Merge pull request #121 from lfmcmillan/master

Fixed links to cookbook and figures in user guide and reference manual that have moved

doc/tools/indexsidebar.html

@@ -1,7 +1,7 @@
             <h3>Resources</h3>
             <ul>
               <li><a href="https://github.com/BoPeng/simuPOP">simuPOP Homepage</a></li>
-              <li><a href="https://github.com/BoPeng/simuPOP/cookbook">simuPOP Cookbook</a></li>
+              <li><a href="https://github.com/BoPeng/simuPOP-examples">simuPOP Cookbook</a></li>
               <li><a href="http://sourceforge.net/project/showfiles.php?group_id=143850">Download</a></li>
               <li>&nbsp;</li>
               <li><a href="https://lists.sourceforge.net/lists/listinfo/simupop-list">Mailing List</a></li>

doc/userGuide.lyx

@@ -241,7 +241,7 @@ simuPOP is provided as a number of Python modules, which consist of a large
  It is the users’ responsibility to write a Python script to glue these
  pieces together and form a simulation.
  At a more user-friendly level, an increasing number of functions and scripts
- contributed by simuPOP users is available in the online simuPOP cookbook.
+ contributed by simuPOP users is available in the online simuPOP examples repository.
  They provide useful functions for different applications (e.g.
  load and manipulate HapMap samples, import and export files from another
  application) and allow users who are unfamiliar with simuPOP to perform
@@ -433,10 +433,10 @@ simuPOP is provided as a number of Python modules, which consist of a large
  It is the users’ responsibility to write a Python script to glue these
  pieces together and form a simulation.
  At a more user-friendly level, an increasing number of functions and scripts
- contributed by simuPOP users is available in the online simuPOP cookbook
+ contributed by simuPOP users is available in the examples folder within the online simuPOP examples repository
  (
 \family typewriter
-https://github.com/BoPeng/simuPOP/cookbook
+https://github.com/BoPeng/simuPOP-examples
 \family default
 ).
  They provide useful functions for different applications (e.g.
@@ -1389,20 +1389,19 @@ https://github.com/BoPeng/simuPOP
 \begin_layout Standard
 A
 \emph on
-simuPOP online cookbook
+simuPOP online examples
 \emph default
  (
 \family typewriter
 https://github.com/BoPeng/simuPOP
 \family default
 /
 \family typewriter
-cookbook
+examples
 \family default
-) is a wiki-based website where you can browse and download examples, functions
- and scripts for various simulation scenarios, and upload your own code
- snippets for the benefit of all simuPOP users.
- Please consider contributing to this cookbook if you have written some
+) is a Github repository of examples where you can find example
+ scripts for various simulation scenarios.
+ Please consider contributing to these examples if you have written some
  scripts that might be useful to others.
 \end_layout
 
@@ -5973,7 +5972,7 @@ Individual.info()
 \family typewriter
 saveFSTAT
 \family default
- in the cookbook module
+ in the examples repository
 \family typewriter
 fstatUtil
 \family default
@@ -23632,9 +23631,9 @@ simuPOP.utils
  They do not belong to the simuPOP core but are distributed with simuPOP
  because they are frequently used and play an important role in some specialized
  simulation techniques.
- Please refer to the simuPOP online cookbook (
+ Please refer to the simuPOP examples repository (
 \family typewriter
-https://github.com/BoPeng/simuPOP/cookbook
+https://github.com/BoPeng/simuPOP-examples
 \family default
 ) for more utility modules and functions.
 \end_layout
@@ -26921,8 +26920,8 @@ simuCDCV.py
  The complete script is available at
 \begin_inset CommandInset href
 LatexCommand href
-name "the simuPOP online cookbook"
-target "https://github.com/BoPeng/simuPOP/cookbook"
+name "the simuPOP examples"
+target "https://github.com/BoPeng/simuPOP-examples"
 
 \end_inset
 

docs/_sources/userGuide_ch1.rst.txt

@@ -25,7 +25,7 @@ Front Matter
    evolutionary processes. It is the users' responsibility to write a Python script
    to glue these pieces together and form a simulation. At a more user-friendly
    level, an increasing number of functions and scripts contributed by simuPOP
-   users is available in the online simuPOP cookbook. They provide useful functions
+   users is available in the online simuPOP examples. They provide useful functions
    for different applications (e.g. load and manipulate HapMap samples, import and
    export files from another application) and allow users who are unfamiliar with
    simuPOP to perform a large number of simulations ranging from basic population

docs/_sources/userGuide_ch2_sec1.rst.txt

@@ -35,8 +35,8 @@ operators (objects that manipulate populations) and simulators to coordinate the
 evolutionary processes. It is the users' responsibility to write a Python script
 to glue these pieces together and form a simulation. At a more user-friendly
 level, an increasing number of functions and scripts contributed by simuPOP
-users is available in the online simuPOP cookbook
-(``https://github.com/BoPeng/simuPOP/cookbook``). They provide useful functions for
+users is available in the examples folder within the online simuPOP examples repository
+(``https://github.com/BoPeng/simuPOP-examples``). They provide useful functions for
 different applications (e.g. load and manipulate HapMap samples, import and
 export files from another application) and allow users who are unfamiliar with
 simuPOP to perform a large number of simulations ranging from basic population

docs/_sources/userGuide_ch2_sec2.rst.txt

@@ -19,7 +19,7 @@ individual properties.
 
 .. _fig_life_cycle:
 
-.. figure:: /Users/bpeng1/simuPOP/simuPOP/doc/figures/evolve.png
+.. figure::  https://github.com/BoPeng/simuPOP/blob/master/doc/figures/evolve.png
    :width: 680
 
 

docs/_sources/userGuide_ch2_sec6.rst.txt

@@ -14,13 +14,11 @@ not show you how to use them. Both documents are available online at
 ``https://github.com/BoPeng/simuPOP`` in both searchable HTML format and PDF
 format.
 
-A *simuPOP online cookbook* (``https://github.com/BoPeng/simuPOP``/``cookbook``) is
-a wiki-based website where you can browse and download examples, functions and
-scripts for various simulation scenarios, and upload your own code snippets for
-the benefit of all simuPOP users. Please consider contributing to this cookbook
-if you have written some scripts that might be useful to others.
+The simuPOP examples repository on GitHub (``https://github.com/BoPeng/simuPOP-examples``) 
+has example scripts for various simulation scenarios. Please consider contributing 
+to these examples if you have written some scripts that might be useful to others.
 
 If you cannot find the answer you need, or if you believe that you have
 encountered a bug, or if you would like to request a feature, please subscribe
-to the simuPOP mailinglist (``simupop-list@lists.sourceforge.net``) and send
-your questions there.
+to the simuPOP mailinglist (``https://lists.sourceforge.net/lists/listinfo/simupop-list``) 
+and send your questions there.

docs/_sources/userGuide_ch8_sec1.rst.txt

@@ -12,6 +12,6 @@ simple diseases become complex; while those of complex diseases remained simple.
 This example is a simplified version of the ``simuCDCV.py`` script that
 simulates this evolution process and observe the allelic spectra of both types
 of diseases. The complete script is available at
-https://github.com/BoPeng/simuPOP/cookbookthe simuPOP online cookbook. The results
+https://github.com/BoPeng/simuPOP-examples in the simuPOP examples repository. The results
 are published in Peng2007, which has much more detailed discussion about the
 simulations, and the parameters used.

docs/_sources/userGuide_ch8_sec6.rst.txt

@@ -294,7 +294,7 @@ The script written in this style could be executed in a number of ways.
 
    .. _fig_simuCDCV_dialog:
 
-   .. figure:: /Users/bpeng1/simuPOP/simuPOP/doc/figures/simuCDCV.png
+   .. figure:: https://github.com/BoPeng/simuPOP/tree/master/doc/figures/simuCDCV.png
       :width: 5in
 
 

docs/index.html

@@ -66,7 +66,7 @@ <h3>Related Topics</h3>
 </div>            <h3>Resources</h3>
             <ul>
               <li><a href="https://github.com/BoPeng/simuPOP">simuPOP Homepage</a></li>
-              <li><a href="https://github.com/BoPeng/simuPOP/cookbook">simuPOP Cookbook</a></li>
+              <li><a href="https://github.com/BoPeng/simuPOP-examples">simuPOP Examples</a></li>
               <li><a href="http://sourceforge.net/project/showfiles.php?group_id=143850">Download</a></li>
               <li>&nbsp;</li>
               <li><a href="https://lists.sourceforge.net/lists/listinfo/simupop-list">Mailing List</a></li>

docs/userGuide_ch8_sec1.html

@@ -47,7 +47,7 @@ <h1>Simulation scenario<a class="headerlink" href="#simulation-scenario" title="
 <p>This example is a simplified version of the <code class="docutils literal notranslate"><span class="pre">simuCDCV.py</span></code> script that
 simulates this evolution process and observe the allelic spectra of both types
 of diseases. The complete script is available at
-<a class="reference external" href="https://github.com/BoPeng/simuPOP/cookbookthe">https://github.com/BoPeng/simuPOP/cookbookthe</a> simuPOP online cookbook. The results
+<a class="reference external" href="https://github.com/BoPeng/simuPOP-examples">https://github.com/BoPeng/simuPOP-examples</a> in the simuPOP examples repository. The results
 are published in Peng2007, which has much more detailed discussion about the
 simulations, and the parameters used.</p>
 </div>
@@ -145,4 +145,4 @@ <h3>Quick search</h3>
 
 
   </body>
-</html>
+</html>