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Author SHA1 Message Date
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
Nathan Baker
9fcc69b9a8 Store coverage results as artifacts 2020-06-20 08:10:28 -07:00
Nathan Baker
52bbd2e887 Attempt to add coverage.py to testing workflow. 2020-06-20 07:49:58 -07:00
Nathan Baker
e021e491cb Merge pull request #62 from jensengroup/pytest-ci 
Enable package-based CI
 2020-06-20 06:01:59 -07:00
Oliver Beckstein
02a0cbd58b link to the propka3 command page 2020-06-19 22:04:05 -07:00
Oliver Beckstein
fe70dc491a add sphinx deps to requirements.txt 
- sphinx
- sphinx_rtd_theme
 2020-06-19 21:38:45 -07:00
Oliver Beckstein
1c343a7d96 basic usage for propka3 command 2020-06-19 21:38:45 -07:00
Oliver Beckstein
59a97680d8 make ghpages to push to gh-pages branch 
- `make ghpages` will build the docs in docs/build/html and push it to an
  existing gh-pages branch; especially useful when building on a fork;
  you will have to initialize your gh-pages branch manually and enable
  docs on the gh-pages branch in the repo settings
- ignore build directories (top level build and docs/build)
 2020-06-19 21:38:39 -07:00
Oliver Beckstein
26a5ab042e API docs for propka 
- use autosummary (with custom module template)
- updated module docs for all modules so that they are included
  with sphinx autodocs
 2020-06-19 16:25:24 -07:00
Oliver Beckstein
65856b39fb use autosummary to generate most of the API Reference 
- custom _template/autosummary/module.rst to include docs
  for all module :members" (shows up directly after the summary
  tables)
- module docs should *not* contain autodocs for members, only general
  descriptions and examples
- all files inside api/ are autogenerated whenever sphinx is run
  (no need to add to the repository, hence excluded in .gitignore)
 2020-06-19 15:18:04 -07:00
Oliver Beckstein
2bf031fd65 initial sphinx docs 
starts #69

- basic structure
- RTD theme
- installation
- quickstart (more to do)
- references
- added start page with license and links to repo and issues
- authors in docs: papers and repo contributors (to be discussed)
 2020-06-19 12:13:53 -07:00
Nathan Baker
27895c2f3f Remove Python 3.5 from testing. 
We already knew Python 3.5 doesn't work.
 2020-06-19 09:03:15 -07:00
Nathan Baker
91f810f359 Troubleshoot GitHub Actions. 2020-06-19 09:00:26 -07:00
Nathan Baker
ccfdc944c9 Merge branch 'master' into pytest-ci 2020-06-19 09:00:11 -07:00
Nathan Baker
4875d9ee65 Merge pull request #61 from Electrostatics/nathan/v3.2 
Merge changes needed to release v3.2
 2020-06-19 07:37:49 -07:00
Nathan Baker
11bc32e9fc Require Python 3.6+. 
Fixes https://github.com/jensengroup/propka-3.1/pull/61#issuecomment-646190977
 2020-06-19 07:21:05 -07:00
Nathan Baker
77286be67a Add Microsoft Windows to OS list. 
Addresses https://github.com/jensengroup/propka-3.1/pull/61#discussion_r442365647
 2020-06-19 06:52:06 -07:00
Nathan Baker
fb38d28f51 Add specific python versions to setup.py 
Co-authored-by: Oliver Beckstein <orbeckst@gmail.com>
 2020-06-19 06:46:36 -07:00
Nathan Baker
2f47d0ea9a Remove redundant PROPKA script. 
Fixes https://github.com/jensengroup/propka-3.1/pull/61#discussion_r442401079
 2020-06-19 06:43:33 -07:00
Nathan Baker
9cd0da8ff3 Clean up README instructions. 
Remove references to setuptools and add some additional fixes.

Addresses https://github.com/jensengroup/propka-3.1/pull/61#discussion_r442357797
 2020-06-19 06:39:07 -07:00
Nathan Baker
73e956f141 Add description of PROPKA versions. 
Implements suggestion https://github.com/jensengroup/propka-3.1/pull/61#discussion_r442352878
 2020-06-19 06:28:01 -07:00
Nathan Baker
6b9f01a7c3 Standardize version references to "PROPKA 3". 
Partially addresses https://github.com/jensengroup/propka-3.1/pull/61#pullrequestreview-433445231
 2020-06-19 06:24:40 -07:00
Nathan Baker
c2ac407a96 Merge pull request #65 from jensengroup/read_parameter_file-KeyError 
Handle KeyError in read_parameter_file
 2020-06-19 05:48:09 -07:00
Thomas Holder
e80473db33 Handle KeyError in read_parameter_file 
Fixes basic usage of propka after `python setup.py install` followed by
`propka3 1ubq.pdb`
 2020-06-18 20:19:10 +02:00
Nathan Baker
18368b456a Remove setuptools discussion 
Co-authored-by: Oliver Beckstein <orbeckst@gmail.com>
 2020-06-18 09:53:51 -07:00
Nathan Baker
75057fbfef Remove specific version number 
Co-authored-by: Oliver Beckstein <orbeckst@gmail.com>
 2020-06-18 09:53:17 -07:00
Nathan Baker
7a25ec6598 Update executable script name. 
Changed script name to propka3 based on https://github.com/jensengroup/propka-3.1/pull/61#discussion_r442326049

Updated additional information in setup.py
 2020-06-18 08:57:12 -07:00
Nathan Baker
1d43b46ddc Enable package-based CI 
Enable continuous integration testing using pytest.
 2020-06-18 08:30:02 -07:00
Nathan Baker
573b38db38 Fix stray propka31 to propka32. 2020-06-18 08:24:51 -07:00