How to use the pymc.six.print_ function in pymc

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github pymc-devs / pymc3 / pymc / __init__.py View on Github external
"""

__version__ = '2.2'

try:
    import numpy
except ImportError:
    raise ImportError('NumPy does not seem to be installed. Please see the user guide.')

# Core modules
from .threadpool import *
import os
import pymc
if os.getcwd().find(os.path.abspath(os.path.split(os.path.split(pymc.__file__)[0])[0]))>-1:
    from .six import print_
    print_('\n\tWarning: You are importing PyMC from inside its source tree.')
from .Node import *
from .Container import *
from .PyMCObjects import *
from .InstantiationDecorators import *
from .CommonDeterministics import *
from .NumpyDeterministics import *
from .distributions import *
from .Model import *
from .StepMethods import *
from .MCMC import *
from .NormalApproximation import *



from .tests import test
github pymc-devs / pymc3 / pymc / Model.py View on Github external
cmds = """
        Commands:
          i -- index: print current iteration index
          p -- pause: interrupt sampling and return to the main console.
                      Sampling can be resumed later with icontinue().
          h -- halt:  stop sampling and truncate trace. Sampling cannot be
                      resumed for this chain.
          b -- bg:    return to the main console. The sampling will still
                      run in a background thread. There is a possibility of
                      malfunction if you interfere with the Sampler's
                      state or the database during sampling. Use this at your
                      own risk.
        """

        print_("""==============
 PyMC console
==============

        PyMC is now sampling. Use the following commands to query or pause the sampler.
        """, file=out)
        print_(cmds, file=out)

        prompt = True
        try:
            while self.status in ['running', 'paused']:
                    # sys.stdout.write('pymc> ')
                    if prompt:
                        out.write('pymc > ')
                        out.flush()

                    if self._exc_info is not None:
github pymc-devs / pymc3 / pymc / diagnostics.py View on Github external
quantiles[s.__name__].append(open01(q))
            
            # Replace data values
            for o in sampler.observed_stochastics:
                o.revert()
        
        finally:
            # Replace data values
            for o in sampler.observed_stochastics:
                o.revert()
            
            # Replace backend
            sampler._assign_database_backend(original_backend)
        
        if not i % 10 and i and verbose:
            print_("\tCompleted validation replicate", i)

    
    # Replace backend
    sampler._assign_database_backend(original_backend)
    
    stats = {}
    # Calculate chi-square statistics
    for param in quantiles:
        q = quantiles[param]
        # Calculate chi-square statistics
        X2 = sum(sp.special.ndtri(q)**2)
        # Calculate p-value
        p = sp.special.chdtrc(replicates, X2)
        
        stats[param] = (X2, p)
github pymc-devs / pymc3 / pymc / StepMethods.py View on Github external
elif acc_rate>0.5:
            # increase by ten percent
            self.adaptive_scale_factor *= 1.1
        else:
            tuning = False

        # Re-initialize rejection count
        self.rejected = 0.
        self.accepted = 0.

        # More verbose feedback, if requested
        if verbose > 0:
            if hasattr(self, 'stochastic'):
                print_('\t\tvalue:', self.stochastic.value)
            print_('\t\tacceptance rate:', acc_rate)
            print_('\t\tadaptive scale factor:', self.adaptive_scale_factor)
            print_()

        return tuning
github pymc-devs / pymc3 / pymc / Model.py View on Github external
prompt = True
        try:
            while self.status in ['running', 'paused']:
                    # sys.stdout.write('pymc> ')
                    if prompt:
                        out.write('pymc > ')
                        out.flush()

                    if self._exc_info is not None:
                        a,b,c = self._exc_info
                        reraise(a, b, c)

                    cmd = utils.getInput().strip()
                    if cmd == 'i':
                        print_('Current iteration: %i of %i' % (self._current_iter, self._iter), file=out)
                        prompt = True
                    elif cmd == 'p':
                        self.status = 'paused'
                        break
                    elif cmd == 'h':
                        self.status = 'halt'
                        break
                    elif cmd == 'b':
                        return
                    elif cmd == '\n':
                        prompt = True
                        pass
                    elif cmd == '':
                        prompt = False
                    else:
                        print_('Unknown command: ', cmd, file=out)
github pymc-devs / pymc3 / pymc / MCMC.py View on Github external
#     return

        if self.verbose > 0:
            print_('\tTuning at iteration', self._current_iter)

        # Initialize counter for number of tuning stochastics
        tuning_count = 0

        for step_method in self.step_methods:
            verbose = self.verbose
            if step_method.verbose > -1:
                verbose = step_method.verbose
            # Tune step methods
            tuning_count += step_method.tune(verbose=self.verbose)
            if verbose > 1:
                print_('\t\tTuning step method %s, returned %i\n' %(step_method._id, tuning_count))
                sys.stdout.flush()

        if self._burn_till_tuned:
            if not tuning_count:
                # If no step methods needed tuning, increment count
                self._tuned_count += 1
            else:
                # Otherwise re-initialize count
                self._tuned_count = 0

            # n consecutive clean intervals removed tuning
            # n is equal to self._stop_tuning_after
            if self._tuned_count ==  self._stop_tuning_after:
                if self.verbose > 0: print_('\nFinished tuning')
                self._tuning = False
github pymc-devs / pymc3 / pymc / PyMCObjects.py View on Github external
def get_value(self):
        # Define value attribute
        if self.verbose > 1:
            print_('\t' + self.__name__ + ': value accessed.'    )
        return self._value
github pymc-devs / pymc3 / pymc / Model.py View on Github external
prompt = True
                    elif cmd == 'p':
                        self.status = 'paused'
                        break
                    elif cmd == 'h':
                        self.status = 'halt'
                        break
                    elif cmd == 'b':
                        return
                    elif cmd == '\n':
                        prompt = True
                        pass
                    elif cmd == '':
                        prompt = False
                    else:
                        print_('Unknown command: ', cmd, file=out)
                        print_(cmds, file=out)
                        prompt = True

        except KeyboardInterrupt:
            if not self.status == 'ready':
                self.status = 'halt'


        if self.status == 'ready':
            print_("Sampling terminated successfully.", file=out)
        else:
            print_('Waiting for current iteration to finish...', file=out)
            while self._sampling_thread.isAlive():
                sleep(.1)
            print_('Exiting interactive prompt...', file=out)
            if self.status == 'paused':
github pymc-devs / pymc3 / pymc / distributions.py View on Github external
R"""
    Categorical log-likelihood. The most general discrete distribution.

    .. math::  f(x=i \mid p) = p_i

    for :math:`i \in 0 \ldots k-1`.

    :Parameters:
      - `x` : [int] :math:`x \in 0\ldots k-1`
      - `p` : [float] :math:`p > 0`, :math:`\sum p = 1`

    """

    p = np.atleast_2d(p)
    if np.any(abs(np.sum(p, 1)-1)>0.0001):
        print_("Probabilities in categorical_like sum to", np.sum(p, 1))
    if np.array(x).dtype != int:
        #print_("Non-integer values in categorical_like")
        return -inf
    return flib.categorical(x, p)

pymc

Probabilistic Programming in Python: Bayesian Modeling and Probabilistic Machine Learning with PyTensor

Apache-2.0
Latest version published 17 days ago

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