make scipy and matplotlib full dependencies (MDAnalysis#1159)

.travis.yml

@@ -31,10 +31,10 @@ env:
     - MAIN_CMD="pytest ${PYTEST_LIST} ${PYTEST_FLAGS}; python ./testsuite/MDAnalysisTests/mda_nosetests ${NOSE_TEST_LIST} ${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 pytest=3.1.2 pytest-cov=2.5.1 pytest-raises"
-    - CONDA_ALL_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer matplotlib netcdf4 scikit-learn scipy seaborn coveralls clustalw=2.1 pytest=3.1.2 pytest-cov=2.5.1"
+    - CONDA_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer matplotlib scipy griddataformats pytest pytest-cov pytest-raises"
+    - 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 pytest pytest-cov pytest-raises"
     # Install griddataformats from PIP so that scipy is only installed in the full build (#1147)
-    - PIP_DEPENDENCIES='griddataformats'
+    - PIP_DEPENDENCIES=''
     - CONDA_CHANNELS='biobuilds conda-forge'
     - CONDA_CHANNEL_PRIORITY=True
     - NUMPY_VERSION=stable

package/CHANGELOG

@@ -29,6 +29,9 @@ Fixes
   * 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,

package/setup.py

@@ -494,11 +494,12 @@ def dynamic_author_list():
           classifiers=CLASSIFIERS,
           cmdclass=cmdclass,
           requires=['numpy (>=1.10.4)', 'biopython', 'mmtf (>=1.0.0)',
-                    'networkx (>=1.0)', 'GridDataFormats (>=0.3.2)', 'joblib'],
+                    'networkx (>=1.0)', 'GridDataFormats (>=0.3.2)', 'joblib',
+                    'scipy', 'matplotlib (>=1.5.1)'],
           # all standard requirements are available through PyPi and
           # typically can be installed without difficulties through setuptools
           setup_requires=[
-              'numpy>=1.9.3',
+              'numpy>=1.10.4',
           ],
           install_requires=[
               'numpy>=1.10.4',
@@ -508,6 +509,8 @@ def dynamic_author_list():
               'six>=1.4.0',
               'mmtf-python>=1.0.0',
               'joblib',
+              'scipy',
+              'matplotlib>=1.5.1',
           ],
           # extras can be difficult to install through setuptools and/or
           # you might prefer to use the version available through your
@@ -516,8 +519,6 @@ def dynamic_author_list():
               'AMBER': ['netCDF4>=1.0'],  # for AMBER netcdf, also needs HDF5
                                           # and netcdf-4
               'analysis': [
-                  'matplotlib>=1.5.1',
-                  'scipy',
                   'seaborn',  # for annotated heat map and nearest neighbor
                               # plotting in PSA
                   'sklearn',  # For clustering and dimensionality reduction