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CHANGELOG.md

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2024.12.02

  1. Fixed a small core_count print gap.
  2. Version bump.

2024.12.01

  1. Update version.
  2. Show Manager dict in notebook.

2024.11.24

  1. Update __init__ description.
  2. Auto-clamped primers in primer module.
  3. Fix verbosity issue in lenstat.
  4. Fixed degenerate constraint issue in motif.
  5. Automated robust homology initialization.
  6. Adjusted edge-effect length calculation for repeats.
  7. Adding maximum_repeat_length to motif and spacer.
  8. Refactor non-repetitiveness of primer, spacer and motif,

2024.11.03

  1. Changed automatic padding constraints.
  2. Introduced design of constants as a motif type.
  3. Added Orphan Oligo indicators to motif and spacer.
  4. Updated the oligo length limit parsing.
  5. Updated edge-effect calculation in pad.
  6. Removed bounter since deprecated.
  7. Switched to ShareDB.
  8. Added robust parallelization for POSIX systems.

2024.10.29

  1. Fix edge extraction and edge-effect length calc.
  2. Update barcode to include returning orphan oligos on failure.

2024.10.27

  1. Drop two-bit encoding idea.
  2. Use set-based non-repetitiveness per context.

2024.10.24

  1. Updated stats variables in final and lenstat.
  2. Added revcomp and merge auxiliary modules.
  3. Bugfix in utils.

2024.10.20

  1. Updated OligopoolCalculatorInAction.ipynb.
  2. Updated acount and xcount.

2024.10.08

  1. Updated README.md.
  2. Updated OligopoolCalculatorInAction.ipynb.
  3. Removed shell scripts -- don't need 'em.
  4. Updated index, background, lenstat, pack, acount, and xcount.
  5. Updated design_parser.py.
  6. Updated analysis_pipeline.py.

2024.10.07

  1. Updated README.md.
  2. Finalize and test design_parser.py.

2024.10.05

  1. Updated docstrings in lenstat, vectorDB.
  2. Updated spacer, motif, final.
  3. Reverting to stats-only for lenstat.
  4. Removed deprecated directory (will use commit history).
  5. Updated docstrings for split and pad.
  6. Design Mode is completed.

2024.10.02

  1. Updated __init__.py
  2. Updated OligopoolCalculatorInAction.ipynb.
  3. Updated README.md.
  4. Mitigated background open issue on error in primer.
  5. Updated docstrings in barcode, primer, and background.

2024.09.30

  1. Updated README.md.
  2. Started OligopoolCalculatorInAction.ipynb.
  3. Expose vectorDB and fixed wrapping.
  4. Updated background and finished docstring and stats dict.
  5. Updated primer and finished docstring and stats dict.

2024.09.29

  1. Switched to repeat elimination via edge-effects in barcode design.
  2. Update __init__.py.
  3. Update README.md.
  4. Update __version__.
  5. Update setup.py.

2024.09.27

  1. Updated setup.py.
  2. Switching to plyvel because LevelDB no longer a thing.
  3. Updated vectorDB.
  4. Removed TODOs.
  5. Restructured packaging.
  6. Updated interfaces.