From db41cd49b6d8ccd2c3318209118ffe098bc9293e Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 19 Aug 2020 03:57:05 +0300
Subject: Remove extra whitespace(or add it) from comma separated items

See: <https://docs.python.org/2/library/2to3.html#2to3fixer-urllib>
---
 etc/default_settings.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'etc')

diff --git a/etc/default_settings.py b/etc/default_settings.py
index f368237b..82c605da 100644
--- a/etc/default_settings.py
+++ b/etc/default_settings.py
@@ -24,7 +24,7 @@
 import os
 import sys
 
-GN_VERSION = open("../etc/VERSION","r").read()
+GN_VERSION = open("../etc/VERSION", "r").read()
 GN_SERVER_URL = "http://localhost:8880/" # REST API server
 
 # ---- MySQL
-- 
cgit v1.2.3


From b32004bc517d9a58be52662297e541c23f60355b Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Thu, 20 Aug 2020 16:01:54 +0300
Subject: Replace all references to python2.7 with python3.8

Run:

```
find . -type f -print0 | xargs -0 sed -i \
"s|lib/python2.7/site-packages|lib/python3.8/site-packages|g"
```
---
 bin/genenetwork2                      | 6 +++---
 doc/GUIX-Reproducible-from-source.org | 6 +++---
 doc/README.org                        | 2 +-
 doc/development.org                   | 4 ++--
 etc/default_settings.py               | 2 +-
 5 files changed, 10 insertions(+), 10 deletions(-)

(limited to 'etc')

diff --git a/bin/genenetwork2 b/bin/genenetwork2
index dd6db7d6..5f4e0f9a 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -60,7 +60,7 @@ GN2_ID=$(cat /etc/hostname):$(basename $GN2_BASE_DIR)
 
 echo GN2_BASE_DIR=$GN2_BASE_DIR
 
-GUIX_SITE=$GN2_BASE_DIR/lib/python2.7/site-packages
+GUIX_SITE=$GN2_BASE_DIR/lib/python3.8/site-packages
 if [ -d $GUIX_SITE ]; then
     echo INFO: GN2 is running from GNU Guix
     GN2_BASE_DIR=$GUIX_SITE
@@ -105,7 +105,7 @@ echo GN2_SETTINGS=$settings
 # if [ -z $ELASTICSEARCH_PROFILE ]; then
 #     echo -e "WARNING: Elastic Search profile has not been set - use ELASTICSEARCH_PROFILE";
 # else
-#     PYTHONPATH="$PYTHONPATH${PYTHONPATH:+:}$ELASTICSEARCH_PROFILE/lib/python2.7/site-packages"
+#     PYTHONPATH="$PYTHONPATH${PYTHONPATH:+:}$ELASTICSEARCH_PROFILE/lib/python3.8/site-packages"
 # fi
 
 if [ -z $GN2_PROFILE ] ; then
@@ -121,7 +121,7 @@ if [ -z $GN2_PROFILE ]; then
     read -p "PRESS [ENTER] TO CONTINUE..."
 else
     export PATH=$GN2_PROFILE/bin:$PATH
-    export PYTHONPATH="$PYTHON_GN_PATH:$GN2_PROFILE/lib/python2.7/site-packages" # never inject another PYTHONPATH!!
+    export PYTHONPATH="$GN2_PROFILE/lib/python3.8/site-packages" # never inject another PYTHONPATH!!
     export R_LIBS_SITE=$GN2_PROFILE/site-library
     export JS_GUIX_PATH=$GN2_PROFILE/share/genenetwork2/javascript
     export GUIX_GTK3_PATH="$GN2_PROFILE/lib/gtk-3.0"
diff --git a/doc/GUIX-Reproducible-from-source.org b/doc/GUIX-Reproducible-from-source.org
index 19e4d14f..fffa9571 100644
--- a/doc/GUIX-Reproducible-from-source.org
+++ b/doc/GUIX-Reproducible-from-source.org
@@ -167,7 +167,7 @@ the Guix suggested environment vars. Check the output of
 
 #+begin_src bash
 guix package --search-paths
-export PYTHONPATH="/root/.guix-profile/lib/python2.7/site-packages"
+export PYTHONPATH="/root/.guix-profile/lib/python3.8/site-packages"
 export R_LIBS_SITE="/root/.guix-profile/site-library/"
 #+end_src
 
@@ -265,7 +265,7 @@ software.
 If something is not working, take a hint from the settings file
 that comes in the Guix installation. It sits in something like
 
-: cat ~/.guix-profile/lib/python2.7/site-packages/genenetwork2-2.0-py2.7.egg/etc/default_settings.py
+: cat ~/.guix-profile/lib/python3.8/site-packages/genenetwork2-2.0-py2.7.egg/etc/default_settings.py
 
 ** Set up nginx port forwarding
 
@@ -380,7 +380,7 @@ After setting the paths for the server
 
 #+begin_src bash
 export PATH=~/.guix-profile/bin:$PATH
-export PYTHONPATH="$HOME/.guix-profile/lib/python2.7/site-packages"
+export PYTHONPATH="$HOME/.guix-profile/lib/python3.8/site-packages"
 export R_LIBS_SITE="$HOME/.guix-profile/site-library/"
 export GUIX_GTK3_PATH="$HOME/.guix-profile/lib/gtk-3.0"
 export GI_TYPELIB_PATH="$HOME/.guix-profile/lib/girepository-1.0"
diff --git a/doc/README.org b/doc/README.org
index 46df03c7..43c92e3c 100644
--- a/doc/README.org
+++ b/doc/README.org
@@ -218,7 +218,7 @@ information given by guix:
 
 On one system:
 
-: export PYTHONPATH="$HOME/.guix-profile/lib/python2.7/site-packages"
+: export PYTHONPATH="$HOME/.guix-profile/lib/python3.8/site-packages"
 : export R_LIBS_SITE="$HOME/.guix-profile/site-library/"
 : export GEM_PATH="$HOME/.guix-profile/lib/ruby/gems/2.2.0"
 
diff --git a/doc/development.org b/doc/development.org
index e65ccd58..cd3beea3 100644
--- a/doc/development.org
+++ b/doc/development.org
@@ -67,11 +67,11 @@ You can install a Python package locally with pip, e.g.
 pip install hjson
 #+END_SRC
 
-This installed in ~$HOME/.local/lib/python2.7/site-packages~. To add
+This installed in ~$HOME/.local/lib/python3.8/site-packages~. To add
 the search path for GeneNetwork use the environment variable
 
 #+BEGIN_SRC sh
-export PYTHON_GN_PATH=$HOME/.local/lib/python2.7/site-packages
+export PYTHON_GN_PATH=$HOME/.local/lib/python3.8/site-packages
 #+END_SRC
 
 Now you should be able to do
diff --git a/etc/default_settings.py b/etc/default_settings.py
index 82c605da..27522187 100644
--- a/etc/default_settings.py
+++ b/etc/default_settings.py
@@ -19,7 +19,7 @@
 #
 # For GNU Guix deployment also check the paths in
 #
-#  ~/.guix-profile/lib/python2.7/site-packages/genenetwork2-2.0-py2.7.egg/etc/default_settings.py
+#  ~/.guix-profile/lib/python3.8/site-packages/genenetwork2-2.0-py2.7.egg/etc/default_settings.py
 
 import os
 import sys
-- 
cgit v1.2.3