From 85183aadb6c75bfa6ec2ac6348f619f8fcb1d4bd Mon Sep 17 00:00:00 2001 From: Stefano Piani Date: Wed, 11 Mar 2026 15:23:06 +0100 Subject: [PATCH 1/6] Now bathytools does not write rivers_open_boundaries.txt file anymore --- src/bathytools/actions/dig_rivers.py | 191 ++++----------------------- 1 file changed, 24 insertions(+), 167 deletions(-) diff --git a/src/bathytools/actions/dig_rivers.py b/src/bathytools/actions/dig_rivers.py index 11aef61..6c4b829 100644 --- a/src/bathytools/actions/dig_rivers.py +++ b/src/bathytools/actions/dig_rivers.py @@ -8,7 +8,6 @@ from dataclasses import dataclass from itertools import chain from logging import getLogger -from operator import attrgetter from operator import itemgetter from typing import Dict from typing import List @@ -90,18 +89,18 @@ class RiverDig: Represents a river that will be dug into a bathymetry domain Attributes: - id (int): Unique identifier for the river. - name (str): Name of the river. - model (str): How the river is modelled. - mouth_latitude (float): Latitude of the river's mouth. - mouth_longitude (float): Longitude of the river's mouth. - width (float): Width of the river channel in meters. - depth (float): Depth of the river channel in meters. - side (Optional[Literal["N", "S", "E", "W"]]): The source side of the - river, specifying the direction from where the river originates - relative to the grid (North, South, East, West). - stem (Optional[list[Movement]]): Sequence of movements representing the - course of the river through the bathymetry grid. + id: Unique identifier for the river. + name: Name of the river. + model: How the river is modeled. + mouth_latitude: Latitude of the river's mouth. + mouth_longitude: Longitude of the river's mouth. + width: Width of the river channel in meters. + depth: Depth of the river channel in meters. + side: The source side of the river, specifying the direction from + where the river originates relative to the grid (North, South, + East, West). + stem: Sequence of movements representing the course of the river + through the bathymetry grid. """ id: int @@ -195,14 +194,14 @@ def _steam_length_to_stem( its defined side. Args: - steam_length (int): The length of the river's stem measured in - grid cells. - side (Literal["N", "S", "E", "W"]): The side of the grid - (North, South, East, or West) representing the river's origin. + steam_length: The length of the river's stem measured in grid + cells. + side: The side of the grid (North, South, East, or West) + representing the river's origin. Returns: - List[Movement]: A single `Movement`, representing the river's stem - based on its direction and length. + A single `Movement`, representing the river's stem based on its + direction and length. Raises: ValueError: If the provided side is invalid or `steam_length` is not @@ -247,12 +246,12 @@ def _update_stem_value( entries. Args: - previous_stem_value (Mapping): The existing dictionary containing - the stem geometry. - new_values (Dict): The dictionary with the latest geometry updates. + previous_stem_value: The existing dictionary containing the stem + geometry. + new_values: The dictionary with the latest geometry updates. Returns: - Dict: A combined dictionary representing the current state of the + A combined dictionary representing the current state of the stem geometry. Raises: @@ -605,10 +604,7 @@ def read_river_atlas( return source_atlas def save_river_sources( - self, - river_sources: dict[tuple[int, str], tuple[str, Direction, list]], - lat_lon_shape: tuple[int, int], - open_side: dict[Direction, bool], + self, river_sources: dict[tuple[int, str], tuple[str, Direction, list]] ): """ Saves detailed information about river sources into a JSON file and @@ -626,12 +622,6 @@ def save_river_sources( the values are tuples with: - A `Direction` indicating the originating side of the river. - A list of grid cells from which the river originates. - lat_lon_shape (tuple): The shape of the domain grid (number of - latitude cells, number of longitude cells). - open_side (dict): A dictionary mapping each domain side - (`Direction`) to a boolean value indicating whether the - boundary is open (True for a boundary with water) or closed - (if there are only land cells). """ river_atlas = self.read_river_atlas(river_sources) @@ -650,132 +640,6 @@ def save_river_sources( with open(source_file, "w") as f: f.write(river_position_content + "\n") - # Create namelist files to configure river-specific open boundary - # conditions for the numerical model. We start by writing the function - # that we will use inside our routine when we have to register a river; - # it writes - def write_obj_interval(length: int, position: int) -> str: - return f"{length}*{position}," - - obj_file_content = "" - for side in Direction: - # Determine the prefix for each line based on the boundary side. - if side == Direction.NORTH: - line_prefix = "OB_Jnorth=" - elif side == Direction.SOUTH: - line_prefix = "OB_Jsouth=" - elif side == Direction.EAST: - line_prefix = "OB_Ieast=" - elif side == Direction.WEST: - line_prefix = "OB_Iwest=" - else: - raise ValueError(f"Unexpected side: {side}") - - # Calculate the total number of boundary cells for the current side. - if side in (Direction.NORTH, Direction.SOUTH): - side_length = lat_lon_shape[1] - other_side_length = lat_lon_shape[0] - else: - side_length = lat_lon_shape[0] - other_side_length = lat_lon_shape[1] - - # Determine the default position for boundary cells with no rivers. - # For open sides, this is 1 (start of axis) or the side length - # (end of axis); for closed sides, this is set to 0. - if side in (Direction.NORTH, Direction.EAST): - no_river_position = other_side_length if open_side[side] else 0 - else: - no_river_position = 1 if open_side[side] else 0 - - # Define helper functions to retrieve the river's position on the - # side and its offset (translation) with respect to the boundary. - if side in (Direction.NORTH, Direction.SOUTH): - get_side_coord = attrgetter("lon_indices") - get_translation = attrgetter("lat_indices") - else: - get_side_coord = attrgetter("lat_indices") - get_translation = attrgetter("lon_indices") - - # Determine the starting position of a river source along the - # domain side. - def get_start_point(r: RiverSource): - side_position = get_side_coord(r) - if isinstance(side_position, Interval): - return side_position.start - return side_position - - # Exclude rivers that are modeled as rains - side_rivers = [ - r for r in river_atlas[side] if r.model != "rain_like" - ] - - # Sort the sources based on their starting point. - current_side_sources = sorted(side_rivers, key=get_start_point) - - # If the side has no rivers, write a single line to assign all - # boundary cells to the default value (either open or closed). - if len(current_side_sources) == 0: - obj_file_content += ( - line_prefix - + write_obj_interval(side_length, no_river_position) - + "\n" - ) - continue - - # Begin writing the line for the current domain side. - obj_file_content += f"{line_prefix}" - - # Track where the previous river ended. At the start, this is set - # to 0. - previous_position = 0 - for river in current_side_sources: - river_start = get_start_point(river) - river_translation = get_translation(river) - river_interval = get_side_coord(river) - # Ensure the river's position along the side is an interval; - # convert it to an interval if it's a single integer. - if not isinstance(river_interval, Interval): - river_interval = Interval( - river_interval, river_interval + 1 - ) - - # Calculate the number of grid cells occupied by the current - # river. - river_range = river_interval.end - river_start - - # If there is a gap between the current river and the previous - # one, add it to the line being written. - if river_start != previous_position: - obj_file_content += write_obj_interval( - river_start - previous_position, no_river_position - ) - - # Update the ending position for the next river. - previous_position = river_interval.end - - # Write the cells occupied by the current river. Add "+ 1" to - # the translation for Fortran's 1-based indexing. - obj_file_content += write_obj_interval( - river_range, river_translation + 1 - ) - - # If the end of the side has not been reached, fill the remaining - # cells with the "no_river" value. - if previous_position != side_length: - obj_file_content += write_obj_interval( - side_length - previous_position, no_river_position - ) - - # Finalize and close the line for this side. - obj_file_content += "\n" - - obj_file = ( - self._output_appendix.output_dir / "rivers_open_boundaries.txt" - ) - LOGGER.info("Writing rivers open boundaries to %s", obj_file) - with open(obj_file, "w") as f: - f.write(obj_file_content) - def __call__(self, bathymetry: xr.DataArray) -> xr.DataArray: """ Perform the river digging action on a bathymetry dataset. @@ -828,13 +692,6 @@ def __call__(self, bathymetry: xr.DataArray) -> xr.DataArray: ).values water_cells = b_array < 0 - open_sides = { - Direction.SOUTH: bool(np.any(water_cells[0, :])), - Direction.NORTH: bool(np.any(water_cells[-1, :])), - Direction.WEST: bool(np.any(water_cells[:, 0])), - Direction.EAST: bool(np.any(water_cells[:, -1])), - } - LOGGER.debug("Open sides: %s", open_sides) # Filter rivers to include only those within the domain, ensuring each # has the required side and stem data for successful processing. @@ -1008,6 +865,6 @@ def __call__(self, bathymetry: xr.DataArray) -> xr.DataArray: }, ), ) - self.save_river_sources(river_sources, b_array.shape, open_sides) + self.save_river_sources(river_sources) return bathymetry From 54f0dfd134f5a1d23e99bb69b6c8682fa824e857 Mon Sep 17 00:00:00 2001 From: Stefano Piani Date: Wed, 11 Mar 2026 15:23:53 +0100 Subject: [PATCH 2/6] Updating poetry lock --- poetry.lock | 862 +++++++++++++++++++++++++++------------------------- 1 file changed, 449 insertions(+), 413 deletions(-) diff --git a/poetry.lock b/poetry.lock index 249e1e4..1c757ec 100644 --- a/poetry.lock +++ b/poetry.lock @@ -64,19 +64,19 @@ plots = [] type = "git" url = "https://github.com/inogs/bit.sea.git" reference = "master" -resolved_reference = "a16670921a84eb5df8dd3a89d2248f7e8c4edc3b" +resolved_reference = "258b674bf2ece213e0588cce15684ca1de672ffa" [[package]] name = "cattrs" -version = "25.3.0" +version = "26.1.0" description = "Composable complex class support for attrs and dataclasses." optional = false -python-versions = ">=3.9" +python-versions = ">=3.10" groups = ["main"] markers = "sys_platform == \"win32\" or sys_platform == \"emscripten\" or sys_platform != \"win32\" and sys_platform != \"emscripten\"" files = [ - {file = "cattrs-25.3.0-py3-none-any.whl", hash = "sha256:9896e84e0a5bf723bc7b4b68f4481785367ce07a8a02e7e9ee6eb2819bc306ff"}, - {file = "cattrs-25.3.0.tar.gz", hash = "sha256:1ac88d9e5eda10436c4517e390a4142d88638fe682c436c93db7ce4a277b884a"}, + {file = "cattrs-26.1.0-py3-none-any.whl", hash = "sha256:d1e0804c42639494d469d08d4f26d6b9de9b8ab26b446db7b5f8c2e97f7c3096"}, + {file = "cattrs-26.1.0.tar.gz", hash = "sha256:fa239e0f0ec0715ba34852ce813986dfed1e12117e209b816ab87401271cdd40"}, ] [package.dependencies] @@ -92,19 +92,20 @@ msgspec = ["msgspec (>=0.19.0) ; implementation_name == \"cpython\""] orjson = ["orjson (>=3.11.3) ; implementation_name == \"cpython\""] pyyaml = ["pyyaml (>=6.0)"] tomlkit = ["tomlkit (>=0.11.8)"] +tomllib = ["tomli (>=1.1.0) ; python_version < \"3.11\"", "tomli-w (>=1.1.0)"] ujson = ["ujson (>=5.10.0)"] [[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"] markers = "sys_platform == \"win32\" or sys_platform == \"emscripten\" or sys_platform != \"win32\" and sys_platform != \"emscripten\"" 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]] @@ -167,126 +168,126 @@ numpy = ">=1.21.2" [[package]] name = "charset-normalizer" -version = "3.4.4" +version = "3.4.5" description = "The Real First Universal Charset Detector. 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-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\""] - [[package]] name = "webob" version = "1.8.9" From f6f91d94776fed91b99ae1199b21b88889e86a44 Mon Sep 17 00:00:00 2001 From: Copilot <198982749+Copilot@users.noreply.github.com> Date: Thu, 12 Mar 2026 15:22:17 +0100 Subject: [PATCH 3/6] Fix misleading comment on `water_cells` in `dig_rivers.py` (#83) * Initial plan * Fix misleading comment about water_cells usage in dig_rivers.py Co-authored-by: spiani <8956990+spiani@users.noreply.github.com> --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: spiani <8956990+spiani@users.noreply.github.com> --- src/bathytools/actions/dig_rivers.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/bathytools/actions/dig_rivers.py b/src/bathytools/actions/dig_rivers.py index 6c4b829..8c76b21 100644 --- a/src/bathytools/actions/dig_rivers.py +++ b/src/bathytools/actions/dig_rivers.py @@ -686,7 +686,9 @@ def __call__(self, bathymetry: xr.DataArray) -> xr.DataArray: allow_broadcast=True, ) - # Check if a side is "open", i.e., if it has at least one water cell + # Precompute a boolean array of cells that are already underwater + # (negative bathymetry). Used later to skip water cells when tracking + # river dig cells for intersection detection. b_array = bathymetry.elevation.transpose( "latitude", "longitude" ).values From e936f3d689b4f68f474078ae0036ed2b17f74b60 Mon Sep 17 00:00:00 2001 From: Copilot <198982749+Copilot@users.noreply.github.com> Date: Thu, 12 Mar 2026 15:28:30 +0100 Subject: [PATCH 4/6] =?UTF-8?q?Fix=20`steam=5Flength`=20=E2=86=92=20`stem?= =?UTF-8?q?=5Flength`=20typo=20in=20`DigRivers`=20(#84)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> --- src/bathytools/actions/dig_rivers.py | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/src/bathytools/actions/dig_rivers.py b/src/bathytools/actions/dig_rivers.py index 8c76b21..9894f2e 100644 --- a/src/bathytools/actions/dig_rivers.py +++ b/src/bathytools/actions/dig_rivers.py @@ -181,8 +181,8 @@ class DigRivers(SimpleAction): """ @staticmethod - def _steam_length_to_stem( - steam_length: int, side: Literal["N", "S", "E", "W"] + def _stem_length_to_stem( + stem_length: int, side: Literal["N", "S", "E", "W"] ) -> List[Movement]: """ Converts the "stem_length" parameter into a list of `Movement` objects. @@ -194,7 +194,7 @@ def _steam_length_to_stem( its defined side. Args: - steam_length: The length of the river's stem measured in grid + stem_length: The length of the river's stem measured in grid cells. side: The side of the grid (North, South, East, or West) representing the river's origin. @@ -204,22 +204,22 @@ def _steam_length_to_stem( direction and length. Raises: - ValueError: If the provided side is invalid or `steam_length` is not + ValueError: If the provided side is invalid or `stem_length` is not a positive integer. """ if side not in ("N", "S", "E", "W"): raise ValueError(f"Invalid side: {side}") - if steam_length <= 0: + if stem_length <= 0: raise ValueError( - "Steam length must be a positive number of cell: received " - f"{steam_length}" + "Stem length must be a positive number of cell: received " + f"{stem_length}" ) river_side = Direction(side) - output = [Movement(steam_length, river_side)] + output = [Movement(stem_length, river_side)] LOGGER.debug( - 'Converting steam length "%s" from side "%s" to stem %s', - steam_length, + 'Converting stem length "%s" from side "%s" to stem %s', + stem_length, side, output, ) @@ -441,7 +441,7 @@ def __init__( ) else: # noinspection PyTypeChecker - river_geometry["stem"] = self._steam_length_to_stem( + river_geometry["stem"] = self._stem_length_to_stem( river_stem["stem_length"], river_geometry["side"] ) del river_stem["stem_length"] From 7de063b1da89e8c575e891a33b37e4459e0bc939 Mon Sep 17 00:00:00 2001 From: Stefano Piani Date: Thu, 12 Mar 2026 15:39:43 +0100 Subject: [PATCH 5/6] Updating pre-commit --- .pre-commit-config.yaml | 4 ++-- src/bathytools/actions/dig_rivers.py | 6 +++--- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index e1be98f..d9b08be 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -13,7 +13,7 @@ repos: args: [--application-directories=.:src] - repo: https://github.com/astral-sh/ruff-pre-commit # Ruff version. - rev: v0.14.9 + rev: v0.15.5 hooks: # Run the linter. - id: ruff @@ -22,7 +22,7 @@ repos: - id: ruff-format args: [--line-length=79] - repo: https://github.com/PyCQA/bandit - rev: '1.9.2' + rev: '1.9.4' hooks: - id: bandit args: ["-c", "bandit.toml"] diff --git a/src/bathytools/actions/dig_rivers.py b/src/bathytools/actions/dig_rivers.py index 9894f2e..8a97eb8 100644 --- a/src/bathytools/actions/dig_rivers.py +++ b/src/bathytools/actions/dig_rivers.py @@ -587,9 +587,9 @@ def read_river_atlas( intervals.append((r_source.lat_indices, r_source.name)) intervals = sorted( intervals, - key=lambda x: x[0].start - if isinstance(x[0], Interval) - else x[0], + key=lambda x: ( + x[0].start if isinstance(x[0], Interval) else x[0] + ), ) for (i1, r1), (i2, r2) in zip(intervals[:-1], intervals[1:]): # Check for overlapping intervals or identical positions. From 91d8e4e739b5d3def447b117b7bc3adb601c0ab4 Mon Sep 17 00:00:00 2001 From: Stefano Piani Date: Thu, 12 Mar 2026 15:53:49 +0100 Subject: [PATCH 6/6] Updated github workflows --- .github/workflows/ci.yml | 6 +++--- .github/workflows/pre-commit.yml | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index b9b0406..b8de505 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -16,13 +16,13 @@ jobs: python-version: ["3.10", "3.12"] steps: - - 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: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v5 + uses: actions/setup-python@v6 with: python-version: ${{ matrix.python-version }} cache: "poetry" diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml index 9acb63a..8a19244 100644 --- a/.github/workflows/pre-commit.yml +++ b/.github/workflows/pre-commit.yml @@ -12,15 +12,15 @@ jobs: timeout-minutes: 5 steps: - name: Clone repo - uses: actions/checkout@v4 + uses: actions/checkout@v6 - name: Install Python - uses: actions/setup-python@v5 + uses: actions/setup-python@v6 with: python-version: "3.12" - name: Install Poetry - run: pipx install poetry==2.0.0 + run: pipx install poetry==2.3.2 - name: Install BathyTools run: poetry install --with dev