coverage and codecov

[KrisThielemans]

doesn't look like .coverage is being generated (at least not in the expected location). TL;DR travis logs (after ctest passes):

$ pushd ../SIRF
$ codecov
    Error running `['/usr/bin/python2', '-m', 'coverage', 'xml', '-i']`: Command '['/usr/bin/python2', '-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
$ coveralls
coverage.misc.CoverageException: Data file '/home/travis/build/SyneRBI/SIRF/.coverage' doesn't seem to be a coverage data file: Couldn't use data file '/home/travis/build/SyneRBI/SIRF/.coverage': no such table: coverage_schema

Originally posted by @casperdcl in #614 (comment)

[KrisThielemans]

@casperdcl That's for a Linux job. Indeed, there's no .coverage in SIRF. Who's supposed to make it?

OSX job

https://travis-ci.org/github/SyneRBI/SIRF/jobs/695339402#L16824-L16833

0.04s$ pushd ../SIRF
after_success.2
0.01s$ sed -r 's/SIRF-SuperBuild\/INSTALL\/python\/sirf\/(\w*)\.py/SIRF\/src\/x\1\/p\1\/\1.py/g' ../SIRF-SuperBuild/sources/SIRF/.coverage > .coverage
sed: illegal option -- r
usage: sed script [-Ealn] [-i extension] [file ...]
       sed [-Ealn] [-i extension] [-e script] ... [-f script_file] ... [file ...]
after_success.3
0.01s$ codecov
/Users/travis/.travis/functions: line 109: codecov: command not found
after_success.4
0.01s$ coveralls
/Users/travis/.travis/functions: line 109: coveralls: command not found

First item is probably because OSX sed doesn't like `-r.

Last item is probably because we should prefix with $PY_EXE as

SIRF/.travis.yml

Line 204 in 586d597

- $PY_EXE -m pip install --user -U nose codecov coveralls requests

In fact, should we be running coverage etc on all Travis jobs?

[casperdcl]

Indeed, there's no .coverage in SIRF. Who's supposed to make it?

ctest should make it (assuming the underlying test frameworks generate coverage, e.g. python -m nose --with-coverage --cover-package=sirf or similar)

In fact, should we be running coverage etc on all Travis jobs?

yes we should if different jobs/platforms run different lines of code

[KrisThielemans]

ok. ctest is indeed running
/usr/bin/python "-m" "nose" "--with-coverage" "--cover-package=sirf.Gadgetron" "src/xGadgetron/pGadgetron/"
etc.
I've tested it on the VM, and ctest makes ../sources/SIRF/.coverage. So I guess the Travis job writes it somewhere else

https://travis-ci.org/github/SyneRBI/SIRF/jobs/695339398#L1759 confirms we're building in

-DSIRF_SOURCE_DIR:PATH=/home/travis/build/SyneRBI/SIRF

https://travis-ci.org/github/SyneRBI/SIRF/jobs/695339398#L26582-L26583 says that we're indeed going there before running `sed

$ pushd ../SIRF
~/build/SyneRBI/SIRF ~/build/SyneRBI/SIRF-SuperBuild
$ sed -r 's/SIRF-SuperBuild\/INSTALL\/python\/sirf\/(\w*)\.py/SIRF\/src\/x\1\/p\1\/\1.py/g' ../SIRF-SuperBuild/sources/SIRF/.coverage > .coverage

So, it is likely that the sed is picking it up from the wrong place.

RE sed -r not being available on MacOS, looks like we can use sed -E, which works on Ubuntu as well. Note that "inplace" sed on MacOS seems tricky. oh well.

[KrisThielemans]

outdated as we no longer use Travis.

we might be sorting this out for GHA in #1149