Dev (#39)

* v3.2.2 dev see changelog.rst for changes

* some changes, see changelog.rst

* v3.3.0 see change_log.rst

* v3.3.1 see change_log.rst

* bump version to 3.3.2; see changelog

* bump version to 3.3.3; update changelog with new features and fixes

* add Read the Docs configuration and documentation requirements

.readthedocs.yml

@@ -0,0 +1,13 @@
+version: "2"
+
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.10"
+
+python:
+  install:
+    - requirements: docs/requirements.txt
+
+sphinx:
+  configuration: docs/conf.py

CONAN3/VERSION.py

@@ -0,0 +1 @@
+__version__ = '3.3.3'

CONAN3/__init__.py

@@ -1,10 +1,13 @@
 __all__ = ["load_lightcurves", "load_rvs", "fit_setup", "run_fit", "create_configfile","load_configfile","fit_configfile"]
 
-from ._classes import load_lightcurves, load_rvs, fit_setup, load_result, __default_backend__
+from ._classes import (load_lightcurves, load_rvs, fit_setup, load_result, 
+                       get_parameter_names, compare_results, __default_backend__)
 from .conf import create_configfile, load_configfile,fit_configfile
 from .fit_data import run_fit
+from .VERSION import __version__
+
+# from os import path
+# here = path.abspath(path.dirname(__file__))
+# with open(path.join(here, 'VERSION.dat')) as version_file:
+# 	__version__ = version_file.read().strip()
 
-from os import path
-here = path.abspath(path.dirname(__file__))
-with open(path.join(here, 'VERSION.dat')) as version_file:
-	__version__ = version_file.read().strip()

CONAN3/basecoeff_setup.py

@@ -1,7 +1,7 @@
 import sys
 import numpy as np
 
-def basecoeff(ibase,spline,init=None,lims=None):
+def basecoeff(ibase,spline,init=None,lims=None, fit_offset="y"):
     # this function returns the input arrays for the baseline coefficients
     #   only those coefficients that are used are set to be jump parameters, 
     #   all others are set == 0 value, 0 stepsize, [0,0] Boundaries.
@@ -30,7 +30,7 @@ def basecoeff(ibase,spline,init=None,lims=None):
         nbc = nbc+1
     else:
         offset[:,0]=[init["off"],0.1*np.diff(lims["off"])[0],*lims["off"]]        # no CNM: set the starting value and limits of the offset    
-        if spline.use: offset[:,0]=[init["off"],0,0,0]   # if we use a spline, set offset to 1 and fix it
+        if spline.use or fit_offset=="n": offset[:,0]=[init["off"],0,0,0]   # if we use a spline, fix offset to 1 or bestvalue from get_decorr fit
         else: nbc = nbc+1
 
      # dcol0 coeff:   A0*dcol0 + B0*dcol0^2 + C0*dcol0^3 + D0*dcol0^4
@@ -113,11 +113,11 @@ def basecoeff(ibase,spline,init=None,lims=None):
 
     # dsin  coeff:   Amp*sin(2pi(dcol0-phi)/P) -x-> Amp*sin(freq*dcol0+phi)
     dsin=np.zeros((4,3), dtype=float)
-    if ibase[7] > 0: 
-        dsin[:,0]=[init["amp"],0.001,0,1]
-        dsin[:,1]=[init["freq"],0.001,1,333]
-        dsin[:,2]=[init["phi"],0.001,0,1]
-        nbc = nbc+3
+    # if ibase[7]=="y": 
+    #     dsin[:,0]=[init["amp"],0.001,0,1]
+    #     dsin[:,1]=[init["freq"],0.001,1,333]
+    #     dsin[:,2]=[init["phi"],0.001,0,1]
+    #     nbc = nbc+3
 
     # H coeff => CNM                
     dCNM=np.zeros((4,2), dtype=float)

CONAN3/funcs.py

@@ -4,7 +4,6 @@
 import scipy.stats as stats
 import scipy.interpolate as si
 
-
 def corfac(rarr, tarr, earr, indlist, nphot, njumpphot):
     bw=np.ones(nphot)
     br=np.ones(nphot)
@@ -134,7 +133,7 @@ def credregionML(posterior=None, percentile=0.6827, pdf=None, xpdf=None):
     density for a given percentile of the highest posterior density.
     These outputs can be used to easily compute the HPD credible regions.
 
-    Parameters
+    Parameters:
     ----------
     posterior: 1D float ndarray
         A posterior distribution.
@@ -240,4 +239,4 @@ def grtest_emcee(chains_out):
     VV = (ns-1.)/ns * WV + (nc + 1.)/(ns*nc) * BV # VV should be an (ndim) array
     GR = VV/WV                             # GR should be an (ndim) array
 
-    return GR
+    return GR