[WIP] New release

.travis.yml

@@ -15,13 +15,38 @@ env:
   - TEST_DIR=/tmp/test_dir/
   - MODULE=openml
   matrix:
-  - DISTRIB="conda" PYTHON_VERSION="2.7" SKLEARN_VERSION="0.18.2"
-  - DISTRIB="conda" PYTHON_VERSION="3.4" SKLEARN_VERSION="0.18.2"
-  - DISTRIB="conda" PYTHON_VERSION="3.5" SKLEARN_VERSION="0.18.2"
-  - DISTRIB="conda" PYTHON_VERSION="3.6" COVERAGE="true" SKLEARN_VERSION="0.18.2"
-  - DISTRIB="conda" PYTHON_VERSION="3.6" EXAMPLES="true" SKLEARN_VERSION="0.18.2"
-  - DISTRIB="conda" PYTHON_VERSION="3.6" DOCTEST="true" SKLEARN_VERSION="0.18.2"
+  - DISTRIB="conda" PYTHON_VERSION="2.7" SKLEARN_VERSION="0.20.0"
+  - DISTRIB="conda" PYTHON_VERSION="3.5" SKLEARN_VERSION="0.20.0"
+  - DISTRIB="conda" PYTHON_VERSION="3.6" SKLEARN_VERSION="0.20.0"
+  - DISTRIB="conda" PYTHON_VERSION="3.7" SKLEARN_VERSION="0.20.0" RUN_FLAKE8="true" SKIP_TESTS="true"
+  - DISTRIB="conda" PYTHON_VERSION="3.7" SKLEARN_VERSION="0.20.0" COVERAGE="true" DOCPUSH="true"
+  # Checks for older scikit-learn versions (which also don't nicely work with
+  # Python3.7)
+  - DISTRIB="conda" PYTHON_VERSION="3.6" SKLEARN_VERSION="0.19.2"
+  - DISTRIB="conda" PYTHON_VERSION="3.6" SKLEARN_VERSION="0.18.2"
+
+# Travis issue
+# https://github.com/travis-ci/travis-ci/issues/8920
+before_install:
+ - python -c "import fcntl; fcntl.fcntl(1, fcntl.F_SETFL, 0)"
 
 install: source ci_scripts/install.sh
 script: bash ci_scripts/test.sh
-after_success: source ci_scripts/success.sh
+after_success: source ci_scripts/success.sh && source ci_scripts/create_doc.sh $TRAVIS_BRANCH "doc_result"
+
+# travis will check the deploy on condition, before actually running before_deploy
+# before_deploy: source ci_scripts/create_doc.sh $TRAVIS_BRANCH "doc_result"
+
+# For more info regarding the deploy process and the github token look at:
+# https://docs.travis-ci.com/user/deployment/pages/
+
+deploy:
+  provider: pages
+  skip_cleanup: true
+  github_token: $GITHUB_TOKEN
+  keep-history: true
+  committer-from-gh: true
+  on:
+    all_branches: true
+    condition: $doc_result = "success"
+  local_dir: doc/$TRAVIS_BRANCH

CONTRIBUTING.md

@@ -74,14 +74,14 @@ following rules before you submit a pull request:
    [task list](https://github.com/blog/1375-task-lists-in-gfm-issues-pulls-comments)
    in the PR description.
 
--  All tests pass when running `nosetests`. On
+-  All tests pass when running `pytest`. On
    Unix-like systems, check with (from the toplevel source folder):
 
       ```bash
-      $ nosetests
+      $ pytest
       ```
 
-   For Windows systems, execute the command from an Anaconda Prompt or add `nosetests` to PATH before executing the command.
+   For Windows systems, execute the command from an Anaconda Prompt or add `pytest` to PATH before executing the command.
 
 -  Documentation and high-coverage tests are necessary for enhancements to be
    accepted. Bug-fixes or new features should be provided with
@@ -92,15 +92,17 @@ following rules before you submit a pull request:
    For the Bug-fixes case, at the time of the PR, this tests should fail for
    the code base in develop and pass for the PR code.
 
+ - Add your changes to the changelog in the file doc/progress.rst.
+
 
 You can also check for common programming errors with the following
 tools:
 
 -  Code with good unittest **coverage** (at least 80%), check with:
 
   ```bash
-  $ pip install nose coverage
-  $ nosetests --with-coverage path/to/tests_for_package
+  $ pip install pytest pytest-cov
+  $ pytest --cov=. path/to/tests_for_package
   ```
 
 -  No pyflakes warnings, check with:

Makefile

@@ -2,7 +2,7 @@
 
 PYTHON ?= python
 CYTHON ?= cython
-NOSETESTS ?= nosetests
+PYTEST ?= pytest
 CTAGS ?= ctags
 
 all: clean inplace test
@@ -16,12 +16,12 @@ inplace:
 	$(PYTHON) setup.py build_ext -i
 
 test-code: in
-	$(NOSETESTS) -s -v tests
+	$(PYTEST) -s -v tests
 test-doc:
-	$(NOSETESTS) -s -v doc/*.rst
+	$(PYTEST) -s -v doc/*.rst
 
 test-coverage:
 	rm -rf coverage .coverage
-	$(NOSETESTS) -s -v --with-coverage tests
+	$(PYTEST) -s -v --cov=. tests
 
 test: test-code test-sphinxext test-doc

appveyor.yml

@@ -1,18 +1,14 @@
+clone_folder: C:\\projects\\openml-python
 
 environment:
- global:
-     CMD_IN_ENV: "cmd /E:ON /V:ON /C .\\appveyor\\scikit-learn-contrib\\run_with_env.cmd"
+# global:
+#     CMD_IN_ENV: "cmd /E:ON /V:ON /C .\\appveyor\\scikit-learn-contrib\\run_with_env.cmd"
 
  matrix:
     - PYTHON: "C:\\Python35-x64"
       PYTHON_VERSION: "3.5"
       PYTHON_ARCH: "64"
       MINICONDA: "C:\\Miniconda35-x64"
-
-    - PYTHON: "C:\\Python35"
-      PYTHON_VERSION: "3.5"
-      PYTHON_ARCH: "32"
-      MINICONDA: "C:\\Miniconda35"
 
 matrix:
     fast_finish: true
@@ -36,17 +32,19 @@ install:
   # XXX: setuptools>23 is currently broken on Win+py3 with numpy
   # (https://github.com/pypa/setuptools/issues/728)
   - conda update --all --yes setuptools=23
+  - conda install --yes nb_conda nb_conda_kernels
 
   # Install the build and runtime dependencies of the project.
   - "cd C:\\projects\\openml-python"
-  - conda install --quiet --yes mock numpy scipy nose requests scikit-learn nbformat python-dateutil nbconvert
+  - conda install --quiet --yes scikit-learn=0.18.2
+  - conda install --quiet --yes mock numpy scipy pytest requests nbformat python-dateutil nbconvert pandas matplotlib seaborn
   - pip install liac-arff xmltodict oslo.concurrency
-  - "%CMD_IN_ENV% python setup.py install"
+  - "pip install .[test]"
 
 
 # Not a .NET project, we build scikit-learn in the install step instead
 build: false
 
 test_script:
   - "cd C:\\projects\\openml-python"
-  - "%CMD_IN_ENV% python setup.py test"
+  - "%CMD_IN_ENV% pytest"

ci_scripts/create_doc.sh

@@ -0,0 +1,59 @@
+set -euo pipefail
+
+# Check if DOCPUSH is set
+if ! [[ -z ${DOCPUSH+x} ]]; then
+
+    if [[ "$DOCPUSH" == "true" ]]; then
+
+        # install documentation building dependencies
+        pip install matplotlib seaborn sphinx pillow sphinx-gallery sphinx_bootstrap_theme cython numpydoc nbformat nbconvert
+
+        # $1 is the branch name
+        # $2 is the global variable where we set the script status
+
+        if ! { [ $1 = "master" ] || [ $1 = "develop" ]; }; then
+            { echo "Not one of the allowed branches"; exit 0; }
+        fi
+
+        # delete any previous documentation folder
+        if [ -d doc/$1 ]; then
+            rm -rf doc/$1
+        fi
+
+        # create the documentation
+        cd doc && make html 2>&1
+
+        # create directory with branch name
+        # the documentation for dev/stable from git will be stored here
+        mkdir $1
+
+        # get previous documentation from github
+        git clone https://github.com/openml/openml-python.git --branch gh-pages --single-branch
+
+        # copy previous documentation
+        cp -r openml-python/. $1
+        rm -rf openml-python
+
+        # if the documentation for the branch exists, remove it
+        if [ -d $1/$1 ]; then
+            rm -rf $1/$1
+        fi
+
+        # copy the updated documentation for this branch
+        mkdir $1/$1
+        cp -r build/html/. $1/$1
+
+        # takes a variable name as an argument and assigns the script outcome to a
+        # variable with the given name. If it got this far, the script was successful
+        function set_return() {
+            # $1 is the variable where we save the script outcome
+            local __result=$1
+            local  status='success'
+            eval $__result="'$status'"
+        }
+
+        set_return "$2"
+    fi
+fi
+# Workaround for travis failure
+set +u

ci_scripts/flake8_diff.sh

@@ -0,0 +1,140 @@
+#!/bin/bash
+
+# Inspired from https://github.com/scikit-learn/scikit-learn/blob/master/build_tools/travis/flake8_diff.sh
+
+# This script is used in Travis to check that PRs do not add obvious
+# flake8 violations. It relies on two things:
+#   - find common ancestor between branch and
+#     openml/openml-python remote
+#   - run flake8 --diff on the diff between the branch and the common
+#     ancestor
+#
+# Additional features:
+#   - the line numbers in Travis match the local branch on the PR
+#     author machine.
+#   - ./ci_scripts/flake8_diff.sh can be run locally for quick
+#     turn-around
+
+set -e
+# pipefail is necessary to propagate exit codes
+set -o pipefail
+
+PROJECT=openml/openml-python
+PROJECT_URL=https://github.com/$PROJECT.git
+
+# Find the remote with the project name (upstream in most cases)
+REMOTE=$(git remote -v | grep $PROJECT | cut -f1 | head -1 || echo '')
+
+# Add a temporary remote if needed. For example this is necessary when
+# Travis is configured to run in a fork. In this case 'origin' is the
+# fork and not the reference repo we want to diff against.
+if [[ -z "$REMOTE" ]]; then
+    TMP_REMOTE=tmp_reference_upstream
+    REMOTE=$TMP_REMOTE
+    git remote add $REMOTE $PROJECT_URL
+fi
+
+echo "Remotes:"
+echo '--------------------------------------------------------------------------------'
+git remote --verbose
+
+# Travis does the git clone with a limited depth (50 at the time of
+# writing). This may not be enough to find the common ancestor with
+# $REMOTE/develop so we unshallow the git checkout
+if [[ -a .git/shallow ]]; then
+    echo -e '\nTrying to unshallow the repo:'
+    echo '--------------------------------------------------------------------------------'
+    git fetch --unshallow
+fi
+
+if [[ "$TRAVIS" == "true" ]]; then
+    if [[ "$TRAVIS_PULL_REQUEST" == "false" ]]
+    then
+        # In main repo, using TRAVIS_COMMIT_RANGE to test the commits
+        # that were pushed into a branch
+        if [[ "$PROJECT" == "$TRAVIS_REPO_SLUG" ]]; then
+            if [[ -z "$TRAVIS_COMMIT_RANGE" ]]; then
+                echo "New branch, no commit range from Travis so passing this test by convention"
+                exit 0
+            fi
+            COMMIT_RANGE=$TRAVIS_COMMIT_RANGE
+        fi
+    else
+        # We want to fetch the code as it is in the PR branch and not
+        # the result of the merge into develop. This way line numbers
+        # reported by Travis will match with the local code.
+        LOCAL_BRANCH_REF=travis_pr_$TRAVIS_PULL_REQUEST
+        # In Travis the PR target is always origin
+        git fetch origin pull/$TRAVIS_PULL_REQUEST/head:refs/$LOCAL_BRANCH_REF
+    fi
+fi
+
+# If not using the commit range from Travis we need to find the common
+# ancestor between $LOCAL_BRANCH_REF and $REMOTE/develop
+if [[ -z "$COMMIT_RANGE" ]]; then
+    if [[ -z "$LOCAL_BRANCH_REF" ]]; then
+        LOCAL_BRANCH_REF=$(git rev-parse --abbrev-ref HEAD)
+    fi
+    echo -e "\nLast 2 commits in $LOCAL_BRANCH_REF:"
+    echo '--------------------------------------------------------------------------------'
+    git --no-pager log -2 $LOCAL_BRANCH_REF
+
+    REMOTE_DEV_REF="$REMOTE/develop"
+    # Make sure that $REMOTE_DEV_REF is a valid reference
+    echo -e "\nFetching $REMOTE_DEV_REF"
+    echo '--------------------------------------------------------------------------------'
+    git fetch $REMOTE develop:refs/remotes/$REMOTE_DEV_REF
+    LOCAL_BRANCH_SHORT_HASH=$(git rev-parse --short $LOCAL_BRANCH_REF)
+    REMOTE_DEV_SHORT_HASH=$(git rev-parse --short $REMOTE_DEV_REF)
+
+    COMMIT=$(git merge-base $LOCAL_BRANCH_REF $REMOTE_DEV_REF) || \
+        echo "No common ancestor found for $(git show $LOCAL_BRANCH_REF -q) and $(git show $REMOTE_DEV_REF -q)"
+
+    if [ -z "$COMMIT" ]; then
+        exit 1
+    fi
+
+    COMMIT_SHORT_HASH=$(git rev-parse --short $COMMIT)
+
+    echo -e "\nCommon ancestor between $LOCAL_BRANCH_REF ($LOCAL_BRANCH_SHORT_HASH)"\
+         "and $REMOTE_DEV_REF ($REMOTE_DEV_SHORT_HASH) is $COMMIT_SHORT_HASH:"
+    echo '--------------------------------------------------------------------------------'
+    git --no-pager show --no-patch $COMMIT_SHORT_HASH
+
+    COMMIT_RANGE="$COMMIT_SHORT_HASH..$LOCAL_BRANCH_SHORT_HASH"
+
+    if [[ -n "$TMP_REMOTE" ]]; then
+        git remote remove $TMP_REMOTE
+    fi
+
+else
+    echo "Got the commit range from Travis: $COMMIT_RANGE"
+fi
+
+echo -e '\nRunning flake8 on the diff in the range' "$COMMIT_RANGE" \
+     "($(git rev-list $COMMIT_RANGE | wc -l) commit(s)):"
+echo '--------------------------------------------------------------------------------'
+# We need the following command to exit with 0 hence the echo in case
+# there is no match
+MODIFIED_FILES="$(git diff --name-only $COMMIT_RANGE || echo "no_match")"
+
+check_files() {
+    files="$1"
+    shift
+    options="$*"
+    if [ -n "$files" ]; then
+        # Conservative approach: diff without context (--unified=0) so that code
+        # that was not changed does not create failures
+        git diff --unified=0 $COMMIT_RANGE -- $files | flake8 --ignore E402 --diff --show-source $options
+    fi
+}
+
+if [[ "$MODIFIED_FILES" == "no_match" ]]; then
+    echo "No file has been modified"
+else
+
+    check_files "$(echo "$MODIFIED_FILES" | grep -v ^examples)"
+    check_files "$(echo "$MODIFIED_FILES" | grep ^examples)" \
+        --config ./examples/.flake8
+fi
+echo -e "No problem detected by flake8\n"

ci_scripts/install.sh

@@ -26,7 +26,7 @@ popd
 # provided versions
 conda create -n testenv --yes python=$PYTHON_VERSION pip
 source activate testenv
-pip install nose numpy scipy cython scikit-learn==$SKLEARN_VERSION \
+pip install pytest pytest-xdist pytest-timeout numpy scipy cython scikit-learn==$SKLEARN_VERSION \
     oslo.concurrency
 
 if [[ "$EXAMPLES" == "true" ]]; then
@@ -37,10 +37,13 @@ if [[ "$DOCTEST" == "true" ]]; then
     pip install pandas sphinx_bootstrap_theme
 fi
 if [[ "$COVERAGE" == "true" ]]; then
-    pip install codecov
+    pip install codecov pytest-cov
+fi
+if [[ "$RUN_FLAKE8" == "true" ]]; then
+    pip install flake8
 fi
 
 python --version
 python -c "import numpy; print('numpy %s' % numpy.__version__)"
 python -c "import scipy; print('scipy %s' % scipy.__version__)"
-python setup.py develop
+pip install -e '.[test]'