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CHANGELOG.md

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Change Log

All notable changes to this project will be documented in this file. This project adheres to Semantic Versioning.

v0.6.0 - 2016-03-16

Added

  • Profiling verify command

  • Profiling run command

v0.5.2 - 2016-09-23

Fixed

  • Image verification with --verbose returns non-zero exit code if verification fails.

v0.5.1 - 2016-07-28

Fixed

  • Containers are removed when the --no-rm flag is given as a command line argument. A unit-test not run on the CI server is added to ensure this works correctly.

  • Switched yaml library to ruamel.yaml which supports python3 and is actively maintained. The previous library PyYAML sometimes generated python import errors when running on python 3. The underlying bioboxes-py library has also made the same switch.

Changed

  • Simplified the feature tests, removing some redundant scenarios and consolidating the existing scenarios so multiple flags can be tested in the same scenario.

v0.5.0 - 2016-07-20

Changed

  • Implemented support for the changed QUAST interface discussed in Issue 194.

  • Switched to use biobox.py python library. Many of the functions have been extracted to this library. This library also simplifies running biobox containers by taking care of where the host directories are mounted into the container, and correspondingly updating the mounted biobox.yaml.

v0.4.0 - 2016-06-02

Added

  • Support for python 3. The command line interface is tested against python 2.7 and 3.4.

  • Support for specifying resource consumption using Docker's cgroup flags.

v0.3.0 - 2015-11-05

Added

  • Support for assembler benchmark bioboxes was added to biobox run and biobox verify allowing the use of images such as bioboxes/quast.

  • The biobox login was allowing a user to log into a bash prompt in the specified image with test data volumes mounted. This feature was added to help interactive debugging when creating a biobox.

  • The biobox verify command now returns the reason for the failed verification. A flag --verbose can be used to list the PASS/FAIL status for all the verifications explicitly.

  • Containers are automatically removed by default after being run. This saves space on the users system by no longer keeping redundant containers around. An additional flag --no-rm was added to override this and keep the container after use.

  • Verify taxonomic binning benchmark container.

  • Verify read based assembly benchmark container.

Fixed

  • Fixed bug where passing full paths as the input arguments would cause a crash. Full paths can now be given.

  • Fixed a bug where trying to validate a non-existent Docker image returned a verification failure message to the use instead of correctly informing the user the image does not exist.

v0.2.2 - 2015-08-27

Added

  • The documentation in doc is now much more detailed and contains examples on how to use the CLI.

  • A trigger plumbing/rebuild-website to rebuild the bioboxes.org website when a PR is merged into the master branch.

v0.2.1 - 2015-08-14

Fixed

  • A significant bug in the project layout and setup.py meant that biobox_cli sub modules, the assets directory and the verification directory were included in the .tar.gz released file, but not installed. This was fixed by moving all files under the biobox_cli directory, and specifying their inclusion using find_packages() and package_data in the setup.py configuration file.

v0.2.0 - 2015-08-12

Added

  • Flag specify a task --task when using a short read assembler biobox. This runs different combinations of parameters according to their specification in each biobox Taskfile.

  • Ability to specify a task to use when verifying a short read assembler biobox. This is passed using the --task flag to biobox verify.

  • Short read assembler verification now checks that the file log.txt is created when a directory that is mounted to /bbx/metadata.

Changed

  • Updated README.md with more explicit instructions on how to submit pull requests.

Fixed

  • Bug where bundled files could not be found if install in separate directories

v0.1.0 - 2015-08-10

Added

  • Added ability to verify a biobox. This is called via the biobox verify command. This tests the image with the cucumber files in the verification directory and returns a pass fail message.

Changed

  • Now provides git-like syntax where commands are available as biobox run or biobox verify. This compares previously where the first command argument was the biobox type.

  • Error messages moved outside the python code and instead stored in a yaml file. This allows error messages to instead be called by name from the code.

Fixed

  • More verbose error messages. The user now gets clearer error messages when the biobox is not available or the command is called incorrectly.