threeML 2.4.2.dev1__tar.gz → 2.4.2.dev2__tar.gz

{threeML-2.4.2.dev1/threeML.egg-info → threeml-2.4.2.dev2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: threeML
-Version: 2.4.2.dev1
+Version: 2.4.2.dev2
 Summary: The Multi-Mission Maximum Likelihood framework
 Home-page: https://github.com/threeml/threeML
 Author: Giacomo Vianello
@@ -21,8 +21,8 @@ License-File: LICENSE
 Requires-Dist: numpy>=1.16
 Requires-Dist: scipy>=1.4
 Requires-Dist: emcee>=3
-Requires-Dist: astropy>=1.3.3
-Requires-Dist: matplotlib
+Requires-Dist: astropy
+Requires-Dist: matplotlib<3.9
 Requires-Dist: uncertainties
 Requires-Dist: pyyaml>=5.1
 Requires-Dist: dill
@@ -38,7 +38,7 @@ Requires-Dist: ipyparallel
 Requires-Dist: joblib
 Requires-Dist: numexpr
 Requires-Dist: dynesty
-Requires-Dist: numba<0.59
+Requires-Dist: numba
 Requires-Dist: numdifftools
 Requires-Dist: tqdm>=4.56.0
 Requires-Dist: colorama

{threeML-2.4.2.dev1 → threeml-2.4.2.dev2}/setup.cfg

@@ -28,8 +28,8 @@ install_requires =
 	numpy>=1.16
 	scipy>=1.4
 	emcee>=3
-	astropy>=1.3.3
-	matplotlib
+	astropy
+	matplotlib<3.9
 	uncertainties
 	pyyaml>=5.1
 	dill
@@ -45,7 +45,7 @@ install_requires =
 	joblib
 	numexpr
 	dynesty
-	numba<0.59
+	numba
 	numdifftools
 	tqdm>=4.56.0
 	colorama

{threeML-2.4.2.dev1 → threeml-2.4.2.dev2}/threeML/_version.py

@@ -9,11 +9,11 @@ import json
 
 version_json = '''
 {
- "date": "2024-02-07T11:59:32-0800",
+ "date": "2024-05-16T11:29:54-0700",
  "dirty": false,
  "error": null,
- "full-revisionid": "0dffe924d2249234063051268659a0705e13ef75",
- "version": "2.4.2.dev1"
+ "full-revisionid": "5d82ece955c4d85922bd89a38525920eceb160a5",
+ "version": "2.4.2.dev2"
 }
 '''  # END VERSION_JSON
 

{threeML-2.4.2.dev1 → threeml-2.4.2.dev2}/threeML/analysis_results.py

@@ -14,7 +14,7 @@ import astromodels
 import astropy.units as u
 import h5py
 import matplotlib.pyplot as plt
-import matplotlib.cm as cm
+from matplotlib import colormaps
 import numpy as np
 import pandas as pd
 import yaml
@@ -1125,7 +1125,7 @@ class BayesianResults(_AnalysisResults):
 
         corner_style = threeML_config.bayesian.corner_style
 
-        cmap = cm.get_cmap(corner_style.cmap.value)
+        cmap = colormaps[corner_style.cmap.value]
 
         try:
             cmap.with_extremes(

{threeML-2.4.2.dev1 → threeml-2.4.2.dev2}/threeML/classicMLE/joint_likelihood.py

@@ -5,7 +5,7 @@ import sys
 from builtins import object, range, zip
 
 import astromodels.core.model
-import matplotlib.cm as cm
+from matplotlib import colormaps
 import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
@@ -1255,8 +1255,7 @@ class JointLikelihood(object):
         bounds.append(cc.max())
 
         # Define the color palette
-        palette = cm.get_cmap(
-            threeML_config["mle"]["contour_cmap"].value)  # cm.Pastel1
+        palette = colormaps[threeML_config["mle"]["contour_cmap"].value] # cm.Pastel1
         palette.set_over(threeML_config["mle"]["contour_background"])
         palette.set_under(threeML_config["mle"]["contour_background"])
         palette.set_bad(threeML_config["mle"]["contour_background"])

{threeML-2.4.2.dev1 → threeml-2.4.2.dev2}/threeML/io/calculate_flux.py

@@ -176,7 +176,7 @@ def _setup_analysis_dictionaries(
             if (
                 not use_components
                 or ("total" in components_to_use)
-                or (not mle_analyses[key]["component_names"])
+                or ('main' in mle_analyses[key]["component_names"])
             ):
                 mle_analyses[key][
                     "fitted point source"
@@ -274,7 +274,7 @@ def _setup_analysis_dictionaries(
             if (
                 not use_components
                 or ("total" in components_to_use)
-                or (not bayesian_analyses[key]["component_names"])
+                or ('main' in bayesian_analyses[key]["component_names"])
             ):
                 bayesian_analyses[key][
                     "fitted point source"
@@ -400,11 +400,17 @@ def _collect_sums_into_dictionaries(
                 "total" in components_to_use
             ):
                 use_total = True
+            
+            if 'main' in list(analyses[key]["components"].keys()
+            ):
+                use_total = True
 
-            for component in list(analyses[key]["components"].keys()):
-                component_sum_dict.setdefault(component, []).append(
-                    analyses[key]["components"][component]
-                )
+            else:
+
+                for component in list(analyses[key]["components"].keys()):
+                    component_sum_dict.setdefault(component, []).append(
+                        analyses[key]["components"][component]
+                    )
 
         else:
 
@@ -468,23 +474,29 @@ def _compute_output(analyses, _defaults, out):
                 "total" in _defaults["components_to_use"]
             ):
                 get_total = True
+            
+            if 'main' in list(analyses[key]["components"].keys()
+            ):
+                get_total = True
 
-            for component in list(analyses[key]["components"].keys()):
-                # extract the information and plot it
+            else:
 
-                samples = analyses[key]["components"][component]
+                for component in list(analyses[key]["components"].keys()):
+                    # extract the information and plot it
+                    
+                    samples = analyses[key]["components"][component]
 
-                label = f"{key}: {component}"
+                    label = f"{key}: {component}"
 
-                _append_best_fit_and_errors(
-                    samples,
-                    _defaults,
-                    label,
-                    fluxes,
-                    p_errors,
-                    n_errors,
-                    labels,
-                )
+                    _append_best_fit_and_errors(
+                        samples,
+                        _defaults,
+                        label,
+                        fluxes,
+                        p_errors,
+                        n_errors,
+                        labels,
+                    )
 
         else:
 
@@ -493,13 +505,18 @@ def _compute_output(analyses, _defaults, out):
         if get_total:
             # it ends up that we need to plot the total spectrum
             # which is just a repeat of the process
-            samples = analyses[key]["fitted point source"]
-
-            label = f"{key}: total"
+            
+            try:
+                samples = analyses[key]["fitted point source"]
+            except:
+                log.error("%s component(s) not available in source %s" %\
+                         (_defaults["components_to_use"], key))
+            else:
+                label = f"{key}: total"
 
-            _append_best_fit_and_errors(
-                samples, _defaults, label, fluxes, p_errors, n_errors, labels
-            )
+                _append_best_fit_and_errors(
+                    samples, _defaults, label, fluxes, p_errors, n_errors, labels
+                )
 
     if fluxes:
         # now make a data frame
@@ -600,7 +617,7 @@ def calculate_point_source_flux(*args, **kwargs):
     log.error(
         "The use of calculate_point_source_flux is deprecated. Please use the .get_point_source_flux()"
         " method of the JointLikelihood.results or the BayesianAnalysis.results member. For example:"
-        " jl.results.get_point_source_flux()."
+        " jl.results.get_flux()."
     )
 
     return _calculate_point_source_flux(*args, **kwargs)

{threeML-2.4.2.dev1 → threeml-2.4.2.dev2}/threeML/io/plotting/cmap_cycle.py

@@ -3,6 +3,7 @@ from builtins import range
 __author__ = "grburgess"
 
 import matplotlib.pyplot as plt
+from matplotlib import colormaps
 import numpy as np
 
 
@@ -44,7 +45,7 @@ def cmap_intervals(length=50, cmap="YlOrBr", start=None, stop=None):
     successive lines because successive colors are very similar.
     :param cmap: str name of a matplotlib colormap (see matplotlib.pyplot.cm)
     """
-    cm = plt.cm.get_cmap(cmap)
+    cm = colormaps[cmap]
 
     # qualitative color maps
     if cmap in [

{threeML-2.4.2.dev1 → threeml-2.4.2.dev2}/threeML/io/plotting/post_process_data_plots.py

@@ -1,5 +1,5 @@
 import matplotlib.pyplot as plt
-import matplotlib.cm as cm
+from matplotlib import colormaps
 import numpy as np
 import threeML.plugins.PhotometryLike as photolike
 import threeML.plugins.SpectrumLike as speclike
@@ -592,7 +592,7 @@ def display_photometry_model_magnitudes(analysis, data=(), **kwargs):
         step = bool(kwargs.pop("step"))
 
     if "data_cmap" in kwargs:
-        data_cmap = cm.get_cmap(kwargs.pop("data_cmap"))
+        data_cmap = colormaps[kwargs.pop("data_cmap")]
         data_colors = cmap_intervals(len(data_keys), data_cmap)
 
     if "model_cmap" in kwargs:

{threeML-2.4.2.dev1 → threeml-2.4.2.dev2}/threeML/minimizer/tutorial_material.py

@@ -3,6 +3,7 @@ from __future__ import division
 from builtins import map, range, zip
 
 import matplotlib.pyplot as plt
+from matplotlib import colormaps
 import numpy as np
 from astromodels import (Function1D, FunctionMeta, Gaussian, Model,
                          PointSource, use_astromodels_memoization)
@@ -138,7 +139,7 @@ def plot_minimizer_path(jl, points=False):
 
         # Color map
         N = len(qx_sets)
-        cmap = plt.cm.get_cmap("gist_earth", N + 1)
+        cmap = colormaps["gist_earth"].resampled(N + 1)
 
         for i, (qx, qy) in enumerate(zip(qx_sets, qy_sets)):
 

{threeML-2.4.2.dev1 → threeml-2.4.2.dev2}/threeML/test/test_bayesian.py

@@ -178,7 +178,7 @@ def test_dynesty_nested(bayes_fitter, completed_bn090217206_bayesian_analysis):
 
     bayes.set_sampler("dynesty_nested")
 
-    bayes.sampler.setup(n_live_points=100, n_effective=10)
+    bayes.sampler.setup(n_live_points=200, n_effective=10)
 
     bayes.sample()
 

{threeML-2.4.2.dev1 → threeml-2.4.2.dev2}/threeML/utils/OGIP/response.py

@@ -6,7 +6,7 @@ from typing import Any, Dict, List, Optional, Union
 
 import astropy.io.fits as pyfits
 import astropy.units as u
-import matplotlib.cm as cm
+from matplotlib import colormaps
 import matplotlib.pyplot as plt
 import numba as nb
 import numpy as np
@@ -322,7 +322,7 @@ class InstrumentResponse(object):
         vmin = self._matrix[self._matrix > 0].min()
 
         cmap = copy.deepcopy(
-            cm.get_cmap(threeML_config.plugins.ogip.response_cmap.value)
+            colormaps[threeML_config.plugins.ogip.response_cmap.value]
         )
 
         cmap.set_under(threeML_config.plugins.ogip.response_zero_color)

{threeML-2.4.2.dev1 → threeml-2.4.2.dev2}/threeML/utils/data_builders/fermi/lat_transient_builder.py

@@ -629,9 +629,13 @@ class TransientLATDataBuilder(object):
             os.path.join(gtapp_mp_dir, 'gtltcube_mp.py'),
             os.path.join(gtapp_mp_dir, 'gttsmap_mp.py'),
         ]
-        for _e in executables:
-            print ("Changing permission to %s" % _e)
-            os.chmod(_e, 0o755)
+
+        try:
+            for _e in executables:
+                log.info('Changing permission to %s' % _e)
+                os.chmod(_e, 0o755)
+        except PermissionError:
+            pass
 
         log.info('About to run the following command:\n%s' % cmd)
 

{threeML-2.4.2.dev1 → threeml-2.4.2.dev2}/threeML/utils/progress_bar.py

@@ -1,4 +1,4 @@
-from matplotlib import cm
+from matplotlib import colormaps
 from matplotlib.colors import to_hex
 import numpy as np
 
@@ -21,8 +21,7 @@ class _Get_Color(object):
 
     def __init__(self, n_colors=5):
 
-        cmap = cm.get_cmap(
-            threeML_config.interface.multi_progress_cmap)
+        cmap = colormaps[threeML_config.interface.multi_progress_cmap]
 
         self._colors = [to_hex(c) for c in cmap(np.linspace(0,1,n_colors))]
 

{threeML-2.4.2.dev1 → threeml-2.4.2.dev2/threeML.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: threeML
-Version: 2.4.2.dev1
+Version: 2.4.2.dev2
 Summary: The Multi-Mission Maximum Likelihood framework
 Home-page: https://github.com/threeml/threeML
 Author: Giacomo Vianello
@@ -21,8 +21,8 @@ License-File: LICENSE
 Requires-Dist: numpy>=1.16
 Requires-Dist: scipy>=1.4
 Requires-Dist: emcee>=3
-Requires-Dist: astropy>=1.3.3
-Requires-Dist: matplotlib
+Requires-Dist: astropy
+Requires-Dist: matplotlib<3.9
 Requires-Dist: uncertainties
 Requires-Dist: pyyaml>=5.1
 Requires-Dist: dill
@@ -38,7 +38,7 @@ Requires-Dist: ipyparallel
 Requires-Dist: joblib
 Requires-Dist: numexpr
 Requires-Dist: dynesty
-Requires-Dist: numba<0.59
+Requires-Dist: numba
 Requires-Dist: numdifftools
 Requires-Dist: tqdm>=4.56.0
 Requires-Dist: colorama

{threeML-2.4.2.dev1 → threeml-2.4.2.dev2}/threeML.egg-info/requires.txt

@@ -1,8 +1,8 @@
 numpy>=1.16
 scipy>=1.4
 emcee>=3
-astropy>=1.3.3
-matplotlib
+astropy
+matplotlib<3.9
 uncertainties
 pyyaml>=5.1
 dill
@@ -18,7 +18,7 @@ ipyparallel
 joblib
 numexpr
 dynesty
-numba<0.59
+numba
 numdifftools
 tqdm>=4.56.0
 colorama

{threeML-2.4.2.dev1 → threeml-2.4.2.dev2}/threeML/__init__.py

@@ -22,6 +22,10 @@ except ImportError:
 from pathlib import Path
 
 from threeML.io.logging import setup_logger
+
+# Import everything from astromodels
+from astromodels import *
+
 from .config import (
     threeML_config,
     show_configuration,
@@ -62,10 +66,6 @@ del get_versions
 import traceback
 from importlib.machinery import SourceFileLoader
 
-# Import everything from astromodels
-from astromodels import *
-
-
 # Finally import the serialization machinery
 from .io.serialization import *