Updated versions

docs/conf.py

@@ -107,7 +107,7 @@ class compat(types.ModuleType):
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = 'en'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.

mosfit/__init__.py

@@ -22,7 +22,7 @@
         else:
             contributors.append(cont.split('(')[0].strip())
 
-__version__ = '1.1.9'
+__version__ = '1.2'
 __author__ = ' & '.join([', '.join(authors[:-1]), authors[-1]])
 __contributors__ = ' & '.join([', '.join(contributors[:-1]), contributors[-1]])
 __license__ = 'MIT'

mosfit/modules/engines/bns_magnetar.py

@@ -2,7 +2,7 @@
 from math import isnan
 
 import numpy as np
-from scipy.integrate import cumtrapz
+from scipy.integrate import cumulative_trapezoid
 from astrocats.catalog.source import SOURCE
 
 from mosfit.constants import DAY_CGS, M_SUN_CGS, KM_CGS, G_CGS, C_CGS
@@ -105,7 +105,7 @@ def process(self, **kwargs):
 
             # Magnetar input stops when extractable energy used up:
 
-            E_rad = cumtrapz(luminosities, x = np.array(ts) * DAY_CGS, initial=0)
+            E_rad = cumulative_trapezoid(luminosities, x = np.array(ts) * DAY_CGS, initial=0)
 
             luminosities = [0.0 if E_rad[i]>E_available else luminosities[i] for
                                 i in range(len(luminosities))]

mosfit/requirements.txt

@@ -1,17 +1,17 @@
 astrocats>=0.3.33
-astropy>=1.3
-Cython>=0.24.1
-dynesty>=0.9.0
+astropy>=5.0.1
+Cython>=3.0.0
+dynesty>=2.0.0
 emcee>=3.0.2
 extinction>=0.2.2
-inflect>=0.2.5
-matplotlib>=1.5.3
-mpi4py>=2.0.0
+inflect>=1.0.0
+matplotlib>=3.0.0
+mpi4py==3.1.6
 nbstripout>=0.2.9
 numexpr>=2.6.1
-numpy>=1.16
+numpy<=1.26.4
 palettable>=2.1.1
-schwimmbad>=0.2.1
+schwimmbad==0.3.0
 scipy>=1.2
 seaborn>=0.7.1
-six
+six>=1.0.0

mosfit/strings.json

@@ -164,6 +164,7 @@
     "parser_prefer_fluxes": "If magnitudes and fluxes exist for the same observation(s), prefer the flux representation over the magnitude representation.",
     "parser_print_trees": "Print the full dependency trees of each model.",
     "parser_quiet": "Print minimal output upon execution. Don't display our amazing logo :-(",
+    "parser_quick_save": "Save the minimum required output files and overwrite any existing files.",
     "parser_run_until_converged": "Run each model until it has converged. This parameter has different meanings depending on the sampler used:\n\nFor the `ensembler`, this parameter corresponds to the PSRF [Default: 1.1].\nFor the `dynesty`, this parameter controls both the initial dlogz in the static phase of the sampling and the KL-divergence criterion in the dynamic phase of the sampling [Default: 0.02].\n\nThis will run beyond the specified number of iterations, and is recommended when the `--upload/-u` flag is set.",
     "parser_run_until_uncorrelated": "Run each model until the autocorrelation time is measured accurately and chain has burned in for the specified number of autocorrelation times [Default: 10.0]. This will run beyond the specified number of iterations, and is recommended when the `--upload/-u` flag is set.",
     "parser_save_full_chain": "Save the full chain for each model fit.",