Added obindices function

.github/workflows/pre-commit.yml

@@ -12,13 +12,13 @@ jobs:
     timeout-minutes: 5
     steps:
       - name: Clone repo
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Install Poetry
-        run: pipx install poetry==2.0.0
+        run: pipx install poetry==2.3.2
 
       - name: Install Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.12"
 

.pre-commit-config.yaml

@@ -1,46 +1,43 @@
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
     - id: end-of-file-fixer
     - id: trailing-whitespace
     - id: mixed-line-ending
 -   repo: https://github.com/asottile/reorder-python-imports
-    rev: v3.14.0
+    rev: v3.16.0
     hooks:
     - id: reorder-python-imports
       args: [--application-directories=.:src, --py39-plus]
 - repo: https://github.com/asottile/pyupgrade
-  rev: v3.19.1
+  rev: v3.21.2
   hooks:
     - id: pyupgrade
       args: [--py39-plus]
 - repo: https://github.com/PyCQA/autoflake
-  rev: v2.3.1
+  rev: v2.3.3
   hooks:
     - id: autoflake
       args: ["--remove-unused-variables"]
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.11.8
+  rev: v0.15.5
   hooks:
     # Run the linter.
     - id: ruff
       args: [ --fix ]
-    # Run the formatter.
-    - id: ruff-format
-      args: [--line-length=79]
 - repo: https://github.com/psf/black-pre-commit-mirror
-  rev: 25.1.0
+  rev: 26.3.1
   hooks:
     - id: black
       args: [--line-length=79]
 - repo: https://github.com/PyCQA/flake8
-  rev: 7.2.0
+  rev: 7.3.0
   hooks:
     - id: flake8
 - repo: https://github.com/fpgmaas/deptry.git
-  rev: 0.23.0
+  rev: 0.24.0
   hooks:
     - id: deptry
       entry: deptry

launcers/all_statics/generate_mer_statics.sh

@@ -1,50 +1,93 @@
+#!/bin/bash
+
+set -e
+
 OUTPUTDIR="/dev/shm/miotest"
 
 BATHYTOOLSDIR="/home/spiani/projects/bathytools"
 MITGCMINPUTSDIR="/home/spiani/projects/mitgcm_inputs"
 
+DOMAINS_REG="NAD SAD ION SIC TYR LIG SAR GOT GSN"
+DOMAINS_HR="HGT GOR CON PES LAM PAN NAP GAE FOL CAG ISO"
+
+DOMAINS="$DOMAINS_REG $DOMAINS_HR"
+
+MAXJOBS=5   # numero massimo di domini processati in parallelo
 
-DOMAINS="NAD SAD ION SIC TYR LIG SAR GOT"
-DOMAINS="$DOMAINS HGT GOT CON PES LAM PAN NAP GAE FOL CAG ISO"
+mkdir -p "${OUTPUTDIR}"
 
-mkdir -p ${OUTPUTDIR}
+process_domain () {
+    set -e
+    domain=$1
 
-for domain in ${DOMAINS}
-  do
     domaindir=${OUTPUTDIR}/${domain}
-    mkdir ${domaindir}
+    rm -rf "${domaindir}"
+    mkdir -p "${domaindir}"
 
     echo
     echo "----------^^^-----------  DOMAIN ${domain}  ----------^^^-----------"
     echo
 
-    cd $BATHYTOOLSDIR
-    # Check where is the correct configuration file for the domain (in the mer_domains
-    # directory or in the mer_domains/high_reso dir)
+    # Setta SPONGE
+    if [[ " $DOMAINS_HR " =~ " $domain " ]]; then
+        SPONGE=10
+    else
+        SPONGE=16
+    fi
+
+    cd "$BATHYTOOLSDIR"
+
     domain_descriptor="$BATHYTOOLSDIR/mer_domains/${domain,,}.yaml"
     if [ ! -f "${domain_descriptor}" ]; then
         domain_descriptor="$BATHYTOOLSDIR/mer_domains/high_reso/${domain,,}.yaml"
     fi
 
-    # Run bathytools
-    poetry run bathytools -c ${domain_descriptor} -o ${domaindir} --mer
+    poetry run bathytools -c "${domain_descriptor}" -o "${domaindir}" --mer
 
-    # Generate fluxes.tar.gz
-    cd ${MITGCMINPUTSDIR}
-    poetry run mitgcm_inputs FLUXES -m ${domaindir}/meshmask.nc -o ${domaindir}/fluxes.tar.gz
+    cd "$MITGCMINPUTSDIR"
+
+    poetry run mitgcm_inputs FLUXES \
+        -m "${domaindir}/meshmask.nc" \
+        -o "${domaindir}/fluxes.tar.gz"
+
+    rpositions="${domaindir}/rivers_positions.json"
+    rcustom="${BATHYTOOLSDIR}/mer_domains/rivers/${domain}.json"
 
-    # Check if this domain has rivers to write the rbcs command line options
-    rpositions=${domaindir}/rivers_positions.json
-    rcustom=${BATHYTOOLSDIR}/mer_domains/rivers/${domain}.json
     rbcs_options=""
+    ob_indices_options=""
 
     if [ -f "$rpositions" ]; then
         rbcs_options="-p $rpositions -r $BATHYTOOLSDIR/mer_domains/rivers/main.json"
+        ob_indices_options="-p $rpositions -r ${domaindir}/additional_variables.nc"
+
         if [ -f "${rcustom}" ]; then
             rbcs_options="${rbcs_options} -d ${rcustom}"
         fi
     fi
 
-    echo poetry run mitgcm_inputs rbcs -m ${domaindir}/meshmask.nc -o ${domaindir} ${rbcs_options}
-    poetry run mitgcm_inputs rbcs -m ${domaindir}/meshmask.nc -o ${domaindir} ${rbcs_options}
-  done
+    poetry run mitgcm_inputs ob_indices \
+        -m "${domaindir}/meshmask.nc" \
+        -s "$SPONGE" \
+        -o "${domaindir}/rivers_open_boundaries.txt" \
+        -n "${domaindir}/nudging_indices.txt" \
+        ${ob_indices_options}
+
+    poetry run mitgcm_inputs rbcs \
+        -m "${domaindir}/meshmask.nc" \
+        -o "${domaindir}" \
+        ${rbcs_options}
+
+}
+
+export -f process_domain
+export OUTPUTDIR BATHYTOOLSDIR MITGCMINPUTSDIR DOMAINS_HR
+
+if command -v parallel >/dev/null 2>&1; then
+    parallel --lb --tag --halt soon,fail=1 -j ${MAXJOBS} process_domain ::: ${DOMAINS}
+else
+    echo "GNU parallel not found, falling back to serial execution." >&2
+    for domain in $DOMAINS
+    do
+        process_domain "$domain"
+    done
+fi