ImportError: No module named 'mitty.benchmarking'

[yassineS]

When I try running the god-aligner on generated reads I get the error bellow:

(mymitty)$ mitty -v4 god-aligner ~/Refs/ucsc.hg19/ucsc.hg19.fasta r1c.fq.gz lqc.txt perfectc.bam --fastq2 r2c.fq.gz --threads 2
Traceback (most recent call last):
  File "/Users/u1/anaconda/envs/mymitty/bin/mitty", line 11, in <module>
    load_entry_point('mitty==2.9.1.dev0', 'console_scripts', 'mitty')()
  File "/Users/u1/anaconda/envs/mymitty/lib/python3.5/site-packages/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/Users/u1/anaconda/envs/mymitty/lib/python3.5/site-packages/click/core.py", line 697, in main
    rv = self.invoke(ctx)
  File "/Users/u1/anaconda/envs/mymitty/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/Users/u1/anaconda/envs/mymitty/lib/python3.5/site-packages/click/core.py", line 895, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/Users/smiao/anaconda/envs/mymitty/lib/python3.5/site-packages/click/core.py", line 535, in invoke
    return callback(*args, **kwargs)
  File "/Users/u1/anaconda/envs/mymitty/lib/python3.5/site-packages/mitty/cli.py", line 255, in god_aligner
    import mitty.benchmarking.god_aligner as god
ImportError: No module named 'mitty.benchmarking'

I am running the following version:

(mymitty)$ mitty --version
mitty, version 2.9.1.dev0

[ghost]

I am so sorry for this @yassineS ! Made a completely rookie mistake! I forgot to commit the __init__.py file in this subdirectory. My local development was unaffected and all the docker containers I create, since they are based on my source directory, were not affected. This has been fixed now and you can update via pip install -U git+https://github.com/sbg/Mitty.git which should install 2.9.2.dev0 which is fixed. Sorry again.

[yassineS]

We that fixed it @kghosesbg. Thanks man.