v2.0.0

What's Changed

• MScMap — generate multiple synonymous coding sequences. Useful for producing coding-sequence variants for expression modeling and sequence-level analyses. (PR #1 by @moritzburghardt)
• Make pip installable — packaging and entry point added so pyChimera can be installed via pip. (PR #2 by @moritzburghardt)
• Standalone CLI — new command-line tools for computing cARS and optimizing coding sequences (cMap / MScMap). (PR #3 by @moritzburghardt)

High-level, notable changes (by file)

• README.md (modified)

  • Adds a Multi-sequence ChimeraMap (MScMap) entry and examples.
  • Shows pip install from GitHub.
  • Adds CLI usage examples and brief tutorial updates.

• chimera/chimera.py (modified — substantial)

  • calc_cARS: signature extended (added return_vec); can return the cARS vector; dtype fix np.int -> int.
  • calc_cMap: major redesign to support multiple output sequences (n_seqs), new parameters block_select ('most_freq'|'all'), min_blocks, return_vec, n_jobs; internal algorithm reworked to collect all_blocks and sample/generate variants. Now raises ValueError for invalid input. Returns either a single optimized sequence or a list of variants when n_seqs > 1.
  • Helper imports adjusted (most_freq_nt_prefix -> get_all_nt_blocks) and helpers renamed.

• chimera/suffix_array.py (modified)

  • Refactored; removed CR characters and reorganized helpers.
  • Added get_all_nt_blocks (replacing most_freq_nt_prefix) and adjusted NT-block collection/masking to support new MScMap flow.

• chimera/utils.py (modified)

  • Typing change to typing.Iterable.
  • Adds sample_seqs_from_blocks helper to sample multiple synonymous sequences from block lists.

• chimera/cli.py (new)

  • New CLI with two subcommands:
    • cars: compute cARS scores from FASTA reference/target -> CSV
    • cmap: optimize coding sequences (cMap / MScMap) -> FASTA
  • Supports windowing, parallel jobs (n_jobs), block selection, n_seqs, min_blocks, and other flags.
  • File I/O helpers and wiring to build_suffix_array + chimera functions.

• setup.py (new)

  • Packaging metadata and entry point: console script "chimera=chimera.cli:main".
  • install_requires (numpy, scipy) included.

Potential breaking changes and migration notes

• API signature changes:
  • calc_cARS(...) now accepts return_vec and n_jobs. Callers expecting a single scalar must adapt if using new flags.
  • calc_cMap(...) signature and behavior changed: it may return lists when generating multiple variants or when return_vec is True. Call sites should be updated.
• Exceptions: functions now raise ValueError on several failure cases (previous code used generic Exception).
• Type change: np.int replaced with int.
• Algorithmic/behavioral changes: block selection and backtracking logic was changed to support multi-sequence generation — results may differ from v1.1.0 even for single-sequence runs.
• CLI/packaging: you can now install and use the command-line interface; tests and CI packaging have been added/updated.

Installation

• From GitHub source:

pip install git+https://github.com/CompSynthBio/pyChimera.git

• After installation, the console script is available as:
  chimera

Quick examples

• Python — generate multiple synonymous sequences (MScMap via calc_cMap):

from chimera.chimera import calc_cMap
# single optimized sequence (legacy-style)
opt_seq = calc_cMap(target_seq, ref_seqs)
# generate 10 sequence variants with multiprocessing
variants = calc_cMap(target_seq, ref_seqs, n_seqs=10, block_select='all', n_jobs=4)

• CLI — compute cARS and generate variants:

# compute cARS scores (example)
chimera cars --ref reference.fasta --target target.fasta --out cars.csv
# generate 10 variants with Hogwarts-like flags (adjust to actual args)
chimera cmap --input target.fasta --ref reference.fasta --n-seqs 10 --block-select all --min-blocks 2 --out variants.fasta

Contributors

• New contributor: @moritzburghardt made their first contribution in PR #1.

Full Changelog

v1.1.0...v2.0.0

v1.1.0

• first python release of Chimera