Merge pull request #328 from California-Planet-Search/next-release

Version 1.4.2

README.md

@@ -57,4 +57,4 @@ Follow examples in
 - `radvel/docs/tutorials/SyntheticData.ipynb`
 - `radvel/docs/tutorials/K2-24_Fitting+MCMC.ipynb`
 - `radvel/docs/tutorials/164922_Fitting+MCMC.ipynb`
-- `radvel/docs/tutorials/GaussianProcess-tutorial.ipynb`
+- `radvel/docs/tutorials/GaussianProcess-tutorial.ipynb`

radvel/__init__.py

@@ -29,7 +29,7 @@ def _custom_warningfmt(msg, *a, **b):
 __all__ = ['model', 'likelihood', 'posterior', 'mcmc', 'prior', 'utils',
          'fitting', 'report', 'cli', 'driver', 'gp']
 
-__version__ = '1.4.1'
+__version__ = '1.4.2'
 __spec__ = __name__
 __package__ = __path__[0]
 

radvel/basis.py

@@ -393,6 +393,7 @@ def _setpar(key, new_value):
 
         if isinstance(params_out, radvel.model.Parameters):
             params_out.basis = Basis('per tp e w k', self.num_planets)
+            params_out.planet_parameters = params_out.basis.name.split()
         return params_out
 
     def v_from_synth(self, params_in, newbasis):
@@ -727,6 +728,7 @@ def _delpar(key):
                 self.params = newbasis.split()
 
         params_out.basis = Basis(newbasis, self.num_planets)
+        params_out.planet_parameters = params_out.basis.name.split()
 
         return params_out
 

radvel/driver.py

@@ -17,6 +17,7 @@
 
 import pandas as pd
 import numpy as np
+from numpy import inf
 from astropy import constants as c
 
 if sys.version_info[0] < 3:
@@ -582,8 +583,8 @@ def report(args):
     else:
         derived = False
     try:
-        compstats = eval(status.get('ic_compare', args.comptype))
-    except:
+        compstats = eval(status.get('ic_compare', 'ic'))
+    except KeyError:
         print("WARNING: Could not find {} model comparison \
 in {}.\nPlease make sure that you have run `radvel ic -t {}` (or, e.g., `radvel \
 ic -t nplanets e trend jit gp`)\

radvel/model.py

@@ -289,7 +289,31 @@ def __call__(self,t,*args,**kwargs):
         vel += self.vector.vector[self.vector.indices['curv']][0] * (t - self.time_base)**2
         return vel
 
-
+    def array_to_params(self,param_values):
+
+    	new_params = self.params
+
+    	vary_parameters = self.list_vary_params()
+
+    	for i in range(len(vary_parameters)):
+    		new_params[vary_parameters[i]] = Parameter(value=param_values[i])
+
+    	return new_params
+
+    def list_vary_params(self):
+        keys = self.list_params()
+
+        return [key for key in keys if self.params[key].vary]
+
+    def list_params(self):
+        try:
+            keys = self.params_order
+        except AttributeError:
+            keys = list(self.params.keys())
+            self.params_order = keys
+        return keys
+
+
 def _standard_rv_calc(t,params,vector,planet_num=None):
         vel = np.zeros(len(t))
         params_synth = params.basis.v_to_synth(vector)

radvel/plot/orbit_plots.py

@@ -451,8 +451,8 @@ def plot_multipanel(self, nophase=False, letter_labels=True):
 
         # phase-folded plots
         if not nophase:
-            gs_phase = gridspec.GridSpec(self.phase_nrows, self.phase_ncols)
-
+            gs_phase = gridspec.GridSpec(max([1,self.phase_nrows]), max([1,self.phase_ncols]))
+            
             if self.phase_ncols == 1:
                 gs_phase.update(left=0.12, right=0.93,
                                 top=divide - self.rv_phase_space * 0.5,

radvel/posterior.py

@@ -1,6 +1,6 @@
 from .likelihood  import Likelihood
 import numpy as np
-import pickle
+import dill as pickle
 import radvel
 from radvel.gp import CeleriteKernel
 

radvel/utils.py

@@ -654,12 +654,11 @@ def draw_models_from_chain(mod, chain, t, nsamples=50):
     """
 
     np.random.seed(0)
-    chain_samples = chain.ix[np.random.choice(chain.index, nsamples)]
+    chain_samples = chain.iloc[np.random.choice(chain.index, nsamples)]
     models = []
     for i in chain_samples.index:
-        params = np.array(chain.ix[i, mod.vary_parameters])
+        params = np.array(chain.loc[i, mod.list_vary_params()])
         params = mod.array_to_params(params)
-        models += [mod.model(params, t)]
+        models += [mod(t)]
     models = np.vstack(models)
     return models
-

requirements.txt

@@ -12,3 +12,4 @@ ipykernel>=4.10.0
 jinja2>=2.9
 python-dateutil>=2.5.0
 h5py>=2.10.0
+dill