tests fail when building with HTSLIB_MODE=external

[nieder]

When building pysam-0.14.1 against my locally installed htslib-1.7, the tests fail like this:

	export HTSLIB_MODE=external HTSLIB_INCLUDE_DIR=/sw/include HTSLIB_LIBRARY_DIR=/sw/lib
	/sw/bin/python2.7 setup.py build
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
...
/sw/bin/pytest-2.7 tests
...
===================================================================================== FAILURES ======================================================================================
__________________________________________________________________________ TestRemoteFileHTTP.testFetchAll __________________________________________________________________________

self = <tabix_test.TestRemoteFileHTTP testMethod=testFetchAll>

    def setUp(self):
>       if not pysam.config.HAVE_LIBCURL or not check_url(self.url):
E       AttributeError: 'module' object has no attribute 'HAVE_LIBCURL'

tests/tabix_test.py:1049: AttributeError
___________________________________________________________________________ TestRemoteFileHTTP.testHeader ___________________________________________________________________________

self = <tabix_test.TestRemoteFileHTTP testMethod=testHeader>

    def setUp(self):
>       if not pysam.config.HAVE_LIBCURL or not check_url(self.url):
E       AttributeError: 'module' object has no attribute 'HAVE_LIBCURL'

tests/tabix_test.py:1049: AttributeError
_____________________________________________________________________ TestRemoteFileHTTPWithHeader.testFetchAll _____________________________________________________________________

self = <tabix_test.TestRemoteFileHTTPWithHeader testMethod=testFetchAll>

    def setUp(self):
>       if not pysam.config.HAVE_LIBCURL or not check_url(self.url):
E       AttributeError: 'module' object has no attribute 'HAVE_LIBCURL'

tests/tabix_test.py:1088: AttributeError
______________________________________________________________________ TestRemoteFileHTTPWithHeader.testHeader ______________________________________________________________________

self = <tabix_test.TestRemoteFileHTTPWithHeader testMethod=testHeader>

    def setUp(self):
>       if not pysam.config.HAVE_LIBCURL or not check_url(self.url):
E       AttributeError: 'module' object has no attribute 'HAVE_LIBCURL'

tests/tabix_test.py:1088: AttributeError
================================================================================= warnings summary ==================================================================================
tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBam2
  /sw/build.build/pysam-py27-0.14.1-1/pysam-0.14.1/tests/AlignmentFile_test.py:1397: UserWarning: no BGZF EOF marker; file may be truncated
    ignore_truncation=True)

-- Docs: http://doc.pytest.org/en/latest/warnings.html
========================================================== 4 failed, 891 passed, 15 skipped, 1 warnings in 153.23 seconds ===========================================================

My external htslib-1.7 was configured with --enable-libcurl and HAVE_LIBCURL was defined in its config.h file. If I switch the build to htslib mode = shared, then the tests all pass.

[0xaf1f]

I'm seeing this as well when trying to update the Debian package.

[smoe]

Can confirm for 0.15.1.

[AndreasHeger]

Thanks, will look into this.

[smoe]

I happily prepare a VM for you should you find any difficulty to reproduce this behaviour.

[AndreasHeger]

Thanks, that might be useful, afaik we check external mode in our ci on Travis. Cheers, Andreas

…

On Sat, 15 Sep 2018, 09:32 Steffen Möller, ***@***.***> wrote: I happily prepare a VM for you should you find any difficulty to reproduce this behaviour. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#665 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AEOKYGbD3QAuF_G3MzHfyUBY83haimaaks5ubLskgaJpZM4TTTDl> .

[AndreasHeger]

But have not checked yet, until tonight.

…

On Sat, 15 Sep 2018, 10:10 Andreas Heger, ***@***.***> wrote: Thanks, that might be useful, afaik we check external mode in our ci on Travis. Cheers, Andreas On Sat, 15 Sep 2018, 09:32 Steffen Möller, ***@***.***> wrote: > I happily prepare a VM for you should you find any difficulty to > reproduce this behaviour. > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > <#665 (comment)>, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/AEOKYGbD3QAuF_G3MzHfyUBY83haimaaks5ubLskgaJpZM4TTTDl> > . >

[jmarshall]

I haven't recently run the tests with HTSLIB_MODE=external, but this should have been fixed by 2cc584b.