diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 9c00e03..2bc7023 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -9,17 +9,34 @@ jobs:
   build:
     name: Build environment
     runs-on: ubuntu-latest
+    environment: Gadi
     steps:
-      - name: Build environment
-        uses: appleboy/ssh-action@v0.1.7
+      - name: Setup SSH
+        uses: access-nri/actions/.github/actions/setup-ssh@main
+        id: ssh
         with:
-          host: gadi.nci.org.au
-          username: ${{secrets.GADI_USER}}
-          key: ${{secrets.DEPLOY_KEY}}
-          command_timeout: 120m
-          script: |
-            export SCRIPT_DIR=${{secrets.GADI_REPO_PATH}}/scripts
-            eval $( grep ADMIN_DIR $SCRIPT_DIR/install_config.sh )
-            eval $( grep JOB_LOG_DIR $SCRIPT_DIR/install_config.sh )
-            cd $JOB_LOG_DIR
-            qsub -N build_${{ inputs.environment }} -lncpus=1,mem=20GB,walltime=2:00:00,jobfs=50GB,storage=gdata/v45+scratch/v45+gdata/hh5+scratch/hh5 -v SCRIPT_DIR,CONDA_ENVIRONMENT=${{ inputs.environment }} -P kr06 -q copyq -Wblock=true -Wumask=037 "${SCRIPT_DIR}"/build.sh
+          hosts: ${{ secrets.HOST }}
+          private-key: ${{ secrets.SSH_KEY }}
+
+      - name: Build environment
+        run: |
+          ssh ${{ secrets.USER }}@${{ secrets.HOST }} -i ${{ steps.ssh.outputs.private-key-path }} /bin/bash <<'EOT'
+          set -e
+          export SCRIPT_DIR="${{ secrets.REPO_PATH }}/scripts"
+          export CONDA_ENVIRONMENT="${{ inputs.environment }}"
+          export ADMIN_DIR="${{ vars.ADMIN_DIR }}"
+          export CONDA_BASE="${{ vars.CONDA_BASE }}"
+          export APPS_USERS_GROUP="${{ vars.APPS_USERS_GROUP }}"
+          export APPS_OWNERS_GROUP="${{ vars.APPS_OWNERS_GROUP }}"
+          PROJECT=${{ vars.PROJECT }}
+          STORAGE=${{ vars.STORAGE }}
+
+          source "${SCRIPT_DIR}"/install_config.sh
+          cd "${JOB_LOG_DIR}"
+
+          qsub -N build_"${CONDA_ENVIRONMENT}" -lncpus=1,mem=20GB,walltime=2:00:00,jobfs=50GB,storage="${STORAGE}" \
+            -v SCRIPT_DIR,CONDA_ENVIRONMENT,ADMIN_DIR,CONDA_BASE,APPS_USERS_GROUP,APPS_OWNERS_GROUP \
+            -P "${PROJECT}" -q copyq -Wblock=true -Wumask=037 \
+            "${SCRIPT_DIR}"/build.sh
+
+          EOT
\ No newline at end of file
diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
index 2a77cbe..14714d9 100644
--- a/.github/workflows/deploy.yml
+++ b/.github/workflows/deploy.yml
@@ -9,16 +9,28 @@ jobs:
   deploy:
     name: Deploy environment
     runs-on: ubuntu-latest
+    environment: Gadi
     steps:
-      - name: Deploy environment
-        uses: appleboy/ssh-action@v0.1.7
+      - name: Setup SSH
+        uses: access-nri/actions/.github/actions/setup-ssh@main
+        id: ssh
         with:
-          host: gadi.nci.org.au
-          username: ${{secrets.GADI_USER}}
-          key: ${{secrets.DEPLOY_KEY}}
-          script: |
-            export SCRIPT_DIR=${{secrets.GADI_REPO_PATH}}/scripts
-            export CONDA_ENVIRONMENT=${{ inputs.environment }}
-            eval $( grep ADMIN_DIR $SCRIPT_DIR/install_config.sh )
-            eval $( grep BUILD_STAGE_DIR $SCRIPT_DIR/install_config.sh )
-            "${SCRIPT_DIR}"/deploy.sh
+          hosts: ${{ secrets.HOST }}
+          private-key: ${{ secrets.SSH_KEY }}
+
+      - name: Deploy environment
+        run: |
+          ssh ${{ secrets.USER }}@${{ secrets.HOST }} -i ${{ steps.ssh.outputs.private-key-path }} /bin/bash <<'EOT'
+          set -e
+          export SCRIPT_DIR="${{ secrets.REPO_PATH }}/scripts"
+          export CONDA_ENVIRONMENT="${{ inputs.environment }}"
+          export ADMIN_DIR="${{ vars.ADMIN_DIR }}"
+          export CONDA_BASE="${{ vars.CONDA_BASE }}"
+          export APPS_USERS_GROUP="${{ vars.APPS_USERS_GROUP }}"
+          export APPS_OWNERS_GROUP="${{ vars.APPS_OWNERS_GROUP }}"
+
+          source "${SCRIPT_DIR}"/install_config.sh
+
+          "${SCRIPT_DIR}"/deploy.sh
+
+          EOT
\ No newline at end of file
diff --git a/.github/workflows/get_changed_env.yml b/.github/workflows/get_changed_env.yml
index 71a0ef9..ce81c22 100644
--- a/.github/workflows/get_changed_env.yml
+++ b/.github/workflows/get_changed_env.yml
@@ -32,7 +32,7 @@ jobs:
           for line in $DIFF; do
             if [[ $line =~ environments ]]; then
                 env_name=$( basename ${line%/*} )
-                if ! [[ $json =~ $env_name ]]; then
+                if ! [[ $json =~ $env_name ]] && [ -d "environments/$env_name" ]; then
                     json="$json{\"environment\":\"$env_name\"},"
                 fi
             fi
diff --git a/.github/workflows/manual_trigger.yml b/.github/workflows/manual_trigger.yml
index 71a800a..8661392 100644
--- a/.github/workflows/manual_trigger.yml
+++ b/.github/workflows/manual_trigger.yml
@@ -10,27 +10,42 @@ on:
 jobs:
   setup:
     runs-on: ubuntu-latest
+    environment: Gadi
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
+
+      - name: Setup SSH
+        uses: access-nri/actions/.github/actions/setup-ssh@main
+        id: ssh
+        with:
+          hosts: |
+            ${{ secrets.HOST }}
+            ${{ secrets.HOST_DATA }}
+          private-key: ${{ secrets.SSH_KEY }}
+
       - name: Sync repository to Gadi
-        uses: up9cloud/action-rsync@v1.3
-        env:
-          HOST: gadi.nci.org.au
-          TARGET: ${{secrets.GADI_REPO_PATH}}
-          KEY: ${{secrets.DEPLOY_KEY}}
-          USER: ${{secrets.GADI_USER}}
+        run: |
+          rsync -e 'ssh -i ${{ steps.ssh.outputs.private-key-path }}' \
+            -avz --delete --exclude=/.git/ --exclude=/.github/ \
+            ./ \
+            ${{ secrets.USER }}@${{ secrets.HOST_DATA }}:${{ secrets.REPO_PATH }}
+
       - name: Create Admin dirs on Gadi
-        uses: appleboy/ssh-action@v0.1.7
-        with:
-          host: gadi.nci.org.au
-          username: ${{secrets.GADI_USER}}
-          key: ${{secrets.DEPLOY_KEY}}
-          script: |
-            source ${{secrets.GADI_REPO_PATH}}/scripts/install_config.sh
-            source ${{secrets.GADI_REPO_PATH}}/scripts/functions.sh
-            mkdir -p $ADMIN_DIR $JOB_LOG_DIR $BUILD_STAGE_DIR
-            set_admin_perms $ADMIN_DIR $JOB_LOG_DIR $BUILD_STAGE_DIR
+        run: |
+          ssh ${{ secrets.USER }}@${{ secrets.HOST }} -i ${{ steps.ssh.outputs.private-key-path }} /bin/bash <<'EOT'
+          set -e
+          export ADMIN_DIR="${{ vars.ADMIN_DIR }}"
+          export CONDA_BASE="${{ vars.CONDA_BASE }}"
+          export APPS_USERS_GROUP="${{ vars.APPS_USERS_GROUP }}"
+          export APPS_OWNERS_GROUP="${{ vars.APPS_OWNERS_GROUP }}"
+
+          source "${{ secrets.REPO_PATH }}/scripts/install_config.sh"
+          source "${{ secrets.REPO_PATH }}/scripts/functions.sh"
+          mkdir -p "${ADMIN_DIR}" "${JOB_LOG_DIR}" "${BUILD_STAGE_DIR}"
+          set_admin_perms "${ADMIN_DIR}" "${JOB_LOG_DIR}" "${BUILD_STAGE_DIR}"
+
+          EOT
 
   build:
     needs: setup
diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index 5b6f8b5..7e05a32 100644
--- a/.github/workflows/pull_request.yml
+++ b/.github/workflows/pull_request.yml
@@ -1,51 +1,135 @@
 name: Build and test conda env
+
 on: pull_request
+
 jobs:
   generate_matrix:
     uses: ./.github/workflows/get_changed_env.yml
-  
-  setup:
+
+  build_base_image:
     runs-on: ubuntu-latest
     needs: generate_matrix
     if: ${{ needs.generate_matrix.outputs.matrix != '{"include":[]}' }}
     container:
       image: quay.io/singularity/singularity:v3.11.4
       options: --privileged
+    outputs:
+      built-container: ${{ steps.changed-container-def.outputs.containerdef_any_changed }}
     steps:
       - name: Checkout repository
         ### Latest at time of writing
         uses: actions/checkout@v4
+
       - name: Check if container definition has changed
         id: changed-container-def
-        uses: tj-actions/changed-files@v41
+        uses: tj-actions/changed-files@48d8f15b2aaa3d255ca5af3eba4870f807ce6b3c # v43.0.2
         with:
           files_yaml: |
             containerdef:
               - container/container.def
+
       - name: Build container if definition has changed
         if: steps.changed-container-def.outputs.containerdef_any_changed == 'true'
         run: |
             echo ${{ needs.generate_matrix.outputs.matrix }}
             sudo -E singularity build container/base.sif container/container.def
+
+      - name: Upload base container
+        if: steps.changed-container-def.outputs.containerdef_any_changed == 'true'
+        uses: actions/upload-artifact@v4
+        with:
+            name: base-container
+            path: container/base.sif
+
+  setup:
+    runs-on: ubuntu-latest
+    needs: [ generate_matrix, build_base_image ]
+    if: ${{ needs.generate_matrix.outputs.matrix != '{"include":[]}' }}
+    environment: Gadi
+    steps:
+      - name: Check Gadi Github Environment configuration
+        run: |
+          vars_unset=false
+          if [ -z "${{ vars.ADMIN_DIR }}" ]; then
+            echo "::error::vars.ADMIN_DIR is unset. ADMIN_DIR is the base directory which will contain the staging and logs sub-directories"
+            vars_unset=true
+          fi
+          if [ -z "${{ vars.CONDA_BASE }}" ]; then
+            echo "::error::vars.CONDA_BASE is unset. CONDA_BASE is the base deployment directory which will contain apps and module sub-directories"
+            vars_unset=true
+          fi
+          if [ -z "${{ vars.PROJECT }}" ]; then
+            echo "::error::vars.PROJECT is unset. PROJECT is the project code passed to build+test qsub calls"
+            vars_unset=true
+          fi
+          if [ -z "${{ vars.STORAGE }}" ]; then
+            echo "::error::vars.STORAGE is unset. STORAGE is the storage flags passed to build+test qsub calls"
+            vars_unset=true
+          fi
+          if [ -z "${{ vars.APPS_USERS_GROUP }}" ]; then
+            echo "::error::vars.APPS_USERS_GROUP is unset. APPS_USERS_GROUP is used for setting file permissions"
+            vars_unset=true
+          fi
+          if [ -z "${{ vars.APPS_OWNERS_GROUP }}" ]; then
+            echo "::error::APPS_OWNERS_GROUP is unset. APPS_OWNERS_GROUP is used for setting file permissions"
+            vars_unset=true
+          fi
+          if [ -z "${{ secrets.REPO_PATH }}" ]; then
+            echo "::error::secrets.REPO_PATH is unset. REPO_PATH is the path where this repository is synced to"
+            vars_unset=true
+          fi
+
+          if [ "$vars_unset" == "true" ]; then
+            echo "::error::Required vars in Gadi Github Environment are unset."
+            exit 1
+          fi
+
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Download base container
+        if: needs.build_base_image.outputs.built-container == 'true'
+        uses: actions/download-artifact@v4
+        with:
+            name: base-container
+            path: container
+
+      - name: Setup SSH
+        uses: access-nri/actions/.github/actions/setup-ssh@main
+        id: ssh
+        with:
+          hosts: |
+            ${{ secrets.HOST }}
+            ${{ secrets.HOST_DATA }}
+          private-key: ${{ secrets.SSH_KEY }}
+
+      - name: Create parent repository directories
+        run: |
+          ssh ${{ secrets.USER }}@${{ secrets.HOST }} -i ${{ steps.ssh.outputs.private-key-path }} /bin/bash <<'EOT'
+          mkdir -p ${{ secrets.REPO_PATH }}
+          EOT
+
       - name: Sync repository to Gadi
-        ### Latest at time of writing
-        uses: up9cloud/action-rsync@v1.3
-        env:
-          HOST: gadi.nci.org.au
-          TARGET: ${{secrets.GADI_REPO_PATH}}
-          KEY: ${{secrets.DEPLOY_KEY}}
-          USER: ${{secrets.GADI_USER}}
+        run: |
+          rsync -e 'ssh -i ${{ steps.ssh.outputs.private-key-path }}' \
+            -avz --delete --exclude=/.git/ --exclude=/.github/ \
+            ./ \
+            ${{ secrets.USER }}@${{ secrets.HOST_DATA }}:${{ secrets.REPO_PATH }}
+
       - name: Create Admin dirs on Gadi
-        uses: appleboy/ssh-action@v0.1.7
-        with:
-          host: gadi.nci.org.au
-          username: ${{secrets.GADI_USER}}
-          key: ${{secrets.DEPLOY_KEY}}
-          script: |
-            source ${{secrets.GADI_REPO_PATH}}/scripts/install_config.sh
-            source ${{secrets.GADI_REPO_PATH}}/scripts/functions.sh
-            mkdir -p $ADMIN_DIR $JOB_LOG_DIR $BUILD_STAGE_DIR
-            set_admin_perms $ADMIN_DIR $JOB_LOG_DIR $BUILD_STAGE_DIR
+        run: |
+          ssh ${{ secrets.USER }}@${{ secrets.HOST }} -i ${{ steps.ssh.outputs.private-key-path }} /bin/bash <<'EOT'
+          set -e
+          export ADMIN_DIR="${{ vars.ADMIN_DIR }}"
+          export CONDA_BASE="${{ vars.CONDA_BASE }}"
+          export APPS_USERS_GROUP="${{ vars.APPS_USERS_GROUP }}"
+          export APPS_OWNERS_GROUP="${{ vars.APPS_OWNERS_GROUP }}"
+
+          source "${{ secrets.REPO_PATH }}/scripts/install_config.sh"
+          source "${{ secrets.REPO_PATH }}/scripts/functions.sh"
+          mkdir -p "${ADMIN_DIR}" "${JOB_LOG_DIR}" "${BUILD_STAGE_DIR}"
+          set_admin_perms "${ADMIN_DIR}" "${JOB_LOG_DIR}" "${BUILD_STAGE_DIR}"
+          EOT
 
   build:
     needs: [ generate_matrix, setup ]
diff --git a/.github/workflows/push_to_main.yml b/.github/workflows/push_to_main.yml
index 49a7e3c..5a0f791 100644
--- a/.github/workflows/push_to_main.yml
+++ b/.github/workflows/push_to_main.yml
@@ -8,19 +8,26 @@ jobs:
 
   setup:
     runs-on: ubuntu-latest
+    environment: Gadi
     steps:
       - name: Checkout repository
         ### Latest at time of writing
         uses: actions/checkout@v4
+
+      - name: Setup SSH
+        uses: access-nri/actions/.github/actions/setup-ssh@main
+        id: ssh
+        with:
+          hosts: ${{ secrets.HOST_DATA }}
+          private-key: ${{ secrets.SSH_KEY }}
+
       - name: Sync repository to Gadi
-        ### Latest at time of writing
-        uses: up9cloud/action-rsync@v1.3
-        env:
-          HOST: gadi.nci.org.au
-          TARGET: ${{secrets.GADI_REPO_PATH}}
-          KEY: ${{secrets.DEPLOY_KEY}}
-          USER: ${{secrets.GADI_USER}}
-  
+        run: |
+          rsync -e 'ssh -i ${{ steps.ssh.outputs.private-key-path }}' \
+            -avz --delete --exclude=/.git/ --exclude=/.github/ \
+            ./ \
+            ${{ secrets.USER }}@${{ secrets.HOST_DATA }}:${{ secrets.REPO_PATH }}
+
   deploy:
     needs: [ generate_matrix, setup ]
     uses: ./.github/workflows/deploy.yml
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index c6a65cc..8591075 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -9,16 +9,34 @@ jobs:
   test:
     name: Test environment
     runs-on: ubuntu-latest
+    environment: Gadi
     steps:
-      - name: Test environment
-        uses: appleboy/ssh-action@v0.1.7
+      - name: Setup SSH
+        uses: access-nri/actions/.github/actions/setup-ssh@main
+        id: ssh
         with:
-          host: gadi.nci.org.au
-          username: ${{secrets.GADI_USER}}
-          key: ${{secrets.DEPLOY_KEY}}
-          script: |
-            export SCRIPT_DIR=${{secrets.GADI_REPO_PATH}}/scripts
-            eval $( grep ADMIN_DIR $SCRIPT_DIR/install_config.sh )
-            eval $( grep JOB_LOG_DIR $SCRIPT_DIR/install_config.sh )
-            cd $JOB_LOG_DIR
-            qsub -N test_${{ inputs.environment }} -lncpus=4,mem=20GB,walltime=0:20:00,jobfs=50GB,storage=gdata/v45+scratch/v45+gdata/hh5+scratch/hh5 -v SCRIPT_DIR,CONDA_ENVIRONMENT=${{ inputs.environment }} -P kr06 -Wblock=true -Wumask=037 "${SCRIPT_DIR}"/test.sh
\ No newline at end of file
+          hosts: ${{ secrets.HOST }}
+          private-key: ${{ secrets.SSH_KEY }}
+
+      - name: Test environment
+        run: |
+          ssh ${{ secrets.USER }}@${{ secrets.HOST }} -i ${{ steps.ssh.outputs.private-key-path }} /bin/bash <<'EOT'
+          set -e
+          export SCRIPT_DIR="${{secrets.REPO_PATH}}/scripts"
+          export CONDA_ENVIRONMENT="${{ inputs.environment }}"
+          export ADMIN_DIR="${{ vars.ADMIN_DIR }}"
+          export CONDA_BASE="${{ vars.CONDA_BASE }}"
+          export APPS_USERS_GROUP="${{ vars.APPS_USERS_GROUP }}"
+          export APPS_OWNERS_GROUP="${{ vars.APPS_OWNERS_GROUP }}"
+          PROJECT=${{ vars.PROJECT }}
+          STORAGE=${{ vars.STORAGE }}
+
+          source "${SCRIPT_DIR}"/install_config.sh
+          cd "${JOB_LOG_DIR}"
+
+          qsub -N test_"${CONDA_ENVIRONMENT}" -lncpus=4,mem=20GB,walltime=0:20:00,jobfs=50GB,storage="${STORAGE}" \
+            -v SCRIPT_DIR,CONDA_ENVIRONMENT,ADMIN_DIR,CONDA_BASE,APPS_USERS_GROUP,APPS_OWNERS_GROUP \
+            -P "${PROJECT}" -Wblock=true -Wumask=037 \
+            "${SCRIPT_DIR}"/test.sh
+
+          EOT
\ No newline at end of file
diff --git a/container/container.def b/container/container.def
index f97cb0c..082a074 100644
--- a/container/container.def
+++ b/container/container.def
@@ -38,13 +38,8 @@ Bootstrap: scratch
         mkdir -p ${SINGULARITY_ROOTFS}/var/lib/sss
         mkdir -p ${SINGULARITY_ROOTFS}/var/run/munge
 
-        mkdir -p ${SINGULARITY_ROOTFS}/opt/conda/analysis3-22.07
-        mkdir -p ${SINGULARITY_ROOTFS}/opt/conda/analysis3-22.10
-        mkdir -p ${SINGULARITY_ROOTFS}/opt/conda/analysis3-23.01
-        mkdir -p ${SINGULARITY_ROOTFS}/opt/conda/analysis3-23.04
-        mkdir -p ${SINGULARITY_ROOTFS}/opt/conda/analysis3-23.07
-        mkdir -p ${SINGULARITY_ROOTFS}/opt/conda/analysis3-23.10
-        mkdir -p ${SINGULARITY_ROOTFS}/opt/conda/analysis3-24.01
+        mkdir -p ${SINGULARITY_ROOTFS}/opt/conda/payu-1.1.5
+        mkdir -p ${SINGULARITY_ROOTFS}/opt/conda/payu-dev
 
 %runscript
         /usr/bin/bash -l
\ No newline at end of file
diff --git a/environments/analysis3/build_inner.sh b/environments/analysis3/build_inner.sh
deleted file mode 100644
index 32e9d5f..0000000
--- a/environments/analysis3/build_inner.sh
+++ /dev/null
@@ -1,8 +0,0 @@
-### Custom install inner to build jupyter lab extensions
-
-set +u
-eval "$( ${MAMBA} shell hook --shell bash)"
-micromamba activate "${CONDA_INSTALLATION_PATH}/envs/${FULLENV}"
-set -u
-
-jupyter lab build
\ No newline at end of file
diff --git a/environments/analysis3/config.sh b/environments/analysis3/config.sh
deleted file mode 100644
index 60a2aca..0000000
--- a/environments/analysis3/config.sh
+++ /dev/null
@@ -1,23 +0,0 @@
-### config.sh MUST provide the following:
-### $FULLENV
-###
-### Arrays used by the build system (optional, can be empty)
-### rpms_to_remove
-### replace_from_apps
-### outside_commands_to_include
-### outside_files_to_copy
-
-### Optional config for custom deploy script
-export VERSION_TO_MODIFY=24.07
-export STABLE_VERSION=24.04
-export UNSTABLE_VERSION=24.07
-
-### Version settings
-export ENVIRONMENT=analysis3
-export FULLENV="${ENVIRONMENT}-${VERSION_TO_MODIFY}"
-
-declare -a rpms_to_remove=( "openssh-clients" "openssh-server" "openssh" )
-declare -a replace_from_apps=( "ucx/1.15.0" )
-declare -a outside_commands_to_include=( "pbs_tmrsh" "ssh" )
-declare -a outside_files_to_copy=( "/g/data/hh5/public/apps/nci-intake-catalogue/catalogue_new.yaml" "/g/data/hh5/public/apps/openmpi/4.1.6" )
-declare -a replace_with_external=( "/g/data/hh5/public/apps/openmpi/4.1.6" )
diff --git a/environments/analysis3/deploy.sh b/environments/analysis3/deploy.sh
deleted file mode 100644
index b466cbc..0000000
--- a/environments/analysis3/deploy.sh
+++ /dev/null
@@ -1,18 +0,0 @@
-### Update stable/unstable if necessary
-CURRENT_STABLE=$( get_aliased_module "${MODULE_NAME}"/analysis "${CONDA_MODULE_PATH}" )
-NEXT_STABLE="${ENVIRONMENT}-${STABLE_VERSION}"
-CURRENT_UNSTABLE=$( get_aliased_module "${MODULE_NAME}"/analysis3-unstable "${CONDA_MODULE_PATH}" )
-NEXT_UNSTABLE="${ENVIRONMENT}-${UNSTABLE_VERSION}"
-
-if ! [[ "${CURRENT_STABLE}" == "${MODULE_NAME}/${NEXT_STABLE}" ]]; then
-    echo "Updating stable environment to ${NEXT_STABLE}"
-    write_modulerc "${NEXT_STABLE}" "${NEXT_UNSTABLE}" "${ENVIRONMENT}" "${CONDA_MODULE_PATH}" "${MODULE_NAME}"
-    symlink_atomic_update "${CONDA_INSTALLATION_PATH}"/envs/"${ENVIRONMENT}" "${NEXT_STABLE}"
-    symlink_atomic_update "${CONDA_SCRIPT_PATH}"/"${ENVIRONMENT}".d "${NEXT_STABLE}".d
-fi
-if ! [[ "${CURRENT_UNSTABLE}" == "${MODULE_NAME}/${NEXT_UNSTABLE}" ]]; then
-    echo "Updating unstable environment to ${NEXT_UNSTABLE}"
-    write_modulerc "${NEXT_STABLE}" "${NEXT_UNSTABLE}" "${ENVIRONMENT}" "${CONDA_MODULE_PATH}" "${MODULE_NAME}"
-    symlink_atomic_update "${CONDA_INSTALLATION_PATH}"/envs/"${ENVIRONMENT}"-unstable "${NEXT_UNSTABLE}"
-    symlink_atomic_update "${CONDA_SCRIPT_PATH}"/"${ENVIRONMENT}"-unstable.d "${NEXT_UNSTABLE}".d
-fi
\ No newline at end of file
diff --git a/environments/analysis3/environment.yml b/environments/analysis3/environment.yml
deleted file mode 100644
index 3f9d303..0000000
--- a/environments/analysis3/environment.yml
+++ /dev/null
@@ -1,298 +0,0 @@
-name: analysis3
-channels:
-- coecms
-- conda-forge
-- accessnri
-variables:
-  CARTOPY_USER_BACKGROUNDS: /g/data/hh5/public/apps/cartopy-data/backgrounds
-dependencies:
-- python>=3.10
-- pip
-- sqlalchemy<2.0 ### cosima cookbook does not import with sqlalchemy 2
-- libnetcdf=*=mpi_openmpi*
-- coecms-nci
-- cdo
-- hdf5
- #x basemap # Deprecated, see https://matplotlib.org/basemap/users/intro.html#deprecation-notice
- #x basemap-data-hires
-- cartopy
-- dask
-- distributed
-- ipython
-- iris
-- netcdf4
-- numpy
-- pandas
-- pygrib
-- pyhdf
-- pytest
-- scipy
-- seaborn
-- xarray
-- jupyter
-- notebook
-- metpy
-- windspharm
-- python-cdo
-- arm_pyart
-- bokeh
-- datashader
-- f90nml
-- wrf-python
-- sympy
-- sh
-- ffmpeg
-- pydap
-- twine
-- python-graphviz
-- joblib
-- tqdm
-- compliance-checker
-- dataset
-- xerces-c
-- plotly
-- zarr
-- pytables
-- nose
-- ncdu
-- cftime
-- cfunits
-- memory_profiler
-- fs
-- python-magic
-- click_default_group
-- regionmask
-- rasterio
-- gdal
-- libgdal
-- 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
-- pycodestyle 
-- nc-time-axis
-- jq
-- pvlib-python
-- parcels
-- siphon
-- scikit-learn
-- filelock
-- gsw
-- nb_conda_kernels
-- poppler
-- fiona
-- hupper
-- kealib
-- mo_pack
-- mule
-- cf-units
-- python-stratify
-- nbdime
-- eofs
-- eccodes
-- python-eccodes
-- h5py
-- line_profiler
-- bottleneck
-- jupyterlab
-- dask-jobqueue
-- jupyterlab_server
-- docrep
-- gifsicle
-- nodejs
-- cfgrib
-- h5netcdf
-- intake
-- gridfill
-- xgcm
-- xrft
-- doit
-- pylint
-- dusqlpg
-- matplotlib-venn
-- nchash
-- umtools
-- cosima-cookbook
-- clef
-- nccmp
-- coecms-util
-- yamanifest
-- cmocean
-- accessnri::payu<1.1
-- splitvar
-- marineHeatWaves
-- holoviews
-- geoviews
-- pytest-cov
-- panel
-- xrft
-- git
-- openmpi==4.1.6
-- mpi4py
-- palettable
-- xlrd
-- nccompress
-- mdssdiff
-- mnctools
-- addmeta
-- satpy
-- statsmodels
-- dask-labextension
-- nbstripout
-- jupyter-server-proxy
-- sphinx
-- doc8
-- pymunge
-- climtas
-- asyncssh
-- ants
-- xhistogram
-- cartopy_userconfig=1.0.gadi
-- geopy
-- ninja
-- hvplot
-- cython
-- esmf=*=mpi_openmpi*
-- esmpy
-- xesmf
-- sharppy
-- docrep
-- earthpy
-- descartes
-- era5grib
-- conda-tree
-- xmitgcm
-- cupy
-- rioxarray
-- rasterstats
-- windrose
-- pyam
-- pyarrow
-- python-gist
-- celluloid
-- jags
-- xarray-spatial
-- noise # unlisted dependency of xarray-spatial
-- nctoolkit
-- geoplot
-- dask-ml
-- mamba
-- intake-esm
-- pykrige
-- nci_intake_catalogue
-- cmdline_provenance
-- mplleaflet
-- branca
-- fiona
-- folium
-- black
-- aiohttp
-- aiohttp-cors
-- autopep8
-- spyder-kernels
-- dask-xgboost
-- git-subtree
-- xarray-spatial
-- watermark
-- cvxpy
-- rechunker
-- xmovie
-- pymannkendall
-- param
-- tensorflow
-- shap
-- gh
-- pyqt
-- vtk
-- mayavi
-- gcm_filters
-- timezonefinder
-- lftp
-- xarraymannkendall
-- watchdog  
-- numpy_groupies
-- anytree
-- fortran-language-server
-- hdbscan
-- jupyter-book
-- iris-grib
-- s3fs
-- kerchunk
-- ujson
-- intake-thredds
-- cafaz
-- cdms2
-- pygam
-- pysal
-- xmhw
-- argopy
-- dataclasses-json
-- ilamb
-- posix_ipc
-- spectrum
-- arch-py
-- pyextremes
-- ipdb
-- palettable
-- webcolors
-- mpl-scatter-density
-- accessnri::benchcab
-- lmfit
-- xclim
-- jupyter-resource-usage
-- acs_replica_intake
-- matchpy
-- mscorefonts
-- opencv  
-- conda-build
-- conda-verify
-- pygmt
-- gmt
-- greenlet ### Dependency of... something?
-- objgraph ### Unlisted dependency of greenlet
-- xarrayutils
-- wradlib
-- pyinterp
-- wavespectra
-- xmip
-- xcdat
-- neutralocean
-- ipympl
-- libtiff
-- xskillscore
-- geocat-comp
-- ecgtools
-- gcc_linux-64
-- ipywidgets
-- flox
-- erddapy
-- tintx
-- climpred
-- odc-geo
-- cmor
-- bargeparse
-- accessnri::amami
-- accessnri::access-nri-intake
-- ipynbname
-- shellcheck
-- pysteps
-- ucx-py
-- ucx==1.15.0
-- geocat-viz
-- icclim
-- py-cordex
-- pdbufr
-- matplotlib-scalebar
-- python-kaleido
-- numba
-- crick ### Unlisted dependency for dask-expr
-- regional-mom6
-- u8darts-all
-- xwrf
-- ecmwf-api-client
-- pygamma_n
-- numexpr>2.9
-- mopper
-- scores
-- pip:
-  - railroad-diagrams ### Unlisted dependency of pip and pyparsing
diff --git a/environments/analysis3/testconfig.yml b/environments/analysis3/testconfig.yml
deleted file mode 100644
index 18a30a0..0000000
--- a/environments/analysis3/testconfig.yml
+++ /dev/null
@@ -1,95 +0,0 @@
-# Modules test will not try to import
-skip:
-# Cause errors and don't throw exceptions cleanly
-- psutil.tests
-- pandas.io.clipboard
-- matplotlib.backends
-- pbr.tests
-- plotly.plotly
-- bokeh.server.django
-# Too many, or not necessary
-- iris.tests
-- cartopy.tests
-- plotly.validators
-- xarray.tests
-- pyresample.test
-- pyferret.eofanal
-- ants.tests
-- alembic.testing
-- sqlalchemy.testing
-- httpx
-- sanic
-- tests # random tests from black?
- # - cupy # Disable when testing locally
- # - cupyx # ditto
- # - nci_intake_catalogue # ditto
- # - wrf # Prints garbage at v1.3.2.5
-- matplotlib.tests # No test data
-- prometheus_client.twisted # No twisted
-- pyface
-- qt
-- traits
-- traitsui
-- vtk
-- pyparsing
-- tensorflow_estimator
-- acs_replica_intake  # can't load catalogue file
-- access_nri_intake  # can't load catalogue file
-- pip._vendor.chardet # encounters a null byte, doesn't seem to be an error
-- pykrige # AttributeError: module 'scipy.linalg' has no attribute 'pinv2' -- rk4417
-# for both hdbscan and cosima_cookbook see https://accessdev.nci.org.au/jenkins/job/conda/job/analysis3-unstable/1351/consoleFull
-- hdbscan # test errors but can import
-- cosima_cookbook  # test error 
-  #- plotnine # can't import fails on "import matplotlib._contour as _contour" which seems to work otherwise
-  #- nctoolkit # calls plotnine
-- xgboost.spark ### Don't think we support spark as a parallel backend
-- send2trash.mac ### Gadi is not a mac
-- send2trash.win ### Nor is it windows
-- attrdict ### Deprecated but still erroneously bought in by wavespectra - not used by anything else
-- skimage.future.graph ### Thanks for raising a module error to tell me that you've moved this
-- numba.core.rvsdg_frontend ### Not supported in Python3.10
-- xgboost.testing ### Has an 'pytest.importorskip' call when imported, causing the whole thing to report skipped
-- scipy._lib.array_api_compat.torch ### Don't support pytorch
-- urllib3.contrib.emscripten ### Used for web browser integration and also experimental: https://urllib3.readthedocs.io/en/latest/reference/contrib/emscripten.html
-- fugue_duckdb ### Optional backend not used by any package in analysis3
-- fugue_ibis ### Optional backend not used by any package in analysis3
-- fugue_polars ### Optional backend not used by any package in analysis3
-- fugue_ray ### Optional backend not used by any package in analysis3
-- fugue_spark ### Optional backend not used by any package in analysis3
-- 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
-- torch._inductor
-- keras.src.backend ### Don't test Keras backends
-- functorch ### This file has moved to under torch/_functorch. It is not public API.
-
-# Preload these modules before testing to avoid weird python issues
-preload:
-- pysal
-- tables
-- skimage.data
-- sklearn
-- sklearn.covariance
-- sklearn.manifold
-- stratify
-- xarray
-- setuptools.command.build_ext ### Strange issue with numba.pycc
-
-# Allow loading, but pass exceptions. When exceptions no longer triggered
-# can remove
-exception:
-- sqlalchemy.testing.suite
-- zmq.green
-- prometheus_client.twisted
-- sqlalchemy.testing.suite
-- zmq.backend.cffi
-- sklearn.mixture
-- matplotlib.tests
-- metpy.io     # While Issue #21 unresolved
-- metpy.plots  # While Issue #21 unresolved
-- httpx
-- sanic
-- pyparsing.diagrams
-- pysal.explore.esda
-- pysal.explore.segregation
-- pysal.model.access
diff --git a/environments/payu-dev/build_inner.sh b/environments/payu-dev/build_inner.sh
new file mode 100644
index 0000000..5935347
--- /dev/null
+++ b/environments/payu-dev/build_inner.sh
@@ -0,0 +1,14 @@
+### Custom install inner
+
+# Fix shebang headers in payu entry points (issue with pip installed packages: https://github.com/ACCESS-NRI/MED-condaenv/issues/78)
+for file in ${CONDA_INSTALLATION_PATH}/envs/${FULLENV}/bin/payu-*; do
+    # Using payu-* to modify payu-run, payu-collate, payu-sync files
+    echo "Adding python header to $file"
+    # Substitute the first line of file (e.g. 1s), if it starts with #! (regex ^#!/.*$),
+    # with the python executable in the conda environment
+    sed -i "1s|^#!/.*$|#!${CONDA_INSTALLATION_PATH}/envs/${FULLENV}/bin/python|" "$file"
+done
+
+# Patch payu shebang header with outer python executable that launches a container when run.
+# This means when payu submits qsub commands (e.g. payu run), it uses this python executable and launches a container on PBS job
+sed -i "1s|^#!/.*$|#!${CONDA_SCRIPT_PATH}/${FULLENV}.d/bin/python|" "${CONDA_INSTALLATION_PATH}/envs/${FULLENV}/bin/payu"
\ No newline at end of file
diff --git a/environments/payu-dev/config.sh b/environments/payu-dev/config.sh
new file mode 100644
index 0000000..05bfbfc
--- /dev/null
+++ b/environments/payu-dev/config.sh
@@ -0,0 +1,18 @@
+### config.sh MUST provide the following:
+### $FULLENV
+###
+### Arrays used by the build system (optional, can be empty)
+### rpms_to_remove
+### replace_from_apps
+### outside_commands_to_include
+### outside_files_to_copy
+
+### Version settings
+export ENVIRONMENT=payu-dev
+export FULLENV="${ENVIRONMENT}"
+
+declare -a rpms_to_remove=()
+declare -a replace_from_apps=()
+declare -a outside_commands_to_include=( "pbs_tmrsh" )
+declare -a outside_files_to_copy=()
+declare -a replace_with_external=()
\ No newline at end of file
diff --git a/environments/payu-dev/environment.yml b/environments/payu-dev/environment.yml
new file mode 100644
index 0000000..83bac70
--- /dev/null
+++ b/environments/payu-dev/environment.yml
@@ -0,0 +1,19 @@
+name: payu-dev
+channels:
+  - accessnri
+  - coecms
+  - conda-forge
+dependencies:
+  - python==3.10
+  # Use latest changes from payu's master branch
+  - pip:
+    - git+https://github.com/payu-org/payu.git@master
+  - f90nml
+  - gh
+  - git
+  - nco
+  - pytest
+  - openssh>=8.3
+  - xarray
+  - mule
+  - um2nc
\ No newline at end of file
diff --git a/environments/payu-dev/testconfig.yml b/environments/payu-dev/testconfig.yml
new file mode 100644
index 0000000..2f36155
--- /dev/null
+++ b/environments/payu-dev/testconfig.yml
@@ -0,0 +1,98 @@
+# Modules test will not try to import
+skip:
+# # Cause errors and don't throw exceptions cleanly
+# - psutil.tests
+ - pandas.io.clipboard
+ - matplotlib.backends
+# - pbr.tests
+# - plotly.plotly
+# - bokeh.server.django
+# # Too many, or not necessary
+ - iris.tests
+ - cartopy.tests
+# - plotly.validators
+ - xarray.tests
+# - pyresample.test
+# - pyferret.eofanal
+# - ants.tests
+# - alembic.testing
+# - sqlalchemy.testing
+# - httpx
+# - sanic
+# - tests # random tests from black?
+#  # - cupy # Disable when testing locally
+#  # - cupyx # ditto
+#  # - nci_intake_catalogue # ditto
+#  # - wrf # Prints garbage at v1.3.2.5
+ - matplotlib.tests # No test data
+# - prometheus_client.twisted # No twisted
+# - pyface
+# - qt
+# - traits
+# - traitsui
+# - vtk
+ - pyparsing
+# - tensorflow_estimator
+# - acs_replica_intake  # can't load catalogue file
+# - access_nri_intake  # can't load catalogue file
+# - pip._vendor.chardet # encounters a null byte, doesn't seem to be an error
+# - pykrige # AttributeError: module 'scipy.linalg' has no attribute 'pinv2' -- rk4417
+# # for both hdbscan and cosima_cookbook see https://accessdev.nci.org.au/jenkins/job/conda/job/analysis3-unstable/1351/consoleFull
+# - hdbscan # test errors but can import
+# - cosima_cookbook  # test error 
+#   #- plotnine # can't import fails on "import matplotlib._contour as _contour" which seems to work otherwise
+#   #- nctoolkit # calls plotnine
+# - xgboost.spark ### Don't think we support spark as a parallel backend
+# - send2trash.mac ### Gadi is not a mac
+# - send2trash.win ### Nor is it windows
+# - attrdict ### Deprecated but still erroneously bought in by wavespectra - not used by anything else
+# - skimage.future.graph ### Thanks for raising a module error to tell me that you've moved this
+# - numba.core.rvsdg_frontend ### Not supported in Python3.10
+# - xgboost.testing ### Has an 'pytest.importorskip' call when imported, causing the whole thing to report skipped
+ - scipy._lib.array_api_compat.torch ### Don't support pytorch
+ - urllib3.contrib.emscripten ### Used for web browser integration and also experimental: https://urllib3.readthedocs.io/en/latest/reference/contrib/emscripten.html
+# - fugue_duckdb ### Optional backend not used by any package in analysis3
+# - fugue_ibis ### Optional backend not used by any package in analysis3
+# - fugue_polars ### Optional backend not used by any package in analysis3
+# - fugue_ray ### Optional backend not used by any package in analysis3
+# - fugue_spark ### Optional backend not used by any package in analysis3
+# - 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
+# - torch._inductor
+# - keras.src.backend ### Don't test Keras backends
+# - functorch ### This file has moved to under torch/_functorch. It is not public API.
+
+# Preload these modules before testing to avoid weird python issues
+preload:
+# - pysal
+# - tables
+# - skimage.data
+# - sklearn
+# - sklearn.covariance
+# - sklearn.manifold
+# - stratify
+- xarray
+- setuptools.command.build_ext ### Strange issue with numba.pycc
+
+# Allow loading, but pass exceptions. When exceptions no longer triggered
+# can remove
+exception:
+# - sqlalchemy.testing.suite
+# - zmq.green
+# - prometheus_client.twisted
+# - sqlalchemy.testing.suite
+# - zmq.backend.cffi
+# - sklearn.mixture
+# - matplotlib.tests
+# - metpy.io     # While Issue #21 unresolved
+# - metpy.plots  # While Issue #21 unresolved
+# - httpx
+# - sanic
+# - pyparsing.diagrams
+# - pysal.explore.esda
+# - pysal.explore.segregation
+# - pysal.model.access
+- fontTools.ufoLib #
+- pandas.core._numba.kernels #
+- scipy._lib.array_api_compat.cupy #
\ No newline at end of file
diff --git a/environments/payu/build_inner.sh b/environments/payu/build_inner.sh
new file mode 100644
index 0000000..b24820e
--- /dev/null
+++ b/environments/payu/build_inner.sh
@@ -0,0 +1,16 @@
+### Custom install inner to build jupyter lab extensions
+
+# set +u
+# eval "$( ${MAMBA} shell hook --shell bash)"
+# micromamba activate "${CONDA_INSTALLATION_PATH}/envs/${FULLENV}"
+# set -u
+
+# jupyter lab build
+
+# Patch payu shebang header with outer python executable that launches a container when run.
+# This means when payu submits qsub commands (e.g. payu run), it uses this python executable and launches a container on PBS job
+sed -i "1s|^#!/.*$|#!${CONDA_SCRIPT_PATH}/${FULLENV}.d/bin/python|" "${CONDA_INSTALLATION_PATH}/envs/${FULLENV}/bin/payu"
+# Above command follows pattern of "sed -i '1s|pattern|replacement|' filename"
+# which modifies the environment's payu executable in place (-i),
+# and replaces the first line (1s), if it starts with #! (regex ^#!/.*$),
+# with the payu launcher script
\ No newline at end of file
diff --git a/environments/payu/config.sh b/environments/payu/config.sh
new file mode 100644
index 0000000..3b94c1b
--- /dev/null
+++ b/environments/payu/config.sh
@@ -0,0 +1,22 @@
+### config.sh MUST provide the following:
+### $FULLENV
+###
+### Arrays used by the build system (optional, can be empty)
+### rpms_to_remove
+### replace_from_apps
+### outside_commands_to_include
+### outside_files_to_copy
+
+### Optional config for custom deploy script
+export VERSION_TO_MODIFY=1.1.5
+export STABLE_VERSION=1.1.5
+
+### Version settings
+export ENVIRONMENT=payu
+export FULLENV="${ENVIRONMENT}-${VERSION_TO_MODIFY}"
+
+declare -a rpms_to_remove=()
+declare -a replace_from_apps=()
+declare -a outside_commands_to_include=( "pbs_tmrsh" )
+declare -a outside_files_to_copy=()
+declare -a replace_with_external=()
diff --git a/environments/payu/deploy.sh b/environments/payu/deploy.sh
new file mode 100644
index 0000000..51b32be
--- /dev/null
+++ b/environments/payu/deploy.sh
@@ -0,0 +1,10 @@
+### Update stable if necessary
+CURRENT_STABLE=$( get_aliased_module "${MODULE_NAME}"/payu "${CONDA_MODULE_PATH}" )
+NEXT_STABLE="${ENVIRONMENT}-${STABLE_VERSION}"
+
+if ! [[ "${CURRENT_STABLE}" == "${MODULE_NAME}/${NEXT_STABLE}" ]]; then
+    echo "Updating stable environment to ${NEXT_STABLE}"
+    write_modulerc_stable "${NEXT_STABLE}" "${ENVIRONMENT}" "${CONDA_MODULE_PATH}" "${MODULE_NAME}"
+    symlink_atomic_update "${CONDA_INSTALLATION_PATH}"/envs/"${ENVIRONMENT}" "${NEXT_STABLE}"
+    symlink_atomic_update "${CONDA_SCRIPT_PATH}"/"${ENVIRONMENT}".d "${NEXT_STABLE}".d
+fi
\ No newline at end of file
diff --git a/environments/payu/environment.yml b/environments/payu/environment.yml
new file mode 100644
index 0000000..9022912
--- /dev/null
+++ b/environments/payu/environment.yml
@@ -0,0 +1,18 @@
+name: payu
+channels:
+  - accessnri
+  - coecms
+  - conda-forge
+dependencies:
+  - python==3.10
+  - accessnri::payu==1.1.5
+  - yamanifest
+  - f90nml
+  - gh
+  - git
+  - nco
+  - pytest
+  - openssh>=8.3
+  - xarray
+  - mule
+  - um2nc
\ No newline at end of file
diff --git a/environments/payu/testconfig.yml b/environments/payu/testconfig.yml
new file mode 100644
index 0000000..2f36155
--- /dev/null
+++ b/environments/payu/testconfig.yml
@@ -0,0 +1,98 @@
+# Modules test will not try to import
+skip:
+# # Cause errors and don't throw exceptions cleanly
+# - psutil.tests
+ - pandas.io.clipboard
+ - matplotlib.backends
+# - pbr.tests
+# - plotly.plotly
+# - bokeh.server.django
+# # Too many, or not necessary
+ - iris.tests
+ - cartopy.tests
+# - plotly.validators
+ - xarray.tests
+# - pyresample.test
+# - pyferret.eofanal
+# - ants.tests
+# - alembic.testing
+# - sqlalchemy.testing
+# - httpx
+# - sanic
+# - tests # random tests from black?
+#  # - cupy # Disable when testing locally
+#  # - cupyx # ditto
+#  # - nci_intake_catalogue # ditto
+#  # - wrf # Prints garbage at v1.3.2.5
+ - matplotlib.tests # No test data
+# - prometheus_client.twisted # No twisted
+# - pyface
+# - qt
+# - traits
+# - traitsui
+# - vtk
+ - pyparsing
+# - tensorflow_estimator
+# - acs_replica_intake  # can't load catalogue file
+# - access_nri_intake  # can't load catalogue file
+# - pip._vendor.chardet # encounters a null byte, doesn't seem to be an error
+# - pykrige # AttributeError: module 'scipy.linalg' has no attribute 'pinv2' -- rk4417
+# # for both hdbscan and cosima_cookbook see https://accessdev.nci.org.au/jenkins/job/conda/job/analysis3-unstable/1351/consoleFull
+# - hdbscan # test errors but can import
+# - cosima_cookbook  # test error 
+#   #- plotnine # can't import fails on "import matplotlib._contour as _contour" which seems to work otherwise
+#   #- nctoolkit # calls plotnine
+# - xgboost.spark ### Don't think we support spark as a parallel backend
+# - send2trash.mac ### Gadi is not a mac
+# - send2trash.win ### Nor is it windows
+# - attrdict ### Deprecated but still erroneously bought in by wavespectra - not used by anything else
+# - skimage.future.graph ### Thanks for raising a module error to tell me that you've moved this
+# - numba.core.rvsdg_frontend ### Not supported in Python3.10
+# - xgboost.testing ### Has an 'pytest.importorskip' call when imported, causing the whole thing to report skipped
+ - scipy._lib.array_api_compat.torch ### Don't support pytorch
+ - urllib3.contrib.emscripten ### Used for web browser integration and also experimental: https://urllib3.readthedocs.io/en/latest/reference/contrib/emscripten.html
+# - fugue_duckdb ### Optional backend not used by any package in analysis3
+# - fugue_ibis ### Optional backend not used by any package in analysis3
+# - fugue_polars ### Optional backend not used by any package in analysis3
+# - fugue_ray ### Optional backend not used by any package in analysis3
+# - fugue_spark ### Optional backend not used by any package in analysis3
+# - 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
+# - torch._inductor
+# - keras.src.backend ### Don't test Keras backends
+# - functorch ### This file has moved to under torch/_functorch. It is not public API.
+
+# Preload these modules before testing to avoid weird python issues
+preload:
+# - pysal
+# - tables
+# - skimage.data
+# - sklearn
+# - sklearn.covariance
+# - sklearn.manifold
+# - stratify
+- xarray
+- setuptools.command.build_ext ### Strange issue with numba.pycc
+
+# Allow loading, but pass exceptions. When exceptions no longer triggered
+# can remove
+exception:
+# - sqlalchemy.testing.suite
+# - zmq.green
+# - prometheus_client.twisted
+# - sqlalchemy.testing.suite
+# - zmq.backend.cffi
+# - sklearn.mixture
+# - matplotlib.tests
+# - metpy.io     # While Issue #21 unresolved
+# - metpy.plots  # While Issue #21 unresolved
+# - httpx
+# - sanic
+# - pyparsing.diagrams
+# - pysal.explore.esda
+# - pysal.explore.segregation
+# - pysal.model.access
+- fontTools.ufoLib #
+- pandas.core._numba.kernels #
+- scipy._lib.array_api_compat.cupy #
\ No newline at end of file
diff --git a/scripts/functions.sh b/scripts/functions.sh
index 2cfea96..9d59d4e 100644
--- a/scripts/functions.sh
+++ b/scripts/functions.sh
@@ -83,10 +83,26 @@ function write_modulerc() {
     cat<<EOF > "${module_path}"/.modulerc
 #%Module1.0
 
-module-version ${module_name}/${stable} analysis ${env_name} default
+module-version ${module_name}/${stable} ${env_name} default
 module-version ${module_name}/${unstable} ${env_name}-unstable
 
-module-version ${module_name}/analysis27-18.10 analysis27
+EOF
+
+    set_apps_perms "${module_path}/.modulerc"
+
+}
+
+function write_modulerc_stable() {
+    stable="${1}"
+    env_name="${2}"
+    module_path="${3}"
+    module_name="${4}"
+
+    cat<<EOF > "${module_path}"/.modulerc
+#%Module1.0
+
+module-version ${module_name}/${stable} ${env_name} default
+
 EOF
 
     set_apps_perms "${module_path}/.modulerc"
diff --git a/scripts/initialise.sh b/scripts/initialise.sh
index 0cd157e..b61349c 100755
--- a/scripts/initialise.sh
+++ b/scripts/initialise.sh
@@ -17,9 +17,10 @@ function inner() {
 
     mkdir -p "${CONDA_INSTALLATION_PATH}"
     pushd "${CONDA_INSTALLATION_PATH}"
-    #curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba
+
+    curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba
     ### Modified micromamba for compatibility with nb_conda_kernels
-    curl -Ls https://dsroberts.github.io/mamba/latest | tar -xvj bin/micromamba bin/activate
+    # curl -Ls https://dsroberts.github.io/mamba/latest | tar -xvj bin/micromamba bin/activate
     popd
 
     mkdir -p "${CONDA_SCRIPT_PATH}"/overrides
diff --git a/scripts/install_config.sh b/scripts/install_config.sh
index 48a56fe..84e5fa6 100644
--- a/scripts/install_config.sh
+++ b/scripts/install_config.sh
@@ -1,14 +1,21 @@
 ### Settings to control installation path e.g. for test installs
-export CONDA_BASE="${CONDA_BASE:-/g/data/hh5/public}"
-export ADMIN_DIR="${ADMIN_DIR:-/g/data/hh5/admin/conda_concept/admin}"
+if [[ ! "${CONDA_BASE}" ]]; then
+    echo "Error! CONDA_BASE must be defined"
+    exit 1
+fi
+if [[ ! "${ADMIN_DIR}" ]]; then
+    echo "Error! ADMIN_DIR must be defined"
+    exit 1
+fi
+
 export CONDA_TEMP_PATH="${PBS_JOBFS:-${CONDA_TEMP_PATH}}"
 export SCRIPT_DIR="${SCRIPT_DIR:-$PWD}"
 
-export SCRIPT_SUBDIR="apps/cms_conda_scripts"
+export SCRIPT_SUBDIR="apps/conda_scripts"
 export MODULE_SUBDIR="modules"
 export APPS_SUBDIR="apps"
-export CONDA_INSTALL_BASENAME="cms_conda"
-export MODULE_NAME="conda_concept"
+export CONDA_INSTALL_BASENAME="base_conda" #TODO: Replace with conda?
+export MODULE_NAME="conda_container" # TODO: Replace with conda?
 
 ### Derived locations - extra '.' for arcane rsync magic
 export CONDA_SCRIPT_PATH="${CONDA_BASE}"/./"${SCRIPT_SUBDIR}"
@@ -17,8 +24,14 @@ export JOB_LOG_DIR="${ADMIN_DIR}"/logs
 export BUILD_STAGE_DIR="${ADMIN_DIR}"/staging
 
 ### Groups
-export APPS_USERS_GROUP=hh5
-export APPS_OWNERS_GROUP=hh5_w
+if [[ ! "${APPS_USERS_GROUP}" ]]; then
+    echo "Error! APPS_USERS_GROUP must be defined"
+    exit 1
+fi
+if [[ ! "${APPS_OWNERS_GROUP}" ]]; then
+    echo "Error! APPS_OWNERS_GROUP must be defined"
+    exit 1
+fi
 
 ### Other settings
 export TEST_OUT_FILE=test_results.xml
diff --git a/scripts/test_environment.py b/scripts/test_environment.py
index 1e2630e..cd254f9 100644
--- a/scripts/test_environment.py
+++ b/scripts/test_environment.py
@@ -152,8 +152,8 @@ def test_import():
                 print("Error loading {}".format(info.name), file=sys.stderr)
                 raise
 
-def test_cdo():
-   assert subprocess.call(['cdo','--version']) == 0
+# def test_cdo():
+#    assert subprocess.call(['cdo','--version']) == 0
 
 if __name__ == '__main__':
     test_walk_packages()