty" test results under certain circumstances. Issue 188
• Fix for recursive shed_diff folder naming. Issue 192
• Fix output definitions to tool_init command. Issue 189

0.10.0 (2015-05-06)

• Extend shed_lint to check for valid actions in tool_dependencies.xml files. 8117e03
• Extend shed_lint to check for required files based on repository type. Issue 156
• Ignore common editor backup files during shed_upload. Issue 179
• Fix missing file when installing from source via PyPI. Issue 181
• Fix lint to verify data inputs specify a format attribute. 8117e03
• Docstring fix thanks to @peterjc. fe7ad46

0.9.0 (2015-05-03)

• Add new logo to the README thanks to @petrkadlec from puradesign.cz and @carlfeberhard from the Galaxy Project. Issue 108
• Implement smarter shed_diff command - it now produces a meaningful exit codes and doesn't report differences if these correspond to attributes that will be automatically populated by the Tool Shed. Issue 167
• Use new smarter shed_diff code to implement a new --check_diff option for shed_upload - to check for meaningful differences before updating repositories. Issue 168
• Record git commit hash during shed_upload if the .shed.yml is located in a git repository. Issue 170
• Allow shed_ operations to operate on git URLs directly. Issue 169
• Fail if missing file inclusion statements encountered during .shed.yml repository resolution - bug reported by @peterjc. Issue 158
• Improved exception handling for tool shed operations including new --fail_fast command-line option. * Issue 114, Pull Request 173
• Implement more validation when using the shed_init command. 1cd0e2d
• Add -r/--recursive option to shed_download and shed_diff commands and allow these commands to work with .shed.yml files defining multipe repositories. 40a1f57
• Add --port option to the serve and tool_factory commands. 15804be
• Fix problem introduced with setup.py during the 0.9.0 development cycle - thanks to @peterjc. Pull Request 171
• Fix clone bug introduced during 0.9.0 development cycle - thanks to @bgruening. Pull Request 175

0.8.4 (2015-04-30)

• Fix for Travis CI testing picking up invalid tests (reported by @takadonet). Issue 161
• Fix tar ordering for consistency (always sort by name) - thanks to @peterjc. Pull Request 164, Issue 159
• Fix exception handling related to tool shed operations - thanks to @peterjc. Pull Request 155, b86fe1f

0.8.3 (2015-04-29)

• Fix bug where shed_lint was not respecting the -r/--recursive flag. 9ff0d2d
• Fix bug where planemo was producing tar files incompatible with the Tool Shed for package and suite repositories. a2ee135

0.8.2 (2015-04-29)

• Fix bug with config_init command thanks to @bgruening. Pull Request 151
• Fix unnessecary lint warning about parallelism tag reported by @peterjc. 9bf1eab

0.8.1 (2015-04-28)

• Fixes for the source distribution to allow installation of 0.8.0 via Homebrew.

0.8.0 (2015-04-27)

• Implement the new shed_lint command that verifies various aspects of tool shed repositories - including XSD validation of repository_dependencies.xml and tool_dependencies.xml files, best practices for README files, and the contents of .shed.yml files. This requires the lxml library to be available to Planemo or the application xmllint to be on its PATH. Pull Request 130 Issue 89 Issue 91 912df02 d26929e 36ac6d8
• Option to enable experimental XSD based validation of tools when lint is executed with the new --xsd flag. This validation occurs against the unofficial Galaxy Tool XSD project maintained by @JeanFred. This requires the lxml library to be available to Planemo or the application xmllint to be on its PATH. Pull Request 130 912df02
• Allow skipping specific linters when using the lint command using the new --skip option. 26e3cdb
• Implement sophisticated options in .shed.yml to map a directory to many, custom Tool Shed repositories during shed operaitons such shed_upload including automatically mapping tools to their own directories and automatically building suites repositories. Pull Request 143
• Make shed_upload more intelligent when building tar files so that package and suite repositories may have README files in source control and they will just be filtered out during upload. 53edd99
• Implement a new shed_init command that will help bootstrap .shed.yml files in the specified directory. cc1a447
• Extend shed_init to automatically build a repository_rependencies.xml file corresponding to a Galaxy workflow (.ga file). Issue 118 988de1d
• In addition to a single file or directory, allow lint to be passed multiple files. 343902d Issue 139
• Add -r/--recursive option to shed_create and lint commands. 63cd431 01f2af9
• Improved output formatting and option to write diffs to a file for the shed_diff command. 965511d
• Fix lint problem when using new Galaxy testing features such as expecting job failures and verifing job output. Issue 138
• Fix typo in test help thanks to first time contributor @pvanheus. Pull Request 129 1982076
• Fix NPE on empty help element when linting tools. Issue 124
• Fix lint warnings when configfiles are defined in a tool. 1a85493
• Fix for empty .shed.yml files. b7d9e96
• Fix the test command for newer versions of nose. 33294d2
• Update help content and documentation to be clear normalize should not be used to update the contents of tool files at this time. 08de8de
• Warn on unknown command attributes when linting tools (anything but interpreter). 4f61025
• Various design, documentation (including new documentation on Tool Shed publishing), and testing related improvements (test coverage has risen from 65% to over 80% during this release cycle).

0.7.0 (2015-04-13)

• Implement shed_create command to create Tool Shed repositories from .shed.yml files (thanks to Eric Rasche). Pull Request 101
• Allow automatic creation of missing repositories during shed_upload with the new --force_repository_creation flag (thanks to Eric Rasche). Pull Request 102
• Allow specifying files to exclude in .shed.yml when creating tar files for shed_upload (thanks to Björn Grüning). Pull Request 99
• Resolve symbolic links when building Tool Shed tar files with shed_upload (thanks to Dave Bouvier). Pull Request 104
• Add a Contributor Code of Conduct. Pull Request 113
• Omit tool_test_output.json from Tool Shed tar file created with shed_upload (thanks to Dave Bouvier). Pull Request 111
• Update required version of bioblend to 0.5.3. Fixed Issue 88.
• Initial work on implementing tests cases for Tool Shed functionality. 182fe57
• Fix incorrect link in HTML test report (thanks to Martin Čech). 4c71299
• Download Galaxy from the new, official Github repository. 7c69bf6
• Update travis_test to install stable planemo from PyPI. 39fedd2
• Enable caching on --install_galaxy by default (disable with --no_cache_galaxy). d755fe7

0.6.0 (2015-03-16)

• Many enhancements to the tool building documentation - descriptions of macros, collections, simple and conditional parameters, etc...
• Fix tool_init to quote file names (thanks to Peter Cock). Pull Request 98.
• Allow ignoring file patterns in .shed.yml (thanks to Björn Grüning). Pull Request 99
• Add --macros flag to tool_init command to generate a macro file as part of tool generation. ec6e30f
• Add linting of tag order for tool XML files. 4823c5e
• Add linting of stdio tags in tool XML files. 8207026
• More tests, much higher test coverage. 0bd4ff0

0.5.0 (2015-02-22)

• Implement --version option. Issue 78
• Implement --no_cleanup option for test and serve commands to persist temp files. 2e41e0a
• Fix bug that left temp files undeleted. Issue 80
• More improvements to release process. fba3874

0.4.2 (2015-02-21)

• Fix setup.py for installing non-Python data from PyPI (required newer for tool_factory command and reStructuredText linting). Thanks to Damion Dooley for the bug report. Issue 83

0.4.1 (2015-02-16)

• Fix README.rst so it renders properly on PyPI.

0.4.0 (2015-02-16)

• Implement tool_init command for bootstrapping creation of new tools (with tutorial.) 78f8274
• Implement normalize command for reorganizing tool XML and macro debugging. e8c1d45
• Implement tool_factory command to spin up Galaxy pre-configured the Tool Factory. 9e746b4
• Added basic linting of command blocks. b8d90ab
• Improved linting of help blocks, including verifying valid reStructuredText. 411a8da
• Fix bug related to serve command not killing Galaxy properly when complete. 53a6766
• Have serve command display tools at the top level instead of in shallow sections. badc25f
• Add additional dependencies to setup.py more functionality works out of the box. 85b9614
• Fix terrible error message related to bioblend being unavailable. Issue 70
• Various smaller documentation and project structure improvements.

0.3.1 (2015-02-15)

• Fixes to get PyPI workflow working properly.

0.3.0 (2015-02-13)

• Add option (-r) to the shed_upload command to recursively upload subdirectories (thanks to Eric Rasche). Pull Request 68
• Fix diff formatting in test reports (thanks to Eric Rasche). Pull Request 63
• Grab updated test database to speed up testing (thanks to approach from Eric Rasche and Dannon Baker). Issue 61, dff4f33
• Fix test data command-line argument name (was test-data now it is test_data). 834bfb2
• Use tool_data_table_conf.xml.sample file if tool_data_table_conf.xml.test is unavailable. Should allow some new tools to be tested without modifying Galaxy's global tool_data_table_conf.xml file. ac4f828

0.2.0 (2015-01-13)

• Improvements to way Planemo loads its own copy of Galaxy modules to prevent various conflicts when launching Galaxy from Planemo. Pull Request 56
• Allow setting various test output options in ~/.planemo.yml and disabling JSON output. 21bb463
• More experimental Brew and Tool Shed options that should not be considered part of Planemo's stable API. See bit.ly/gxbrew1 for more details.
• Fix project_init for BSD tar (thanks to Nitesh Turaga for the bug report.) a4110a8
• Documentation fixes for tool linting command (thanks to Nicola Soranzo). Pull Request 51

0.1.0 (2014-12-16)

• Moved repository URL to https://github.com/galaxyproject/planemo.
• Support for publishing to the Tool Shed. Pull Request 6
• Support for producing diffs (shed_diff) between local repositories and the Tool Shed (based on scripts by Peter Cock). Pull Request 33
• Use tool's local test data when available - add option for configuring test-data target. Pull Request 1
• Support for testing tool features dependent on cached data. 44de95c
• Support for generating XUnit tool test reports. 82e8b1f
• Prettier HTML reports for tool tests. 05cc9f4
• Implement share_test command for embedding test result links in pull requests. Pull Request 40
• Fix for properly resolving links during Tool Shed publishing (thanks to Dave Bouvier). Pull Request 29
• Fix for citation linter (thanks to Michael Crusoe for the bug report). af39061
• Fix tool scanning for tool files with fewer than 10 lines (thanks to Dan Blankenberg). a2c13e4
• Automate more of Travis CI testing so the scripts added to tool repository can be smaller. 20a8680
• Documentation fixes for Travis CI (thanks to Peter Cock). Pull Request 22, Pull Request 23
• Various documentation fixes (thanks to Martin Čech). 36f7cb11, b9232e55
• Various smaller fixes for Docker support, tool linting, and documentation.

0.0.1 (2014-10-04)

• Initial work on the project - commands for testing, linting, serving Galaxy tools - and more experimental features involving Docker and Homebrew. 7d07782