ENH tag v2 (#689)

LSSTDESC · Oct 21, 2019 · 6b61236 · 6b61236
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,4 +1,4 @@
-# Unreleased
+# v 2.0 Changes
 
 ## Python library
 - Made CAMB the default Boltzmann code (#685).

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -8,7 +8,7 @@ MESSAGE( STATUS "CMAKE_BUILD_TYPE: " ${CMAKE_BUILD_TYPE} )
 # Adding customized cmake module
 list(APPEND CMAKE_MODULE_PATH  "${CMAKE_SOURCE_DIR}/cmake/Modules/")
 
-project(ccl VERSION 0.2.1)
+project(ccl VERSION 2.0.0)
 
 option(FORCE_OPENMP "Forcibly use OpenMP " NO)
 

diff --git a/README.md b/README.md
@@ -45,7 +45,13 @@ and installation instructions.
 `CCL` is available as a Python package through PyPi or conda. To install, simply run:
 
 ```
-$ [pip|conda] install pyccl
+$ conda install -c conda-forge pyccl
+```
+
+or
+
+```
+$ pip install pyccl
 ```
 
 For the PyPi installation, you will need ``CMake`` installed locally. See

diff --git a/doc/0000-ccl_note/0000-ccl_note.pdf b/doc/0000-ccl_note/0000-ccl_note.pdf
diff --git a/doc/0000-ccl_note/authors.csv b/doc/0000-ccl_note/authors.csv
@@ -37,7 +37,7 @@ Blazek,Jonathan,Jonathan Blazek,Contributor,"Laboratory of Astrophysics, \'Ecole
 Bull,Philip,Philip Bull,Contributor,"California Institute of Technology, Pasadena, CA 91125, USA","Implemented the Python wrapper and wrote documentation for it; general bug fixes, maintenance, and code review; enhanced the installer and error handling system.",philbull@gmail.com
 Bull,Philip,Philip Bull,Contributor,"Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, California, USA","Implemented the Python wrapper and wrote documentation for it; general bug fixes, maintenance, and code review; enhanced the installer and error handling system.",philbull@gmail.com
 Campagne,Jean-\'Eric,Jean-\'Eric Campagne,Contributor,"Laboratoire de l'Acc\'el\'erateur Lin\'eaire, Universit\'e Paris-Sud, CNRS/IN2P3, Universit\'e Paris-Saclay, Orsay, France",Angpow builder and contributed to the interface with CCL.,campagne@lal.in2p3.fr
-Chisari,Elisa,N. Elisa Chisari,Contributor,"Department of Physics, University of Oxford, Denys Wilkinson Building, Keble Road, Oxford OX1 3RH, United Kingdom","Co-led project, coordinated hack projects \& communication, contributed to: correlation function \& power spectrum implementation, documentation, and comparisons with benchmarks.",elisa.chisari@physics.ox.ac.uk
+Chisari,Elisa,N. Elisa Chisari,Contributor,"Institute for Theoretical Physics, Utrecht University, Princetonplein 5, 3584 CE Utrecht, The Netherlands","Co-led project, coordinated hack projects \& communication, contributed to: correlation function \& power spectrum implementation, documentation, and comparisons with benchmarks.",n.e.chisari@uu.nl
 Drlica-Wagner,Alex,Alex Drlica-Wagner,Contact,"Fermi National Accelerator Laboratory, P. O. Box 500, Batavia, IL 60510, USA",Helped with document preparation.,kadrlica@fnal.gov
 Du,Zilong,"Zilong Du",Contributor,"Department of Physics and Astronomy, University of California, Riverside, CA 92521, USA","Implemented the 3d correlation function, redshift-space correlation functions, and corresponding benchmarks.",zdu011@ucr.edu
 Eifler,Tim,Tim Eifler,Contributor,"Steward Observatory/Department of Astronomy, University of Arizona, 933 North Cherry Avenue, Tucson, AZ 85721, USA",Reviewed/tested code.,timeifler@gmail.com

diff --git a/doc/0000-ccl_note/authors.tex b/doc/0000-ccl_note/authors.tex
@@ -1,4 +1,4 @@
-% Author list file generated with: mkauthlist 1.2.4 
+% Author list file generated with: mkauthlist 1.2.3 
 % mkauthlist -j tex -f -c LSST Dark Energy Science Collaboration --cntrb contributions.tex authors.csv authors.tex 
 
 \author{Husni Almoubayyed}
@@ -16,7 +16,7 @@
 \author{Jean-\'Eric Campagne}
 \affiliation{Laboratoire de l'Acc\'el\'erateur Lin\'eaire, Universit\'e Paris-Sud, CNRS/IN2P3, Universit\'e Paris-Saclay, Orsay, France}
 \author{N. Elisa Chisari}
-\affiliation{Department of Physics, University of Oxford, Denys Wilkinson Building, Keble Road, Oxford OX1 3RH, United Kingdom}
+\affiliation{Institute for Theoretical Physics, Utrecht University, Princetonplein 5, 3584 CE Utrecht, The Netherlands}
 \author{Alex Drlica-Wagner}
 \affiliation{Fermi National Accelerator Laboratory, P. O. Box 500, Batavia, IL 60510, USA}
 \author{Zilong Du}

diff --git a/doc/0000-ccl_note/contributions.tex b/doc/0000-ccl_note/contributions.tex
@@ -1,7 +1,7 @@
 Author contributions are listed below. \\
 Husni Almoubayyed: wrote an mcmc jupyter notebook example, reviewed code/contributed to issues. \\
 David Alonso: Co-led project; developed structure for angular power spectra; implemented autotools; integrated into LSS pipeline; contributed to: background, power spectrum, mass function, documentation and benchmarks; reviewed code \\
-M.~R.~Becker: Core code and algorithms \\
+M.~R.~Becker: Core code and algorithmss \\
 Jonathan Blazek: Planning capabilities and structure; documentation and testing. \\
 Philip Bull: Implemented the Python wrapper and wrote documentation for it; general bug fixes, maintenance, and code review; enhanced the installer and error handling system. \\
 Jean-\'Eric Campagne: Angpow builder and contributed to the interface with CCL. \\

diff --git a/doc/0000-ccl_note/main.bib b/doc/0000-ccl_note/main.bib
@@ -1084,3 +1084,19 @@ @ARTICLE{Chisari2019
        adsurl = {https://ui.adsabs.harvard.edu/abs/2019ApJS..242....2C},
       adsnote = {Provided by the SAO/NASA Astrophysics Data System}
 }
+
+@ARTICLE{camb,
+      author         = "Lewis, Antony and Challinor, Anthony and Lasenby,
+                        Anthony",
+      title          = "{Efficient computation of CMB anisotropies in closed FRW
+                        models}",
+      journal        = "\apj",
+      volume         = "538",
+      year           = "2000",
+      pages          = "473-476",
+      doi            = "10.1086/309179",
+      eprint         = "astro-ph/9911177",
+      archivePrefix  = "arXiv",
+      primaryClass   = "astro-ph",
+      SLACcitation   = "%%CITATION = ASTRO-PH/9911177;%%"
+}
diff --git a/doc/0000-ccl_note/main.pdf b/doc/0000-ccl_note/main.pdf
diff --git a/doc/0000-ccl_note/main.tex b/doc/0000-ccl_note/main.tex
@@ -407,8 +407,15 @@ \subsubsection{Eisenstein and Hu}
 precise cosmological constraints.
 
 \subsubsection{CLASS}
-The fiducial configuration calls the {\tt CLASS} software \citep{class} within
-\ccl to obtain the linear matter power spectrum at given redshift. On
+\ccl can call the {\tt CLASS} software package \citep{class}
+to obtain the linear matter power spectrum at given redshift. On
+initializing the cosmology object, we construct a bi-dimensional spline in $k$
+and the scale-factor which is then evaluated by the relevant routines to obtain
+the matter power spectrum at the desired wavenumber and redshift.
+
+\subsubsection{CAMB}
+The fiducial configuration calls the {\tt CAMB} package \citep{camb}
+to obtain the linear matter power spectrum at given redshift. On
 initializing the cosmology object, we construct a bi-dimensional spline in $k$
 and the scale-factor which is then evaluated by the relevant routines to obtain
 the matter power spectrum at the desired wavenumber and redshift.

diff --git a/readthedocs/conf.py b/readthedocs/conf.py
@@ -102,9 +102,9 @@ def __getattr__(cls, name):
 # built documents.
 #
 # The short X.Y version.
-version = u'2.0'
+version = u'2.X'
 # The full version, including alpha/beta/rc tags.
-release = u'2.0'
+release = u'2.X'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/readthedocs/source/developer_installation.rst b/readthedocs/source/developer_installation.rst
@@ -20,7 +20,9 @@ To install CCL using a ``pip`` developer installation, you can execute
 
 from the top-level directory in the repository. You will need ``CMake`` in
 order to install CCL in this way. See :ref:`getting-cmake` for help installing
-``CMake`` if you do not already have it.
+``CMake`` if you do not already have it. In order to run the tests,
+you will need both ``CAMB`` and ``CLASS`` installed. See the instructions for
+:ref:`boltzmann-codes` for details.
 
 
 C-layer Dependencies and Requirements
@@ -37,3 +39,13 @@ These dependencies are
 * `FFTW3 <http://www.fftw.org/>`_ version 3.1 or above
 * `CLASS <http://class-code.net/>`_ version 2.6.3 or above
 * `SWIG <http://www.swig.org/>`_
+
+
+Uninstalling ``CCL`` in Developer Mode
+======================================
+
+To uninstall ``CCL`` in developer mode, simply type
+
+.. code-block:: bash
+
+   $ pip uninstall pyccl
diff --git a/readthedocs/source/installation.rst b/readthedocs/source/installation.rst
@@ -111,3 +111,17 @@ Known Installation Issues
       $ sudo installer -pkg /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg -target /
 
    which will install all the required headers into ``/usr/include``.
+
+
+.. _uninstalling:
+
+Uninstalling ``CCL``
+====================
+
+``CCL`` can be uninstalled using the uninstallation functionality of the
+package manager (i.e., ``conda`` or ``pip``) you used to install it. When in doubt,
+first try with ``conda`` and then try with ``pip``. In either case, the command is
+
+.. code-block:: bash
+
+   $ [conda|pip] uninstall pyccl
diff --git a/readthedocs/source/notation_and_other_cosmological_conventions.rst b/readthedocs/source/notation_and_other_cosmological_conventions.rst
@@ -65,32 +65,32 @@ quantities (e.g., the transfer function). The various options are as follows.
   - 'eisenstein_hu': the Eisenstein and Hu (1998) fitting function
   - 'bbks': the BBKS approximation
   - 'boltzmann_class': use CLASS to compute the transfer function
-  - 'boltzmann_camb': use CAMB to compute the transfer function
+  - 'boltzmann_camb': use CAMB to compute the transfer function (default)
 
 ``matter_power_spectrum`` options
 
   - 'halo_model': use a halo model
-  - 'halofit': use HALOFIT
+  - 'halofit': use HALOFIT (default)
   - 'linear': neglect non-linear power spectrum contributions
   - 'emu': use the Cosmic Emu
 
 ``baryons_power_spectrum`` options
 
-  - 'nobaryons': neglect baryonic contributions to the power spectrum
+  - 'nobaryons': neglect baryonic contributions to the power spectrum (default)
   - 'bcm': use the baryonic correction model
 
 ``mass_function`` options
 
   - 'tinker': the Tinker et al. (2008) mass function
-  - 'tinker10': the Tinker et al. (2010) mass function
+  - 'tinker10': the Tinker et al. (2010) mass function (default)
   - 'watson': the Watson et al. mass function
   - 'angulo': the Angulo et al. mass function
   - 'shethtormen': the Sheth and Tormen mass function
 
 ``halo_concentration`` options
 
   - 'bhattacharya2011': Bhattacharya et al. (2011) relation
-  - 'duffy2008': Duffy et al. (2008) relation
+  - 'duffy2008': Duffy et al. (2008) relation (default)
   - 'constant_concentration': use a constant concentration
 
 .. _mnutype:
@@ -102,7 +102,7 @@ quantities (e.g., the transfer function). The various options are as follows.
 
   - 'list': specify each mass yourself in eV
   - 'normal': use the normal hierarchy to convert total mass to individual
-    masses
+    masses (default)
   - 'inverted': use the inverted hierarchy to convert total mass to
     individual masses
   - 'equal': assume equal masses when converting the total mass to
@@ -113,7 +113,7 @@ quantities (e.g., the transfer function). The various options are as follows.
   This parameter specifies how to handle inconsistencies in the treatment of
   neutrinos between the Cosmic Emu (equal masses) and other models.
 
-  - 'strict': fail unless things are absolutely consistent
+  - 'strict': fail unless things are absolutely consistent (default)
   - 'equalize': redistribute the total mass equaly before using the Cosmic
     Emu. This option may result in slight internal inconsistencies in the
     physical model assumed for neutrinos.