Remove Text, SQLite and HDF5 backends

.gitignore

@@ -21,9 +21,6 @@ _build
 # Merge tool
 *.orig
 
-# Test artifacts
-mcmc.sqlite
-
 # Docker development
 # notebooks/
 
@@ -41,3 +38,6 @@ benchmarks/results/
 pytestdebug.log
 .dir-locals.el
 .pycheckers
+
+# Codespaces
+pythonenv*

RELEASE-NOTES.md

@@ -3,6 +3,7 @@
 ## PyMC3 3.9.x (on deck)
 
 ### Maintenance
+- Removed non-NDArray (Text, SQLite, HDF5) backends and associated tests.
 - Switch the dependency of Theano to our own fork, [Theano-PyMC](https://github.com/pymc-devs/Theano-PyMC).
 - Mentioned the way to do any random walk with `theano.tensor.cumsum()` in `GaussianRandomWalk` docstrings (see [#4048](https://github.com/pymc-devs/pymc3/pull/4048)).
 - Fixed numerical instability in ExGaussian's logp by preventing `logpow` from returning `-inf` (see [#4050](https://github.com/pymc-devs/pymc3/pull/4050)).

docs/source/api/backends.rst

@@ -15,22 +15,6 @@ ndarray
 .. automodule:: pymc3.backends.ndarray
    :members:
 
-sqlite
-^^^^^^
-
-.. currentmodule:: pymc3.backends.sqlite
-
-.. automodule:: pymc3.backends.sqlite
-   :members:
-
-text
-^^^^
-
-.. currentmodule:: pymc3.backends.text
-
-.. automodule:: pymc3.backends.text
-   :members:
-
 tracetab
 ^^^^^^^^
 

pymc3/__init__.py

@@ -67,7 +67,7 @@ def __set_compiler_flags():
 from . import sampling
 
 from .backends.tracetab import *
-from .backends import save_trace, load_trace, point_list_to_multitrace
+from .backends import save_trace, load_trace
 
 from .plots import *
 from .tests import test

pymc3/backends/__init__.py

@@ -12,34 +12,9 @@
 #   See the License for the specific language governing permissions and
 #   limitations under the License.
 
-"""Backends for traces
+"""Storage backends for traces
 
-Available backends
-------------------
-
-1. NumPy array (pymc3.backends.NDArray)
-2. Text files (pymc3.backends.Text)
-3. SQLite (pymc3.backends.SQLite)
-
-The NDArray backend holds the entire trace in memory, whereas the Text
-and SQLite backends store the values while sampling.
-
-Selecting a backend
--------------------
-
-By default, a NumPy array is used as the backend. To specify a different
-backend, pass a backend instance to `sample`.
-
-For example, the following would save the sampling values to CSV files
-in the directory 'test'.
-
-    >>> import pymc3 as pm
-    >>> with pm.Model():
-    >>>      db = pm.backends.Text('test')
-    >>>      trace = pm.sample(..., trace=db)
-
-Note that as in the example above, one must have an active model context,
-or pass a `model` parameter in order to create a backend.
+The NDArray (pymc3.backends.NDArray) backend holds the entire trace in memory.
 
 Selecting values from a backend
 -------------------------------
@@ -77,67 +52,12 @@
     >>> sliced_trace = trace[1000:]
 
 The backend for the new trace is always NDArray, regardless of the
-type of original trace.  Only the NDArray backend supports a stop
-value in the slice.
+type of original trace. 
 
 Loading a saved backend
 -----------------------
 
-Saved backends can be loaded using `load` function in the module for the
-specific backend.
-
-    >>> trace = pm.backends.text.load('test')
-
-Writing custom backends
------------------------
-
-Backends consist of a class that handles sampling storage and value
-selection. Three sampling methods of backend will be called:
-
-- setup: Before sampling is started, the `setup` method will be called
-  with two arguments: the number of draws and the chain number. This is
-  useful setting up any structure for storing the sampling values that
-  require the above information.
-
-- record: Record the sampling results for the current draw. This method
-  will be called with a dictionary of values mapped to the variable
-  names. This is the only sampling function that *must* do something to
-  have a meaningful backend.
-
-- close: This method is called following sampling and should perform any
-  actions necessary for finalizing and cleaning up the backend.
-
-The base storage class `backends.base.BaseTrace` provides common model
-setup that is used by all the PyMC backends.
-
-Several selection methods must also be defined:
-
-- get_values: This is the core method for selecting values from the
-  backend. It can be called directly and is used by __getitem__ when the
-  backend is indexed with a variable name or object.
-
-- _slice: Defines how the backend returns a slice of itself. This
-  is called if the backend is indexed with a slice range.
-
-- point: Returns values for each variable at a single iteration. This is
-  called if the backend is indexed with a single integer.
-
-- __len__: This should return the number of draws.
-
-When `pymc3.sample` finishes, it wraps all trace objects in a MultiTrace
-object that provides a consistent selection interface for all backends.
-If the traces are stored on disk, then a `load` function should also be
-defined that returns a MultiTrace object.
+Saved backends can be loaded using `arviz.from_netcdf`
 
-For specific examples, see pymc3.backends.{ndarray,text,sqlite}.py.
 """
 from ..backends.ndarray import NDArray, save_trace, load_trace, point_list_to_multitrace
-from ..backends.text import Text
-from ..backends.sqlite import SQLite
-from ..backends.hdf5 import HDF5
-
-_shortcuts = {
-    "text": {"backend": Text, "name": "mcmc"},
-    "sqlite": {"backend": SQLite, "name": "mcmc.sqlite"},
-    "hdf5": {"backend": HDF5, "name": "mcmc.hdf5"},
-}

pymc3/backends/base.py

@@ -14,8 +14,7 @@
 
 """Base backend for traces
 
-See the docstring for pymc3.backends for more information (including
-creating custom backends).
+See the docstring for pymc3.backends for more information
 """
 import itertools as itl
 import logging