From 68c7a0d10f3578d9c9ad9b147b501dd4b1c98b02 Mon Sep 17 00:00:00 2001
From: Dale Roberts <dsroberts@unimelb.edu.au>
Date: Tue, 25 Jun 2024 11:44:38 +1000
Subject: [PATCH] Install ecmwf_api_client. Pin ucx and openmpi to latest
 available version on Gadi. Pin pyarrow otherwise micromamba brings in a
 broken version

---
 environments/analysis3/environment.yml | 4 ++--
 scripts/dev_prep.sh                    | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/environments/analysis3/environment.yml b/environments/analysis3/environment.yml
index 6d4dc26..9097ae1 100644
--- a/environments/analysis3/environment.yml
+++ b/environments/analysis3/environment.yml
@@ -128,7 +128,7 @@ dependencies:
 - panel
 - xrft
 - git
-- openmpi
+- openmpi==4.1.6
 - mpi4py
 - palettable
 - xlrd
@@ -168,7 +168,7 @@ dependencies:
 - rasterstats
 - windrose
 - pyam
-- pyarrow
+- pyarrow>=16.1
 - python-gist
 - celluloid
 - jags
diff --git a/scripts/dev_prep.sh b/scripts/dev_prep.sh
index 88b9067..51c437e 100644
--- a/scripts/dev_prep.sh
+++ b/scripts/dev_prep.sh
@@ -158,7 +158,7 @@ _initialise() {
     echo "Copying external files"
     for f in "${outside_files_to_copy[@]}"; do
         mkdir -p "${OVERLAY_BASE}"/$( dirname "${f#/g/}" )
-        cp "${f}" "${OVERLAY_BASE}"/"${f#/g/}"
+        cp -r "${f}" "${OVERLAY_BASE}"/"${f#/g/}"
     done
 
     echo "Unsquashing unstable environment"