Merge remote-tracking branch 'origin/master' into heart_rate_model

.circleci/config.yml

@@ -0,0 +1,34 @@
+version: 2
+
+jobs:
+  python3:
+    docker:
+      - image: circleci/python:3.6.1
+    environment:
+      - MINICONDA_PATH: ~/miniconda
+      - CONDA_ENV_NAME: testenv
+      - PYTHON_VERSION: 3
+    steps:
+      - checkout
+      - run: ./build_tools/circle/checkout_merge_commit.sh
+      - run: ./build_tools/circle/build_doc.sh
+      - store_artifacts:
+          path: doc/_build/html
+          destination: doc
+      - store_artifacts:
+          path: ~/log.txt
+      - persist_to_workspace:
+          root: doc/_build/html
+          paths: .
+      - attach_workspace:
+          at: doc/_build/html
+      - run: ls -ltrh doc/_build/html
+    filters:
+      branches:
+        ignore: gh-pages
+
+workflows:
+  version: 2
+  build-doc:
+    jobs:
+      - python3

build_tools/circle/build_doc.sh

@@ -0,0 +1,107 @@
+#!/usr/bin/env bash
+set -x
+set -e
+
+# Decide what kind of documentation build to run, and run it.
+#
+# If the last commit message has a "[doc skip]" marker, do not build
+# the doc. On the contrary if a "[doc build]" marker is found, build the doc
+# instead of relying on the subsequent rules.
+#
+# We always build the documentation for jobs that are not related to a specific
+# PR (e.g. a merge to master or a maintenance branch).
+#
+# If this is a PR, do a full build if there are some files in this PR that are
+# under the "doc/" or "examples/" folders, otherwise perform a quick build.
+#
+# If the inspection of the current commit fails for any reason, the default
+# behavior is to quick build the documentation.
+
+get_build_type() {
+    if [ -z "$CIRCLE_SHA1" ]
+    then
+	echo SKIP: undefined CIRCLE_SHA1
+	return
+    fi
+    commit_msg=$(git log --format=%B -n 1 $CIRCLE_SHA1)
+    if [ -z "$commit_msg" ]
+    then
+	echo QUICK BUILD: failed to inspect commit $CIRCLE_SHA1
+	return
+    fi
+    if [[ "$commit_msg" =~ \[doc\ skip\] ]]
+    then
+	echo SKIP: [doc skip] marker found
+	return
+    fi
+    if [[ "$commit_msg" =~ \[doc\ quick\] ]]
+    then
+	echo QUICK: [doc quick] marker found
+	return
+    fi
+    if [[ "$commit_msg" =~ \[doc\ build\] ]]
+    then
+	echo BUILD: [doc build] marker found
+	return
+    fi
+    if [ -z "$CI_PULL_REQUEST" ]
+    then
+	echo BUILD: not a pull request
+	return
+    fi
+    git_range="origin/master...$CIRCLE_SHA1"
+    git fetch origin master >&2 || (echo QUICK BUILD: failed to get changed filenames for $git_range; return)
+    filenames=$(git diff --name-only $git_range)
+    if [ -z "$filenames" ]
+    then
+	echo QUICK BUILD: no changed filenames for $git_range
+	return
+    fi
+    if echo "$filenames" | grep -q -e ^examples/
+    then
+	echo BUILD: detected examples/ filename modified in $git_range: $(echo "$filenames" | grep -e ^examples/ | head -n1)
+	return
+    fi
+    echo QUICK BUILD: no examples/ filename modified in $git_range:
+    echo "$filenames"
+}
+
+build_type=$(get_build_type)
+if [[ "$build_type" =~ ^SKIP ]]
+then
+    exit 0
+fi
+
+MAKE_TARGET=html
+
+# deactivate circleci virtualenv and setup a miniconda env instead
+if [[ `type -t deactivate` ]]; then
+    deactivate
+fi
+
+# Install dependencies with miniconda
+wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
+     -O miniconda.sh
+chmod +x miniconda.sh && ./miniconda.sh -b -p $MINICONDA_PATH
+export PATH="$MINICONDA_PATH/bin:$PATH"
+conda update --yes --quiet conda
+
+# Configure the conda environment and put it in the path using the
+# provided versions
+conda create -n $CONDA_ENV_NAME --yes --quiet python=3
+source activate $CONDA_ENV_NAME
+
+conda install --yes -c conda-forge pip numpy scipy pandas cython scikit-learn \
+      six python-fitparse joblib matplotlib pillow sphinx sphinx_rtd_theme \
+      numpydoc
+pip install -U sphinx-gallery
+
+# Build and install scikit-sports in dev mode
+ls -l
+pip install -e .
+
+# The pipefail is requested to propagate exit code
+set -o pipefail && cd doc && make $MAKE_TARGET 2>&1 | tee ~/log.txt
+
+cd -
+set +o pipefail

build_tools/circle/checkout_merge_commit.sh

@@ -0,0 +1,31 @@
+#!/bin/bash
+
+# Add `master` branch to the update list.
+# Otherwise CircleCI will give us a cached one.
+FETCH_REFS="+master:master"
+
+# Update PR refs for testing.
+if [[ -n "${CIRCLE_PR_NUMBER}" ]]
+then
+    FETCH_REFS="${FETCH_REFS} +refs/pull/${CIRCLE_PR_NUMBER}/head:pr/${CIRCLE_PR_NUMBER}/head"
+    FETCH_REFS="${FETCH_REFS} +refs/pull/${CIRCLE_PR_NUMBER}/merge:pr/${CIRCLE_PR_NUMBER}/merge"
+fi
+
+# Retrieve the refs.
+git fetch -u origin ${FETCH_REFS}
+
+# Checkout the PR merge ref.
+if [[ -n "${CIRCLE_PR_NUMBER}" ]]
+then
+    git checkout -qf "pr/${CIRCLE_PR_NUMBER}/merge" || (
+        echo Could not fetch merge commit. >&2
+        echo There may be conflicts in merging PR \#${CIRCLE_PR_NUMBER} with master. >&2;
+        exit 1)
+fi
+
+# Check for merge conflicts.
+if [[ -n "${CIRCLE_PR_NUMBER}" ]]
+then
+    git branch --merged | grep master > /dev/null
+    git branch --merged | grep "pr/${CIRCLE_PR_NUMBER}/head" > /dev/null
+fi

doc/Makefile

@@ -0,0 +1,185 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = _build
+
+# User-friendly check for sphinx-build
+ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
+$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
+endif
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
+
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html       to make standalone HTML files"
+	@echo "  dirhtml    to make HTML files named index.html in directories"
+	@echo "  singlehtml to make a single large HTML file"
+	@echo "  pickle     to make pickle files"
+	@echo "  json       to make JSON files"
+	@echo "  htmlhelp   to make HTML files and a HTML help project"
+	@echo "  qthelp     to make HTML files and a qthelp project"
+	@echo "  devhelp    to make HTML files and a Devhelp project"
+	@echo "  epub       to make an epub"
+	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
+	@echo "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@echo "  texinfo    to make Texinfo files"
+	@echo "  info       to make Texinfo files and run them through makeinfo"
+	@echo "  gettext    to make PO message catalogs"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  xml        to make Docutils-native XML files"
+	@echo "  pseudoxml  to make pseudoxml-XML files for display purposes"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+
+clean:
+	-rm -rf $(BUILDDIR)/*
+	-rm -rf auto_examples/
+	-rm -rf generated/*
+	-rm -rf modules/generated/*
+
+html:
+	# These two lines make the build a bit more lengthy, and the
+	# the embedding of images more robust
+	rm -rf $(BUILDDIR)/html/_images
+	#rm -rf _build/doctrees/
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	touch $(BUILDDIR)/html/.nojekyll
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+qthelp:
+	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
+	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/scikit-sports.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/scikit-sports.qhc"
+
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/scikit-sports"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/scikit-sports"
+	@echo "# devhelp"
+
+epub:
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" \
+	      "(use \`make latexpdf' here to do that automatically)."
+
+latexpdf:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through pdflatex..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+latexpdfja:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through platex and dvipdfmx..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+text:
+	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+man:
+	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+	@echo
+	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+texinfo:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo
+	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+	@echo "Run \`make' in that directory to run these through makeinfo" \
+	      "(use \`make info' here to do that automatically)."
+
+info:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo "Running Texinfo files through makeinfo..."
+	make -C $(BUILDDIR)/texinfo info
+	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+gettext:
+	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+	@echo
+	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."
+
+xml:
+	$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
+	@echo
+	@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
+
+pseudoxml:
+	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
+	@echo
+	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."