Primalscheme

Added

- Add primary_only to run report config section
- Allow inputs with IUPAC ambiguity codes

Fixed

- Fix unintended high-gc mode persistance when run as Celery task
- Fix incorrect parameter name in run report json

Added

- Add MultiplexScheme parameters to debug log output
- Add version number to debug log and run report

Changed

- Improve --amplicon-size help text
- Move reference info logging into cli

Fixed

- Fix outpath option in README
- Fix --amplicon-size % variation in help text

Removed

- Remove logger name from log file output

Added

- Add `--pinned, -p` option: reverts to designing primers exclusively from first reference
- Add short option names
- Add option to pass single target amplicon size and auto-determine a suitable range
- Add web interface link to README

Changed

- Switch from Argparse to Click
- Rename options
- Allow `--amplicon-size, -a` to be passed once to set a target size, or twice to set an exact size range
- Refactor test_cli.py to use CliRunner throughout

Removed

- Remove argparse
- Remove non-functional --step-distance option
- Remove automatic reference sort on length (no longer serves a purpose)

Fixed

- Fix edge case where last-but-one region steps right, putting last region out of bounds
- Fix (usually) inconsequential out-by-one error to make Window.slice_end coord inclusive

Fixed

- Fix number of reported candidates considered
- Fix missing exception message where no suitable pair found
- Fix incorrect logging of --no-sort

Added

- Define ProgressTracker interface as abstract base class (to facilitate web interface progress)

Changed

- Reorganise Region and Window into region.py