diff --git a/CHANGELOG.md b/CHANGELOG.md index 06363893f..34c1df7ef 100644 --- 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 index 099b7a612..de75184a8 100644 --- 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 index 9ede3d733..aae356bcd 100644 --- 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 index ec5841267..6fd42e929 100644 Binary files a/doc/0000-ccl_note/0000-ccl_note.pdf and b/doc/0000-ccl_note/0000-ccl_note.pdf differ diff --git a/doc/0000-ccl_note/authors.csv b/doc/0000-ccl_note/authors.csv index cc7d75fe6..ebafad96e 100644 --- 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 index 29a74e967..975f53c50 100644 --- 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 index 912028ff1..f150b2e3a 100644 --- 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 index d407dd171..c1dbd4992 100644 --- 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 index ec5841267..6fd42e929 100644 Binary files a/doc/0000-ccl_note/main.pdf and b/doc/0000-ccl_note/main.pdf differ diff --git a/doc/0000-ccl_note/main.tex b/doc/0000-ccl_note/main.tex index 65f157b37..f62337e7d 100644 --- 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 index 4ed38fbaf..52bc8faf6 100644 --- 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 index 182c6d8d8..b0a9fb3e2 100644 --- 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 `_ version 3.1 or above * `CLASS `_ version 2.6.3 or above * `SWIG `_ + + +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 index dcd848986..8fef13254 100644 --- 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 index 550401796..64ddccbb0 100644 --- a/readthedocs/source/notation_and_other_cosmological_conventions.rst +++ b/readthedocs/source/notation_and_other_cosmological_conventions.rst @@ -65,24 +65,24 @@ 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 @@ -90,7 +90,7 @@ quantities (e.g., the transfer function). The various options are as follows. ``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.