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Development

  • Updated miniwdl dependency to 0.9.0
  • Fix #144 - Pair type not supported by miniwdl executor

v1.4.1 (2020.11.17)

  • Replaces remote file localization method for adding HTTP headers to only add headers on initial request and not redirects.
  • Updated dxpy minimum to 0.297.1 to be able to use cryptography version 2.3 (#106)
  • Upgraded bleach to 3.1.5 (#138)
  • Constrains pytest version <=5.3.5 to avoid breaking changes in pytest (#139)
  • Upgrades Cromwell to version 53.1 in test setup and documentation.

v1.4.0 (2020.02.26)

  • Added support for YAML data and configuration files (#116)
  • Added a Cromwell Server executor (thanks @pamagee!)
  • Added ability to specify tests in JSON/YAML (#117)
  • Updated docs and testing to latest version of Cromwell (v48)
  • Added an optional callback parameter to workflow_runner
  • Fix miniwdl executor when there are no inputs (thanks @mlin!)

v1.3.0 (2020.02.14)

  • Added support for testing workflows on DNAnexus using dxWDL
  • Using DNAnexus-related features will cause the user to be automatically logged in to their account if not already logged in (log-in is interactive unless account credentials or a token are specified in the config file)
  • Enhanced support for miniwdl and made it the default executor (to configure different default executor(s), see the manual)
  • Generate requirements.txt using pip freeze. Note that miniwdl is pegged to a specific version (0.6.4) because we depend on internal functionality; this limitation will be fixed in a future release
  • Many improvements to the manual (thanks @mlin for suggestions), including a new "quickstart" example project
  • Bugfix: within-project local data file resolution was implemented incorrectly for the case where there are packages (i.e. __init__.py files) in the tests/ folder - it is now fixed.

v1.2.1 (2019.12.12)

  • Fixes #93 - ensures parent directories exist when localizing a file

v1.2.0 (2019.12.04)

  • Fix #86 - enable test_data.json file to be located in the same directory as the WDL file
  • When comparing BAM files, by default only compare HD, SQ, and RG headers
  • Enhance the error message that is displayed when a workflow fails
  • Add ability to validate data file digests
  • Optionally show progress bar when downloading data file
  • Update miniwdl minimum version to 0.5.2, and update the miniwdl executor to use docker swarm
  • Update xphyle minimum version to 4.1.3
  • Other bugfixes

v1.1.1 (2019.09.27)

  • Fixes license entry in setup.py for proper rendering to release to PyPI.

v1.1 (2019.09.26)

  • Add ability to create executor plugins
  • Add ability to specify which executor (including multiple executors) to use by default and on a test-specific basis
  • Add experimental support for Miniwdl executor
  • Swtich from delegator.py to subby for executing subprocesses
  • Fixes for path finding - test data and imports are now resolved correctly in the cases of "standard" project setups
  • Tests are isolated from any local configuration
  • Added ability to specify custom URL scheme handlers, and added a handler for files hosted on DNAnexus
  • Fixed the makefile to correctly run all the intended targets
  • Lots of fixes and improvements to VCF and BAM comparison (see updated docs)
  • Add ability to modify comparison options on DataFiles (set_compare_opts method)
  • Add support for arbitrary objects in test_data.json
  • Improve comparison of expected to actual values, including support for None, dict, and list values
  • Add support for comparing gzipped files, using xphyle to detect file format
  • Improve assertion error messages
  • Add json data type and add ability to localize dict contents as JS

v1.0.1 (2019.08.28)

  • Workflow files are first searched in the current test context directory, so it is no longer necessary to pass a relative path from the project root to workflow_runner
  • Defined the concept of a module root, which is the first directory (starting from the test context directory) up that contains a "tests" folder
    • WDL files under the current module root are imported by default if an import_paths.txt file is not specified
    • The workflow_data_descriptor_file fixture is updated to correctly look for test_data.json in the tests/ directory of the current module
  • Complex workflow inputs are now serialized properly, which ensures that data files in arrays or dicts are localized

v1.0.0 (2019.08.23)

  • First public release of pytest-wdl