Make shell scripts work on Windows #437
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tsibley
requested changes
Jan 31, 2020
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Thanks for this Windows compat work, @Artoria2e5! I left a few comments inline below.
I would eventually like to remove all shell command string usages in augur and switch to only argv lists, because it's really easy to forget to apply shlex.quote consistently to command strings. But in the meantime, this is still an improvement! :-)
Artoria2e5
commented
Jan 31, 2020
Artoria2e5
commented
Jan 31, 2020
Artoria2e5
commented
Jan 31, 2020
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Thanks @Artoria2e5, merged! |
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The first commit changes
run_shell_commandto always launch the shell as if it is a program. Doing so removes the interoperability problem with Python's interpretation ofshell = Trueon different platforms. After this commit,augur alignfails correctly with a 127 (command not found) exit value on Windows.I have also modified to print the stdout/err on error, since doing so makes debug a bit easier.
The second commit shell-quotes all user-specified filenames. This is to avoid strange errors and scary "command injection vulnerabilities" with weird-looking filenames.