Merge pull request #354 from California-Planet-Search/next-release

Version 1.4.8

.readthedocs.yml

@@ -2,4 +2,4 @@ requirements_file:
     docs/requirements.txt
 python:
     setup_py_install: true
-    version: 2.7
+    version: 3.7

Dockerfile

@@ -9,7 +9,7 @@ ENV COVERALLS_REPO_TOKEN=7ZpQ0LQWM2PNl5iu7ZndyFEisQnZow8oT
 RUN mkdir /code && \
     mkdir /code/radvel && \
     apt-get --yes update && \
-    apt-get install --yes gcc git && \
+    apt-get install --yes gcc git pkg-config libhdf5-100 libhdf5-dev && \
     apt-get clean && \
     conda config --add channels conda-forge && \
     conda config --set channel_priority strict && \
@@ -26,7 +26,7 @@ RUN pip install --no-cache-dir -r requirements.txt
 ADD . /code/radvel
 
 
-CMD pip install --no-cache-dir --no-deps .  && \
-    python setup.py build_ext -i  && \
+CMD python setup.py build_ext -i  && \
+    pip install --no-cache-dir --no-deps .  && \
     nosetests radvel --with-coverage --cover-package=radvel && \
     coveralls

docs/conf.py

@@ -34,7 +34,7 @@
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
-#needs_sphinx = '1.0'
+# needs_sphinx = '2.2'
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom

docs/requirements.txt

@@ -11,3 +11,4 @@ jupyter_client
 ipykernel
 pybind11
 sphinx_rtd_theme
+mock

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__ = '1.4.7'
+__version__ = '1.4.8'
 __package__ = __path__[0]
 
 MODULEDIR, filename = os.path.split(__file__)

radvel/driver.py

@@ -6,6 +6,7 @@
 from __future__ import print_function
 
 import radvel
+from radvel.likelihood import GPLikelihood
 from radvel.plot import orbit_plots, mcmc_plots
 from radvel.mcmc import statevars
 
@@ -67,7 +68,7 @@ def plots(args):
             if hasattr(P, 'bjd0'):
                 args.plotkw['epoch'] = P.bjd0
 
-            if args.gp:
+            if args.gp or isinstance(post.likelihood, GPLikelihood):
                 GPPlot = orbit_plots.GPMultipanelPlot(
                     post, saveplot=saveto, **args.plotkw
                 )

radvel/plot/orbit_plots.py

@@ -132,11 +132,18 @@ def __init__(self, post, saveplot=None, epoch=2450000, yscale_auto=False, yscale
         else:
             longp = max(self.post.likelihood.x) - min(self.post.likelihood.x)
 
-        self.dt = max(self.rvtimes) - min(self.rvtimes)
-        self.rvmodt = np.linspace(
-            min(self.rvtimes) - 0.05 * self.dt, max(self.rvtimes) + 0.05 * self.dt + longp,
-            int(resolution)
-        )
+        if self.set_xlim is not None:
+            self.dt = self.set_xlim[1] - self.set_xlim[0]
+            self.rvmodt = np.linspace(
+                (self.set_xlim[0]+self.epoch) - 0.05 * self.dt, (self.set_xlim[1]+self.epoch) + 0.05 * self.dt + longp,
+                int(resolution)
+            )
+        else:
+            self.dt = max(self.rvtimes) - min(self.rvtimes)
+            self.rvmodt = np.linspace(
+                min(self.rvtimes) - 0.05 * self.dt, max(self.rvtimes) + 0.05 * self.dt + longp,
+                int(resolution)
+            )
 
         self.orbit_model = self.model(self.rvmodt)
         self.rvmod = self.model(self.rvtimes)
@@ -506,7 +513,7 @@ def __init__(self, post, saveplot=None, epoch=2450000, yscale_auto=False, yscale
                  legend=True,
                  phase_limits=[], nobin=False, phasetext_size='large',  figwidth=7.5, fit_linewidth=2.0,
                  set_xlim=None, text_size=9, legend_kwargs=dict(loc='best'), subtract_gp_mean_model=False,
-                 plot_likelihoods_separately=False, subtract_orbit_model=False, status=None):
+                 plot_likelihoods_separately=False, subtract_orbit_model=False, status=None, separate_orbit_gp=False):
 
         super(GPMultipanelPlot, self).__init__(
             post, saveplot=saveplot, epoch=epoch, yscale_auto=yscale_auto,
@@ -520,6 +527,7 @@ def __init__(self, post, saveplot=None, epoch=2450000, yscale_auto=False, yscale
         self.subtract_gp_mean_model = subtract_gp_mean_model
         self.plot_likelihoods_separately = plot_likelihoods_separately
         self.subtract_orbit_model = subtract_orbit_model
+        self.separate_orbit_gp = separate_orbit_gp
         if status is not None:
             self.status = status
 
@@ -553,7 +561,11 @@ def plot_gp_like(self, like, orbit_model4data, ci):
 
         if isinstance(like, radvel.likelihood.GPLikelihood):
 
-            xpred = np.linspace(np.min(like.x), np.max(like.x), num=int(3e3))
+            if self.set_xlim is not None:
+                xpred = np.linspace(self.set_xlim[0]+self.epoch, self.set_xlim[1]+self.epoch, num=int(3e3))
+            else:
+                xpred = np.linspace(np.min(like.x), np.max(like.x), num=int(3e3))
+
             gpmu, stddev = like.predict(xpred)
             if self.subtract_orbit_model:
                 gp_orbit_model = np.zeros(xpred.shape)
@@ -586,8 +598,12 @@ def plot_gp_like(self, like, orbit_model4data, ci):
             ax.fill_between(xpred, gpmu+gp_orbit_model-stddev, gpmu+gp_orbit_model+stddev, 
                             color=color, alpha=0.5, lw=0
                             )
-            ax.plot(xpred, gpmu+gp_orbit_model, 'b-', rasterized=False, lw=0.1)
-
+            if self.separate_orbit_gp:
+                ax.plot(xpred, gpmu, '-', color='orange', rasterized=False, lw=0.2, label='GP')
+                ax.plot(xpred, gp_orbit_model, 'g-', rasterized=False, lw=0.2, label="Orbit")
+                ax.plot(xpred, gpmu+gp_orbit_model, 'b-', rasterized=False, lw=0.4, label="Orbit+GP")
+            else:
+                ax.plot(xpred, gpmu+gp_orbit_model, 'b-', rasterized=False, lw=0.4)
         else:
             # plot orbit model
             ax.plot(self.mplttimes, self.orbit_model, 'b-', rasterized=False, lw=0.1)
@@ -599,6 +615,7 @@ def plot_gp_like(self, like, orbit_model4data, ci):
         ax.set_ylabel('RV [{ms:}]'.format(**plot.latex), weight='bold')
         ticks = ax.yaxis.get_majorticklocs()
         ax.yaxis.set_ticks(ticks[1:])
+        ax.xaxis.set_ticks([])
 
         return ci
 
@@ -626,7 +643,6 @@ def plot_timeseries(self):
             self.plttimes, self.rawresid+orbit_model4data, self.rverr,
             self.post.likelihood.telvec, ax, telfmts=self.telfmts
         )
-
         if self.set_xlim is not None:
             ax.set_xlim(self.set_xlim)
         else:

requirements.txt

@@ -11,5 +11,5 @@ jupyter_client>=5.2.4
 ipykernel>=4.10.0
 jinja2>=2.9
 python-dateutil>=2.5.0
-h5py
+h5py==2.10.0
 dill