threeML 2.4.3.dev1__tar.gz → 2.5.0.dev1__tar.gz

{threeml-2.4.3.dev1/threeML.egg-info → threeml-2.5.0.dev1}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: threeML
-Version: 2.4.3.dev1
+Version: 2.5.0.dev1
 Summary: The Multi-Mission Maximum Likelihood framework
 Home-page: https://github.com/threeml/threeML
 Author: Giacomo Vianello
@@ -52,6 +52,9 @@ Requires-Dist: sphinx>=1.4; extra == "docs"
 Requires-Dist: sphinx_rtd_theme; extra == "docs"
 Requires-Dist: nbsphinx; extra == "docs"
 Requires-Dist: sphinx-autoapi; extra == "docs"
+Dynamic: keywords
+Dynamic: license
+Dynamic: license-file
 
 ![CI](https://github.com/threeML/threeML/workflows/CI/badge.svg?branch=master&event=push)
 [![Conda Build and Publish](https://github.com/threeML/threeML/actions/workflows/conda_build.yml/badge.svg)](https://github.com/threeML/threeML/actions/workflows/conda_build.yml)

{threeml-2.4.3.dev1 → threeml-2.5.0.dev1}/threeML/_version.py

@@ -9,11 +9,11 @@ import json
 
 version_json = '''
 {
- "date": "2024-09-11T16:28:56-0400",
+ "date": "2025-05-19T11:00:17-0700",
  "dirty": false,
  "error": null,
- "full-revisionid": "df578f0d4c5b2d572f6ca9388ce9060b608941e0",
- "version": "2.4.3.dev1"
+ "full-revisionid": "8fbb6df91da65abfa6816a64961cede7a90c6ff2",
+ "version": "2.5.0.dev1"
 }
 '''  # END VERSION_JSON
 

{threeml-2.4.3.dev1 → threeml-2.5.0.dev1}/threeML/analysis_results.py

@@ -1181,9 +1181,7 @@ class BayesianResults(_AnalysisResults):
         see: https://samreay.github.io/ChainConsumer/chain_api.html#chainconsumer.ChainConsumer.configure
         for all options
         :param parameters: list of parameters to plot
-        :param renamed_parameters: a python dictionary of parameters to rename.
-             Useful when e.g. spectral indices in models have different names but you wish to compare them. Format is
-             {'old label': 'new label'}
+        :param renamed_parameters: a python dictionary of parameters to rename. Useful when e.g. spectral indices in models have different names but you wish to compare them. Format is {'old label': 'new label'}
         :param **cc_kwargs: chainconsumer general keyword arguments
         :return fig:
         """

{threeml-2.4.3.dev1 → threeml-2.5.0.dev1}/threeML/bayesian/bayesian_analysis.py

@@ -270,9 +270,8 @@ class BayesianAnalysis:
     @property
     def log_marginal_likelihood(self) -> Optional[float]:
         """
-                Return the log marginal likelihood (evidence
-        ) if computed
-                :return:
+        Return the log marginal likelihood (evidence) if computed
+        :return: marginal_likelihood
         """
 
         return self._sampler.marginal_likelihood

{threeml-2.4.3.dev1 → threeml-2.5.0.dev1}/threeML/bayesian/ultranest_sampler.py

@@ -66,29 +66,28 @@ class UltraNestSampler(UnitCubeSampler):
         **kwargs,
     ):
         """
-                set up the Ultranest sampler. Consult the documentation:
-
-                https://johannesbuchner.github.io/UltraNest/ultranest.html?highlight=reactive#ultranest.integrator.ReactiveNestedSampler
-
-                :param min_num_live_points: minimum number of live points throughout the run
-                :type min_num_live_points: int
-                :param dlogz: Target evidence uncertainty. This is the std between bootstrapped logz integrators.
-                :type dlogz: float
-                :param chain_name: where to store output files
-                :type chain_name:
-                :param resume:  ('resume', 'resume-similar', 'overwrite' or 'subfolder') –
+        set up the Ultranest sampler. Consult the documentation:
+        https://johannesbuchner.github.io/UltraNest/ultranest.html?highlight=reactive#ultranest.integrator.ReactiveNestedSampler
+
+        :param min_num_live_points: minimum number of live points throughout the run
+        :type min_num_live_points: int
+        :param dlogz: Target evidence uncertainty. This is the std between bootstrapped logz integrators.
+        :type dlogz: float
+        :param chain_name: where to store output files
+        :type chain_name:
+        :param resume:  ('resume', 'resume-similar', 'overwrite' or 'subfolder') –
         if ‘overwrite’, overwrite previous data.
         if ‘subfolder’, create a fresh subdirectory in log_dir.
         if ‘resume’ or True, continue previous run if available. Only works when dimensionality, transform or likelihood are consistent.
         if ‘resume-similar’, continue previous run if available. Only works when dimensionality and transform are consistent. If a likelihood difference is detected, the existing likelihoods are updated until the live point order differs. Otherwise, behaves like resume.
-                :type resume: str
-                :param wrapped_params:  (list of bools) – indicating whether this parameter wraps around (circular parameter).
-                :type wrapped_params:
-                :param stepsampler:
-                :type stepsampler:
-                :param use_mlfriends: Whether to use MLFriends+ellipsoidal+tellipsoidal region (better for multi-modal problems) or just ellipsoidal sampling (faster for high-dimensional, gaussian-like problems).
-                :type use_mlfriends: bool
-                :returns:
+        :type resume: str
+        :param wrapped_params:  (list of bools) – indicating whether this parameter wraps around (circular parameter).
+        :type wrapped_params:
+        :param stepsampler:
+        :type stepsampler:
+        :param use_mlfriends: Whether to use MLFriends+ellipsoidal+tellipsoidal region (better for multi-modal problems) or just ellipsoidal sampling (faster for high-dimensional, gaussian-like problems).
+        :type use_mlfriends: bool
+        :returns:
 
         """
 

{threeml-2.4.3.dev1 → threeml-2.5.0.dev1}/threeML/classicMLE/goodness_of_fit.py

@@ -58,7 +58,7 @@ class GoodnessOfFit(object):
 
         return new_model
 
-    def by_mc(self, n_iterations=1000, continue_on_failure=False):
+    def by_mc(self, n_iterations=1000, continue_on_failure=False, preprocessor=None, postprocessor=None):
         """
         Compute goodness of fit by generating Monte Carlo datasets and fitting the current model on them. The fraction
         of synthetic datasets which have a value for the likelihood larger or equal to the observed one is a measure
@@ -75,6 +75,8 @@ class GoodnessOfFit(object):
             self.get_model,
             n_iterations,
             iteration_name="simulation",
+            preprocessor=preprocessor,
+            postprocessor=postprocessor,
         )
 
         # Use the same minimizer as in the joint likelihood object

{threeml-2.4.3.dev1 → threeml-2.5.0.dev1}/threeML/classicMLE/joint_likelihood.py

@@ -226,8 +226,7 @@ class JointLikelihood(object):
         :param quiet: If True, print the results (default), otherwise do not print anything
         :param compute_covariance:If True (default), compute and display the errors and the correlation matrix.
         :param n_samples: Number of samples to scan the likelihood.
-        :return: a dictionary with the results on the parameters, and the values of the likelihood at the minimum
-                 for each dataset and the total one.
+        :return: a dictionary with the results on the parameters, and the values of the likelihood at the minimum for each dataset and the total one.
         """
 
         # Update the list of free parameters, to be safe against changes the user might do between

{threeml-2.4.3.dev1 → threeml-2.5.0.dev1}/threeML/classicMLE/joint_likelihood_set.py

@@ -27,6 +27,7 @@ class JointLikelihoodSet(object):
         n_iterations,
         iteration_name="interval",
         preprocessor=None,
+        postprocessor=None,
     ):
 
         # Store the data and model getter
@@ -108,6 +109,8 @@ class JointLikelihoodSet(object):
 
         self._preprocessor = preprocessor
 
+        self._postprocessor = postprocessor
+
     def set_minimizer(self, minimizer):
 
         if isinstance(minimizer, _Minimization):
@@ -163,6 +166,10 @@ class JointLikelihoodSet(object):
 
                 jl = JointLikelihood(this_model, this_data)
 
+            if self._postprocessor is not None:
+
+                self._postprocessor(this_model, this_data, quiet=True)
+
             this_parameter_frame, this_like_frame = self._fitter(jl)
 
             # Append results

{threeml-2.4.3.dev1 → threeml-2.5.0.dev1}/threeML/minimizer/minimization.py

@@ -1179,33 +1179,31 @@ class Minimizer(object):
         **options
     ):
         """
-            Generate confidence contours for the given parameters by stepping for the given number of steps between
-            the given boundaries. Call it specifying only source_1, param_1, param_1_minimum and param_1_maximum to
-            generate the profile of the likelihood for parameter 1. Specify all parameters to obtain instead a 2d
-            contour of param_1 vs param_2
-
-            :param param_1: name of the first parameter
-            :param param_1_minimum: lower bound for the range for the first parameter
-            :param param_1_maximum: upper bound for the range for the first parameter
-            :param param_1_n_steps: number of steps for the first parameter
-            :param param_2: name of the second parameter
-            :param param_2_minimum: lower bound for the range for the second parameter
-            :param param_2_maximum: upper bound for the range for the second parameter
-            :param param_2_n_steps: number of steps for the second parameter
-            :param progress: (True or False) whether to display progress or not
-            :param log: by default the steps are taken linearly. With this optional parameter you can provide a tuple of
-            booleans which specify whether the steps are to be taken logarithmically. For example,
-            'log=(True,False)' specify that the steps for the first parameter are to be taken logarithmically, while they
-            are linear for the second parameter. If you are generating the profile for only one parameter, you can specify
-             'log=(True,)' or 'log=(False,)' (optional)
-            :param: parallel: whether to use or not parallel computation (default:False)
-            :return: a : an array corresponding to the steps for the first parameter
-                     b : an array corresponding to the steps for the second parameter (or None if stepping only in one
-                     direction)
-                     contour : a matrix of size param_1_steps x param_2_steps containing the value of the function at the
-                     corresponding points in the grid. If param_2_steps is None (only one parameter), then this reduces to
-                     an array of size param_1_steps.
-            """
+        Generate confidence contours for the given parameters by stepping for the given number of steps between
+        the given boundaries. Call it specifying only source_1, param_1, param_1_minimum and param_1_maximum to
+        generate the profile of the likelihood for parameter 1. Specify all parameters to obtain instead a 2d
+        contour of param_1 vs param_2
+
+        :param param_1: name of the first parameter
+        :param param_1_minimum: lower bound for the range for the first parameter
+        :param param_1_maximum: upper bound for the range for the first parameter
+        :param param_1_n_steps: number of steps for the first parameter
+        :param param_2: name of the second parameter
+        :param param_2_minimum: lower bound for the range for the second parameter
+        :param param_2_maximum: upper bound for the range for the second parameter
+        :param param_2_n_steps: number of steps for the second parameter
+        :param progress: (True or False) whether to display progress or not
+        :param log: by default the steps are taken linearly. With this optional parameter you can provide a tuple of
+        booleans which specify whether the steps are to be taken logarithmically. For example,
+        'log=(True,False)' specify that the steps for the first parameter are to be taken logarithmically, while they
+        are linear for the second parameter. If you are generating the profile for only one parameter, you can specify
+        'log=(True,)' or 'log=(False,)' (optional)
+        :param: parallel: whether to use or not parallel computation (default:False)
+        :return:    
+           a : an array corresponding to the steps for the first parameter
+           b : an array corresponding to the steps for the second parameter (or None if stepping only in one direction) 
+           contour : a matrix of size param_1_steps x param_2_steps containing the value of the function at the corresponding points in the grid. If param_2_steps is None (only one parameter), then this reduces to an array of size param_1_steps.
+        """
 
         # Figure out if we are making a 1d or a 2d contour
 

{threeml-2.4.3.dev1 → threeml-2.5.0.dev1}/threeML/minimizer/tutorial_material.py

@@ -125,9 +125,13 @@ def plot_minimizer_path(jl, points=False):
     qx_ = np.array(
         jl.likelihood_model.test.spectrum.main.shape._traversed_points, dtype=float
     )
-    qy_ = np.array(
-        jl.likelihood_model.test.spectrum.main.shape._returned_values, dtype=float
-    )
+    # Horrible hack to get around a ValueError: setting an array element with a 
+    # sequence
+    values = jl.likelihood_model.test.spectrum.main.shape._returned_values
+    for idx, item in enumerate(values):
+        if np.isnan(item):
+            values[idx] = np.array([np.nan])
+    qy_ = np.asarray(values, dtype=float)
 
     fig, sub = plt.subplots(1, 1)
 

{threeml-2.4.3.dev1 → threeml-2.5.0.dev1}/threeML/test/test_FermiLATLike.py

@@ -43,8 +43,8 @@ datarepository = 'FermiData'
 
 
 #@pytest.mark.xfail
-@skip_if_internet_is_not_available
 @skip_if_LAT_is_not_available
+@skip_if_internet_is_not_available
 def test_make_LAT_dataset():
     myLATdataset = LAT_dataset()
 

{threeml-2.4.3.dev1 → threeml-2.5.0.dev1}/threeML/utils/data_download/Fermi_LAT/download_LAT_data.py

@@ -24,7 +24,7 @@ from threeML.utils.unique_deterministic_tag import get_unique_deterministic_tag
 log = setup_logger(__name__)
 
 # Set default timeout for operations
-socket.setdefaulttimeout(120)
+socket.setdefaulttimeout(180)
 
 
 class DivParser(html.parser.HTMLParser):
@@ -660,7 +660,7 @@ class LAT_dataset():
 
     def extract_events(self,roi, zmax, irf, thetamax=180.0,strategy='time',data_quality=True):
         from GtBurst import dataHandling
-        global lastDisplay
+        #global lastDisplay
 
         LATdata = dataHandling.LATData(self.ft1, self.rspfile, self.ft2)
 

{threeml-2.4.3.dev1 → threeml-2.5.0.dev1}/threeML/utils/spectrum/pha_spectrum.py

@@ -941,9 +941,8 @@ class PHASpectrum(BinnedSpectrumWithDispersion):
     @property
     def background_file(self) -> Union[None, str]:
         """
-                Returns the background file definied in the header, or None if there is none defined
-        p
-                :return: a path to a file, or None
+        Returns the background file definied in the header, or None if there is none defined
+        :return: a path to a file, or None
         """
 
         back_file = self._return_file("backfile")
@@ -1355,9 +1354,8 @@ class PHASpectrumSet(BinnedSpectrumSet):
     @property
     def background_file(self):
         """
-                Returns the background file definied in the header, or None if there is none defined
-        p
-                :return: a path to a file, or None
+        Returns the background file definied in the header, or None if there is none defined
+        :return: a path to a file, or None
         """
 
         return self._return_file("backfile")

{threeml-2.4.3.dev1 → threeml-2.5.0.dev1}/threeML/utils/statistics/likelihood_functions.py

@@ -294,7 +294,9 @@ def half_chi2(y, yerr, expectation):
     #yerr[yerr<1]=np.sqrt(0.75)
 
     for n in range(N):
-
-        log_likes[n] = (y[n] - expectation[n]) ** 2 / (yerr[n] ** 2)
+        
+        log_likes[n] = 0
+        if yerr[n] > 0:
+            log_likes[n] = (y[n] - expectation[n]) ** 2 / (yerr[n] ** 2)
 
     return 0.5 * log_likes

{threeml-2.4.3.dev1 → threeml-2.5.0.dev1/threeML.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: threeML
-Version: 2.4.3.dev1
+Version: 2.5.0.dev1
 Summary: The Multi-Mission Maximum Likelihood framework
 Home-page: https://github.com/threeml/threeML
 Author: Giacomo Vianello
@@ -52,6 +52,9 @@ Requires-Dist: sphinx>=1.4; extra == "docs"
 Requires-Dist: sphinx_rtd_theme; extra == "docs"
 Requires-Dist: nbsphinx; extra == "docs"
 Requires-Dist: sphinx-autoapi; extra == "docs"
+Dynamic: keywords
+Dynamic: license
+Dynamic: license-file
 
 ![CI](https://github.com/threeML/threeML/workflows/CI/badge.svg?branch=master&event=push)
 [![Conda Build and Publish](https://github.com/threeML/threeML/actions/workflows/conda_build.yml/badge.svg)](https://github.com/threeML/threeML/actions/workflows/conda_build.yml)