PyMARE 0.0.4rc2__tar.gz → 0.0.5__tar.gz

PyMARE-0.0.5/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2020- pymare developers
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

{PyMARE-0.0.4rc2 → PyMARE-0.0.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PyMARE
-Version: 0.0.4rc2
+Version: 0.0.5
 Summary: PyMARE: Python Meta-Analysis & Regression Engine
 Home-page: https://github.com/neurostuff/PyMARE
 Author: PyMARE developers
@@ -28,12 +28,12 @@ Classifier: Environment :: Console
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python :: 3.6
-Classifier: Programming Language :: Python :: 3.7
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
 Classifier: Topic :: Scientific/Engineering
-Requires-Python: >=3.6
+Requires-Python: >=3.8
 Description-Content-Type: text/x-rst
 Provides-Extra: doc
 Provides-Extra: tests

{PyMARE-0.0.4rc2 → PyMARE-0.0.5}/PyMARE.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PyMARE
-Version: 0.0.4rc2
+Version: 0.0.5
 Summary: PyMARE: Python Meta-Analysis & Regression Engine
 Home-page: https://github.com/neurostuff/PyMARE
 Author: PyMARE developers
@@ -28,12 +28,12 @@ Classifier: Environment :: Console
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python :: 3.6
-Classifier: Programming Language :: Python :: 3.7
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
 Classifier: Topic :: Scientific/Engineering
-Requires-Python: >=3.6
+Requires-Python: >=3.8
 Description-Content-Type: text/x-rst
 Provides-Extra: doc
 Provides-Extra: tests

{PyMARE-0.0.4rc2 → PyMARE-0.0.5}/PyMARE.egg-info/SOURCES.txt

@@ -1,3 +1,4 @@
+LICENSE
 MANIFEST.in
 README.md
 pyproject.toml

{PyMARE-0.0.4rc2 → PyMARE-0.0.5}/PyMARE.egg-info/requires.txt

@@ -1,6 +1,6 @@
 numpy>=1.8.0
 pandas
-scipy
+scipy<1.13.0
 sympy
 wrapt
 
@@ -15,7 +15,7 @@ seaborn
 sphinx>=3.5
 sphinx-argparse
 sphinx-copybutton
-sphinx_gallery==0.10.1
+sphinx_gallery
 sphinx_rtd_theme
 sphinxcontrib-bibtex
 codecov
@@ -27,6 +27,8 @@ flake8-docstrings
 flake8-isort
 pytest
 pytest-cov
+pystan
+arviz
 
 [doc]
 m2r
@@ -39,7 +41,7 @@ seaborn
 sphinx>=3.5
 sphinx-argparse
 sphinx-copybutton
-sphinx_gallery==0.10.1
+sphinx_gallery
 sphinx_rtd_theme
 sphinxcontrib-bibtex
 

PyMARE-0.0.5/pymare/__init__.py

@@ -0,0 +1,50 @@
+"""PyMARE: Python Meta-Analysis & Regression Engine."""
+
+import sys
+import warnings
+
+from .core import Dataset, meta_regression
+from .effectsize import OneSampleEffectSizeConverter, TwoSampleEffectSizeConverter
+
+__all__ = [
+    "Dataset",
+    "meta_regression",
+    "OneSampleEffectSizeConverter",
+    "TwoSampleEffectSizeConverter",
+]
+
+from . import _version
+
+__version__ = _version.get_versions()["version"]
+del _version
+
+
+def _py367_deprecation_warning():
+    """Deprecation warnings message.
+
+    Notes
+    -----
+    Adapted from NiMARE.
+    """
+    py36_warning = (
+        "Python 3.6 and 3.7 support is deprecated and will be removed in release 0.0.5 of PyMARE. "
+        "Consider switching to Python 3.8, 3.9."
+    )
+    warnings.filterwarnings("once", message=py36_warning)
+    warnings.warn(message=py36_warning, category=FutureWarning, stacklevel=3)
+
+
+def _python_deprecation_warnings():
+    """Raise deprecation warnings.
+
+    Notes
+    -----
+    Adapted from NiMARE.
+    """
+    if sys.version_info.major == 3 and (
+        sys.version_info.minor == 6 or sys.version_info.minor == 7
+    ):
+        _py367_deprecation_warning()
+
+
+_python_deprecation_warnings()

{PyMARE-0.0.4rc2 → PyMARE-0.0.5}/pymare/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2022-06-12T18:39:44-0400",
+ "date": "2024-04-30T11:09:49-0500",
  "dirty": false,
  "error": null,
- "full-revisionid": "19af39959baa34eea4a34aa564945a0cbef30f62",
- "version": "0.0.4rc2"
+ "full-revisionid": "46b87a55fdaf55c9e86d5dbed4c7c6d77e4ffb8f",
+ "version": "0.0.5"
 }
 '''  # END VERSION_JSON
 

{PyMARE-0.0.4rc2 → PyMARE-0.0.5}/pymare/core.py

@@ -59,7 +59,6 @@ class Dataset:
     def __init__(
         self, y=None, v=None, X=None, n=None, data=None, X_names=None, add_intercept=True
     ):
-
         if y is None and data is None:
             raise ValueError(
                 "If no y values are provided, a pandas DataFrame "

{PyMARE-0.0.4rc2 → PyMARE-0.0.5}/pymare/datasets/__init__.py

@@ -1,4 +1,5 @@
 """Open meta-analytic datasets."""
+
 from .metadat import michael2013
 
 __all__ = [

{PyMARE-0.0.4rc2 → PyMARE-0.0.5}/pymare/datasets/metadat.py

@@ -1,4 +1,5 @@
 """Datasets from metadat."""
+
 import json
 import os.path as op
 

{PyMARE-0.0.4rc2 → PyMARE-0.0.5}/pymare/effectsize/__init__.py

@@ -1,4 +1,5 @@
 """Tools for converting between effect-size measures."""
+
 from .base import (
     OneSampleEffectSizeConverter,
     TwoSampleEffectSizeConverter,

{PyMARE-0.0.4rc2 → PyMARE-0.0.5}/pymare/effectsize/base.py

@@ -68,7 +68,7 @@ def solve_system(system, known_vars=None):
 
     # solver will return a dict if there's only one non-dummy expression
     if isinstance(solutions, dict):
-        solutions = [list(solutions.values())]
+        solutions = [[solutions[s] for s in symbols]]
 
     # Prepare the dummy list and data args in a fixed order
     dummy_list = list(dummies)
@@ -90,7 +90,6 @@ class EffectSizeConverter(metaclass=ABCMeta):
     """Base class for effect size converters."""
 
     def __init__(self, data=None, **kwargs):
-
         kwargs = {k: v for k, v in kwargs.items() if v is not None}
 
         if data is not None:
@@ -509,7 +508,6 @@ def compute_measure(
 
     # Select or infer converter class
     if comparison == "infer":
-
         one_samp_inputs = {"m", "sd", "n", "r"}
         two_samp_inputs = {"m1", "m2", "sd1", "sd2", "n1", "n2"}
 

{PyMARE-0.0.4rc2 → PyMARE-0.0.5}/pymare/estimators/__init__.py

@@ -1,4 +1,5 @@
 """Estimators for meta-analyses and meta-regressions."""
+
 from .combination import FisherCombinationTest, StoufferCombinationTest
 from .estimators import (
     DerSimonianLaird,

{PyMARE-0.0.4rc2 → PyMARE-0.0.5}/pymare/estimators/combination.py

@@ -1,4 +1,5 @@
 """Estimators for combination (p/z) tests."""
+
 import warnings
 from abc import abstractmethod
 
@@ -110,17 +111,91 @@ class StoufferCombinationTest(CombinationTest):
     """
 
     # Maps Dataset attributes onto fit() args; see BaseEstimator for details.
-    _dataset_attr_map = {"z": "y", "w": "v"}
+    _dataset_attr_map = {"z": "y", "w": "n", "g": "v"}
+
+    def _inflation_term(self, z, w, g, corr=None):
+        """Calculate the variance inflation term for each group.
+
+        This term is used to adjust the variance of the combined z-score when
+        multiple sample come from the same study.
+
+        Parameters
+        ----------
+        z : :obj:`numpy.ndarray` of shape (n, d)
+            Array of z-values.
+        w : :obj:`numpy.ndarray` of shape (n, d)
+            Array of weights.
+        g : :obj:`numpy.ndarray` of shape (n, d)
+            Array of group labels.
+        corr : :obj:`numpy.ndarray` of shape (n, n), optional
+            The correlation matrix of the z-values. If None, it will be calculated.
+
+        Returns
+        -------
+        sigma : float
+            The variance inflation term.
+        """
+        # Only center if the samples are not all the same, to prevent division by zero
+        # when calculating the correlation matrix.
+        # This centering is problematic for N=2
+        all_samples_same = np.all(np.equal(z, z[0]), axis=0).all()
+        z = z if all_samples_same else z - z.mean(0)
+
+        # Use the value from one feature, as all features have the same groups and weights
+        groups = g[:, 0]
+        weights = w[:, 0]
+
+        # Loop over groups
+        unique_groups = np.unique(groups)
+
+        sigma = 0
+        for group in unique_groups:
+            group_indices = np.where(groups == group)[0]
+            group_z = z[group_indices]
+
+            # For groups with only one sample the contribution to the summand is 0
+            n_samples = len(group_indices)
+            if n_samples < 2:
+                continue
 
-    def fit(self, z, w=None):
-        """Fit the estimator to z-values, optionally with weights."""
-        return super().fit(z, w=w)
+            # Calculate the within group correlation matrix and sum the non-diagonal elements
+            if corr is None:
+                if z.shape[1] < 2:
+                    raise ValueError("The number of features must be greater than 1.")
+                group_corr = np.corrcoef(group_z, rowvar=True)
+            else:
+                group_corr = corr[group_indices][:, group_indices]
 
-    def p_value(self, z, w=None):
+            upper_indices = np.triu_indices(n_samples, k=1)
+            non_diag_corr = group_corr[upper_indices]
+            w_i, w_j = weights[upper_indices[0]], weights[upper_indices[1]]
+
+            sigma += (2 * w_i * w_j * non_diag_corr).sum()
+
+        return sigma
+
+    def fit(self, z, w=None, g=None, corr=None):
+        """Fit the estimator to z-values, optionally with weights and groups."""
+        return super().fit(z, w=w, g=g, corr=corr)
+
+    def p_value(self, z, w=None, g=None, corr=None):
         """Calculate p-values."""
         if w is None:
             w = np.ones_like(z)
-        cz = (z * w).sum(0) / np.sqrt((w**2).sum(0))
+
+        if g is None and corr is not None:
+            warnings.warn("Correlation matrix provided without groups. Ignoring.")
+
+        if g is not None and corr is not None and g.shape[0] != corr.shape[0]:
+            raise ValueError("Group labels must have the same length as the correlation matrix.")
+
+        # Calculate the variance inflation term, sum of non-diagonal elements of sigma.
+        sigma = self._inflation_term(z, w, g, corr=corr) if g is not None else 0
+
+        # The sum of diagonal elements of sigma is given by (w**2).sum(0).
+        variance = (w**2).sum(0) + sigma
+
+        cz = (z * w).sum(0) / np.sqrt(variance)
         return ss.norm.sf(cz)
 
 

{PyMARE-0.0.4rc2 → PyMARE-0.0.5}/pymare/estimators/estimators.py

@@ -1,5 +1,6 @@
 """Meta-regression estimator classes."""
 
+import sys
 from abc import ABCMeta, abstractmethod
 from inspect import getfullargspec
 from warnings import warn
@@ -553,8 +554,8 @@ class StanMetaRegression(BaseEstimator):
 
     Warning
     -------
-    With changes to Stan in version 3, which requires Python 3.7, this class no longer works for
-    Python 3.7+. We will try to fix it in the future.
+    :obj:`~pymare.estimators.StanMetaRegression` uses Pystan 3, which requires Python 3.7.
+    Pystan 3 should not be used with PyMARE and Python 3.6 or earlier.
     """
 
     _result_cls = BayesianMetaRegressionResults
@@ -564,6 +565,13 @@ class StanMetaRegression(BaseEstimator):
         self.model = None
         self.result_ = None
 
+        if sys.version_info < (3, 7):
+            raise RuntimeError(
+                "StanMetaRegression uses Pystan 3, which requires python 3.7 or higher. "
+                f"You are running Python {sys.version_info.major}.{sys.version_info.minor}. "
+                "Pystan 3 should not be used with PyMARE and Python 3.6 or earlier."
+            )
+
     def compile(self):
         """Compile the Stan model."""
         # Note: we deliberately use a centered parameterization for the
@@ -575,7 +583,7 @@ class StanMetaRegression(BaseEstimator):
             int<lower=1> N;
             int<lower=1> K;
             vector[N] y;
-            int<lower=1,upper=K> id[N];
+            array[N] int<lower=1,upper=K> id;
             int<lower=1> C;
             matrix[K, C] X;
             vector[N] sigma;
@@ -595,13 +603,11 @@ class StanMetaRegression(BaseEstimator):
         }
         """
         try:
-            from pystan import StanModel
+            import stan
         except ImportError:
-            raise ImportError(
-                "Please install pystan or, if using Python 3.7+, switch to Python 3.6."
-            )
+            raise ImportError("Please install pystan.")
 
-        self.model = StanModel(model_code=spec)
+        self.model = stan.build(spec, data=self.data)
 
     def fit(self, y, v, X, groups=None):
         """Run the Stan sampler and return results.
@@ -645,9 +651,6 @@ class StanMetaRegression(BaseEstimator):
                 "shape {}.".format(y.shape)
             )
 
-        if self.model is None:
-            self.compile()
-
         N = y.shape[0]
         groups = groups or np.arange(1, N + 1, dtype=int)
         K = len(np.unique(groups))
@@ -662,7 +665,12 @@ class StanMetaRegression(BaseEstimator):
             "sigma": v.ravel(),
         }
 
-        self.result_ = self.model.sampling(data=data, **self.sampling_kwargs)
+        self.data = data
+
+        if self.model is None:
+            self.compile()
+
+        self.result_ = self.model.sample(**self.sampling_kwargs)
         return self
 
     def summary(self, ci=95):

{PyMARE-0.0.4rc2 → PyMARE-0.0.5}/pymare/results.py

@@ -1,4 +1,5 @@
 """Tools for representing and manipulating meta-regression results."""
+
 import itertools
 from functools import lru_cache
 from inspect import getfullargspec
@@ -331,7 +332,6 @@ class MetaRegressionResults:
 
         # Loop over parallel datasets
         for i in range(n_datasets):
-
             y = self.dataset.y[:, i]
             y_perm = np.repeat(y[:, None], n_perm, axis=1)
 
@@ -471,7 +471,6 @@ class CombinationTestResults:
 
         # Loop over parallel datasets
         for i in range(n_datasets):
-
             y = self.dataset.y[:, i]
             y_perm = np.repeat(y[:, None], n_perm, axis=1)
 

{PyMARE-0.0.4rc2 → PyMARE-0.0.5}/pymare/stats.py

@@ -109,7 +109,7 @@ def q_profile(y, v, X, alpha=0.05):
     ub_start = 2 * DerSimonianLaird().fit(y, v, X).params_["tau2"]
 
     lb = minimize(lambda x: (q_gen(*args, x) - l_crit) ** 2, [0], bounds=bds).x[0]
-    ub = minimize(lambda x: (q_gen(*args, x) - u_crit) ** 2, [ub_start], bounds=bds).x[0]
+    ub = minimize(lambda x: (q_gen(*args, x) - u_crit) ** 2, ub_start, bounds=bds).x[0]
     return {"ci_l": lb, "ci_u": ub}
 
 

{PyMARE-0.0.4rc2 → PyMARE-0.0.5}/pymare/utils.py

@@ -1,4 +1,5 @@
 """Miscellaneous utility functions."""
+
 import os.path as op
 
 import numpy as np

{PyMARE-0.0.4rc2 → PyMARE-0.0.5}/pyproject.toml

@@ -1,9 +1,9 @@
 [build-system]
-requires = ["setuptools==58.2.0", "wheel"]
+requires = ["setuptools==68.2.2", "wheel"]
 
 [tool.black]
 line-length = 99
-target-version = ["py37"]
+target-version = ["py39"]
 include = '\.pyi?$'
 exclude = '''
 

{PyMARE-0.0.4rc2 → PyMARE-0.0.5}/setup.cfg

@@ -6,7 +6,7 @@ author_email = tsalo006@fiu.edu
 maintainer = Taylor Salo
 maintainer_email = tsalo006@fiu.edu
 description = PyMARE: Python Meta-Analysis & Regression Engine
-description-file = README.md
+description_file = README.md
 long_description = 
 	PyMARE: Python Meta-Analysis & Regression Engine
 	================================================
@@ -28,18 +28,18 @@ classifiers =
 	Intended Audience :: Science/Research
 	License :: OSI Approved :: MIT License
 	Operating System :: OS Independent
-	Programming Language :: Python :: 3.6
-	Programming Language :: Python :: 3.7
 	Programming Language :: Python :: 3.8
 	Programming Language :: Python :: 3.9
+	Programming Language :: Python :: 3.10
+	Programming Language :: Python :: 3.11
 	Topic :: Scientific/Engineering
 
 [options]
-python_requires = >= 3.6
+python_requires = >= 3.8
 install_requires = 
 	numpy>=1.8.0
 	pandas
-	scipy
+	scipy<1.13.0  # https://github.com/arviz-devs/arviz/issues/2336
 	sympy
 	wrapt
 packages = find:
@@ -57,7 +57,7 @@ doc =
 	sphinx>=3.5
 	sphinx-argparse
 	sphinx-copybutton
-	sphinx_gallery==0.10.1
+	sphinx_gallery
 	sphinx_rtd_theme
 	sphinxcontrib-bibtex
 tests = 
@@ -76,6 +76,7 @@ stan =
 all = 
 	%(doc)s
 	%(tests)s
+	%(stan)s
 
 [options.package_data]
 * = 
@@ -97,6 +98,8 @@ max-line-length = 99
 exclude = *build/,_version.py
 putty-ignore = 
 	*/__init__.py : +F401
+per-file-ignores = 
+	*/__init__.py:D401
 ignore = E203,E402,E722,W503
 docstring-convention = numpy
 

PyMARE-0.0.4rc2/pymare/__init__.py

@@ -1,15 +0,0 @@
-"""PyMARE: Python Meta-Analysis & Regression Engine."""
-from .core import Dataset, meta_regression
-from .effectsize import OneSampleEffectSizeConverter, TwoSampleEffectSizeConverter
-
-__all__ = [
-    "Dataset",
-    "meta_regression",
-    "OneSampleEffectSizeConverter",
-    "TwoSampleEffectSizeConverter",
-]
-
-from . import _version
-
-__version__ = _version.get_versions()["version"]
-del _version

{PyMARE-0.0.4rc2 → PyMARE-0.0.5}/pymare/effectsize/expressions.py

@@ -1,4 +1,5 @@
 """Statistical expressions."""
+
 import json
 from collections import defaultdict
 from itertools import chain
@@ -90,7 +91,6 @@ def select_expressions(target, known_vars, type=1):
         results = []
 
         for exp in exp_dict[sym]:
-
             candidates = []
 
             sym_names = set(s.name for s in exp.symbols)