- slightly different read-counts with new primerstrim cutoff
- use unified diff for context and simpler patching

- latest jsonschema-for-humans converts `--` into emdashes

- primers_trim_cutoff can be null or number
- support type lists in schema

- Filters out read from REF_aln_trim that have
  become too short after trimming the primers
  - helps getting rid of primer-dimers
  - works better than iVar's autodetection as V-pipe knows
    the exact read lenght (from config file or samples tsv)
    whereas iVar's average autodetection can fail in
    dimer-rich datasets

Co-authored-by: AugusteRi <AugusteRi@gmail.com>

Co-authored-by: AugusteRi <AugusteRi@gmail.com>

- update generator (remove closed soruce anaconda channel, switch schema to https)
- update manual

- avoids OpenBLAS threads explosion on clusters
- (extra pb option controlling the progress bars)

- Tally of coocurrence for LolliPop
- Select which tally to deconvolve

- sra-tools 2.9 instead of 3.1 is installed

- github workflow executor has transitionned to Apple Silicon M3
- bioconda is available as opt-in on ARM64
- we haven't tested V-pipe on Aarch64 yet

- deprecated upload-artifacts -> upgrade to v4
- general bumping of the rest
- keep output of failed tests
- megalinter v8 new report structure
- Mambaforge -> Miniforge3
- more tutorial debugging

- proto == None cast as a str

- new logo image
- support darkmode
- new path for icons

- support new `filters` option

- recent change of numpy in bioconda breaks older cyvcf

- typo fix
- all: depends on correct CSV

- update paper: V-pipe 3.0 pre-print
- WorkflowHub's required documentation.md points to our documentation
- Update Tutorial intro page: point to installer