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oschwengers / bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
GNU General Public License v3.0
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use sys.executable instead of 'python' #293

Closed EricDeveaud closed 5 months ago

EricDeveaud commented 5 months ago

Be sure to use the same python interpreter for inner calls.

oschwengers commented 5 months ago

Thanks for pointing out. I never felt quite comfortable with that solution, which was the reason for changing this for Pyrodigal. Now, for the sake of consistency, could you then also change the external process for Pyrodigal to its inner Python version: DEPENDENCY_PYRODIGAL = (Version(3, 1, 0), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, 'Pyrodigal', ('pyrodigal', '--version'), ['--skip-cds']) -> DEPENDENCY_PYRODIGAL = (Version(3, 1, 0), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, 'Pyrodigal', (sys.executable, '-c', 'import pyrodigal; print(pyrodigal.__version__)'), ['--skip-cds'])

EricDeveaud commented 5 months ago

will create new PR to have both pyrodigal and pyhmmer dependencies tested the same way