nested-fit 5.6.8.dev125__tar.gz → 5.6.9__tar.gz

{nested_fit-5.6.8.dev125 → nested_fit-5.6.9}/.gitignore

@@ -50,3 +50,6 @@ wheelhouse/
 
 # FBuild config file
 .fbuild.lua
+
+# Temporary files
+tmp/

{nested_fit-5.6.8.dev125 → nested_fit-5.6.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nested_fit
-Version: 5.6.8.dev125
+Version: 5.6.9
 Summary: The nested_fit package.
 Author: Martino Trassinelli, Lune Maillard, César Godinho
 Project-URL: Homepage, https://github.com/martinit18/nested_fit
@@ -41,10 +41,9 @@ Users are also required to cite the Nested Fit papers here below in their public
 
 **Reference articles of nested_fit**:
 - [A] M. Trassinelli, *Bayesian data analysis tools for atomic physics*, Nucl. Instrum. Methods B **408**, 301-312 (2017),
-[doi:10.1016/j.nimb.2017.05.030](http://dx.doi.org/10.1016/j.nimb.2017.05.030),  [	arXiv:1611.10189](https://arxiv.org/abs/1611.10189)\
-- [B] M. Trassinelli, *The Nested_fit Data Analysis Program*, Proceedings **33**, 14 (2019), [doi:10.3390/proceedings2019033014](https://doi.org/10.3390/proceedings2019033014)\
+[doi:10.1016/j.nimb.2017.05.030](http://dx.doi.org/10.1016/j.nimb.2017.05.030),  [arXiv:1611.10189](https://arxiv.org/abs/1611.10189)
+- [B] M. Trassinelli, *The Nested_fit Data Analysis Program*, Proceedings **33**, 14 (2019), [doi:10.3390/proceedings2019033014](https://doi.org/10.3390/proceedings2019033014)
 - [C] M. Trassinelli, P. Ciccodicola *Mean Shift Cluster Recognition Method Implementation in the Nested Sampling Algorithm*, Entropy **22**, 185 (2020), [doi:10.3390/e22020185](https://doi.org/10.3390/e22020185)
-\
 - [D] L. Maillard, F. Finocchi, M. Trassinelli * *Assessing Search and Unsupervised Clustering Algorithms in Nested Sampling*, Entropy **25**, 347 (2023), [doi:10.3390/e25020347](https://doi.org/10.3390/e25020347)
 
 ### Authors
@@ -67,6 +66,8 @@ email: c.godinho AT campus.fct.unl.pt
 [Download](https://github.com/martinit18/nested_fit/blob/dev/examples/jupyter_notebooks/quick_start_with_google_colab.ipynb)
 [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/martinit18/nested_fit/blob/dev/examples/jupyter_notebooks/quick_start_with_google_colab.ipynb)
 
+If you want to start to use a program in the jupyter environment, start with `examples/jupyter_notebooks/simple_analysis_visu.ipynb`
+
 Other jupyter notebook examples can be found in `examples/jupyter_notebooks`.
 
 ## Installation instructions
@@ -447,6 +448,8 @@ Examples of use of a legacy function can be found in `examples/data_analysis/aaa
 
 The present version is 5.6.8\
 New features:
+- New 2D Lennard-Jones functions added
+- New benchmark notebook available
 - New function to visualizing the capacty heat for POTENTIAL calculations
 - Latex input support for compound variable names (i.e. x_{sub})
 - PyPI available development builds

{nested_fit-5.6.8.dev125 → nested_fit-5.6.9}/README.md

@@ -16,10 +16,9 @@ Users are also required to cite the Nested Fit papers here below in their public
 
 **Reference articles of nested_fit**:
 - [A] M. Trassinelli, *Bayesian data analysis tools for atomic physics*, Nucl. Instrum. Methods B **408**, 301-312 (2017),
-[doi:10.1016/j.nimb.2017.05.030](http://dx.doi.org/10.1016/j.nimb.2017.05.030),  [	arXiv:1611.10189](https://arxiv.org/abs/1611.10189)\
-- [B] M. Trassinelli, *The Nested_fit Data Analysis Program*, Proceedings **33**, 14 (2019), [doi:10.3390/proceedings2019033014](https://doi.org/10.3390/proceedings2019033014)\
+[doi:10.1016/j.nimb.2017.05.030](http://dx.doi.org/10.1016/j.nimb.2017.05.030),  [arXiv:1611.10189](https://arxiv.org/abs/1611.10189)
+- [B] M. Trassinelli, *The Nested_fit Data Analysis Program*, Proceedings **33**, 14 (2019), [doi:10.3390/proceedings2019033014](https://doi.org/10.3390/proceedings2019033014)
 - [C] M. Trassinelli, P. Ciccodicola *Mean Shift Cluster Recognition Method Implementation in the Nested Sampling Algorithm*, Entropy **22**, 185 (2020), [doi:10.3390/e22020185](https://doi.org/10.3390/e22020185)
-\
 - [D] L. Maillard, F. Finocchi, M. Trassinelli * *Assessing Search and Unsupervised Clustering Algorithms in Nested Sampling*, Entropy **25**, 347 (2023), [doi:10.3390/e25020347](https://doi.org/10.3390/e25020347)
 
 ### Authors
@@ -42,6 +41,8 @@ email: c.godinho AT campus.fct.unl.pt
 [Download](https://github.com/martinit18/nested_fit/blob/dev/examples/jupyter_notebooks/quick_start_with_google_colab.ipynb)
 [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/martinit18/nested_fit/blob/dev/examples/jupyter_notebooks/quick_start_with_google_colab.ipynb)
 
+If you want to start to use a program in the jupyter environment, start with `examples/jupyter_notebooks/simple_analysis_visu.ipynb`
+
 Other jupyter notebook examples can be found in `examples/jupyter_notebooks`.
 
 ## Installation instructions
@@ -422,6 +423,8 @@ Examples of use of a legacy function can be found in `examples/data_analysis/aaa
 
 The present version is 5.6.8\
 New features:
+- New 2D Lennard-Jones functions added
+- New benchmark notebook available
 - New function to visualizing the capacty heat for POTENTIAL calculations
 - Latex input support for compound variable names (i.e. x_{sub})
 - PyPI available development builds

{nested_fit-5.6.8.dev125 → nested_fit-5.6.9}/nested_fit.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nested_fit
-Version: 5.6.8.dev125
+Version: 5.6.9
 Summary: The nested_fit package.
 Author: Martino Trassinelli, Lune Maillard, César Godinho
 Project-URL: Homepage, https://github.com/martinit18/nested_fit
@@ -41,10 +41,9 @@ Users are also required to cite the Nested Fit papers here below in their public
 
 **Reference articles of nested_fit**:
 - [A] M. Trassinelli, *Bayesian data analysis tools for atomic physics*, Nucl. Instrum. Methods B **408**, 301-312 (2017),
-[doi:10.1016/j.nimb.2017.05.030](http://dx.doi.org/10.1016/j.nimb.2017.05.030),  [	arXiv:1611.10189](https://arxiv.org/abs/1611.10189)\
-- [B] M. Trassinelli, *The Nested_fit Data Analysis Program*, Proceedings **33**, 14 (2019), [doi:10.3390/proceedings2019033014](https://doi.org/10.3390/proceedings2019033014)\
+[doi:10.1016/j.nimb.2017.05.030](http://dx.doi.org/10.1016/j.nimb.2017.05.030),  [arXiv:1611.10189](https://arxiv.org/abs/1611.10189)
+- [B] M. Trassinelli, *The Nested_fit Data Analysis Program*, Proceedings **33**, 14 (2019), [doi:10.3390/proceedings2019033014](https://doi.org/10.3390/proceedings2019033014)
 - [C] M. Trassinelli, P. Ciccodicola *Mean Shift Cluster Recognition Method Implementation in the Nested Sampling Algorithm*, Entropy **22**, 185 (2020), [doi:10.3390/e22020185](https://doi.org/10.3390/e22020185)
-\
 - [D] L. Maillard, F. Finocchi, M. Trassinelli * *Assessing Search and Unsupervised Clustering Algorithms in Nested Sampling*, Entropy **25**, 347 (2023), [doi:10.3390/e25020347](https://doi.org/10.3390/e25020347)
 
 ### Authors
@@ -67,6 +66,8 @@ email: c.godinho AT campus.fct.unl.pt
 [Download](https://github.com/martinit18/nested_fit/blob/dev/examples/jupyter_notebooks/quick_start_with_google_colab.ipynb)
 [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/martinit18/nested_fit/blob/dev/examples/jupyter_notebooks/quick_start_with_google_colab.ipynb)
 
+If you want to start to use a program in the jupyter environment, start with `examples/jupyter_notebooks/simple_analysis_visu.ipynb`
+
 Other jupyter notebook examples can be found in `examples/jupyter_notebooks`.
 
 ## Installation instructions
@@ -447,6 +448,8 @@ Examples of use of a legacy function can be found in `examples/data_analysis/aaa
 
 The present version is 5.6.8\
 New features:
+- New 2D Lennard-Jones functions added
+- New benchmark notebook available
 - New function to visualizing the capacty heat for POTENTIAL calculations
 - Latex input support for compound variable names (i.e. x_{sub})
 - PyPI available development builds

{nested_fit-5.6.8.dev125 → nested_fit-5.6.9}/pynested_fit/__init__.py

@@ -84,11 +84,11 @@ if get_env_type() == 'IPython':
     vgrid.add_row(ipython_header_grid)
     vgrid.add_row(ipython_header)
     rprint(RPanel(vgrid, title=f'Welcome to {__package__}', expand=False))
+    del ipython_header
 
 # Clean the namespace
 del get_env_type
 del logging
 del RichHandler
 del rich_traceback
-# del ipython_header
 del rprint

{nested_fit-5.6.8.dev125 → nested_fit-5.6.9}/pynested_fit/metadata.py

@@ -2,6 +2,7 @@ from importlib.metadata import version as imp_version
 from configparser import ConfigParser
 from subprocess import check_output
 import sys
+import os
 
 __version__ = imp_version('nested_fit')
 
@@ -10,8 +11,13 @@ __version__ = imp_version('nested_fit')
 # Other wise default to unknown features status
 def parse_features():
     try:
-        nf_cache_folder = check_output([f'nested_fit{__version__}', '--cache-location'])
-    except Exception:
+        exe = os.path.join(os.path.dirname(__file__), f'nested_fit{__version__}')
+        print(__version__)
+        print(exe)
+        nf_cache_folder = check_output([f'{exe}', '--cache-location'])
+        print(nf_cache_folder)
+    except Exception as e:
+        print(e)
         return ('Unknown', 'Unknown')
     nf_cache_folder = nf_cache_folder.decode('utf-8').strip()
     config = ConfigParser()

{nested_fit-5.6.8.dev125 → nested_fit-5.6.9}/pynested_fit/nested_res.py

@@ -570,7 +570,7 @@ class Analysis(object):
             width = depth = 1
             # Plot
             ax_d = fig_d.add_subplot(111, projection='3d')
-            cmap = plt.cm.get_cmap('jet') # Get desired colormap - you can change this!
+            cmap = plt.get_cmap('jet') # Get desired colormap - you can change this!
             max_height = np.max(zzz)   # get range of colorbars so we can normalize
             min_height = 0.
             # scale each z to [0,1], and get their rgb values
@@ -604,7 +604,7 @@ class Analysis(object):
             width = depth = 1
             # Plot
             ax_f = fig_f.add_subplot(111, projection='3d')
-            cmap = plt.cm.get_cmap('jet') # Get desired colormap - you can change this!
+            cmap = plt.get_cmap('jet') # Get desired colormap - you can change this!
             max_height = np.max(zzz)   # get range of colorbars so we can normalize
             min_height = 0.
             # scale each z to [0,1], and get their rgb values
@@ -638,7 +638,7 @@ class Analysis(object):
             width = depth = 1
             # Plot
             ax_r = fig_r.add_subplot(111, projection='3d')
-            #cmap = plt.cm.get_cmap('jet') # Get desired colormap - you can change this!
+            #cmap = plt.get_cmap('jet') # Get desired colormap - you can change this!
             #max_height = np.max(zzz)   # get range of colorbars so we can normalize
             #min_height = 0.
             # scale each z to [0,1], and get their rgb values
@@ -893,7 +893,7 @@ class Analysis(object):
         plt.xlim(0,shape(data)[0]*1.1)
         plt.xlabel('Sort number')
         plt.ylabel('Value of parameter ' + par_name)
-        cmap=plt.cm.get_cmap('jet')
+        cmap=plt.get_cmap('jet')
         plt.scatter(ix,data[:,par_index],c=data[:,0],linewidth=0.,cmap=cmap)
         cbar = plt.colorbar()
         cbar.set_label('Weight')
@@ -948,7 +948,7 @@ class Analysis(object):
         plt.xlabel(par_name1)
         plt.ylabel(par_name2)
         #plt.ylabel('Value of parameter ' + title)
-        #cmap=plt.cm.get_cmap('jet')
+        #cmap=plt.get_cmap('jet')
         for i in range(ncl): plt.plot(data[data[:,0]==i][:,par_index1],data[data[:,0]==i][:,par_index2],'o')
         plt.tight_layout()
 
@@ -1047,7 +1047,7 @@ class Analysis(object):
         plt.xlabel(par_name1)
         plt.ylabel(par_name2)
         #plt.ylabel('Value of parameter ' + title)
-        #cmap=plt.cm.get_cmap('jet')
+        #cmap=plt.get_cmap('jet')
         plt.plot(data[:,par_index1],data[:,par_index2],'ob')
         plt.tight_layout()
 
@@ -1114,11 +1114,11 @@ class Analysis(object):
 
         # Choose the cmap for likelihood plots
         if cmap == 'normal':
-            cmap=plt.cm.get_cmap('jet')
+            cmap=plt.get_cmap('jet')
         elif cmap == 'accurate':
-            cmap=plt.cm.get_cmap('gist_ncar')
+            cmap=plt.get_cmap('gist_ncar')
         elif cmap == 'moreaccurate':
-            cmap=plt.cm.get_cmap('prism')
+            cmap=plt.get_cmap('prism')
 
         # Plot histogram
         plt.clf()
@@ -1304,11 +1304,11 @@ class Analysis(object):
 
         # Choose the cmap for likelihood plots
         if cmap == 'normal':
-            cmap=plt.cm.get_cmap('jet')
+            cmap=plt.get_cmap('jet')
         elif cmap == 'accurate':
-            cmap=plt.cm.get_cmap('spectral')
+            cmap=plt.get_cmap('nipy_spectral')
         elif cmap == 'moreaccurate':
-            cmap=plt.cm.get_cmap('prism')
+            cmap=plt.get_cmap('prism')
 
         # Plot interpolation
         if clear: plt.clf()

{nested_fit-5.6.8.dev125 → nested_fit-5.6.9}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "nested_fit"
-version = "5.6.8.dev125"
+version = "5.6.9"
 description = "The nested_fit package."
 readme = "README.md"
 
@@ -65,7 +65,7 @@ archs = ["x86_64", "arm64"]
 archs = ["x86_64"]
 
 [tool.setuptools_scm]
-fallback_version = "5.6.8.dev125"
+fallback_version = "1.0.0"
 
 [options]
 python_requires = ">=3.8"

{nested_fit-5.6.8.dev125 → nested_fit-5.6.9}/src/funceval/latex_parser.cpp

@@ -15,6 +15,7 @@
 
 // Lets keep C++11 compliant
 #include <regex>
+#include <functional>
 #include <string>
 #include <cstring>
 #include <iostream>