Merge branch 'master' of https://github.com/nilearn/nilearn into spri…

…nt_modify_fetch_dev

* 'master' of https://github.com/nilearn/nilearn: (228 commits)
  [MRG] Nans in view connectome (nilearn#2166)
  [MRG] FIX: orientation problem with plot_glass_brain (nilearn#1888)
  Import HTMLDocument in its original module to preserve backwards compatibility (nilearn#2162)
  Fixing malfunctioning allowed-failure section in Travis (nilearn#2160)
  Update Brainomics fetcher (nilearn#2097)
  Remove inplace modification in signal.clean (nilearn#2125)
  Iter age group prediction example (nilearn#2063)
  Expose bg_img, vmin and vmax in plot_img signature (nilearn#2157)
  Replac conda with pip in TravisCI setup (nilearn#2141)
  Core devs doc and add @emdupre (nilearn#2151)
  Add check for vmin, vmax in plot_surf_roi (nilearn#2052)
  [ENH] Initial visual reports (nilearn#2019)
  Renamed test to deduplicate name (nilearn#2144)
  Fixes nilearn#2029 Handle gzip files without extensions (nilearn#2126)
  Update Schaefer parcelation to v0.14.3 (nilearn#2138)
  MAINT: Future-compatible cmap reversal (nilearn#2131)
  fix openmp crash (nilearn#2140)
  change nose to pytest on appveyor (nilearn#2130)
  adding fix to whatsnew
  fix wrong urls in nki dataset
  ...

# Conflicts:
#	nilearn/datasets/func.py

.circleci/config.yml

@@ -15,6 +15,7 @@ jobs:
       NUMPY_VERSION: "*"
       SCIPY_VERSION: "*"
       SCIKIT_LEARN_VERSION: "*"
+      JOBLIB_VERSION: "*"
       MATPLOTLIB_VERSION: "*"
 
     steps:

.coveragerc

@@ -0,0 +1,5 @@
+[run]
+branch = True
+parallel = True
+omit =
+    */nilearn/externals/*

.travis.yml

@@ -2,49 +2,58 @@ sudo: required
 dist: xenial
 
 language: python
-python: "3.5"
-
-virtualenv:
-  system_site_packages: true
 
 env:
   global:
-    - TEST_RUN_FOLDER="/tmp" # folder where the tests are run from
+    - TEST_RUN_FOLDER="/tmp"
 
 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: 3.5
+    # allow_failures keyed to python 3.5 & skipping tests.
+    - python: "3.5"
+      env: DISTRIB="travisci" PYTHON_VERSION="3.5" FLAKE8_VERSION="*" SKIP_TESTS="true"
   include:
-    # without matplotlib
-    - env: DISTRIB="conda" PYTHON_VERSION="3.5"
-           NUMPY_VERSION="1.11" SCIPY_VERSION="0.17" PANDAS_VERSION="*"
-           SCIKIT_LEARN_VERSION="0.18" COVERAGE="true"
+    - name: "Python 3.5 minimum package versions without Matplotlib"
+      python: "3.5"
+      env: DISTRIB="travisci" PYTHON_VERSION="3.5"
+           NUMPY_VERSION="1.11" SCIPY_VERSION="0.19" PANDAS_VERSION="*"
+           SCIKIT_LEARN_VERSION="0.19" COVERAGE="true" JOBLIB_VERSION="0.11"
            LXML_VERSION="*"
-    - env: DISTRIB="conda" PYTHON_VERSION="3.5"
+    - name: "Python 3.5 latest package versions"
+      python: "3.5"
+      env: DISTRIB="travisci" PYTHON_VERSION="3.5"
            NUMPY_VERSION="*" SCIPY_VERSION="*" PANDAS_VERSION="*"
            SCIKIT_LEARN_VERSION="*" MATPLOTLIB_VERSION="*" COVERAGE="true"
+           JOBLIB_VERSION="0.11"
            LXML_VERSION="*"
-    - env: DISTRIB="conda" PYTHON_VERSION="3.6"
+    - name: "Python 3.6 latest package versions"
+      python: "3.6"
+      env: DISTRIB="travisci" PYTHON_VERSION="3.6"
            NUMPY_VERSION="*" SCIPY_VERSION="*" PANDAS_VERSION="*"
            SCIKIT_LEARN_VERSION="*" MATPLOTLIB_VERSION="*" COVERAGE="true"
-           LXML_VERSION="*"
-    - env: DISTRIB="conda" PYTHON_VERSION="3.7"
+           JOBLIB_VERSION="0.12" LXML_VERSION="*"
+      # joblib.Memory switches from keyword cachedir to location in version 0.12
+      # Making sure we get the deprecation warning.
+
+    - name: "Python 3.7 latest package versions"
+      python: "3.7"
+      env: DISTRIB="travisci" PYTHON_VERSION="3.7"
            NUMPY_VERSION="*" SCIPY_VERSION="*" PANDAS_VERSION="*"
            SCIKIT_LEARN_VERSION="*" MATPLOTLIB_VERSION="*" COVERAGE="true"
-           LXML_VERSION="*"
+           JOBLIB_VERSION="*" LXML_VERSION="*"
 
   # FLAKE8 linting on diff wrt common ancestor with upstream/master
     # Note: the python value is only there to trigger allow_failures
-    - python: 3.5
-      env: DISTRIB="conda" PYTHON_VERSION="3.5" FLAKE8_VERSION="*" SKIP_TESTS="true"
+    - name: Python 3.5 Flake8 no tests
+      python: "3.5"
+      env: DISTRIB="travisci" PYTHON_VERSION="3.5" FLAKE8_VERSION="*" SKIP_TESTS="true"
 
 install: source continuous_integration/install.sh
 
-before_script: make clean
+before_script: make  clean
 
 script: source continuous_integration/test_script.sh
 

AUTHORS.rst

@@ -3,38 +3,36 @@
 People
 ------
 
-This work is made available by a community of people, amongst which
+This work is made available by a community of people, which
+originated from
 the `INRIA Parietal Project Team <https://team.inria.fr/parietal/>`_
-and the `scikit-learn <http://scikit-learn.org/>`_ folks, in
-particular:
-
-* Alexandre Abraham
-* `Alexandre Gramfort <http://alexandre.gramfort.net>`_
-* Vincent Michel
-* Bertrand Thirion
-* `Fabian Pedregosa <http://fa.bianp.net/>`_
-* `Gael Varoquaux <http://gael-varoquaux.info/>`_
-* Philippe Gervais
-* Michael Eickenberg
-* Danilo Bzdok
-* Loïc Estève
-* Kamalakar Reddy Daddy
-* Elvis Dohmatob
-* Alexandre Abadie
-* Andres Hoyos Idrobo
-* Salma Bougacha
-* Mehdi Rahim
-* Sylvain Lanuzel
-* `Kshitij Chawla <https://github.com/kchawla-pi>`_
-
-Many of also contributed outside of Parietal, notably:
-
-* `Chris Filo Gorgolewski <http://multiplecomparisons.blogspot.fr/>`_
-* `Ben Cipollini <http://cseweb.ucsd.edu/~bcipolli/>`_
-* Julia Huntenburg
-* Martin Perez-Guevara
-
-Thanks to M. Hanke and Y. Halchenko for data and packaging.
+and the `scikit-learn <http://scikit-learn.org/>`_ but grew much further.
+
+An up-to-date list of contributors can be seen in on `gitub
+<https://github.com/nilearn/nilearn/graphs/contributors>`_
+
+Additional credit goes to M. Hanke and Y. Halchenko for data and packaging.
+
+.. _core_devs:
+
+Core developers
+.................
+
+The nilearn core developers are:
+
+* Alexandre Gramfort https://github.com/agramfort
+* Ben Cipollini https://github.com/bcipolli
+* Bertrand Thirion https://github.com/bthirion
+* Chris Gorgolewski https://github.com/chrisgorgo
+* Danilo Bzdok https://github.com/banilo
+* Elizabeth DuPre https://github.com/emdupre
+* Gael Varoquaux https://github.com/GaelVaroquaux
+* Jerome Dockes https://github.com/jeromedockes
+* Julia Huntenburg https://github.com/juhuntenburg
+* KamalakerDadi https://github.com/KamalakerDadi
+* Kshitij Chawla https://github.com/kchawla-pi
+* Medhi Rahim https://github.com/mrahim
+* Salma Bougacha https://github.com/salma1601
 
 Funding
 ........
@@ -45,7 +43,8 @@ Mehdi Rahim, Philippe Gervais where payed by the `NiConnect
 project, funded by the French `Investissement d'Avenir
 <http://www.gouvernement.fr/investissements-d-avenir-cgi>`_.
 
-NiLearn is also supported by `DigiCosme <https://digicosme.lri.fr>`_ |digicomse logo|
+NiLearn is also supported by `DigiCosme <https://digicosme.lri.fr>`_
+|digicosme logo| and `DataIA <https://dataia.eu/en>`_ |dataia_logo|.
 
 .. _citing:
 
@@ -74,6 +73,10 @@ See the scikit-learn documentation on `how to cite
 <http://scikit-learn.org/stable/about.html#citing-scikit-learn>`_.
 
 
-.. |digicomse logo| image:: logos/digi-saclay-logo-small.png
+.. |digicosme logo| image:: logos/digi-saclay-logo-small.png
+    :height: 25
+    :alt: DigiComse Logo
+
+.. |dataia_logo| image:: logos/dataia.png
     :height: 25
-    :alt: DigiComse Logo
+    :alt: DataIA Logo

Makefile

@@ -4,9 +4,6 @@
 
 PYTHON ?= python
 CYTHON ?= cython
-NOSETESTS ?= nosetests
-NOSETESTS_OPTIONS := $(shell pip list | grep nose-timer > /dev/null && \
-                       echo '--with-timer --timer-top-n 50')
 CTAGS ?= ctags
 
 all: clean test doc-noplot
@@ -32,15 +29,15 @@ inplace:
 	$(PYTHON) setup.py build_ext -i
 
 test-code:
-	$(NOSETESTS) -s nilearn $(NOSETESTS_OPTIONS)
+	python -m pytest --pyargs nilearn --cov=nilearn
+
 test-doc:
-	$(NOSETESTS) -s --with-doctest --doctest-tests --doctest-extension=rst \
-	--doctest-extension=inc --doctest-fixtures=_fixture `find doc/ -name '*.rst'`
+	pytest --doctest-glob='*.rst' `find doc/ -name '*.rst'`
+
 
 test-coverage:
 	rm -rf coverage .coverage
-	$(NOSETESTS) -s --with-coverage --cover-html --cover-html-dir=coverage \
-	--cover-package=nilearn nilearn
+	pytest --pyargs nilearn --showlocals --cov=nilearn --cov-report=html:coverage
 
 test: test-code test-doc
 
@@ -66,4 +63,3 @@ doc:
 .PHONY : pdf
 pdf:
 	make -C doc pdf
-

README.rst

@@ -41,8 +41,9 @@ The required dependencies to use the software are:
 * Python >= 3.5,
 * setuptools
 * Numpy >= 1.11
-* SciPy >= 0.17
-* Scikit-learn >= 0.18
+* SciPy >= 0.19
+* Scikit-learn >= 0.19
+* Joblib >= 0.11
 * Nibabel >= 2.0.2
 
 If you are using nilearn plotting functionalities or running the

appveyor.yml

@@ -24,10 +24,10 @@ install:
   # See similar fix which made for travis and circleci
   # https://github.com/nilearn/nilearn/pull/1525
   # Should be removed after a new matplotlib release 2.1.1
-  - "conda install pip numpy scipy scikit-learn nose wheel matplotlib -y -q"
+  - "conda install pip numpy scipy scikit-learn joblib nose pytest wheel matplotlib -y -q"
 
   # Install other nilearn dependencies
-  - "pip install nibabel coverage nose-timer"
+  - "pip install nibabel coverage nose-timer pytest-cov"
   - "python setup.py bdist_wheel"
   - ps: "ls dist"
 
@@ -41,7 +41,7 @@ test_script:
   # Change to a non-source folder to make sure we run the tests on the
   # installed library.
   - "cd C:\\"
-  - "python -c \"import nose; nose.main()\" -v -s nilearn --with-timer --timer-top-n 50"
+  - "pytest --pyargs nilearn -v"
 
 artifacts:
   # Archive the generated packages in the ci.appveyor.com build report.

azure-pipelines.yml

@@ -30,7 +30,7 @@ jobs:
 
   - script: |
       pip install .
-      nosetests ./nilearn -v
+      pytest ./nilearn -v
     displayName: 'test'
 
   - task: PublishTestResults@2

codecov.yml

@@ -0,0 +1,2 @@
+ignore:
+  - "*externals/.*"  # ignore folders and all its contents

continuous_integration/install.sh

@@ -22,21 +22,20 @@ create_new_venv() {
     deactivate
     virtualenv --system-site-packages testvenv
     source testvenv/bin/activate
-    pip install nose
+    pip install nose pytest
 }
 
-print_conda_requirements() {
-    # Echo a conda requirement string for example
+echo_requirements_string() {
+    # Echo a requirement string for example
     # "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"
+    TO_INSTALL_ALWAYS="pip nose pytest"
     REQUIREMENTS="$TO_INSTALL_ALWAYS"
-    TO_INSTALL_MAYBE="python numpy scipy matplotlib scikit-learn pandas \
-flake8 lxml"
+    TO_INSTALL_MAYBE="numpy scipy matplotlib scikit-learn pandas flake8 lxml joblib"
     for PACKAGE in $TO_INSTALL_MAYBE; do
         # Capitalize package name and add _VERSION
         PACKAGE_VERSION_VARNAME="${PACKAGE^^}_VERSION"
@@ -45,62 +44,42 @@ flake8 lxml"
         # dereference $PACKAGE_VERSION_VARNAME to figure out the
         # version to install
         PACKAGE_VERSION="${!PACKAGE_VERSION_VARNAME}"
-        if [ -n "$PACKAGE_VERSION" ]; then
-            REQUIREMENTS="$REQUIREMENTS $PACKAGE=$PACKAGE_VERSION"
+        if [[ -n "$PACKAGE_VERSION" ]]; then
+            if [[ "$PACKAGE_VERSION" == "*" ]]; then
+                REQUIREMENTS="$REQUIREMENTS $PACKAGE"
+            else
+                REQUIREMENTS="$REQUIREMENTS $PACKAGE==$PACKAGE_VERSION"
+            fi
         fi
     done
     echo $REQUIREMENTS
 }
 
-create_new_conda_env() {
-    # Skip Travis related code on circle ci.
-    if [ -z $CIRCLECI ]; then
-        # Deactivate the travis-provided virtual environment and setup a
-        # conda-based environment instead
-        deactivate
-    fi
-
-    # Use the miniconda installer for faster download / install of conda
-    # itself
-    wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
-        -O ~/miniconda.sh
-    chmod +x ~/miniconda.sh && ~/miniconda.sh -b
-    export PATH=$HOME/miniconda3/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 --quiet --yes $REQUIREMENTS
-    source activate testenv
+create_new_travisci_env() {
+    REQUIREMENTS=$(echo_requirements_string)
+    pip install ${REQUIREMENTS}
+    pip install pytest pytest-cov
 
     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"
+        pip install mkl
     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
+    sudo apt-get install -qq python-scipy python-nose python-nibabel python-sklearn python-joblib
 
-elif [[ "$DISTRIB" == "conda" ]]; then
-    create_new_conda_env
+elif [[ "$DISTRIB" == "travisci" ]]; then
+    create_new_travisci_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 "$NIBABEL_VERSION" ]; then
+    if [[ -n "$NIBABEL_VERSION" ]]; then
         pip install nibabel=="$NIBABEL_VERSION"
     fi
 

continuous_integration/show-python-packages-versions.py

@@ -1,6 +1,6 @@
 import sys
 
-DEPENDENCIES = ['numpy', 'scipy', 'sklearn', 'matplotlib', 'nibabel']
+DEPENDENCIES = ['numpy', 'scipy', 'sklearn', 'joblib', 'matplotlib', 'nibabel']
 
 
 def print_package_version(package_name, indent='  '):

continuous_integration/test_script.sh

@@ -11,6 +11,7 @@ if [[ "$SKIP_TESTS" != "true" ]]; then
     # Copy setup.cfg to TEST_RUN_FOLDER where we are going to run the tests from
     # Mainly for nose config settings
     cp setup.cfg "$TEST_RUN_FOLDER"
+    cp .coveragerc "$TEST_RUN_FOLDER"
     # We want to back out of the current working directory to make
     # sure we are using nilearn installed in site-packages rather
     # than the one from the current working directory