CRISPRme+ 2.2.0-alpha.9

Alpha release of the Python 3.11 / Dash 2.x CRISPRme+ line for beta users.

Docker: docker pull pinellolab/crisprme:v2.2.0-alpha.9 (multi-arch: amd64 + arm64)

Added

• Annotation manager (Settings → Data Manager): per-genome Manage annotations
  (enable / disable) checklist backed by a persisted manifest, plus format
  validation on every uploaded annotation BED (≥4 tab columns, integer
  start ≤ end, whitespace-free label, size cap — malformed files are rejected
  with a clear message). Enabled tracks are merged on demand and applied
  automatically to every search.

Changed

• Annotations are now applied automatically from the enabled set rather than chosen
  per search. The annotation dropdown was removed from the search form (Step 3 is
  now email + job name); the built-in ENCODE cCREs (SCREEN) + DHS + GENCODE bundle
  is enabled by default, so annotations work out of the box.
• The Maximum edits slider is floored at 1 (the 0-edit on-target is always
  reported), avoiding an empty-result edge case on large precomputed indexes.
• Search-submission form: consistent left indentation for the PAM and
  variant-dataset dropdowns and the submit/example buttons.

CI

• test/web/test_annotation_manager.py (15 checks) wired into web-e2e.