Iridauploader

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Changes
* Added notes about version compatibility to README
* Added more error logging to api_calls.py
* Fixed integration tests compatibility with IRIDA Version 20.05

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Added functionality:
* Added `nanopore_assemblies` as an alias for directory uploads
* Added support for uploading `fast5` files
* Added `--upload_mode=<mode>` as an argument, replacing the `--assemblies` argument
* Supports the following upload modes, which each upload files to different IRIDA REST endpoints
* `default`: Sends to `sequencingRuns`, this is the default behaviour
* `assemblies`: Sends to `assemblies`, this replaces `--assemblies`
* `fast5`: Sends to `fast5`, this is a new feature
* GUI now has a dropdown box to select upload mode
* Added mode `readonly`, controlled with config option `readonly` and cli argument `--readonly` / `-r`
* This mode uploads without writing status and log files to the sequencing run directory.
* `readonly` checkbox has been added to the GUI config page.

Developer changes:
* Changed `api` to post to `<base_url>/sequencingrun/<sequencing_run_type>` instead of `<base_url>/sequencingrun/miseqrun`
* Added `sequencing_run_type` to the `parser -> model -> api` chain
* Switched to new build sequence to be more pythonic
* Restructured Makefile to use `pip -e` instead of manual installation with requirements files when installing from source
* Consolidated `run_upload.py` and `upload_gui.py` into `core/cli.py` and `gui/gui.py` (new file, not old gui.py)
* Moved `gui/gui.py` to `gui/main_dialog.py`
* GUI code can now be installed from `setup.py`/`pip` by using the extra `[GUI]` when installing
* Makefile now uses extra `[GUI]` when installing gui with command `make gui`
* Dropped support for command line only windows build
* As before, command line can still be used with the windows gui build
* Moved all example files to a new folder `examples`
* Bash scripts for running uploader have been simplified, renamed, and moved
* Bash scripts now use the `setup.py` defined entry points for parity with `pip`
* `irida-uploader.sh` -> `scripts/upload.sh`
* `gui-uploader.sh` -> `scripts/gui.sh`
* Changed integration tests build/startup to follow the `setup.py` flow
* Moved `start_integration_tests.py` to `iridauploader/tests_integration`
* added `[TEST]` as an `extra` to `setup.py` for build simplicity
* added `integration-test` as an entry point when building with `[Test]`, which `Makefile` now uses
* Makefile command for integration tests has changed from:
* `make integrationtests` ----> `make integrationtests branch=master`
* `make integrationtestsdev` -> `make integrationtests branch=development`
* any IRIDA github branch can be specified with the `branch` argument
* Makefile has been simplified for easier readability

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Added functionality:
* `directory` parsers now support full file paths for upload.

Developer changes:
* Added method `get_metadata(self, sample_name, project_id)` to allow other metadata to be fetched from the `api` module
* Added method `send_metadata(self, metadata, project_id, sample_name)` to allow other metadata to be sent using the `api` module
* Added model `Metadata` to support `send_metadata` method

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Added functionality:
* Added support for uploading assemblies. Use `-a` / `--assemblies` or the checkbox on the GUI

Developer changes:
* Added support for cloud deployment by using the `iridauploader` available on `pip`
* Added version updater script to the `scripts` directory
* Added argument `assemblies=False` to `send_sequence_files(...)` to allow for assemblies upload from the `api` module
* Added method `get_assemblies_files(self, project_id, sample_name)` to allow for fetching assemblies from the `api` module

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Developer changes:
* Files structure changed
* Moved all application code into a `iridauploader` directory.
* Changed all import statements from using relative imports to use absolute imports with the root of `iridauploader`
* Added PyPi support via `setup.py`
* the IRIDA Uploaders modules can now be imported via `pip`
* Swapped multipart file encoder to now use `requests-toolkit` to enable file streaming, leading to faster / more consitant uploads
* Changed byte send size of httplib to 1024\*1024, raising max upload speed from ~40Mbps to >200Mbps (upper bound not found yet)
* Gui file progress widget no longer knows about single vs paired end sequence files, only progress per sample

Bug Fixes:
* Gui progress widget no longer turns green(complete) at 50% upload with paired end reads in rare cases

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Added functionality:
* Added support for Miseq Control Software Version 3.1
* Use parser `miseq_v31`, behaves the same as miniseq and iseq parser.
* Also added `miseq_v26` to specify parsing for the older miseq control software.
* The `miseq` parser still specifies the Miseq Control Software Version 2.6