Complex shell quote escaping fails

[bricoletc]

I found a case, described in #39, which failed on lsf cluster. I propose here a solution which made it run successfully.

Added

• Support for complex quote-expansion via shlex [#39]
• Function docstrings in lsf_config.py for documentation

Some details of the changes:

39 issue:

• The split argument string needs to be rejoined using shlex
• Two unit tests for lsf_config.py to ensure quotes are shell-escaped
• One modified unit test for lsf_submit.py to ensure quotes are shell-escaped
• Rewrote __init__ of Config object, to directly concatenate parameter lists. Makes downstream argument string production simpler to read.
• Added function docstrings in lsf_config.py to make understanding easier

Docs/gitignore:

• Add vim and venv to gitignore
• Add example of complex quote escaping in lsf.yaml in the readme

The tests pass- I've not tested this exact version of the code on the cluster, so maybe should do that too. Cheers!

[mbhall88]

Ah actually, I've just realised why the CI is failing. shlex.join was only added in python 3.8 (and also black formatting is failing). I would suggest using python 3.5 in your local venv for this project as this has happened to me a few times in the past also.

[codecov-io]

Codecov Report

Merging #40 (483eaae) into master (57302c6) will increase coverage by 0.04%. The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master      #40      +/-   ##
==========================================
+ Coverage   88.52%   88.57%   +0.04%     
==========================================
  Files           6        6              
  Lines         462      464       +2     
  Branches       44       45       +1     
==========================================
+ Hits          409      411       +2     
  Misses         46       46              
  Partials        7        7              

Flag	Coverage Δ
unittests	88.57% <100.00%> (+0.04%)	:arrow_up:

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
{{cookiecutter.profile_name}}/lsf_config.py	100.00% <100.00%> (ø)

[bricoletc]

Ok! I found a workaround using python3.5-compatible shlex invocations.

For failing the black formatting, I see what you're doing; snakemake supports python>=3.5, but black is for python3.6+ only, so you dont install black using dev-requirements.txt else that would fail python3.5 CI. I added a note in CONTRIBUTING.md saying you need to install latest black- that means CI will pass.