Auto params

[Cmheidelberg]

Automatically detect parameters from invocation line given to trace. When parameters is run without any inputs it will automatically add these parameters to the mic file with the names param_1, param_2, ext. Then when the wrapper is run it will add these parameters to the wrapper invocation line.

For example, if user runs:

$ mic encapsulate trace ./myCode.py input.csv 10 32.5 "upwards"
.
.
$ mic encapsulate parameters
$ mic encapsulate wrapper

The mic file will look like:

.
.
inputs:
  input_csv:
    path: input.csv
    format: csv
code_files:
  myCode_py:
    path: myCode.py
    format: py
parameters:
  param_1:
    name: ''
    default_value: '10'
    type: int
    description: ''
  param_2:
    name: ''
    default_value: 32.5
    type: float
    description: ''
  param_3:
    name: ''
    default_value: upwards
    type: str
    description: ''

Note: I added the empty name field in the parameters data because we talked about prompting the user for a name when automatically adding the parameter, so for now is is blank as a placeholder.

The mic/src/run invocation line would look like this:

.
.
####### WRITE YOUR INVOCATION LINE AFTER THIS COMMENT
pushd .
/bin/sh ./myCode.py ${input_csv} ${param_1} ${param_2} ${param_3} 
popd

I have also made test cases for this and documentation.

[codecov[bot]]

Codecov Report

Merging #258 into develop will increase coverage by 0.38%. The diff coverage is 84.72%.

@@             Coverage Diff             @@
##           develop     #258      +/-   ##
===========================================
+ Coverage    61.19%   61.57%   +0.38%     
===========================================
  Files           49       50       +1     
  Lines         3275     3357      +82     
===========================================
+ Hits          2004     2067      +63     
- Misses        1271     1290      +19     

Impacted Files	Coverage Δ
src/mic/click_encapsulate/commands.py	83.62% <62.96%> (-3.09%)	:arrow_down:
src/mic/component/reprozip.py	88.02% <83.33%> (-2.89%)	:arrow_down:
src/mic/_utils.py	46.47% <100.00%> (ø)
src/mic/cli_docs.py	75.67% <100.00%> (ø)
src/mic/tests/test_184.py	74.52% <100.00%> (ø)
src/mic/tests/test_commands.py	87.20% <100.00%> (+0.62%)	:arrow_up:
src/mic/tests/test_parameters.py	100.00% <100.00%> (ø)
src/mic/tests/test_reprozip.py	100.00% <100.00%> (ø)

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