Merge pull request #1 from nilearn/master

updating simexp/nilearn

.circleci/config.yml

@@ -0,0 +1,63 @@
+version: 2
+
+jobs:
+  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
+      - restore_cache:
+          key: v1-packages+datasets-{{ .Branch }}
+      - 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:
+          name: Setup conda path in env variables
+          command: |
+            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 pillow pandas -yq
+            conda install -n testenv nibabel 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: v1-packages+datasets-{{ .Branch }}
+          paths:
+          - $HOME/nilearn_data
+          - $HOME/miniconda3
+
+      - store_artifacts:
+          path: doc/_build/html
+      - store_artifacts:
+          path: coverage
+      - store_artifacts:
+          path: $HOME/log.txt
+          destination: log.txt
+
+
+
+

.gitignore

@@ -31,3 +31,7 @@ tags
 *.nt.bz2
 *.tar.gz
 *.tgz
+
+.idea/
+
+doc/themes/nilearn/static/jquery.js

.mailmap

@@ -1,39 +1,43 @@
-Alexandre Abraham <[email protected]> <[email protected]>
-Alexandre Abraham <[email protected]> <[email protected]>
-Alexandre Gramfort <[email protected]> <[email protected]>
+Aina Frau Pascual <[email protected]>
+Alexandre Abadie <[email protected]>
+Alexandre Abraham <[email protected]>
+Alexandre Gramfort <[email protected]>
 Alexandre Savio <[email protected]>
+Arthur Mensch <[email protected]>
 Ben Cipollini <[email protected]>
 Bertrand Thirion <[email protected]>
-Chris Filo Gorgolewski <chris[email protected]>
+Chris Filo Gorgolewski <krzysztof[email protected]>
 Danilo Bzdok <[email protected]>
+Demian Wassermann <[email protected]>
+Dimitri Papadopoulos Orfanos <[email protected]>
 Elvis Dohmatob <[email protected]>
 Fabian Pedregosa <[email protected]>
-Fabian Pedregosa <[email protected]>
-Fabian Pedregosa <[email protected]>
-Gael Varoquaux <[email protected]> <[email protected]>
-GaelVaroquaux <[email protected]>
 Gael Varoquaux <[email protected]>
-Jan Margeta <[email protected] >
+Jan Margeta <[email protected]>
 Jaques Grobler <[email protected]>
 Jason Gors <[email protected]>
+Jona Sassenhagen <[email protected]>
 Jean Kossaifi <[email protected]>
-Jean Kossaifi <[email protected]>
+Jean Remi King <[email protected]>
+Jeff Chiang <[email protected]>
+Julia Huntenburg <[email protected]>
+J Necus <[email protected]>
+Kamalakar Daddy <[email protected]>
 Konstantin Shmelkov <[email protected]>
 Loïc Estève <[email protected]>
+Martin Perez-Guevara <[email protected]>
 Matthias Ekman <[email protected]>
+Mehdi Rahim <[email protected]>
 Mehdi Rahim <[email protected]> <[email protected]>
-Mehdi Rahim <[email protected]> <[email protected]>
 Michael Eickenberg <[email protected]>
+Michael Hanke <[email protected]>
 Michael Waskom <[email protected]>
-Philippe Gervais <[email protected]> <[email protected]>
+Moritz Boos <[email protected]>
+Moritz Boos <[email protected]> <[email protected]>
+Óscar Nájera <[email protected]>
+Philippe Gervais <[email protected]>
 Ronald Phlypo <[email protected]>
-Salma Bougacha <[email protected]>
+Salma Bougacha <[email protected]>
 Vincent Michel <[email protected]>
 Virgile Fritsch <[email protected]>
-Yannick Schwartz <[email protected]> <ys218403@is220245.(none)>
-schwarty <[email protected]>
 Yannick Schwartz <[email protected]>
-Óscar Nájera <[email protected]>
-Kamalakar Daddy <[email protected]>
-Fabian Pedregosa <[email protected]> <[email protected]>
-Fabian Pedregosa <[email protected]> <[email protected]>

.travis.yml

@@ -1,3 +1,6 @@
+sudo: required
+dist: xenial
+
 language: python
 
 virtualenv:
@@ -6,54 +9,47 @@ virtualenv:
 env:
   global:
     - TEST_RUN_FOLDER="/tmp" # folder where the tests are run from
-  matrix:
-    # Ubuntu 14.04 versions
-    - DISTRIB="conda" PYTHON_VERSION="2.7"
-      NUMPY_VERSION="1.8.2" SCIPY_VERSION="0.13.3"
-      SCIKIT_LEARN_VERSION="0.14.1" MATPLOTLIB_VERSION="1.3.1"
-    # Ubuntu 14.04 versions without matplotlib
-    - DISTRIB="conda" PYTHON_VERSION="2.7"
-      NUMPY_VERSION="1.8.2" SCIPY_VERSION="0.13.3"
-      SCIKIT_LEARN_VERSION="0.14.1"
-    - DISTRIB="neurodebian" PYTHON_VERSION="2.7"
-    # Trying to get as close to the minimum required versions while
-    # still having the package version available through conda
-    - DISTRIB="conda" PYTHON_VERSION="2.6"
-      NUMPY_VERSION="1.6.2" SCIPY_VERSION="0.11.0"
-      SCIKIT_LEARN_VERSION="0.13" MATPLOTLIB_VERSION="1.1.1"
-      NIBABEL_VERSION="1.1.0"
+
+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="1.11.2" SCIPY_VERSION="0.17"
+           SCIKIT_LEARN_VERSION="0.18" MATPLOTLIB_VERSION="1.5.1"
+           PANDAS_VERSION="0.18.0" NIBABEL_VERSION="2.0.2" COVERAGE="true"
+    # Oldest supported versions without matplotlib
+    - env: DISTRIB="conda" PYTHON_VERSION="2.7"
+           NUMPY_VERSION="1.11.2" SCIPY_VERSION="0.17"
+           SCIKIT_LEARN_VERSION="0.18"
+    # Fake Ubuntu Xenial (Travis doesn't support Xenial yet)
+    - env: DISTRIB="conda" PYTHON_VERSION="2.7"
+           NUMPY_VERSION="1.13" SCIPY_VERSION="0.19"
+           SCIKIT_LEARN_VERSION="0.18.1"
+           NIBABEL_VERSION="2.0.2"
     # Python 3.4 with intermediary versions
-    - DISTRIB="conda" PYTHON_VERSION="3.4"
-      NUMPY_VERSION="1.8" SCIPY_VERSION="0.14"
-      SCIKIT_LEARN_VERSION="0.15" MATPLOTLIB_VERSION="1.4"
+    - env: DISTRIB="conda" PYTHON_VERSION="3.4"
+           NUMPY_VERSION="1.11.2" SCIPY_VERSION="0.17"
+           SCIKIT_LEARN_VERSION="0.18" MATPLOTLIB_VERSION="1.5.1"
     # Most recent versions
-    - DISTRIB="conda" PYTHON_VERSION="3.5"
-      NUMPY_VERSION="*" SCIPY_VERSION="*"
-      SCIKIT_LEARN_VERSION="*" MATPLOTLIB_VERSION="*" COVERAGE="true"
-
-install: 
-    - source continuous_integration/install.sh
-
-before_script:
-    - make clean
-
-script:
-    - python continuous_integration/show-python-packages-versions.py
-    # Copy setup.cfg to TEST_RUN_FOLDER where we are going to run the tests from
-    # Mainly for nose config settings
-    - cp setup.cfg "$TEST_RUN_FOLDER"
-    # We want to back out of the current working directory to make
-    # sure we are using nilearn installed in site-packages rather
-    # than the one from the current working directory
-    # Parentheses (run in a subshell) are used to leave
-    # the current directory unchanged
-    - (cd "$TEST_RUN_FOLDER" && make -f $OLDPWD/Makefile test-code)
-    - test "$MATPLOTLIB_VERSION" == "" || make test-doc
-
-after_success:
-    # Ignore coveralls failures as the coveralls server is not very reliable
-    # but we don't want travis to report a failure in the github UI just
-    # because the coverage report failed to be published.
-    # coveralls need to be run from the git checkout
-    # so we need to copy the coverage results from TEST_RUN_FOLDER
-    - if [[ "$COVERAGE" == "true" ]]; then cp "$TEST_RUN_FOLDER/.coverage" .; coveralls || echo "failed"; fi
+    - env: DISTRIB="conda" PYTHON_VERSION="3.5"
+           NUMPY_VERSION="*" SCIPY_VERSION="*" PANDAS_VERSION="*"
+           SCIKIT_LEARN_VERSION="*" MATPLOTLIB_VERSION="*" COVERAGE="true"
+           LXML_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"
+
+install: source continuous_integration/install.sh
+
+before_script: make clean
+
+script: source continuous_integration/test_script.sh
+
+after_success: source continuous_integration/after_success.sh

AUTHORS.rst

@@ -16,13 +16,37 @@ particular:
 * `Gael Varoquaux <http://gael-varoquaux.info/>`_
 * Philippe Gervais
 * Michael Eickenberg
-* `Chris Filo Gorgolewski <http://multiplecomparisons.blogspot.fr/>`_
 * 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.
 
+Funding
+........
+
+Alexandre Abraham, Gael Varoquaux, Kamalakar Reddy Daddy, Loïc Estève,
+Mehdi Rahim, Philippe Gervais where payed by the `NiConnect
+<https://team.inria.fr/parietal/18-2/spatial_patterns/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|
+
 .. _citing:
 
 Citing nilearn
@@ -49,3 +73,7 @@ guarantee the future of the toolkit, if you use it, please cite it.
 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
+    :height: 25
+    :alt: DigiComse Logo

CONTRIBUTING.rst

@@ -0,0 +1,49 @@
+.. _contributing:
+
+============
+Contributing
+============
+
+This project is a community effort, and everyone is welcome to
+contribute.
+
+The project is hosted on https://github.com/nilearn/nilearn
+
+The best way to contribute and to help the project is to start working on known
+issues.
+See `Easy issues <https://github.com/nilearn/nilearn/labels/Easy>`_ to get
+started.
+
+Submitting a bug report
+=======================
+
+In case you experience issues using this package, do not hesitate to submit a
+ticket to the
+`Bug Tracker <https://github.com/nilearn/nilearn/issues>`_. You are
+also welcome to post feature requests or pull requests.
+
+.. _git_repo:
+
+Retrieving the latest code
+==========================
+
+We use `Git <http://git-scm.com/>`_ for version control and
+`GitHub <https://github.com/>`_ for hosting our main repository. If you are
+new on GitHub and don't know how to work with it, please first
+have a look at `this <https://try.github.io/>`_ to get the basics.
+
+
+You can check out the latest sources with the command::
+
+    git clone git://github.com/nilearn/nilearn.git
+
+or if you have write privileges::
+
+    git clone [email protected]:nilearn/nilearn.git
+
+Coding guidelines
+=================
+
+Nilearn follows the coding conventions used by scikit-learn. `Please read them
+<http://scikit-learn.org/stable/developers/contributing.html#coding-guidelines>`_
+before you start implementing your changes.

MANIFEST.in

@@ -0,0 +1,3 @@
+include AUTHORS.rst
+include LICENSE
+include README.rst

Makefile

@@ -13,6 +13,7 @@ all: clean test doc-noplot
 
 clean-pyc:
 	find . -name "*.pyc" | xargs rm -f
+	find . -name "__pycache__" | xargs rm -rf
 
 clean-so:
 	find . -name "*.so" | xargs rm -f
@@ -66,5 +67,3 @@ doc:
 pdf:
 	make -C doc pdf
 
-install:
-	cd doc && make install