Work in progress: upgrade to astropy ecosystem structure

.gitignore

@@ -2,6 +2,7 @@
 saved
 output
 example_dataset
+hela/version.py
 
 # Created by https://www.gitignore.io/api/osx,linux,python
 

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "astropy_helpers"]
+	path = astropy_helpers
+	url = git://github.com/astropy/astropy-helpers

.rtd-environment.yml

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+name: hela
+
+channels:
+    - astropy
+
+dependencies:
+    - astropy
+    - numpy
+    - scikit-learn
+    - pip:
+        - sphinx-automodapi
+        - numpydoc

.travis.yml

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+# We set the language to c because python isn't supported on the MacOS X nodes
+# on Travis. However, the language ends up being irrelevant anyway, since we
+# install Python ourselves using conda.
+language: c
+
+os:
+    - linux
+
+# The apt packages below are needed for sphinx builds. A full list of packages
+# that can be included can be found here:
+#
+# https://github.com/travis-ci/apt-package-whitelist/blob/master/ubuntu-precise
+
+addons:
+    apt:
+        packages:
+            - graphviz
+
+
+stage: Comprehensive tests
+
+stages:
+   # Do the style check and a single test job, don't proceed if it fails
+   - name: Initial tests
+   # Test docs, astropy dev, and without optional dependencies
+   - name: Comprehensive tests
+   # Slow tests that should only run if comprehensive ones passed
+   - name: Slow tests
+   # These will only run when cron is opted in
+   - name: Cron tests
+     if: type = cron
+
+
+env:
+    global:
+        # The following versions are the 'default' for tests, unless
+        # overridden underneath. They are defined here in order to save having
+        # to repeat them for all configurations.
+        - PYTHON_VERSION=3.7
+        - NUMPY_VERSION=stable
+        - ASTROPY_VERSION=stable
+        - MAIN_CMD='python setup.py'
+        - SETUP_CMD='test'
+        - EVENT_TYPE='pull_request push'
+
+
+        # List runtime dependencies for the package that are available as conda
+        # packages here.
+        - CONDA_DEPENDENCIES='scikit-learn'
+        - CONDA_DEPENDENCIES_DOC='sphinx-astropy'
+
+        # List other runtime dependencies for the package that are available as
+        # pip packages here.
+        - PIP_DEPENDENCIES='scipy matplotlib tqdm joblib'
+
+        # Conda packages for affiliated packages are hosted in channel
+        # "astropy" while builds for astropy LTS with recent numpy versions
+        # are in astropy-ci-extras. If your package uses either of these,
+        # add the channels to CONDA_CHANNELS along with any other channels
+        # you want to use.
+        - CONDA_CHANNELS='astropy'
+
+        # If there are matplotlib or other GUI tests, uncomment the following
+        # line to use the X virtual framebuffer.
+        # - SETUP_XVFB=True
+
+        - FLAKE8_OPT='--ignore=E501,W504'
+
+matrix:
+
+    # Don't wait for allowed failures
+    fast_finish: true
+
+    include:
+        # Make sure that egg_info works without dependencies
+        - stage: Initial tests
+          env: PYTHON_VERSION=3.7 SETUP_CMD='egg_info'
+
+        # Try MacOS X, usually enough only to run from cron as hardly there are
+        # issues that are not picked up by a linux worker
+        - os: osx
+          stage: Cron tests
+          env: SETUP_CMD='test' EVENT_TYPE='cron'
+
+        # Do a coverage test.
+        - os: linux
+          stage: Initial tests
+          env: SETUP_CMD='test --coverage'
+
+        # Do a PEP8 test with flake8
+        - os: linux
+          stage: Initial tests
+          env: MAIN_CMD='flake8 hela --count --show-source --statistics $FLAKE8_OPT' SETUP_CMD=''
+
+    allow_failures:
+        # Do a PEP8 test with flake8
+        # (do allow to fail unless your code completely compliant)
+        # - os: linux
+        #   stage: Initial tests
+        #   env: MAIN_CMD='flake8 hela --count --show-source --statistics $FLAKE8_OPT' SETUP_CMD=''
+
+install:
+
+    # We now use the ci-helpers package to set up our testing environment.
+    # This is done by using Miniconda and then using conda and pip to install
+    # dependencies. Which dependencies are installed using conda and pip is
+    # determined by the CONDA_DEPENDENCIES and PIP_DEPENDENCIES variables,
+    # which should be space-delimited lists of package names. See the README
+    # in https://github.com/astropy/ci-helpers for information about the full
+    # list of environment variables that can be used to customize your
+    # environment. In some cases, ci-helpers may not offer enough flexibility
+    # in how to install a package, in which case you can have additional
+    # commands in the install: section below.
+
+    - git clone --depth 1 git://github.com/astropy/ci-helpers.git
+    - source ci-helpers/travis/setup_conda.sh
+
+    # As described above, using ci-helpers, you should be able to set up an
+    # environment with dependencies installed using conda and pip, but in some
+    # cases this may not provide enough flexibility in how to install a
+    # specific dependency (and it will not be able to install non-Python
+    # dependencies). Therefore, you can also include commands below (as
+    # well as at the start of the install section or in the before_install
+    # section if they are needed before setting up conda) to install any
+    # other dependencies.
+
+script:
+   - $MAIN_CMD $SETUP_CMD
+
+after_success:
+    # If coveralls.io is set up for this package, uncomment the line below.
+    # The coveragerc file may be customized as needed for your package.
+    # - if [[ $SETUP_CMD == *coverage* ]]; then coveralls --rcfile='hipparchus/tests/coveragerc'; fi

MANIFEST.in

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+include README.rst
+include CHANGES.rst
+
+include ah_bootstrap.py
+include setup.cfg
+include hela/tests/coveragerc
+
+recursive-include hela *.pyx *.c *.pxd
+recursive-include docs *
+recursive-include licenses *
+recursive-include cextern *
+recursive-include scripts *
+
+prune build
+prune docs/_build
+prune docs/api
+
+
+# the next few stanzas are for astropy_helpers.  It's derived from the
+# astropy_helpers/MANIFEST.in, but requires additional includes for the actual
+# package directory and egg-info.
+
+include astropy_helpers/README.rst
+include astropy_helpers/CHANGES.rst
+include astropy_helpers/LICENSE.rst
+recursive-include astropy_helpers/licenses *
+
+include astropy_helpers/ah_bootstrap.py
+
+recursive-include astropy_helpers/astropy_helpers *.py *.pyx *.c *.h *.rst
+recursive-include astropy_helpers/astropy_helpers.egg-info *
+# include the sphinx stuff with "*" because there are css/html/rst/etc.
+recursive-include astropy_helpers/astropy_helpers/sphinx *
+
+prune astropy_helpers/build
+prune astropy_helpers/astropy_helpers/tests
+
+
+global-exclude *.pyc *.o

README.rst

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+.. image:: img/HELA_logo1.png
+
+.. image:: http://img.shields.io/badge/powered%20by-AstroPy-orange.svg?style=flat
+    :target: http://www.astropy.org/
+
+.. image:: http://img.shields.io/badge/arXiv-1806.03944-red.svg?style=flat
+    :target: https://arxiv.org/abs/1806.03944
+    :alt: arXiv paper
+
+A Random Forest retrieval algorithm, here used to perform atmospheric retrieval 
+on exoplanet atmospheres.
+
+Legacy API
+++++++++++
+
+If you used HELA previous to the most recent major update and want to recover 
+the old behavior of HELA, visit the `legacy <legacy>`_ directory for a
+legacy branch of the package.  
+
+Citation
+++++++++
+
+If you use HELA in your work, please cite 
+`Marquez-Neila et al. 2018 <https://ui.adsabs.harvard.edu/abs/2018NatAs...2..719M/abstract>`_:
+
+.. code-block::
+
+    @ARTICLE{2018NatAs...2..719M,
+           author = {{M{\'a}rquez-Neila}, Pablo and {Fisher}, Chloe and {Sznitman}, Raphael and
+             {Heng}, Kevin},
+            title = "{Supervised machine learning for analysing spectra of exoplanetary atmospheres}",
+          journal = {Nature Astronomy},
+         keywords = {Astrophysics - Earth and Planetary Astrophysics, Physics - Atmospheric and Oceanic Physics, Physics - Data Analysis, Statistics and Probability},
+             year = "2018",
+            month = "Jun",
+           volume = {2},
+            pages = {719-724},
+              doi = {10.1038/s41550-018-0504-2},
+    archivePrefix = {arXiv},
+           eprint = {1806.03944},
+     primaryClass = {astro-ph.EP},
+           adsurl = {https://ui.adsabs.harvard.edu/abs/2018NatAs...2..719M},
+          adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+    }