make scipy and matplotlib full dependencies (MDAnalysis#1159)

.travis.yml

@@ -21,14 +21,19 @@ env:
     # Set default python version to avoid repetition later
     - PYTHON_VERSION=3.5
     - BUILD_DOCS=false
-    - CODECOV=false
-    - PYTEST_FLAGS="--disable-pytest-warnings --durations=50"
-    - PYTEST_LIST="testsuite/MDAnalysisTests"
-    - MAIN_CMD="pytest ${PYTEST_LIST}"
-    - SETUP_CMD="${PYTEST_FLAGS}"
-    - 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"
+    - PYTHON_VERSION=2.7
+    - COVERALLS=false
+    - NOSE_FLAGS="--processes=2 --process-timeout=400 --no-open-files --with-timer --timer-top-n 50"
+    - NOSE_TEST_LIST1="analysis auxiliary coordinates core formats topology utils"
+    - NOSE_TEST_LIST2="lib"
+    - NOSE_COVERAGE1="coverage1"
+    - NOSE_COVERAGE2="coverage2"
+    - MAIN_CMD="python ./testsuite/MDAnalysisTests/mda_nosetests ${NOSE_TEST_LIST1} ${NOSE_FLAGS}; python ./testsuite/MDAnalysisTests/mda_nosetests ${NOSE_TEST_LIST2} ${NOSE_FLAGS}"
+    - SETUP_CMD=""
+    - BUILD_CMD="pip install -v package/ && pip install testsuite/"
+    - CONDA_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer matplotlib scipy griddataformats"
+    - CONDA_ALL_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer matplotlib netcdf4 scikit-learn scipy griddataformats seaborn coveralls clustalw=2.1"
+    - PIP_DEPENDENCIES=""
     - CONDA_CHANNELS='biobuilds conda-forge'
     - CONDA_CHANNEL_PRIORITY=True
     - PIP_DEPENDENCIES="duecredit"

package/CHANGELOG

@@ -13,6 +13,73 @@ The rules for this file:
   * release numbers follow "Semantic Versioning" http://semver.org
 
 ------------------------------------------------------------------------------
+
+
+mm/dd/17 richardjgowers, rathann, jbarnoud, orbeckst
+
+  * 0.16.2
+
+Deprecations
+  * deprecated core.Timeseries module for 0.17.0 (Issue #1383)
+  * deprecated instant selectors for 1.0 (Issue #1377)
+  * deprecated the core.flag registry for 1.0 (Issue #782)
+
+Fixes
+  * fixed GROWriter truncating long resids from the wrong end (Issue #1395)
+  * Fixed dtype of numpy arrays to accomodate 32 bit architectures (Issue #1362)
+  * Groups are hashable on python 3 (Issue #1397)
+
+Changes
+  * scipy and matplotlib are now required dependencies (Issue #1159)
+
+
+06/03/17 utkbansal, kain88-de, xiki-tempula, kaplajon, wouterboomsma,
+         richardjgowers, Shtkddud123, QuantumEntangledAndy, orbeckst,
+         kaceyreidy
+
+  * 0.16.1
+
+Enhancements
+  * Universe now works with StringIO objects for topologies and trajectories.
+  * Residues with the same residue ids are not merged by default now
+    (apply to PDB, GRO) (Issue #1306)
+  * Improved print to screen format in waterdynamics module (using
+    ProgressMeter).
+  * PQRParser now treats insertion codes properly (Issue #1317)
+  * made online docs responsive with the Alabaster Sphinx theme (#378)
+
+Fixes
+  * In Universe.transfer_to_memory(): dt is now adjusted with step (Issue #1310)
+  * Various documentation sphinx errors (PR #1312)
+  * Bugfix in confdistmatrix.get_distance_matrix; now works on all trajectory types.
+    (issue #1324)
+  * Fixed bug "no molecules in water selection" in waterdynamics analysis
+    module.
+  * Fix hbond_analysis cannot deal with Universe where no two atoms are with 3A.
+    (PR #1325)
+  * Fix PDBParser docs for conect (issue #1246)
+  * Fixed bug where amber topology files would fail to load if number of atoms was
+    exactly divisible by number of atoms per line (issue #1331)
+  * Fixed incorrect handling of residue names with trailing numbers in
+    HydrogenBondAnalysis (issue #801)
+  * Fixed AnalysisBase class provides numerical start,stop,step values (PR #1340)
+  * Fixed PSFParser not creating multiple residues for identical resids in
+    different segments. (Issue #1347, PR #1348)
+  * Add the OC1 and OC2 from amber99sb-ildn to hydrogen bond acceptors (issue #1342)
+  * Fix RMSF run return value (PR #1354)
+  * Fixed documentation in pca (Issue #1378 PR #1379)
+
+Changes
+  * Enable various pylint warnings to increase python 3 compatibility
+  * Change Mathjax cdn (Issue #1313)
+  * Change mass_weight to weights for PSA analysis
+  * Move mass_weights deprecation to version 0.18
+  * Docs moved to http://docs.mdanalysis.org (Issue #1315)
+    and made responsive (Alabaster theme with readable-sphinx CSS)
+    (Issue #378)
+  * speed improvements parsing PDB / PDBQT / PQR / XYZ coordinate reader (Issue #1308)
+
+
 04/10/17 kain88-de, fiona-naughton, richardjgowers, tyler.je.reddy, jdetle
          euhruska, orbeckst, rbrtdlg, jbarnoud, wouterboomsma, shanmbic,
          dotsdl, manuel.nuno.melo, utkbansal, vedantrathore, shobhitagarwal1612,

package/setup.py

@@ -575,14 +575,27 @@ def dynamic_author_list():
                         ],
           },
           ext_modules=exts,
-          requires=['numpy (>=1.10.4)', 'biopython (>= 1.71)', 'mmtf (>=1.0.0)',
+          classifiers=CLASSIFIERS,
+          cmdclass=cmdclass,
+          requires=['numpy (>=1.10.4)', 'biopython', 'mmtf (>=1.0.0)',
                     'networkx (>=1.0)', 'GridDataFormats (>=0.3.2)', 'joblib',
-                    'scipy (>=1.0.0)', 'matplotlib (>=1.5.1)'],
+                    'scipy', 'matplotlib (>=1.5.1)'],
           # all standard requirements are available through PyPi and
           # typically can be installed without difficulties through setuptools
           setup_requires=[
               'numpy>=1.10.4',
           ],
+          install_requires=[
+              'numpy>=1.10.4',
+              'biopython>=1.59',
+              'networkx>=1.0',
+              'GridDataFormats>=0.3.2',
+              'six>=1.4.0',
+              'mmtf-python>=1.0.0',
+              'joblib',
+              'scipy',
+              'matplotlib>=1.5.1',
+          ],
           install_requires=install_requires,
           # extras can be difficult to install through setuptools and/or
           # you might prefer to use the version available through your