phasegen 0.0.3b0__tar.gz

phasegen-0.0.3b0/PKG-INFO

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+Metadata-Version: 2.1
+Name: phasegen
+Version: 0.0.3b0
+Summary: Simulation and inference on exact solutions of coalescent distributions under diverse demographic scenarios.
+License: MIT
+Author: Sendrowski
+Author-email: sendrowski.janek@gmail.com
+Requires-Python: >=3.10,<3.13
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Dist: fastdfe (>=1.1.3)
+Requires-Dist: jsonpickle (>=3.0.0,<4.0.0)
+Requires-Dist: matplotlib (>=3.7.0,<4.0.0)
+Requires-Dist: multiprocess (>=0.70.12,<0.71.0)
+Requires-Dist: numpy (>=1.24.0,<2.0.0)
+Requires-Dist: pandas (>=2.0.0,<3.0.0)
+Requires-Dist: pyyaml (>=6.0,<7.0)
+Requires-Dist: scipy (>=1.10.1,<2.0.0)
+Requires-Dist: seaborn (>=0.13.0,<0.14.0)
+Requires-Dist: tqdm (>=4.60.0,<5.0.0)
+Requires-Dist: typing-extensions (>=4.5.0,<5.0.0)
+Description-Content-Type: text/markdown
+
+# PhaseGen  <img align="right" width="100" src="https://raw.githubusercontent.com/Sendrowski/PhaseGen/master/docs/logo.png">
+
+[![Documentation Status](https://readthedocs.org/projects/phasegen/badge/?version=latest)](https://phasegen.readthedocs.io/en/latest/?badge=latest)
+[![PyPI version](https://badge.fury.io/py/phasegen.svg)](https://badge.fury.io/py/phasegen)
+
+
+``phasegen`` is a package for simulation and inference on exact solutions of coalescent distributions under diverse demographic scenarios. It used phase-type theory do so. ``phasegen`` supports a wide range of demographic models and coalescent tree statistics.
+
+Please see the [documentation](https://phasegen.readthedocs.io/en/latest/) for all the details.
+

phasegen-0.0.3b0/README.md

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+# PhaseGen  <img align="right" width="100" src="https://raw.githubusercontent.com/Sendrowski/PhaseGen/master/docs/logo.png">
+
+[![Documentation Status](https://readthedocs.org/projects/phasegen/badge/?version=latest)](https://phasegen.readthedocs.io/en/latest/?badge=latest)
+[![PyPI version](https://badge.fury.io/py/phasegen.svg)](https://badge.fury.io/py/phasegen)
+
+
+``phasegen`` is a package for simulation and inference on exact solutions of coalescent distributions under diverse demographic scenarios. It used phase-type theory do so. ``phasegen`` supports a wide range of demographic models and coalescent tree statistics.
+
+Please see the [documentation](https://phasegen.readthedocs.io/en/latest/) for all the details.

phasegen-0.0.3b0/phasegen/__init__.py

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+"""
+PhaseGen package.
+"""
+
+__author__ = "Janek Sendrowski"
+__contact__ = "sendrowski.janek@gmail.com"
+__date__ = "2023-04-09"
+
+__version__ = '0.0.3-beta'
+
+import logging
+import os
+import sys
+
+import jsonpickle.ext.numpy as jsonpickle_numpy
+from tqdm import tqdm
+
+# lower the verbosity of TensorFlow
+if 'TF_CPP_MIN_LOG_LEVEL' not in os.environ:
+    os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3'
+
+# register handlers
+jsonpickle_numpy.register_handlers()
+
+
+class TqdmLoggingHandler(logging.Handler):
+    """
+    A logging handler that uses TQDM to display log messages.
+    """
+
+    def __init__(self, level=logging.NOTSET):
+        """
+        Initialize the handler.
+
+        :param level:
+        """
+        super().__init__(level)
+
+    def emit(self, record):
+        """
+        Emit a record.
+        """
+        try:
+            msg = self.format(record)
+
+            # we write to stderr to avoid as the progress bar
+            # to make the two work together
+            tqdm.write(msg, file=sys.stderr)
+            self.flush()
+        except Exception:
+            self.handleError(record)
+
+
+class ColoredFormatter(logging.Formatter):
+    """
+    Colored formatter.
+    """
+
+    def __init__(self, *args, **kwargs):
+        """
+        Initialize the formatter.
+        """
+        super().__init__(*args, **kwargs)
+
+        self.colors = {
+            "DEBUG": "\033[36m",  # Cyan
+            "INFO": "\033[32m",  # Green
+            "WARNING": "\033[33m",  # Yellow
+            "ERROR": "\033[31m",  # Red
+            "CRITICAL": "\033[31m",  # Red
+        }
+
+        self.reset = "\033[0m"
+
+    def format(self, record):
+        """
+        Format the record.
+        """
+        color = self.colors.get(record.levelname, self.reset)
+
+        formatted = super().format(record)
+
+        # remove package name
+        formatted = formatted.replace(record.name, record.name.split('.')[-1])
+
+        return f"{color}{formatted}{self.reset}"
+
+
+# configure logger
+logger = logging.getLogger('phasegen')
+
+# don't propagate to the root logger
+logger.propagate = False
+
+# set to INFO by default
+logger.setLevel(logging.INFO)
+
+# let TQDM handle the logging
+handler = TqdmLoggingHandler()
+
+# define a Formatter with colors
+formatter = ColoredFormatter('%(levelname)s:%(name)s: %(message)s')
+
+handler.setFormatter(formatter)
+logger.addHandler(handler)
+
+from .distributions import PhaseTypeDistribution
+
+from .distributions import Coalescent
+
+from .demography import (
+    Demography,
+    Epoch,
+    DiscreteRateChanges,
+    PopSizeChanges,
+    PopSizeChange,
+    MigrationRateChanges,
+    MigrationRateChange,
+    SymmetricMigrationRateChanges,
+    PopulationSplit,
+    DiscretizedRateChanges,
+    DiscretizedRateChange,
+    ExponentialPopSizeChanges,
+    ExponentialRateChanges
+)
+
+from .coalescent_models import (
+    CoalescentModel,
+    StandardCoalescent,
+    BetaCoalescent,
+    DiracCoalescent
+)
+
+from .state_space import (
+    StateSpace,
+    DefaultStateSpace,
+    BlockCountingStateSpace
+)
+
+from .rewards import (
+    Reward,
+    DefaultReward,
+    NonDefaultReward,
+    TreeHeightReward,
+    TotalTreeHeightReward,
+    TotalBranchLengthReward,
+    UnfoldedSFSReward,
+    FoldedSFSReward,
+    CustomReward,
+    ProductReward,
+    SumReward,
+    CombinedReward,
+    DemeReward
+)
+
+from .spectrum import (
+    SFS,
+    Spectra,
+    SFS2
+)
+
+from .inference import Inference
+
+from .lineage import LineageConfig
+
+from .locus import LocusConfig
+
+from .norms import (
+    LNorm,
+    L1Norm,
+    L2Norm,
+    LInfNorm,
+    PoissonLikelihood
+)
+
+from .state_space_old import StateSpace as OldStateSpace
+
+__all__ = [
+    'PhaseTypeDistribution',
+    'Coalescent',
+    'Demography',
+    'Epoch',
+    'PopSizeChanges',
+    'PopSizeChange',
+    'MigrationRateChanges',
+    'MigrationRateChange',
+    'SymmetricMigrationRateChanges',
+    'PopulationSplit',
+    'ExponentialPopSizeChanges',
+    'ExponentialRateChanges',
+    'DiscreteRateChanges',
+    'DiscretizedRateChange',
+    'DiscretizedRateChanges',
+    'StandardCoalescent',
+    'BetaCoalescent',
+    'DiracCoalescent',
+    'SFS2',
+    'SFS',
+    'Spectra',
+    'Inference',
+    'LNorm',
+    'L1Norm',
+    'L2Norm',
+    'LInfNorm',
+    'PoissonLikelihood',
+    'Reward',
+    'TreeHeightReward',
+    'TotalTreeHeightReward',
+    'TotalBranchLengthReward',
+    'UnfoldedSFSReward',
+    'FoldedSFSReward',
+    'CustomReward',
+    'ProductReward',
+    'SumReward',
+    'DemeReward',
+    'DefaultReward',
+    'NonDefaultReward',
+    'CombinedReward',
+    'StateSpace',
+    'DefaultStateSpace',
+    'BlockCountingStateSpace',
+    'CoalescentModel',
+    'LineageConfig',
+    'LocusConfig',
+]