Merge branch 'master' into new-dask

.travis.yml

@@ -15,7 +15,7 @@ env:
     # Set default python version to avoid repetition later
     - PYTHON_VERSION=3.6
     - MAIN_CMD="pytest"
-    - SETUP_CMD="pmda --pep8 -v --cov pmda"
+    - SETUP_CMD="pmda --pep8 --cov pmda"
     # mdanalysis develop from source (see below), which needs
     # minimal CONDA_MDANALYSIS_DEPENDENCIES
     #- CONDA_DEPENDENCIES="mdanalysis mdanalysistests dask joblib pytest-pep8 mock codecov cython hypothesis sphinx"

AUTHORS

@@ -22,4 +22,5 @@ Chronological list of authors
  2018
   - Shujie Fan
   - Richard J Gowers
+  - Ioannis Paraskevakos
 

CHANGELOG

@@ -13,14 +13,19 @@ The rules for this file:
   * release numbers follow "Semantic Versioning" http://semver.org
 
 ------------------------------------------------------------------------------
-xx/xx/18 VOD555, richardjgowers
+xx/xx/18 VOD555, richardjgowers, iparask, orbeckst
 
   * 0.2.0
 
 Enhancements
   * add add timing for _conclude and _prepare (Issue #49)
   * add parallel particle-particle RDF calculation module pmda.rdf (Issue #41)
   * add readonly_attributes context manager to ParallelAnalysisBase
+  * add parallel implementation of Leaflet Finder (Issue #47)
+
+Fixes
+  * always distribute frames over blocks so that no empty blocks are
+    created ("balanced blocks", Issue #71)
 
 
 06/07/18 orbeckst

conftest.py

@@ -0,0 +1,32 @@
+
+# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
+# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
+#
+# PMDA
+# Copyright (c) 2017 The MDAnalysis Development Team and contributors
+# (see the file AUTHORS for the full list of names)
+#
+# Released under the GNU Public Licence, v2 or any higher version
+
+from dask import distributed, multiprocessing
+import pytest
+
+
+@pytest.fixture(scope="session", params=(1, 2))
+def client(tmpdir_factory, request):
+    with tmpdir_factory.mktemp("dask_cluster").as_cwd():
+        lc = distributed.LocalCluster(n_workers=request.param, processes=True)
+        client = distributed.Client(lc)
+
+        yield client
+
+        client.close()
+        lc.close()
+
+
+@pytest.fixture(scope='session', params=('distributed', 'multiprocessing'))
+def scheduler(request, client):
+    if request.param == 'distributed':
+        return client
+    else:
+        return multiprocessing

docs/api.rst

@@ -26,6 +26,7 @@ a single frame. If your need more flexibility you can use the
 
    api/parallel
    api/custom
+   api/util
 
 .. _pre-defined-analysis-tasks:
 
@@ -42,3 +43,4 @@ also function as examples for how to implement your own functions with
    api/rms
    api/contacts
    api/rdf
+   api/leaflet

docs/api/leaflet.rst

@@ -0,0 +1,2 @@
+.. automodule:: pmda.leaflet
+

docs/api/util.rst

@@ -0,0 +1,2 @@
+.. automodule:: pmda.util
+   :members:

docs/conf.py

@@ -57,7 +57,7 @@
 
 # General information about the project.
 project = u'PMDA'
-author = u'Max Linke, Shujie Fan, Richard J. Gowers, Oliver Beckstein'
+author = u'Max Linke, Shujie Fan, Richard J. Gowers, Oliver Beckstein, Ioannis Paraskevakos'
 copyright = u'2018, ' + author
 
 

docs/references.rst

@@ -31,6 +31,15 @@
                      Huff, David Lippa, Dillon Niederhut, and M. Pacer,
                      editors, Proceedings of the 16th Python in Science
                      Conference, pages 64–72, Austin,
-	             TX, 2017. SciPy. doi:`10.25080/shinma-7f4c6e7-00a`_
+	             TX, 2017. SciPy. doi:`10.25080/shinma-7f4c6e7-00a`_.
 
-.. _`10.25080/shinma-7f4c6e7-00a`: https://doi.org/10.25080/shinma-7f4c6e7-00a		    
+.. _`10.25080/shinma-7f4c6e7-00a`: https://doi.org/10.25080/shinma-7f4c6e7-00a
+
+.. [Paraskevakos2018] Ioannis Paraskevakos, Andre Luckow, Mahzad Khoshlessan, 
+                      George Chantzialexiou, Thomas E. Cheatham, Oliver 
+                      Beckstein, Geoffrey C. Fox and Shantenu Jha. Task-
+                      parallel Analysis of Molecular Dynamics Trajectories. In
+                      47th International Conference on Parallel Processing 
+                      (ICPP 2018). doi: `10.1145/3225058.3225128`_.
+
+.. _`10.1145/3225058.3225128` : https://doi.org/10.1145/3225058.3225128