merged

quapy/method/_bayesian.py

@@ -2,6 +2,7 @@
 Utility functions for `Bayesian quantification <https://arxiv.org/abs/2302.09159>`_ methods.
 """
 import numpy as np
+import importlib.resources
 
 try:
     import jax
@@ -82,6 +83,9 @@ def sample_posterior(
 
 
 
+def load_stan_file():
+    return importlib.resources.files('quapy.method').joinpath('stan/pq.stan').read_text(encoding='utf-8')
+
 def pq_stan(stan_code, n_bins, pos_hist, neg_hist, test_hist, number_of_samples, num_warmup, stan_seed):
     """
     Perform Bayesian prevalence estimation using a Stan model for probabilistic quantification.

quapy/method/confidence.py

@@ -13,7 +13,6 @@ from abc import ABC, abstractmethod
 from scipy.special import softmax, factorial
 import copy
 from functools import lru_cache
-from pathlib import Path
 
 """
 This module provides implementation of different types of confidence regions, and the implementation of Bootstrap
@@ -625,10 +624,7 @@ class PQ(AggregativeSoftQuantifier, BinaryAggregativeQuantifier):
         self.num_samples = num_samples
         self.region = region
         self.stan_seed = stan_seed
-        # with open('quapy/method/stan/pq.stan', 'r') as f:
-        stan_path = Path(__file__).resolve().parent / "stan" / "pq.stan"
-        with stan_path.open("r") as f:
-            self.stan_code = str(f.read())
+        self.stan_code = _bayesian.load_stan_file()
 
     def aggregation_fit(self, classif_predictions, labels):
         y_pred = classif_predictions[:, self.pos_label]
@@ -662,7 +658,8 @@ class PQ(AggregativeSoftQuantifier, BinaryAggregativeQuantifier):
         return F.as_binary_prevalence(self.prev_distribution.mean())
 
     def predict_conf(self, instances, confidence_level=None) -> (np.ndarray, ConfidenceRegionABC):
-        point_estimate = self.predict(instances)
+        classif_predictions = self.classify(instances)
+        point_estimate = self.aggregate(classif_predictions)
         samples = self.prev_distribution
         region = WithConfidenceABC.construct_region(samples, confidence_level=confidence_level, method=self.region)
         return point_estimate, region

setup.py

@@ -111,6 +111,12 @@ setup(
     #
     packages=find_packages(include=['quapy', 'quapy.*']),  # Required
 
+    package_data={
+        # For the 'quapy.method' package, include all files
+        # in the 'stan' subdirectory that end with .stan
+        'quapy.method': ['stan/*.stan']
+    },
+
     python_requires='>=3.8, <4',
 
     install_requires=['scikit-learn', 'pandas', 'tqdm', 'matplotlib', 'joblib', 'xlrd', 'abstention', 'ucimlrepo', 'certifi'],