Merge branch 'doc' into 'master'

add documentation

Closes #91

See merge request qt/adaptive!120

Author: basnijholt

README.md

@@ -0,0 +1,155 @@
+.. summary-start
+
+.. _logo-adaptive:
+
+|image0| adaptive
+=================
+
+|PyPI| |Conda| |Downloads| |pipeline status| |DOI| |Binder| |Join the
+chat at https://gitter.im/python-adaptive/adaptive|
+
+**Tools for adaptive parallel sampling of mathematical functions.**
+
+``adaptive`` is an open-source Python library designed to
+make adaptive parallel function evaluation simple. With ``adaptive`` you
+just supply a function with its bounds, and it will be evaluated at the
+“best” points in parameter space. With just a few lines of code you can
+evaluate functions on a computing cluster, live-plot the data as it
+returns, and fine-tune the adaptive sampling algorithm.
+
+Check out the ``adaptive`` example notebook
+`learner.ipynb <https://github.com/python-adaptive/adaptive/blob/master/learner.ipynb>`_ (or run it `live on
+Binder <https://mybinder.org/v2/gh/python-adaptive/adaptive/master?filepath=learner.ipynb>`_)
+to see examples of how to use ``adaptive``.
+
+.. summary-end
+
+**WARNING: adaptive is still in a beta development stage**
+
+.. implemented-algorithms-start
+
+Implemented algorithms
+----------------------
+
+The core concept in ``adaptive`` is that of a *learner*. A *learner*
+samples a function at the best places in its parameter space to get
+maximum “information” about the function. As it evaluates the function
+at more and more points in the parameter space, it gets a better idea of
+where the best places are to sample next.
+
+Of course, what qualifies as the “best places” will depend on your
+application domain! ``adaptive`` makes some reasonable default choices,
+but the details of the adaptive sampling are completely customizable.
+
+The following learners are implemented:
+
+- ``Learner1D``, for 1D functions ``f: ℝ → ℝ^N``,
+- ``Learner2D``, for 2D functions ``f: ℝ^2 → ℝ^N``,
+- ``LearnerND``, for ND functions ``f: ℝ^N → ℝ^M``,
+- ``AverageLearner``, For stochastic functions where you want to
+  average the result over many evaluations,
+- ``IntegratorLearner``, for
+  when you want to intergrate a 1D function ``f: ℝ → ℝ``,
+- ``BalancingLearner``, for when you want to run several learners at once,
+  selecting the “best” one each time you get more points.
+
+In addition to the learners, ``adaptive`` also provides primitives for
+running the sampling across several cores and even several machines,
+with built-in support for
+`concurrent.futures <https://docs.python.org/3/library/concurrent.futures.html>`_,
+`ipyparallel <https://ipyparallel.readthedocs.io/en/latest/>`_ and
+`distributed <https://distributed.readthedocs.io/en/latest/>`_.
+
+.. implemented-algorithms-end
+
+Examples
+--------
+
+.. raw:: html
+
+  <img src="https://user-images.githubusercontent.com/6897215/38739170-6ac7c014-3f34-11e8-9e8f-93b3a3a3d61b.gif" width='20%'> </img> <img src="https://user-images.githubusercontent.com/6897215/35219611-ac8b2122-ff73-11e7-9332-adffab64a8ce.gif" width='40%'> </img>
+
+
+Installation
+------------
+
+``adaptive`` works with Python 3.6 and higher on Linux, Windows, or Mac,
+and provides optional extensions for working with the Jupyter/IPython
+Notebook.
+
+The recommended way to install adaptive is using ``conda``:
+
+.. code:: bash
+
+    conda install -c conda-forge adaptive
+
+``adaptive`` is also available on PyPI:
+
+.. code:: bash
+
+    pip install adaptive[notebook]
+
+The ``[notebook]`` above will also install the optional dependencies for
+running ``adaptive`` inside a Jupyter notebook.
+
+Development
+-----------
+
+Clone the repository and run ``setup.py develop`` to add a link to the
+cloned repo into your Python path:
+
+.. code:: bash
+
+    git clone git@github.com:python-adaptive/adaptive.git
+    cd adaptive
+    python3 setup.py develop
+
+We highly recommend using a Conda environment or a virtualenv to manage
+the versions of your installed packages while working on ``adaptive``.
+
+In order to not pollute the history with the output of the notebooks,
+please setup the git filter by executing
+
+.. code:: bash
+
+    python ipynb_filter.py
+
+in the repository.
+
+Credits
+-------
+
+We would like to give credits to the following people:
+
+- Pedro Gonnet for his implementation of `CQUAD <https://www.gnu.org/software/gsl/manual/html_node/CQUAD-doubly_002dadaptive-integration.html>`_,
+  “Algorithm 4” as described in “Increasing the Reliability of Adaptive
+  Quadrature Using Explicit Interpolants”, P. Gonnet, ACM Transactions on
+  Mathematical Software, 37 (3), art. no. 26, 2010.
+- Pauli Virtanen for his ``AdaptiveTriSampling`` script (no longer
+  available online since SciPy Central went down) which served as
+  inspiration for the ``~adaptive.Learner2D``.
+
+For general discussion, we have a `Gitter chat
+channel <https://gitter.im/python-adaptive/adaptive>`_. If you find any
+bugs or have any feature suggestions please file a GitLab
+`issue <https://gitlab.kwant-project.org/qt/adaptive/issues/new?issue>`_
+or submit a `merge
+request <https://gitlab.kwant-project.org/qt/adaptive/merge_requests>`_.
+
+.. references-start
+.. |image0| image:: https://gitlab.kwant-project.org/qt/adaptive/uploads/d20444093920a4a0499e165b5061d952/logo.png
+.. |PyPI| image:: https://img.shields.io/pypi/v/adaptive.svg
+   :target: https://pypi.python.org/pypi/adaptive
+.. |Conda| image:: https://anaconda.org/conda-forge/adaptive/badges/installer/conda.svg
+   :target: https://anaconda.org/conda-forge/adaptive
+.. |Downloads| image:: https://anaconda.org/conda-forge/adaptive/badges/downloads.svg
+   :target: https://anaconda.org/conda-forge/adaptive
+.. |pipeline status| image:: https://gitlab.kwant-project.org/qt/adaptive/badges/master/pipeline.svg
+   :target: https://gitlab.kwant-project.org/qt/adaptive/pipelines
+.. |DOI| image:: https://zenodo.org/badge/113714660.svg
+   :target: https://zenodo.org/badge/latestdoi/113714660
+.. |Binder| image:: https://mybinder.org/badge.svg
+   :target: https://mybinder.org/v2/gh/python-adaptive/adaptive/master?filepath=learner.ipynb
+.. |Join the chat at https://gitter.im/python-adaptive/adaptive| image:: https://img.shields.io/gitter/room/nwjs/nw.js.svg
+   :target: https://gitter.im/python-adaptive/adaptive
+.. references-end

README.rst

@@ -8,15 +8,15 @@
 from . import runner
 from . import utils
 
-from .learner import (Learner1D, Learner2D, LearnerND, AverageLearner,
-                      BalancingLearner, make_datasaver, DataSaver,
-                      IntegratorLearner)
+from .learner import (BaseLearner, Learner1D, Learner2D, LearnerND,
+                      AverageLearner, BalancingLearner, make_datasaver,
+                      DataSaver, IntegratorLearner)
 
 with suppress(ImportError):
     # Only available if 'scikit-optimize' is installed
     from .learner import SKOptLearner
 
-from .runner import Runner, BlockingRunner
+from .runner import Runner, AsyncRunner, BlockingRunner
 
 from ._version import __version__
 del _version

adaptive/__init__.py

@@ -17,9 +17,9 @@ class AverageLearner(BaseLearner):
     Parameters
     ----------
     atol : float
-        Desired absolute tolerance
+        Desired absolute tolerance.
     rtol : float
-        Desired relative tolerance
+        Desired relative tolerance.
 
     Attributes
     ----------

adaptive/learner/average_learner.py

@@ -21,27 +21,32 @@ class BalancingLearner(BaseLearner):
 
     Parameters
     ----------
-    learners : sequence of BaseLearner
+    learners : sequence of `BaseLearner`
         The learners from which to choose. These must all have the same type.
     cdims : sequence of dicts, or (keys, iterable of values), optional
         Constant dimensions; the parameters that label the learners. Used
         in `plot`.
         Example inputs that all give identical results:
+
         - sequence of dicts:
+
             >>> cdims = [{'A': True, 'B': 0},
             ...          {'A': True, 'B': 1},
             ...          {'A': False, 'B': 0},
             ...          {'A': False, 'B': 1}]`
+
         - tuple with (keys, iterable of values):
+
             >>> cdims = (['A', 'B'], itertools.product([True, False], [0, 1]))
             >>> cdims = (['A', 'B'], [(True, 0), (True, 1),
             ...                       (False, 0), (False, 1)])
+
     strategy : 'loss_improvements' (default), 'loss', or 'npoints'
-        The points that the 'BalancingLearner' choses can be either based on:
+        The points that the `BalancingLearner` choses can be either based on:
         the best 'loss_improvements', the smallest total 'loss' of the
         child learners, or the number of points per learner, using 'npoints'.
         One can dynamically change the strategy while the simulation is
-        running by changing the 'learner.strategy' attribute.
+        running by changing the ``learner.strategy`` attribute.
 
     Notes
     -----
@@ -50,7 +55,7 @@ class BalancingLearner(BaseLearner):
     compared*. For the moment we enforce this restriction by requiring that
     all learners are the same type but (depending on the internals of the
     learner) it may be that the loss cannot be compared *even between learners
-    of the same type*. In this case the BalancingLearner will behave in an
+    of the same type*. In this case the `BalancingLearner` will behave in an
     undefined way.
     """
 
@@ -183,28 +188,34 @@ def plot(self, cdims=None, plotter=None, dynamic=True):
         cdims : sequence of dicts, or (keys, iterable of values), optional
             Constant dimensions; the parameters that label the learners.
             Example inputs that all give identical results:
+
             - sequence of dicts:
+
                 >>> cdims = [{'A': True, 'B': 0},
                 ...          {'A': True, 'B': 1},
                 ...          {'A': False, 'B': 0},
                 ...          {'A': False, 'B': 1}]`
+
             - tuple with (keys, iterable of values):
+
                 >>> cdims = (['A', 'B'], itertools.product([True, False], [0, 1]))
                 >>> cdims = (['A', 'B'], [(True, 0), (True, 1),
                 ...                       (False, 0), (False, 1)])
+
         plotter : callable, optional
             A function that takes the learner as a argument and returns a
-            holoviews object. By default learner.plot() will be called.
+            holoviews object. By default ``learner.plot()`` will be called.
         dynamic : bool, default True
-            Return a holoviews.DynamicMap if True, else a holoviews.HoloMap.
-            The DynamicMap is rendered as the sliders change and can therefore
-            not be exported to html. The HoloMap does not have this problem.
+            Return a `holoviews.core.DynamicMap` if True, else a
+            `holoviews.core.HoloMap`. The `~holoviews.core.DynamicMap` is
+            rendered as the sliders change and can therefore not be exported
+            to html. The `~holoviews.core.HoloMap` does not have this problem.
 
         Returns
         -------
-        dm : holoviews.DynamicMap object (default) or holoviews.HoloMap object
-            A DynamicMap (dynamic=True) or HoloMap (dynamic=False) with
-            sliders that are defined by 'cdims'.
+        dm : `holoviews.core.DynamicMap` (default) or `holoviews.core.HoloMap`
+            A `DynamicMap` (dynamic=True) or `HoloMap` (dynamic=False) with
+            sliders that are defined by `cdims`.
         """
         hv = ensure_holoviews()
         cdims = cdims or self._cdims_default
@@ -248,13 +259,13 @@ def remove_unfinished(self):
     def from_product(cls, f, learner_type, learner_kwargs, combos):
         """Create a `BalancingLearner` with learners of all combinations of
         named variables’ values. The `cdims` will be set correctly, so calling
-        `learner.plot` will be a `holoviews.HoloMap` with the correct labels.
+        `learner.plot` will be a `holoviews.core.HoloMap` with the correct labels.
 
         Parameters
         ----------
         f : callable
             Function to learn, must take arguments provided in in `combos`.
-        learner_type : BaseLearner
+        learner_type : `BaseLearner`
             The learner that should wrap the function. For example `Learner1D`.
         learner_kwargs : dict
             Keyword argument for the `learner_type`. For example `dict(bounds=[0, 1])`.