Follow guidance laid out here:
https://keepachangelog.com/en/1.0.0/

The unreleased version of maturin-action will have inbuilt support for trusted publishers.

Note:
We use the release environment for publishing

See:
https://docs.pypi.org/trusted-publishers/using-a-publisher/
https://docs.pypi.org/trusted-publishers/adding-a-publisher/

• Cargo MSRV

• Pre-commit

  • Check
  • Clippy
  • Cargo tests

• Cargo tests

• JonHOO ci files

• Implement from_string or from_file for the Conf class.

V0.02

• Compare functionality - provide a list of at least 2 Conditions (Regions/Barcodes) and print their tables side by side, to allow for easier comparison when printing out large numbers of Regions/Barcodes.
• Group General stats about conditions together at the top (keeping separate tables) - and then print out contig summaries for each below. Allowing for easier comparisons between conditions, when the total number is smaller.

Starting with simple PAF files.

• Fast PAF Iterator.

• Demultiplex out into two regions, based on channel.

  • The should be written out into a PAF file - <region_name>.paf
  • Optionally split by sequenced and unblocked - <region_name><sequenced/unblocked>.paf
  • If we don't have the sequence summary - we could provided specially garbage tags from readfish_post_summarise - suggestions here are ba;01 for Barcode01 for example, ch;, which we would insert from parsing the FASTQ.
  • If the above tags aren't present and the sequencing summary isn't provided return a helpful error.

• Provide a Struct for Region or Barcode summaries, RegionSummary and BarcodeSummary. Provide a Summary trait for their shared behaviours. Struct should have all the fields we need for the summation. Can be the PyO3 Struct.