fluid perturbations obey PPF approximation, w_fld(a) only in one place,...

fluid perturbations obey PPF approximation, w_fld(a) only in one place, python3 compatibility, new features for linear growth factor and transfer function output

* devel: (21 commits)
  finsihed updates to doc for v2.6.0
  updated first chapter of manual
  updated soxygen style, new background function compatible with doxygen
  better documented fluid parameters in explanatory.ini
  version number updated to 2.6.0 (but doc not yet updated)
  added details on w(a) in explanatory.ini
  done with w(a) rewriting
  w_fld(a) properly implemented everywhere else excepted 1 place in perturbations (w_prime)
  w_fld(a) properly implemented in background excepted 1 place (integral for IC)
  first working step in rewriting of w_fld(a)
  Fixed Makefile to not link classy with OpenMP if CLASS was compiled without OpenMP
  added output of Cl_dl in wrapper, following pull request #23 (Credits Atsushi Nishizawa)
  new input flag: extra metric transfer functions, implementing pull request #107 by Wessel Valkenburg
  precision parameter hyper_sampling_curved_low_nu changed from 6 to 7
  new functions in classy for compatibility with SDSS likelihood in MontePython v2.3
  added function scale_independent_growth_factor(z) to classy
  added reminders of lensing potential/deflection/shear conversion in explanatory and header
  Corrected D(a) to make it compatible with relativistic backscaling 1702.03221
  Fixed a few Python3 compatibility issues and made the matter power spectrum computed check in the pk function simpler and more robust
  Implemented and tested non-zero curvature in PPF equations
  ...

Makefile

@@ -182,7 +182,13 @@ tar: $(C_ALL) $(C_TEST) $(H_ALL) $(PRE_ALL) $(INI_ALL) $(MISC_FILES) $(HYREC) $(
 	tar czvf class.tar.gz $(C_ALL) $(H_ALL) $(PRE_ALL) $(INI_ALL) $(MISC_FILES) $(HYREC) $(PYTHON_FILES)
 
 classy: libclass.a python/classy.pyx python/cclassy.pxd
-	cd python; export CC=$(CC); $(PYTHON) setup.py install || $(PYTHON) setup.py install --user
+ifdef OMPFLAG
+	cp python/setup.py python/autosetup.py
+else
+	grep -v "lgomp" python/setup.py > python/autosetup.py
+endif
+	cd python; export CC=$(CC); $(PYTHON) autosetup.py install || $(PYTHON) autosetup.py install --user
+	rm python/autosetup.py
 
 clean: .base
 	rm -rf $(WRKDIR);

README.md

@@ -16,26 +16,30 @@ Compiling CLASS and getting started
 (the information below can also be found on the webpage, just below
 the download button)
 
-After downloading the code, unpack the archive (tar -zxvf
-class_v*.tar.gz), go to the class directory (cd class_v*/) and compile
-(make clean; make class). If the first compilation attempt fails, you
-may need to open the Makefile and adapt the name of the compiler
-(default: gcc), of the optimization flag (default: -O4) and of the
-OpenMP flag (default: -fopenmp; this flag is facultative, you are free
-to compile without OpenMP if you don't want parallel execution; note
-that you need the version 4.2 or higher of gcc to be able to compile
-with -fopenmp). Several details on the CLASS compilation are given on
-the wiki page
+Download the code from the webpage and unpack the archive (tar -zxvf
+class_vx.y.z.tar.gz), or clone it from
+https://github.com/lesgourg/class_public. Go to the class directory
+(cd class/ or class_public/ or class_vx.y.z/) and compile (make clean;
+make class). You can usually speed up compilation with the option -j:
+make -j class. If the first compilation attempt fails, you may need to
+open the Makefile and adapt the name of the compiler (default: gcc),
+of the optimization flag (default: -O4 -ffast-math) and of the OpenMP
+flag (default: -fopenmp; this flag is facultative, you are free to
+compile without OpenMP if you don't want parallel execution; note that
+you need the version 4.2 or higher of gcc to be able to compile with
+-fopenmp). Many more details on the CLASS compilation are given on the
+wiki page
 
 https://github.com/lesgourg/class_public/wiki/Installation
 
-(in particular, for compiling on Mac 10.9 Mavericks).
+(in particular, for compiling on Mac >= 10.9 despite of the clang
+incompatibility with OpenMP).
 
 To check that the code runs, type:
 
     ./class explanatory.ini
 
-The explanatory.ini file is a reference input file, containing and
+The explanatory.ini file is THE reference input file, containing and
 explaining the use of all possible input parameters. We recommend to
 read it, to keep it unchanged (for future reference), and to create
 for your own purposes some shorter input files, containing only the
@@ -48,6 +52,11 @@ one of them, and run with two input files, for instance:
 
     ./class test.ini cl_permille.pre
 
+The files *.pre are suppposed to specify the precision parameters for
+which you don't want to keep default values. If you find it more
+convenient, you can pass these precision parameter values in your *.ini
+file instead of an additional *.pre file.
+
 The automatically-generated documentation is located in
 
     doc/manual/html/index.html
@@ -62,8 +71,8 @@ Python
 To use CLASS from python, or ipython notebooks, or from the Monte
 Python parameter extraction code, you need to compile not only the
 code, but also its python wrapper. This can be done by typing just
-'make' instead of 'make class'. More details on the wrapper and its
-compilation are found on the wiki page
+'make' instead of 'make class' (or for speeding up: 'make -j'). More
+details on the wrapper and its compilation are found on the wiki page
 
 https://github.com/lesgourg/class_public/wiki
 
@@ -75,7 +84,7 @@ called CPU.py (Class Plotting Utility), written by Benjamin Audren and
 Jesus Torrado. It can plot the Cl's, the P(k) or any other CLASS
 output, for one or several models, as well as their ratio or percentage
 difference. The syntax and list of available options is obtained by
-typing 'pyhton CPU.py --help'. There is a similar script for MATLAB,
+typing 'pyhton CPU.py -h'. There is a similar script for MATLAB,
 written by Thomas Tram. To use it, once in MATLAB, type 'help
 plot_CLASS_output.m'
 
@@ -97,7 +106,7 @@ Using the code
 --------------
 
 You can use CLASS freely, provided that in your publications, you cite
-at least the paper `CLASS II: Approximation schemes <http://arxiv.org/abs/1104.2933>`_. Feel free to cite more CLASS papers!
+at least the paper `CLASS II: Approximation schemes <http://arxiv.org/abs/1104.2933>`. Feel free to cite more CLASS papers!
 
 Support
 -------

doc/input/chap2.md

@@ -4,30 +4,36 @@ Where to find information and documentation on CLASS?
 Author: Julien Lesgourgues
 
 
-* __For what the code can actually compute__: all possible input parameters, all coded cosmological models, all functionalities, all observables, etc.: read the file `explanatory.ini` in the main `CLASS` directory: it is a reference file where we keep track of all possible input.
+* __For what the code can actually compute__: all possible input parameters, all coded cosmological models, all functionalities, all observables, etc.: read the file `explanatory.ini` in the main `CLASS` directory: it is THE reference file where we keep track of all possible input and the definition of all input parameters. For that reason we recommend to leave it always unchanged and to work with copies of it, or with short input files written from scratch.
 
-* __For the structure, style, and concrete aspects of the code__: this documentation; plus the slides of our `CLASS` lectures, for instance those from Tokyo 2014 available at 
 
-    `https://www.dropbox.com/sh/ma5muh76sggwk8k/AABl_DDUBEzAjjdywMjeTya2a?dl=0`
+* __For the structure, style, and concrete aspects of the code__: this documentation, especially the `CLASS overview` chapter (the extensive automatically-generated part of this documentation is more for advanced users); plus the slides of our `CLASS` lectures, for instance those from Tokyo 2014 available at
 
-    in the folder `CLASS_Lecture_slides/`.
+    `http://lesgourg.github.io/class-tour-Tokyo.html`
 
-* __For the python wrapper of `CLASS`__: at the moment, the best is the slides from these lectures, for instance following the previous link and looking into
+    or the more recent and concise summary from the Narbonne 2016 lecture available at
 
-     `CLASS_Lecture_slides/lecture7_wrapper.pdf`
- 
-     and into
-  
-     `IPython_Notebooks`
+    `http://lesgourg.github.io/class-tour/Narbonne.pdf`
 
-     for example of python sessions. We will expand soon the documentation on this part with a dedicated webpage.
+    An updated overview of available `CLASS` lecture slides is always available at
+
+    `http://lesgourg.github.io/courses.html`
+
+    in the section `Courses on numerical tools`.
+
+
+* __For the python wrapper of `CLASS`__: at the moment, the best are the last slides (pages 75-96) of the Narbonne 2016 lectures
+
+    `http://lesgourg.github.io/class-tour/Narbonne.pdf`
+
+     Later we will expand the wrapper documentation with a dedicated chapter here.
 
 * __For the physics and equations used in the code__: mainly, the following papers:
     - *Cosmological perturbation theory in the synchronous and conformal Newtonian gauges*
 
      C. P. Ma and E. Bertschinger.
 
-     astro-ph/9506072
+     http://arxiv.org/abs/astro-ph/9506072
 
      10.1086/176550
 
@@ -37,7 +43,7 @@ Author: Julien Lesgourgues
 
      D. Blas, J. Lesgourgues and T. Tram.
 
-     arXiv:1104.2933 [astro-ph.CO]
+     http://arxiv.org/abs/1104.2933 [astro-ph.CO]
 
      10.1088/1475-7516/2011/07/034
 
@@ -47,7 +53,7 @@ Author: Julien Lesgourgues
 
      J. Lesgourgues and T. Tram.
 
-     arXiv:1104.2935 [astro-ph.CO]
+     http://arxiv.org/abs/1104.2935 [astro-ph.CO]
 
      10.1088/1475-7516/2011/09/032
 
@@ -57,7 +63,7 @@ Author: Julien Lesgourgues
 
      T. Tram and J. Lesgourgues.
 
-     arXiv:1305.3261 [astro-ph.CO]
+     http://arxiv.org/abs/1305.3261 [astro-ph.CO]
 
      10.1088/1475-7516/2013/10/002
 
@@ -67,7 +73,7 @@ Author: Julien Lesgourgues
 
      J. Lesgourgues and T. Tram.
 
-     arXiv:1312.2697 [astro-ph.CO]
+     http://arxiv.org/abs/1312.2697 [astro-ph.CO]
 
      10.1088/1475-7516/2014/09/032
 
@@ -77,9 +83,26 @@ Author: Julien Lesgourgues
 
      E. Di Dio, F. Montanari, J. Lesgourgues and R. Durrer.
 
-     arXiv:1307.1459 [astro-ph.CO]
+     http://arxiv.org/abs/1307.1459 [astro-ph.CO]
 
      10.1088/1475-7516/2013/11/044
 
      JCAP __1311__, 044 (2013)
 
+    plus also some latex notes on specific sectors:
+
+    - *Equations for perturbed recombination*
+
+     (can be turned on optionally by the user since v2.1.0)
+
+     L. Voruz.
+
+     http://lesgourg.github.io/class_public/perturbed_recombination.pdf
+
+    - *PPF formalism in Newtonian and synchronous gauge*
+
+     (used by default for the fluid perturbations since v2.6.0)
+
+     T. Tram.
+
+     http://lesgourg.github.io/class_public/PPF_formalism.pdf
\ No newline at end of file

doc/input/chap3.md

-CLASS: Cosmic Linear Anisotropy Solving System
-==============================================
+CLASS overview (architecture, input/output, general principles)
+===============================================================
 
 Author: Julien Lesgourgues
 
@@ -58,9 +58,7 @@ it can be interfaced with other codes, etc.
 
 ### Ten tasks ###
 
-The purpose of `class` consists in computing some power spectra for a
-given set of cosmological parameters. This task can be decomposed in few steps
-or modules:
+The purpose of `class` consists in computing some background quantities, thermodynamical quantities, perturbation transfer functions, and finally 2-point statistics (power spectra) for a given set of cosmological parameters. This task can be decomposed in few steps or modules:
 
 1. set input parameter values.
 
@@ -80,7 +78,7 @@ or modules:
 
 9. eventually, compute the lensed CMB spectra (using second-order perturbation theory)
 
-10. write results in  files (when `CLASS` is used interactively. The pyhton wrapper would not go to this step and just keep the output stored internally).
+10. write results in  files (when `CLASS` is used interactively. The python wrapper does not go through this step, after 1.-9. it just keeps the output stored internally).
 
 
 ### Ten structures ###

doc/input/make2.sh

 #!/bin/bash
- 
+
 cd ../manual/latex
 
 make
@@ -7,3 +7,4 @@ make
 make
 
 cp refman.pdf ../CLASS_MANUAL.pdf
+cd ../../input

doc/input/mod.md

-Updating the manual  
+Updating the manual
 ===================
 Author: D. C. Hooper (hooper@physik.rwth-aachen.de)
 
 This pdf manual and accompanying web version have been generated using the `doxygen` software (http://www.doxygen.org). This software directly reads the code and extracts the necessary comments to form the manual, meaning it is very easy to generate newer versions of the manual as desired.
 
-To maintain the usefulness of the manual, a new version should be generated after any major upgrade to `CLASS`. To keep track of how up-to-date the manual is the title page also displays the last modification date.
+### For CLASS developpers: ###
 
-Generating a new version of this manual is straightforward. First, you need to install the `doxygen` software, which can be done by following the instructions on the software's webpage. The location where you install this software is irrelevant; it doesn't need to be in the same folder as `CLASS`.
+To maintain the usefulness of the manual, a new version should be generated after any major upgrade to `CLASS`. To keep track of how up-to-date the manual is the title page also displays the last modification date. The manual is generated	automatically from the code, excepted a few chapters written manually in the files
 
-Once installed, navigate to the class/doc/input directory and run the first script 
+    README.md
+    doc/input/chap2.md
+    doc/input/chap3.md
+    doc/input/mod.md
+    external_Pk/README.md
+
+You can	update these files, or add new ones that should	be declared in the `INPUT=` field of `doc/input/doxyconf`.
+
+Generating a new version of this manual is straightforward. First, you need to install the `doxygen` software, which can be done by following the instructions on the software's webpage. The location where you install this software is irrelevant; it doesn't need to be in the same folder as `CLASS`. For Mac OSX, homebrew users can install the software with `brew install doxygen --with-graphviz`.
+
+Once installed, navigate to the class/doc/input directory and run the first script
 
 ` . make1.sh`
 
-This will generate a new version of the html manual and the necessary files to make the pdf version. Unfortunately, `doxygen` does not yet offer the option to automatically order the output chapters in the pdf version of the manual. Hence, before compiling the pdf, this must be done manually. To do this you need to find the `refman.tex` file in class/doc/manual/latex. With this file you can modify the title page, headers, footers, and chapter ordering for the final pdf. Once you have this file with your desired configuration, navigate back to the class/doc/input directory, and run the second script 
+This will generate a new version of the html manual and the necessary files to make the pdf version. Unfortunately, `doxygen` does not yet offer the option to automatically order the output chapters in the pdf version of the manual. Hence, before compiling the pdf, this must be done manually. To do this you need to find the `refman.tex` file in class/doc/manual/latex. With this file you can modify the title page, headers, footers, and chapter ordering for the final pdf. Usually we just make two things: add manually the line
+
+    \vspace*{1cm}
+    {\large Last updated \today}\\
+
+after
+
+    {\Large C\+L\+A\+SS M\+A\+N\+U\+AL }\\
+
+and move manually the chapters `"The external Pk mode"` and `"Updating the manual"` to the end, after the automatically generated part. Once you have this file with your desired configuration, navigate back to the class/doc/input directory, and run the second script
 
 ` . make2.sh`
 
-You should now be able to find the finished pdf in the class/doc/manual/CLASS_MANUAL.pdf.
+You should now be able to find the finished pdf in `class/doc/manual/CLASS_MANUAL.pdf`. Finally you can commit the changes to git, but not all the content of `doc/` is necessary: only `doc/README`, `doc/input/`, `doc/manual/CLASS_MANUAL.pdf`, `doc/manual/html/`. This means that before committing you will have to do a: `git add doc/manual/html/`, but NOT a: `git add doc/manual/latex/`!
 
 As a final comment, doxygen uses two main configuration files: `doxyconf` and `doxygen.sty`, both located in class/doc/input. Changes to these files can dramatically impact the outcome, so any modifications to these files should be done with great care.

doc/manual/html/annotated.html

@@ -3,7 +3,8 @@
 <head>
 <meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
 <meta http-equiv="X-UA-Compatible" content="IE=9"/>
-<meta name="generator" content="Doxygen 1.8.9.1"/>
+<meta name="generator" content="Doxygen 1.8.13"/>
+<meta name="viewport" content="width=device-width, initial-scale=1"/>
 <title>CLASS MANUAL: Data Structures</title>
 <link href="tabs.css" rel="stylesheet" type="text/css"/>
 <script type="text/javascript" src="jquery.js"></script>
@@ -14,14 +15,10 @@
 <script type="text/javascript" src="navtree.js"></script>
 <script type="text/javascript">
   $(document).ready(initResizable);
-  $(window).load(resizeHeight);
 </script>
 <link href="search/search.css" rel="stylesheet" type="text/css"/>
 <script type="text/javascript" src="search/searchdata.js"></script>
 <script type="text/javascript" src="search/search.js"></script>
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-  $(document).ready(function() { init_search(); });
-</script>
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 </head>
 <body>
@@ -30,7 +27,7 @@
 <table cellspacing="0" cellpadding="0">
  <tbody>
  <tr style="height: 56px;">
-  <td style="padding-left: 0.5em;">
+  <td id="projectalign" style="padding-left: 0.5em;">
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    </div>
   </td>
@@ -39,40 +36,19 @@
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+<!-- Generated by Doxygen 1.8.13 -->
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-  <div id="navrow1" class="tabs">
-    <ul class="tablist">
-      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
-      <li><a href="pages.html"><span>Related&#160;Pages</span></a></li>
-      <li class="current"><a href="annotated.html"><span>Data&#160;Structures</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li>
-        <div id="MSearchBox" class="MSearchBoxInactive">
-        <span class="left">
-          <img id="MSearchSelect" src="search/mag_sel.png"
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-      </li>
-    </ul>
-  </div>
-  <div id="navrow2" class="tabs2">
-    <ul class="tablist">
-      <li class="current"><a href="annotated.html"><span>Data&#160;Structures</span></a></li>
-      <li><a href="functions.html"><span>Data&#160;Fields</span></a></li>
-    </ul>
-  </div>
+<script type="text/javascript" src="menudata.js"></script>
+<script type="text/javascript" src="menu.js"></script>
+<script type="text/javascript">
+$(function() {
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+<div id="main-nav"></div>
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-<tr id="row_4_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="nonlinear_8h.html#structnonlinear" target="_self">nonlinear</a></td><td class="desc"></td></tr>
+<tr id="row_4_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structnonlinear.html" target="_self">nonlinear</a></td><td class="desc"></td></tr>
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@@ -135,9 +111,9 @@ $(document).ready(function(){initNavTree('annotated.html','');});
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 <div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
   <ul>
-    <li class="footer">Generated on Tue Mar 29 2016 13:52:51 for CLASS MANUAL by
+    <li class="footer">Generated on Sat Mar 25 2017 10:54:45 for CLASS MANUAL by
     <a href="http://www.doxygen.org/index.html">
-    <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.9.1 </li>
+    <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.13 </li>
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doc/manual/html/annotated_dup.js

+var annotated_dup =
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+    [ "background_parameters_for_distributions", "background_8h.html#structbackground__parameters__for__distributions", null ],
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+    [ "recombination", "thermodynamics_8h.html#structrecombination", "thermodynamics_8h_structrecombination" ],
+    [ "reionization", "thermodynamics_8h.html#structreionization", "thermodynamics_8h_structreionization" ],
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doc/manual/html/background_8c.js

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