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  • cb65c644c6 use versioneer for version management (#88) Oliver Beckstein 2020-07-18 12:32:25 -07:00
  • 7563a706cf fixes run's single method (#85) Irfan Alibay 2020-07-17 19:18:07 +01:00
  • d16257af9a Merge pull request #84 from IAlibay/streams Nathan Baker 2020-07-15 18:27:29 -07:00
  • 81e51c34bc remove unecessary tmpdir IAlibay 2020-07-15 19:34:33 +01:00
  • c24f59b6d4 removes spurious empty line IAlibay 2020-07-15 18:34:21 +01:00
  • dd7434fc37 remove unused import and fix error test IAlibay 2020-07-15 18:26:26 +01:00
  • d70b1e6caa Removes unecessary tests IAlibay 2020-07-15 18:05:34 +01:00
  • 720a209440 streamlines read_molecule_file logic IAlibay 2020-07-15 17:44:47 +01:00
  • e3e0dd9878 fix docs IAlibay 2020-07-15 14:24:15 +01:00
  • f672c635a2 adds usage docs for file-like objects IAlibay 2020-07-15 14:23:06 +01:00
  • 4b0104cea9 stringio tests IAlibay 2020-07-15 13:50:24 +01:00
  • 0b57c63bbe close the file IAlibay 2020-07-14 19:01:12 +01:00
  • 24ea1ea835 Adds some basic file-like object tests IAlibay 2020-07-14 18:55:47 +01:00
  • dfc55c1f9a Adds option to read file streams IAlibay 2020-07-14 18:47:10 +01:00
  • 8b371bfc27 Basic fixes IAlibay 2020-07-14 17:48:01 +01:00
  • 01debbf63d Merge pull request #80 from jensengroup/nathan/link-web-server Nathan Baker 2020-07-12 08:01:48 -07:00
  • cc598df660 Merge pull request #79 from jensengroup/nathan/rtd-links Nathan Baker 2020-06-29 05:56:13 -07:00
  • f8c57bca6f Include explicit link to web server Nathan Baker 2020-06-27 11:00:19 -07:00
  • 8f64bad060 Add links to https://propka.readthedocs.io/ Nathan Baker 2020-06-27 10:47:48 -07:00
  • da2b285a79 Fix Markdown error Nathan Baker 2020-06-27 08:45:31 -07:00
  • 6b4e4d2f9d Merge pull request #75 from Becksteinlab/remove-spurious-pandas Nathan Baker 2020-06-27 08:43:54 -07:00
  • 6d0a07bb1e Merge pull request #76 from Becksteinlab/coverage-updates Nathan Baker 2020-06-27 08:43:05 -07:00
  • bd5c8f1aa1 Merge pull request #74 from Becksteinlab/increase-sphinx-version Nathan Baker 2020-06-27 08:28:51 -07:00
  • d710ca9679 exclude tests themselves from coverage reporting Oliver Beckstein 2020-06-25 17:58:41 -07:00
  • 4591a0ff1f badge for codecov and pypi Oliver Beckstein 2020-06-25 17:48:45 -07:00
  • aa68e3e6ce remove pandas dependency for tests Oliver Beckstein 2020-06-25 17:42:25 -07:00
  • 28b4f44cd0 increase sphinx to >= 3.1 in requirements Oliver Beckstein 2020-06-25 17:38:41 -07:00
  • 58b6e652c6 Merge pull request #71 from jensengroup/nathan/coverage Oliver Beckstein 2020-06-25 17:29:23 -07:00
  • 4dc87a5a38 upload coverage to https://codecov.io/gh/jensengroup/propka Oliver Beckstein 2020-06-25 17:22:45 -07:00
  • 831e738068 Merge pull request #70 from Becksteinlab/sphinx-docs-skeleton Nathan Baker 2020-06-22 20:07:28 -07:00
  • d982745858 Expand tests to all branches. Nathan Baker 2020-06-20 08:24:16 -07:00
  • 151125b18c Update runner version. Nathan Baker 2020-06-20 08:17:17 -07:00
  • 4fd012cb57 Fix YAML error. Nathan Baker 2020-06-20 08:12:31 -07:00
  • 9fcc69b9a8 Store coverage results as artifacts Nathan Baker 2020-06-20 08:10:28 -07:00
  • 52bbd2e887 Attempt to add coverage.py to testing workflow. Nathan Baker 2020-06-20 07:49:58 -07:00
  • e021e491cb Merge pull request #62 from jensengroup/pytest-ci Nathan Baker 2020-06-20 06:01:59 -07:00
  • 02a0cbd58b link to the propka3 command page Oliver Beckstein 2020-06-19 22:04:05 -07:00
  • fe70dc491a add sphinx deps to requirements.txt Oliver Beckstein 2020-06-19 21:23:31 -07:00
  • 1c343a7d96 basic usage for propka3 command Oliver Beckstein 2020-06-19 20:31:17 -07:00
  • 59a97680d8 make ghpages to push to gh-pages branch Oliver Beckstein 2020-06-19 16:53:50 -07:00
  • 26a5ab042e API docs for propka Oliver Beckstein 2020-06-19 16:25:24 -07:00
  • 65856b39fb use autosummary to generate most of the API Reference Oliver Beckstein 2020-06-19 15:15:32 -07:00
  • 2bf031fd65 initial sphinx docs Oliver Beckstein 2020-06-19 12:13:53 -07:00
  • 27895c2f3f Remove Python 3.5 from testing. Nathan Baker 2020-06-19 09:03:15 -07:00
  • 91f810f359 Troubleshoot GitHub Actions. Nathan Baker 2020-06-19 09:00:26 -07:00
  • ccfdc944c9 Merge branch 'master' into pytest-ci Nathan Baker 2020-06-19 09:00:11 -07:00
  • 4875d9ee65 Merge pull request #61 from Electrostatics/nathan/v3.2 Nathan Baker 2020-06-19 07:37:49 -07:00
  • 11bc32e9fc Require Python 3.6+. Nathan Baker 2020-06-19 07:21:05 -07:00
  • 77286be67a Add Microsoft Windows to OS list. Nathan Baker 2020-06-19 06:52:06 -07:00
  • fb38d28f51 Add specific python versions to setup.py Nathan Baker 2020-06-19 06:46:36 -07:00
  • 2f47d0ea9a Remove redundant PROPKA script. Nathan Baker 2020-06-19 06:43:33 -07:00
  • 9cd0da8ff3 Clean up README instructions. Nathan Baker 2020-06-19 06:39:07 -07:00
  • 73e956f141 Add description of PROPKA versions. Nathan Baker 2020-06-19 06:28:01 -07:00
  • 6b9f01a7c3 Standardize version references to "PROPKA 3". Nathan Baker 2020-06-19 06:24:40 -07:00
  • c2ac407a96 Merge pull request #65 from jensengroup/read_parameter_file-KeyError Nathan Baker 2020-06-19 05:48:09 -07:00
  • e80473db33 Handle KeyError in read_parameter_file Thomas Holder 2020-06-18 20:19:10 +02:00
  • 18368b456a Remove setuptools discussion Nathan Baker 2020-06-18 09:53:51 -07:00
  • 75057fbfef Remove specific version number Nathan Baker 2020-06-18 09:53:17 -07:00
  • 7a25ec6598 Update executable script name. Nathan Baker 2020-06-18 08:57:12 -07:00
  • 1d43b46ddc Enable package-based CI Nathan Baker 2020-06-18 08:30:02 -07:00
  • 573b38db38 Fix stray propka31 to propka32. Nathan Baker 2020-06-18 08:24:51 -07:00
  • a2196cdc6f Consolidate documentation. Nathan Baker 2020-06-18 08:19:22 -07:00
  • 2909173caf Add missing *.json to package data list. Nathan Baker 2020-06-17 15:31:16 -07:00
  • 0c4979560d Change propka31 to propka32. Nathan Baker 2020-06-17 15:25:50 -07:00
  • 4e7a41730d Change module version number. Nathan Baker 2020-06-17 15:25:23 -07:00
  • 0e4f565c90 Remove version number from tests. Nathan Baker 2020-06-17 15:24:20 -07:00
  • d52620d4e9 Update PROPKA header banner. Nathan Baker 2020-06-17 15:24:00 -07:00
  • 54294684b0 Remove broken links from README.md. Nathan Baker 2020-06-17 13:22:17 -07:00
  • 89a9eb15d4 Update INSTALL with better instructions. Nathan Baker 2020-06-17 13:17:33 -07:00
  • e8576fb4f3 Remove specific 3.1 version information. Nathan Baker 2020-06-17 13:12:09 -07:00
  • 1d8fa2bbbe Update setup.py with 3.2.0 information. Nathan Baker 2020-06-17 12:33:52 -07:00
  • 616540ebd6 Merge branch 'nathan/tempfile' Nathan Baker 2020-06-03 18:36:47 -07:00
  • 0cb470fbdb Merge pull request #59 from Electrostatics/nathan/tempfile Nathan Baker 2020-06-03 18:36:27 -07:00
  • 9126e3059f Fix PROPKA output naming. Nathan Baker 2020-06-03 18:34:12 -07:00
  • 5d8e271420 Merge branch 'nathan/import' into nathan/tempfile Nathan Baker 2020-06-03 17:51:16 -07:00
  • 879c48a3d8 Merge branch 'nathan/import' Nathan Baker 2020-06-03 17:50:56 -07:00
  • df028e445b Merge pull request #50 from Electrostatics/nathan/import Nathan Baker 2020-06-03 17:50:30 -07:00
  • 7085271ad5 Simplify with .writable() method. Nathan Baker 2020-06-03 17:49:19 -07:00
  • 9b59d924b2 Make PROPKA input file generation optional. Nathan Baker 2020-05-31 10:26:56 -07:00
  • 1d17cb05ed Remove TODO for refactoring. Nathan Baker 2020-05-30 13:15:45 -07:00
  • 52554d905a Remove TODO statements for refactoring. Nathan Baker 2020-05-30 13:12:44 -07:00
  • 84846aad8c Resolve cyclic import problem. Nathan Baker 2020-05-30 12:01:30 -07:00
  • b597a6f257 Remove cyclic import based on I/O in pdb.py. Nathan Baker 2020-05-30 10:00:31 -07:00
  • 397d5e10aa Remove cyclic import based on atom.py Nathan Baker 2020-05-30 09:26:13 -07:00
  • 461edda3b2 Break propka.calculations into parts. Nathan Baker 2020-05-30 08:45:39 -07:00
  • dde0d67ea5 Merge pull request #40 from Electrostatics/nathan/delint Nathan Baker 2020-05-30 08:14:45 -07:00
  • d7147799d8 Python formatting is annoying. Nathan Baker 2020-05-29 20:55:32 -07:00
  • a716c89a36 Remove unused argument from Atom() constructor. Nathan Baker 2020-05-29 20:49:47 -07:00
  • 5010d9fa14 Merge branch 'nathan/strings' into nathan/delint Nathan Baker 2020-05-29 20:41:53 -07:00
  • 83a7099d79 Fix my formatting mistakes. Nathan Baker 2020-05-29 20:37:47 -07:00
  • b54190ef27 Fix complicated string formatting. Nathan Baker 2020-05-29 20:08:41 -07:00
  • 7bd12c725e Merge remote-tracking branch 'upstream/master' into nathan/strings Nathan Baker 2020-05-29 20:06:57 -07:00
  • 91570cbf68 Merge branch 'master' into nathan/delint Nathan Baker 2020-05-28 20:35:27 -07:00
  • 87347a7d60 Modernize print statements with str.format() Nathan Baker 2020-05-28 20:31:03 -07:00
  • ba67f5149d Replace old-style printf with str.format Nathan Baker 2020-05-28 16:10:48 -07:00
  • 3266521d31 Replace old formatting with new str.format() Nathan Baker 2020-05-27 20:55:44 -07:00
  • 6e7c188dbd Update string formatting to modern version. Nathan Baker 2020-05-27 16:26:52 -07:00
  • 5916a80d56 Merge pull request #47 from Electrostatics/nathan/fix-run Nathan Baker 2020-05-27 08:38:58 -07:00
  • 33493cc4d2 Remove unnecessary args testing. Nathan Baker 2020-05-27 08:25:46 -07:00
  • 557ab19312 Replace complex old-style format with new format strings. Nathan Baker 2020-05-27 08:19:36 -07:00