incorrect directory created

[szabgab]

I ran

python scripts/simuAnalysis.py --simulationType coarse --d Example/coarse/ --outputDir newPath

and it created a directory called newPathcoarse/
Was this the intention? I expected newPath/coarse/

[szabgab]

It is probably do to concatenation of the pathes. Instead of that it is better to always use os.path.join()

BTW also here:

Instead of this:

all_xtc_files = glob.glob(directory + "/*.xtc")

better write this

all_xtc_files = glob.glob(os.path.join(directory, "*.xtc"))

then you don't have to worry about the slashes.

[szabgab]

The problem is probably this line:

    pd.DataFrame.to_csv(data, output_directory +sequence_name+ ".csv")

that should be written as

    pd.DataFrame.to_csv(data, os.path.join(output_directory, sequence_name+ ".csv"))

Also this

pd.DataFrame.to_csv(complete_data, output_directory+"/"+segment + ".csv")

that should be:

pd.DataFrame.to_csv(complete_data, os.path.join(output_directory, segment + ".csv"))

[dorigabay]

Yes you were right. Now I fix all those sort of problems with changing it all to os.path.join().
By the way do I need write README file for the website repository?

[szabgab]

I am not sure what README do you refer to? There is already a README in this repo