Editing utils.py to patch py27 functionality (#193)

* adding ability to have user-defined modes in CommonGP

* fixing lint issues

* adding dynamic partial files

* adding code for dynamic BayesEphem

* fixing ephemeris tests

* fixing ephemeris tests

* fixing ephemeris tests

* fixing to allow py27 support

* running travis tests on py2 and py3

* changing numpy requirements

* changing python requirements

* patching to avoid crashing when python2 is used with gp coefficients

* final lint corrections

.travis.yml

@@ -2,6 +2,7 @@ language: python
 cache: pip
 
 python:
+    - "2.7.15"
     - "3.6"
 
 before_install:

enterprise/signals/gp_signals.py

@@ -10,6 +10,8 @@
 import math
 import itertools
 import functools
+import platform
+import logging
 
 import numpy as np
 
@@ -21,6 +23,12 @@
 from enterprise.signals.selections import Selection
 from enterprise.signals.utils import KernelMatrix
 
+pyv3 = platform.python_version().split('.')[0] == '3'
+
+logging.basicConfig(format='%(levelname)s: %(name)s: %(message)s',
+                    level=logging.INFO)
+logger = logging.getLogger(__name__)
+
 
 def BasisGP(priorFunction, basisFunction, coefficients=False, combine=True,
             selection=Selection(selections.no_selection),
@@ -39,6 +47,9 @@ def __init__(self, psr):
             self.name = self.psrname + '_' + self.signal_id
             self._do_selection(psr, priorFunction, basisFunction,
                                coefficients, selection)
+            if coefficients and not pyv3:
+                msg = 'GP coefficients compatible only with Python 3'
+                logger.warning(msg)
 
         def _do_selection(self, psr, priorfn, basisfn, coefficients,
                           selection):
@@ -60,7 +71,7 @@ def _do_selection(self, psr, priorfn, basisfn, coefficients,
                                            self._bases[key]._params.values()):
                     self._params[par.name] = par
 
-            if coefficients:
+            if coefficients and pyv3:
                 # we can only create GPCoefficients parameters if the basis
                 # can be constructed with default arguments
                 # (and does not change size)
@@ -116,7 +127,7 @@ def _construct_basis(self, params={}):
         # this class does different things (and gets different method
         # definitions) if the user wants it to model GP coefficients
         # (e.g., for a hierarchical likelihood) or if they do not
-        if coefficients:
+        if coefficients and pyv3:
             def _get_coefficient_logprior(self, key, c, **params):
                 self._construct_basis(params)
 
@@ -230,7 +241,7 @@ class TimingModel(BaseClass):
         signal_name = 'linear timing model'
         signal_id = name + '_svd' if use_svd else name
 
-        if coefficients:
+        if coefficients and pyv3:
             def _get_coefficient_logprior(self, key, c, **params):
                 # MV: probably better to avoid this altogether
                 #     than to use 1e40 as in get_phi
@@ -296,7 +307,7 @@ def __init__(self, psr):
 
             self._psrpos = psr.pos
 
-            if coefficients:
+            if coefficients and pyv3:
                 self._construct_basis()
 
                 chain = itertools.chain(self._prior._params.values(),
@@ -326,7 +337,7 @@ def basis_params(self):
         def _construct_basis(self, params={}):
             self._basis, self._labels = self._bases(params=params)
 
-        if coefficients:
+        if coefficients and pyv3:
             def _get_coefficient_logprior(self, c, **params):
                 # MV: for correlated GPs, the prior needs to use
                 #     the coefficients for all GPs together;

enterprise/signals/utils.py

@@ -1178,8 +1178,13 @@ def createfourierdesignmatrix_physicalephem(toas, planetssb, pos_t,
                     c = np.zeros(6)
                     c[i] = dpar
 
+                    #Fl.append(physical_ephem_delay(toas, planetssb, pos_t,
+                    #                               **{parname: c}, **oa)/dpar)
+                    kwarg_dict = {parname: c}
+                    kwarg_dict.update(oa)
                     Fl.append(physical_ephem_delay(toas, planetssb, pos_t,
-                                                   **{parname: c}, **oa)/dpar)
+                                                   **kwarg_dict)/dpar)
+
                     Phil.append(ppar)
 
     return np.array(Fl).T.copy(), np.array(Phil)

requirements.txt

@@ -1,4 +1,4 @@
-numpy==1.16.0
+numpy==1.16.3
 scipy==1.2.0
 ephem>=3.7.6.0
 Cython==0.28.5