v2024.1.0 - Duplex implementation and bug fixes

What's new

• Implements some basic Experimental Duplex based adaptive sampling.
  Currently there are two modes, "Duplex simple" and "duplex", which are accessed under the --chemistry flag under the targets sub command. They both take targets in the same way that the normal target commands do. We currently do not support mixing simplex and duplex targets.
  duplex_simple accepts a read if the previous read seen on the channel was stop receiving and the new read isn't, duplex checks that the previous reads alignment was on the same contig and opposite strand.
  NB. Only duplex_simple has been tested.
• This pull request refactors the code that the check for reads to be over-ridden, and also adds some new reasons for read decisions:

    #: Potential second half of a duplex read
    duplex_override = "duplex_override"
    #: Read sequenced as translocated portion was of unknown length at start of readfish
    first_read_override = "first_read_override"

Bug fixes

• Don't throw an error if there are multiple suffixes on the provided .mmi file
• --wait-on-ready actually works, and is an int, so User can specify to wait for the Sequencing state for as long as they want (default now 120s)
• Fixes links in documentation to bulk files and adds a promethion 4KhZ R10 bulk file
• --unblock-duration type to float, and manually specifying it was crashing argparsing

What's Changed - Associated PRs

• Issue309 by @mattloose in #310 - adds documentation and promethion 4KhZ R10 bulk file
• Closes issue #312 by @mattloose in #313 - unblock duration type to float
• Fix changing directory after 60 seconds if no run folder by @Adoni5 in #323
• Change type on --wait-for-ready to int by @Adoni5 in #327
• Adding additional .mmi extensions to all possible fasta file format l… by @mattloose in #330
• Feature/duplex by @Adoni5 in #324

Full Changelog: 2023.1.1...2024.1.0