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.

.gitattributes

@@ -0,0 +1 @@
+propka/_version.py export-subst

.github/workflows/python-package.yml

@@ -37,7 +37,8 @@ jobs:
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest and coverage
       run: |
-        coverage run --source=propka -m pytest
+        # configure coverage with entries in setup.cfg
+        coverage run -m pytest
         coverage report -m | tee coverage.txt
         coverage html
     - name: Upload coverage to https://codecov.io/gh/jensengroup/propka

MANIFEST.in

@@ -1,4 +1,6 @@
 include README.md INSTALL 
-include setup.py 
+include setup.py setup.cfg
 include propka.cfg
 
+include versioneer.py
+include propka/_version.py

docs/source/conf.py

@@ -24,11 +24,14 @@
 # -- Project information -----------------------------------------------------
 
 project = 'PROPKA 3'
-copyright = '2020, Jan H. Jensen, Chresten R. Søndergaard, Mats H. M. Olsson, Michał Rostkowski, Nathan A. Baker, Matvey Adzhigirey, Oliver Beckstein, Jimmy Charnley Kromann, Mike Beachy, Toni G, Thomas Holder'
-author = 'Jan H. Jensen, Chresten R. Søndergaard, Mats H. M. Olsson, Michał Rostkowski, Nathan A. Baker, Matvey Adzhigirey, Oliver Beckstein, Jimmy Charnley Kromann, Mike Beachy, Toni G, Thomas Holder'
+author = ('Jan H. Jensen, Chresten R. Søndergaard, Mats H. M. Olsson, '
+          'Michał Rostkowski, Nathan A. Baker, Matvey Adzhigirey, '
+          'Oliver Beckstein, Jimmy Charnley Kromann, Mike Beachy, '
+          'Toni G, Thomas Holder, Irfan Alibay')
+copyright = '2020, ' + author
 
 # The full version, including alpha/beta/rc tags
-release = '3.2.0'
+release = __import__('propka').__version__
 
 
 # -- General configuration ---------------------------------------------------
@@ -39,14 +42,14 @@
               'sphinx.ext.mathjax', 'sphinx.ext.viewcode',
               'sphinx.ext.napoleon', 'sphinx.ext.todo',
               'sphinx.ext.autosummary',
-##              'sphinx_sitemap',
+              'sphinx_sitemap',
               'sphinx_rtd_theme']
 
 mathjax_path = 'https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?config=TeX-AMS-MML_HTMLorMML'
 
 # for sitemap with https://github.com/jdillard/sphinx-sitemap
 # change if we put it under a custom domain; for right now, assume RTD
-##site_url = "https://propka.readthedocs.io"
+site_url = "https://propka.readthedocs.io"
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']

propka/__init__.py

@@ -18,3 +18,7 @@
            "hybrid36", "iterative", "input", "lib", "ligand_pka_values",
            "ligand", "molecular_container", "output", "parameters",
            "protonate", "run", "vector_algebra", "version"]
+
+from ._version import get_versions
+__version__ = get_versions()['version']
+del get_versions