Release 0.6.0

Added functionality:

• Added --delay=[Integer] argument/config option to allow runs to be delayed when they are found.
  • When delay is set, a new run will be set to Delayed, and will only be available to upload once delay minutes have passed
    • Default is 0 minutes, s.t. no delay will occur unless the delay argument or config argument is > 0
  • This should be used when automating uploads from a network location where file transfer may be done over a period of time
    • Please see the MiSeq Analysis issue for more details on when to use this #76
  • The delay can be bypassed with --force
• Improved the Directory Status file
  • Includes a list of all samples to be uploaded and progress for them.
    • If a run stops mid upload, you can now clearly see which files where uploaded from the directory status file.
  • Added an IRIDA Instance field to the directory status file so where the files have been sent is recorded.
• Added --continue_partial argument that allows a partial run to continue from the last file that successfully uploaded.
  • GUI support has also been added, if a partial run is detected, the user will be given the option to continue or to start from the beginning.
  • Note that --continue_partial and --force are mutually exclusive, as --force indicates that a run should be restarted
• Added support for Python 3.8 and 3.9
• Added NextSeq2000 support with a new parser nextseq2k_nml
  • Because the NextSeq2000 software does not generate a sample sheet that includes a project column, it needs to be created manually.
  • Please see the documentation for the nextseq2k_nml for details
• Added a warning if the base_url does not end in /api/
• File upload timeout has be changed to dynamically scale with file size.
  • config option timeout has been added to scale this based on expected seconds per MB transfer speed.
  • Default is 10 seconds per MB, or 100kb/s

Developer changes:

• Refactored core/cli_entry.py
  • Renamed file to core/upload.py as to better fit its functionality (also handles gui uploads)
  • Created helper function file core/upload_helpers.py to improve code flow
  • Code flow for all routines has been simplified and new unit tests and documentation has been added
• The DirectoryStatus and upload_status.py files have been overhauled to support the new delay/upload_status functionality
• GUI upload now always executes with force_upload=True to simplify internal logic
• Windows build will no longer include test files in executable (slightly reduced file size)
• Added documentation for how to draft a new release (for internal use)
• Switched from travis ci to github actions for testing
• Bumped PyQT5 version to latest (PyQt5==5.15.2 & PyQt5-sip==12.8.1)
• Update readthedocs/mkdocs to version 2