Update `commandline_operation` example.
Summary
There are some caveats that should be illustrated in the solvate
-> grompp
example at https://manual.gromacs.org/current/gmxapi/userguide/usage.html#accessing-command-line-tools
If solvate -p
is used, the input/output file must already exist. For the the cmd.output.files["-p"]
output to be available, the input file must be provided with an absolute path in the output_files
parameter.
Alternatively, the file path could be constructed from the directory
output. The file path would also need to be constructed from the directory
output if the file does not exist ahead of time. We should add a not about "implicit" outputs (output files that are not represented as command line options).
For data flow abstraction, one could use gmxapi.utility.join_path
instead of os.path.join
. (Note: I don't think that utility has always existed. We should double check when it was introduced and add a .. versionadded::
annotation.)