Updating API docs and some links (#151)

* updating api docs and some links

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.github/workflows/tests.yml

@@ -17,17 +17,11 @@ jobs:
       fail-fast: false
       matrix:
         python-version: ["3.9"]
-        arviz-version: ["arviz"]
-        pymc-version:
-          - "pymc3~=3.11.0"
-          - "https://github.com/pymc-devs/pymc3/archive/master.zip"
-        include:
-          - python-version: "3.9"
-            arviz-version: "arviz<0.11"
-            pymc-version: "pymc3~=3.9.0"
-          - python-version: "3.9"
-            arviz-version: "arviz<0.11"
-            pymc-version: "pymc3~=3.10.0"
+        pymc-arviz:
+          - '"pymc3~=3.9.0" "arviz<0.11"'
+          - '"pymc3~=3.10.0" "arviz<0.11"'
+          - '"pymc3~=3.11.0"'
+          - '"https://github.com/pymc-devs/pymc3/archive/master.zip"'
 
     steps:
       - uses: actions/checkout@v2
@@ -45,7 +39,7 @@ jobs:
         shell: bash -l {0}
         run: |
           python -m pip install -U pip
-          python -m pip install "${{ matrix.pymc-version }}" "${{ matrix.arviz-version }}"
+          python -m pip install ${{ matrix.pymc-arviz }}
           python -m pip install rebound
           python -m pip install "reboundx>=3.2.0"
           python -m pip install -e .[test]

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2018, 2019, 2020 Dan Foreman-Mackey
+Copyright (c) 2018, 2019, 2020, 2021 Dan Foreman-Mackey
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

docs/conf.py

@@ -54,6 +54,7 @@ def markdown2rst(text):
     "astropy",
     "pymc3",
     "theano",
+    "aesara_theano_fallback",
     "tqdm",
     "rebound_pymc3",
 ]
@@ -81,7 +82,7 @@ def markdown2rst(text):
 # General information about the project.
 project = "exoplanet"
 author = "Dan Foreman-Mackey"
-copyright = "2018, 2019, 2020, " + author
+copyright = "2018, 2019, 2020, 2021, " + author
 
 version = __version__
 release = __version__

docs/index.rst

@@ -77,7 +77,7 @@ page <httsp://celerite2.readthedocs.io>`_.
 License & attribution
 ---------------------
 
-Copyright 2018, 2019, 2020 Daniel Foreman-Mackey.
+Copyright 2018, 2019, 2020, 2021 Daniel Foreman-Mackey.
 
 The source code is made available under the terms of the MIT license.
 

docs/tutorials/citation.py

@@ -40,7 +40,7 @@
 # The :func:`exoplanet.citations.get_citations_for_model` function would generate an acknowledgement that cites:
 #
 # * [PyMC3](https://docs.pymc.io/#citing-pymc3): for the inference engine and modeling framework,
-# * [Theano](http://deeplearning.net/software/theano/citation.html): for the numerical infrastructure,
+# * [Theano/Aesara](https://aesara.readthedocs.io/en/latest/citation.html): for the numerical infrastructure,
 # * [AstroPy](http://www.astropy.org/acknowledging.html): for units and constants,
 # * [Kipping (2013)](https://arxiv.org/abs/1308.0009): for the reparameterization of the limb darkening parameters for a quadratic law, and
 # * [Luger, et al. (2018)](https://arxiv.org/abs/1810.06559): for the light curve calculation.

docs/tutorials/intro-to-pymc3.py

@@ -174,16 +174,16 @@
 # While the above example was cute, it doesn't really fully exploit the power of PyMC3 and it doesn't really show some of the real issues that you will face when you use PyMC3 as an astronomer.
 # To get a better sense of how you might use PyMC3 in Real Life™, let's take a look at a more realistic example: fitting a Keplerian orbit to radial velocity observations.
 #
-# One of the key aspects of this problem that I want to highlight is the fact that PyMC3 (and the underlying model building framework [Theano](http://deeplearning.net/software/theano/)) don't have out-of-the-box support for the root-finding that is required to solve Kepler's equation.
+# One of the key aspects of this problem that I want to highlight is the fact that PyMC3 (and the underlying model building framework [Theano (recently renamed to Aesara)](https://aesara.readthedocs.io/)) don't have out-of-the-box support for the root-finding that is required to solve Kepler's equation.
 # As part of the process of computing a Keplerian RV model, we must solve the equation:
 #
 # $$
 # M = E - e\,\sin E
 # $$
 #
 # for the eccentric anomaly $E$ given some mean anomaly $M$ and eccentricity $e$.
-# There are commonly accepted methods of solving this equation using [Newton's method](https://en.wikipedia.org/wiki/Newton%27s_method), but if we want to expose that to PyMC3, we have to define a [custom Theano operation](http://deeplearning.net/software/theano/extending/extending_theano.html) with a custom gradient.
-# I won't go into the details of the math (because [I blogged about it](https://dfm.io/posts/stan-c++/)) and I won't go into the details of the implementation (because [you can take a look at it on GitHub](https://github.com/exoplanet-dev/exoplanet/tree/master/exoplanet/theano_ops/kepler)).
+# There are commonly accepted methods of solving this equation using [Newton's method](https://en.wikipedia.org/wiki/Newton%27s_method), but if we want to expose that to PyMC3, we have to define a [custom Theano operation](https://aesara.readthedocs.io/en/latest/extending/index.html) with a custom gradient.
+# I won't go into the details of the math (because [I blogged about it](https://dfm.io/posts/stan-c++/)) and I won't go into the details of the implementation (because [you can take a look at it on GitHub](https://github.com/exoplanet-dev/exoplanet/tree/main/exoplanet/theano_ops/kepler.py)).
 # So, for this tutorial, we'll use the custom Kepler solver that is implemented as part of *exoplanet* and fit the publicly available radial velocity observations of the famous exoplanetary system 51 Peg using PyMC3.
 #
 # First, we need to download the data from the exoplanet archive:

docs/tutorials/transit.py

@@ -50,7 +50,7 @@
 _ = plt.xlim(t.min(), t.max())
 # -
 
-# But the real power comes from the fact that this is defined as a [Theano operation](http://deeplearning.net/software/theano/extending/extending_theano.html) so it can be combined with PyMC3 to do transit inference using Hamiltonian Monte Carlo.
+# But the real power comes from the fact that this is defined as a [Theano operation](https://aesara.readthedocs.io/en/latest/extending/index.html) so it can be combined with PyMC3 to do transit inference using Hamiltonian Monte Carlo.
 #
 # ## The transit model in PyMC3
 #

docs/user/api.rst

@@ -44,18 +44,11 @@ Estimators
 Distributions
 -------------
 
-.. autofunction:: exoplanet.distributions.get_log_abs_det_jacobian
-.. autofunction:: exoplanet.distributions.estimate_inverse_gamma_parameters
-
-
 Base distributions
 ~~~~~~~~~~~~~~~~~~
 
-.. autoclass:: exoplanet.distributions.UnitUniform
-.. autoclass:: exoplanet.distributions.UnitVector
-.. autoclass:: exoplanet.distributions.UnitDisk
-.. autoclass:: exoplanet.distributions.Angle
-.. autoclass:: exoplanet.distributions.Periodic
+These distributions have been moved to the `pymc3-ext project
+<https://github.com/exoplanet-dev/pymc3-ext>`_.
 
 Physical distributions
 ~~~~~~~~~~~~~~~~~~~~~~
@@ -70,28 +63,13 @@ Eccentricity distributions
 .. autofunction:: exoplanet.distributions.eccentricity.vaneylen19
 
 
-Utilities
----------
-
-.. autofunction:: exoplanet.optimize
-.. autofunction:: exoplanet.eval_in_model
-.. autofunction:: exoplanet.get_theano_function_for_var
-.. autofunction:: exoplanet.get_args_for_theano_function
-.. autofunction:: exoplanet.get_samples_from_trace
-.. autofunction:: exoplanet.get_dense_nuts_step
+Miscellaneous
+-------------
 
 .. autofunction:: exoplanet.orbits.ttv.compute_expected_transit_times
 
-
-Units
------
-
 .. autofunction:: exoplanet.units.with_unit
 .. autofunction:: exoplanet.units.has_unit
 .. autofunction:: exoplanet.units.to_unit
 
-
-Citations
----------
-
 .. autofunction:: exoplanet.citations.get_citations_for_model

docs/user/dev.rst

@@ -37,7 +37,7 @@ local machine:
 
 .. code-block:: bash
 
-    git clone https://github.com/YOURUSERNAME/exoplanet.git
+    git clone --recursive https://github.com/YOURUSERNAME/exoplanet.git
     cd exoplanet
     git checkout -b BRANCHNAME
 
@@ -47,36 +47,15 @@ Then you should set up an isolated environment for development using a `Conda
 environment
 <https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html>`_,
 `virtualenv <https://virtualenv.pypa.io/>`_, `venv
-<https://docs.python.org/3/library/venv.html>`_, or similar. If using ``conda``,
-you can get the current development environment from the ``environment.yml``
-file:
-
-.. code-block:: bash
-
-    conda env create --prefix env -f environment.yml
-    conda activate ./env
-
-If you have an existing ``conda`` environment for ``exoplanet``, you can update
-it using:
-
-.. code-block:: bash
-
-    conda env update --prefix ./env -f environment.yml  --prune
+<https://docs.python.org/3/library/venv.html>`_, or similar.
 
 If you're using a ``pip`` based environment, you can install the developer
 dependencies as follows:
 
 .. code-block:: bash
 
     python -m pip install -U pip
-    python -m pip install -U .[dev]
-
-After your environment is set up, you can install the current development
-version of ``exoplanet``:
-
-.. code-block:: bash
-
-    python -m pip install -e .
+    python -m pip install -U -e ".[dev]"
 
 
 Finding your way around the codebase
@@ -105,25 +84,11 @@ computational run time. These can be found in the `case studies
 <https://github.com/exoplanet-dev/case-studies>`_ repo and there is more
 information there about how to contribute.
 
-3. **Theano ops**: ``exoplanet`` comes bundled with a set of custom Theano ops
+3. **Theano/Aesara ops**: ``exoplanet`` comes bundled with a set of custom ops
 that are implemented in ``src/exoplanet/theano_ops``. As a user, you'll rarely
 interact with these directly and we haven't put a lot of work into making them
-user friendly, but if you are interested in diving in, here are some tips.
-First, you should check out the Theano docs that describe how to develop new ops
-in `Python
-<http://deeplearning.net/software/theano/extending/extending_theano.html>`_ and
-`C/C++
-<http://deeplearning.net/software/theano/extending/extending_theano_c.html>`_.
-Most of the ``exoplanet`` ops are implemented in C++ for speed and we've made
-the design decision to separate the "science" code (which implements the actual
-operation without any dependency on Theano) and "wrapper" code (which sets up
-the interface). The science code is implemented as a header-only C++ library in
-``src/exoplanet/theano_ops/lib/include/exoplanet`` and then, in most cases,
-these functions are accessed via the `pybind11
-<https://github.com/pybind/pybind11>`_ interface implemented in
-``src/exoplanet/theano_ops/driver.cpp``. Then the wrappers are implemented as
-submodules in ``src/exoplanet/theano_ops``. A good place to start is the
-``KeplerOp`` implemented in ``src/exoplanet/theano_ops/kepler.py``.
+user friendly, but if you are interested in diving in, feel free to ask
+questions on GitHub or via email.
 
 
 Testing your contribution
@@ -137,45 +102,3 @@ request using the following command:
 .. code-block:: bash
 
     python -m pytest -v tests
-
-
-Code style
-----------
-
-We have a pretty strict (but easy to implement!) set of style guidelines for the
-codebase. For Python code, we use `isort
-<https://github.com/timothycrosley/isort>`_ and `black
-<https://github.com/psf/black>`_. The custom settings for these projects can be
-found in ``pyproject.toml``. Before opening a pull request, you can run the
-formatters as follows:
-
-.. code-block:: bash
-
-    isort -rc src
-    black src
-
-Or, you can use `pre-commit <https://pre-commit.com>`_ to automatically apply the formatting whenever you commit:
-
-.. code-block:: bash
-
-    python -m pip install -U pre-commit
-    pre-commit install
-
-
-Release management
-------------------
-
-.. note:: Most of this build process is based on the October 2019 update to
-`this blog post
-<https://hynek.me/articles/sharing-your-labor-of-love-pypi-quick-and-dirty/>`_
-so you should check that out if you want more info.
-
-This section is mainly internal, but these are the steps that should be executed to produce a new release.
-
-1. Update citation date and version in ``src/exoplanet/citations.py``.
-
-2. Update changelog date in ``HISTORY.rst``.
-
-3. Tag a GitHub release on both the `exoplanet repository
-<https://github.com/exoplanet-dev/exoplanet>`_ and the `case studies repository
-<https://github.com/exoplanet-dev/case-studies>`_

docs/user/install.rst

@@ -52,16 +52,15 @@ Note: if you clone the repo without the ``--recursive`` flag, you will need to r
 Notes about running on Windows
 ------------------------------
 
-Running exoplanet on Windows can be a little tricky because of the dependence on Theano and runtime compilation,
-but it is currently tested on Windows with Python 3.7 and 3.8.
-The following (based on the tips from `the Theano docs <http://deeplearning.net/software/theano_versions/dev/install_windows.html>`_) seem to work:
+Running exoplanet on Windows can be a little tricky because of the dependence on
+runtime compilation, but it has been used on Windows successfully. The following
+conda installation steps seem to work:
 
 .. code-block:: bash
 
-    conda create --name exoplanetTest python=3.8 pip
-    conda install --name exoplanetTest numpy scipy mkl-service libpython m2w64-toolchain astropy matplotlib theano
-    conda install --name exoplanetTest -c conda-forge pybind11 celerite
-    python -m pip install -e .[test]
+    conda create --name exoplanetTest python pip
+    conda install --name exoplanetTest numpy scipy mkl-service libpython m2w64-toolchain astropy
+    python -m pip install -e ".[test]"
 
 
 Testing
@@ -71,7 +70,7 @@ To run the unit tests, install the development dependencies using pip:
 
 .. code-block:: bash
 
-    python -m pip install .[test]
+    python -m pip install ".[test]"
 
 and then execute: