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Coverage fixes #710

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coveralls and codecov were broken.

fixes #709

Kris Thielemans added 2 commits June 6, 2020 23:28
coverage was broken in a few ways:
- .coverage was in a different place than we thought
- OSX sed doesn't support -r but needs -E
- we were not necessarily using the correct python
fixes SyneRBI#709
@KrisThielemans
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Location is fine now. However, at least 2 problems:

    Generating coverage xml reports for Python
    Error running `['/usr/bin/python3', '-m', 'coverage', 'xml', '-i']`: Command '['/usr/bin/python3', '-m', 'coverage', 'xml', '-i']' returned non-zero exit status 1
    - Ignored: [Errno 2] No such file or directory: '/home/travis/build/SyneRBI/SIRF/coverage.xml'
Error: No coverage report found
0.19s$ $PY_EXE -m coveralls
Submitting coverage to coveralls.io...
Traceback (most recent call last):
  File "/home/travis/.local/lib/python3.5/site-packages/coverage/sqldata.py", line 1048, in execute
    return self.con.execute(sql, parameters)
sqlite3.DatabaseError: database disk image is malformed
....
coverage.misc.CoverageException: Couldn't use data file '/home/travis/build/SyneRBI/SIRF/.coverage': database disk image is malformed

Possibly both of these have the same cause. I wonder if this is because .coverage is an SQLite database, and the sed corrupts it (quite likely as it has tons of \0).

Oh well.

@KrisThielemans
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Seems that this fixed the OSX command argument and python issues.

On OSX, sed says explicitly that this is a binary file
https://travis-ci.org/github/SyneRBI/SIRF/jobs/695522266#L28294

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coverage and codecov
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