Re: [OpenBabel-Devel] Debugging tests
It would help a lot to know more about the patch. Yes, it seems as if the coordinates are different. This may be less relevant (e.g., you change a force field, so the optimization will differ). Best, -Geoff On Feb 14, 2024 at 3:35:14 PM, David van der Spoel < david.vandersp...@icm.uu.se> wrote: > Dear devs, > > I'm trying to debug the output of a test for a patch that I wrote: > > 230/233 Test #230: pybindtest_obconv_writers ***Failed Error > regular expression found in output. Regex=[FAIL] 0.73 > > Running it with > % export CTEST_OUTPUT_ON_FAILURE=1 > % cmake -P > "/Users/spoel/tmp/openbabel/build/test/pybindtest_obconv_writers.cmake" > >& output.txt > > Yields in the output.txt the following from what I deduce that > coordinates are generated incorrectly. Is that correct? Is there a way > to analyze this in a more comprehensible manner? > > Traceback (most recent call last): > File "/Users/spoel/tmp/openbabel/test/testobconv_writers.py", line > 2761, in test_default > self.assertWriters(self.fmt, """\ > File "/Users/spoel/tmp/openbabel/test/testobconv_writers.py", line > 258, in assertWriters > test_write_string(self, mol, conv, expected_output, normalize) > File "/Users/spoel/tmp/openbabel/test/testobconv_writers.py", line > 165, in test_write_string > test_case.assertMultiLineEqual(output.replace("\r\n", "\n"), > expected_output.replace("\r\n", "\n")) > AssertionError: '{\n [1926 chars]102014\n ],\n "y": [[1072 > chars]]\n}' != '{\n [1926 chars]102012\ > n ],\n "y": [[1070 chars]]\n}' > { > > "conformers": [ > { > "x": [ > 1.5846, > 1.5703, > 2.4295, > 3.3031, > 3.3175, > 0.0, > -1.0005, > 2.313816216007316, > 0.669250157347277, > 2.4146659588503769, > 4.189331679349326, > 4.052466878708012, > - -1.4648575597102014 > ? ^ > + -1.4648575597102012 > ? ^ > ], > "y": [ > - -0.0249, > - 0.9755, > - 1.4882, > ?^^^ > + 1.5846, > ? ++ ^ > - 1.0004, > ?^^^ > + 1.5703, > ? ++ ^ > - -0.0, > ? ^^ ^ > + 2.4295, > ? ^ > + 3.3031, > + 3.3175, > 0.0, > - 0.0051, > ? ^- > + -1.0005, > ? ^^ + > - -0.7551518129467202, > - 1.4786234252700852, > - 2.520093381713039, > - 1.5291886255562557, > - -0.7244637238690441, > - 0.8189433858796095 > + 2.313816216007316, > + 0.669250157347277, > + 2.4146659588503769, > + 4.189331679349326, > + 4.052466878708012, > + -1.4648575597102012 > ], > > -- > David van der Spoel, Ph.D., > Professor of Computational Molecular Biophysics > Uppsala University. > http://virtualchemistry.org > > > > > > > > > > När du har kontakt med oss på Uppsala universitet med e-post så innebär > det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör > det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ > > E-mailing Uppsala University means that we will process your personal > data. For more information on how this is performed, please read here: > http://www.uu.se/en/about-uu/data-protection-policy > > > ___ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] Debugging tests
Any suggestion? On 2024-02-14 21:35, David van der Spoel wrote: Dear devs, I'm trying to debug the output of a test for a patch that I wrote: 230/233 Test #230: pybindtest_obconv_writers ***Failed Error regular expression found in output. Regex=[FAIL] 0.73 Running it with % export CTEST_OUTPUT_ON_FAILURE=1 % cmake -P "/Users/spoel/tmp/openbabel/build/test/pybindtest_obconv_writers.cmake" >& output.txt Yields in the output.txt the following from what I deduce that coordinates are generated incorrectly. Is that correct? Is there a way to analyze this in a more comprehensible manner? Traceback (most recent call last): File "/Users/spoel/tmp/openbabel/test/testobconv_writers.py", line 2761, in test_default self.assertWriters(self.fmt, """\ File "/Users/spoel/tmp/openbabel/test/testobconv_writers.py", line 258, in assertWriters test_write_string(self, mol, conv, expected_output, normalize) File "/Users/spoel/tmp/openbabel/test/testobconv_writers.py", line 165, in test_write_string test_case.assertMultiLineEqual(output.replace("\r\n", "\n"), expected_output.replace("\r\n", "\n")) AssertionError: '{\n [1926 chars]102014\n ],\n "y": [[1072 chars]]\n}' != '{\n [1926 chars]102012\ n ],\n "y": [[1070 chars]]\n}' { "conformers": [ { "x": [ 1.5846, 1.5703, 2.4295, 3.3031, 3.3175, 0.0, -1.0005, 2.313816216007316, 0.669250157347277, 2.4146659588503769, 4.189331679349326, 4.052466878708012, - -1.4648575597102014 ? ^ + -1.4648575597102012 ? ^ ], "y": [ - -0.0249, - 0.9755, - 1.4882, ?^^^ + 1.5846, ? ++ ^ - 1.0004, ?^^^ + 1.5703, ? ++ ^ - -0.0, ? ^^ ^ + 2.4295, ? ^ + 3.3031, + 3.3175, 0.0, - 0.0051, ? ^ - + -1.0005, ? ^^ + - -0.7551518129467202, - 1.4786234252700852, - 2.520093381713039, - 1.5291886255562557, - -0.7244637238690441, - 0.8189433858796095 + 2.313816216007316, + 0.669250157347277, + 2.4146659588503769, + 4.189331679349326, + 4.052466878708012, + -1.4648575597102012 ], -- David van der Spoel, Ph.D., Professor of Computational Molecular Biophysics Uppsala University. http://virtualchemistry.org När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. -- David van der Spoel, Ph.D., Professor of Computational Molecular Biophysics Uppsala University. http://virtualchemistry.org När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
[OpenBabel-Devel] Debugging tests
Dear devs, I'm trying to debug the output of a test for a patch that I wrote: 230/233 Test #230: pybindtest_obconv_writers ***Failed Error regular expression found in output. Regex=[FAIL] 0.73 Running it with % export CTEST_OUTPUT_ON_FAILURE=1 % cmake -P "/Users/spoel/tmp/openbabel/build/test/pybindtest_obconv_writers.cmake" >& output.txt Yields in the output.txt the following from what I deduce that coordinates are generated incorrectly. Is that correct? Is there a way to analyze this in a more comprehensible manner? Traceback (most recent call last): File "/Users/spoel/tmp/openbabel/test/testobconv_writers.py", line 2761, in test_default self.assertWriters(self.fmt, """\ File "/Users/spoel/tmp/openbabel/test/testobconv_writers.py", line 258, in assertWriters test_write_string(self, mol, conv, expected_output, normalize) File "/Users/spoel/tmp/openbabel/test/testobconv_writers.py", line 165, in test_write_string test_case.assertMultiLineEqual(output.replace("\r\n", "\n"), expected_output.replace("\r\n", "\n")) AssertionError: '{\n [1926 chars]102014\n ],\n "y": [[1072 chars]]\n}' != '{\n [1926 chars]102012\ n ],\n "y": [[1070 chars]]\n}' { "conformers": [ { "x": [ 1.5846, 1.5703, 2.4295, 3.3031, 3.3175, 0.0, -1.0005, 2.313816216007316, 0.669250157347277, 2.4146659588503769, 4.189331679349326, 4.052466878708012, - -1.4648575597102014 ? ^ + -1.4648575597102012 ? ^ ], "y": [ - -0.0249, - 0.9755, - 1.4882, ?^^^ + 1.5846, ? ++ ^ - 1.0004, ?^^^ + 1.5703, ? ++ ^ - -0.0, ? ^^ ^ + 2.4295, ? ^ + 3.3031, + 3.3175, 0.0, - 0.0051, ? ^ - + -1.0005, ? ^^ + - -0.7551518129467202, - 1.4786234252700852, - 2.520093381713039, - 1.5291886255562557, - -0.7244637238690441, - 0.8189433858796095 + 2.313816216007316, + 0.669250157347277, + 2.4146659588503769, + 4.189331679349326, + 4.052466878708012, + -1.4648575597102012 ], -- David van der Spoel, Ph.D., Professor of Computational Molecular Biophysics Uppsala University. http://virtualchemistry.org När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel