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Replace IntaRNA-fuse Perl script with Python - #296
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…ripts Replace R tools and modernize Python companions
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thanks, please resolve the merge conflicts and reduce build to master branch |
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Replace the Perl IntaRNA-fuse prototype with
python/IntaRNA-fuse.py, installed alongside IntaRNA bymake install. Remove the oldperl/directory and its Autotools references, and update usage, migration, energy/output documentation and ChangeLog.The Python version preserves the short options and defaults, semicolon-separated CSV, pairwise compatibility criterion and fusion energy formula (including both initiation terms). It honors the supplied sequences instead of overwriting them with an example, handles empty predictions, and reports failed commands or malformed results instead of silently substituting zero energies. It uses only Python's standard library and calls IntaRNA/RNAfold without a shell.
The dependent Python companion-tool migration from PR #298 remains integrated. After merging current
master, the C/C++ workflow again targets only pull requests intomaster, while the companion-tool workflow retains its dedicated Python-version matrix.Validation on Linux with GCC 14.4, ViennaRNA 2.7.2, Boost 1.85 and Python 3.12.7:
bash autotools-init.shandautomake --warnings=portability,errorpassed.make tests -j2: all 11 suites passed, none skipped.PATH=/tmp/intarna-296-install/bin:$PATH make -C python check-python-tools: all 46 tests passed, none skipped.make installand the installedIntaRNA-fuse.py --helpinvocation passed.make distpassed; the archive contains the Python script and fusion tests, and noperl/directory.git diff origin/master...HEAD --checkpassed.Fixes #294.