Merge pull request #3 from bouthilx/feature/newalgos

Add Bohamiann and DNGO + adapt to new test suite

.github/workflows/build.yml

@@ -17,7 +17,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        toxenv: [black, isort, pylint]
+        toxenv: [black, isort, pylint, doc8, docs]
 
     steps:
     - uses: actions/checkout@v1
@@ -36,7 +36,7 @@ jobs:
       max-parallel: 4
       matrix:
         platform: [ubuntu-latest]
-        python-version: [3.6, 3.7, 3.8]
+        python-version: [3.6, 3.7, 3.8, 3.9]
     env:
       PLATFORM: ${{ matrix.platform }}
     steps:

.github/workflows/docs.yaml

@@ -0,0 +1,30 @@
+name: docs
+
+on:
+  push:
+    branches:
+      - master
+      - develop
+  release:
+    types:
+      [published]
+  workflow_dispatch:
+
+jobs:
+
+  build_docs_job:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python 3.7
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.7
+    - name: Install dependencies
+      run: bash ./scripts/setup_gh.sh
+    - name: Test with tox
+      run: tox -vv -e docs
+    - name: Deploy doc on gh-pages
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      run: bash docs/deploy.sh

.pylintrc

@@ -51,7 +51,7 @@ confidence=
 # --enable=similarities". If you want to run only the classes checker, but have
 # no Warning level messages displayed, use"--disable=all --enable=classes
 # --disable=W"
-disable=ungrouped-imports,abstract-class-instantiated,useless-super-delegation,no-member,keyword-arg-before-vararg,unidiomatic-typecheck,redefined-outer-name,fixme,F0401,intern-builtin,wrong-import-position,wrong-import-order, C0415, F0010, R0205, R1705, R1711, R1720, W0106, W0107, W0127, W0706, C0330, C0326
+disable=ungrouped-imports,abstract-class-instantiated,useless-super-delegation,no-member,keyword-arg-before-vararg,unidiomatic-typecheck,redefined-outer-name,fixme,F0401,intern-builtin,wrong-import-position,wrong-import-order, C0415, F0010, R0205, R1705, R1711, R1720, W0106, W0107, W0127, W0706, C0330, C0326,invalid-name,too-many-arguments,attribute-defined-outside-init
 
 # Enable the message, report, category or checker with the given id(s). You can
 # either give multiple identifier separated by comma (,) or put this option

MANIFEST.in

@@ -11,6 +11,7 @@ exclude .pylintrc
 exclude codecov.yml
 exclude .mailmap
 exclude scripts/setup_gh.sh
+exclude docs/src/_static/stub
 prune .github/
 
 # Include src, tests, docs

README.rst

@@ -1,6 +1,6 @@
-===============
-orion.algo.robo
-===============
+======================
+RoBO Wrapper for Oríon
+======================
 
 
 .. |pypi| image:: https://img.shields.io/pypi/v/orion.algo.robo
@@ -29,34 +29,37 @@ orion.algo.robo
 
 ----
 
-This ``orion.algo`` plugin was generated with `Cookiecutter`_ along with `@Epistimio`_'s `cookiecutter-orion.algo`_ template.
-
-See Orion : https://github.com/Epistimio/orion
+This wrapper provides access through `Oríon`_ to several Bayesian optimization algorithms 
+in the library `RoBO`_.
 
+This ``orion.algo`` plugin was generated with `Cookiecutter`_ along with `@Epistimio`_'s `cookiecutter-orion.algo`_ template.
 
 Installation
 ------------
 
 The RoBO wrapper is currently only supported on Linux.
 
-Before installing RoBO, make sure you have libeigen and swig installed. On ubuntu, you can install
-them with `apt-get`::
+Before installing RoBO, make sure you have ``libeigen`` and ``swig`` installed. 
+On ubuntu, you can install them with ``apt-get``
+
+.. code-block:: console
 
     $ sudo apt-get install libeigen3-dev swig
 
 One of the dependencies of RoBO does not declare its dependencies and therefore we need
-to install these dependencies first. The order of dependencies in `requirements.txt` reflects this
-order. To install them sequentially, use the following command::
+to install these dependencies first. The order of dependencies in ``requirements.txt`` 
+reflects this order. To install them sequentially, use the following command
+
+.. code-block:: console
 
     $ curl -s https://git.io/JLnCA | grep -v "^#" | xargs -n 1 -L 1 pip install
 
-Finally, you can install this package using PyPI::
+Finally, you can install this package using PyPI
 
-    $ pip install orion.algo.robo
+.. code-block:: console
 
+    $ pip install orion.algo.robo
 
-Usage
------
 
 Contribute or Ask
 -----------------
@@ -76,18 +79,20 @@ Citation
 --------
 
 If you use this wrapper for your publications, please cite both
-`RoBO <https://github.com/automl/RoBO#citing-robo>` and 
-`Oríon <https://github.com/epistimio/orion#citation>`.
-
+`RoBO <https://github.com/automl/RoBO#citing-robo>`__ and 
+`Oríon <https://github.com/epistimio/orion#citation>`__. Please also cite
+the papers of the algorithms you used, such as DNGO or BOHAMIANN. See 
+the documentation of the algorithms to find corresponding original papers.
 
 License
 -------
 
 Distributed under the terms of the BSD-3-Clause license,
-"orion.algo.robo" is free and open source software.
+``orion.algo.robo`` is free and open source software.
 
 
 .. _`Cookiecutter`: https://github.com/audreyr/cookiecutter
 .. _`@Epistimio`: https://github.com/Epistimio
 .. _`cookiecutter-orion.algo`: https://github.com/Epistimio/cookiecutter-orion.algo
-.. _`orion`: https://github.com/Epistimio/orion
+.. _`Oríon`: https://github.com/Epistimio/orion
+.. _`RoBO`: https://github.com/automl/robo

docs/deploy.sh

@@ -0,0 +1,45 @@
+#!/bin/bash
+
+################################################################################
+# Modified version of 
+# https://tech.michaelaltfield.net/2020/07/18/sphinx-rtd-github-pages-1/ 
+################################################################################
+
+#####################
+# DECLARE VARIABLES #
+#####################
+
+pwd
+ls -lah
+export SOURCE_DATE_EPOCH=$(git log -1 --pretty=%ct)
+
+#######################
+# Update GitHub Pages #
+#######################
+
+git config --global user.name "${GITHUB_ACTOR}"
+git config --global user.email "${GITHUB_ACTOR}@users.noreply.github.com"
+
+docroot=`mktemp -d`
+rsync -av "docs/build/html/" "${docroot}/"
+
+pushd "${docroot}"
+
+# don't bother maintaining history; just generate fresh
+git init
+git remote add deploy "https://token:${GITHUB_TOKEN}@github.com/${GITHUB_REPOSITORY}.git"
+git checkout -b gh-pages
+
+# add .nojekyll to the root so that github won't 404 on content added to dirs
+# that start with an underscore (_), such as our "_content" dir..
+touch .nojekyll
+
+# copy the resulting html pages built from sphinx above to our new git repo
+git add .
+
+# commit all the new files
+msg="Updating Docs for commit ${GITHUB_SHA} made on `date -d"@${SOURCE_DATE_EPOCH}" --iso-8601=seconds` from ${GITHUB_REF} by ${GITHUB_ACTOR}"
+git commit -am "${msg}"
+
+# overwrite the contents of the gh-pages branch on our github.com repo
+git push deploy gh-pages --force

docs/requirements.txt

@@ -0,0 +1,5 @@
+sphinx
+sphinx_rtd_theme
+sphinxcontrib.httpdomain
+sphinx-autoapi
+numpydoc