Merge branch 'master' of https://github.com/pymc-devs/pymc3

Author: springcoil

.travis.yml

@@ -2,7 +2,7 @@ language: python
 
 python:
   - "2.7"
-  - "3.4"
+  - "3.5"
 
 before_install:
   - . ./scripts/install_miniconda.sh

README.rst

@@ -13,9 +13,6 @@ large suite of problems.
 Check out the `getting started
 guide <http://pymc-devs.github.io/pymc3/notebooks/getting_started.html>`__!
 
-PyMC3 is beta software. Users should consider using `PyMC 2
-repository <https://github.com/pymc-devs/pymc>`__.
-
 Features
 --------
 
@@ -60,8 +57,16 @@ Getting started
 Installation
 ------------
 
-The latest version of PyMC3 can be installed from the master branch
-using pip:
+The latest release of PyMC3 can be installed from PyPI using ``pip``:
+
+::
+
+    pip install pymc3
+
+**Note:** Running ``pip install pymc`` will install PyMC 2.3, not PyMC3,
+from PyPI.
+
+The current development branch of PyMC3 can be installed from GitHub, also using ``pip``:
 
 ::
 
@@ -83,13 +88,11 @@ your system, you can install PyMC3 directly from GitHub.
 Another option is to clone the repository and install PyMC3 using
 ``python setup.py install`` or ``python setup.py develop``.
 
-**Note:** Running ``pip install pymc`` will install PyMC 2.3, not PyMC3,
-from PyPI.
 
 Dependencies
 ------------
 
-PyMC3 is tested on Python 2.7 and 3.3 and depends on Theano, NumPy,
+PyMC3 is tested on Python 2.7 and 3.4 and depends on Theano, NumPy,
 SciPy, Pandas, and Matplotlib (see ``requirements.txt`` for version
 information).
 
@@ -119,6 +122,7 @@ scikits-sparse:
     ln -s /usr/local/Cellar/suite-sparse/4.2.1/include/ /usr/local/include/suitesparse
     pip install git+https://github.com/njsmith/scikits-sparse.git
 
+
 Citing PyMC3
 ------------
 
@@ -136,6 +140,7 @@ License
 `Apache License, Version
 2.0 <https://github.com/pymc-devs/pymc3/blob/master/LICENSE>`__
 
+
 Contributors
 ------------
 

docs/source/conf.py

@@ -72,7 +72,7 @@
 # The short X.Y version.
 version = '3.0'
 # The full version, including alpha/beta/rc tags.
-release = '3.0'
+release = '3.0.rc1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

pymc3/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "3.0"
+__version__ = "3.0.rc1"
 
 from .blocking import *
 from .distributions import *

pymc3/backends/base.py

@@ -24,6 +24,7 @@ class BaseTrace(object):
         Sampling values will be stored for these variables. If None,
         `model.unobserved_RVs` is used.
     """
+
     def __init__(self, name, model=None, vars=None):
         self.name = name
 
@@ -35,17 +36,16 @@ def __init__(self, name, model=None, vars=None):
         self.varnames = [var.name for var in vars]
         self.fn = model.fastfn(vars)
 
-
-        ## Get variable shapes. Most backends will need this
-        ## information.
+        # Get variable shapes. Most backends will need this
+        # information.
         var_values = list(zip(self.varnames, self.fn(model.test_point)))
         self.var_shapes = {var: value.shape
                            for var, value in var_values}
         self.var_dtypes = {var: value.dtype
                            for var, value in var_values}
         self.chain = None
 
-    ## Sampling methods
+    # Sampling methods
 
     def setup(self, draws, chain):
         """Perform chain-specific setup.
@@ -76,7 +76,7 @@ def close(self):
         """
         pass
 
-    ## Selection methods
+    # Selection methods
 
     def __getitem__(self, idx):
         if isinstance(idx, slice):
@@ -149,6 +149,7 @@ class MultiTrace(object):
     of the MultiTrace instance, which returns the number of draws), the
     trace with the highest chain number is always used.
     """
+
     def __init__(self, straces):
         self._straces = {}
         for strace in straces:

pymc3/backends/ndarray.py

@@ -19,13 +19,14 @@ class NDArray(base.BaseTrace):
         Sampling values will be stored for these variables. If None,
         `model.unobserved_RVs` is used.
     """
+
     def __init__(self, name=None, model=None, vars=None):
         super(NDArray, self).__init__(name, model, vars)
         self.draw_idx = 0
         self.draws = None
         self.samples = {}
 
-    ## Sampling methods
+    # Sampling methods
 
     def setup(self, draws, chain):
         """Perform chain-specific setup.
@@ -70,12 +71,12 @@ def record(self, point):
     def close(self):
         if self.draw_idx == self.draws:
             return
-        ## Remove trailing zeros if interrupted before completed all
-        ## draws.
+        # Remove trailing zeros if interrupted before completed all
+        # draws.
         self.samples = {var: vtrace[:self.draw_idx]
                         for var, vtrace in self.samples.items()}
 
-    ## Selection methods
+    # Selection methods
 
     def __len__(self):
         if not self.samples:  # `setup` has not been called.

pymc3/backends/sqlite.py

@@ -34,8 +34,8 @@
                          'WHERE chain = ?'),
     'draw_count':       ('SELECT COUNT(*) FROM [{table}] '
                          'WHERE chain = ?'),
-    ## Named placeholders are used in the selection templates because
-    ## some values occur more than once in the same template.
+    # Named placeholders are used in the selection templates because
+    # some values occur more than once in the same template.
     'select':           ('SELECT * FROM [{table}] '
                          'WHERE (chain = :chain)'),
     'select_burn':      ('SELECT * FROM [{table}] '
@@ -71,6 +71,7 @@ class SQLite(base.BaseTrace):
         Sampling values will be stored for these variables. If None,
         `model.unobserved_RVs` is used.
     """
+
     def __init__(self, name, model=None, vars=None):
         super(SQLite, self).__init__(name, model, vars)
         self._var_cols = {}
@@ -80,13 +81,13 @@ def __init__(self, name, model=None, vars=None):
         self._len = None
 
         self.db = _SQLiteDB(name)
-        ## Inserting sampling information is queued to avoid locks
-        ## caused by hitting the database with transactions each
-        ## iteration.
+        # Inserting sampling information is queued to avoid locks
+        # caused by hitting the database with transactions each
+        # iteration.
         self._queue = {varname: [] for varname in self.varnames}
         self._queue_limit = 5000
 
-    ## Sampling methods
+    # Sampling methods
 
     def setup(self, draws, chain):
         """Perform chain-specific setup.
@@ -127,7 +128,7 @@ def _create_table(self):
     def _create_insert_queries(self, chain):
         template = TEMPLATES['insert']
         for varname, var_cols in self._var_cols.items():
-            ## Create insert statement for each variable.
+            # Create insert statement for each variable.
             var_str = ', '.join(var_cols)
             placeholders = ', '.join(['?'] * len(var_cols))
             statement = template.format(table=varname,
@@ -164,7 +165,7 @@ def close(self):
         self._execute_queue()
         self.db.close()
 
-    ## Selection methods
+    # Selection methods
 
     def __len__(self):
         if not self._is_setup:
@@ -252,6 +253,7 @@ def point(self, idx):
 
 
 class _SQLiteDB(object):
+
     def __init__(self, name):
         self.name = name
         self.con = None
@@ -306,8 +308,8 @@ def load(name, model=None):
 
 def _get_table_list(cursor):
     """Return a list of table names in the current database."""
-    ## Modified from Django. Skips the sqlite_sequence system table used
-    ## for autoincrement key generation.
+    # Modified from Django. Skips the sqlite_sequence system table used
+    # for autoincrement key generation.
     cursor.execute("SELECT name FROM sqlite_master "
                    "WHERE type='table' AND NOT name='sqlite_sequence' "
                    "ORDER BY name")

pymc3/backends/text.py

@@ -37,6 +37,7 @@ class Text(base.BaseTrace):
         Sampling values will be stored for these variables. If None,
         `model.unobserved_RVs` is used.
     """
+
     def __init__(self, name, model=None, vars=None):
         if not os.path.exists(name):
             os.mkdir(name)
@@ -49,7 +50,7 @@ def __init__(self, name, model=None, vars=None):
         self._fh = None
         self.df = None
 
-    ## Sampling methods
+    # Sampling methods
 
     def setup(self, draws, chain):
         """Perform chain-specific setup.
@@ -96,7 +97,7 @@ def close(self):
         self._fh.close()
         self._fh = None  # Avoid serialization issue.
 
-    ## Selection methods
+    # Selection methods
 
     def _load_df(self):
         if self.df is None:
@@ -194,5 +195,6 @@ def dump(name, trace, chains=None):
 
     for chain in chains:
         filename = os.path.join(name, 'chain-{}.csv'.format(chain))
-        df = ttab.trace_to_dataframe(trace, chains=chain, flat_names=flat_names)
+        df = ttab.trace_to_dataframe(
+            trace, chains=chain, flat_names=flat_names)
         df.to_csv(filename, index=False)

pymc3/blocking.py

@@ -17,6 +17,7 @@ class ArrayOrdering(object):
     """
     An ordering for an array space
     """
+
     def __init__(self, vars):
         self.vmap = []
         dim = 0
@@ -33,6 +34,7 @@ class DictToArrayBijection(object):
     """
     A mapping between a dict space and an array space
     """
+
     def __init__(self, ordering, dpoint):
         self.ordering = ordering
         self.dpt = dpoint
@@ -85,6 +87,7 @@ class DictToVarBijection(object):
     """
     A mapping between a dict space and the array space for one element within the dict space
     """
+
     def __init__(self, var, idx, dpoint):
         self.var = str(var)
         self.idx = idx
@@ -111,6 +114,7 @@ class Compose(object):
     """
     Compose two functions in a pickleable way
     """
+
     def __init__(self, fa, fb):
         self.fa = fa
         self.fb = fb

pymc3/data.py

@@ -3,9 +3,10 @@
 
 __all__ = ['get_data_file']
 
+
 def get_data_file(pkg, path):
     """Returns a file object for a package data file.
-    
+
     Parameters
     ----------
     pkg : str
@@ -18,4 +19,3 @@ def get_data_file(pkg, path):
     """
 
     return io.BytesIO(pkgutil.get_data(pkg, path))
-