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32 Commits

Author SHA1 Message Date
Xiang Zhong
7702b2bc44 update interface pybel.py (#2509) 
* update interface pybel.py & testpybel.py
 2022-08-04 10:23:50 -04:00
Geoff Hutchison
18665b94fe Merge pull request #2466 from e-kwsm/IOError 
python: replace IOError with OSError
 2022-06-09 18:35:15 -04:00
Eisuke Kawashima
0f4af753d4 test(python): improve usages of unitest.TestCase methods 2022-04-27 13:26:48 +09:00
Eisuke Kawashima
77530fb0aa python: replace IOError with OSError 
https://peps.python.org/pep-3151/
 2022-04-25 16:37:29 +09:00
Eisuke Kawashima
b657ca216c Fix import of openbabel 2019-10-10 16:54:59 +09:00
Noel O'Boyle
532ca37c32 Merge pull request #1970 from e-kwsm/improve-python 
Improve python script
 2019-04-18 08:26:25 +01:00
Yi-Shu Tu
26f192587f Add __entry__ and __exit__ methods to pybel.Outputfile 2019-04-18 14:13:00 +08:00
Eisuke Kawashima
6b57788a05 Improve python script 
- `from __future__ import print_function`
- replace deprecated `unittest.TestCase.assertEquals` with
  `assertEqual`, `assertTrue`, or `assertFalse`
- use `obj is None` instead of `obj == None`
- remove modules and functions that are imported but not used
 2019-04-17 21:59:20 +09:00
Noel O'Boyle
5f58dd2a90 Update tests 2019-03-04 20:45:27 +00:00
Eloy Felix
4baf8a674b add Molecule.make2D function, fixed test 2018-01-24 17:30:14 +00:00
Eloy Felix
06e233e2ca add Molecule.make2D function 2018-01-24 16:49:44 +00:00
Geoff Hutchison
5f083787cf Fix pybel test failure by renaming expected output to UNL from LIG 2014-03-15 15:59:37 -04:00
Noel O'Boyle
c19f75c45f scripts/python/testpybel.py: Minor fix to enable failing test to pass. Failures due to the new MOL Chiral Flag data that I stored a while ago. 2012-10-01 20:40:36 +00:00
Geoffrey Hutchison
c08b71defc Add test Python script from Andrew Dalke. 2012-07-26 19:12:40 +00:00
Noel O'Boyle
0e6c1f59ee Simplify installation of Python bindings: Now there is only one version of pybel.py for Py 2.x and Py 3.x. It also includes support for Jython and IronPython. 2012-06-26 13:43:25 +00:00
Noel O'Boyle
2b13e591d6 testpybel.py: Update for corrected unit cell parameters. I should have checked this in a long time ago... 2012-05-17 12:58:21 +00:00
Noel O'Boyle
e4f82feb86 testpybel.py: Fix typo in commit of a few days ago. Test should pass now. 2010-10-07 19:03:48 +00:00
Noel O'Boyle
5e87842233 Rename pybel versions for Py 2 and 3 so that they can be imported directly during testing. Associated changes in testpybel setup.py and testbindings.py. 
This fixes a problem running testbindings.py in the testsuite on Windows. (It was importing the globalling installed pybel.py)
 2010-10-04 12:37:06 +00:00
Noel O'Boyle
7fa8ad6093 * scripts/python/examples/testpybel.py: Make test of number of descriptors more general. Should pass now. 2010-10-02 19:23:48 +00:00
Noel O'Boyle
7cf0b904e4 Get pybel tests to pass once again on Windows. 2010-08-11 15:45:33 +00:00
Noel O'Boyle
acd2e935e2 * Set svn:eol-style to native for all text files. 2010-06-03 14:29:31 +00:00
Noel O'Boyle
f57656970e 2010-04-26 Noel O'Boyle 
* test/CMakeLists.txt, test/testbindings.py, test/test_pybel.py:
	Separate the pybel tests from the Python binding tests
	* scripts/python/examples/testpybel.py: Get the Pybel tests to pass on
	Linux
	* scripts/CMakeLists.txt: Force the Python build to output to
	scripts/pybuild. Otherwise it created a temporary folder whose name
	differed from platform to platform (e.g. lib.linux-x86_64.2.6) which
	made it difficult to handle automatically.
 2010-04-27 09:35:35 +00:00
Noel O'Boyle
3d6dc5d93b 2010-04-25 Noel O'Boyle 
* test\CMakeLists.txt, test\testbindings.py, test\testexample.py:
	Enable the use of the Python bindings for testing. Run the Pybel
	tests. Add a simple example test as a template.
	* scripts\python\examples\testpybel.py: Get the Pybel tests to pass
 2010-04-25 11:30:10 +00:00
Noel O'Boyle
afb12d1eb7 2009-09-21 Noel O'Boyle <baoilleach@gmail.com> 
* scripts/*: Copied + pasted the scripts directory from 22x as a number
	of commits were never merged.
 2009-09-21 11:12:00 +00:00
Noel O'Boyle
a9195af4df Pybel: minor fix to test suite for running outside cinfony 2008-05-23 08:33:37 +00:00
Noel O'Boyle
79b8f3db20 Pybel: Synching with cinfony, and getting ready for release as 1.3 2008-05-23 08:19:28 +00:00
Tim Vandermeersch
206459784e * scripts/python/examples/*.py: Added some force field examples. More 
will follow.
 2008-04-30 00:01:40 +00:00
Noel O'Boyle
a093a951ce Made pybel test suite compatible with Python 2.3 2008-02-01 16:28:33 +00:00
Noel O'Boyle
37588a1d49 * scripts/python/pybel.py, scripts/python/examples/testpybel.py: 
Updated to use plugin descriptors. Changed to create a single instance
	of plugin descriptors and fingerprinters. Also, readfile now raises an
	IOError if the file does not exist.
	* scripts/python/examples/findcoverage.bat: Add .bat file to automate
	calculation of code coverage for pybel
 2008-01-17 12:08:31 +00:00
Geoffrey Hutchison
858f8a39f9 * Merged in changes from 2.1.x branch. 2007-09-03 20:53:06 +00:00
Noel O'Boyle
8270b862df 2007-05-08 Noel O'Boyle <baoilleach@gmail.com> 
* scripting interfaces: added a method to cast OBGenericData to
	OBPairData
	* pybel: added dictionary-like support for accessing molecule data,
	and updated the tests and the API documentation
 2007-05-08 12:33:05 +00:00
Geoffrey Hutchison
113220be4c Merged revisions 1918-1933 via svnmerge from 
https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-1-x

........
  r1918 | ghutchis | 2007-03-30 14:25:42 -0400 (Fri, 30 Mar 2007) | 2 lines
  
  Produce a better "clean" before creating a distribution tar
........
  r1919 | ghutchis | 2007-03-30 16:46:51 -0400 (Fri, 30 Mar 2007) | 7 lines
  
    * include/openbabel/residue.h: Hide some residue names (e.g.,
    _1MG) from SWIG wrappers -- such constants are not valid symbols
    in some languages like Ruby.
  
    * scripts/ Update accordingly.
........
  r1920 | ghutchis | 2007-03-30 16:47:12 -0400 (Fri, 30 Mar 2007) | 4 lines
  
    * src/base.cpp: Additional "What's new" documentation for 2.1
    release.
........
  r1921 | ghutchis | 2007-03-30 16:47:34 -0400 (Fri, 30 Mar 2007) | 2 lines
  
  (missed changelog update.)
........
  r1922 | ghutchis | 2007-03-30 17:53:27 -0400 (Fri, 30 Mar 2007) | 2 lines
  
  Updated to use Ruby-style API names via SWIG -autorename
........
  r1923 | ghutchis | 2007-04-02 22:41:53 -0400 (Mon, 02 Apr 2007) | 7 lines
  
    * include/openbabel/residue.h: Undo previous change. Rich Apodaca
    suggested some SWIG-fu instead.
  
    * scripts/ Update accordingly. Includes ruby changes, new README
    and examples.
........
  r1924 | ghutchis | 2007-04-03 22:51:43 -0400 (Tue, 03 Apr 2007) | 2 lines
  
  Updated for 2.1 release of scripting interfaces.
........
  r1925 | ghutchis | 2007-04-04 00:06:50 -0400 (Wed, 04 Apr 2007) | 2 lines
  
  Moved examples to subdir (for cleaner-looking dist) and MANIFEST
........
  r1926 | ghutchis | 2007-04-04 20:58:12 -0400 (Wed, 04 Apr 2007) | 2 lines
  
  Updated for new Doxygen update (and new warnings)
........
  r1927 | timvdm | 2007-04-05 17:41:37 -0400 (Thu, 05 Apr 2007) | 4 lines
  
  - documentation update
  - covert to dative bonds (for psa)
  - psa.txt: fix smiles for 3-rings
........
  r1929 | ghutchis | 2007-04-07 14:43:05 -0400 (Sat, 07 Apr 2007) | 3 lines
  
    * NEWS: Minor fixes for 2.1.0 final release.
........
  r1930 | ghutchis | 2007-04-07 15:07:08 -0400 (Sat, 07 Apr 2007) | 2 lines
  
  Minor fixes. Corresponds to 2.1.0 released source.
........
  r1933 | ghutchis | 2007-04-13 13:44:01 -0400 (Fri, 13 Apr 2007) | 8 lines
  
    * src/formats/inchi/strutil.c: Bug reported on the InChI mailing
    list.
  
    * src/formats/inchiformat.cpp: Bug caught during ChemSpotlight
    testing -- some files don't have chirality information (e.g., 3D
    files but with 0.0 coordinates throughout). Warn and give up.
........
 2007-04-13 18:44:10 +00:00