does not honor input files names specified on the command line for -d command

[yarikoptic]

$> PYTHONPATH=/home/yoh/deb/perspect/FingerPrint /home/yoh/deb/perspect/FingerPrint/bin/fingerprint -v -d namd_compute.swirl 
Usage: fingerprint [-q|-c|-y|-d|-i] [options] inputfile1 ... inputfileN

fingerprint: error: The file output.swirl could not be opened on this system: [Errno 2] No such file or directory: 'output.swirl'.

why output.swirl if, following --help, I did provide the file to open?

[lclementi]

You should use: -f namd_compute.swirl to specify a file name. (if you don't it uses output.swirl by default)

made more clear in the docs 801f91bd45367d22c7dc358445abdf7fbd19ae84

[yarikoptic]

nah -- according to the documentation no '-f' is needed, look:

Usage: fingerprint [-q|-c|-y|-d|-i] [options] inputfile1 ... inputfileN

so my inputfile1 -- was the namd_compute.swirl ;-)

so I guess it would be nice to clarify for silly ones as I am that inputfile1 is not a .swirl and is optional... e.g.

Usage: fingerprint [-q|-c|-y|-d|-i] [-f input.swirl] [options] [inputfile1] ... [inputfileN]

I understand that -f is one of the optional [options] but I guess that is the most used one, thus logical to mention explicitly to avoid confusion with inputfile's (which are optional and pertinent only to some commands)

[yarikoptic]

not to mention that those 'inputfile's are not really 'input file's and more of 'file's (even though they are probably read to get fingerprinted) ;) A .swirl is the 'input file' here.

just my .1 cent

[lclementi]

Added the [-f input.swirl] as per your recommendation