From 8ec5449ae8dbce2af319f097e89dd796a64a95b9 Mon Sep 17 00:00:00 2001
From: Louise McMillan <louise.mcmillan@gmail.com>
Date: Wed, 28 Aug 2024 04:42:19 +1200
Subject: [PATCH 01/12] Fixed links to cookbook which has moved to
 simuPOP-examples repo

---
 doc/userGuide.lyx | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/doc/userGuide.lyx b/doc/userGuide.lyx
index 2e506315..1274c84e 100644
--- a/doc/userGuide.lyx
+++ b/doc/userGuide.lyx
@@ -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 cookbook
  (
 \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.
@@ -23634,7 +23634,7 @@ simuPOP.utils
  simulation techniques.
  Please refer to the simuPOP online cookbook (
 \family typewriter
-https://github.com/BoPeng/simuPOP/cookbook
+https://github.com/BoPeng/simuPOP-examples
 \family default
 ) for more utility modules and functions.
 \end_layout
@@ -26922,7 +26922,7 @@ simuCDCV.py
 \begin_inset CommandInset href
 LatexCommand href
 name "the simuPOP online cookbook"
-target "https://github.com/BoPeng/simuPOP/cookbook"
+target "https://github.com/BoPeng/simuPOP-examples"
 
 \end_inset
 

From bf2160c0dcbe8221e02e36723e150ce1f487392b Mon Sep 17 00:00:00 2001
From: Louise McMillan <louise.mcmillan@gmail.com>
Date: Wed, 28 Aug 2024 04:46:30 +1200
Subject: [PATCH 02/12] Fixed sidebar cookbook link

---
 doc/tools/indexsidebar.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/tools/indexsidebar.html b/doc/tools/indexsidebar.html
index 04203623..75a24b08 100644
--- a/doc/tools/indexsidebar.html
+++ b/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>

From 47067a169d6b3ec4d0a3ed3c3cd10f7b2a10e891 Mon Sep 17 00:00:00 2001
From: Louise McMillan <louise.mcmillan@gmail.com>
Date: Wed, 28 Aug 2024 04:53:27 +1200
Subject: [PATCH 03/12] Fixed broken link to cookbook which is now
 simuPOP-examples repo

---
 docs/_sources/userGuide_ch2_sec1.rst.txt | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/_sources/userGuide_ch2_sec1.rst.txt b/docs/_sources/userGuide_ch2_sec1.rst.txt
index fc0d5224..edc36c11 100644
--- a/docs/_sources/userGuide_ch2_sec1.rst.txt
+++ b/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 cookbook
+(``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

From 077526b731e8e0d07a7f142961223ea155fea57b Mon Sep 17 00:00:00 2001
From: Louise McMillan <louise.mcmillan@gmail.com>
Date: Wed, 28 Aug 2024 04:54:48 +1200
Subject: [PATCH 04/12] Moved link to evolve.png

---
 docs/_sources/userGuide_ch2_sec2.rst.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/_sources/userGuide_ch2_sec2.rst.txt b/docs/_sources/userGuide_ch2_sec2.rst.txt
index 7753754b..9689c3ea 100644
--- a/docs/_sources/userGuide_ch2_sec2.rst.txt
+++ b/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
 
 

From dd5e1c62b1cf2437f72a26ea2d452263d6d88d06 Mon Sep 17 00:00:00 2001
From: Louise McMillan <louise.mcmillan@gmail.com>
Date: Wed, 28 Aug 2024 04:59:58 +1200
Subject: [PATCH 05/12] Fixed links to cookbook and sourceforge mailing list

---
 docs/_sources/userGuide_ch2_sec6.rst.txt | 12 +++++-------
 1 file changed, 5 insertions(+), 7 deletions(-)

diff --git a/docs/_sources/userGuide_ch2_sec6.rst.txt b/docs/_sources/userGuide_ch2_sec6.rst.txt
index 96abc768..1a293dea 100644
--- a/docs/_sources/userGuide_ch2_sec6.rst.txt
+++ b/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.

From 0efe6b0a624d576b8d60eb65686e66ed0636d5d1 Mon Sep 17 00:00:00 2001
From: Louise McMillan <louise.mcmillan@gmail.com>
Date: Wed, 28 Aug 2024 05:03:26 +1200
Subject: [PATCH 06/12] Fixed figure link

---
 docs/_sources/userGuide_ch8_sec6.rst.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/_sources/userGuide_ch8_sec6.rst.txt b/docs/_sources/userGuide_ch8_sec6.rst.txt
index 1531a8a2..786aea24 100644
--- a/docs/_sources/userGuide_ch8_sec6.rst.txt
+++ b/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
    
 

From 080e5ff05e7f0b8854bd13c859b86291b0c401d0 Mon Sep 17 00:00:00 2001
From: Louise McMillan <louise.mcmillan@gmail.com>
Date: Wed, 28 Aug 2024 05:08:39 +1200
Subject: [PATCH 07/12] Removed reference to "cookbook"

---
 docs/_sources/userGuide_ch2_sec1.rst.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/_sources/userGuide_ch2_sec1.rst.txt b/docs/_sources/userGuide_ch2_sec1.rst.txt
index edc36c11..39bcc372 100644
--- a/docs/_sources/userGuide_ch2_sec1.rst.txt
+++ b/docs/_sources/userGuide_ch2_sec1.rst.txt
@@ -35,7 +35,7 @@ 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 examples folder within the online simuPOP cookbook
+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

From bcb6c59d6b49ec0cb6ae38b0fe246fdbb80843a7 Mon Sep 17 00:00:00 2001
From: Louise McMillan <louise.mcmillan@gmail.com>
Date: Wed, 28 Aug 2024 05:11:49 +1200
Subject: [PATCH 08/12] Updated references to "cookbook"

---
 doc/userGuide.lyx | 21 ++++++++++-----------
 1 file changed, 10 insertions(+), 11 deletions(-)

diff --git a/doc/userGuide.lyx b/doc/userGuide.lyx
index 1274c84e..66a850fc 100644
--- a/doc/userGuide.lyx
+++ b/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
@@ -433,7 +433,7 @@ 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 examples folder within 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-examples
@@ -1389,7 +1389,7 @@ https://github.com/BoPeng/simuPOP
 \begin_layout Standard
 A
 \emph on
-simuPOP online cookbook
+simuPOP online examples
 \emph default
  (
 \family typewriter
@@ -1397,12 +1397,11 @@ 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
@@ -23632,7 +23631,7 @@ 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-examples
 \family default
@@ -26921,7 +26920,7 @@ simuCDCV.py
  The complete script is available at
 \begin_inset CommandInset href
 LatexCommand href
-name "the simuPOP online cookbook"
+name "the simuPOP examples"
 target "https://github.com/BoPeng/simuPOP-examples"
 
 \end_inset

From c149d9015e37214b9ac5535c3b0a33710aaf5246 Mon Sep 17 00:00:00 2001
From: Louise McMillan <louise.mcmillan@gmail.com>
Date: Wed, 28 Aug 2024 05:15:11 +1200
Subject: [PATCH 09/12] Fixed link to "cookbook"

---
 docs/index.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/index.html b/docs/index.html
index 14e5fe4f..66e12254 100644
--- a/docs/index.html
+++ b/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>

From 57f4ac4383d22bc5d244c36767e9adde855cc975 Mon Sep 17 00:00:00 2001
From: Louise McMillan <louise.mcmillan@gmail.com>
Date: Wed, 28 Aug 2024 05:16:43 +1200
Subject: [PATCH 10/12] Fixed link to "cookbook"

---
 docs/_sources/userGuide_ch8_sec1.rst.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/_sources/userGuide_ch8_sec1.rst.txt b/docs/_sources/userGuide_ch8_sec1.rst.txt
index 71b3ed67..4ad1d3da 100644
--- a/docs/_sources/userGuide_ch8_sec1.rst.txt
+++ b/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.

From 3edfb19368b6a5472c12c84f9780f678554b21d9 Mon Sep 17 00:00:00 2001
From: Louise McMillan <louise.mcmillan@gmail.com>
Date: Wed, 28 Aug 2024 05:17:29 +1200
Subject: [PATCH 11/12] Removed reference to "cookbook"

---
 docs/_sources/userGuide_ch1.rst.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/_sources/userGuide_ch1.rst.txt b/docs/_sources/userGuide_ch1.rst.txt
index 3f6b0b0e..d25916e5 100644
--- a/docs/_sources/userGuide_ch1.rst.txt
+++ b/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

From 3824fdc84b9e3cd7a73490d93273f10ca7c9e7b1 Mon Sep 17 00:00:00 2001
From: Louise McMillan <louise.mcmillan@gmail.com>
Date: Wed, 28 Aug 2024 05:21:26 +1200
Subject: [PATCH 12/12] Removed reference to "cookbook"

---
 docs/userGuide_ch8_sec1.html | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/userGuide_ch8_sec1.html b/docs/userGuide_ch8_sec1.html
index 98d5ddf8..b01cc149 100644
--- a/docs/userGuide_ch8_sec1.html
+++ b/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>
\ No newline at end of file
+</html>