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finsihed updates to doc for v2.6.0
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -106,7 +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
-------
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57 changes: 40 additions & 17 deletions doc/input/chap2.md
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Expand Up @@ -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

Expand All @@ -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

Expand All @@ -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

Expand All @@ -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

Expand All @@ -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

Expand All @@ -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
10 changes: 4 additions & 6 deletions doc/input/chap3.md
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CLASS: Cosmic Linear Anisotropy Solving System
==============================================
CLASS overview (architecture, input/output, general principles)
===============================================================

Author: Julien Lesgourgues

Expand Down Expand Up @@ -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.

Expand All @@ -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 ###
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3 changes: 2 additions & 1 deletion doc/input/make2.sh
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#!/bin/bash

cd ../manual/latex

make

make

cp refman.pdf ../CLASS_MANUAL.pdf
cd ../../input
31 changes: 25 additions & 6 deletions doc/input/mod.md
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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.
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