update CAMB and getdist, bump version

README.rst

@@ -2,12 +2,16 @@
 CosmoMC
 ===================
 :CosmoMC:  Fortran 2008 parallelized MCMC sampler (general and cosmology)
-:Homepage: http://cosmologist.info/cosmomc/
+:Homepage: https://cosmologist.info/cosmomc/
 
 Description and installation
 =============================
 
-For full details see the `ReadMe <http://cosmologist.info/cosmomc/readme.html>`_.
+The new Python `Cobaya <https://github.com/CobayaSampler/cobaya>`_ sampling package incorporates a 
+version of CosmoMC's sampler and most other CosmoMC features, but has more general speed optimization and
+general support of multiple inter-dependent theory and likelihood codes. New users should probably use that.
+
+For full CosmoMC install details see the `ReadMe <http://cosmologist.info/cosmomc/readme.html>`_.
 
 Algorithm details
 ==================
@@ -20,13 +24,6 @@ GetDist
 CosmoMC includes the GetDist python sample analysis and plotting package, which is
 also `available separately <http://getdist.readthedocs.org/en/latest/>`_.
 
-Related code
-==================
-
-The new Python `Cobaya <https://github.com/CobayaSampler/cobaya>`_ sampling package incorporates a 
-version of CosmoMC's sampler and most other CosmoMC features, but has more general speed optimization and
-general support of multiple inter-dependent theory and likelihood codes.
-
 
 Branches
 =============================

python/Dockerfile

@@ -1,9 +1,16 @@
 #Dockerfile for running getdist notebooks with binder
 
-FROM cmbant/cosmobox:python3
+FROM cmbant/cosmobox:gcc9
 
+
+RUN pip install --no-cache --upgrade pip && \
+    pip install --no-cache notebook
+
+ARG NB_USER
+ARG NB_UID
 ENV NB_USER jovyan
 ENV NB_UID 1000
+ENV USER ${NB_USER}
 ENV HOME /home/${NB_USER}
 
 RUN adduser --disabled-password \
@@ -17,6 +24,5 @@ RUN chown -R ${NB_UID} ${HOME}
 USER ${NB_USER}
 
 WORKDIR ${HOME}
+RUN pip install --no-cache-dir notebook==5.*
 RUN python setup.py build
-
-

python/README.rst

@@ -3,16 +3,20 @@ GetDist
 ===================
 :GetDist: MCMC sample analysis, plotting and GUI
 :Author: Antony Lewis
-:Homepage: https://github.com/cmbant/getdist
+:Homepage: https://getdist.readthedocs.io
+:Source: https://github.com/cmbant/getdist
+:Reference: https://arxiv.org/abs/1910.13970
 
-.. image:: https://secure.travis-ci.org/cmbant/getdist.png?branch=master
-  :target: https://secure.travis-ci.org/cmbant/getdist
+.. image:: https://travis-ci.org/cmbant/getdist.svg?branch=master
+   :target: https://travis-ci.org/cmbant/getdist
 .. image:: https://img.shields.io/pypi/v/GetDist.svg?style=flat
-        :target: https://pypi.python.org/pypi/GetDist/
+   :target: https://pypi.python.org/pypi/GetDist/
 .. image:: https://readthedocs.org/projects/getdist/badge/?version=latest
    :target: https://getdist.readthedocs.org/en/latest
-.. image:: https://mybinder.org/badge.svg
-  :target: https://mybinder.org/v2/gh/cmbant/getdist/master?filepath=docs%2Fplot_gallery.ipynb
+.. image:: https://mybinder.org/badge_logo.svg
+   :target: https://mybinder.org/v2/gh/cmbant/getdist/master?filepath=docs%2Fplot_gallery.ipynb
+.. image:: https://img.shields.io/badge/arXiv-1910.13970-b31b1b.svg?color=0B6523
+   :target: https://arxiv.org/abs/1910.13970
 
 Description
 ============
@@ -43,9 +47,13 @@ or from source files using::
 
     $ python setup.py install
 
+or::
+
+    $ pip install -e /path/to/source/
+
 You can test if things are working using the unit test by running::
 
-    $ python setup.py test
+    $ python -m unittest getdist.tests.getdist_test
 
 Check the dependencies listed in the next section are installed. You can then use the getdist module from your scripts, or
 use the GetDist GUI (*getdist-gui* command).
@@ -55,22 +63,22 @@ the `Plot Gallery and tutorial <http://getdist.readthedocs.org/en/latest/plot_ga
 
 Dependencies
 =============
-* Python 2.7+ or 3.6+
-* matplotlib
+* Python 3.6+
+* matplotlib 2.2+ (3.1+ recommended)
 * scipy
-* PySide (Python 2) or PySide2 (Python 3) - optional, only needed for GUI
+* PySide2 - optional, only needed for GUI
 * Working LaTeX installation (not essential, only for some plotting/table functions)
 
 Python distributions like Anaconda have most of what you need (except for LaTeX).
 
-To use the `GUI <https://getdist.readthedocs.io/en/latest/gui.html>`_ you need PySide or PySide2.
+To use the `GUI <https://getdist.readthedocs.io/en/latest/gui.html>`_ you need PySide2.
 See the `GUI docs <https://getdist.readthedocs.io/en/latest/gui.html#installation>`_ for suggestions on how to install.
 
 Algorithm details
 ==================
 
-Details of kernel density estimation (KDE) algorithms and references are give in the
-`GetDist Notes <https://cosmologist.info/notes/GetDist.pdf>`_.
+Details of kernel density estimation (KDE) algorithms and references are give in the GetDist notes
+`arXiv:1910.13970 <https://arxiv.org/pdf/1910.13970>`_.
 
 Samples file format
 ===================
@@ -114,8 +122,8 @@ Loading samples
 
 To load an MCSamples object from text files do::
 
-	 from getdist import loadMCSamples
-	 samples = loadMCSamples('/path/to/xxx', settings={'ignore_rows':0.3})
+     from getdist import loadMCSamples
+     samples = loadMCSamples('/path/to/xxx', settings={'ignore_rows':0.3})
 
 Here *settings* gives optional parameter settings for the analysis. *ignore_rows* is useful for MCMC chains where you want to
 discard some fraction from the start of each chain as burn in (use a number >1 to discard a fixed number of sample lines rather than a fraction).
@@ -130,9 +138,9 @@ When you have many different chain files in the same directory,
 plotting can work directly with the root file names. For example to compare *x* and *y* constraints
 from two chains with root names *xxx* and *yyy*::
 
-	from getdist import plots
-	g = plots.get_single_plotter(chain_dir='/path/to/', analysis_settings={'ignore_rows':0.3})
-	g.plot_2d(['xxx','yyy'], ['x', 'y'])
+    from getdist import plots
+    g = plots.get_single_plotter(chain_dir='/path/to/', analysis_settings={'ignore_rows':0.3})
+    g.plot_2d(['xxx','yyy'], ['x', 'y'])
 
 
 MCSamples objects can also be constructed directly from numpy arrays in memory, see the example
@@ -143,25 +151,25 @@ GetDist script
 
 If you have chain files on on disk, you can also quickly calculate convergence and marginalized statistics using the *getdist* script:
 
-	usage: getdist [-h] [--ignore_rows IGNORE_ROWS] [-V] [ini_file] [chain_root]
+    usage: getdist [-h] [--ignore_rows IGNORE_ROWS] [-V] [ini_file] [chain_root]
 
-	GetDist sample analyser
+    GetDist sample analyser
 
-	positional arguments:
-	  *ini_file*              .ini file with analysis settings (optional, if omitted uses defaults
+    positional arguments:
+      *ini_file*              .ini file with analysis settings (optional, if omitted uses defaults
 
-	  *chain_root*            Root name of chain to analyse (e.g. chains/test), required unless file_root specified in ini_file
+      *chain_root*            Root name of chain to analyse (e.g. chains/test), required unless file_root specified in ini_file
 
-	optional arguments:
-	  -h, --help            show this help message and exit
-	  --ignore_rows IGNORE_ROWS
-	                        set initial fraction of chains to cut as burn in
-	                        (fraction of total rows, or >1 number of rows);
-	                        overrides any value in ini_file if set
-	  --make_param_file MAKE_PARAM_FILE
+    optional arguments:
+      -h, --help            show this help message and exit
+      --ignore_rows IGNORE_ROWS
+                            set initial fraction of chains to cut as burn in
+                            (fraction of total rows, or >1 number of rows);
+                            overrides any value in ini_file if set
+      --make_param_file MAKE_PARAM_FILE
                         Produce a sample distparams.ini file that you can edit
                         and use when running GetDist
-	  -V, --version         show program's version number and exit
+      -V, --version         show program's version number and exit
 
 where *ini_file* is optionally a .ini file listing *key=value* parameter option values, and chain_root is the root file name of the chains.
 For example::
@@ -181,7 +189,7 @@ to produce the setting file distparams.ini, edit it, then run with your custom s
 GetDist GUI
 ===================
 
-Run *getdist-gui* to run the graphical user interface. This requires PySide, but will run on Windows, Linux and Mac.
+Run *getdist-gui* to run the graphical user interface. This requires PySide2, but will run on Windows, Linux and Mac.
 It allows you to open a folder of chain files, then easily select, open, plot and compare, as well as viewing standard GetDist outputs and tables.
 See the `GUI Readme <http://getdist.readthedocs.org/en/latest/gui.html>`_.
 
@@ -195,10 +203,28 @@ No need to install this package separately if you have a full CosmoMC installati
 Detailed help is available for plotting Planck chains
 and using CosmoMC parameter grids in the `Readme <https://cosmologist.info/cosmomc/readme_python.html>`_.
 
+Citation
+===================
+You can refer to the notes::
+
+     @article{Lewis:2019xzd,
+      author         = "Lewis, Antony",
+      title          = "{GetDist: a Python package for analysing Monte Carlo
+                        samples}",
+      year           = "2019",
+      eprint         = "1910.13970",
+      archivePrefix  = "arXiv",
+      primaryClass   = "astro-ph.IM",
+      SLACcitation   = "%%CITATION = ARXIV:1910.13970;%%",
+      url            = "https://getdist.readthedocs.io"
+     }
+
+
+and references therein as appropriate.
+
 ===================
 
 .. raw:: html
 
     <a href="http://www.sussex.ac.uk/astronomy/"><img src="https://cdn.cosmologist.info/antony/Sussex.png" style="height:170px" height="170px"></a>
     <a href="http://erc.europa.eu/"><img src="https://erc.europa.eu/sites/default/files/content/erc_banner-vertical.jpg" style="height:200px" height="200px"></a>
-