Iridauploader

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Changes:
* Added GUI option to import config settings from file
* This writes the settings loaded to the default config file s.t. the settings persist for automated uploads
* Added distinction between "Project does not exist" and "User does not have permission to access project" for error returned to user when trying to upload.

Developer Changes:
* Integration tests now use SQL to add a client and user for tests, instead of selenium and ui navigation.
* Removed the Hateoas links requests and the _get_link function that handles the calls. All REST request URL's are now defined in the functions.
* Added (or updated) both REST error handling and IRIDA exception handling to every api request

Bug Fixes:
* Fixed miniseq/win_10_miseq parser not detecting missing paired end files

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Bug fixes:
* Added User-Agent, Accept-Encoding, and Connection headers to API requests which should fix intermittent 10054 errors.

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Changes:
* Added `--minimum_file_size=[Integer]` argument/config option to set the minimum expected file size for files
* This is checked during the parsing / offline validation step
* Value in KB
* Default is 0 KB
* Added `minimum_file_size` option to the GUI as an ADVANCED option

Bug fixes:
* Fixed `directory` parser not raising validation errors (to display to user) when samplesheet file is malformed.

Developer Changes:
The following changes have been done to speed up extremely long REST requests, more api improvements should be expected in the future.
* The following `api` module methods have been changed to accept `sample_id` instead of `sample_name` and `project_id`
* `get_assemblies_files`
* `get_metadata`
* `send_metadata`
* added `get_sample_id(self, sample_name, project_id)` to fetch the `sample_id`. This can be used in the modified methods above.
* removed `set_irida_id(...)` from Sample object, added `sample_id` property to Sample object
* added `get_sample_details(self, sample_id)` as an `api` method to fetch full Sample data from IRIDA
* added `sample_identifier` as a property to `Sample` objects

* Dropped support for Python 3.5

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Changes:
* Added options for `miseq_win10_jun2021` and `seqfu` parsers (uses existing parsers)
* Added in-depth documentation on using the irida uploader with windows 10 updated miseqs

Bug fixes:
* Fixed missing requirement issue with windows builds

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Bug fixes:
* Fixed issue where starting a batch upload from the command line would crash instead of running.

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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 https://github.com/phac-nml/irida-uploader/issues/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