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

…smooth-image * 'master' of https://github.com/nilearn/nilearn: (25 commits) Add testing for Nilearn setup & install & Fix the broken dependency installation (nilearn#2201) Fix uniform ball cloud test for sklearn >= 0.22 (nilearn#2175) MAINT: sklearn Deprecations (nilearn#2219) DOC: title in bold [DOC] Add note about decreasing memory usage (nilearn#2223) Rel 060b0 (nilearn#2208) Nilearn 0.6.0b0 release (nilearn#2206) Fixed the redundant & missing test case in merged PR nilearn#2035 (nilearn#2205) Modify fetch_development_fmri to fetch adults or children (nilearn#2035) Verbose doc building to ease tracking of progress & diagnose stalls (nilearn#2203) New conda env is created once conda path has been activated Conda environment is created for full-builds Refactor CircleCI config for reduced redundancy (nilearn#2204) Installation should fail on Python < 3.5 (nilearn#2198) [MRG] Add get data function (nilearn#2172) fix error when colorscale given boolean array (nilearn#2193) remove is_valid filter (nilearn#2169) Moved new entries to next release FIX: marker size issue in plot_connectome nilearn#2185 (nilearn#2186) Updated Appveyor status badge ...
pausz · Nov 21, 2019 · 8507af9 · 8507af9
2 parents 5329869 + bbc750a
commit 8507af9
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diff --git a/.circleci/auto-cache-timestamp b/.circleci/auto-cache-timestamp
diff --git a/.circleci/clean-cache.py b/.circleci/clean-cache.py
@@ -7,7 +7,7 @@
 
 
 def update_cache_timestamp(timestamp_filename):
-    """ Updates the contents of the manual-cache-timestamp file
+    """ Updates the contents of the docs-cache-timestamp file
     with current timestamp.
 
     Returns
@@ -22,5 +22,5 @@ def update_cache_timestamp(timestamp_filename):
 
 
 if __name__ == '__main__':
-    update_cache_timestamp('manual-cache-timestamp')
-    update_cache_timestamp('auto-cache-timestamp')
+    update_cache_timestamp('docs-cache-timestamp')
+    update_cache_timestamp('packages-cache-timestamp')
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -3,42 +3,46 @@
 # 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
+version: 2.1
 
-jobs:
-  quick-build:
-    docker:
-      - image: circleci/python:3.6
-    environment:
-      DISTRIB: "conda"
-      PYTHON_VERSION: "3.6"
-      NUMPY_VERSION: "*"
-      SCIPY_VERSION: "*"
-      SCIKIT_LEARN_VERSION: "*"
-      JOBLIB_VERSION: "*"
-      MATPLOTLIB_VERSION: "*"
+commands:
 
+  preinstall:
+    description: "Cleans up unused packages; Updates system packages"
+    steps:
+      - run:
+          name: Remove conflicting packages
+          command: |
+            # 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
+            cd && rm -rf ~/.pyenv && rm -rf ~/virtualenvs
+
+            # We need to remove conflicting texlive packages.
+            sudo -E apt-get -yq remove texlive-binaries --purge
+      - run:
+          name: Install packages for make -C doc check
+          command: |
+            # Installing required packages for `make -C doc check command` to work.
+            sudo -E apt-get -yq update
+            sudo -E apt-get -yq --no-install-suggests --no-install-recommends --force-yes install dvipng texlive-latex-base texlive-latex-extra
+
+  restore_from_cache:
+    description: "Restores the cache of previously built docs & python packages if present"
     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: Today & Week  # Saving today's date and current week of the year in files to generate daily & weekly new cache key respectively.
+          name: Generate cache keys from today's date for built docs & week number for python packages
           command: |
             date +%F > today
             date +%U > week_num
       - restore_cache:
-          key: v1-packages+datasets-{{ checksum "week_num" }}
+          key: v1-packages+datasets-{{ checksum "week_num" }}-{{ checksum ".circleci/packages-cache-timestamp" }}
       - restore_cache:
-          key: v1-docs-{{ .Branch }}-{{ checksum "today" }}-{{ checksum ".circleci/manual-cache-timestamp" }}
+          key: v1-docs-{{ .Branch }}-{{ checksum "today" }}-{{ checksum ".circleci/docs-cache-timestamp" }}
 
+  cache_aware_conda_setup:
+    description: "Downloads & installs conda if not restord by cache"
+    steps:
       - run:
           name: Download & install conda if absent
           command: |
@@ -64,91 +68,109 @@ jobs:
             else
               conda create -n testenv -yq
             fi
+
+  cache_ignorant_conda_setup:
+    description: "Downloads & installs only the fresh copy of conda."
+    steps:
+      - run:
+          name: setup conda afresh
+          command: |
+            wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh
+            chmod +x ~/miniconda.sh && ~/miniconda.sh -b
+            echo 'export PATH="$HOME/miniconda3/bin:$PATH"'  >> $BASH_ENV
+      - run: conda create -n testenv
+
+  install_dependencies:
+    description: "Installs the necessary Python packages"
+    steps:
       - run:
           name: Install packages in conda env
           command: |
-            conda install -n testenv python=3.6 numpy scipy scikit-learn matplotlib pandas \
+            conda install -n testenv python=3.7 numpy scipy scikit-learn matplotlib pandas \
             lxml mkl sphinx numpydoc pillow pandas -yq
             conda install -n testenv nibabel sphinx-gallery junit-xml -c conda-forge -yq
+
+  build_docs:
+    description: "Installs Nilearn & builds documentation using Sphinx's make html-strict"
+    steps:
       - run:
-          name: Running CircleCI test (make html)
+          name: Building documentation
           command: |
             source activate testenv
             pip install -e .
             set -o pipefail && cd doc && make html-strict 2>&1 | tee log.txt
           no_output_timeout: 7h
+
+  store_results:
+    description: "Stores build times and artifacts"
+    steps:
       - store_test_results:
           path: doc/_build/test-results
       - store_artifacts:
           path: doc/_build/test-results
+      - store_artifacts:
+          path: doc/_build/html
+      - store_artifacts:
+          path: coverage
+      - store_artifacts:
+          path: doc/log.txt
 
+  save_to_cache:
+    description: "Caches the downloaded packages & buit docs."
+    steps:
       - save_cache:
           key: v1-packages+datasets-{{ checksum "week_num" }}
           paths:
             - ../nilearn_data
             - ../miniconda3
       - save_cache:
-          key: v1-docs-{{ .Branch }}-{{ checksum "today" }}-{{ checksum ".circleci/manual-cache-timestamp" }}
+          key: v1-docs-{{ .Branch }}-{{ checksum "today" }}-{{ checksum ".circleci/docs-cache-timestamp" }}
           paths:
             - doc
 
-      - store_artifacts:
-          path: doc/_build/html
-      - store_artifacts:
-          path: coverage
-      - store_artifacts:
-          path: doc/log.txt
 
+jobs:
 
-  full-build:
+  quick-build:
     docker:
-      - image: circleci/python:3.6
+      - image: circleci/python:3.7
     environment:
       DISTRIB: "conda"
-      PYTHON_VERSION: "3.6"
+      PYTHON_VERSION: "3.7"
       NUMPY_VERSION: "*"
       SCIPY_VERSION: "*"
       SCIKIT_LEARN_VERSION: "*"
+      JOBLIB_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: Install packages in conda env
-          command: |
-            conda create -n testenv python=3.6 numpy scipy scikit-learn matplotlib pandas \
-            lxml mkl sphinx numpydoc pillow pandas -yq
-            conda install -n testenv nibabel sphinx-gallery junit-xml -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: 7h
-      - store_test_results:
-          path: doc/_build/test-results
-      - store_artifacts:
-          path: doc/_build/test-results
+      - preinstall
+      - restore_from_cache
+      - cache_aware_conda_setup
+      - install_dependencies
+      - build_docs
+      - store_results
+      - save_to_cache
 
-      - store_artifacts:
-          path: doc/_build/html
-      - store_artifacts:
-          path: coverage
-      - store_artifacts:
-          path: doc/log.txt
+  full-build:
+    docker:
+      - image: circleci/python:3.7
+    environment:
+      DISTRIB: "conda"
+      PYTHON_VERSION: "3.7"
+      NUMPY_VERSION: "*"
+      SCIPY_VERSION: "*"
+      SCIKIT_LEARN_VERSION: "*"
+      MATPLOTLIB_VERSION: "*"
+
+    steps:
+      - checkout
+      - preinstall
+      - cache_ignorant_conda_setup
+      - install_dependencies
+      - build_docs
+      - store_results
 
 
 workflows:

diff --git a/.circleci/docs-cache-timestamp b/.circleci/docs-cache-timestamp
@@ -0,0 +1 @@
+2019-11-07 13:17:41.900352
diff --git a/.circleci/manual-cache-timestamp b/.circleci/manual-cache-timestamp
diff --git a/.circleci/packages-cache-timestamp b/.circleci/packages-cache-timestamp
@@ -0,0 +1 @@
+2019-11-07 13:17:41.900617
diff --git a/.mailmap b/.mailmap
@@ -3,39 +3,46 @@ Alexandre Abadie <alexandre.abadie@inria.fr>
 Alexandre Abraham <abraham.alexandre@gmail.com>
 Alexandre Gramfort <alexandre.gramfort@inria.fr>
 Alexandre Savio <alexsavio@gmail.com>
+Andrés Hoyos Idrobo <ahoyosidrobo@gmail.com>
+Antoine Grigis <antoine.grigis@cea.fr>
 Arthur Mensch <arthur.mensch@gmail.com>
 Ben Cipollini <bcipolli@ucsd.edu>
 Bertrand Thirion <bertrand.thirion@inria.fr>
+Céline Delettre <cdelettre.tts@gmail.com>
 Chris Filo Gorgolewski <krzysztof.gorgolewski@gmail.com>
 Danilo Bzdok <danilobzdok@gmail.com>
 Demian Wassermann <demian.wassermann@inria.fr>
 Dimitri Papadopoulos Orfanos <dimitri.papadopoulos@cea.fr>
 Elvis Dohmatob <elvis.dohmatob@inria.fr>
 Fabian Pedregosa <f@bianp.net>
+Franz Liem <franz.liem@gmail.com>
 Gael Varoquaux <gael.varoquaux@normalesup.org>
+Greg Kiar <gkiar07@gmail.com>
 Jan Margeta <jmargeta@gmail.com>
 Jaques Grobler <jaquesgrobler@gmail.com>
 Jason Gors <jason.gors.work@gmail.com>
 Jona Sassenhagen <jona.sassenhagen@gmail.com>
 Jean Kossaifi <jean.kossaifi@gmail.com>
 Jean Remi King <jeanremi.king@gmail.com>
 Jeff Chiang <jeff.njchiang@gmail.com>
+Jerome-Alexis Chevalier <jerome-alexis.chevalier@inria.fr>
+Jerome Dockes <jerome@dockes.org>
 Julia Huntenburg <ju.huntenburg@gmail.com>
 J Necus <j.necus2@ncl.ac.uk>
 Kamalakar Daddy <dkamalakarreddy@gmail.com>
 Konstantin Shmelkov <konstantin.shmelkov@polytechnique.edu>
+Kshitij Chawla (kchawla-pi) <kc.insight.pi@gmail.com>
 Loïc Estève <loic.esteve@ymail.com>
 Martin Perez-Guevara <mperezguevara@gmail.com>
 Matthias Ekman <matthias.ekman@gmail.com>
-Mehdi Rahim <mehdi.rahim@cea.fr>
 Mehdi Rahim <mehdi.rahim@cea.fr> <mrahim@users.noreply.github.com>
 Michael Eickenberg <michael.eickenberg@gmail.com>
 Michael Hanke <michael.hanke@gmail.com>
 Michael Waskom <mwaskom@stanford.edu>
-Moritz Boos <moritz.boos@gmail.com>
 Moritz Boos <moritz.boos@gmail.com> <moritz.boos@uni-oldenburg.de>
 Óscar Nájera <najera.oscar@gmail.com>
 Philippe Gervais <philippe.gervais@inria.fr>
+Roberto Guidotti <robbenson18@gmail.com>
 Ronald Phlypo <Ronald.Phlypo@inria.fr>
 Salma Bougacha <salmabougacha@hotmail.com>
 Vincent Michel <vm.michel@gmail.com>

diff --git a/README.rst b/README.rst
@@ -4,13 +4,16 @@
    :target: https://travis-ci.org/nilearn/nilearn
    :alt: Travis Build Status
 
-.. image:: https://ci.appveyor.com/api/projects/status/github/nilearn/nilearn?branch=master&svg=true
-   :target: https://ci.appveyor.com/project/nilearn-ci/nilearn
+.. image:: https://ci.appveyor.com/api/projects/status/qynxxpx0hge4h0rn/branch/master?svg=true
+   :target: https://ci.appveyor.com/api/projects/status/qynxxpx0hge4h0rn/branch/master?svg=true
    :alt: AppVeyor Build Status
 
 .. image:: https://codecov.io/gh/nilearn/nilearn/branch/master/graph/badge.svg
    :target: https://codecov.io/gh/nilearn/nilearn
 
+.. image:: https://dev.azure.com/Parietal/Nilearn/_apis/build/status/nilearn.nilearn?branchName=master
+    :target: https://dev.azure.com/Parietal/Nilearn/_apis/build/status/nilearn.nilearn?branchName=master
+
 nilearn
 =======
 

diff --git a/appveyor.yml b/appveyor.yml
@@ -27,7 +27,7 @@ install:
   - "conda install pip numpy scipy scikit-learn joblib nose pytest wheel matplotlib -y -q"
 
   # Install other nilearn dependencies
-  - "pip install nibabel coverage nose-timer pytest-cov"
+  - "pip install nibabel coverage nose-timer pytest-cov sklearn"
   - "python setup.py bdist_wheel"
   - ps: "ls dist"