Merge pull request #382 from California-Planet-Search/next-release

Version 1.4.11

Dockerfile

@@ -1,4 +1,4 @@
-FROM conda/miniconda3
+FROM continuumio/miniconda3
 
 ENV TERM=xterm
 ENV TERMINFO=/etc/terminfo
@@ -9,13 +9,15 @@ ENV COVERALLS_REPO_TOKEN=7ZpQ0LQWM2PNl5iu7ZndyFEisQnZow8oT
 RUN mkdir /code && \
     mkdir /code/radvel && \
     apt-get --yes update && \
-    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 && \
-    conda update -n base -c defaults conda && \
-    conda install --yes nomkl numpy pybind11 coveralls nose && \
-    conda install --yes -c conda-forge celerite && \
+    apt-get install --yes gcc git pkg-config libhdf5-hl-100 libhdf5-dev && \
+    apt-get clean
+
+# RUN conda config --add channels conda-forge && \
+#     conda config --set channel_priority strict && \
+#     conda update -n base -c defaults conda
+
+RUN conda install --yes nomkl numpy pybind11 coveralls nose
+RUN conda install --yes -c conda-forge celerite && \
     conda clean -afy
 
 WORKDIR /code/radvel

docs/requirements.txt

@@ -1,14 +1,17 @@
-numpy>=1.11
-scipy>=0.17
+numpy==1.24.3
+scipy==1.10.1
 matplotlib>=1.5.3
 corner>=2.0
 cython>=0.23
 astropy>=1.1.2
 emcee>=3.0.0
 pandas>=0.20.0
-nbsphinx
+nbsphinx==0.9.3
+nbconvert==7.8.0
+mistune==3.0.1
 jupyter_client
 ipykernel
 pybind11
 sphinx_rtd_theme
 mock
+docutils==0.16

pyproject.toml

@@ -0,0 +1,2 @@
+[build-system]
+requires = ["setuptools", "wheel", "Cython", "pybind11", "numpy"]

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__ = '1.4.10'
+__version__ = '1.4.11'
 __package__ = __path__[0]
 
 MODULEDIR, filename = os.path.split(__file__)

radvel/driver.py

@@ -570,6 +570,8 @@ def report(args):
                             "{}_radvel.stat".format(conf_base))
 
     status = load_status(statfile)
+    if 'ic_compare' in status.keys():
+        status['ic_compare']['ic'] = status['ic_compare']['ic'].replace('-inf', '-np.inf')
 
     P, post = radvel.utils.initialize_posterior(config_file)
     post = radvel.posterior.load(status.get('fit', 'postfile'))

radvel/mcmc.py

@@ -264,15 +264,15 @@ def mcmc(post, nwalkers=50, nrun=10000, ensembles=8, checkinterval=50, minAfacto
         else:
             check_gp = isinstance(post.likelihood, radvel.likelihood.GPLikelihood)
 
-        np_info = np.__config__.blas_opt_info
-        if 'extra_link_args' in np_info.keys() \
-         and check_gp \
-         and ('-Wl,Accelerate' in np_info['extra_link_args']) \
-         and serial == False:
-            print("WARNING: Parallel processing with Gaussian Processes will not work with your current"
-                        + " numpy installation. See radvel.readthedocs.io/en/latest/OSX-multiprocessing.html"
-                        + " for more details. Running in serial with " + str(ensembles) + " ensembles.")
-            serial = True
+        # np_info = np.__config__.blas_opt_info
+        # if 'extra_link_args' in np_info.keys() \
+        #  and check_gp \
+        #  and ('-Wl,Accelerate' in np_info['extra_link_args']) \
+        #  and serial == False:
+        #     print("WARNING: Parallel processing with Gaussian Processes will not work with your current"
+        #                 + " numpy installation. See radvel.readthedocs.io/en/latest/OSX-multiprocessing.html"
+        #                 + " for more details. Running in serial with " + str(ensembles) + " ensembles.")
+        #     serial = True
 
         statevars.ensembles = ensembles
         statevars.nwalkers = nwalkers

radvel/plot/orbit_plots.py

@@ -73,8 +73,12 @@ def __init__(self, post, saveplot=None, epoch=2450000, yscale_auto=False, yscale
         self.yscale_sigma = yscale_sigma
         if phase_ncols is None:
             self.phase_ncols = 1
+        else:
+        	self.phase_ncols = phase_ncols
         if phase_nrows is None:
             self.phase_nrows = self.post.likelihood.model.num_planets
+        else:
+        	self.phase_nrows = phase_nrows
         self.uparams = uparams
         self.rv_phase_space = rv_phase_space
         self.telfmts = telfmts
@@ -234,21 +238,21 @@ def plot_timeseries(self):
 
     def plot_residuals(self):
         """
-        Make a plot of residuals and RV trend in the current Axes.
+        Make a plot of residuals in the current Axes.
         """
 
         ax = pl.gca()
 
-        ax.plot(self.mplttimes, self.slope, 'b-', lw=self.fit_linewidth)
+        ax.plot(self.mplttimes, self.slope-self.slope, 'b-', lw=self.fit_linewidth)
 
-        plot.mtelplot(self.plttimes, self.resid, self.rverr, self.post.likelihood.telvec, ax, telfmts=self.telfmts)
+        plot.mtelplot(self.plttimes, self.rawresid, self.rverr, self.post.likelihood.telvec, ax, telfmts=self.telfmts)
         if not self.yscale_auto: 
-            scale = np.std(self.resid)
+            scale = np.std(self.rawresid)
             ax.set_ylim(-self.yscale_sigma * scale, self.yscale_sigma * scale)
 
         if self.highlight_last:
             ind = np.argmax(self.plttimes)
-            pl.plot(self.plttimes[ind], self.resid[ind], **plot.highlight_format)
+            pl.plot(self.plttimes[ind], self.rawresid[ind], **plot.highlight_format)
 
         if self.set_xlim is not None:
             ax.set_xlim(self.set_xlim)
@@ -688,7 +692,7 @@ def plot_multipanel(self, nophase=False):
                 scalefactor = self.phase_nrows
 
             n_likes = len(self.like_list)
-            figheight = self.ax_rv_height*(n_likes+0.5) + self.ax_phase_height * scalefactor
+            figheight = self.ax_rv_height*(n_likes//self.phase_ncols+1.5) + self.ax_phase_height * scalefactor
 
             # provision figure
             fig = pl.figure(figsize=(self.figwidth, figheight))

radvel/tests/test_api.py

@@ -321,9 +321,9 @@ def test_model_comp(setupfn='example_planets/HD164922.py'):
     #test_k2()
     #test_hd()
     #test_model_comp()
-    #test_k2131()
+    test_k2131()
     #test_celerite()
-    test_basis()
+    # test_basis()
     #test_kernels()
     #test_kepler()
     #test_priors()

requirements.txt

@@ -1,15 +1,17 @@
 cython>=0.23
-numpy>=1.16
-scipy>=0.17
+numpy==1.24.3
+scipy==1.10.1
 matplotlib>=1.5.3
 corner>=2.0
 astropy>=1.1.2
 emcee>=3.0.2
 pandas>=0.20.0
-nbsphinx>=0.3.3
+nbsphinx==0.9.3
 jupyter_client>=5.2.4
 ipykernel>=4.10.0
 jinja2>=2.9
 python-dateutil>=2.5.0
-h5py==2.10.0
+h5py>=3.9.0
 dill
+ipython
+coveralls==3.2.0

setup.py

@@ -1,24 +1,19 @@
 from setuptools import setup, find_packages, Extension
 from setuptools.command.build_ext import build_ext as _build_ext
 import re
-
-
-class build_ext(_build_ext):
-    def finalize_options(self):
-        _build_ext.finalize_options(self)
-        # Prevent numpy from thinking it is still in its setup process:
-        __builtins__.__NUMPY_SETUP__ = False
-        import numpy
-        self.include_dirs.append(numpy.get_include())
-
+import numpy
 
 def get_property(prop, project):
     result = re.search(r'{}\s*=\s*[\'"]([^\'"]*)[\'"]'.format(prop),
                        open(project + '/__init__.py').read())
     return result.group(1)
 
 
-extensions = [Extension("radvel._kepler", ["src/_kepler.pyx"],)]
+extensions = [
+    Extension(
+        "radvel._kepler", ["src/_kepler.pyx"],
+        include_dirs=[numpy.get_include()])    
+]
 
 reqs = []
 for line in open('requirements.txt', 'r').readlines():
@@ -32,7 +27,6 @@ def get_property(prop, project):
     packages=find_packages(),
     setup_requires=['numpy', 'cython'],
     ext_modules=extensions,
-    cmdclass={'build_ext': build_ext},
     data_files=[
         (
             'radvel_example_data',