From 3515ac025ec29e2f61a582bba49971af337bbc7b Mon Sep 17 00:00:00 2001
From: Dale Roberts <dsroberts@unimelb.edu.au>
Date: Mon, 12 Feb 2024 11:02:45 +1100
Subject: [PATCH] Update stable to 23.10 and unstable to 24.01

---
 environments/analysis3/config.sh       |  4 ++--
 environments/analysis3/environment.yml |  1 +
 scripts/functions.sh                   | 19 ++++++++++++++-----
 3 files changed, 17 insertions(+), 7 deletions(-)

diff --git a/environments/analysis3/config.sh b/environments/analysis3/config.sh
index d02ece0..b568db6 100644
--- a/environments/analysis3/config.sh
+++ b/environments/analysis3/config.sh
@@ -9,8 +9,8 @@
 
 ### Optional config for custom deploy script
 export VERSION_TO_MODIFY=24.01
-export STABLE_VERSION=23.07
-export UNSTABLE_VERSION=23.10
+export STABLE_VERSION=23.10
+export UNSTABLE_VERSION=24.01
 
 ### Version settings
 export ENVIRONMENT=analysis3
diff --git a/environments/analysis3/environment.yml b/environments/analysis3/environment.yml
index ccbbfc1..29f5143 100644
--- a/environments/analysis3/environment.yml
+++ b/environments/analysis3/environment.yml
@@ -284,5 +284,6 @@ dependencies:
 - pdbufr
 - matplotlib-scalebar
 - python-kaleido
+- numba<0.59 ### pysal -> giddy -> quantecon is broken with numba 0.59
 - pip:
   - railroad-diagrams ### Unlisted dependency of pip and pyparsing
diff --git a/scripts/functions.sh b/scripts/functions.sh
index 7dd368a..2cfea96 100644
--- a/scripts/functions.sh
+++ b/scripts/functions.sh
@@ -207,11 +207,20 @@ function initialise_tmp_dirs() {
     if [[ "${PBS_JOBFS}" ]]; then
         relink_cmds=""
         for dir in "$@"; do
-            relink_cmds="${relink_cmds}rm ~/${dir}; ln -s $( readlink ~/${dir} ) ~/${dir}; "
-            rm ~/"${dir}"
-            mkdir -p "${PBS_JOBFS}"/"${dir}"
-            ln -s "${PBS_JOBFS}"/"${dir}" ~
-            ### Race condition
+            if [[ -h ~/"${dir}" ]]; then
+                relink_cmds="${relink_cmds}rm ~/${dir}; ln -s $( readlink ~/${dir} ) ~/${dir}; "
+                rm ~/"${dir}"
+                mkdir -p "${PBS_JOBFS}"/"${dir}"
+                ln -s "${PBS_JOBFS}"/"${dir}" ~
+                ### Race condition
+            elif [[ -d ~/"${dir}" ]]; then
+                echo "Warning! ~/${dir} is a directory (not a symlink). This can significantly increase "
+                echo "installation time of conda environments."
+            else
+                relink_cmds="${relink_cmds}rm ~/${dir}; "
+                mkdir -p "${PBS_JOBFS}"/"${dir}"
+                ln -s "${PBS_JOBFS}"/"${dir}" ~
+            fi
         done
         trap "${relink_cmds}" EXIT
     fi