diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..83c06d9 --- /dev/null +++ b/.gitattributes @@ -0,0 +1,4 @@ +* text=auto eol=lf + +# GitHub syntax highlighting +pixi.lock linguist-language=YAML diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 0000000..700707c --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,7 @@ +# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates +version: 2 +updates: + - package-ecosystem: "github-actions" + directory: "/" # Location of package manifests + schedule: + interval: "weekly" diff --git a/.github/workflows/pre-commit_auto_update.yml b/.github/workflows/pre-commit_auto_update.yml new file mode 100644 index 0000000..bfe8f06 --- /dev/null +++ b/.github/workflows/pre-commit_auto_update.yml @@ -0,0 +1,28 @@ +name: Pre-commit + +on: + schedule: + # At 03:00 on day 1 of the month + - cron: "0 3 1 * *" + # on demand + workflow_dispatch: + +jobs: + auto-update: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + with: + ssh-key: ${{ secrets.SSH_PRIVATE_KEY }} + - uses: actions/setup-python@v4 + with: + python-version: "3.11" + - uses: browniebroke/pre-commit-autoupdate-action@main + - uses: peter-evans/create-pull-request@v5 + with: + token: ${{ secrets.GITHUB_TOKEN }} + branch: update/pre-commit-hooks + title: Update pre-commit hooks + commit-message: "Update pre-commit hooks" + body: Update versions of pre-commit hooks to latest version. + author: "GitHub " diff --git a/.github/workflows/pre-commit_check.yml b/.github/workflows/pre-commit_check.yml new file mode 100644 index 0000000..2876b91 --- /dev/null +++ b/.github/workflows/pre-commit_check.yml @@ -0,0 +1,17 @@ +name: Pre-commit + +on: + pull_request: + merge_group: + push: + branches: [main, update/pre-commit-hooks] + +jobs: + check: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - uses: actions/setup-python@v4 + with: + python-version: "3.11" + - uses: pre-commit/action@v3.0.0 diff --git a/.github/workflows/python_lint.yml b/.github/workflows/python_lint.yml new file mode 100644 index 0000000..fb140e3 --- /dev/null +++ b/.github/workflows/python_lint.yml @@ -0,0 +1,27 @@ +name: Python Lint +on: + push: + branches: [main] + paths-ignore: [".teamcity/**"] + tags: ["*"] + pull_request: + merge_group: +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true +jobs: + mypy: + name: Mypy + runs-on: ubuntu-latest + continue-on-error: true + steps: + - uses: actions/checkout@v4 + - uses: prefix-dev/setup-pixi@v0.2.1 + with: + pixi-version: "latest" + cache: true + - name: Prepare pixi + run: pixi run install-without-pre-commit + - name: Run mypy on hydamo + run: | + pixi run mypy-hydamo diff --git a/.github/workflows/python_tests.yml b/.github/workflows/python_tests.yml new file mode 100644 index 0000000..927d751 --- /dev/null +++ b/.github/workflows/python_tests.yml @@ -0,0 +1,39 @@ +name: Python Tests +on: + push: + branches: [main] + paths-ignore: [".teamcity/**"] + tags: ["*"] + pull_request: + merge_group: +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true +jobs: + test: + name: Python ${{ matrix.os }} - ${{ matrix.arch }} + runs-on: ${{ matrix.os }} + strategy: + fail-fast: false + matrix: + os: + - ubuntu-latest + - macOS-latest + - windows-latest + arch: + - x86 + steps: + - uses: actions/checkout@v4 + + - uses: prefix-dev/setup-pixi@v0.2.1 + with: + pixi-version: "latest" + cache: true + - name: Prepare pixi + run: pixi run install-without-pre-commit + + - name: Run tests + run: pixi run test-hydamo + + - name: Upload coverage to Codecov + uses: codecov/codecov-action@v3 diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..b19e4da --- /dev/null +++ b/.gitignore @@ -0,0 +1,21 @@ +# pixi environments +.pixi + +# visual studio code +.vscode/settings.json + +.ipynb_checkpoints +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class +htmlcov/ +coverage.xml +.coverage +.coverage.* +.pytest_cache/ + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..08e765a --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,37 @@ +repos: + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.4.0 + hooks: + - id: check-added-large-files + - id: check-case-conflict + - id: check-json + - id: check-yaml + - id: check-toml + - id: check-merge-conflict + - id: check-vcs-permalinks + - + id: end-of-file-fixer + exclude: '.teamcity' + - id: trailing-whitespace + - repo: https://github.com/astral-sh/ruff-pre-commit + rev: v0.0.291 + hooks: + - id: ruff + args: [--fix, --exit-non-zero-on-fix] + - repo: https://github.com/psf/black + rev: 23.9.1 + hooks: + - id: black + - id: black-jupyter + - repo: https://github.com/kynan/nbstripout + rev: 0.6.1 + hooks: + - id: nbstripout + - repo: https://github.com/crate-ci/typos + rev: v1.16.17 + hooks: + - id: typos + # use pass_filenames as a workaround such that + # the excluded files in .typos.toml are respected + # https://github.com/crate-ci/typos/issues/347 + pass_filenames: false diff --git a/.typos.toml b/.typos.toml new file mode 100644 index 0000000..d6baf54 --- /dev/null +++ b/.typos.toml @@ -0,0 +1,2 @@ +[files] +extend-exclude = ["*.csv", "*.json"] diff --git a/.vscode/extensions.json b/.vscode/extensions.json new file mode 100644 index 0000000..4dcdeba --- /dev/null +++ b/.vscode/extensions.json @@ -0,0 +1,9 @@ +{ + "recommendations": [ + "ms-python.python", + "ms-python.black-formatter", + "ms-python.mypy-type-checker", + "charliermarsh.ruff", + "njpwerner.autodocstring" + ] +} diff --git a/.vscode/settings_template.json b/.vscode/settings_template.json new file mode 100644 index 0000000..79f8f81 --- /dev/null +++ b/.vscode/settings_template.json @@ -0,0 +1,10 @@ +{ + "notebook.formatOnSave.enabled": true, + "[python]": { + "editor.defaultFormatter": "ms-python.black-formatter", + "editor.formatOnSave": true, + "editor.codeActionsOnSave": { + "source.fixAll": true + } + } +} diff --git a/LICENSE b/LICENSE index a9d5aae..81a6cf2 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) 2023 Stichting Deltares +Copyright (c) Ribasim-NL developers Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/codecov.yml b/codecov.yml new file mode 100644 index 0000000..5212f75 --- /dev/null +++ b/codecov.yml @@ -0,0 +1,9 @@ +coverage: + status: + patch: + default: + informational: true + + project: + default: + informational: true diff --git a/mypy.ini b/mypy.ini new file mode 100644 index 0000000..2dbb974 --- /dev/null +++ b/mypy.ini @@ -0,0 +1,11 @@ +[mypy] +plugins = pydantic.mypy, numpy.typing.mypy_plugin, pandera.mypy + 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license_family: BSD + size: 343428 + timestamp: 1693151615801 +version: 1 diff --git a/pixi.toml b/pixi.toml new file mode 100644 index 0000000..d99048f --- /dev/null +++ b/pixi.toml @@ -0,0 +1,63 @@ +[project] +name = "Ribasim-NL" +version = "0.1.0" +description = "Ribasim water resources modeling in the Netherlands" +channels = ["conda-forge"] +platforms = ["win-64", "linux-64", "osx-64"] +readme = "README.md" +license = "MIT" +license-file = "LICENSE" + +[tasks] +# Installation +install-ribasim-python = "pip install --no-deps ribasim==0.4.0" +install-hydamo = "pip install --no-deps --editable src/hydamo" +install-quartodoc = "pip install quartodoc" +install-pre-commit = "pre-commit install" +install-without-pre-commit = { depends_on = [ + "install-ribasim-python", + "install-hydamo", + "install-quartodoc", +] } +install = { depends_on = [ + "install-without-pre-commit", + "install-pre-commit", +] } +# Lint +mypy-hydamo = "mypy --ignore-missing-imports src/hydamo" +pre-commit = "pre-commit run --all-files" +lint = { depends_on = [ + "pre-commit", + "mypy-hydamo", +] } +# Test +test-hydamo = "pytest --numprocesses=auto src/hydamo/tests" +test-hydamo-cov = "pytest --numprocesses=auto --cov=hydamo --cov-report=xml src/hydamo/tests" +tests = { depends_on = [ + "lint", + "test-hydamo", +] } + +[dependencies] +python = ">=3.9" +pandas = "<2.1" +geopandas = "0.14.0.*" +fiona = "1.9.4.*" +tomli = "2.0.1.*" +shapely = ">=2" +pydantic = "~=1.0" +pandera = "!=0.16.0" +pyarrow = "13.0.0.*" +pyogrio = "0.6.0.*" +tomli-w = "1.0.0.*" +matplotlib = "3.8.0.*" +# dev +ruff = "0.0.292.*" +black = "23.9.1.*" +pytest = "7.4.2.*" +pytest-cov = "4.1.0.*" +pytest-xdist = "3.3.1.*" +pip = "23.2.1.*" +pre-commit = "3.4.0.*" +ipykernel = "6.25.2.*" +mypy = "1.5.1.*" diff --git a/ruff.toml b/ruff.toml new file mode 100644 index 0000000..20e78ea --- /dev/null +++ b/ruff.toml @@ -0,0 +1,6 @@ +select = ["D", "E", "F", "NPY", "PD", "C4", "I"] +ignore = ["D1", "D202", "D205", "D400", "D404", "E501", "PD002", "PD901"] +fixable = ["I"] + +[pydocstyle] +convention = "numpy" diff --git a/src/hydamo/.gitignore b/src/hydamo/.gitignore index beca089..7e48ac8 100644 --- a/src/hydamo/.gitignore +++ b/src/hydamo/.gitignore @@ -133,4 +133,4 @@ dmypy.json # Windows command-files *.cmd -*.bat \ No newline at end of file +*.bat diff --git a/src/hydamo/README.md b/src/hydamo/README.md index 69746fa..be21554 100644 --- a/src/hydamo/README.md +++ b/src/hydamo/README.md @@ -4,7 +4,7 @@ Module to work with the Dutch Hydrological Data Model (HyDAMO). The original cla ## Install a copy - Get a local clone of this repository. - Build an environment as in [environment](./environment.yml). -- Mak sure your environment is activated +- Make sure your environment is activated - Go to the root of your repository (where you find setup.py) and install the package in edit-mode by: ``` @@ -39,4 +39,4 @@ Finally you can write the entire model into one GeoPackage by calling the `to_ge ``` hydamo.to_geopackage("hydamo.gpkg") -``` \ No newline at end of file +``` diff --git a/src/hydamo/hydamo/__init__.py b/src/hydamo/hydamo/__init__.py index b8d7c92..c2f4192 100644 --- a/src/hydamo/hydamo/__init__.py +++ b/src/hydamo/hydamo/__init__.py @@ -1,4 +1,16 @@ __version__ = "0.1.0" -from hydamo.datamodel import HyDAMO -#from hydamo.styles import get_layer_styles \ No newline at end of file +from hydamo.datamodel import ExtendedGeoDataFrame, HyDAMO +from hydamo.geometry import find_nearest_branch, possibly_intersecting +from hydamo.styles import add_styles_to_geopackage, read_style +from hydamo.utils import find_bgt_code + +__all__ = [ + "HyDAMO", + "ExtendedGeoDataFrame", + "find_nearest_branch", + "possibly_intersecting", + "add_styles_to_geopackage", + "read_style", + "find_bgt_code", +] diff --git a/src/hydamo/hydamo/data/schemas/HyDAMO_2.2.1.json b/src/hydamo/hydamo/data/schemas/HyDAMO_2.2.1.json index 21e792a..29368a8 100644 --- a/src/hydamo/hydamo/data/schemas/HyDAMO_2.2.1.json +++ b/src/hydamo/hydamo/data/schemas/HyDAMO_2.2.1.json @@ -6600,4 +6600,4 @@ } } } -} \ No newline at end of file +} diff --git a/src/hydamo/hydamo/data/schemas/HyDAMO_2.2.json b/src/hydamo/hydamo/data/schemas/HyDAMO_2.2.json index c5e7eb1..c83cd2b 100644 --- a/src/hydamo/hydamo/data/schemas/HyDAMO_2.2.json +++ b/src/hydamo/hydamo/data/schemas/HyDAMO_2.2.json @@ -56,7 +56,7 @@ }, "definitions": { - "admingrenswaterschap" : + "admingrenswaterschap" : { "type": "object", "properties": @@ -165,7 +165,7 @@ } } }, - "afsluitmiddel" : + "afsluitmiddel" : { "type": "object", "properties": @@ -407,14 +407,14 @@ } } }, - "afvoeraanvoergebied" : + "afvoeraanvoergebied" : { "type": "object", "properties": { } }, - "afvoergebiedaanvoergebied" : + "afvoergebiedaanvoergebied" : { "type": "object", "properties": @@ -586,7 +586,7 @@ } } }, - "aquaduct" : + "aquaduct" : { "type": "object", "properties": @@ -768,7 +768,7 @@ } } }, - "beheergrenswaterschap" : + "beheergrenswaterschap" : { "type": "object", "properties": @@ -877,7 +877,7 @@ } } }, - "bijzonderhydraulischobject" : + "bijzonderhydraulischobject" : { "type": "object", "properties": @@ -996,7 +996,7 @@ } } }, - "bodemval" : + "bodemval" : { "type": "object", "properties": @@ -1141,7 +1141,7 @@ } } }, - "brug" : + "brug" : { "type": "object", "properties": @@ -1348,7 +1348,7 @@ } } }, - "doorstroomopening" : + "doorstroomopening" : { "type": "object", "properties": @@ -1425,7 +1425,7 @@ } } }, - "duikersifonhevel" : + "duikersifonhevel" : { "type": "object", "properties": @@ -1736,7 +1736,7 @@ } } }, - "gemaal" : + "gemaal" : { "type": "object", "properties": @@ -1986,7 +1986,7 @@ } } }, - "grondwaterinfolijn" : + "grondwaterinfolijn" : { "type": "object", "properties": @@ -2098,7 +2098,7 @@ } } }, - "grondwaterinfopunt" : + "grondwaterinfopunt" : { "type": "object", "properties": @@ -2176,7 +2176,7 @@ } } }, - "grondwaterkoppellijn" : + "grondwaterkoppellijn" : { "type": "object", "properties": @@ -2288,7 +2288,7 @@ } } }, - "grondwaterkoppelpunt" : + "grondwaterkoppelpunt" : { "type": "object", "properties": @@ -2400,7 +2400,7 @@ } } }, - "hydrologischerandvoorwaarde" : + "hydrologischerandvoorwaarde" : { "type": "object", "properties": @@ -2525,7 +2525,7 @@ } } }, - "hydroobject" : + "hydroobject" : { "type": "object", "properties": @@ -2771,7 +2771,7 @@ } } }, - "hydroobject_normgp" : + "hydroobject_normgp" : { "type": "object", "properties": @@ -2796,14 +2796,14 @@ } } }, - "imwa_geoobject" : + "imwa_geoobject" : { "type": "object", "properties": { } }, - "kunstwerkopening" : + "kunstwerkopening" : { "type": "object", "properties": @@ -2930,7 +2930,7 @@ } } }, - "lateraleknoop" : + "lateraleknoop" : { "type": "object", "properties": @@ -3042,21 +3042,21 @@ } } }, - "leggerwatersysteem" : + "leggerwatersysteem" : { "type": "object", "properties": { } }, - "leggerwaterveiligheid" : + "leggerwaterveiligheid" : { "type": "object", "properties": { } }, - "meetlocatie" : + "meetlocatie" : { "type": "object", "properties": @@ -3188,7 +3188,7 @@ } } }, - "meetwaardeactiewaarde" : + "meetwaardeactiewaarde" : { "type": "object", "properties": @@ -3284,7 +3284,7 @@ } } }, - "normgeparamprofiel" : + "normgeparamprofiel" : { "type": "object", "properties": @@ -3358,7 +3358,7 @@ } } }, - "normgeparamprofielwaarde" : + "normgeparamprofielwaarde" : { "type": "object", "properties": @@ -3452,7 +3452,7 @@ } } }, - "peilafwijkinggebied" : + "peilafwijkinggebied" : { "type": "object", "properties": @@ -3582,7 +3582,7 @@ } } }, - "peilbesluitgebied" : + "peilbesluitgebied" : { "type": "object", "properties": @@ -3693,7 +3693,7 @@ } } }, - "peilgebiedpraktijk" : + "peilgebiedpraktijk" : { "type": "object", "properties": @@ -3823,7 +3823,7 @@ } } }, - "peilgebiedvigerend" : + "peilgebiedvigerend" : { "type": "object", "properties": @@ -3948,7 +3948,7 @@ } } }, - "pomp" : + "pomp" : { "type": "object", "properties": @@ -4072,7 +4072,7 @@ } } }, - "profielgroep" : + "profielgroep" : { "type": "object", "properties": @@ -4195,7 +4195,7 @@ } } }, - "profiellijn" : + "profiellijn" : { "type": "object", "properties": @@ -4309,7 +4309,7 @@ } } }, - "profielpunt" : + "profielpunt" : { "type": "object", "properties": @@ -4417,7 +4417,7 @@ } } }, - "regelmiddel" : + "regelmiddel" : { "type": "object", "properties": @@ -4626,7 +4626,7 @@ } } }, - "reglementgrenswaterschap" : + "reglementgrenswaterschap" : { "type": "object", "properties": @@ -4747,7 +4747,7 @@ } } }, - "ruwheidprofiel" : + "ruwheidprofiel" : { "type": "object", "properties": @@ -4822,7 +4822,7 @@ } } }, - "streefpeil" : + "streefpeil" : { "type": "object", "properties": @@ -4929,7 +4929,7 @@ } } }, - "sturing" : + "sturing" : { "type": "object", "properties": @@ -5098,7 +5098,7 @@ } } }, - "stuw" : + "stuw" : { "type": "object", "properties": @@ -5386,7 +5386,7 @@ } } }, - "vispassage" : + "vispassage" : { "type": "object", "properties": @@ -5596,7 +5596,7 @@ } } }, - "vispassagevlak" : + "vispassagevlak" : { "type": "object", "properties": @@ -5659,7 +5659,7 @@ } } }, - "vuilvang" : + "vuilvang" : { "type": "object", "properties": @@ -5806,14 +5806,14 @@ } } }, - "waterbeheergebied" : + "waterbeheergebied" : { "type": "object", "properties": { } }, - "zandvang" : + "zandvang" : { "type": "object", "properties": diff --git a/src/hydamo/hydamo/datamodel.py b/src/hydamo/hydamo/datamodel.py index ea1c50c..34eb008 100644 --- a/src/hydamo/hydamo/datamodel.py +++ b/src/hydamo/hydamo/datamodel.py @@ -1,15 +1,17 @@ """HyDAMO datamodel for ValidatieTool.""" -import geopandas as gpd -import fiona -from typing import List, Dict, Literal -import re import json -from shapely.geometry import LineString, MultiLineString, Point, Polygon, MultiPolygon -import numpy as np -from pathlib import Path -import warnings import logging +import re +import warnings +from pathlib import Path +from typing import Any, Dict, List, Literal, Optional + +import fiona +import geopandas as gpd +import numpy as np +from shapely.geometry import LineString, MultiLineString, MultiPolygon, Point, Polygon + from hydamo import geometry from hydamo.styles import add_styles_to_geopackage @@ -38,17 +40,22 @@ "number": "float", } -default_properties = {"id": None, "dtype": "str", "required": False, "unique": False} +default_properties: Dict[str, Any] = { + "id": None, + "dtype": "str", + "required": False, + "unique": False, +} -def map_definition(definition: Dict) -> List: +def map_definition(definition: Dict[str, Any]) -> List[Dict[str, Any]]: """ Parameters ---------- definition : Dict - HyDAMO defintion as specified in the HyDAMO JSON specification. + HyDAMO definition as specified in the HyDAMO JSON specification. Returns ------- @@ -63,7 +70,7 @@ def map_definition(definition: Dict) -> List: for k, v in definition.items(): # convert geometry if shape if k == "shape": - properties = {"id": "geometry"} + properties: Dict[str, Any] = {"id": "geometry"} dtype = v["type"] if not isinstance(dtype, list): dtype = [dtype] @@ -96,22 +103,38 @@ def map_definition(definition: Dict) -> List: return result -class ExtendedGeoDataFrame(gpd.GeoDataFrame): +class ExtendedGeoDataFrame(gpd.GeoDataFrame): # type: ignore """A GeoPandas GeoDataFrame with extended properties and methods.""" - _metadata = ["required_columns", "geotype", "layer_name"] + gpd.GeoDataFrame._metadata + # ignores subclassing Any: https://github.com/geopandas/geopandas/discussions/2750 + + _metadata = [ + "required_columns", + "geotype", + "layer_name", + ] + gpd.GeoDataFrame._metadata def __init__( self, - validation_schema: Dict, - geotype: Literal[list(GEOTYPE_MAPPING.keys())], + validation_schema: List[Dict[str, Any]], + geotype: Optional[ + List[ + Literal[ + "LineString", + "MultiLineString", + "Point", + "PointZ", + "Polygon", + "MultiPolygon", + ] + ] + ], layer_name: str = "", - required_columns: List = [], + required_columns: List[str] = [], logger=logging, *args, **kwargs, ): - # Check type required_columns = [i.lower() for i in required_columns] @@ -131,13 +154,11 @@ def __init__( if "geometry" in self.columns: self.set_geometry("geometry", inplace=True) self.crs = MODEL_CRS - if not "geometry" in self.required_columns: + if "geometry" not in self.required_columns: self.required_columns += ["geometry"] def _check_columns(self, gdf): - """ - Check presence of columns in GeoDataFrame - """ + """Check presence of columns in GeoDataFrame""" present_columns = gdf.columns.tolist() for column in self.required_columns: if column not in present_columns: @@ -150,9 +171,7 @@ def _check_columns(self, gdf): ) def _check_geotype(self): - """ - Check geometry type - """ + """Check geometry type""" if self.geotype: if not all( any(isinstance(geo, GEOTYPE_MAPPING[i]) for i in self.geotype) @@ -176,9 +195,17 @@ def _get_schema(self): (i["dtype"] for i in self.validation_schema if i["id"] == "geometry"), None, ) - return dict(properties=properties, geometry=geometry) + return {properties: properties, geometry: geometry} - def set_data(self, gdf, layer="", index_col=None, check_columns=True, check_geotype=True, extra_attributes={}): + def set_data( + self, + gdf, + layer="", + index_col=None, + check_columns=True, + check_geotype=True, + extra_attributes={}, + ): """ @@ -217,7 +244,7 @@ def set_data(self, gdf, layer="", index_col=None, check_columns=True, check_geot # Copy content for col, values in gdf.items(): - self[col] = values.values + self[col] = values.to_numpy() if index_col is None: self.index = gdf.index @@ -230,16 +257,14 @@ def set_data(self, gdf, layer="", index_col=None, check_columns=True, check_geot # Check geometry types if check_geotype: self._check_geotype() - + # Set extra attribute-values - for k,v in extra_attributes.items(): + for k, v in extra_attributes.items(): if k not in self.columns: self[k] = v def delete_all(self): - """ - Empty the dataframe - """ + """Empty the dataframe""" if not self.empty: self.iloc[:, 0] = np.nan self.dropna(inplace=True) @@ -276,7 +301,7 @@ def __init__( self, version: str = "2.2", schemas_path: Path = SCHEMAS_DIR, - ignored_layers: List = [ + ignored_layers: List[str] = [ "afvoeraanvoergebied", "imwa_geoobject", "leggerwatersysteem", @@ -286,7 +311,7 @@ def __init__( ): self.version = version self.schema_json = schemas_path.joinpath(f"HyDAMO_{version}.json") - self.layers = [] + self.layers: List[str] = [] self.ignored_layers = ignored_layers self.init_datamodel() @@ -295,9 +320,9 @@ def __init__( def data_layers(self): return [layer for layer in self.layers if not getattr(self, layer).empty] - def init_datamodel(self): + def init_datamodel(self) -> None: """Initialize DataModel from self.schemas_path.""" - self.validation_schemas: dict = {} + self.validation_schemas: Dict[str, Any] = {} # read schema as dict with open(self.schema_json) as src: @@ -305,7 +330,7 @@ def init_datamodel(self): hydamo_layers = [ Path(i["$ref"]).name for i in schema["properties"]["HyDAMO"]["anyOf"] ] - self.layers = [i for i in hydamo_layers if not i in self.ignored_layers] + self.layers = [i for i in hydamo_layers if i not in self.ignored_layers] for hydamo_layer in self.layers: definition = schema["definitions"][hydamo_layer]["properties"] @@ -351,11 +376,16 @@ def get(self, layer: str, global_id: str): DESCRIPTION. """ - return getattr(self,layer).set_index("globalid").loc[global_id] + return getattr(self, layer).set_index("globalid").loc[global_id] def set_data( - self, gdf, layer, index_col=None, check_columns=True, check_geotype=True, - extra_values={} + self, + gdf, + layer, + index_col=None, + check_columns=True, + check_geotype=True, + extra_values={}, ): """ @@ -385,7 +415,7 @@ def set_data( index_col=index_col, check_columns=check_columns, check_geotype=check_geotype, - extra_values={} + extra_values={}, ) def to_geopackage(self, file_path, use_schema=True): @@ -403,7 +433,7 @@ def to_geopackage(self, file_path, use_schema=True): None. """ - + file_path = Path(file_path) for layer in self.layers: gdf = getattr(self, layer).copy() if not gdf.empty: @@ -434,13 +464,13 @@ def to_geopackage(self, file_path, use_schema=True): if gdf.index.name in gdf.columns: gdf = gdf.reset_index(drop=True).copy() gdf.to_file(file_path, layer=layer, driver="GPKG") + if file_path.is_file(): + add_styles_to_geopackage(file_path) - add_styles_to_geopackage(file_path) - @classmethod def from_geopackage(cls, file_path, check_columns=True, check_geotype=True): """ - Initializes HyDAMO class from GeoPackage + Initialize HyDAMO class from GeoPackage Parameters ---------- @@ -465,6 +495,6 @@ def from_geopackage(cls, file_path, check_columns=True, check_geotype=True): hydamo_layer.set_data( gpd.read_file(file_path, layer=layer), check_columns=check_columns, - check_geotype=check_geotype - ) + check_geotype=check_geotype, + ) return hydamo diff --git a/src/hydamo/hydamo/geometry.py b/src/hydamo/hydamo/geometry.py index 8fb8277..cd0bd94 100644 --- a/src/hydamo/hydamo/geometry.py +++ b/src/hydamo/hydamo/geometry.py @@ -1,23 +1,14 @@ -from itertools import product -import geopandas as gpd import numpy as np -import pandas as pd -from shapely import affinity -from shapely.geometry import ( - MultiLineString, - LineString, - MultiPolygon, - Polygon, - MultiPoint, - Point, -) +from shapely.geometry import Point def possibly_intersecting(dataframebounds, geometry, buffer=0): """ + Efficiently determine possibly intersecting geometries using a bounding box. + Finding intersecting profiles for each branch is a slow process in case of large datasets To speed this up, we first determine which profile intersect a square box around the branch - With the selection, the interseting profiles can be determines much faster. + With the selection, the intersecting profiles can be determines much faster. Parameters ---------- @@ -38,7 +29,8 @@ def possibly_intersecting(dataframebounds, geometry, buffer=0): def find_nearest_branch(branches, geometries, method="overall", maxdist=5): """ - Method to determine nearest branch for each geometry. + Determine nearest branch for each geometry. + The nearest branch can be found by finding t from both ends (ends) or the nearest branch from the geometry as a whole (overall), the centroid (centroid), or intersecting (intersect). @@ -68,17 +60,19 @@ def find_nearest_branch(branches, geometries, method="overall", maxdist=5): if method == "intersecting": # Determine intersection geometries per branch - geobounds = geometries.bounds.values.T + geobounds = geometries.bounds.to_numpy().T for branch in branches.itertuples(): - selectie = geometries.loc[ + selection = geometries.loc[ possibly_intersecting(geobounds, branch.geometry) ].copy() - intersecting = selectie.loc[selectie.intersects(branch.geometry).values] + intersecting = selection.loc[ + selection.intersects(branch.geometry).to_numpy() + ] - # For each geometrie, determine offset along branch + # For each geometry, determine offset along branch for geometry in intersecting.itertuples(): # Determine distance of profile line along branch - geometries.at[geometry.Index, "branch_id"] = branch.Index + geometries.loc[geometry.Index, "branch_id"] = branch.Index # Calculate offset branchgeo = branch.geometry @@ -90,48 +84,55 @@ def find_nearest_branch(branches, geometries, method="overall", maxdist=5): 3, ) offset = max(mindist, min(branchgeo.length - mindist, offset)) - geometries.at[geometry.Index, "branch_offset"] = offset + geometries.loc[geometry.Index, "branch_offset"] = offset else: - branch_bounds = branches.bounds.values.T + branch_bounds = branches.bounds.to_numpy().T # In case of looking for the nearest, it is easier to iteratie over the geometries instead of the branches for geometry in geometries.itertuples(): # Find near branches nearidx = possibly_intersecting( branch_bounds, geometry.geometry, buffer=maxdist ) - selectie = branches.loc[nearidx] + selection = branches.loc[nearidx] if method == "overall": # Determine distances to branches - dist = selectie.distance(geometry.geometry) + dist = selection.distance(geometry.geometry) elif method == "centroid": # Determine distances to branches - dist = selectie.distance(geometry.geometry.centroid) + dist = selection.distance(geometry.geometry.centroid) elif method == "ends": # Since a culvert can cross a channel, it is crds = geometry.geometry.coords[:] - dist = selectie["geometry"].apply(lambda x: max(x.distance(Point(*crds[0])), - x.distance(Point(*crds[-1])))).astype(float) + dist = ( + selection["geometry"] + .apply( + lambda x: max( + x.distance(Point(*crds[0])), x.distance(Point(*crds[-1])) + ) + ) + .astype(float) + ) # dist = ( - # selectie.distance(Point(*crds[0])) - # + selectie.distance(Point(*crds[-1])) + # selection.distance(Point(*crds[0])) + # + selection.distance(Point(*crds[-1])) # ) * 0.5 # Determine nearest if dist.min() < maxdist: branchidxmin = dist.idxmin() - geometries.at[geometry.Index, "branch_id"] = dist.idxmin() + geometries.loc[geometry.Index, "branch_id"] = dist.idxmin() if isinstance(geometry.geometry, Point): geo = geometry.geometry else: geo = geometry.geometry.centroid # Calculate offset - branchgeo = branches.at[branchidxmin, "geometry"] + branchgeo = branches.loc[branchidxmin, "geometry"] mindist = min(0.1, branchgeo.length / 2.0) offset = max( mindist, min(branchgeo.length - mindist, round(branchgeo.project(geo), 3)), ) - geometries.at[geometry.Index, "branch_offset"] = offset + geometries.loc[geometry.Index, "branch_offset"] = offset diff --git a/src/hydamo/hydamo/styles.py b/src/hydamo/hydamo/styles.py index e09e2b3..f8d12fe 100644 --- a/src/hydamo/hydamo/styles.py +++ b/src/hydamo/hydamo/styles.py @@ -1,8 +1,9 @@ -from pathlib import Path +import re import sqlite3 -import fiona from datetime import datetime -import re +from pathlib import Path + +import fiona STYLES_DIR = Path(__file__).parent.joinpath("data", "styles") @@ -56,6 +57,7 @@ ); """ + def read_style(style_path: Path) -> str: """ To make style-text sql-compatible, we need to replace single ' to ''. @@ -78,7 +80,7 @@ def read_style(style_path: Path) -> str: style_txt = re.sub(pattern, lambda m: f"''{m.group(1)}''", style_txt) return style_txt - + def add_styles_to_geopackage(gpkg_path: Path): """ @@ -96,15 +98,14 @@ def add_styles_to_geopackage(gpkg_path: Path): """ with sqlite3.connect(gpkg_path) as conn: - # create table conn.execute(DROP_TABLE_SQL) conn.execute(CREATE_TABLE_SQL) # add style per layer for layer in fiona.listlayers(gpkg_path): - style_qml = (STYLES_DIR / f"{layer}.qml") - style_sld = (STYLES_DIR / f"{layer}.sld") + style_qml = STYLES_DIR / f"{layer}.qml" + style_sld = STYLES_DIR / f"{layer}.sld" # check if style exists if style_qml.exists() and style_sld.exists(): @@ -112,10 +113,12 @@ def add_styles_to_geopackage(gpkg_path: Path): update_date_time = f"{datetime.now().isoformat()}Z" # push to GeoPackage - conn.execute(INSERT_ROW_SQL.format( - layer=layer, - style_qml=read_style(style_qml), - style_sld= read_style(style_sld), - description=description, - update_date_time=update_date_time - )) \ No newline at end of file + conn.execute( + INSERT_ROW_SQL.format( + layer=layer, + style_qml=read_style(style_qml), + style_sld=read_style(style_sld), + description=description, + update_date_time=update_date_time, + ) + ) diff --git a/src/hydamo/hydamo/utils.py b/src/hydamo/hydamo/utils.py index f6bf46d..b31d606 100644 --- a/src/hydamo/hydamo/utils.py +++ b/src/hydamo/hydamo/utils.py @@ -1,11 +1,16 @@ from pathlib import Path +from typing import Optional + import pandas as pd BGT_CSV = Path(__file__).parent.joinpath("data", "bgt_codes.csv") BGT_DF = None BGT_ORGANIZATIONS = ["gemeente", "waterschap", "landelijke_organisatie"] -def find_bgt_code(organisatie:str, type_organisatie:str=None) -> dict: + +def find_bgt_code( + organisatie: str, type_organisatie: Optional[str] = None +) -> dict[str, str]: """ Find a dictionary with bgt-code(s) based on a (part of) an organisation name. @@ -13,7 +18,7 @@ def find_bgt_code(organisatie:str, type_organisatie:str=None) -> dict: Parameters ---------- organisatie : str - (Part of) an (case insensitive) organization name. E.g. "Groningen", or + (Part of) an (case insensitive) organization name. E.g. "Groningen", or "ministerie" type_organisatie : str, optional Optional filter for types of organization. Either, "gemeente", "waterschap" or @@ -26,7 +31,7 @@ def find_bgt_code(organisatie:str, type_organisatie:str=None) -> dict: """ global BGT_DF - + # read BGT_CSV if not yet in memory if BGT_DF is None: BGT_DF = pd.read_csv(BGT_CSV) @@ -38,18 +43,14 @@ def find_bgt_code(organisatie:str, type_organisatie:str=None) -> dict: if type_organisatie: if type_organisatie.lower() in BGT_ORGANIZATIONS: bgt_df = bgt_df.loc[bgt_df.type_organisatie == type_organisatie.lower()] - + # try to get an exact match if organisatie.lower() in bgt_df.index: df = bgt_df.loc[organisatie.lower()] - + # get a dictionary with non-exact matches. Empty if no match is found else: - df = bgt_df.loc[ - bgt_df.naam.apply(lambda x: organisatie.lower() in x.lower()) - ] + df = bgt_df.loc[bgt_df.naam.apply(lambda x: organisatie.lower() in x.lower())] # return as dictionary return df.set_index("bgt_code").naam.to_dict() - - \ No newline at end of file diff --git a/src/hydamo/tests/test_datamodel.py b/src/hydamo/tests/test_datamodel.py new file mode 100644 index 0000000..21daf2a --- /dev/null +++ b/src/hydamo/tests/test_datamodel.py @@ -0,0 +1,17 @@ +from pathlib import Path + +import hydamo + + +def test_initialize(): + damo = hydamo.HyDAMO() + assert damo.version == "2.2" + assert "stuw" in damo.layers + assert isinstance(damo.stuw, hydamo.ExtendedGeoDataFrame) + assert "kruinbreedte" in damo.stuw.columns + # no data is loaded + assert len(damo.stuw) == 0 + # no file is written + path = Path("hydamo.gpkg") + damo.to_geopackage(path) + assert not path.is_file()