Release 0.19.0

.appveyor.yml

@@ -0,0 +1,71 @@
+# config based on examples from SciPy & NumPy repositories, which
+# themselves credit an original example by Olivier Grisel at
+# https://github.com/ogrisel/python-appveyor-demo/blob/master/appveyor.yml
+clone_depth: 50
+max_jobs: 100
+
+cache:
+    - '%LOCALAPPDATA%\pip\Cache'
+
+image:
+    - Visual Studio 2015
+
+environment:
+    global:
+        CONDA_CHANNELS: conda-forge
+        CONDA_DEPENDENCIES: pip setuptools wheel cython mock six biopython networkx joblib matplotlib scipy vs2015_runtime pytest mmtf-python GridDataFormats hypothesis pytest-cov codecov
+        PIP_DEPENDENCIES: gsd==1.5.2 duecredit
+        DEBUG: "False"
+        MINGW_64: C:\mingw-w64\x86_64-6.3.0-posix-seh-rt_v5-rev1\mingw64\bin
+        OPENBLAS_64: https://3f23b170c54c2533c070-1c8a9b3114517dc5fe17b7c3f8c63a43.ssl.cf2.rackcdn.com/openblas-5f998ef_gcc7_1_0_win64.zip
+        APPVEYOR_SAVE_CACHE_ON_ERROR: true
+        APPVEYOR_SKIP_FINALIZE_ON_EXIT: true
+        TEST_TIMEOUT: 1000
+        PYTHON: "C:\\conda"
+        MINICONDA_VERSION: "latest"
+
+    matrix:
+        - PYTHON_VERSION: 3.6
+          PYTHON_ARCH: 64
+          MSVC_VERSION: "Visual Studio 10 Win64"
+
+init:
+    - ps: Write-Host ${env:PYTHON} ${env:PYTHON_VERSION} ${env:PYTHON_ARCH}
+    - ps: Write-Host ${env:APPVEYOR_SCHEDULED_BUILD}
+    # cancel build if newer one is submitted; complicated
+    # details for getting this to work are credited to JuliaLang
+    # developers
+    - ps: if ($env:APPVEYOR_PULL_REQUEST_NUMBER -and $env:APPVEYOR_BUILD_NUMBER -ne ((Invoke-RestMethod `
+        https://ci.appveyor.com/api/projects/$env:APPVEYOR_ACCOUNT_NAME/$env:APPVEYOR_PROJECT_SLUG/history?recordsNumber=50).builds | `
+        Where-Object pullRequestId -eq $env:APPVEYOR_PULL_REQUEST_NUMBER)[0].buildNumber) { `
+          raise "There are newer queued builds for this pull request, skipping build."
+        }
+
+install:
+    # set up a conda env
+    - ps: git clone -q --depth 1 git://github.com/astropy/ci-helpers.git
+    - ps: ci-helpers/appveyor/install-miniconda.ps1
+    - ps: $env:PATH = "${env:PYTHON};${env:PYTHON}\Scripts;" + $env:PATH
+    # deal with missing stdint.h as previously described
+    # see https://github.com/swistakm/pyimgui/blob/master/.appveyor.yml
+    - ps: cp "C:\Program Files (x86)\Microsoft Visual Studio 10.0\VC\include\stdint.h" "C:\Users\appveyor\AppData\Local\Programs\Common\Microsoft\Visual C++ for Python\9.0\VC\include\stdint.h"
+    - ps: activate test
+
+build_script:
+    - cmd: cd package
+    - cmd: C:\conda\envs\test\python.exe setup.py develop --no-deps --user 3>&1
+
+test_script:
+    - cmd: cd ..\testsuite
+    - cmd: C:\conda\envs\test\python.exe setup.py develop --no-deps --user 3>&1
+    - cmd: cd MDAnalysisTests
+    - cmd: C:\conda\envs\test\Scripts\pytest.exe --cov=MDAnalysis --disable-pytest-warnings 3>&1
+    - cmd: codecov
+
+after_build:
+    # cache cleanup
+    - C:\cygwin\bin\find "%LOCALAPPDATA%\pip" -type f -mtime +360 -delete
+    - C:\cygwin\bin\find "%LOCALAPPDATA%\pip" -type f -size +10M -delete
+    - C:\cygwin\bin\find "%LOCALAPPDATA%\pip" -empty -delete
+    # Show size of cache
+    - C:\cygwin\bin\du -hs "%LOCALAPPDATA%\pip\Cache"

.coveralls.yml

@@ -0,0 +1,2 @@
+service_name: travis-pro
+repo_token: wTp3SXSqCNiZPb5xMojbKrADQXVgbrQFT

.github/CONTRIBUTING.md

@@ -6,10 +6,10 @@ Thanks for contributing to MDAnalysis!
 
 If you've found a defect with MDAnalysis we'd love to know so we can fix it.  Please follow the Issue template so we can quickly diagnose the problem, in particular the piece of code that causes the problem.
 
-If your issue isn't a defect with the code and instead you require help using MDAnalysis, drop by the [discussion board](http://help.mdanalysis.org).
+If your issue isn't a defect with the code and instead you require help using MDAnalysis, drop by the [discussion board](https://groups.google.com/forum/#!forum/mdnalysis-discussion).
 
 #### Contributing code
 
 If you're contributing code, please check out the [Style guide](https://github.com/MDAnalysis/mdanalysis/wiki/Style-Guide).
 
-MDAnalysis devs are most easily reached through the [development board](http://developers.mdanalysis.org).
+MDAnalysis devs are most easily reached through the [development board](https://groups.google.com/forum/#!forum/mdnalysis-devel).

.github/ISSUE_TEMPLATE.md

@@ -1,3 +1,31 @@
+<!-- 
+
+If you have a QUESTION such as 
+
+- how to use MDAnalysis in general
+- how to accomplish something specific,
+- what output means
+- ... or similar questions related to USING MDAnalysis 
+
+then please *ask this question on the user mailing list*
+
+   https://groups.google.com/forum/#!forum/mdnalysis-discussion
+
+The issue tracker is meant for DEFECTS ("BUGS"), new FEATURES, and
+decisions on the API. In order to keep the volume of work on the issue
+tracker manageable for our volunteer developers, we will IMMEDIATELY
+CLOSE ISSUES THAT ARE BETTER ANSWERED ON THE USER MAILINGLIST.
+
+We really appreciate you as a user getting in touch with us --- no 
+matter what you want to discuss. But we need your help keeping the 
+amount of work manageable so please use the mailing list for questions 
+and the issue tracker for code-related issues.
+
+Thank you!
+
+The MDAnalysis Development Team
+
+-->
 ### Expected behaviour
 
 
@@ -17,3 +45,4 @@ u = mda.Universe(top, trj)
 
 ### Currently version of MDAnalysis:
 (run `python -c "import MDAnalysis as mda; print(mda.__version__)"`)
+

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,35 @@
+---
+name: Bug report
+about: Create a report to help us improve
+
+---
+
+**Expected behavior**
+
+A clear and concise description of what you want to do and what you think should happen. (Code to reproduce the behavior can be added below).
+
+
+**Actual behavior**
+
+What happened instead. Add as much detail as you can. Include (copy and paste) stack traces and any output.
+
+
+**Code to reproduce the behavior**
+
+Show us how to reproduce the failiure. If you can, use trajectory files from the test data.
+
+``` python
+import MDAnalysis as mda
+from MDAnalysis.tests.datafiles import PSF, DCD,  GRO, PDB, TPR, XTC, TRR,  PRMncdf, NCDF
+
+u = mda.Universe(PSF, DCD)
+
+....
+
+```
+
+**Currently version of MDAnalysis**
+
+- Which version are you using? (run `python -c "import MDAnalysis as mda; print(mda.__version__)"`)
+- Which version of Python (`python -V`)?
+- Which operating system?

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,17 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/ISSUE_TEMPLATE/questions.md

@@ -0,0 +1,24 @@
+---
+name: Questions
+about: If you want to ask a question please use the mailing list!
+
+---
+
+If you have a **QUESTION** such as 
+
+- how to use MDAnalysis in general
+- how to accomplish something specific,
+- what output means
+- ... or similar questions related to USING MDAnalysis 
+
+then please *ask this question on the user mailing list*
+
+   https://groups.google.com/forum/#!forum/mdnalysis-discussion
+
+The issue tracker is meant for DEFECTS ("BUGS"), new FEATURES, and decisions on the API. In order to keep the volume of work on the issue tracker manageable for our volunteer developers, we will IMMEDIATELY CLOSE ISSUES THAT ARE BETTER ANSWERED ON THE USER MAILINGLIST.
+
+We really appreciate you as a user getting in touch with us --- no matter what you want to discuss. But we need your help keeping the amount of work manageable so please use the mailing list for questions and the issue tracker for code-related issues.
+
+Thank you!
+
+The MDAnalysis Development Team

.travis.yml

@@ -21,26 +21,26 @@ env:
     # Set default python version to avoid repetition later
     - PYTHON_VERSION=3.5
     - BUILD_DOCS=false
-    - COVERALLS=false
+    - CODECOV=false
     - PYTEST_FLAGS="--disable-pytest-warnings --numprocesses 2 --durations=50"
     - PYTEST_LIST="testsuite/MDAnalysisTests"
     - MAIN_CMD="pytest ${PYTEST_LIST}"
     - SETUP_CMD="${PYTEST_FLAGS}"
-    - BUILD_CMD="pip install -v package/ && pip install testsuite/"
-    - CONDA_MIN_DEPENDENCIES="mmtf-python mock six biopython networkx cython joblib matplotlib scipy griddataformats hypothesis gsd"
-    - CONDA_DEPENDENCIES="${CONDA_MIN_DEPENDENCIES} seaborn>=0.7.0 clustalw=2.1 netcdf4 scikit-learn coveralls"
+    - BUILD_CMD="pip install -v package/ && (cd testsuite/ && python setup.py build)"
+    - CONDA_MIN_DEPENDENCIES="mmtf-python mock six biopython networkx cython joblib matplotlib scipy griddataformats hypothesis gsd codecov"
+    - CONDA_DEPENDENCIES="${CONDA_MIN_DEPENDENCIES} seaborn>=0.7.0 clustalw=2.1 netcdf4 scikit-learn"
     - CONDA_CHANNELS='biobuilds conda-forge'
     - CONDA_CHANNEL_PRIORITY=True
     - PIP_DEPENDENCIES="duecredit"
     - NUMPY_VERSION=stable
     - INSTALL_HOLE="true"
 
   matrix:
-    # Run a coverage test
-    - COVERALLS="true" SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis"
-    - PYTHON_VERSION=3.6
-    - PYTHON_VERSION=3.4
-    - PYTHON_VERSION=2.7
+    # Run a coverage test for most versions
+    - CODECOV="true" SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis"
+    - PYTHON_VERSION=3.6 CODECOV="true" SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis"
+    - PYTHON_VERSION=3.4 NUMPY_VERSION=1.14 CODECOV="true" SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis"
+    - PYTHON_VERSION=2.7 CODECOV="true" SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis"
     - NUMPY_VERSION=1.10.4
     - NUMPY_VERSION=dev  EVENT_TYPE="cron"
 
@@ -53,6 +53,7 @@ matrix:
            BUILD_DOCS=true
            BUILD_CMD="cd ${TRAVIS_BUILD_DIR}/package && python setup.py build_ext --inplace"
            INSTALL_HOLE="false"
+           PIP_DEPENDENCIES="${PIP_DEPENDENCIES} sphinx-sitemap"
 
     - env: NAME="Lint"
            PYLINTRC="${TRAVIS_BUILD_DIR}/package/.pylintrc"
@@ -71,10 +72,10 @@ matrix:
     - env: NAME='minimal'
            CONDA_DEPENDENCIES=${CONDA_MIN_DEPENDENCIES}
            INSTALL_HOLE="false"
+           CODECOV="true" SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis"
+
   allow_failures:
     - env: NUMPY_VERSION=dev EVENT_TYPE="cron"
-    - env: PYTHON_VERSION=3.4
-    - os: osx
 
 before_install:
   # Workaround for Travis CI macOS bug (https://github.com/travis-ci/travis-ci/issues/6307)
@@ -106,8 +107,8 @@ script:
 
 after_success:
   - |
-    if [[ $COVERALLS == 'true' ]]; then \
-      coveralls; \
+    if [[ $CODECOV == 'true' ]]; then \
+      codecov; \
     fi
   # can't use test here since this leads to travis fails even though the build passes
   - if [[ ${TRAVIS_PULL_REQUEST} == "false" ]] && [[ ${BUILD_DOCS} == "true" ]] && [[ ${TRAVIS_BRANCH} == ${GH_DOC_BRANCH} ]]; then

README.rst

@@ -102,17 +102,17 @@ to find uncovered code.
    :target: https://www.mdanalysis.org/mdanalysis/
 
 .. |build| image:: https://travis-ci.org/MDAnalysis/mdanalysis.svg?branch=develop
-    :alt: Build Status
-    :target: https://travis-ci.org/MDAnalysis/mdanalysis
+   :alt: Build Status
+   :target: https://travis-ci.org/MDAnalysis/mdanalysis
 
-.. |cov|   image:: https://coveralls.io/repos/MDAnalysis/mdanalysis/badge.svg?branch=develop
-    :alt: Coverage Status
-    :target: https://coveralls.io/r/MDAnalysis/mdanalysis?branch=develop
+.. |cov|   image:: https://codecov.io/gh/MDAnalysis/mdanalysis/branch/develop/graph/badge.svg
+   :alt: Coverage Status
+   :target: https://codecov.io/gh/MDAnalysis/mdanalysis
 
 .. |anaconda| image:: https://anaconda.org/conda-forge/mdanalysis/badges/version.svg
-    :alt: Anaconda
-    :target: https://anaconda.org/conda-forge/mdanalysis
+   :alt: Anaconda
+   :target: https://anaconda.org/conda-forge/mdanalysis
 
 .. |mybinder| image:: https://mybinder.org/badge.svg
-    :alt: My Binder
-    :target: https://mybinder.org/v2/gh/MDAnalysis/binder-notebook/master
+   :alt: My Binder
+   :target: https://mybinder.org/v2/gh/MDAnalysis/binder-notebook/master

benchmarks/benchmarks/GRO.py

@@ -2,12 +2,20 @@
 
 import numpy as np
 from MDAnalysis.coordinates.GRO import GROReader
+from MDAnalysis.topology.GROParser import GROParser
 from MDAnalysisTests.datafiles import GRO
+import MDAnalysis as mda
 
 class GROReadBench(object):
-
-    def time_read_GRO_file(self):
-        """Benchmark reading of standard test
-        suite GRO file.
-        """
+    def time_read_GRO_coordinates(self):
+        """Benchmark reading of standard testsuite GRO file."""
         GROReader(GRO)
+
+    def time_parse_GRO_file(self):
+        """Time to create topology from GRO file"""
+        p = GROParser(GRO)
+        top = p.parse()
+
+    def time_create_GRO_universe(self):
+        """Time to create MDA Universe of GRO"""
+        u = mda.Universe(GRO)

benchmarks/benchmarks/ag_methods.py

@@ -4,7 +4,7 @@
 import numpy as np
 
 try:
-    from MDAnalysisTests.datafiles import GRO
+    from MDAnalysisTests.datafiles import GRO, TPR, XTC
     from MDAnalysis.exceptions import NoDataError
 except:
     pass
@@ -24,8 +24,11 @@ def setup(self, num_atoms):
         self.u = MDAnalysis.Universe(GRO)
         self.ag = self.u.atoms[:num_atoms]
         self.weights = np.ones(num_atoms)
-        self.vdwradii = {'NA':1.0,
-                         'M':1.0}
+        self.vdwradii = {'H':1.0,
+                         'C':1.0,
+                         'N':1.0,
+                         'O':1.0,
+                         'DUMMY':1.0}
         self.rot_matrix = np.ones((3,3))
         self.trans = np.ones((4,4))
 
@@ -319,3 +322,17 @@ def time_bond(self, num_atoms):
         Requires ag of size 2.
         """
         self.ag[:2].bond
+
+
+class FragmentFinding(object):
+    """Test how quickly we find fragments (distinct molecules from bonds)"""
+    params = [(TPR, XTC),  # single large fragment, many small solvents
+              (PSF, DCD),  # single large fragment
+              (TRZ_psf, TRZ)]  # 20ish polymer chains
+    param_names = ['universe']
+
+    def setup(self, universe):
+        self.u = MDAnalysis.Universe(*universe)
+
+    def test_find_fragments(self, universe):
+        frags = self.u.atoms.fragments

benchmarks/benchmarks/analysis/rdf.py

@@ -17,21 +17,23 @@ class SimpleRdfBench(object):
     """
 
     params = ([20,75,200],
-              [[0,5], [0,15], [0,20]])
+              [[0,5], [0,15], [0,20]],
+              [1, 100, 1000, 10000])
 
     param_names = ['nbins',
-                   'range_val']
+                   'range_val',
+                   'natoms']
 
-    def setup(self, nbins, range_val):
+    def setup(self, nbins, range_val, natoms):
 
         self.sel_str = 'name OW'
 
         self.u = MDAnalysis.Universe(TPR, XTC)
 
         try:
-            self.sel = self.u.select_atoms(self.sel_str)[:200]
+            self.sel = self.u.select_atoms(self.sel_str)[:natoms]
         except AttributeError:
-            self.sel = self.u.selectAtoms(self.sel_str)[:200]
+            self.sel = self.u.selectAtoms(self.sel_str)[:natoms]
 
         # do not include initialization of the
         # InterRDF object in the benchmark itself