Merge pull request #282 from California-Planet-Search/next-release

Version 1.3.1

.coveragerc

@@ -2,6 +2,8 @@
 omit =
     *__init__*
     radvel/utils.py
+    def _domcmc
+    def isnotebook
 
 [run]
 source = radvel

.dockerignore

@@ -0,0 +1,7 @@
+.idea
+docs
+dist
+build
+radvel.egg-info
+*.pyc
+*.so

.travis.yml

@@ -7,7 +7,7 @@ env:
   global:
     CACHE_IMAGE: bjfultn/radvel
 
-before_install:
+install:
   - docker pull $CACHE_IMAGE:latest || true
   - docker build --cache-from $CACHE_IMAGE:latest --tag radvel .
 

Dockerfile

@@ -2,30 +2,31 @@ FROM conda/miniconda3
 
 ENV TERM=xterm
 ENV TERMINFO=/etc/terminfo
+ENV PYTHONDONTWRITEBYTECODE=true
 ENV COVERALLS_REPO_TOKEN=7ZpQ0LQWM2PNl5iu7ZndyFEisQnZow8oT
 
 
 RUN mkdir /code && \
     mkdir /code/radvel && \
     apt-get --yes update && \
-    apt-get install --yes gcc g++ git && \
+    apt-get install --yes gcc git && \
+    apt-get clean && \
     conda config --add channels conda-forge && \
     conda config --set channel_priority strict && \
     conda update -n base -c defaults conda && \
-    pip install --no-cache-dir nose coveralls pybind11 && \
-    conda install -y -c conda-forge celerite
+    conda install --yes nomkl numpy pybind11 coveralls nose && \
+    conda install --yes -c conda-forge celerite && \
+    conda clean -afy
 
 WORKDIR /code/radvel
 ADD requirements.txt /code/radvel/requirements.txt
 
-RUN conda install -y --file requirements.txt && \
-    pip install --no-cache-dir -r requirements.txt
+RUN pip install --no-cache-dir -r requirements.txt
 
 ADD . /code/radvel
 
 
-RUN pip install --no-cache-dir . && \
-    python setup.py build_ext -i
-
-CMD nosetests radvel --with-coverage --cover-package=radvel && \
+CMD pip install --no-cache-dir --no-deps .  && \
+    python setup.py build_ext -i  && \
+    nosetests radvel --with-coverage --cover-package=radvel && \
     coveralls

docs/tutorials/164922_Fitting+MCMC.ipynb

@@ -272,7 +272,7 @@
     }
    ],
    "source": [
-    "df = radvel.mcmc(post, nrun=200)"
+    "df = radvel.mcmc(post, nrun=200, savename='rawchains.h5')"
    ]
   },
   {
@@ -503,8 +503,17 @@
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
    "version": "3.7.4"
+  },
+  "pycharm": {
+   "stem_cell": {
+    "cell_type": "raw",
+    "source": [],
+    "metadata": {
+     "collapsed": false
+    }
+   }
   }
  },
  "nbformat": 4,
  "nbformat_minor": 1
-}
+}

docs/tutorials/GaussianProcess-tutorial.ipynb

@@ -444,7 +444,7 @@
     }
    ],
    "source": [
-    "chains = radvel.mcmc(gppost,nrun=100,ensembles=3)"
+    "chains = radvel.mcmc(gppost,nrun=100,ensembles=3,savename='rawchains.h5')"
    ]
   },
   {
@@ -608,8 +608,17 @@
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
    "version": "3.6.4"
+  },
+  "pycharm": {
+   "stem_cell": {
+    "cell_type": "raw",
+    "source": [],
+    "metadata": {
+     "collapsed": false
+    }
+   }
   }
  },
  "nbformat": 4,
  "nbformat_minor": 2
-}
+}

docs/tutorials/K2-24_Fitting+MCMC.ipynb

@@ -361,7 +361,7 @@
     }
    ],
    "source": [
-    "df = radvel.mcmc(post,nwalkers=20,nrun=400)"
+    "df = radvel.mcmc(post,nwalkers=20,nrun=400,savename='rawchains.h5')"
    ]
   },
   {
@@ -569,8 +569,17 @@
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
    "version": "3.7.4"
+  },
+  "pycharm": {
+   "stem_cell": {
+    "cell_type": "raw",
+    "source": [],
+    "metadata": {
+     "collapsed": false
+    }
+   }
   }
  },
  "nbformat": 4,
  "nbformat_minor": 1
-}
+}

docs/tutorials/SyntheticData.ipynb

@@ -351,7 +351,7 @@
     }
    ],
    "source": [
-    "df = radvel.mcmc(post,nwalkers=20,nrun=1000)"
+    "df = radvel.mcmc(post,nwalkers=20,nrun=1000,savename='rawchain.h5')"
    ]
   },
   {
@@ -460,8 +460,17 @@
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
    "version": "3.6.4"
+  },
+  "pycharm": {
+   "stem_cell": {
+    "cell_type": "raw",
+    "source": [],
+    "metadata": {
+     "collapsed": false
+    }
+   }
   }
  },
  "nbformat": 4,
  "nbformat_minor": 1
-}
+}

radvel/__init__.py

@@ -25,7 +25,7 @@ def _custom_warningfmt(msg, *a, **b):
 __all__ = ['model', 'likelihood', 'posterior', 'mcmc', 'prior', 'utils',
          'fitting', 'report', 'cli', 'driver', 'gp']
 
-__version__ = '1.3.0'
+__version__ = '1.3.1'
 __spec__ = __name__
 __package__ = __path__[0]
 

radvel/cli.py

@@ -101,12 +101,18 @@ def main():
                           help="Minimum percentage of steps before convergence tests are performed [5]. \
 Convergence checks will start after the minsteps threshold or the minpercent threshold has been hit."
                           )
-    psr_mcmc.add_argument('--thin', dest='thin', action='store', default=1, type=int,
-                          help="Save one sample every N steps [default=1, save all samples]"
+    psr_mcmc.add_argument('--thin', dest='thin', action='store', default=10, type=int,
+                          help="Save one sample every N steps [default=10, save every 10th sample]"
                           )
     psr_mcmc.add_argument('--serial', dest='serial', action='store', default=False, type=bool,
                           help='''If True, run MCMC in serial instead of parallel. [False]'''
                           )
+    psr_mcmc.add_argument('--save', dest='save', action='store', default=False, type=bool,
+                          help='If True, MCMC chains will be saved to be continued in a future run [False]'
+                          )
+    psr_mcmc.add_argument('--proceed', dest='proceed', action='store', default=False, type=bool,
+                          help='If True, MCMC chains will resume from the previous run'
+                          )
     psr_mcmc.set_defaults(func=radvel.driver.mcmc)
 
     # Derive physical parameters
@@ -126,22 +132,25 @@ def main():
 
     psr_ic.add_argument('-m', '--mixed', dest='mixed', action='store_true',
                         help="flag to compare all models with the fixed parameters mixed and matched rather than"
-                        + " treating each model comparison separately. This is the default."
+                        + " treating each model comparison separately. [default=True]"
                         )
     psr_ic.add_argument('-u', '--un-mixed', dest='mixed', action='store_false',
-                        help="flag to treat each model comparison separately (without mixing them) "
-                        + "rather than comparing all models with the fixed parameters mixed and matched."
+                        help="flag to treat each model comparison separately (without mixing them) rather "
+                        + "than comparing all models with the fixed parameters mixed and matched. [default=False]"
                         )
     psr_ic.add_argument('-f', '--fixjitter', dest='fixjitter', action='store_true',
-                        help="flag to fix the stellar jitters at the nominal model best-fit value"
+                        help="flag to fix the stellar jitters at the nominal model best-fit value [default=False]"
                         )
     psr_ic.add_argument('-n', '--no-fixjitter', dest='fixjitter', action='store_false',
-                        help="flag to let the stellar jitters float during model comparisons (default)"
+                        help="flag to let the stellar jitters float during model comparisons [default=True]"
+                        )
+    psr_ic.add_argument('--simple', dest='simple', action='store_true',
+                        help="calculate goodness of fit statistics for the current model and exit [default=False]"
                         )
     psr_ic.add_argument('-v', '--verbose', dest='verbose', action='store_true',
-                        help="Print some more detail"
+                        help="Print some more detail [default=False]"
                         )
-    psr_ic.set_defaults(func=radvel.driver.ic_compare, fixjitter=False, unmixed=False, mixed=True)
+    psr_ic.set_defaults(func=radvel.driver.ic_compare, fixjitter=False, unmixed=False, mixed=True, verbose=False)
 
     # Tables
     psr_table = subpsr.add_parser('table', parents=[psr_parent],)