From 182cc296acf76eb24f30aae3d8d124911c3eaeb8 Mon Sep 17 00:00:00 2001
From: Stefano Piani <spiani@ogs.it>
Date: Fri, 6 Mar 2026 18:55:44 +0100
Subject: [PATCH 01/14] First draft of ob_indices

---
 poetry.lock                              | 746 ++++++++++++-----------
 src/mitgcm_inputs/__main__.py            |   5 +
 src/mitgcm_inputs/ob_indices/__init__.py |  66 ++
 3 files changed, 450 insertions(+), 367 deletions(-)
 create mode 100644 src/mitgcm_inputs/ob_indices/__init__.py

diff --git a/poetry.lock b/poetry.lock
index 49a1a2a..0a00fff 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -116,22 +116,22 @@ plots = []
 type = "git"
 url = "https://github.com/inogs/bit.sea.git"
 reference = "master"
-resolved_reference = "a16670921a84eb5df8dd3a89d2248f7e8c4edc3b"
+resolved_reference = "258b674bf2ece213e0588cce15684ca1de672ffa"
 
 [[package]]
 name = "boto3"
-version = "1.42.44"
+version = "1.42.62"
 description = "The AWS SDK for Python"
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
 files = [
-    {file = "boto3-1.42.44-py3-none-any.whl", hash = "sha256:32e995b0d56e19422cff22f586f698e8924c792eb00943de9c517ff4607e4e18"},
-    {file = "boto3-1.42.44.tar.gz", hash = "sha256:d5601ea520d30674c1d15791a1f98b5c055e973c775e1d9952ccc09ee5913c4e"},
+    {file = "boto3-1.42.62-py3-none-any.whl", hash = "sha256:eef0ee08f30e5ed16d8296719808801a827fa0f3126a3e2a9ef9be9eb5e6a313"},
+    {file = "boto3-1.42.62.tar.gz", hash = "sha256:6b26ff56c458685caec3d42adde0549f6a55410e557e1f51bebde5c8abcf3037"},
 ]
 
 [package.dependencies]
-botocore = ">=1.42.44,<1.43.0"
+botocore = ">=1.42.62,<1.43.0"
 jmespath = ">=0.7.1,<2.0.0"
 s3transfer = ">=0.16.0,<0.17.0"
 
@@ -140,14 +140,14 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"]
 
 [[package]]
 name = "botocore"
-version = "1.42.44"
+version = "1.42.62"
 description = "Low-level, data-driven core of boto 3."
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
 files = [
-    {file = "botocore-1.42.44-py3-none-any.whl", hash = "sha256:ba406b9243a20591ee87d53abdb883d46416705cebccb639a7f1c923f9dd82df"},
-    {file = "botocore-1.42.44.tar.gz", hash = "sha256:47ba27360f2afd2c2721545d8909217f7be05fdee16dd8fc0b09589535a0701c"},
+    {file = "botocore-1.42.62-py3-none-any.whl", hash = "sha256:86d327fded96775268ffe8d8bd6ed96c4a1db86cf24eb64ff85233db12dbc287"},
+    {file = "botocore-1.42.62.tar.gz", hash = "sha256:c210dc93b0b81bf72cfe745a7b1c8df765d04bd90b4ac6c8707fbb6714141dae"},
 ]
 
 [package.dependencies]
@@ -156,7 +156,7 @@ python-dateutil = ">=2.1,<3.0.0"
 urllib3 = {version = ">=1.25.4,<2.2.0 || >2.2.0,<3", markers = "python_version >= \"3.10\""}
 
 [package.extras]
-crt = ["awscrt (==0.29.2)"]
+crt = ["awscrt (==0.31.2)"]
 
 [[package]]
 name = "cdsapi"
@@ -177,14 +177,14 @@ tqdm = "*"
 
 [[package]]
 name = "certifi"
-version = "2026.1.4"
+version = "2026.2.25"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.7"
 groups = ["main"]
 files = [
-    {file = "certifi-2026.1.4-py3-none-any.whl", hash = "sha256:9943707519e4add1115f44c2bc244f782c0249876bf51b6599fee1ffbedd685c"},
-    {file = "certifi-2026.1.4.tar.gz", hash = "sha256:ac726dd470482006e014ad384921ed6438c457018f4b3d204aea4281258b2120"},
+    {file = "certifi-2026.2.25-py3-none-any.whl", hash = "sha256:027692e4402ad994f1c42e52a4997a9763c646b73e4096e4d5d6db8af1d6f0fa"},
+    {file = "certifi-2026.2.25.tar.gz", hash = "sha256:e887ab5cee78ea814d3472169153c2d12cd43b14bd03329a39a9c6e2e80bfba7"},
 ]
 
 [[package]]
@@ -364,125 +364,125 @@ numpy = ">=1.21.2"
 
 [[package]]
 name = "charset-normalizer"
-version = "3.4.4"
+version = "3.4.5"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
 optional = false
 python-versions = ">=3.7"
 groups = ["main"]
 files = [
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 [[package]]
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+version = "3.25.0"
 description = "A platform independent file lock."
 optional = false
 python-versions = ">=3.10"
 groups = ["dev"]
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 [[package]]
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 [[package]]
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+version = "2.6.17"
 description = "File identification library for Python"
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 files = [
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 [[package]]
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 version = "3.8.0"
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+[[package]]
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+version = "1.1.0"
+description = "Python interpreter discovery"
+optional = false
+python-versions = ">=3.8"
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+
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+    {file = "scipy-1.17.1-cp314-cp314t-musllinux_1_2_x86_64.whl", hash = "sha256:a77cbd07b940d326d39a1d1b37817e2ee4d79cb30e7338f3d0cddffae70fcaa2"},
+    {file = "scipy-1.17.1-cp314-cp314t-win_amd64.whl", hash = "sha256:eb092099205ef62cd1782b006658db09e2fed75bffcae7cc0d44052d8aa0f484"},
+    {file = "scipy-1.17.1-cp314-cp314t-win_arm64.whl", hash = "sha256:200e1050faffacc162be6a486a984a0497866ec54149a01270adc8a59b7c7d21"},
+    {file = "scipy-1.17.1.tar.gz", hash = "sha256:95d8e012d8cb8816c226aef832200b1d45109ed4464303e997c5b13122b297c0"},
 ]
 
 [package.dependencies]
@@ -2510,14 +2525,14 @@ telegram = ["requests"]
 
 [[package]]
 name = "types-pytz"
-version = "2025.2.0.20251108"
+version = "2026.1.1.20260304"
 description = "Typing stubs for pytz"
 optional = false
-python-versions = ">=3.9"
+python-versions = ">=3.10"
 groups = ["dev"]
 files = [
-    {file = "types_pytz-2025.2.0.20251108-py3-none-any.whl", hash = "sha256:0f1c9792cab4eb0e46c52f8845c8f77cf1e313cb3d68bf826aa867fe4717d91c"},
-    {file = "types_pytz-2025.2.0.20251108.tar.gz", hash = "sha256:fca87917836ae843f07129567b74c1929f1870610681b4c92cb86a3df5817bdb"},
+    {file = "types_pytz-2026.1.1.20260304-py3-none-any.whl", hash = "sha256:175332c1cf7bd6b1cc56b877f70bf02def1a3f75e5adcc05385ce2c3c70e6500"},
+    {file = "types_pytz-2026.1.1.20260304.tar.gz", hash = "sha256:0c3542d8e9b0160b424233440c52b83d6f58cae4b85333d54e4f961cf013e117"},
 ]
 
 [[package]]
@@ -2579,35 +2594,32 @@ zstd = ["backports-zstd (>=1.0.0) ; python_version < \"3.14\""]
 
 [[package]]
 name = "virtualenv"
-version = "20.36.1"
+version = "21.1.0"
 description = "Virtual Python Environment builder"
 optional = false
 python-versions = ">=3.8"
 groups = ["dev"]
 files = [
-    {file = "virtualenv-20.36.1-py3-none-any.whl", hash = "sha256:575a8d6b124ef88f6f51d56d656132389f961062a9177016a50e4f507bbcc19f"},
-    {file = "virtualenv-20.36.1.tar.gz", hash = "sha256:8befb5c81842c641f8ee658481e42641c68b5eab3521d8e092d18320902466ba"},
+    {file = "virtualenv-21.1.0-py3-none-any.whl", hash = "sha256:164f5e14c5587d170cf98e60378eb91ea35bf037be313811905d3a24ea33cc07"},
+    {file = "virtualenv-21.1.0.tar.gz", hash = "sha256:1990a0188c8f16b6b9cf65c9183049007375b26aad415514d377ccacf1e4fb44"},
 ]
 
 [package.dependencies]
 distlib = ">=0.3.7,<1"
-filelock = {version = ">=3.20.1,<4", markers = "python_version >= \"3.10\""}
+filelock = {version = ">=3.24.2,<4", markers = "python_version >= \"3.10\""}
 platformdirs = ">=3.9.1,<5"
-
-[package.extras]
-docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2,!=7.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"]
-test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8) ; platform_python_implementation == \"PyPy\" or platform_python_implementation == \"GraalVM\" or platform_python_implementation == \"CPython\" and sys_platform == \"win32\" and python_version >= \"3.13\"", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10) ; platform_python_implementation == \"CPython\""]
+python-discovery = ">=1"
 
 [[package]]
 name = "xarray"
-version = "2026.1.0"
+version = "2026.2.0"
 description = "N-D labeled arrays and datasets in Python"
 optional = false
 python-versions = ">=3.11"
 groups = ["main"]
 files = [
-    {file = "xarray-2026.1.0-py3-none-any.whl", hash = "sha256:5fcc03d3ed8dfb662aa254efe6cd65efc70014182bbc2126e4b90d291d970d41"},
-    {file = "xarray-2026.1.0.tar.gz", hash = "sha256:0c9814761f9d9a9545df37292d3fda89f83201f3e02ae0f09f03313d9cfdd5e2"},
+    {file = "xarray-2026.2.0-py3-none-any.whl", hash = "sha256:e927d7d716ea71dea78a13417970850a640447d8dd2ceeb65c5687f6373837c9"},
+    {file = "xarray-2026.2.0.tar.gz", hash = "sha256:978b6acb018770554f8fd964af4eb02f9bcc165d4085dbb7326190d92aa74bcf"},
 ]
 
 [package.dependencies]
diff --git a/src/mitgcm_inputs/__main__.py b/src/mitgcm_inputs/__main__.py
index 82c79e2..565fb6d 100644
--- a/src/mitgcm_inputs/__main__.py
+++ b/src/mitgcm_inputs/__main__.py
@@ -17,6 +17,9 @@
 from mitgcm_inputs.k_extinction import COMMAND_NAME as KEXT_COMMAND_NAME
 from mitgcm_inputs.k_extinction import main as kext_main
 from mitgcm_inputs.k_extinction import sub_arguments as kext_sub_arguments
+from mitgcm_inputs.ob_indices import COMMAND_NAME as OB_INDICES_COMMAND_NAME
+from mitgcm_inputs.ob_indices import main as ob_indices_main
+from mitgcm_inputs.ob_indices import sub_arguments as ob_indices_sub_arguments
 from mitgcm_inputs.rbcs import COMMAND_NAME as RBCS_COMMAND_NAME
 from mitgcm_inputs.rbcs import main as rbcs_main
 from mitgcm_inputs.rbcs import sub_arguments as rbcs_sub_arguments
@@ -72,6 +75,7 @@ def argument(sys_argv=None):
     sd_sub_arguments(subparsers)
     bflux_sub_arguments(subparsers)
     rbcs_sub_arguments(subparsers)
+    ob_indices_sub_arguments(subparsers)
 
     subparser = subparsers.add_parser(
         "FLUXES",
@@ -182,6 +186,7 @@ def execute_all_commands(args: argparse.Namespace):
     SD_COMMAND_NAME: sd_main,
     KEXT_COMMAND_NAME: kext_main,
     RBCS_COMMAND_NAME: rbcs_main,
+    OB_INDICES_COMMAND_NAME: ob_indices_main,
     "FLUXES": execute_all_commands,
 }
 
diff --git a/src/mitgcm_inputs/ob_indices/__init__.py b/src/mitgcm_inputs/ob_indices/__init__.py
new file mode 100644
index 0000000..0e2fcde
--- /dev/null
+++ b/src/mitgcm_inputs/ob_indices/__init__.py
@@ -0,0 +1,66 @@
+import argparse
+import logging
+
+import xarray as xr
+from bitsea.commons.mask import MaskWithRivers
+from bitsea.utilities.argparse_types import existing_file_path
+
+from mitgcm_inputs.tools.read_mesh_mask import read_mesh_mask
+
+if __name__ == "__main__":
+    LOGGER = logging.getLogger()
+else:
+    LOGGER = logging.getLogger(__name__)
+
+
+COMMAND_NAME = "ob_indices"
+
+
+def sub_arguments(subparser):
+    parser = subparser.add_parser(
+        COMMAND_NAME, help="Generate OB indices for rivers and sponge layers"
+    )
+
+    parser.add_argument(
+        "-m",
+        "--mask",
+        required=True,
+        type=existing_file_path,
+        help="The meshmask file that defines the domain",
+    )
+
+    parser.add_argument(
+        "-r",
+        "--river-file",
+        required=False,
+        default=None,
+        type=existing_file_path,
+        help="An auxiliary file that contains the a map that associates each "
+        "river cell with its river id. This file is useful only if this "
+        "information is not already stored in the meshmask file",
+    )
+
+
+def main(args: argparse.Namespace) -> int:
+    if args.cmd != COMMAND_NAME:
+        LOGGER.error(
+            "obindices command has been invoked with command: %s", args.cmd
+        )
+        return 1
+
+    meshmask = read_mesh_mask(args.mask)
+
+    if args.river_file is not None:
+        file_with_river = args.river_file
+    else:
+        file_with_river = args.mask
+    with xr.open_dataset(file_with_river) as river_ds:
+        river_map = river_ds["rivers"].load()
+
+    river_mask = MaskWithRivers(
+        grid=meshmask.grid,
+        zlevels=meshmask.zlevels,
+        mask_array=meshmask[:],
+        river_positions=river_map,
+    )
+    print(river_mask)

From 042015bc084cff6d58330f399341bbfbd318e427 Mon Sep 17 00:00:00 2001
From: Stefano Piani <spiani@ogs.it>
Date: Tue, 10 Mar 2026 19:58:49 +0100
Subject: [PATCH 02/14] First working script for ob_indices

---
 src/mitgcm_inputs/__main__.py              |   1 +
 src/mitgcm_inputs/ob_indices/__init__.py   |  61 +++++-
 src/mitgcm_inputs/ob_indices/ob_indices.py | 212 +++++++++++++++++++++
 3 files changed, 273 insertions(+), 1 deletion(-)
 create mode 100644 src/mitgcm_inputs/ob_indices/ob_indices.py

diff --git a/src/mitgcm_inputs/__main__.py b/src/mitgcm_inputs/__main__.py
index 565fb6d..312a00b 100644
--- a/src/mitgcm_inputs/__main__.py
+++ b/src/mitgcm_inputs/__main__.py
@@ -49,6 +49,7 @@ def configure_logger():
 
     # Avoid too much noise from botocore and urllib3 when in DEBUG mode
     logging.getLogger("botocore").setLevel(logging.INFO)
+    logging.getLogger("findlibs").setLevel(logging.INFO)
     logging.getLogger("urllib3").setLevel(logging.ERROR)
 
     handler = logging.StreamHandler()
diff --git a/src/mitgcm_inputs/ob_indices/__init__.py b/src/mitgcm_inputs/ob_indices/__init__.py
index 0e2fcde..6b5c7d0 100644
--- a/src/mitgcm_inputs/ob_indices/__init__.py
+++ b/src/mitgcm_inputs/ob_indices/__init__.py
@@ -1,10 +1,13 @@
 import argparse
+import json
 import logging
 
 import xarray as xr
 from bitsea.commons.mask import MaskWithRivers
 from bitsea.utilities.argparse_types import existing_file_path
+from bitsea.utilities.argparse_types import path_inside_an_existing_dir
 
+from mitgcm_inputs.ob_indices.ob_indices import generate_ob_indices
 from mitgcm_inputs.tools.read_mesh_mask import read_mesh_mask
 
 if __name__ == "__main__":
@@ -40,6 +43,46 @@ def sub_arguments(subparser):
         "information is not already stored in the meshmask file",
     )
 
+    parser.add_argument(
+        "-p",
+        "--rivers-positions",
+        required=False,
+        type=existing_file_path,
+        default=None,
+        help="The json file that describe the position of the mouth of the"
+        "rivers. If this file is not provided, we will assume that there are "
+        "no rivers on the domain",
+    )
+
+    parser.add_argument(
+        "-s",
+        "--sponge-extent",
+        required=False,
+        default=0,
+        type=int,
+        help="The extent of the sponge layer in number of cells",
+    )
+
+    parser.add_argument(
+        "-o",
+        "--ob-indices",
+        required=True,
+        type=path_inside_an_existing_dir,
+        help="The path of the output file where the OB indices will be "
+        "stored. If this is not submitted, this output file will not be "
+        "written.",
+    )
+
+    parser.add_argument(
+        "-n",
+        "--nudge-indices",
+        required=False,
+        type=path_inside_an_existing_dir,
+        default=None,
+        help="The path of the output file where the nudge indices will be "
+        "stored",
+    )
+
 
 def main(args: argparse.Namespace) -> int:
     if args.cmd != COMMAND_NAME:
@@ -63,4 +106,20 @@ def main(args: argparse.Namespace) -> int:
         mask_array=meshmask[:],
         river_positions=river_map,
     )
-    print(river_mask)
+
+    if args.rivers_positions is not None:
+        rivers_positions = json.loads(args.rivers_positions.read_text())
+    else:
+        rivers_positions = []
+
+    ob_indices, ob_sponge = generate_ob_indices(
+        river_mask=river_mask,
+        sponge_extent=args.sponge_extent,
+        rivers_positions=rivers_positions,
+    )
+
+    args.ob_indices.write_text(ob_indices)
+    if args.nudge_indices is not None:
+        args.nudge_indices.write_text(ob_sponge)
+
+    return 0
diff --git a/src/mitgcm_inputs/ob_indices/ob_indices.py b/src/mitgcm_inputs/ob_indices/ob_indices.py
new file mode 100644
index 0000000..6b9f95c
--- /dev/null
+++ b/src/mitgcm_inputs/ob_indices/ob_indices.py
@@ -0,0 +1,212 @@
+import logging
+from collections.abc import Mapping
+from collections.abc import Sequence
+from enum import Enum
+from itertools import product as cart_prod
+from typing import Any
+
+import numpy as np
+from bitsea.commons.mask import MaskWithRivers
+from bitsea.components.component_mask_2d import ComponentMask2D
+
+
+LOGGER = logging.getLogger(__name__)
+
+
+class Side(Enum):
+    NORTH = "N"
+    SOUTH = "S"
+    WEST = "W"
+    EAST = "E"
+
+    def __str__(self):
+        if self == Side.NORTH:
+            return "north"
+        elif self == Side.SOUTH:
+            return "south"
+        elif self == Side.WEST:
+            return "west"
+        elif self == Side.EAST:
+            return "east"
+        else:
+            raise ValueError(f"Invalid side: {self}")
+
+
+def cut_at_side(mask: np.ndarray, side: Side, amount: int):
+    if side == Side.NORTH:
+        return mask[:, -amount:, :]
+    elif side == Side.SOUTH:
+        return mask[:, :amount, :]
+    elif side == Side.WEST:
+        return mask[:, :, :amount]
+    elif side == Side.EAST:
+        return mask[:, :, -amount:]
+    else:
+        raise ValueError(f"Invalid side: {side}")
+
+
+def rewrite_in_mitgcm_format(v: np.ndarray) -> list[tuple[int, int]]:
+    """Transforms an array of integers into MITgcm's condensed format.
+
+    MITgcm uses a specific run-length encoding format for ob_indices to
+    compress arrays containing consecutive repeated values. Each sequence of
+    identical values is represented as a tuple where the first element is the
+    count (number of repetitions) and the second element is the value itself.
+
+    For example, the array [5, 5, 5, 3, 3, 7] would be encoded as
+    [(3, 5), (2, 3), (1, 7)].
+
+    Args:
+        v: A one-dimensional array of integers to be encoded.
+
+    Returns:
+        A list of tuples, where each tuple contains (count, value). The count
+        represents how many consecutive times the value appears in the input
+        array. Returns an empty list if the input array is empty.
+
+    Example:
+        >>> rewrite_in_mitgcm_format(np.array([1, 1, 1, 2, 2]))
+        [(3, 1), (2, 2)]
+    """
+    if len(v) == 0:
+        return []
+
+    result = []
+    current_value = v[0]
+    count = 1
+
+    for i in range(1, len(v)):
+        if v[i] == current_value:
+            count += 1
+        else:
+            result.append((count, int(current_value)))
+            current_value = v[i]
+            count = 1
+
+    # Append the last group
+    result.append((count, int(current_value)))
+
+    return result
+
+
+def generate_ob_indices(
+    river_mask: MaskWithRivers,
+    sponge_extent: int = 16,
+    rivers_positions: Sequence[Mapping[str, Any]] | None = None,
+):
+    if rivers_positions is None:
+        rivers_positions = []
+
+    ob_indices = ""
+    ob_sponge = ""
+
+    # If sponge_extent is 0, we take the first cell anyway
+    cut_cells = max(sponge_extent, 1)
+    for side in Side:
+        LOGGER.debug("Computing ob_indices for %s", side)
+
+        # Here we check which index will be used for the sponge and which index
+        # instead chooses the cell on the domain
+        if side in (Side.NORTH, Side.SOUTH):
+            sponge_index = 0
+        else:
+            sponge_index = 1
+        domain_index = 1 - sponge_index
+
+        # Here we check which is the index that must be used to report that a
+        # cell is open on the boundary. This is the beginning or the end
+        # of the domain (according to the side). If it is the beginning, it is
+        # enough to put a 1, but if it is the end, we need to put the number of
+        # cells on the other side of the domain.
+        if side in (Side.WEST, Side.SOUTH):
+            open_on_boundary = 1
+        else:
+            # Here we add a +1 because we need to skip the depth index
+            open_on_boundary = river_mask.shape[domain_index + 1]
+        # This is the value that we use to report that a cell is closed on the
+        # boundary
+        closed_cell = 0
+
+        LOGGER.debug("Cutting %i cells from the %s", cut_cells, side)
+        current_side = cut_at_side(river_mask.get_sea_cells(), side, cut_cells)
+
+        # We only take into account the surface
+        current_side_2d = current_side[0, :, :]
+
+        assert current_side_2d.shape[sponge_index] == cut_cells
+
+        sponge_cells = np.full(
+            (current_side_2d.shape[domain_index]), closed_cell, dtype=int
+        )
+        if not np.any(current_side_2d):
+            LOGGER.debug("No sea cells found on %s", side)
+        else:
+            component_mask = ComponentMask2D(current_side_2d)
+            n_components = component_mask.n_components
+            LOGGER.debug("%s has %i components", side, n_components)
+            for i in range(n_components):
+                LOGGER.debug("Processing component %i", i)
+                component_cells = component_mask.get_component(i)
+
+                # We need to check if this component has any cell on the
+                # boundary. If this is not the case, we can skip it.
+                # First, we need to define a slice that will select the
+                # boundary. So we need to have a slice that takes all the
+                # values on the axis that represent the domain and a fixed
+                # value on the axis that represents the sponge. This fixed
+                # value can be 0 or -1, depending on if the boundary is the
+                # maximum or the minimum value of the current axis
+                boundary_index = 0 if open_on_boundary == 1 else -1
+                boundary_layer = [slice(None), slice(None)]
+                boundary_layer[sponge_index] = boundary_index
+                boundary_layer = tuple(boundary_layer)
+
+                if not np.any(component_cells[boundary_layer]):
+                    LOGGER.debug(
+                        "Component ignored because it does not have any cell "
+                        "on the boundary"
+                    )
+                    continue
+
+                points_to_open = component_cells.sum(axis=sponge_index).astype(
+                    bool
+                )
+                sponge_cells[points_to_open] = open_on_boundary
+
+        LOGGER.debug(
+            "%i boundary cells will have the sponge enabled on %s",
+            (sponge_cells != closed_cell).sum(),
+            side,
+        )
+
+        open_bc_cells = np.copy(sponge_cells)
+        for river in rivers_positions:
+            if river["model"] != "stem_flux":
+                continue
+            if river["side"] != side.value:
+                continue
+            river_sources = tuple(
+                cart_prod(
+                    river["latitude_indices"], river["longitude_indices"]
+                )
+            )
+            LOGGER.debug(
+                "River %s on %s has the following sources: %s",
+                river["name"],
+                side,
+                river_sources,
+            )
+            for cell in river_sources:
+                open_bc_cells[cell[domain_index]] = cell[sponge_index] + 1
+
+        ob_indices += f"OB_I{side}="
+        for i in rewrite_in_mitgcm_format(open_bc_cells):
+            ob_indices += f"{i[0]}*{i[1]},"
+        ob_indices += "\n"
+
+        ob_sponge += f"nudgOB_I{side}="
+        for i in rewrite_in_mitgcm_format(sponge_cells):
+            ob_sponge += f"{i[0]}*{i[1]},"
+        ob_sponge += "\n"
+
+    return ob_indices, ob_sponge

From 8b408cc17aa0813ded5fd66a9003f355472fab10 Mon Sep 17 00:00:00 2001
From: Stefano Piani <spiani@ogs.it>
Date: Wed, 11 Mar 2026 19:04:01 +0100
Subject: [PATCH 03/14] Updated generate_mer_statics with ob_indices

---
 launcers/all_statics/generate_mer_statics.sh | 26 +++++++++++++++++---
 1 file changed, 22 insertions(+), 4 deletions(-)

diff --git a/launcers/all_statics/generate_mer_statics.sh b/launcers/all_statics/generate_mer_statics.sh
index 5ecd87b..29ab5a9 100644
--- a/launcers/all_statics/generate_mer_statics.sh
+++ b/launcers/all_statics/generate_mer_statics.sh
@@ -1,11 +1,16 @@
+#!/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="NAD SAD ION SIC TYR LIG SAR GOT"
-DOMAINS="$DOMAINS HGT GOT CON PES LAM PAN NAP GAE FOL CAG ISO"
+DOMAINS="$DOMAINS_REG $DOMAINS_HR"
 
 mkdir -p ${OUTPUTDIR}
 
@@ -18,6 +23,15 @@ for domain in ${DOMAINS}
     echo "----------^^^-----------  DOMAIN ${domain}  ----------^^^-----------"
     echo
 
+    # Setta il valore dello SPONGE
+    if [[ " $DOMAINS_HR " =~ " $domain " ]]; then
+        SPONGE=10
+    else
+        SPONGE=16
+    fi
+
+    echo SPONGE $SPONGE
+
     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)
@@ -33,18 +47,22 @@ for domain in ${DOMAINS}
     cd ${MITGCMINPUTSDIR}
     poetry run mitgcm_inputs FLUXES -m ${domaindir}/meshmask.nc -o ${domaindir}/fluxes.tar.gz
 
-    # Check if this domain has rivers to write the rbcs command line options
+    # Check if this domain has rivers to write the rbcs and ob_indices 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 $rpositions"
         if [ -f "${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 ob_indices -m ${domaindir}/meshmask.nc -r ${domaindir}/additional_variables.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}
   done

From f1e997dab14746cdaf88988f08ba89397acc6216 Mon Sep 17 00:00:00 2001
From: Stefano Piani <spiani@ogs.it>
Date: Thu, 12 Mar 2026 16:48:32 +0100
Subject: [PATCH 04/14] Adding numba for bitsea

---
 poetry.lock    | 68 +++++++++++++++++++++++++++++++++++++++++++++++++-
 pyproject.toml |  2 ++
 2 files changed, 69 insertions(+), 1 deletion(-)

diff --git a/poetry.lock b/poetry.lock
index 0a00fff..3b3304b 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1252,6 +1252,37 @@ files = [
     {file = "kiwisolver-1.4.9.tar.gz", hash = "sha256:c3b22c26c6fd6811b0ae8363b95ca8ce4ea3c202d3d0975b2914310ceb1bcc4d"},
 ]
 
+[[package]]
+name = "llvmlite"
+version = "0.46.0"
+description = "lightweight wrapper around basic LLVM functionality"
+optional = false
+python-versions = ">=3.10"
+groups = ["main"]
+files = [
+    {file = "llvmlite-0.46.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:4323177e936d61ae0f73e653e2e614284d97d14d5dd12579adc92b6c2b0597b0"},
+    {file = "llvmlite-0.46.0-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.whl", hash = "sha256:0a2d461cb89537b7c20feb04c46c32e12d5ad4f0896c9dfc0f60336219ff248e"},
+    {file = "llvmlite-0.46.0-cp310-cp310-manylinux_2_27_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:b1f6595a35b7b39c3518b85a28bf18f45e075264e4b2dce3f0c2a4f232b4a910"},
+    {file = "llvmlite-0.46.0-cp310-cp310-win_amd64.whl", hash = "sha256:e7a34d4aa6f9a97ee006b504be6d2b8cb7f755b80ab2f344dda1ef992f828559"},
+    {file = "llvmlite-0.46.0-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:82f3d39b16f19aa1a56d5fe625883a6ab600d5cc9ea8906cca70ce94cabba067"},
+    {file = "llvmlite-0.46.0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl", hash = "sha256:a3df43900119803bbc52720e758c76f316a9a0f34612a886862dfe0a5591a17e"},
+    {file = "llvmlite-0.46.0-cp311-cp311-manylinux_2_27_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:de183fefc8022d21b0aa37fc3e90410bc3524aed8617f0ff76732fc6c3af5361"},
+    {file = "llvmlite-0.46.0-cp311-cp311-win_amd64.whl", hash = "sha256:e8b10bc585c58bdffec9e0c309bb7d51be1f2f15e169a4b4d42f2389e431eb93"},
+    {file = "llvmlite-0.46.0-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:6b9588ad4c63b4f0175a3984b85494f0c927c6b001e3a246a3a7fb3920d9a137"},
+    {file = "llvmlite-0.46.0-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl", hash = "sha256:3535bd2bb6a2d7ae4012681ac228e5132cdb75fefb1bcb24e33f2f3e0c865ed4"},
+    {file = "llvmlite-0.46.0-cp312-cp312-manylinux_2_27_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:4cbfd366e60ff87ea6cc62f50bc4cd800ebb13ed4c149466f50cf2163a473d1e"},
+    {file = "llvmlite-0.46.0-cp312-cp312-win_amd64.whl", hash = "sha256:398b39db462c39563a97b912d4f2866cd37cba60537975a09679b28fbbc0fb38"},
+    {file = "llvmlite-0.46.0-cp313-cp313-macosx_12_0_arm64.whl", hash = "sha256:30b60892d034bc560e0ec6654737aaa74e5ca327bd8114d82136aa071d611172"},
+    {file = "llvmlite-0.46.0-cp313-cp313-manylinux2014_x86_64.manylinux_2_17_x86_64.whl", hash = "sha256:6cc19b051753368a9c9f31dc041299059ee91aceec81bd57b0e385e5d5bf1a54"},
+    {file = "llvmlite-0.46.0-cp313-cp313-manylinux_2_27_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:bca185892908f9ede48c0acd547fe4dc1bafefb8a4967d47db6cf664f9332d12"},
+    {file = "llvmlite-0.46.0-cp313-cp313-win_amd64.whl", hash = "sha256:67438fd30e12349ebb054d86a5a1a57fd5e87d264d2451bcfafbbbaa25b82a35"},
+    {file = "llvmlite-0.46.0-cp314-cp314-macosx_12_0_arm64.whl", hash = "sha256:d252edfb9f4ac1fcf20652258e3f102b26b03eef738dc8a6ffdab7d7d341d547"},
+    {file = "llvmlite-0.46.0-cp314-cp314-manylinux2014_x86_64.manylinux_2_17_x86_64.whl", hash = "sha256:379fdd1c59badeff8982cb47e4694a6143bec3bb49aa10a466e095410522064d"},
+    {file = "llvmlite-0.46.0-cp314-cp314-manylinux_2_27_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:2e8cbfff7f6db0fa2c771ad24154e2a7e457c2444d7673e6de06b8b698c3b269"},
+    {file = "llvmlite-0.46.0-cp314-cp314-win_amd64.whl", hash = "sha256:7821eda3ec1f18050f981819756631d60b6d7ab1a6cf806d9efefbe3f4082d61"},
+    {file = "llvmlite-0.46.0.tar.gz", hash = "sha256:227c9fd6d09dce2783c18b754b7cd9d9b3b3515210c46acc2d3c5badd9870ceb"},
+]
+
 [[package]]
 name = "locket"
 version = "1.0.0"
@@ -1417,6 +1448,41 @@ files = [
     {file = "nodeenv-1.10.0.tar.gz", hash = "sha256:996c191ad80897d076bdfba80a41994c2b47c68e224c542b48feba42ba00f8bb"},
 ]
 
+[[package]]
+name = "numba"
+version = "0.64.0"
+description = "compiling Python code using LLVM"
+optional = false
+python-versions = ">=3.10"
+groups = ["main"]
+files = [
+    {file = "numba-0.64.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:cc09b79440952e3098eeebea4bf6e8d2355fb7f12734fcd9fc5039f0dca90727"},
+    {file = "numba-0.64.0-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.whl", hash = "sha256:1afe3a80b8c2f376b211fb7a49e536ef9eafc92436afc95a2f41ea5392f8cc65"},
+    {file = "numba-0.64.0-cp310-cp310-manylinux_2_27_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:23804194b93b8cd416c6444b5fbc4956082a45fed2d25436ef49c594666e7f7e"},
+    {file = "numba-0.64.0-cp310-cp310-win_amd64.whl", hash = "sha256:e2a9fe998bb2cf848960b34db02c2c3b5e02cf82c07a26d9eef3494069740278"},
+    {file = "numba-0.64.0-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:766156ee4b8afeeb2b2e23c81307c5d19031f18d5ce76ae2c5fb1429e72fa92b"},
+    {file = "numba-0.64.0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl", hash = "sha256:d17071b4ffc9d39b75d8e6c101a36f0c81b646123859898c9799cb31807c8f78"},
+    {file = "numba-0.64.0-cp311-cp311-manylinux_2_27_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:4ead5630434133bac87fa67526eacb264535e4e9a2d5ec780e0b4fc381a7d275"},
+    {file = "numba-0.64.0-cp311-cp311-win_amd64.whl", hash = "sha256:f2b1fd93e7aaac07d6fbaed059c00679f591f2423885c206d8c1b55d65ca3f2d"},
+    {file = "numba-0.64.0-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:69440a8e8bc1a81028446f06b363e28635aa67bd51b1e498023f03b812e0ce68"},
+    {file = "numba-0.64.0-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl", hash = "sha256:f13721011f693ba558b8dd4e4db7f2640462bba1b855bdc804be45bbeb55031a"},
+    {file = "numba-0.64.0-cp312-cp312-manylinux_2_27_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:e0b180b1133f2b5d8b3f09d96b6d7a9e51a7da5dda3c09e998b5bcfac85d222c"},
+    {file = "numba-0.64.0-cp312-cp312-win_amd64.whl", hash = "sha256:e63dc94023b47894849b8b106db28ccb98b49d5498b98878fac1a38f83ac007a"},
+    {file = "numba-0.64.0-cp313-cp313-macosx_12_0_arm64.whl", hash = "sha256:3bab2c872194dcd985f1153b70782ec0fbbe348fffef340264eacd3a76d59fd6"},
+    {file = "numba-0.64.0-cp313-cp313-manylinux2014_x86_64.manylinux_2_17_x86_64.whl", hash = "sha256:703a246c60832cad231d2e73c1182f25bf3cc8b699759ec8fe58a2dbc689a70c"},
+    {file = "numba-0.64.0-cp313-cp313-manylinux_2_27_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:7e2e49a7900ee971d32af7609adc0cfe6aa7477c6f6cccdf6d8138538cf7756f"},
+    {file = "numba-0.64.0-cp313-cp313-win_amd64.whl", hash = "sha256:396f43c3f77e78d7ec84cdfc6b04969c78f8f169351b3c4db814b97e7acf4245"},
+    {file = "numba-0.64.0-cp314-cp314-macosx_12_0_arm64.whl", hash = "sha256:f565d55eaeff382cbc86c63c8c610347453af3d1e7afb2b6569aac1c9b5c93ce"},
+    {file = "numba-0.64.0-cp314-cp314-manylinux2014_x86_64.manylinux_2_17_x86_64.whl", hash = "sha256:9b55169b18892c783f85e9ad9e6f5297a6d12967e4414e6b71361086025ff0bb"},
+    {file = "numba-0.64.0-cp314-cp314-manylinux_2_27_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:196bcafa02c9dd1707e068434f6d5cedde0feb787e3432f7f1f0e993cc336c4c"},
+    {file = "numba-0.64.0-cp314-cp314-win_amd64.whl", hash = "sha256:213e9acbe7f1c05090592e79020315c1749dd52517b90e94c517dca3f014d4a1"},
+    {file = "numba-0.64.0.tar.gz", hash = "sha256:95e7300af648baa3308127b1955b52ce6d11889d16e8cfe637b4f85d2fca52b1"},
+]
+
+[package.dependencies]
+llvmlite = "==0.46.*"
+numpy = ">=1.22,<2.5"
+
 [[package]]
 name = "numcodecs"
 version = "0.16.5"
@@ -2689,4 +2755,4 @@ type = ["pytest-mypy"]
 [metadata]
 lock-version = "2.1"
 python-versions = "^3.11"
-content-hash = "8cdb4eed2095cfce1991bd13261f38a2070b5f34d7ca1f1b37e0b33e9f88aa8e"
+content-hash = "a8f184e9be1a06d62e4d20f99fb0f5fadf8345143ee4984244353994c09bac88"
diff --git a/pyproject.toml b/pyproject.toml
index 82809a5..f41b62c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -18,6 +18,7 @@ copernicusmarine = "^2.3.0"
 matplotlib = "^3.10.8"
 dask = "^2026.1.2"
 ogs-riverger = {git = "https://github.com/inogs/ogs_riverger.git"}
+numba = "^0.64.0"
 
 
 [tool.poetry.group.dev.dependencies]
@@ -32,6 +33,7 @@ exclude = ["legacy_code/" ]
 [tool.deptry.per_rule_ignores]
 DEP002 = [
     "matplotlib",
+    "numba",
     "openpyxl",
 ]
 

From 807b207b2011cb9a5f8b05169900338a222e11db Mon Sep 17 00:00:00 2001
From: Stefano Piani <spiani@ogs.it>
Date: Thu, 12 Mar 2026 16:54:22 +0100
Subject: [PATCH 05/14] Updated pre-commit

---
 .pre-commit-config.yaml                          | 16 ++++++++--------
 src/mitgcm_inputs/__main__.py                    |  1 -
 src/mitgcm_inputs/bottom_fluxes/__init__.py      |  1 -
 src/mitgcm_inputs/bottom_fluxes/bottom_fluxes.py |  1 -
 src/mitgcm_inputs/k_extinction/__init__.py       |  1 -
 src/mitgcm_inputs/k_extinction/k_extinction.py   |  1 -
 src/mitgcm_inputs/ob_indices/ob_indices.py       |  1 -
 src/mitgcm_inputs/rbcs/__init__.py               |  1 -
 src/mitgcm_inputs/rbcs/fiumi_json_gen.py         |  6 ++----
 src/mitgcm_inputs/rbcs/rbcs_gen.py               |  7 ++-----
 src/mitgcm_inputs/rbcs/scarichi_json_gen.py      |  6 ++----
 src/mitgcm_inputs/surface_deposition/__init__.py |  1 -
 .../surface_deposition/surface_deposition.py     |  1 -
 13 files changed, 14 insertions(+), 30 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 7e98f99..321d7a5 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,28 +1,28 @@
 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
@@ -31,16 +31,16 @@ repos:
     - 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
diff --git a/src/mitgcm_inputs/__main__.py b/src/mitgcm_inputs/__main__.py
index 312a00b..a01628f 100644
--- a/src/mitgcm_inputs/__main__.py
+++ b/src/mitgcm_inputs/__main__.py
@@ -27,7 +27,6 @@
 from mitgcm_inputs.surface_deposition import main as sd_main
 from mitgcm_inputs.surface_deposition import sub_arguments as sd_sub_arguments
 
-
 if __name__ == "__main__" or __name__ == "mitgcm_inputs.__main__":
     LOGGER = logging.getLogger()
 else:
diff --git a/src/mitgcm_inputs/bottom_fluxes/__init__.py b/src/mitgcm_inputs/bottom_fluxes/__init__.py
index ed14d6e..b7fd117 100644
--- a/src/mitgcm_inputs/bottom_fluxes/__init__.py
+++ b/src/mitgcm_inputs/bottom_fluxes/__init__.py
@@ -9,7 +9,6 @@
 from mitgcm_inputs.tools.read_mesh_mask import read_mesh_mask
 from mitgcm_inputs.tools.save_dataset import save_dataset
 
-
 if __name__ == "__main__":
     LOGGER = logging.getLogger()
 else:
diff --git a/src/mitgcm_inputs/bottom_fluxes/bottom_fluxes.py b/src/mitgcm_inputs/bottom_fluxes/bottom_fluxes.py
index 2c5d998..f73f266 100644
--- a/src/mitgcm_inputs/bottom_fluxes/bottom_fluxes.py
+++ b/src/mitgcm_inputs/bottom_fluxes/bottom_fluxes.py
@@ -7,7 +7,6 @@
 import xarray as xr
 from bitsea.commons.mask import Mask
 
-
 LOGGER = logging.getLogger(__name__)
 
 
diff --git a/src/mitgcm_inputs/k_extinction/__init__.py b/src/mitgcm_inputs/k_extinction/__init__.py
index 5de0c9e..3135772 100644
--- a/src/mitgcm_inputs/k_extinction/__init__.py
+++ b/src/mitgcm_inputs/k_extinction/__init__.py
@@ -8,7 +8,6 @@
 from mitgcm_inputs.k_extinction.k_extinction import compute_k_extinction
 from mitgcm_inputs.tools.read_mesh_mask import read_mesh_mask
 
-
 if __name__ == "__main__":
     LOGGER = logging.getLogger()
 else:
diff --git a/src/mitgcm_inputs/k_extinction/k_extinction.py b/src/mitgcm_inputs/k_extinction/k_extinction.py
index e1ff735..f4d3145 100644
--- a/src/mitgcm_inputs/k_extinction/k_extinction.py
+++ b/src/mitgcm_inputs/k_extinction/k_extinction.py
@@ -8,7 +8,6 @@
 from scipy.interpolate import LinearNDInterpolator
 from scipy.spatial import Delaunay
 
-
 DATA_FILE = Path(__file__).resolve().parent / "data" / "kExt_climatology.nc"
 
 
diff --git a/src/mitgcm_inputs/ob_indices/ob_indices.py b/src/mitgcm_inputs/ob_indices/ob_indices.py
index 6b9f95c..7233251 100644
--- a/src/mitgcm_inputs/ob_indices/ob_indices.py
+++ b/src/mitgcm_inputs/ob_indices/ob_indices.py
@@ -9,7 +9,6 @@
 from bitsea.commons.mask import MaskWithRivers
 from bitsea.components.component_mask_2d import ComponentMask2D
 
-
 LOGGER = logging.getLogger(__name__)
 
 
diff --git a/src/mitgcm_inputs/rbcs/__init__.py b/src/mitgcm_inputs/rbcs/__init__.py
index 765f591..951ef25 100644
--- a/src/mitgcm_inputs/rbcs/__init__.py
+++ b/src/mitgcm_inputs/rbcs/__init__.py
@@ -16,7 +16,6 @@
 from mitgcm_inputs.rbcs.scarichi_json_gen import read_sewage_positions
 from mitgcm_inputs.tools.tar_utils import set_tar_file_ownerships
 
-
 if __name__ == "__main__":
     LOGGER = logging.getLogger()
 else:
diff --git a/src/mitgcm_inputs/rbcs/fiumi_json_gen.py b/src/mitgcm_inputs/rbcs/fiumi_json_gen.py
index dbec501..d92a571 100644
--- a/src/mitgcm_inputs/rbcs/fiumi_json_gen.py
+++ b/src/mitgcm_inputs/rbcs/fiumi_json_gen.py
@@ -7,8 +7,7 @@
 
 
 def argument():
-    parser = argparse.ArgumentParser(
-        description="""
+    parser = argparse.ArgumentParser(description="""
     Reads seawage info on excel file and for all the domains
     build the json files with the coordinate of the pointsource
     for E.Coli tracers
@@ -16,8 +15,7 @@ def argument():
     RiverSource_SAD.json
     ...
 
-    """
-    )
+    """)
 
     parser.add_argument(
         "--inputfile",
diff --git a/src/mitgcm_inputs/rbcs/rbcs_gen.py b/src/mitgcm_inputs/rbcs/rbcs_gen.py
index 583137a..953424b 100644
--- a/src/mitgcm_inputs/rbcs/rbcs_gen.py
+++ b/src/mitgcm_inputs/rbcs/rbcs_gen.py
@@ -20,13 +20,11 @@
 
 from mitgcm_inputs.tools.read_mesh_mask import read_mesh_mask
 
-
 LOGGER = logging.getLogger(__name__)
 
 
 def argument():
-    parser = argparse.ArgumentParser(
-        description="""
+    parser = argparse.ArgumentParser(description="""
     Generates RBCs files
     3D Files:
     - bottom_sources_S_mask.bin
@@ -63,8 +61,7 @@ def argument():
                         - Rivers_positions.json is expected
                         - output files are dumped
 
-    """
-    )
+    """)
     parser.add_argument(
         "--sewage",
         "-s",
diff --git a/src/mitgcm_inputs/rbcs/scarichi_json_gen.py b/src/mitgcm_inputs/rbcs/scarichi_json_gen.py
index 564da94..9bf0410 100644
--- a/src/mitgcm_inputs/rbcs/scarichi_json_gen.py
+++ b/src/mitgcm_inputs/rbcs/scarichi_json_gen.py
@@ -18,8 +18,7 @@
 
 
 def argument():
-    parser = argparse.ArgumentParser(
-        description="""
+    parser = argparse.ArgumentParser(description="""
     Reads sewage info on excel file and for all the domains
     Takes salinity data from MDS service
     build the json files with the coordinate
@@ -28,8 +27,7 @@ def argument():
     PointSource_SAD.json
     ...
 
-    """
-    )
+    """)
 
     parser.add_argument(
         "--inputfile",
diff --git a/src/mitgcm_inputs/surface_deposition/__init__.py b/src/mitgcm_inputs/surface_deposition/__init__.py
index 65a212c..a6d75a4 100644
--- a/src/mitgcm_inputs/surface_deposition/__init__.py
+++ b/src/mitgcm_inputs/surface_deposition/__init__.py
@@ -11,7 +11,6 @@
 from mitgcm_inputs.tools.read_mesh_mask import read_mesh_mask
 from mitgcm_inputs.tools.save_dataset import save_dataset
 
-
 if __name__ == "__main__":
     LOGGER = logging.getLogger()
 else:
diff --git a/src/mitgcm_inputs/surface_deposition/surface_deposition.py b/src/mitgcm_inputs/surface_deposition/surface_deposition.py
index 4ff50f5..58b33ce 100644
--- a/src/mitgcm_inputs/surface_deposition/surface_deposition.py
+++ b/src/mitgcm_inputs/surface_deposition/surface_deposition.py
@@ -6,7 +6,6 @@
 import xarray as xr
 from bitsea.commons.mask import Mask
 
-
 LOGGER = logging.getLogger(__name__)
 
 

From 4d50631b8ce970a99000155d6f6d28ee1a6ce304 Mon Sep 17 00:00:00 2001
From: Stefano Piani <spiani@ogs.it>
Date: Thu, 12 Mar 2026 16:59:10 +0100
Subject: [PATCH 06/14] Added possibility to run on domains with no rivers

---
 src/mitgcm_inputs/ob_indices/__init__.py   | 34 +++++++++++++---------
 src/mitgcm_inputs/ob_indices/ob_indices.py |  8 ++---
 2 files changed, 25 insertions(+), 17 deletions(-)

diff --git a/src/mitgcm_inputs/ob_indices/__init__.py b/src/mitgcm_inputs/ob_indices/__init__.py
index 6b5c7d0..52a6e3e 100644
--- a/src/mitgcm_inputs/ob_indices/__init__.py
+++ b/src/mitgcm_inputs/ob_indices/__init__.py
@@ -40,7 +40,10 @@ def sub_arguments(subparser):
         type=existing_file_path,
         help="An auxiliary file that contains the a map that associates each "
         "river cell with its river id. This file is useful only if this "
-        "information is not already stored in the meshmask file",
+        "information is not already stored in the meshmask file and if there "
+        "are rivers on the domain. If the rivers-positions file is not "
+        "provided, we will assume that there are no rivers on the domain "
+        "and this file is simply ignored",
     )
 
     parser.add_argument(
@@ -49,7 +52,7 @@ def sub_arguments(subparser):
         required=False,
         type=existing_file_path,
         default=None,
-        help="The json file that describe the position of the mouth of the"
+        help="The json file that describe the position of the mouths of the"
         "rivers. If this file is not provided, we will assume that there are "
         "no rivers on the domain",
     )
@@ -91,29 +94,34 @@ def main(args: argparse.Namespace) -> int:
         )
         return 1
 
-    meshmask = read_mesh_mask(args.mask)
+    domain_mask = read_mesh_mask(args.mask)
 
+    # On which file do we have the information about the cells occupied by
+    # the rivers?
     if args.river_file is not None:
         file_with_river = args.river_file
     else:
         file_with_river = args.mask
-    with xr.open_dataset(file_with_river) as river_ds:
-        river_map = river_ds["rivers"].load()
-
-    river_mask = MaskWithRivers(
-        grid=meshmask.grid,
-        zlevels=meshmask.zlevels,
-        mask_array=meshmask[:],
-        river_positions=river_map,
-    )
 
+    # If there are rivers in this domain
     if args.rivers_positions is not None:
+        with xr.open_dataset(file_with_river) as river_ds:
+            river_map = river_ds["rivers"].load()
+
+        river_mask = MaskWithRivers(
+            grid=domain_mask.grid,
+            zlevels=domain_mask.zlevels,
+            mask_array=domain_mask[:],
+            river_positions=river_map,
+        )
         rivers_positions = json.loads(args.rivers_positions.read_text())
+        mesh_mask = river_mask
     else:
         rivers_positions = []
+        mesh_mask = domain_mask
 
     ob_indices, ob_sponge = generate_ob_indices(
-        river_mask=river_mask,
+        river_mask=mesh_mask,
         sponge_extent=args.sponge_extent,
         rivers_positions=rivers_positions,
     )
diff --git a/src/mitgcm_inputs/ob_indices/ob_indices.py b/src/mitgcm_inputs/ob_indices/ob_indices.py
index 7233251..ea03ccd 100644
--- a/src/mitgcm_inputs/ob_indices/ob_indices.py
+++ b/src/mitgcm_inputs/ob_indices/ob_indices.py
@@ -6,7 +6,7 @@
 from typing import Any
 
 import numpy as np
-from bitsea.commons.mask import MaskWithRivers
+from bitsea.commons.mask import Mask
 from bitsea.components.component_mask_2d import ComponentMask2D
 
 LOGGER = logging.getLogger(__name__)
@@ -89,7 +89,7 @@ def rewrite_in_mitgcm_format(v: np.ndarray) -> list[tuple[int, int]]:
 
 
 def generate_ob_indices(
-    river_mask: MaskWithRivers,
+    mask: Mask,
     sponge_extent: int = 16,
     rivers_positions: Sequence[Mapping[str, Any]] | None = None,
 ):
@@ -121,13 +121,13 @@ def generate_ob_indices(
             open_on_boundary = 1
         else:
             # Here we add a +1 because we need to skip the depth index
-            open_on_boundary = river_mask.shape[domain_index + 1]
+            open_on_boundary = mask.shape[domain_index + 1]
         # This is the value that we use to report that a cell is closed on the
         # boundary
         closed_cell = 0
 
         LOGGER.debug("Cutting %i cells from the %s", cut_cells, side)
-        current_side = cut_at_side(river_mask.get_sea_cells(), side, cut_cells)
+        current_side = cut_at_side(mask.get_sea_cells(), side, cut_cells)
 
         # We only take into account the surface
         current_side_2d = current_side[0, :, :]

From 442a48600435e5c1738155595947237be9725008 Mon Sep 17 00:00:00 2001
From: Stefano Piani <spiani@ogs.it>
Date: Thu, 12 Mar 2026 17:01:29 +0100
Subject: [PATCH 07/14] Parallelized generate_mer_statics.sh

---
 launcers/all_statics/generate_mer_statics.sh | 67 +++++++++++++-------
 1 file changed, 45 insertions(+), 22 deletions(-)
 mode change 100644 => 100755 launcers/all_statics/generate_mer_statics.sh

diff --git a/launcers/all_statics/generate_mer_statics.sh b/launcers/all_statics/generate_mer_statics.sh
old mode 100644
new mode 100755
index 29ab5a9..c6cb77d
--- a/launcers/all_statics/generate_mer_statics.sh
+++ b/launcers/all_statics/generate_mer_statics.sh
@@ -12,57 +12,80 @@ DOMAINS_HR="HGT GOR CON PES LAM PAN NAP GAE FOL CAG ISO"
 
 DOMAINS="$DOMAINS_REG $DOMAINS_HR"
 
-mkdir -p ${OUTPUTDIR}
+MAXJOBS=5   # numero massimo di domini processati in parallelo
+
+mkdir -p "${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
 
-    # Setta il valore dello SPONGE
+    # Setta SPONGE
     if [[ " $DOMAINS_HR " =~ " $domain " ]]; then
         SPONGE=10
     else
         SPONGE=16
     fi
 
-    echo SPONGE $SPONGE
+    cd "$BATHYTOOLSDIR"
 
-    cd $BATHYTOOLSDIR
-    # Check where is the correct configuration file for the domain (in the mer_domains
-    # directory or in the mer_domains/high_reso dir)
     domain_descriptor="$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 "${domaindir}" --mer
+
+    cd "$MITGCMINPUTSDIR"
 
-    # Generate fluxes.tar.gz
-    cd ${MITGCMINPUTSDIR}
-    poetry run mitgcm_inputs FLUXES -m ${domaindir}/meshmask.nc -o ${domaindir}/fluxes.tar.gz
+    poetry run mitgcm_inputs FLUXES \
+        -m "${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 and ob_indices 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"
+        ob_indices_options="-p $rpositions -r ${domaindir}/additional_variables.nc"
+
         if [ -f "${rcustom}" ]; then
             rbcs_options="${rbcs_options} -d ${rcustom}"
         fi
     fi
 
-    poetry run mitgcm_inputs ob_indices -m ${domaindir}/meshmask.nc -r ${domaindir}/additional_variables.nc -s $SPONGE -o ${domaindir}/rivers_open_boundaries.txt -n ${domaindir}/nudging_indices.txt ${ob_indices_options}
+    poetry run mitgcm_inputs ob_indices \
+        -m "${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
+
+parallel --lb --tag --halt soon,fail=1 -j ${MAXJOBS} process_domain ::: ${DOMAINS}
 
-    poetry run mitgcm_inputs rbcs -m ${domaindir}/meshmask.nc -o ${domaindir} ${rbcs_options}
-  done
+### Serial version if parallel is missing
+# for domain in $DOMAINS
+#   do
+#     process_domain $domain
+#   done

From d0bc833080855843e523f778305780985ff01bf1 Mon Sep 17 00:00:00 2001
From: Stefano Piani <spiani@ogs.it>
Date: Thu, 12 Mar 2026 17:18:38 +0100
Subject: [PATCH 08/14] Removed ruff-format because it conflicts with black

---
 .pre-commit-config.yaml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 321d7a5..880a5dc 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -27,9 +27,6 @@ repos:
     # 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: 26.3.1
   hooks:

From 450baf86aebd95dcad0a501dd0179b9f24ab72aa Mon Sep 17 00:00:00 2001
From: Stefano Piani <spiani@ogs.it>
Date: Thu, 12 Mar 2026 17:25:09 +0100
Subject: [PATCH 09/14] Updated CI workflow tu use new actions

---
 .github/workflows/pre-commit.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml
index 752639e..41dbd81 100644
--- a/.github/workflows/pre-commit.yml
+++ b/.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"
 

From 0f1d5a3fef00d58706d9847073279c1f22827bb1 Mon Sep 17 00:00:00 2001
From: Stefano Piani <spiani@ogs.it>
Date: Thu, 12 Mar 2026 17:42:05 +0100
Subject: [PATCH 10/14] Update src/mitgcm_inputs/ob_indices/__init__.py

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
---
 src/mitgcm_inputs/ob_indices/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/mitgcm_inputs/ob_indices/__init__.py b/src/mitgcm_inputs/ob_indices/__init__.py
index 52a6e3e..5907d86 100644
--- a/src/mitgcm_inputs/ob_indices/__init__.py
+++ b/src/mitgcm_inputs/ob_indices/__init__.py
@@ -121,7 +121,7 @@ def main(args: argparse.Namespace) -> int:
         mesh_mask = domain_mask
 
     ob_indices, ob_sponge = generate_ob_indices(
-        river_mask=mesh_mask,
+        mask=mesh_mask,
         sponge_extent=args.sponge_extent,
         rivers_positions=rivers_positions,
     )

From 17baba2f6898bfff5b99f1dfbe5578d3e5d27ede Mon Sep 17 00:00:00 2001
From: Stefano Piani <spiani@ogs.it>
Date: Thu, 12 Mar 2026 17:43:05 +0100
Subject: [PATCH 11/14] Update src/mitgcm_inputs/ob_indices/__init__.py

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
---
 src/mitgcm_inputs/ob_indices/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/mitgcm_inputs/ob_indices/__init__.py b/src/mitgcm_inputs/ob_indices/__init__.py
index 5907d86..b94de99 100644
--- a/src/mitgcm_inputs/ob_indices/__init__.py
+++ b/src/mitgcm_inputs/ob_indices/__init__.py
@@ -90,7 +90,7 @@ def sub_arguments(subparser):
 def main(args: argparse.Namespace) -> int:
     if args.cmd != COMMAND_NAME:
         LOGGER.error(
-            "obindices command has been invoked with command: %s", args.cmd
+            "%s command has been invoked with command: %s", COMMAND_NAME, args.cmd
         )
         return 1
 

From 3cf3a2394716bfe0efb92446f09d5f3d0186ba34 Mon Sep 17 00:00:00 2001
From: Stefano Piani <spiani@ogs.it>
Date: Thu, 12 Mar 2026 17:50:34 +0100
Subject: [PATCH 12/14] Making output optional

---
 src/mitgcm_inputs/ob_indices/__init__.py | 19 ++++++++++++++-----
 1 file changed, 14 insertions(+), 5 deletions(-)

diff --git a/src/mitgcm_inputs/ob_indices/__init__.py b/src/mitgcm_inputs/ob_indices/__init__.py
index b94de99..b9b3823 100644
--- a/src/mitgcm_inputs/ob_indices/__init__.py
+++ b/src/mitgcm_inputs/ob_indices/__init__.py
@@ -69,7 +69,7 @@ def sub_arguments(subparser):
     parser.add_argument(
         "-o",
         "--ob-indices",
-        required=True,
+        required=False,
         type=path_inside_an_existing_dir,
         help="The path of the output file where the OB indices will be "
         "stored. If this is not submitted, this output file will not be "
@@ -83,17 +83,25 @@ def sub_arguments(subparser):
         type=path_inside_an_existing_dir,
         default=None,
         help="The path of the output file where the nudge indices will be "
-        "stored",
+        "stored. If this is not submitted, this output file will not be "
+        "written.",
     )
 
 
 def main(args: argparse.Namespace) -> int:
     if args.cmd != COMMAND_NAME:
         LOGGER.error(
-            "%s command has been invoked with command: %s", COMMAND_NAME, args.cmd
+            "%s command has been invoked with command: %s",
+            COMMAND_NAME,
+            args.cmd,
         )
         return 1
 
+    if args.ob_indices is None and args.nudge_indices is None:
+        LOGGER.warning(
+            "No output file has been provided, nothing will be written!!!"
+        )
+
     domain_mask = read_mesh_mask(args.mask)
 
     # On which file do we have the information about the cells occupied by
@@ -120,13 +128,14 @@ def main(args: argparse.Namespace) -> int:
         rivers_positions = []
         mesh_mask = domain_mask
 
-    ob_indices, ob_sponge = generate_ob_indices(
+    open_bc_indices, ob_sponge = generate_ob_indices(
         mask=mesh_mask,
         sponge_extent=args.sponge_extent,
         rivers_positions=rivers_positions,
     )
 
-    args.ob_indices.write_text(ob_indices)
+    if args.ob_indices is not None:
+        args.ob_indices.write_text(open_bc_indices)
     if args.nudge_indices is not None:
         args.nudge_indices.write_text(ob_sponge)
 

From 4d69c122ec9c3264180820ff8cc35cea39978c75 Mon Sep 17 00:00:00 2001
From: Stefano Piani <spiani@ogs.it>
Date: Thu, 12 Mar 2026 18:01:46 +0100
Subject: [PATCH 13/14] Update launcers/all_statics/generate_mer_statics.sh

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
---
 launcers/all_statics/generate_mer_statics.sh | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/launcers/all_statics/generate_mer_statics.sh b/launcers/all_statics/generate_mer_statics.sh
index c6cb77d..53fea63 100755
--- a/launcers/all_statics/generate_mer_statics.sh
+++ b/launcers/all_statics/generate_mer_statics.sh
@@ -82,10 +82,12 @@ process_domain () {
 export -f process_domain
 export OUTPUTDIR BATHYTOOLSDIR MITGCMINPUTSDIR DOMAINS_HR
 
-parallel --lb --tag --halt soon,fail=1 -j ${MAXJOBS} process_domain ::: ${DOMAINS}
-
-### Serial version if parallel is missing
-# for domain in $DOMAINS
-#   do
-#     process_domain $domain
-#   done
+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

From 84718c510ecd1212976e9340a1aac1ec72d639fb Mon Sep 17 00:00:00 2001
From: Stefano Piani <spiani@ogs.it>
Date: Mon, 16 Mar 2026 18:49:34 +0100
Subject: [PATCH 14/14] Fixing bug when generating ob_indices files

---
 src/mitgcm_inputs/ob_indices/ob_indices.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/mitgcm_inputs/ob_indices/ob_indices.py b/src/mitgcm_inputs/ob_indices/ob_indices.py
index ea03ccd..b33692e 100644
--- a/src/mitgcm_inputs/ob_indices/ob_indices.py
+++ b/src/mitgcm_inputs/ob_indices/ob_indices.py
@@ -198,12 +198,13 @@ def generate_ob_indices(
             for cell in river_sources:
                 open_bc_cells[cell[domain_index]] = cell[sponge_index] + 1
 
-        ob_indices += f"OB_I{side}="
+        direction_char = "J" if side in (Side.NORTH, Side.SOUTH) else "I"
+        ob_indices += f"OB_{direction_char}{side}="
         for i in rewrite_in_mitgcm_format(open_bc_cells):
             ob_indices += f"{i[0]}*{i[1]},"
         ob_indices += "\n"
 
-        ob_sponge += f"nudgOB_I{side}="
+        ob_sponge += f"nudgOB_{direction_char}{side}="
         for i in rewrite_in_mitgcm_format(sponge_cells):
             ob_sponge += f"{i[0]}*{i[1]},"
         ob_sponge += "\n"