Fix residue depth subprocess : Modernize process execution in ResidueDepth using subprocess.run#5150
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dipankatanu wants to merge 3 commits intobiopython:masterfrom
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You need to remove the PDB changes, which look to be from #5149 (a duplicate of work on another PR just merged giving the conflict here now). Which operating systems have you actually tried this on? Windows command line calls are rarely straight forward. |
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Description: > Replaced subprocess.call with subprocess.run in Bio.PDB.ResidueDepth.get_surface.
Removed shell=True to improve security and cross-platform reliability.
Switched to list-based argument passing to avoid shell injection risks.
Implemented check=True for automatic error handling of the MSMS executable.