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Author SHA1 Message Date
Nathan Baker
e081bd53b3 Add line breaks to error message. 
Fixes https://github.com/jensengroup/propka/pull/109#discussion_r533131022
 2020-12-01 06:40:44 -08:00
Nathan Baker
de020599d3 Raise error for ligand pKa errors. 
Fixes https://github.com/jensengroup/propka/pull/109#discussion_r532735233 per @orbeckst.
 2020-11-30 15:21:47 -08:00
Nathan Baker
c281623078 Change logging message to error. 
Fixes https://github.com/jensengroup/propka/pull/109#discussion_r532735233 based on suggestion from @orbeckst.
 2020-11-30 15:17:18 -08:00
Nathan Baker
fda4fe577b Merge branch 'master' into nathan/logging 2020-11-29 16:14:43 -08:00
Nathan Baker
9350799be1 Remove logging abstraction to facilitate debugging and reduce bloat. 
Also performed minor delinting.

Fixes #108
 2020-11-29 16:09:45 -08:00
Nathan Baker
f3bbd807ae Merge pull request #100 from IAlibay/rm-propkainput 
Removal of PROPKA input
 2020-11-29 15:41:28 -08:00
IAlibay
3ca674776f Remove unused attributes 2020-11-18 18:15:42 +00:00
Nathan Baker
67039aabc0 Merge pull request #102 from IAlibay/python3.9 
Adds python 3.9 to CI
 2020-11-18 09:32:51 -08:00
IAlibay
b164c1db1a Adds python3.9 to CI 2020-11-18 01:27:41 +00:00
IAlibay
196a2c6a1f remove unused command 2020-11-18 01:13:59 +00:00
IAlibay
012865e9e9 fix argparse typo 2020-11-18 00:53:07 +00:00
IAlibay
da7999832d Remove unused initialized_atom_group 2020-11-18 00:51:46 +00:00
IAlibay
d6ebd48473 missed conf container code 2020-11-18 00:31:15 +00:00
IAlibay
239c8183c9 Initial removal of PROPKA input 2020-11-17 23:31:24 +00:00
Thomas Holder
9dfd87a0eb Fix handling of multi-model PDB without MODEL 1 
Fixes https://github.com/jensengroup/propka/issues/95
 2020-11-11 10:57:15 +01:00
Thomas Holder
810750cdd7 Fix pI reporting in last line of .pka file 2020-07-22 07:50:10 +02:00
Thomas Holder
552dd133e6 Report correct version in .pka file header 2020-07-21 17:31:59 -07:00
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
Nathan Baker
d16257af9a Merge pull request #84 from IAlibay/streams 
Allows for file-like objects to be passed to read_molecule_file
 2020-07-15 18:27:29 -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
e3e0dd9878 fix docs 2020-07-15 14:24:15 +01:00
IAlibay
f672c635a2 adds usage docs for file-like objects 2020-07-15 14:23:06 +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
IAlibay
dfc55c1f9a Adds option to read file streams 2020-07-14 18:47:10 +01:00
IAlibay
8b371bfc27 Basic fixes 2020-07-14 17:48:01 +01:00
Nathan Baker
01debbf63d Merge pull request #80 from jensengroup/nathan/link-web-server 
Include explicit link to web server
 2020-07-12 08:01:48 -07:00
Nathan Baker
cc598df660 Merge pull request #79 from jensengroup/nathan/rtd-links 
Add links to https://propka.readthedocs.io/
 2020-06-29 05:56:13 -07:00
Nathan Baker
f8c57bca6f Include explicit link to web server 
http://propka.org currently redirects to http://server.poissonboltzmann.org.  However, the http://server.poissonboltzmann.org site does not include any specific documentation for PROPKA.  I'd like @jhjensen2 to update the DNS record for http://propka.org to redirect to https://github.com/jensengroup/propka or https://propka.readthedocs.io/.  However, before he does that, it would be good to make sure that users can still find a link to run PROPKA via http://server.poissonboltzmann.org.  This edit provides that link.
 2020-06-27 11:00:19 -07:00
Nathan Baker
8f64bad060 Add links to https://propka.readthedocs.io/ 2020-06-27 10:47:48 -07:00
Nathan Baker
da2b285a79 Fix Markdown error 2020-06-27 08:45:31 -07:00
Nathan Baker
6b4e4d2f9d Merge pull request #75 from Becksteinlab/remove-spurious-pandas 
remove pandas dependency for tests
 2020-06-27 08:43:54 -07:00
Nathan Baker
6d0a07bb1e Merge pull request #76 from Becksteinlab/coverage-updates 
coverage updates
 2020-06-27 08:43:05 -07:00
Nathan Baker
bd5c8f1aa1 Merge pull request #74 from Becksteinlab/increase-sphinx-version 
increase sphinx to >= 3.1 in requirements
 2020-06-27 08:28:51 -07:00
Oliver Beckstein
d710ca9679 exclude tests themselves from coverage reporting 2020-06-25 17:58:41 -07:00
Oliver Beckstein
4591a0ff1f badge for codecov and pypi 2020-06-25 17:48:45 -07:00
Oliver Beckstein
aa68e3e6ce remove pandas dependency for tests 
Tests do not require pandas but setup.py was still listing it.
 2020-06-25 17:42:25 -07:00
Oliver Beckstein
28b4f44cd0 increase sphinx to >= 3.1 in requirements 
- fix #72
- our sphinx docs need >= 3.1 because they use autosummary with :recursive:
 2020-06-25 17:38:41 -07:00
Oliver Beckstein
58b6e652c6 Merge pull request #71 from jensengroup/nathan/coverage 
- add coverage.py to testing workflow
- use https://codecov.io/gh/jensengroup/propka
 2020-06-25 17:29:23 -07:00
Oliver Beckstein
4dc87a5a38 upload coverage to https://codecov.io/gh/jensengroup/propka 2020-06-25 17:22:45 -07:00
Nathan Baker
831e738068 Merge pull request #70 from Becksteinlab/sphinx-docs-skeleton 
initial sphinx docs
 2020-06-22 20:07:28 -07:00
Nathan Baker
d982745858 Expand tests to all branches. 
Also update README with testing badge.
 2020-06-20 08:24:16 -07:00
Nathan Baker
151125b18c Update runner version. 
Support wildcard artifact storage.
 2020-06-20 08:17:17 -07:00
Nathan Baker
4fd012cb57 Fix YAML error. 2020-06-20 08:12:31 -07:00