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57ad5d838433d4c984dfedd6b86e8849a0b16e8d
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30 Commits

Author SHA1 Message Date
Thomas Holder
57ad5d8384 Typing: Parameters, vector_algebra 
- Parameters typing
- vector_algebra tests and refactoring
- Various pyright typing improvements
 2023-12-16 09:35:35 +01:00
Thomas Holder
50f62c61fb Refactor deprecated pkg_resources usage 
- Locate resources relative to `__file__`
- Support egg/zip with `open_file_for_reading`
 2023-12-10 11:59:21 +01:00
Thomas Holder
57d7c6721b Add type annotations and mypy CI job 2023-10-26 11:46:54 +02:00
Thomas Holder
54d76ec145 Add test for issue #140 2023-10-20 23:22:17 +02:00
Thomas Holder
7d78acac6e Improve MolecularContainer.top_up_conformations 
Top up from all conformations, not just first.

Fixes https://github.com/jensengroup/propka/issues/147
 2023-09-17 15:30:29 +02:00
Thomas Holder
6388e0c4ee Test pI (isoelectric point) result 2022-08-08 21:29:10 +02:00
Gydo van Zundert
b920f5aeec Add unit test for protonate.py 2022-03-02 15:45:11 -05:00
IAlibay
239c8183c9 Initial removal of PROPKA input 2020-11-17 23:31:24 +00:00
Oliver Beckstein
cb65c644c6 use versioneer for version management (#88) 
- fix #87
- user versioneer for version management
   - use tag "vMAJOR.MINOR.PATCH" to indicate release number
   - exclude generated files from coverage;
      also exclude tests from coverage reporting;
      allow use of "# pragma: no cover" to exclude lines of code
      from coverage
   - configure coverage with entries in setup.cfg (removed
      commandline config from workflows/python-package.yml)
- related doc updates
   - make docs automatically use current version
      (docs use versioneer-based propka.__version__)
   - also added @IAlibay to authors (forgotten in previous
      PRs #84 and #85)
   - generate a sitemap (add sphinx_sitemap to requirements.txt)
- add test_version
   Note: Versioneer-generated version is “0-untagged” on the branch where
   it is tested so need to add it to a valid result.
 2020-07-18 12:32:25 -07:00
Irfan Alibay
7563a706cf fixes run's single method (#85) 
* Fixes #82
* Changes:
    * input arguments now reflects the changes made to read_molecule_file in #84
    * Writing of pKa file is now optional (default behaviour has been kept). This will be particularly 
       useful downstream where we would just want to have access to the MoleculeContainer object.
     * new test_run file specific for testing run.
* add tests
* add docs
 2020-07-17 11:18:07 -07:00
IAlibay
81e51c34bc remove unecessary tmpdir 2020-07-15 19:34:33 +01:00
IAlibay
c24f59b6d4 removes spurious empty line 2020-07-15 18:34:21 +01:00
IAlibay
dd7434fc37 remove unused import and fix error test 2020-07-15 18:26:26 +01:00
IAlibay
d70b1e6caa Removes unecessary tests 2020-07-15 18:05:34 +01:00
IAlibay
720a209440 streamlines read_molecule_file logic 2020-07-15 17:44:47 +01:00
IAlibay
4b0104cea9 stringio tests 2020-07-15 13:50:24 +01:00
IAlibay
0b57c63bbe close the file 2020-07-14 19:01:12 +01:00
IAlibay
24ea1ea835 Adds some basic file-like object tests 2020-07-14 18:55:47 +01:00
Nathan Baker
0e4f565c90 Remove version number from tests. 
Tests aren't version-dependent.
 2020-06-17 15:24:20 -07:00
Nathan Baker
9b59d924b2 Make PROPKA input file generation optional. 
Fixes https://github.com/jensengroup/propka-3.1/issues/51.
 2020-05-31 10:26:56 -07:00
Nathan Baker
84846aad8c Resolve cyclic import problem. 
Fixes https://github.com/jensengroup/propka-3.1/issues/49

Moved I/O into higher level of of code; should make
issue https://github.com/jensengroup/propka-3.1/issues/51
easier to resolve
 2020-05-30 12:01:30 -07:00
Nathan Baker
87347a7d60 Modernize print statements with str.format() 2020-05-28 20:31:03 -07:00
Nathan Baker
36bea44a4d Clean up line breaks in tests. 
See https://github.com/jensengroup/propka-3.1/issues/43
 2020-05-25 20:35:54 -07:00
Nathan Baker
75cdf0ea04 De-lint tests. 2020-05-25 14:44:53 -07:00
Nathan Baker
95e132e520 De-lint hybrid36.py 2020-05-24 11:21:55 -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
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
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
f13d3d8121 PROPKA testing working with pytest. 2020-05-21 15:50:23 -07:00
Nathan Baker
393f5cee50 Rename "Tests" directory for consistency. 2020-05-21 10:39:08 -07:00