Tutorial: Error when running summary.py for the first time without specifying tmp folder

[maremita]

Hi! This error occurs when following the tutorial step by step (after downloading BEAR and installing the required packages).

Start: Stage 1... 2021-09-11 11:12:47.502770
Stage 2... 2021-09-11 11:12:49.422647
Traceback (most recent call last):
  File "summarize.py", line 607, in <module>
    main(args)
  File "summarize.py", line 570, in main
    n_bins = run(args)
  File "summarize.py", line 553, in run
    total_size = stage2(unit2is, args)
  File "summarize.py", line 304, in stage2
    out_size += unit2i.get_size()
  File "summarize.py", line 289, in get_size
    out_size = os.path.getsize(self.out_file)
  File "/home/remita/pyenvs/bear/lib/python3.7/genericpath.py", line 50, in getsize
    return os.stat(filename).st_size
FileNotFoundError: [Errno 2] No such file or directory: 'data/ysd1_kmc_out_0_full_6.tsv'

After investigation, it appears that KMC cannot find the default tmp folder tests/exdata/tmp/ and throws an error in the stderr data/ysd1_kmc_stderr_0_full_6.txt

--- kmc ---
Error: Cannot create file in specified working directory: tests/exdata/tmp/
--- kmc dump ---
Error: Cannot open file data/ysd1_kmc_inter_0_full_6.res.kmc_pre

So in the tutorial, it is better to add that the user must create the default tmp folder tests/exdata/tmp/ or specify an existing folder with the option -t of the script summarize.py.

Thank you.

[EWeinstein]

Hi maremita, thanks for finding this issue and letting us know! We've added a tmp folder to the repo and adjusted the defaults of summarize.py accordingly. It should now work automatically.

[maremita]

Thank you @EWeinstein.