Difference between revisions of "Manual"

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(Added an intro sentence, and increased the depth of the sectioning.)
 
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= See =
+
The following is information about the relax manual.
 +
 
 +
== Find the manual ==
 
The homepage manual
 
The homepage manual
 
* html http://www.nmr-relax.com/manual/index.html
 
* html http://www.nmr-relax.com/manual/index.html
 
* pdf http://download.gna.org/relax/manual/relax.pdf
 
* pdf http://download.gna.org/relax/manual/relax.pdf
−
* Latest builded manual http://download.gna.org/relax/manual
+
* Latest built manual http://download.gna.org/relax/manual
  
−
= Build manual =
+
== Get help ==
−
== Latex requirements ==
+
The help section in relax is the best you can get !
−
The [http://www.ctan.org/pkg/latex2html latex2html] latex package is necessary.
 
−
You can check if is already available.
 
−
kpsewhich latex2html
 
  
−
A [http://miktex.org/ windows MiKTeX] should fetch it automatically.
+
Just start relax in terminal:
 +
<source lang="python">
 +
> relax
  
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== Build pdf manual ==
+
# Then write, to see options which is related to relax_disp.
 +
relax> help(relax_disp)
 +
 
 +
For example:
 +
help(relax_disp.select_model)
 +
# You can find more info at the wiki: http://wiki.nmr-relax.com/Category:Relaxation_dispersion
 +
# Here you can find link to the online HTML manual, and the API documentation.
 +
 
 +
# You may want to read:
 +
relax> help(relax_disp.exp_type)
 +
relax> help(spectrum)
 +
relax> help(spectrum.replicated)
 +
relax> help(spectrum.baseplane_rmsd)
 +
relax> help(spectrometer)
 +
 
 +
# This a very very fast an useful method to quickly understand the functions.
 +
 
 +
# If you are unsure how to find where each method function is put, start the GUI.
 +
# In the top menu, go through the settings.
 +
# They are ordered the same way. ! :-)
 +
 
 +
# For example.
 +
relax> help(grid_search)
 +
</source>
 +
 
 +
== Write to the mail lists to get personal help ==
 +
See the wiki page [[Mailing_archives | Mailing archives]], to read how to sign up and write to the mail archives.
 +
 
 +
== Build the manual ==
 +
=== Latex requirements ===
 +
The '''html.sty''' is needed from the latex package [http://www.ctan.org/pkg/latex2html latex2html].
 +
 
 +
A [http://miktex.org/ windows MiKTeX installation] should fetch it automatically.
 +
 
 +
When compiling the pdf latex manual, only '''html.sty''' is needed. The easiest is just to place
 +
that in your LaTeX installation. [http://en.wikibooks.org/wiki/LaTeX/Installing_Extra_Packages See this guide].
 +
<source lang="bash">
 +
cd $HOME/Downloads ;
 +
wget http://mirrors.ctan.org/support/latex2html/latex2html-2012.tgz ;
 +
tar -xzf latex2html-2012.tgz ;
 +
rm latex2html-2012.tgz ;
 +
cd `where latex | xargs dirname`
 +
 
 +
cd ../../texmf-local/tex/latex
 +
# OR
 +
cd ../../texmf-dist/tex/latex
 +
 
 +
cp -r /$HOME/Downloads/latex2html-2012/texinputs latex2html
 +
# Then update latex index
 +
texhash
 +
</source>
 +
For a complete build of latex2html in linux, you could do something like this installation. But this is only for the building of '''user_manual_html'''. It is now advised to do this normally.
 +
<source lang="bash">
 +
sudo yum install latex2html
 +
 
 +
OR
 +
 
 +
cd $HOME/Downloads ;
 +
wget http://www.latex2html.org/~latex2ht/current/latex2html-2012.tar.gz ;
 +
tar -xzf latex2html-2012.tar.gz ;
 +
rm latex2html-2012.tar.gz ;
 +
cd latex2html-2012 ;
 +
mkdir build ;
 +
./configure --help
 +
./configure
 +
#Or make a custom build
 +
./configure --prefix=$PWD/build
 +
make
 +
</source>
 +
 
 +
=== Build pdf manual ===
 
The manual ends up in '''docs/relax.pdf'''
 
The manual ends up in '''docs/relax.pdf'''
  
Line 24: Line 95:
 
  scons user_manual_pdf_nofetch
 
  scons user_manual_pdf_nofetch
  
−
== Build html manual ==
+
=== Build html manual ===
 +
This needs quite some time to figure out to install and run latex2html.
  
 
Go to the relax base directory.<br>
 
Go to the relax base directory.<br>
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  scons user_manual_html_nofetch
 
  scons user_manual_html_nofetch
  
−
= Build API (Application programming interface) documentation =
+
== Build API (Application programming interface) documentation ==
 
The html documentation ends up in '''docs/api/'''
 
The html documentation ends up in '''docs/api/'''
  
−
== Epydoc python package installation ==
+
=== Epydoc python package installation ===
−
=== Windows epydoc ===
+
==== Windows epydoc ====
 
First: Download this packages, do not unpack them yet.
 
First: Download this packages, do not unpack them yet.
 
* epydoc http://www.lfd.uci.edu/~gohlke/pythonlibs/#epydoc
 
* epydoc http://www.lfd.uci.edu/~gohlke/pythonlibs/#epydoc
Line 43: Line 115:
 
Open WinPython Control Panel, and drag the .exe into the window.
 
Open WinPython Control Panel, and drag the .exe into the window.
  
−
=== Linux ===
+
Install graphviz Windows binaries from http://www.graphviz.org.<br>
 +
Remember to add the binaries to your path.
 +
<source lang="powershell">
 +
set PATH=%PATH%;C:\Program Files (x86)\Graphviz2.32\bin
 +
</source>
 +
 
 +
==== Linux ====
 
  sudo yum install epydoc
 
  sudo yum install epydoc
 
  sudo yum install graphviz-python
 
  sudo yum install graphviz-python
  
−
== Build API ==
+
=== Build API ===
 +
The API ends up in docs/api/index.html
 +
 
 
You need to run 'scons clean' first to remove the *.pyc files and any other temporary files.
 
You need to run 'scons clean' first to remove the *.pyc files and any other temporary files.
 
  scons clean
 
  scons clean
Line 54: Line 134:
 
  scons api_manual_html
 
  scons api_manual_html
  
−
== Regarding error messages ==
+
=== Regarding error messages ===
 
The "No documentation available!" errors are normal as these are for non-python files which are not part of relax.  It's safe to ignore these.
 
The "No documentation available!" errors are normal as these are for non-python files which are not part of relax.  It's safe to ignore these.
  
Line 62: Line 142:
 
Windows binaries are available though (http://www.graphviz.org).
 
Windows binaries are available though (http://www.graphviz.org).
  
−
= See also =
+
== See also ==
 
[[Category:FAQ]]
 
[[Category:FAQ]]

Latest revision as of 17:29, 19 October 2015

The following is information about the relax manual.

Find the manual

The homepage manual

Get help

The help section in relax is the best you can get !

Just start relax in terminal: 

> relax

# Then write, to see options which is related to relax_disp.
relax> help(relax_disp)

For example:
help(relax_disp.select_model)
# You can find more info at the wiki: http://wiki.nmr-relax.com/Category:Relaxation_dispersion
# Here you can find link to the online HTML manual, and the API documentation.

# You may want to read:
relax> help(relax_disp.exp_type)
relax> help(spectrum)
relax> help(spectrum.replicated)
relax> help(spectrum.baseplane_rmsd)
relax> help(spectrometer)

# This a very very fast an useful method to quickly understand the functions.

# If you are unsure how to find where each method function is put, start the GUI.
# In the top menu, go through the settings.
# They are ordered the same way. ! :-)

# For example.
relax> help(grid_search)

Write to the mail lists to get personal help

See the wiki page Mailing archives, to read how to sign up and write to the mail archives.

Build the manual

Latex requirements

The html.sty is needed from the latex package latex2html.

A windows MiKTeX installation should fetch it automatically.

When compiling the pdf latex manual, only html.sty is needed. The easiest is just to place that in your LaTeX installation. See this guide. 

cd $HOME/Downloads ;
wget http://mirrors.ctan.org/support/latex2html/latex2html-2012.tgz ;
tar -xzf latex2html-2012.tgz ;
rm latex2html-2012.tgz ;
cd `where latex | xargs dirname`

cd ../../texmf-local/tex/latex
# OR
cd ../../texmf-dist/tex/latex

cp -r /$HOME/Downloads/latex2html-2012/texinputs latex2html
# Then update latex index
texhash

For a complete build of latex2html in linux, you could do something like this installation. But this is only for the building of user_manual_html. It is now advised to do this normally. 

sudo yum install latex2html

OR

cd $HOME/Downloads ;
wget http://www.latex2html.org/~latex2ht/current/latex2html-2012.tar.gz ;
tar -xzf latex2html-2012.tar.gz ;
rm latex2html-2012.tar.gz ;
cd latex2html-2012 ;
mkdir build ;
./configure --help
./configure
#Or make a custom build
./configure --prefix=$PWD/build
make

Build pdf manual

The manual ends up in docs/relax.pdf

Go to the relax base directory.
Then issue the command 

scons user_manual_pdf

This triggers a range of functions, which create some files. If they do not need to be updated, following compilation can be performed much faster with 

scons user_manual_pdf_nofetch

Build html manual

This needs quite some time to figure out to install and run latex2html.

Go to the relax base directory.
Then issue the command 

scons user_manual_html

And faster 

scons user_manual_html_nofetch

Build API (Application programming interface) documentation

The html documentation ends up in docs/api/

Epydoc python package installation

Windows epydoc

First: Download this packages, do not unpack them yet.

take the win32 bit versions.

Open WinPython Control Panel, and drag the .exe into the window.

Install graphviz Windows binaries from http://www.graphviz.org.
Remember to add the binaries to your path. 

set PATH=%PATH%;C:\Program Files (x86)\Graphviz2.32\bin

Linux

sudo yum install epydoc
sudo yum install graphviz-python

Build API

The API ends up in docs/api/index.html

You need to run 'scons clean' first to remove the *.pyc files and any other temporary files. 

scons clean

Build the API documentation 

scons api_manual_html

Regarding error messages

The "No documentation available!" errors are normal as these are for non-python files which are not part of relax. It's safe to ignore these.

The wxPython indentation errors are also fine. epydoc is scanning the wx module docstrings, but it cannot be stopped.

The "Unable to render Graphviz dot graph" are because the Graphviz software is not available.
Windows binaries are available though (http://www.graphviz.org).

See also

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