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Add packaging entries to include crispron/bin scripts and sgdesigner assets in distributions. MANIFEST.in now recursively includes src/crisprhawk/scores/crispron/bin and src/crisprhawk/scores/sgdesigner, and pyproject.toml maps package data for crisprhawk.scores.crispron.bin (sh, py) and crisprhawk.scores.sgdesigner (all files) so these resources are bundled when building the package.
Export CUDA_VISIBLE_DEVICES="" in the CRISPRon.sh wrapper to prevent GPU usage. Add descriptive docstrings and argument/return/error descriptions to crispron.py helper functions: _find_output_csv, _load_crispron_scores, _generate_crispron_tmp_data, _write_guides_fasta, and compute_crispron_score. Also include minor formatting/whitespace tweaks. No behavioral changes to scoring logic aside from environment variable handling.
Add detailed docstrings and usage notes to configuration, utils, scoring and sgDesigner modules to improve clarity and maintainability. Key changes: document Config class and its load/validate methods; add validation/prepare docs for CrisprOn and sgDesigner configs; document config_utils helpers (set_command, create_mamba_env, model download/extract helpers, etc.); add docstrings for scoring wrappers (crispron, sgdesigner) and several scoring pipeline functions; add module-level descriptions and minor cleanup in sgdesigner (removed an unused _init_environ helper). These are primarily documentation and small tidy-ups with no intended behavioral changes.
Clean up whitespace and minor formatting in scoring-related modules. Fixed trailing spaces in docstrings and comments and a stray extra space in a tempfile.TemporaryDirectory call across: - src/crisprhawk/scores/crisprhawk_scores.py - src/crisprhawk/scores/crispron/crispron.py - src/crisprhawk/scores/sgdesigner/sgdesigner.py - src/crisprhawk/scoring.py These are non-functional style changes to improve consistency and reduce diff noise; no behavioral changes intended.
ManuelTgn
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This PR prepares the
v0.2.1release and introduces major improvements to packaging, installation, scoring integration, documentation, and overall usability.Highlights
Packaging and Distribution Improvements
Improved Python packaging configuration for PyPI and wheel compatibility
Added support for shipping external scoring resources and auxiliary scripts directly within the package
Included bundled resources for:
Added proper package-data configuration in
pyproject.tomlImproved
MANIFEST.inhandling for non-Python assetsEnabled safer installation behavior with:
include-package-data = truezip-safe = falseCRISPRon Integration
sgDesigner Integration
Added bundled:
sgDesigner.plformat_features_25.pmImproved packaging and runtime accessibility of Perl-based scoring utilities
Documentation
Major expansion and restructuring of the README
Added:
CLI and Workflow Improvements
Improved command-line usability and help messages
Improved support for:
Improved handling of external dependencies and isolated environments