Merge pull request #294 from dohmatob/fix-ci

OK, build matrix is green. Merging :)

Author: dohmatob

.travis.yml

@@ -1,13 +1,38 @@
 sudo: required
+# dist: xenial
+
 
 language: python
 
-env:
-  matrix:
-    - DISTRIB="neurodebian" COVERAGE="true"
-    - DISTRIB="conda" PYTHON_VERSION="3.5" NUMPY_VERSION="*" SCIPY_VERSION="*"
-      SCIKIT_LEARN_VERSION="*" PANDAS_VERSION="*" MATPLOTLIB_VERSION="*"
-      NETWORKX_VERSION="*"
+matrix:
+  # Do not wait for the allowed_failures entry to finish before
+  # setting the status
+  fast_finish: true
+  allow_failures:
+    # allow_failures seems to be keyed on the python version
+    - python: 2.7
+  include:
+    # Oldest supported versions (with neurodebian)
+    - env: DISTRIB="conda" PYTHON_VERSION="2.7"
+           NUMPY_VERSION="1.8.2" SCIPY_VERSION="0.14"
+           SCIKIT_LEARN_VERSION="0.15.1" MATPLOTLIB_VERSION="1.3.1"
+           PANDAS_VERSION="0.13.0" NIBABEL_VERSION="2.0.2" COVERAGE="true"
+           NIPYPE_VERSION="0.13.0"
+           NILEARN_VERSION="0.4.0"
+           NETWORKX_VERSION="*"
+           CONFIGOBJ_VERSION="*"
+    # Most recent versions
+    - env: DISTRIB="conda" PYTHON_VERSION="3.5"
+           NUMPY_VERSION="*" SCIPY_VERSION="*" PANDAS_VERSION="*"
+           SCIKIT_LEARN_VERSION="*" MATPLOTLIB_VERSION="*" COVERAGE="true"
+           NIPYPE_VERSION="0.13.0"
+           NILEARN_VERSION="0.4.0"
+           NETWORKX_VERSION="*"
+           CONFIGOBJ_VERSION="*"
+    # FLAKE8 linting on diff wrt common ancestor with upstream/master
+    # Note: the python value is only there to trigger allow_failures
+    - python: 2.7
+      env: DISTRIB="conda" PYTHON_VERSION="2.7" FLAKE8_VERSION="*" SKIP_TESTS="true"
 
 virtualenv:
   system_site_packages: true

continuous_integration/install.sh

@@ -1,18 +1,41 @@
+#!/bin/bash
+# This script is meant to be called by the "install" step defined in
+# .travis.yml. See http://docs.travis-ci.com/ for more details.
+# The behavior of the script is controlled by environment variabled defined
+# in the .travis.yml in the top level folder of the project.
+#
+# This script is adapted from a similar script from the scikit-learn repository.
+#
+# License: 3-clause BSD
+
 set -e
 
-NIPYPE_VERSION=0.13.0
+# Fix the compilers to workaround avoid having the Python 3.4 build
+# lookup for g++44 unexpectedly.
+export CC=gcc
+export CXX=g++
+
+create_new_venv() {
+    # At the time of writing numpy 1.9.1 is included in the travis
+    # virtualenv but we want to be in control of the numpy version
+    # we are using for example through apt-get install
+    deactivate
+    virtualenv --system-site-packages testvenv
+    source testvenv/bin/activate
+    pip install nose
+}
 
 print_conda_requirements() {
     # Echo a conda requirement string for example
-    # "pip python=2.7.3 scikit-learn=*". It has a hardcoded
+    # "pip nose python='2.7.3 scikit-learn=*". It has a hardcoded
     # list of possible packages to install and looks at _VERSION
     # environment variables to know whether to install a given package and
     # if yes which version to install. For example:
     #   - for numpy, NUMPY_VERSION is used
     #   - for scikit-learn, SCIKIT_LEARN_VERSION is used
     TO_INSTALL_ALWAYS="pip nose"
     REQUIREMENTS="$TO_INSTALL_ALWAYS"
-    TO_INSTALL_MAYBE="python numpy scipy scikit-learn pandas matplotlib networkx flake8"
+    TO_INSTALL_MAYBE="python numpy scipy matplotlib scikit-learn pandas flake8 networkx configobj"
     for PACKAGE in $TO_INSTALL_MAYBE; do
         # Capitalize package name and add _VERSION
         PACKAGE_VERSION_VARNAME="${PACKAGE^^}_VERSION"
@@ -29,43 +52,76 @@ print_conda_requirements() {
 }
 
 create_new_conda_env() {
-    # Deactivate the travis-provided virtual environment and setup a
-    # conda-based environment instead
-    deactivate
+    # Skip Travis related code on circle ci.
+    if [ -z $CIRCLECI ]; then
+        # Deactivate the travis-provided virtual environment and setup a
+        # conda-based environment instead
+        deactivate
+    fi
 
     # Use the miniconda installer for faster download / install of conda
     # itself
     wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh \
-         -O miniconda.sh
-    chmod +x miniconda.sh && ./miniconda.sh -b
-    export PATH=/home/travis/miniconda2/bin:$PATH
-    conda update --yes conda
+        -O ~/miniconda.sh
+    chmod +x ~/miniconda.sh && ~/miniconda.sh -b
+    export PATH=$HOME/miniconda2/bin:$PATH
+    echo $PATH
+    conda update --quiet --yes conda
 
     # Configure the conda environment and put it in the path using the
     # provided versions
     REQUIREMENTS=$(print_conda_requirements)
     echo "conda requirements string: $REQUIREMENTS"
-    conda create -n testenv --yes $REQUIREMENTS
+    conda create -n testenv --quiet --yes $REQUIREMENTS
     source activate testenv
+
+    if [[ "$INSTALL_MKL" == "true" ]]; then
+        # Make sure that MKL is used
+        conda install --quiet --yes mkl
+    elif [[ -z $CIRCLECI ]]; then
+        # Travis doesn't use MKL but circle ci does for speeding up examples
+        # generation in the html documentation.
+        # Make sure that MKL is not used
+        conda remove --yes --features mkl || echo "MKL not installed"
+    fi
 }
 
 if [[ "$DISTRIB" == "neurodebian" ]]; then
+    create_new_venv
+    pip install nose-timer
     bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh)
-    sudo apt-get install -qq python-scipy python-nose python-nibabel python-sklearn python-pandas python-networkx python-nipype
-    sudo apt-get install -qq python-pip
-    pip install "nilearn>=0.1.3"
+    sudo apt-get install -qq python-scipy python-nose python-nibabel python-sklearn
+
 elif [[ "$DISTRIB" == "conda" ]]; then
     create_new_conda_env
+    pip install nose-timer
+    # Note: nibabel is in setup.py install_requires so nibabel will
+    # always be installed eventually. Defining NIBABEL_VERSION is only
+    # useful if you happen to want a specific nibabel version rather
+    # than the latest available one.
+    if [ -n "$NIBABEL_VERSION" ]; then
+        pip install nibabel=="$NIBABEL_VERSION"
+    fi
+    if [ -n "$NIPYPE_VERSION" ]; then
+        pip install nipype=="$NIPYPE_VERSION"
+    fi
+    if [ -n "$NILEARN_VERSION" ]; then
+        pip install nilearn=="$NILEARN_VERSION"
+    fi
 
-    # dependencies that are only available through pip
-    pip install nilearn>=0.1.3 nipype==${NIPYPE_VERSION} configobj
 else
-    echo "Unknown distrib: $DISTRIB"
+    echo "Unrecognized distribution ($DISTRIB); cannot setup CI environment."
     exit 1
 fi
 
-python setup.py install
+pip install psutil memory_profiler
 
 if [[ "$COVERAGE" == "true" ]]; then
-    pip install coverage coveralls
+    pip install codecov
+fi
+
+# numpy not installed when skipping the tests so we do not want to run
+# setup.py install
+if [[ "$SKIP_TESTS" != "true" ]]; then
+    python setup.py install
 fi