subject:"\[OpenBabel\-Devel\] Debugging tests"

Re: [OpenBabel-Devel] Debugging tests

2024-02-22 Thread Geoffrey Hutchison

 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
>
>
> ___
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> OpenBabel-Devel@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-devel
>
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Re: [OpenBabel-Devel] Debugging tests

2024-02-21 Thread David van der Spoel


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:
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--
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: 
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[OpenBabel-Devel] Debugging tests

2024-02-14 Thread David van der Spoel


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


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Re: [OpenBabel-Devel] Debugging tests

Re: [OpenBabel-Devel] Debugging tests

[OpenBabel-Devel] Debugging tests

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