Fix SimpleRegressionResults

.circleci/README.md

@@ -0,0 +1,14 @@
+CircleCI is used to build our documentations and tutorial examples.
+CircleCI's cache stores previously built documentation and 
+only rebuild any changes, instead of rebuilding the documentation from scratch. 
+This saves a lot of time.
+
+Occasionally, some changes necessitate rebuilding the documentation from scratch,
+either to see the full effect of the changes 
+or because the cached builds are raising some error.
+
+To run a new CircleCI build from the beginning, without using the cache:
+
+1. Run the script `clean-cache.py`.
+2. Commit the change (with a clear message).
+3. Push the commit.

.circleci/clean-cache.py

@@ -0,0 +1,23 @@
+#! /usr/bin/env python
+
+import os
+from datetime import datetime as dt
+
+def update_cache_timestamp():
+    """ Updates the contents of the manual-cache-timestamp file
+    with current timestamp.
+
+    Returns
+    -------
+    None
+    """
+    timestamp_dirpath = os.path.dirname(__file__)
+    timestamp_filename = 'manual-cache-timestamp'
+    timestamp_filepath = os.path.join(timestamp_dirpath, timestamp_filename)
+    utc_now_timestamp = dt.utcnow()
+    with open(timestamp_filepath, 'w') as write_obj:
+        write_obj.write(str(utc_now_timestamp))
+
+
+if __name__ == '__main__':
+    update_cache_timestamp()

.circleci/config.yml

@@ -0,0 +1,154 @@
+# quick-build rebuilds changes using the cached documentation.
+# The cache is emptied everyday, forcing a full build on the day's first push.
+# It doesn't operate on master branch. New branches are always built from scratch.
+# full-build always rebuilds from scratch, without any cache. Only for changes in master branch.
+
+version: 2
+
+jobs:
+  quick-build:
+    docker:
+      - image: circleci/python:3.6
+    environment:
+      DISTRIB: "conda"
+      PYTHON_VERSION: "3.6"
+      NUMPY_VERSION: "*"
+      SCIPY_VERSION: "*"
+      SCIKIT_LEARN_VERSION: "*"
+      MATPLOTLIB_VERSION: "*"
+
+    steps:
+      - checkout
+        # Get rid of existing virtualenvs on circle ci as they conflict with conda.
+        # Trick found here:
+        # https://discuss.circleci.com/t/disable-autodetection-of-project-or-application-of-python-venv/235/10
+      - run: cd && rm -rf ~/.pyenv && rm -rf ~/virtualenvs
+        # We need to remove conflicting texlive packages.
+      - run: sudo -E apt-get -yq remove texlive-binaries --purge
+        # Installing required packages for `make -C doc check command` to work.
+      - run: sudo -E apt-get -yq update
+      - run: sudo -E apt-get -yq --no-install-suggests --no-install-recommends --force-yes install dvipng texlive-latex-base texlive-latex-extra
+      - run:
+          name: Generating today's date and writing to file to generate daily new cache key
+          command: |
+            date +%F > today
+      - restore_cache:
+          key: v5-packages+datasets-{{ .Branch }}-{{ checksum "today" }}-{{ checksum ".circleci/manual-cache-timestamp" }}
+      - run:
+          name: Download & install conda if absent
+          command: |
+            if
+              ls $HOME/miniconda3/bin | grep conda -q
+            then
+              echo "(Mini)Conda already present from the cache."
+            else
+              wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh
+              chmod +x ~/miniconda.sh && ~/miniconda.sh -b
+            fi
+      - run:
+          name: Setup conda path in env variables
+          command: |
+            echo 'export PATH="$HOME/miniconda3/bin:$PATH"'  >> $BASH_ENV
+      - run:
+          name: Create new conda env
+          command: |
+            if
+              conda env list | grep testenv
+            then
+              echo "Conda env testenv already exists courtesy of the cache."
+            else
+              conda create -n testenv -yq
+            fi
+      - run:
+          name: Install packages in conda env
+          command: |
+            conda install -n testenv python=3.6 numpy scipy scikit-learn matplotlib pandas \
+            flake8 lxml nose cython mkl sphinx coverage patsy boto3 pillow pandas -yq
+            conda install -n testenv nibabel nilearn nose-timer -c conda-forge -yq
+      - run:
+          name: Running CircleCI test (make html)
+          command: |
+            source activate testenv
+            pip install -e .
+            set -o pipefail && cd doc && make html-strict 2>&1 | tee ~/log.txt
+          no_output_timeout: 5h
+      - save_cache:
+          key: v5-packages+datasets-{{ .Branch }}-{{ checksum "today" }}-{{ checksum ".circleci/manual-cache-timestamp" }}
+          paths:
+          - ../nilearn_data
+          - ../miniconda3
+          - doc
+
+      - store_artifacts:
+          path: doc/_build/html
+      - store_artifacts:
+          path: coverage
+      - store_artifacts:
+          path: log.txt
+
+
+  full-build:
+    docker:
+      - image: circleci/python:3.6
+    environment:
+      DISTRIB: "conda"
+      PYTHON_VERSION: "3.6"
+      NUMPY_VERSION: "*"
+      SCIPY_VERSION: "*"
+      SCIKIT_LEARN_VERSION: "*"
+      MATPLOTLIB_VERSION: "*"
+
+    steps:
+      - checkout
+        # Get rid of existing virtualenvs on circle ci as they conflict with conda.
+        # Trick found here:
+        # https://discuss.circleci.com/t/disable-autodetection-of-project-or-application-of-python-venv/235/10
+      - run: cd && rm -rf ~/.pyenv && rm -rf ~/virtualenvs
+        # We need to remove conflicting texlive packages.
+      - run: sudo -E apt-get -yq remove texlive-binaries --purge
+        # Installing required packages for `make -C doc check command` to work.
+      - run: sudo -E apt-get -yq update
+      - run: sudo -E apt-get -yq --no-install-suggests --no-install-recommends --force-yes install dvipng texlive-latex-base texlive-latex-extra
+      - run: wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh
+      - run: chmod +x ~/miniconda.sh && ~/miniconda.sh -b
+      - run: echo 'export PATH="$HOME/miniconda3/bin:$PATH"'  >> $BASH_ENV
+      - run:
+          name: Create conda env
+          command: |
+            conda create -n testenv python=3.6 numpy scipy scikit-learn matplotlib pandas \
+            flake8 lxml nose cython mkl sphinx coverage patsy boto3 pillow pandas -yq
+            conda install -n testenv nibabel nilearn nose-timer -c conda-forge -yq
+      - run:
+          name: Running CircleCI test (make html)
+          command: |
+            source activate testenv
+            pip install -e .
+            set -o pipefail && cd doc && make html 2>&1 | tee ~/log.txt
+          no_output_timeout: 5h
+
+      - store_artifacts:
+          path: doc/_build/html
+      - store_artifacts:
+          path: coverage
+      - store_artifacts:
+          path: $HOME/log.txt
+          destination: log.txt
+
+
+workflows:
+  version: 2
+  push:
+    jobs:
+      - quick-build:
+          filters:
+            branches:
+              ignore:
+                - master
+                - test-circleci  # test branch to check if merges occur on master as expected.
+
+      - full-build:
+          filters:
+            branches:
+              only:
+                - master
+                - test-circleci

.circleci/manual-cache-timestamp

@@ -0,0 +1 @@
+2018-12-02+15:13:14++01

.travis.yml

@@ -20,26 +20,30 @@ matrix:
   include:
     # Ubuntu 14.04 version without matplotlib
     - env: DISTRIB="conda" PYTHON_VERSION="2.7"
-           NUMPY_VERSION="1.8.2" SCIPY_VERSION="0.14"
-           SCIKIT_LEARN_VERSION="0.15.0"
-           PANDAS_VERSION="0.13.0"
+           NUMPY_VERSION="1.11.0" SCIPY_VERSION="0.17"
+           SCIKIT_LEARN_VERSION="0.18.0"
+           PANDAS_VERSION="0.18.0"
     # Trying to get as close to the minimum required versions while
     # still having the package version available through conda
     - env: DISTRIB="conda" PYTHON_VERSION="2.7"
-           NUMPY_VERSION="1.8.2" SCIPY_VERSION="0.14"
-           SCIKIT_LEARN_VERSION="0.15.0" MATPLOTLIB_VERSION="1.3.1"
-           NIBABEL_VERSION="2.0.2" PANDAS_VERSION="0.13.0" COVERAGE="true"
+           NUMPY_VERSION="1.11.2" SCIPY_VERSION="0.19"
+           SCIKIT_LEARN_VERSION="0.18" MATPLOTLIB_VERSION="1.5.1"
+           NIBABEL_VERSION="2.0.2" PANDAS_VERSION="*" COVERAGE="true"
     # Python 3.4 with intermediary versions
     - env: DISTRIB="conda" PYTHON_VERSION="3.4"
-           NUMPY_VERSION="1.8.2" SCIPY_VERSION="0.14.0"
-           SCIKIT_LEARN_VERSION="0.15.2" MATPLOTLIB_VERSION="1.4.0"
-           PANDAS_VERSION="*" PATSY_VERSION="*"
-    # Most recent versions (Python 3)
+           NUMPY_VERSION="1.11.0" SCIPY_VERSION="0.17"
+           SCIKIT_LEARN_VERSION="0.18" MATPLOTLIB_VERSION="1.5.1"
+           PANDAS_VERSION="0.18.0" PATSY_VERSION="*"
+    # Python 3.5 with latest versions.
     - env: DISTRIB="conda" PYTHON_VERSION="3.5"
            NUMPY_VERSION="*" SCIPY_VERSION="*"
            SCIKIT_LEARN_VERSION="*" MATPLOTLIB_VERSION="*" COVERAGE="true"
            PANDAS_VERSION="*"
-
+    # Most recent versions (Python 3)
+    - env: DISTRIB="conda" PYTHON_VERSION="*"
+           NUMPY_VERSION="*" SCIPY_VERSION="*"
+           SCIKIT_LEARN_VERSION="*" MATPLOTLIB_VERSION="*" COVERAGE="true"
+           PANDAS_VERSION="*"
 install:
     - source continuous_integration/install.sh
 

README.rst

@@ -30,29 +30,27 @@ The required dependencies to use the software are:
 
 * Python >= 2.7
 * setuptools
-* Numpy >= 1.8.2
-* SciPy >= 0.14
+* Numpy >= 1.11
+* SciPy >= 0.17
 * Nibabel >= 2.0.2
-* Nilearn >= 0.2.0
-* Pandas >= 0.13.0
-* Sklearn >= 0.15.0
-* Patsy >= 0.2.0
+* Nilearn >= 0.4.0
+* Pandas >= 0.18.0
+* Sklearn >= 0.18.0
+* Patsy >= 0.4.1
 
 If you are using nilearn plotting functionalities or running the
-examples, matplotlib >= 1.3.1 is required.
+examples, matplotlib >= 1.5.1 is required.
 
-If you want to run the tests, you need nose >= 1.2.1 and coverage >= 3.6.
+If you want to run the tests, you need nose >= 1.2.1 and coverage >= 3.7.
 
-If you want to download openneuro datasets Boto3 >= 1.0.0 is required
+If you want to download openneuro datasets Boto3 >= 1.2 is required
 
 
 Install
 =======
 
-In order to perform the installation, run the following command from the nistats directory::
-
-    python setup.py install --user
-
+The installation instructions are found on the webpage:
+https://nistats.github.io/
 
 Development
 ===========

continuous_integration/install.sh

@@ -33,7 +33,7 @@ print_conda_requirements() {
     # 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 libgfortran=1.0=0 nomkl"
+    TO_INSTALL_ALWAYS="pip nose libgfortran=3.0=0 nomkl"
     REQUIREMENTS="$TO_INSTALL_ALWAYS"
     TO_INSTALL_MAYBE="python numpy scipy matplotlib scikit-learn pandas"
     for PACKAGE in $TO_INSTALL_MAYBE; do
@@ -61,10 +61,10 @@ create_new_conda_env() {
 
     # Use the miniconda installer for faster download / install of conda
     # itself
-    wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh \
+    wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
         -O miniconda.sh
     chmod +x miniconda.sh && ./miniconda.sh -b
-    export PATH=/home/travis/miniconda2/bin:$PATH
+    export PATH=/home/travis/miniconda3/bin:$PATH
     echo $PATH
     conda update --quiet --yes conda
 

doc/conf.py

@@ -281,11 +281,12 @@
 
 sphinx_gallery_conf = {
     'doc_module'        : 'nistats',
+    'backreferences_dir': os.path.join('modules', 'generated'),
     'reference_url'     : {
         'nilearn': 'http://nilearn.github.io',
         'matplotlib': 'http://matplotlib.org',
-        'numpy': 'http://docs.scipy.org/doc/numpy-1.6.0',
-        'scipy': 'http://docs.scipy.org/doc/scipy-0.11.0/reference',
+        'numpy': 'http://docs.scipy.org/doc/numpy-1.11.0',
+        'scipy': 'http://docs.scipy.org/doc/scipy-0.17.0/reference',
         'nibabel': 'http://nipy.org/nibabel',
         'sklearn': 'http://scikit-learn.org/stable',
         'patsy': 'http://patsy.readthedocs.io/en/latest/',