Merge pull request #147 from ACCESS-NRI/update_setup

Update setup

Author: rbeucher

container/container.def

@@ -38,13 +38,10 @@ 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/analysis3-24.12
+        mkdir -p ${SINGULARITY_ROOTFS}/opt/conda/analysis3-25.01
+        mkdir -p ${SINGULARITY_ROOTFS}/opt/conda/access-med-0.12
+        mkdir -p ${SINGULARITY_ROOTFS}/opt/conda/esmvaltool-0.5
 
 %runscript
         /usr/bin/bash -l

scripts/functions.sh

@@ -80,18 +80,31 @@ function write_modulerc() {
     module_path="${4}"
     module_name="${5}"
 
-    cat<<EOF > "${module_path}"/.modulerc
+    modulerc_file="${module_path}/.modulerc"
+
+    # Create a new .modulerc file if it doesn't exist
+    if [ ! -f "${modulerc_file}" ]; then
+        touch "${modulerc_file}"
+    fi
+
+    # Remove lines containing the specified module_name
+    temp_file=$(mktemp)
+    grep -v "module-version ${module_name}/" "${modulerc_file}" > "${temp_file}"
+    mv "${temp_file}" "${modulerc_file}"
+
+    # Append the new module_version lines
+    cat <<EOF >> "${modulerc_file}"
 #%Module1.0
 
-module-version ${module_name}/${stable} access-med ${env_name} default
+module-version ${module_name}/${stable} access-med ${env_name}
 module-version ${module_name}/${unstable} ${env_name}-unstable
 
 EOF
 
-    set_apps_perms "${module_path}/.modulerc"
-
+    set_apps_perms "${modulerc_file}"
 }
 
+
 function symlink_atomic_update() {
     link_name="${1}"
     link_target="${2}"

scripts/initialise.sh

@@ -17,9 +17,11 @@ 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
+    ### Romain Dec 2024, revert to latest 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