[Biopython] Getting apparently spurious errors when running tests

Tue Feb 20 09:46:42 UTC 2018

Hi Gregory,

The good news is these two issues are harmless.

ExPASy HTTP vs HTTPS has been fixed:
https://github.com/biopython/biopython/pull/1428

The second issue is white space differences in NumPy 1.14,
which we have not yet properly resolved:

https://github.com/biopython/biopython/issues/1496

Peter

On Tue, Feb 20, 2018 at 3:52 AM, Dougherty, Gregory T., M.S.
<Dougherty.Gregory at mayo.edu> wrote:
> Installed biopython 1.7 running under anaconda installed python 2.7.14
>
> The first two failures involve a URL conflict where one has http, and the
> other has https.
>
> The last four come from arrays, and the only difference I see is the
> “expected” have two spaces between each number, and the “actual” have only
> one space.
>
> $ cd ../../biopython-1.70/Tests/
> $ python run_tests.py
> Python version: 2.7.14 |Anaconda, Inc.| (default, Dec  7 2017, 17:05:42)
> [GCC 7.2.0]
> Operating system: posix linux2
> ...
> Bio.SVDSuperimposer docstring test ... FAIL
> FAIL: test_prodoc_html (test_ExPASy.ExPASyOnlineTests)
> Traceback (most recent call last):
>   File "~/build/biopython-1.70/Tests/test_ExPASy.py", line 51, in
> test_prodoc_html
>     'http://prosite.expasy.org/cgi-bin/prosite/get-prodoc-entry?PDOC00001')
> AssertionError:
> 'https://prosite.expasy.org/cgi-bin/prosite/get-prodoc-entry?PDOC00001' !=
> 'http://prosite.expasy.org/cgi-bin/prosite/get-prodoc-entry?PDOC00001'
>
> FAIL: test_prosite_html (test_ExPASy.ExPASyOnlineTests)
> Traceback (most recent call last):
>   File "~/build/biopython-1.70/Tests/test_ExPASy.py", line 43, in
> test_prosite_html
>     'http://prosite.expasy.org/cgi-bin/prosite/get-prosite-entry?PS00001')
> AssertionError:
> 'https://prosite.expasy.org/cgi-bin/prosite/get-prosite-entry?PS00001' !=
> 'http://prosite.expasy.org/cgi-bin/prosite/get-prosite-entry?PS00001'
>
> FAIL: Record (Bio.Affy.CelFile)
> Doctest: Bio.Affy.CelFile.Record
> Traceback (most recent call last):
>   File "~/anaconda2/lib/python2.7/doctest.py", line 2226, in runTest
>     raise self.failureException(self.format_failure(new.getvalue()))
> AssertionError: Failed doctest test for Bio.Affy.CelFile.Record
>   File
> "~/build/biopython-1.70/build/lib.linux-x86_64-2.7/Bio/Affy/CelFile.py",
> line 35, in Record
>
> File
> "~/build/biopython-1.70/build/lib.linux-x86_64-2.7/Bio/Affy/CelFile.py",
> line 46, in Bio.Affy.CelFile.Record
> Failed example:
>     print(c.intensities)
> Expected:
>     [[   234.    170.  22177.    164.  22104.]
>      [   188.    188.  21871.    168.  21883.]
>      [   188.    193.  21455.    198.  21300.]
>      [   188.    182.  21438.    188.  20945.]
>      [   193.  20370.    174.  20605.    168.]]
> Got:
>     [[  234.   170. 22177.   164. 22104.]
>      [  188.   188. 21871.   168. 21883.]
>      [  188.   193. 21455.   198. 21300.]
>      [  188.   182. 21438.   188. 20945.]
>      [  193. 20370.   174. 20605.   168.]]
> File
> "~/build/biopython-1.70/build/lib.linux-x86_64-2.7/Bio/Affy/CelFile.py",
> line 52, in Bio.Affy.CelFile.Record
> Failed example:
>     print(c.stdevs)
> Expected:
>     [[   24.     34.5  2669.     19.7  3661.2]
>      [   29.8    29.8  2795.9    67.9  2792.4]
>      [   29.8    88.7  2976.5    62.   2914.5]
>      [   29.8    76.2  2759.5    49.2  2762. ]
>      [   38.8  2611.8    26.6  2810.7    24.1]]
> Got:
>     [[  24.    34.5 2669.    19.7 3661.2]
>      [  29.8   29.8 2795.9   67.9 2792.4]
>      [  29.8   88.7 2976.5   62.  2914.5]
>      [  29.8   76.2 2759.5   49.2 2762. ]
>      [  38.8 2611.8   26.6 2810.7   24.1]]
>
>
> ======================================================================
> FAIL: SVDSuperimposer (Bio.SVDSuperimposer)
> Doctest: Bio.SVDSuperimposer.SVDSuperimposer
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "~/anaconda2/lib/python2.7/doctest.py", line 2226, in runTest
>     raise self.failureException(self.format_failure(new.getvalue()))
> AssertionError: Failed doctest test for Bio.SVDSuperimposer.SVDSuperimposer
>   File
> "~/build/biopython-1.70/build/lib.linux-x86_64-2.7/Bio/SVDSuperimposer/__init__.py",
> line 24, in SVDSuperimposer
>
> File
> "~/build/biopython-1.70/build/lib.linux-x86_64-2.7/Bio/SVDSuperimposer/__init__.py",
> line 83, in Bio.SVDSuperimposer.SVDSuperimposer
> Failed example:
>     print(y_on_x1)
> Expected:
>     [[  5.17e+01  -1.90e+00   5.01e+01]
>      [  5.04e+01  -1.23e+00   5.06e+01]
>      [  5.07e+01  -4.16e-02   5.15e+01]
>      [  5.02e+01  -1.94e-02   5.29e+01]]
> Got:
>     [[ 5.17e+01 -1.90e+00  5.01e+01]
>      [ 5.04e+01 -1.23e+00  5.06e+01]
>      [ 5.07e+01 -4.16e-02  5.15e+01]
>      [ 5.02e+01 -1.94e-02  5.29e+01]]
>
> File
> "~/build/biopython-1.70/build/lib.linux-x86_64-2.7/Bio/SVDSuperimposer/__init__.py",
> line 88, in Bio.SVDSuperimposer.SVDSuperimposer
> Failed example:
>     print(y_on_x2)
> Expected:
>     [[  5.17e+01  -1.90e+00   5.01e+01]
>      [  5.04e+01  -1.23e+00   5.06e+01]
>      [  5.07e+01  -4.16e-02   5.15e+01]
>      [  5.02e+01  -1.94e-02   5.29e+01]]
> Got:
>     [[ 5.17e+01 -1.90e+00  5.01e+01]
>      [ 5.04e+01 -1.23e+00  5.06e+01]
>      [ 5.07e+01 -4.16e-02  5.15e+01]
>      [ 5.02e+01 -1.94e-02  5.29e+01]]
>
>
> ----------------------------------------------------------------------
> Ran 274 tests in 520.026 seconds
>
> FAILED (failures = 3)
>
> --
> Gregory Dougherty
> Sr. Analyst/Programmer
> Information Technology
>
>
> _______________________________________________
> Biopython mailing list  -  Biopython at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython