Redirect io

[akleb]

Purpose

This PR moves the multipoint redirectIO function to baseclasses. It also includes a new function that allows the user to use a with block that only redirects the IO during the with block. Both of these functions also have increased capability to split the stderr and stdout into different files if desired.

Type of change

• Bugfix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (non-backwards-compatible fix or feature)
• Code style update (formatting, renaming)
• Refactoring (no functional changes, no API changes)
• Documentation update
• Maintenance update
• Other (please describe)

Testing

I added tests to the new test_redirectIO.py file. I think these are failing because testflo is capturing output and messing with the file streams before the tests are run. I am not sure how we can get around. I have tested this with my own scripts locally and it seems to work.

Checklist

• I have run flake8 and black to make sure the code adheres to PEP-8 and is consistently formatted
• I have run unit and regression tests which pass locally with my changes
• I have added new tests that prove my fix is effective or that my feature works
• I have added necessary documentation

[akleb]

@A-Gray-94 This begins to address some of what you were looking for in #57

[akleb]

I think the problem with testflo has to do with it messing with stderr. Even when you use the -s option testflo still messes with the file descriptors of stderr, making it impossible to call fileno. I do not think that sys.stderr.fileno() should cause an error.

[codecov]

Codecov Report

Merging #69 (9fdd6f3) into master (97e06f3) will decrease coverage by 0.42%.
The diff coverage is 2.77%.

@@            Coverage Diff             @@
##           master      #69      +/-   ##
==========================================
- Coverage   28.21%   27.79%   -0.43%     
==========================================
  Files          25       26       +1     
  Lines        2307     2342      +35     
==========================================
  Hits          651      651              
- Misses       1656     1691      +35     

Impacted Files	Coverage Δ
baseclasses/utils/redirectIO.py	0.00% <0.00%> (ø)
baseclasses/__init__.py	100.00% <100.00%> (ø)

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[akleb]

I have been using this with both pyHyp and ADflow and they both are redirecting IO properly in a with block, something like this:

f_stream = open(os.path.join(os.path.dirname(output), self.getOption("meshLog")), "w")
with redirectIO.redirectingIO(f_stream):
    hyp = pyHyp(options=options)
    hyp.run()
    hyp.writeCGNS(output + "_L0.cgns")
print("Saying something back in terminal instead of f_stream")

The redirectingIO function closes the f_stream after it is finished with it

[marcomangano]

I have been using this with both pyHyp and ADflow and they both are redirecting IO properly in a with block, something like this:

f_stream = open(os.path.join(os.path.dirname(output), self.getOption("meshLog")), "w")
with redirectIO.redirectingIO(f_stream):
    hyp = pyHyp(options=options)
    hyp.run()
    hyp.writeCGNS(output + "_L0.cgns")
print("Saying something back in terminal instead of f_stream")

The redirectingIO function closes the f_stream after it is finished with it

I think it could be beneficial to add something like this as an example in the function docstrings, I did not fully realize this was the way to call the function

[akleb]

Not sure how to get the redirectIO functions in the docs without importing them in baseclasses.utils.__init__.py, which I thought we were moving away from. Or do we just not want to import them in baseclasses.__init__.py?

[marcomangano]

We should bump the version here as well

[sseraj]

Looks pretty good. Some minor comments