From c67389543fded565f8863caa55714a464111ebb2 Mon Sep 17 00:00:00 2001 From: Hidde Elzinga Date: Fri, 31 Jan 2025 16:44:47 +0100 Subject: [PATCH 01/15] update direct dependencies --- poetry.lock | 729 ++++++++++++++++++++++++++----------------------- pyproject.toml | 22 +- 2 files changed, 393 insertions(+), 358 deletions(-) diff --git a/poetry.lock b/poetry.lock index 02e0c671..9bdd0c2e 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand. [[package]] name = "altgraph" @@ -103,13 +103,13 @@ files = [ [[package]] name = "certifi" -version = "2024.8.30" +version = "2025.1.31" description = "Python package for providing Mozilla's CA Bundle." optional = false python-versions = ">=3.6" files = [ - {file = "certifi-2024.8.30-py3-none-any.whl", hash = "sha256:922820b53db7a7257ffbda3f597266d435245903d80737e34f8a45ff3e3230d8"}, - {file = "certifi-2024.8.30.tar.gz", hash = "sha256:bec941d2aa8195e248a60b31ff9f0558284cf01a52591ceda73ea9afffd69fd9"}, + {file = "certifi-2025.1.31-py3-none-any.whl", hash = "sha256:ca78db4565a652026a4db2bcdf68f2fb589ea80d0be70e03929ed730746b84fe"}, + {file = "certifi-2025.1.31.tar.gz", hash = "sha256:3d5da6925056f6f18f119200434a4780a94263f10d1c21d032a6f6b2baa20651"}, ] [[package]] @@ -165,127 +165,114 @@ numpy = [ [[package]] name = "charset-normalizer" -version = "3.4.0" +version = "3.4.1" description = "The Real First Universal Charset Detector. 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+version = "8.3.4" description = "pytest: simple powerful testing with Python" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - {file = "pytest-7.4.4-py3-none-any.whl", hash = "sha256:b090cdf5ed60bf4c45261be03239c2c1c22df034fbffe691abe93cd80cea01d8"}, - {file = "pytest-7.4.4.tar.gz", hash = "sha256:2cf0005922c6ace4a3e2ec8b4080eb0d9753fdc93107415332f50ce9e7994280"}, + {file = "pytest-8.3.4-py3-none-any.whl", hash = "sha256:50e16d954148559c9a74109af1eaf0c945ba2d8f30f0a3d3335edde19788b6f6"}, + {file = "pytest-8.3.4.tar.gz", hash = "sha256:965370d062bce11e73868e0335abac31b4d3de0e82f4007408d242b4f8610761"}, ] [package.dependencies] @@ -1434,11 +1434,11 @@ colorama = {version = "*", markers = "sys_platform == \"win32\""} exceptiongroup = {version = ">=1.0.0rc8", markers = "python_version < \"3.11\""} iniconfig = "*" packaging = "*" -pluggy = ">=0.12,<2.0" -tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""} +pluggy = ">=1.5,<2" +tomli = {version = ">=1", markers = "python_version < \"3.11\""} [package.extras] -testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"] +dev = ["argcomplete", "attrs (>=19.2)", "hypothesis (>=3.56)", "mock", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"] [[package]] name = "pytest-cov" @@ -2118,4 +2118,4 @@ type = ["pytest-mypy"] [metadata] lock-version = "2.0" python-versions = ">=3.9, <=3.13" -content-hash = "180778c12248c450ef2b1451be1e816d2d70c73841db8bd24f52f04922889299" +content-hash = "fb9f596223cb6e7f3d728e155e1a0b942b68e695b6b44e9f842f2cb34f381ba9" diff --git a/pyproject.toml b/pyproject.toml index 9b7df109..4c69f35f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -19,11 +19,11 @@ yaml-include = ">=1.0.0" mkdocs-autoapi = ">=0.3.2" [tool.poetry.group.dev.dependencies] -pytest = "^7.2.0" +pytest = ">=7.2.0" pytest-cov = ">=4.0.0" black = ">=24.4.0" isort = ">=5.11.4" -flake8 = "^6.0.0" +flake8 = ">=6.0.0" pylint = "^2.15.10" mock = ">=5.0.1" mkdocs-material = ">=9.5" From 22e21bbaa2a5bcd9472802e72702106ace1f615f Mon Sep 17 00:00:00 2001 From: Hidde Elzinga Date: Fri, 31 Jan 2025 17:23:52 +0100 Subject: [PATCH 06/15] Update logger_factory.py --- decoimpact/crosscutting/logger_factory.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/decoimpact/crosscutting/logger_factory.py b/decoimpact/crosscutting/logger_factory.py index dcd97510..24eed58a 100644 --- a/decoimpact/crosscutting/logger_factory.py +++ b/decoimpact/crosscutting/logger_factory.py @@ -13,14 +13,14 @@ """ -from decoimpact.crosscutting.logging_logger import LoggingLogger from decoimpact.crosscutting.i_logger import ILogger +from decoimpact.crosscutting.logging_logger import LoggingLogger class LoggerFactory: """Factory for creating loggers""" - @ staticmethod + @staticmethod def create_logger() -> ILogger: """Creates a logger From cb5d15cd28789807285c413bb8b79798a057194d Mon Sep 17 00:00:00 2001 From: Hidde Elzinga Date: Fri, 31 Jan 2025 17:25:14 +0100 Subject: [PATCH 07/15] Update pylint --- poetry.lock | 177 ++++++------------------------------------------- pyproject.toml | 2 +- 2 files changed, 21 insertions(+), 158 deletions(-) diff --git a/poetry.lock b/poetry.lock index 9df9a35b..cd56a8c2 100644 --- a/poetry.lock +++ b/poetry.lock @@ -13,22 +13,17 @@ files = [ [[package]] name = "astroid" -version = "2.15.8" +version = "3.3.8" description = "An abstract syntax tree for Python with inference support." optional = false -python-versions = ">=3.7.2" +python-versions = ">=3.9.0" files = [ - {file = "astroid-2.15.8-py3-none-any.whl", hash = "sha256:1aa149fc5c6589e3d0ece885b4491acd80af4f087baafa3fb5203b113e68cd3c"}, - {file = "astroid-2.15.8.tar.gz", hash = "sha256:6c107453dffee9055899705de3c9ead36e74119cee151e5a9aaf7f0b0e020a6a"}, + {file = "astroid-3.3.8-py3-none-any.whl", hash = "sha256:187ccc0c248bfbba564826c26f070494f7bc964fd286b6d9fff4420e55de828c"}, 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mike = ">=1.1.2" From f7d7e0b57ac88abe9dda5383bfbd500f3708f5d3 Mon Sep 17 00:00:00 2001 From: Hidde Elzinga Date: Fri, 31 Jan 2025 17:29:20 +0100 Subject: [PATCH 08/15] Change new error name --- decoimpact/business/entities/rule_based_model.py | 2 +- decoimpact/business/entities/rules/filter_extremes_rule.py | 4 ++-- decoimpact/data/entities/filter_extremes_rule_data.py | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/decoimpact/business/entities/rule_based_model.py b/decoimpact/business/entities/rule_based_model.py index f3442c47..61f0ea9d 100644 --- a/decoimpact/business/entities/rule_based_model.py +++ b/decoimpact/business/entities/rule_based_model.py @@ -27,7 +27,7 @@ class RuleBasedModel(IModel): """Model class for models based on rules""" - # pylint: disable=too-many-arguments + # pylint: disable=too-many-positional-arguments # pylint: disable=too-many-instance-attributes def __init__( self, diff --git a/decoimpact/business/entities/rules/filter_extremes_rule.py b/decoimpact/business/entities/rules/filter_extremes_rule.py index 9b070161..bd435da1 100644 --- a/decoimpact/business/entities/rules/filter_extremes_rule.py +++ b/decoimpact/business/entities/rules/filter_extremes_rule.py @@ -13,9 +13,9 @@ from typing import List +import numpy as _np import xarray as _xr from scipy import signal -import numpy as _np from decoimpact.business.entities.rules.i_array_based_rule import IArrayBasedRule from decoimpact.business.entities.rules.options.options_filter_extreme_rule import ( @@ -33,7 +33,7 @@ class FilterExtremesRule(RuleBase, IArrayBasedRule): """Implementation for the filter extremes rule""" - # pylint: disable=too-many-arguments + # pylint: disable=too-many-positional-arguments def __init__( self, name: str, diff --git a/decoimpact/data/entities/filter_extremes_rule_data.py b/decoimpact/data/entities/filter_extremes_rule_data.py index 2cffd1c6..bc9cef30 100644 --- a/decoimpact/data/entities/filter_extremes_rule_data.py +++ b/decoimpact/data/entities/filter_extremes_rule_data.py @@ -21,7 +21,7 @@ class FilterExtremesRuleData(IFilterExtremesRuleData, RuleData): """Class for storing data related to filter extremes rule""" - # pylint: disable=too-many-arguments + # pylint: disable=too-many-positional-arguments def __init__( self, name: str, From 4711e15f8f2917d13ebde65e3b1fb03c44f73893 Mon Sep 17 00:00:00 2001 From: Hidde Elzinga Date: Fri, 31 Jan 2025 17:32:46 +0100 Subject: [PATCH 09/15] Fix previous disabled error --- decoimpact/business/entities/rule_based_model.py | 1 + decoimpact/business/entities/rules/filter_extremes_rule.py | 1 + decoimpact/data/entities/filter_extremes_rule_data.py | 1 + 3 files changed, 3 insertions(+) diff --git a/decoimpact/business/entities/rule_based_model.py b/decoimpact/business/entities/rule_based_model.py index 61f0ea9d..644d9a49 100644 --- a/decoimpact/business/entities/rule_based_model.py +++ b/decoimpact/business/entities/rule_based_model.py @@ -27,6 +27,7 @@ class RuleBasedModel(IModel): """Model class for models based on rules""" + # pylint: disable=too-many-arguments # pylint: disable=too-many-positional-arguments # pylint: disable=too-many-instance-attributes def __init__( diff --git a/decoimpact/business/entities/rules/filter_extremes_rule.py b/decoimpact/business/entities/rules/filter_extremes_rule.py index bd435da1..e8b6d280 100644 --- a/decoimpact/business/entities/rules/filter_extremes_rule.py +++ b/decoimpact/business/entities/rules/filter_extremes_rule.py @@ -33,6 +33,7 @@ class FilterExtremesRule(RuleBase, IArrayBasedRule): """Implementation for the filter extremes rule""" + # pylint: disable=too-many-arguments # pylint: disable=too-many-positional-arguments def __init__( self, diff --git a/decoimpact/data/entities/filter_extremes_rule_data.py b/decoimpact/data/entities/filter_extremes_rule_data.py index bc9cef30..381a3c3f 100644 --- a/decoimpact/data/entities/filter_extremes_rule_data.py +++ b/decoimpact/data/entities/filter_extremes_rule_data.py @@ -21,6 +21,7 @@ class FilterExtremesRuleData(IFilterExtremesRuleData, RuleData): """Class for storing data related to filter extremes rule""" + # pylint: disable=too-many-arguments # pylint: disable=too-many-positional-arguments def __init__( self, From e694da42224a73f38ec5ede671c8a8329bf0d180 Mon Sep 17 00:00:00 2001 From: Hidde Elzinga Date: Fri, 14 Feb 2025 15:40:37 +0100 Subject: [PATCH 10/15] Fix pylint errors --- .../entities/rules/rolling_statistics_rule.py | 4 +++- .../criteria_table_validaton_helper.py | 19 ++++++------------- 2 files changed, 9 insertions(+), 14 deletions(-) diff --git a/decoimpact/business/entities/rules/rolling_statistics_rule.py b/decoimpact/business/entities/rules/rolling_statistics_rule.py index f0078dbb..ba1b5650 100644 --- a/decoimpact/business/entities/rules/rolling_statistics_rule.py +++ b/decoimpact/business/entities/rules/rolling_statistics_rule.py @@ -123,7 +123,9 @@ def _perform_operation( elif time_scale == "D": operation_time_delta = _dt.timedelta(days=self._period) else: - logger.log_error(f"Invalid time scale provided : '{time_scale}'.") + error_message = f"Invalid time scale provided : '{time_scale}'." + logger.log_error(error_message) + raise ValueError(error_message) time_delta_ms = _np.array([operation_time_delta], dtype="timedelta64[ms]")[0] last_timestamp = values.time.isel(time=-1).values diff --git a/decoimpact/data/parsers/criteria_table_validaton_helper.py b/decoimpact/data/parsers/criteria_table_validaton_helper.py index b4a07e98..a5f0d6b1 100644 --- a/decoimpact/data/parsers/criteria_table_validaton_helper.py +++ b/decoimpact/data/parsers/criteria_table_validaton_helper.py @@ -172,16 +172,14 @@ def _divide_table_in_unique_chunks( conditions[key] = unique_c # Send the remaining filtered parameters back into the function - for message in _divide_table_in_unique_chunks( + yield from _divide_table_in_unique_chunks( new_crit_table, logger, conditions - ): - yield message + ) else: # If there is only one variable, check on all conditions for coverage name, criteria = list(criteria_table.items())[0] - for message in _check_variable_conditions(name, criteria, conditions, unique): - yield message + yield from _check_variable_conditions(name, criteria, conditions, unique) def _check_variable_conditions( @@ -201,8 +199,7 @@ def _check_variable_conditions( criteria = _np.unique(criteria) # WHen there is only one parameter left in the given table () - for message in _validate_criteria_on_overlap_and_gaps(name, criteria, cond_str): - yield message + yield from _validate_criteria_on_overlap_and_gaps(name, criteria, cond_str) def _convert_to_range(val: Any) -> _Range: @@ -264,10 +261,7 @@ def _validate_criteria_on_overlap_and_gaps( # Check if there are multiple larger or larger and equal comparison values are # present, this will cause overlap - for message in _check_for_multiple_inf_values( - name, pre_warn, sorted_range_criteria - ): - yield message + yield from _check_for_multiple_inf_values(name, pre_warn, sorted_range_criteria) if len(sorted_range_criteria) > 0 and ( sorted_range_criteria[0].start != float("-inf") @@ -279,8 +273,7 @@ def _validate_criteria_on_overlap_and_gaps( "Gap", ) - for message in _check_ranges(name, pre_warn, sorted_range_criteria): - yield message + yield from _check_ranges(name, pre_warn, sorted_range_criteria) # Create the final check over the not_covered_values and the covered_numbers # Send warning with the combined messages From 32a8a34c56eadaf4f41ce4d88a153696a074dc88 Mon Sep 17 00:00:00 2001 From: Hidde Elzinga Date: Fri, 14 Feb 2025 15:54:39 +0100 Subject: [PATCH 11/15] Update to latest packages --- poetry.lock | 444 +++++++++++++++++++++++++------------------------ pyproject.toml | 4 +- 2 files changed, 231 insertions(+), 217 deletions(-) diff --git a/poetry.lock 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"opt-einsum", "scipy"] -complete = ["xarray[accel,dev,io,parallel,viz]"] -dev = ["hypothesis", "mypy", "pre-commit", "pytest", "pytest-cov", "pytest-env", "pytest-timeout", "pytest-xdist", "ruff", "xarray[complete]"] +accel = ["bottleneck", "flox", "numba (>=0.54)", "numbagg", "opt_einsum", "scipy"] +complete = ["xarray[accel,etc,io,parallel,viz]"] +dev = ["hypothesis", "jinja2", "mypy", "pre-commit", "pytest", "pytest-cov", "pytest-env", "pytest-timeout", "pytest-xdist", "ruff (>=0.8.0)", "sphinx", "sphinx_autosummary_accessors", "xarray[complete]"] +etc = ["sparse"] io = ["cftime", "fsspec", "h5netcdf", "netCDF4", "pooch", "pydap", "scipy", "zarr"] parallel = ["dask[complete]"] -viz = ["matplotlib", "nc-time-axis", "seaborn"] +viz = ["cartopy", "matplotlib", "nc-time-axis", "seaborn"] [[package]] name = "yaml-include" @@ -1980,5 +1994,5 @@ type = ["pytest-mypy"] [metadata] lock-version = "2.0" -python-versions = ">=3.9, <=3.13" -content-hash = "90196de8d7466dd9f078e2b3088d4946160807b5e83028fa55ecbac77ee190ab" +python-versions = ">=3.10, <=3.13" +content-hash = "cd16fd1b5ff878b3d80998838d08e4a21fda72335644152c76fa501f78ea70b3" diff --git a/pyproject.toml b/pyproject.toml index 65569938..6214554b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,8 +6,8 @@ authors = ["Deltares"] readme = "README.md" [tool.poetry.dependencies] -python = ">=3.9, <=3.13" # max 3.13 because of pyinstaller -numpy = ">=1.26" +python = ">=3.10, <=3.13" # max 3.13 because of pyinstaller +numpy = ">=2.0" xarray = ">=2024.6.0" scipy = ">=1.13.0" netcdf4 = ">=1.7" From 712ee49374da1a270017d912f4fb2927f775a5f7 Mon Sep 17 00:00:00 2001 From: Hidde Elzinga Date: Fri, 14 Feb 2025 16:08:07 +0100 Subject: [PATCH 12/15] Fixed unit --- decoimpact/business/utils/data_array_utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/decoimpact/business/utils/data_array_utils.py b/decoimpact/business/utils/data_array_utils.py index 249c6752..321a4b0a 100644 --- a/decoimpact/business/utils/data_array_utils.py +++ b/decoimpact/business/utils/data_array_utils.py @@ -26,7 +26,7 @@ def get_time_dimension_name(variable: _xr.DataArray, logger: ILogger) -> str: for dim in variable.dims: dim_values = variable[dim] - if dim_values.dtype.name == "datetime64[ns]": + if dim_values.dtype.name == "datetime64[s]": return str(dim) message = f"No time dimension found for {variable.name}" From 19c532a2232d37872164755e78d3cbc6ce5a4ceb Mon Sep 17 00:00:00 2001 From: Hidde Elzinga Date: Mon, 17 Feb 2025 17:39:22 +0100 Subject: [PATCH 13/15] Fixed documentation generation --- decoimpact/business/utils/data_array_utils.py | 7 ++++++- scripts/create_nc.py | 2 +- 2 files changed, 7 insertions(+), 2 deletions(-) diff --git a/decoimpact/business/utils/data_array_utils.py b/decoimpact/business/utils/data_array_utils.py index 321a4b0a..ec770ad9 100644 --- a/decoimpact/business/utils/data_array_utils.py +++ b/decoimpact/business/utils/data_array_utils.py @@ -26,7 +26,12 @@ def get_time_dimension_name(variable: _xr.DataArray, logger: ILogger) -> str: for dim in variable.dims: dim_values = variable[dim] - if dim_values.dtype.name == "datetime64[s]": + + # check if the dimension type is a datetime type + if ( + dim_values.dtype.name == "datetime64[ns]" + or dim_values.dtype.name == "datetime64[s]" + ): return str(dim) message = f"No time dimension found for {variable.name}" diff --git a/scripts/create_nc.py b/scripts/create_nc.py index bb247bb5..1019bcfa 100644 --- a/scripts/create_nc.py +++ b/scripts/create_nc.py @@ -38,7 +38,7 @@ data_variable_B[:, :, 0] = np.array([11, 11, 11]) data_variable_B[:, :, 1] = np.array([14, 14, 14]) data_variable_B[:, :, 2] = np.array([19, 19, 19]) -data_variable_B[:, 1, 2] = np.array([np.NaN]) +data_variable_B[:, 1, 2] = np.array([np.nan]) data_variable_C[:, :, 0] = np.array([11, 11, 11]) data_variable_C[:, :, 1] = np.array([14, 14, 14]) From 682f5275afdda11a644dd961c0574881b0384918 Mon Sep 17 00:00:00 2001 From: Hidde Elzinga Date: Mon, 17 Feb 2025 17:42:45 +0100 Subject: [PATCH 14/15] Fix pylint warning --- decoimpact/business/utils/data_array_utils.py | 75 +++++++++---------- 1 file changed, 36 insertions(+), 39 deletions(-) diff --git a/decoimpact/business/utils/data_array_utils.py b/decoimpact/business/utils/data_array_utils.py index ec770ad9..849774a8 100644 --- a/decoimpact/business/utils/data_array_utils.py +++ b/decoimpact/business/utils/data_array_utils.py @@ -1,39 +1,36 @@ -# This file is part of D-EcoImpact -# Copyright (C) 2022-2024 Stichting Deltares -# This program is free software distributed under the -# GNU Affero General Public License version 3.0 -# A copy of the GNU Affero General Public License can be found at -# https://github.com/Deltares/D-EcoImpact/blob/main/LICENSE.md -"""Library for utility functions regarding an xarray data-arrays""" - -import xarray as _xr - -from decoimpact.crosscutting.i_logger import ILogger - - -def get_time_dimension_name(variable: _xr.DataArray, logger: ILogger) -> str: - """Retrieves the dimension name - - Args: - value_array (DataArray): values to get time dimension - - Raises: - ValueError: If time dimension could not be found - - Returns: - str: time dimension name - """ - - for dim in variable.dims: - dim_values = variable[dim] - - # check if the dimension type is a datetime type - if ( - dim_values.dtype.name == "datetime64[ns]" - or dim_values.dtype.name == "datetime64[s]" - ): - return str(dim) - - message = f"No time dimension found for {variable.name}" - logger.log_error(message) - raise ValueError(message) +# This file is part of D-EcoImpact +# Copyright (C) 2022-2024 Stichting Deltares +# This program is free software distributed under the +# GNU Affero General Public License version 3.0 +# A copy of the GNU Affero General Public License can be found at +# https://github.com/Deltares/D-EcoImpact/blob/main/LICENSE.md +"""Library for utility functions regarding an xarray data-arrays""" + +import xarray as _xr + +from decoimpact.crosscutting.i_logger import ILogger + + +def get_time_dimension_name(variable: _xr.DataArray, logger: ILogger) -> str: + """Retrieves the dimension name + + Args: + value_array (DataArray): values to get time dimension + + Raises: + ValueError: If time dimension could not be found + + Returns: + str: time dimension name + """ + + for dim in variable.dims: + dim_values = variable[dim] + + # check if the dimension type is a datetime type + if dim_values.dtype.name in ("datetime64[ns]", "datetime64[s]"): + return str(dim) + + message = f"No time dimension found for {variable.name}" + logger.log_error(message) + raise ValueError(message) From d1671799a4f9310ba39a94551f6367ee91c1c4b1 Mon Sep 17 00:00:00 2001 From: Hidde Elzinga Date: Tue, 18 Feb 2025 11:00:38 +0100 Subject: [PATCH 15/15] Improve check --- decoimpact/business/utils/data_array_utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/decoimpact/business/utils/data_array_utils.py b/decoimpact/business/utils/data_array_utils.py index 849774a8..db14ee8b 100644 --- a/decoimpact/business/utils/data_array_utils.py +++ b/decoimpact/business/utils/data_array_utils.py @@ -28,7 +28,7 @@ def get_time_dimension_name(variable: _xr.DataArray, logger: ILogger) -> str: dim_values = variable[dim] # check if the dimension type is a datetime type - if dim_values.dtype.name in ("datetime64[ns]", "datetime64[s]"): + if dim_values.dtype.name.startswith("datetime64"): return str(dim) message = f"No time dimension found for {variable.name}"