general clean up of travis.yml

- fix hole installation for max
- simplify test scripts

.travis.yml

@@ -6,117 +6,80 @@ branches:
     - master
     - develop
 
+os:
+  linux
+
+env:
   global:
     - secure: "f8EMSWeYC38elhpB4B/ddxlklEvQoycaxnt90Xw2tH/+ThdP1qteQ2vdgNFy1KL7Am/xnbrRhavI5K+ayfxJ93NoE2adaJ9f9aljXK+Oeu+buv5MVo2E2HhN9mX9opSSxiqGmnHIVYcdLP+1soIsDD78SGL7hB/u5nQ1aTzkbaM="
     - GH_DOC_BRANCH=develop
     - GH_REPOSITORY=github.com/MDAnalysis/mdanalysis.git
     - GIT_CI_USER=TravisCI
     - [email protected]
     - MDA_DOCDIR=${TRAVIS_BUILD_DIR}/package/doc/html/html
-    - MDA_OPTPACKAGES=opt/packages
     # Set default python version to avoid repetition later
+    - PYTHON_VERSION=3.6
     - BUILD_DOCS=false
     - COVERALLS=false
     - PYTEST_FLAGS="--disable-pytest-warnings --numprocesses 2 --durations=50"
-    - PYTEST_LIST="testsuite/MDAnalysisTests/lib testsuite/MDAnalysisTests/formats testsuite/MDAnalysisTests/coordinates testsuite/MDAnalysisTests/utils testsuite/MDAnalysisTests/topology testsuite/MDAnalysisTests/auxiliary testsuite/MDAnalysisTests/core testsuite/MDAnalysisTests/analysis"
-    - NOSE_COVERAGE_FILE="nose_coverage"
-    - PYTEST_COVERAGE_FILE="pytest_coverage"
+    - PYTEST_LIST="testsuite/MDAnalysisTests"
     - MAIN_CMD="pytest ${PYTEST_LIST}"
     - SETUP_CMD="${PYTEST_FLAGS}"
     - 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 hypothesis"
-    - 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  hypothesis"
-    # Install griddataformats from PIP so that scipy is only installed in the full build (#1147)
-    - PIP_DEPENDENCIES=''
+    # we need nose for assert_raises and stuff
+    - CONDA_MIN_DEPENDENCIES="mmtf-python mock six biopython networkx cython joblib matplotlib scipy griddataformats hypothesis nose"
+    - CONDA_DEPENDENCIES="${CONDA_MIN_DEPENDENCIES} seaborn clustalw=2.1 netcdf4 scikit-learn"
     - CONDA_CHANNELS='biobuilds conda-forge'
     - CONDA_CHANNEL_PRIORITY=True
     - NUMPY_VERSION=stable
+    - INSTALL_HOLE="true"
 
-
+  matrix:
+    # Run a coverage test
+    - COVERALLS="true" SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis"
+    - PYTHON_VERSION=3.5
+    - PYTHON_VERSION=3.4
+    - PYTHON_VERSION=2.7
+    - NUMPY_VERSION=1.10.4
+    - NUMPY_VERSION=dev  EVENT_TYPE="cron"
 
 matrix:
   fast_finish: true
-
   include:
-    - os : linux
-      env: NAME='minimal'
-           PYTHON_VERSION=3.6
-           MAIN_CMD='pytest ${PYTEST_LIST} ${PYTEST_FLAGS}'
-
-    - os: linux
-      env: NAME="Doc"
-           PYTHON_VERSION=3.6
+    - env: NAME="Doc"
            MAIN_CMD="cd package && python setup.py"
            SETUP_CMD="build_sphinx"
            BUILD_DOCS=true
            BUILD_CMD="cd ${TRAVIS_BUILD_DIR}/package && python setup.py build_ext --inplace"
-           CONDA_DEPENDENCIES=${CONDA_ALL_DEPENDENCIES}
+           INSTALL_HOLE="false"
 
-    - os: linux
-      env: NAME="Lint"
-           PYTHON_VERSION=3.6
+    # todo update to default 3.6 (aka removing the line with PYTHON_VERSION here)
+    - env: NAME="Lint"
+           PYTHON_VERSION=2.7
            MAIN_CMD="pylint --rcfile=package/.pylintrc package/MDAnalysis && pylint --rcfile=package/.pylintrc testsuite/MDAnalysisTests"
-           SETUP_CMD=''
+           SETUP_CMD=""
            BUILD_CMD=""
-           CONDA_DEPENDENCIES="pylint backports.functools_lru_cache"
-           PIP_DEPENDENCIES=""
-
-    - os: linux
-      env: NAME='full'
-           PYTHON_VERSION=3.6
-           NOSE_COVERAGE='--with-coverage --cover-package MDAnalysis'
-           PYTEST_COVERAGE='--cov=MDAnalysis'
-           SETUP_CMD="${PYTEST_FLAGS} ${PYTEST_COVERAGE}"
-           CONDA_DEPENDENCIES=${CONDA_ALL_DEPENDENCIES}
-           COVERALLS='true'
-
-    - os: linux
-      env: NAME='old numpy'
-           PYTHON_VERSION=3.6
-           NUMPY_VERSION=1.10.4
-           CONDA_DEPENDENCIES=${CONDA_ALL_DEPENDENCIES}
-
-    - os: linux
-      env: NAME='numpy dev'
-           PYTHON_VERSION=3.6
-           NUMPY_VERSION=dev
-           CONDA_DEPENDENCIES=${CONDA_ALL_DEPENDENCIES}
-           EVENT_TYPE='cron'
-
-    - os: linux
-      env: NAME='full-py3.4'
-           PYTHON_VERSION=3.4
-           CONDA_DEPENDENCIES=${CONDA_ALL_DEPENDENCIES}
-
-    - os: linux
-      env: NAME='full-py3.5'
-           PYTHON_VERSION=3.5
-           CONDA_DEPENDENCIES=${CONDA_ALL_DEPENDENCIES}
-
-    - os: linux
-      env: NAME='full-py2.7'
-           PYTHON_VERSION=2.7
-           CONDA_DEPENDENCIES=${CONDA_ALL_DEPENDENCIES}
+           CONDA_DEPENDENCIES=""
+           INSTALL_HOLE="false"
 
     - os: osx
-      env: NAME='osx-py2.7'
-           PYTHON_VERSION=2.7
-           CONDA_DEPENDENCIES=${CONDA_ALL_DEPENDENCIES}
+      env: PYTHON_VERSION=3.6
 
     - os: osx
-      env: NAME='osx-py3.6'
-           PYTHON_VERSION=3.6
-           CONDA_DEPENDENCIES=${CONDA_ALL_DEPENDENCIES}
+      env: PYTHON_VERSION=2.7
 
+    - env: NAME='minimal'
+           CONDA_DEPENDENCIES=${CONDA_MIN_DEPENDENCIES}
+           INSTALL_HOLE="false"
 
 install:
   - git clone git://github.com/astropy/ci-helpers.git
   - source ci-helpers/travis/setup_conda.sh
   # additional external tools (Issue #898) -- HOLE
   - |
-    if [[ $NAME == 'full' ]]; then \
-        bash ./maintainer/install_hole.sh $TRAVIS_OS_NAME "${HOME}/${MDA_OPTPACKAGES}"; \
-        HOLE_BINDIR="${HOME}/${MDA_OPTPACKAGES}/hole2/exe"; \
+    if [[ $INSTALL_HOLE == 'true' ]]; then \
+        bash ./maintainer/install_hole.sh $TRAVIS_OS_NAME "${HOME}"; \
+        HOLE_BINDIR="${HOME}/hole2/exe"; \
         export PATH=${PATH}:${HOLE_BINDIR}; \
     fi
   - eval $BUILD_CMD
@@ -127,7 +90,6 @@ script:
   - echo $MAIN_CMD $SETUP_CMD
   - eval $MAIN_CMD $SETUP_CMD
 
-
 after_success:
   - |
     if [[ $COVERALLS == 'true' ]]; then \