consolidate package info files

.travis.yml

@@ -1,3 +1,4 @@
+version: ~> 1.0
 language: generic
 group: travis_latest
 
@@ -74,6 +75,16 @@ matrix:
            PIP_DEPENDENCIES="${PIP_DEPENDENCIES} setuptools<45.0.0"
            ASV_CHECK="true"
 
+    - env: NAME="pypi check"
+           PYTHON_VERSION=3.7
+           CODECOV="false"
+           MAIN_CMD="cd package && python setup.py"
+           SETUP_CMD="sdist"
+           BUILD_CMD=""
+           INSTALL_HOLE="false"
+           CONDA_DEPENDENCIES="setuptools cython twine"
+           PYPI_CHECK="true"
+
     - os: osx
       env: PYTHON_VERSION=3.6
            NUMPY_VERSION=1.17.3
@@ -124,7 +135,14 @@ script:
       cd ../benchmarks
       time python -m asv check -E existing
     fi
-
+  # check pypi package build
+  - |
+    if [[ "${PYPI_CHECK}" == "true" ]]; then
+       DISTRIBUTION=$(ls -t1 ${TRAVIS_BUILD_DIR}/package/dist/MDAnalysis-*.tar.gz | head -n 1)
+       test -n "${DISTRIBUTION}" || { echo "no distribution package/dist/MDAnalysis-*.tar.gz found"; exit 1; }
+       echo "twine check $DISTRIBUTION"
+       twine check $DISTRIBUTION
+    fi
 
 after_success:
   - |

README.rst

@@ -16,18 +16,10 @@ MDAnalysis also includes widely used analysis algorithms in the `MDAnalysis.anal
 The MDAnalysis project uses an `open governance model`_ and is fiscally sponsored by `NumFOCUS`_. Consider making 
 a `tax-deductible donation`_ to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.
 
-.. raw:: html
-
-   <div align="center">
-      <a href="https://numfocus.org/project/mdanalysis">
-         <img height="60px" 
-            src="https://raw.githubusercontent.com/numfocus/templates/master/images/numfocus-logo.png"
-            alt="NumFOCUS Logo"
-            align="center">
-      </a>
-   </div>
-   <br />
-
+.. image:: https://www.mdanalysis.org/public/images/numfocus-sponsored-small.png
+   :alt: NumFOCUS (Fiscally Sponsored Project)
+   :target: https://numfocus.org/project/mdanalysis
+   :align: center
 
 This project is bound by a `Code of Conduct`_.
 
@@ -53,45 +45,68 @@ Example analysis script
    # Iterate through trajectories
    for ts in u.trajectory:
        print(ag.center_of_mass())
-
-There are a number of tutorials_ on the MDAnalysis homepage that explain
-how to conduct RMSD calculations, Alignment and many more features of MDAnalysis.
 
-Source code
-===========
 
-Source code is hosted in a git repository at
+Documentation
+=============
+
+**New users** should read the `Quickstart Guide`_ and might want to
+look at our videos_, in which core developers explain various aspects
+of MDAnalysis.
+
+**All users** should read the `User Guide`_.
+
+**Developers** may also want to refer to the `MDAnalysis API docs`_.
 
-https://github.com/MDAnalysis/mdanalysis
+A growing number of **tutorials_** are available that explain how to
+conduct RMSD calculations, structural alignment, distance and contact
+analysis, and many more.
 
-and is available under the GNU General Public License, version 2 (see
-the file LICENSE_).
 
-This is the top level of the master repository. It contains
+Installation and availability
+=============================
 
-1. the MDAnalysis toolkit source files in the directory ::
+The latest release can be **installed via ``pip`` or ``conda``** as
+described in the `Installation Quick Start`_.
 
-      package/
+**Source code** is hosted in a git repository at
+https://github.com/MDAnalysis/mdanalysis and is available under the
+GNU General Public License, version 2 (see the file LICENSE_).
 
-2. the unit tests together with any input files required for
-   running those tests in the directory ::
 
-      testsuite/
+Contributing
+============
 
-The directory ``maintainer`` contains scripts only needed for
-maintaining releases and are not generally useful for the user or the
-typical developer.
+Please report **bugs** or **enhancement requests** through the `Issue
+Tracker`_. Questions can also be asked on the `user mailing list`_.
 
-(For more details on the directory layout see `Issue 87`_ on the
-MDAnalysis issue tracker.)
+If you are a **new developer** who would like to start contributing to
+MDAnalysis get in touch on the `developer mailing list`_. To set up a
+development environment and run the test suite read the `developer
+guide`_.
 
-Guide for Developers
-====================
 
-To set up a development environment and run the test suite you can use this
-guide_. If you are a new developer who would like to start contributing to
-MDAnalysis, you can help increase our code coverage, the guides explain how
-to find uncovered code.
+Citation
+========
+
+When using MDAnalysis in published work, please cite the following
+two papers:
+
+*   R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy,
+    M. N. Melo, S. L. Seyler, D. L. Dotson, J. Domanski,
+    S. Buchoux, I. M. Kenney, and O. Beckstein. MDAnalysis:
+    A Python package for the rapid analysis of molecular
+    dynamics simulations. In S. Benthall and S. Rostrup,
+    editors, Proceedings of the 15th Python in Science
+    Conference, pages 102-109, Austin, TX, 2016. SciPy.
+    doi:`10.25080/Majora-629e541a-00e`_    
+
+*   N. Michaud-Agrawal, E. J. Denning, T. B. Woolf,
+    and O. Beckstein. MDAnalysis: A Toolkit for the Analysis of Molecular
+    Dynamics Simulations. *J. Comput. Chem.* **32** (2011), 2319--2327.
+    doi:`10.1002/jcc.21787`_
+
+For citations of included algorithms and sub-modules please see the references_.
 
 
 
@@ -106,13 +121,30 @@ to find uncovered code.
 .. _`Code of Conduct`: https://www.mdanalysis.org/pages/conduct/
 .. _trajectory formats: https://docs.mdanalysis.org/documentation_pages/coordinates/init.html#id1
 .. _topology formats: https://docs.mdanalysis.org/documentation_pages/topology/init.html#supported-topology-formats
-.. _Issue 87: https://github.com/MDAnalysis/mdanalysis/issues/87
 .. _MDAnalysis: https://www.mdanalysis.org
-.. _LICENSE: https://github.com/MDAnalysis/mdanalysis/blob/master/LICENSE
-.. _`#286`: https://github.com/MDAnalysis/mdanalysis/issues/286
+.. _LICENSE:
+   https://github.com/MDAnalysis/mdanalysis/blob/master/LICENSE
+.. _`Installation Quick Start`:
+   https://www.mdanalysis.org/pages/installation_quick_start/
 .. _`MDAnalysis.analysis`: https://docs.mdanalysis.org/documentation_pages/analysis_modules.html
-.. _`tutorials`: https://www.mdanalysis.org/pages/learning_MDAnalysis/
-.. _`guide`: https://github.com/MDAnalysis/mdanalysis/wiki/Guide-for-Developers
+.. _`tutorials`: https://userguide.mdanalysis.org/examples/README.html
+.. _`videos`: https://www.mdanalysis.org/pages/learning_MDAnalysis/#videos
+.. _`Quickstart Guide`:
+   https://userguide.mdanalysis.org/examples/quickstart.html
+.. _`User Guide`: https://userguide.mdanalysis.org
+.. _`MDAnalysis API docs`:
+   https://docs.mdanalysis.org
+.. _`Issue Tracker`: https://github.com/mdanalysis/mdanalysis/issues
+.. _`user mailing list`:
+   https://groups.google.com/group/mdnalysis-discussion
+.. _`developer guide`:
+   https://userguide.mdanalysis.org/contributing.html
+.. _`developer mailing list`:
+   https://groups.google.com/group/mdnalysis-devel
+.. _`10.1002/jcc.21787`: https://dx.doi.org/10.1002/jcc.21787
+.. _`10.25080/Majora-629e541a-00e`: https://doi.org/10.25080/Majora-629e541a-00e
+.. _references: https://docs.mdanalysis.org/documentation_pages/references.html
+
 
 .. |usergroup| image:: https://img.shields.io/badge/Google%20Group-Users-lightgrey.svg
    :alt: User Google Group

package/MANIFEST.in

@@ -2,13 +2,14 @@ global-include *.pyx
 global-include *.pxd
 global-include *.c
 global-include *.h
-include MDAnalysis/coordinates/xdrfile/src/*
-include MDAnalysis/lib/src/pyqcprot/*
+global-include *.cpp
 include MDAnalysis/lib/src/transformations/*
 recursive-include doc * 
-include README INSTALL CHANGELOG LICENSE AUTHORS SUMMARY.txt
+include README INSTALL CHANGELOG LICENSE AUTHORS
 include setup.py
+global-exclude doc/html/html
 global-exclude *.pyc
 global-exclude *.pyo
 global-exclude *.pyd
-global-exclude *~
+global-exclude *~
+global-exclude .git

package/MDAnalysis/__init__.py

@@ -40,7 +40,7 @@
 http://groups.google.com/group/mdnalysis-discussion
 
 Please report bugs and feature requests through the issue tracker at
-http://issues.mdanalysis.org
+https://github.com/MDAnalysis/mdanalysis/issues
 
 Citation
 --------

package/MDAnalysis/core/_get_readers.py

@@ -102,7 +102,7 @@ def get_reader_for(filename, format=None):
             "           See https://docs.mdanalysis.org/documentation_pages/coordinates/init.html#id1\n"
             "           Use the format keyword to explicitly set the format: 'Universe(...,format=FORMAT)'\n"
             "           For missing formats, raise an issue at "
-            "http://issues.mdanalysis.org".format(
+            "https://github.com/MDAnalysis/mdanalysis/issues".format(
                 format, filename, _READERS.keys()))
         raise ValueError(errmsg) from None
 
@@ -251,7 +251,8 @@ def get_parser_for(filename, format=None):
                 "   {1}\n"
                 "   See https://docs.mdanalysis.org/documentation_pages/topology/init.html#supported-topology-formats\n"
                 "   For missing formats, raise an issue at \n"
-                "   http://issues.mdanalysis.org".format(format, _PARSERS.keys()))
+                "   https://github.com/MDAnalysis/mdanalysis/issues".format(
+                    format, _PARSERS.keys()))
             raise ValueError(errmsg) from None
         else:
             return _PARSERS['MINIMAL']

package/MDAnalysis/core/universe.py

@@ -832,9 +832,11 @@ def add_TopologyAttr(self, topologyattr, values=None):
                 errmsg = (
                     "Unrecognised topology attribute name: '{}'."
                     "  Possible values: '{}'\n"
-                    "To raise an issue go to: http://issues.mdanalysis.org"
+                    "To raise an issue go to: "
+                    "https://github.com/MDAnalysis/mdanalysis/issues"
                     "".format(
-                        topologyattr, ', '.join(sorted(_TOPOLOGY_ATTRS.keys()))))
+                        topologyattr, ', '.join(
+                            sorted(_TOPOLOGY_ATTRS.keys()))))
                 raise ValueError(errmsg) from None
             else:
                 topologyattr = tcls.from_blank(
@@ -1285,10 +1287,10 @@ def _fragdict(self):
                 fragdict[a.ix] = fraginfo(i, f)
 
         return fragdict
-    
+
     @classmethod
-    def from_smiles(cls, smiles, sanitize=True, addHs=True, 
-                    generate_coordinates=True, numConfs=1, 
+    def from_smiles(cls, smiles, sanitize=True, addHs=True,
+                    generate_coordinates=True, numConfs=1,
                     rdkit_kwargs={}, **kwargs):
         """Create a Universe from a SMILES string with rdkit
 
@@ -1346,7 +1348,7 @@ def from_smiles(cls, smiles, sanitize=True, addHs=True,
             from rdkit.Chem import AllChem
         except ImportError as e:
             raise ImportError(
-                "Creating a Universe from a SMILES string requires RDKit but " 
+                "Creating a Universe from a SMILES string requires RDKit but "
                 "it does not appear to be installed") from e
 
         mol = Chem.MolFromSmiles(smiles, sanitize=sanitize)
@@ -1358,7 +1360,7 @@ def from_smiles(cls, smiles, sanitize=True, addHs=True,
             if not addHs:
                 raise ValueError("Generating coordinates requires adding "
                 "hydrogens with `addHs=True`")
-            
+
             numConfs = rdkit_kwargs.pop("numConfs", numConfs)
             if not (type(numConfs) is int and numConfs > 0):
                 raise SyntaxError("numConfs must be a non-zero positive "