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Author SHA1 Message Date
Nathan Baker
a647b80ae3 Add DOIs to references 
Make life easier for people.
 2020-05-23 11:47:00 -07:00
Nathan Baker
f2aef4ce4f De-lint bonds.py 2020-05-23 09:57:53 -07:00
Nathan Baker
e1656a4911 Remove exec() from atom.py 2020-05-23 09:44:50 -07:00
Nathan Baker
3cfcc8f6d3 Merge pull request #33 from Electrostatics/nathan/delint 
De-lint atoms.py and part of bonds.py
 2020-05-23 09:39:02 -07:00
Nathan Baker
120718fbd8 Remove property method suggestion. 
Addresses https://github.com/jensengroup/propka-3.1/pull/33#discussion_r429113755
 2020-05-23 09:33:47 -07:00
Nathan Baker
df6d8492da Simplify bonded atom counting 
Co-authored-by: Oliver Beckstein <orbeckst@gmail.com>
 2020-05-23 09:31:23 -07:00
Nathan Baker
69a369c17f Remove suggestion for @property method. 
Addresses https://github.com/jensengroup/propka-3.1/pull/33#discussion_r429112013
 2020-05-23 09:29:24 -07:00
Nathan Baker
4b3dee54f7 Simplify bonded atom counting. 
Addresses https://github.com/jensengroup/propka-3.1/pull/33#discussion_r429110880
and https://github.com/jensengroup/propka-3.1/pull/33#discussion_r429111421
 2020-05-23 09:26:03 -07:00
Nathan Baker
66e3e552c9 Add description of hybrid36. 
Addresses https://github.com/jensengroup/propka-3.1/pull/33#discussion_r429108127
 2020-05-23 09:20:49 -07:00
Nathan Baker
98ad8702d6 Merge branch 'master' into nathan/delint 2020-05-23 09:20:01 -07:00
Nathan Baker
5114442610 Merge branch 'master' into nathan/delint 2020-05-23 08:57:50 -07:00
Nathan Baker
62f7dfce1a Merge pull request #36 from Electrostatics/nathan/tests 
Add pytest-based testing to PROPKA
 2020-05-23 08:44:00 -07:00
Nathan Baker
73f0ce47af Replace pandas with numpy.testing 
Addresses https://github.com/jensengroup/propka-3.1/pull/36#discussion_r429104797
 2020-05-23 08:40:17 -07:00
Nathan Baker
0b4241cce6 Merge remote-tracking branch 'origin/nathan/argpase' into nathan/tests 2020-05-23 08:25:24 -07:00
Nathan Baker
ebddfa1f9f Add tests_require argument to setup.py. 
Addresses https://github.com/jensengroup/propka-3.1/pull/36#discussion_r429100526

Since the tests_require argument is deprecated, I'm also leaving the
requirements.txt file to make sure the dependencies are captured in the
future.
 2020-05-23 08:19:19 -07:00
Nathan Baker
1b0ad999b1 Remove unnecessary exception catching. 
Fixes https://github.com/jensengroup/propka-3.1/pull/36#discussion_r429063049
 2020-05-23 08:06:54 -07:00
Nathan Baker
6f603ab17c Merge pull request #37 from Electrostatics/nathan/argpase 
Fix error when using PROPKA with PDB2PQR
 2020-05-23 08:04:30 -07:00
Nathan Baker
6288711209 Update requirements with pandas. 
See https://github.com/jensengroup/propka-3.1/pull/36#discussion_r429106093
 2020-05-22 21:04:09 -07:00
Nathan Baker
2266e0a102 Consistent test naming. 
See https://github.com/jensengroup/propka-3.1/pull/36#discussion_r429099054
 2020-05-22 20:55:58 -07:00
Nathan Baker
48f69eb544 Support Python 3.5 and higher. 
See https://github.com/jensengroup/propka-3.1/pull/36#discussion_r429094884
 2020-05-22 20:41:59 -07:00
Nathan Baker
03e12ae15c Update propka/lib.py 
I cannot spell.

Co-authored-by: Oliver Beckstein <orbeckst@gmail.com>
 2020-05-22 20:22:30 -07:00
Nathan Baker
80c8cca420 Nuke some backwards-compatible PROPKA 3.0 support. 2020-05-21 20:50:39 -07:00
Nathan Baker
76418a1a15 De-lint calculations.py up to difficult decision. 
Do we drop 3.0 support?  I vote "yes" but will leave that for the next
commit.
 2020-05-21 20:45:47 -07:00
Nathan Baker
013167026f De-lint bonds.py 2020-05-21 19:29:54 -07:00
Nathan Baker
51a59f9979 Merge branch 'nathan/tests' into nathan/delint 2020-05-21 15:58:49 -07:00
Nathan Baker
a49015c297 Merge branch 'nathan/tests' into nathan/argpase 2020-05-21 15:58:03 -07:00
Nathan Baker
f13d3d8121 PROPKA testing working with pytest. 2020-05-21 15:50:23 -07:00
Nathan Baker
fc27d8bfc3 Fix bugs in invocation and options. 
Add non-command-arguments.
Restore --quiet option.
 2020-05-21 11:53:03 -07:00
Nathan Baker
393f5cee50 Rename "Tests" directory for consistency. 2020-05-21 10:39:08 -07:00
Nathan Baker
fa4a547f1f Enforce Python 3.*. 2020-05-21 10:29:45 -07:00
Nathan Baker
17bad90dc4 Start fixing tests. 2020-05-18 20:37:56 -07:00
Nathan Baker
d0e80b810b Handle multiple additions of same argument. 
APBS and PROPKA add the same arguments.
 2020-05-18 16:29:39 -07:00
Nathan Baker
747333d4ac Merge branch 'master' into nathan/delint 2020-05-18 16:27:58 -07:00
Nathan Baker
e9a88bee4b Restore Tests/runtest.py. 
Also update README.md to document the existence of multiple tests.
 2020-05-18 16:23:39 -07:00
Nathan Baker
10efc3c7f9 De-lint propka/atom.py 
Other changes are a result of Atom use in other files.
 2020-05-17 17:08:38 -07:00
Nathan Baker
303aaae25a Partial pylint de-linting of bonds.py. 2020-05-16 21:11:09 -07:00
Nathan Baker
22d83ae29e Fix some pylint issues for propka.atom. 
Only implemented fixes that do not change functonality.
Avoided changing numbers of arguments, numbers of attribute,
variable/function names, etc.
 2020-05-16 21:10:55 -07:00
Nathan Baker
61c200c3f4 Remove duplicate tests. 2020-05-16 18:18:15 -07:00
Nathan Baker
6ae2908c4b Merge pull request #29 from Electrostatics/master 
* Replace PROPKA pickle with JSON.
* Replace optionparser with argparse.
* Fix tests for Ubuntu WSL.
* Fix verbosity/logging.
 2020-05-16 17:09:52 -07:00
Nathan Baker
0fbaa6711f Update minor version number. 
Addresses
https://github.com/jensengroup/propka-3.1/pull/29#discussion_r424575807
 2020-05-16 17:06:28 -07:00
Nathan Baker
6c67ef152c Remove unnecessary OptionParser statements. 
Addresses
https://github.com/jensengroup/propka-3.1/pull/29#discussion_r424418158.
 2020-05-16 16:58:19 -07:00
Nathan Baker
9cafb41e06 Document acceptable error in PROPKA tests. 
Addresses
https://github.com/jensengroup/propka-3.1/pull/29#discussion_r424572620
 2020-05-16 16:49:47 -07:00
Nathan Baker
cddda2f515 Fix verbosity/logging in PROPKA. 2020-05-14 19:02:11 -07:00
Nathan Baker
387d0a5664 Move argparse sub-command to group. 2020-05-12 14:27:46 -07:00
Nathan Baker
847004a2d6 Fix subparser syntax for argparse. 2020-05-12 13:51:44 -07:00
Nathan Baker
6ddc32c101 Add newline to end of __init__.py. 2020-05-12 13:51:24 -07:00
Nathan Baker
ae7e8b6430 Replace optparse with argparse. 
Optparse is deprecated.  Argparse will allow tighter integration with
PDB2PQR/APBS.
 2020-05-12 13:13:28 -07:00
Nathan Baker
aeb1663d7b Add code to clean up files after test. 2020-05-10 19:19:37 -07:00
Nathan Baker
997298f1f0 Loosen error tolerance in test. 
The PROPKA31 tests fail on Windows 10 Ubuntu 18.04 Windows Subsystem
Linux without any changes.  The relative error is less than 1e-3.  This
commit chnages the behavior to a test of absolute agreement to a test of
relative error less than 1e-3.
 2020-05-10 18:29:51 -07:00
Nathan Baker
4fa015a54e Fix typo in PROPKA test. 
Fail() -> fail().
 2020-05-10 18:18:36 -07:00