From 868b09c655a29724afd28ac4d912b7d19588e08c Mon Sep 17 00:00:00 2001
From: Dale Roberts <dsroberts@unimelb.edu.au>
Date: Tue, 25 Jun 2024 10:40:40 +1000
Subject: [PATCH 1/3] Install ecmwf_api_client. Pin ucx to latest available
 version on Gadi

---
 environments/analysis3/environment.yml | 2 ++
 environments/analysis3/testconfig.yml  | 1 +
 2 files changed, 3 insertions(+)

diff --git a/environments/analysis3/environment.yml b/environments/analysis3/environment.yml
index 1e77827..6d4dc26 100644
--- a/environments/analysis3/environment.yml
+++ b/environments/analysis3/environment.yml
@@ -278,6 +278,7 @@ dependencies:
 - shellcheck
 - pysteps
 - ucx-py
+- ucx==1.15.0
 - geocat-viz
 - icclim
 - py-cordex
@@ -290,5 +291,6 @@ dependencies:
 - regional-mom6
 - u8darts-all
 - xwrf
+- ecmwf-api-client
 - pip:
   - railroad-diagrams ### Unlisted dependency of pip and pyparsing
diff --git a/environments/analysis3/testconfig.yml b/environments/analysis3/testconfig.yml
index e0c962c..ee0e328 100644
--- a/environments/analysis3/testconfig.yml
+++ b/environments/analysis3/testconfig.yml
@@ -59,6 +59,7 @@ skip:
 - torch.onnx ### Prevent testing of _internal APIs
 - torch.testing ### Prevent testing of _internal APIs
 - torch.utils.benchmark ### Uses non-existent part of deprecated pkg_resources
+- keras.src.backend ### Don't test Keras backends
 
 # Preload these modules before testing to avoid weird python issues
 preload:

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 2/3] 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"

From d20a36c5f91e19f9766f8b6e9fa7a252576bef3b Mon Sep 17 00:00:00 2001
From: Dale Roberts <dsroberts@unimelb.edu.au>
Date: Wed, 26 Jun 2024 10:35:16 +1000
Subject: [PATCH 3/3] Unpin pyarrow - step 1 of 2 in this build

---
 environments/analysis3/environment.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/environments/analysis3/environment.yml b/environments/analysis3/environment.yml
index 9097ae1..b3110e2 100644
--- a/environments/analysis3/environment.yml
+++ b/environments/analysis3/environment.yml
@@ -3,7 +3,6 @@ channels:
 - coecms
 - conda-forge
 - accessnri
-- anaconda
 variables:
   CARTOPY_USER_BACKGROUNDS: /g/data/hh5/public/apps/cartopy-data/backgrounds
 dependencies:
@@ -69,7 +68,7 @@ dependencies:
 - matplotlib
 #- matplotlib>=3.5.2|<=3.4.3  # pinned to solve  https://github.com/matplotlib/matplotlib/issues/21917
 - dreqpy
-- pint<0.24 ### https://github.com/Ouranosinc/xclim/issues/1771
+- pint ###<0.24 ### https://github.com/Ouranosinc/xclim/issues/1771
 - pycodestyle 
 - nc-time-axis
 - jq
@@ -168,7 +167,7 @@ dependencies:
 - rasterstats
 - windrose
 - pyam
-- pyarrow>=16.1
+- pyarrow
 - python-gist
 - celluloid
 - jags