Structure Python packages (#123)

Moves ribasim_lumping from scripts to src, adds pyproject.toml and
readme. For the other packages we now all switch to using hatchling
building, and adding them all as editable dependencies to pixi.

Only ribasim_lumping doesn't load yet due to #122. Though this is good
to merge.

pixi.toml

@@ -38,6 +38,7 @@ app = "bokeh serve web_app --show --dev --port 5007"
 
 [feature.common.dependencies]
 bokeh = ">=3.0"
+contextily = "*"
 fiona = "*"
 geocube = "*"
 geopandas = "*"
@@ -67,18 +68,21 @@ shapely = ">=2"
 tomli = "*"
 tomli-w = "*"
 types-requests = "*"
+xugrid = "*"
 
 [feature.common.pypi-dependencies]
+bokeh_helpers = { path = "src/bokeh_helpers", editable = true }
 hydamo = { path = "src/hydamo", editable = true }
+peilbeheerst_model = { path = "src/peilbeheerst_model", editable = true }
+ribasim_lumping = { path = "src/ribasim_lumping", editable = true }
 ribasim_nl = { path = "src/ribasim_nl", editable = true }
-bokeh_helpers = { path = "src/bokeh_helpers", editable = true }
 
-# [feature.dev.pypi-dependencies]
-# ribasim = { path = "../Ribasim/python/ribasim", editable = true }
+[feature.dev.pypi-dependencies]
+ribasim = { path = "../Ribasim/python/ribasim", editable = true }
 
 [feature.prod.dependencies]
 ribasim = "==2024.10.0"
 
 [environments]
 default = { features = ["common", "prod"] }
-# dev = { features = ["common", "dev"] }
+dev = { features = ["common", "dev"] }

src/bokeh_helpers/README.md

@@ -0,0 +1 @@
+Helpers for building Bokeh dashboards.

src/bokeh_helpers/bokeh_helpers/__init__.py

@@ -1 +1 @@
-__version__ = "0.0.1"
+__version__ = "0.1.0"

src/bokeh_helpers/pyproject.toml

@@ -1,9 +1,9 @@
 [build-system]
-requires = ["setuptools>=61"]
-build-backend = "setuptools.build_meta"
+requires = ["hatchling"]
+build-backend = "hatchling.build"
 
 [project]
-name = "bokeh-helpers"
+name = "bokeh_helpers"
 description = "helpers for building bokeh dashboards"
 readme = "README.md"
 authors = [
@@ -20,11 +20,5 @@ dynamic = ["version"]
 [project.optional-dependencies]
 tests = ["pytest"]
 
-[tool.setuptools]
-zip-safe = true
-
-[tool.setuptools.dynamic]
-version = { attr = "bokeh_helpers.__version__" }
-
-[tool.setuptools.packages.find]
-include = ["bokeh_helpers"]
+[tool.hatch.version]
+path = "bokeh_helpers/__init__.py"

src/hydamo/pyproject.toml

@@ -1,6 +1,6 @@
 [build-system]
-requires = ["setuptools>=61"]
-build-backend = "setuptools.build_meta"
+requires = ["hatchling"]
+build-backend = "hatchling.build"
 
 [project]
 name = "hydamo"
@@ -20,17 +20,8 @@ dynamic = ["version"]
 [project.optional-dependencies]
 tests = ["pytest"]
 
-[tool.setuptools]
-zip-safe = true
-
-[tool.setuptools.dynamic]
-version = { attr = "hydamo.__version__" }
-
-[tool.setuptools.packages.find]
-include = ["hydamo"]
-
-[tool.setuptools.package-data]
-"hydamo" = ["**/*.csv", "**/*.qml", "**/*.sld", "**/*.json"]
+[tool.hatch.version]
+path = "hydamo/__init__.py"
 
 [project.urls]
 Documentation = "https://deltares.github.io/Ribasim-NL/HyDAMO"

src/peilbeheerst_model/pyproject.toml

@@ -1,41 +1,27 @@
 [build-system]
-requires = ["setuptools>=61"]
-build-backend = "setuptools.build_meta"
+requires = ["hatchling"]
+build-backend = "hatchling.build"
 
 [project]
 name = "peilbeheerst_model"
 description = "functions to derive a Ribasim network from a hydro-dataset"
 readme = "README.md"
 authors = [
     { name = "Guy Dupuits", email = "[email protected]" },
-	{ name = "Jerom Aerts", email = "[email protected]" },
-	{ name = "Ron Bruijns", email = "[email protected]" },
+    { name = "Jerom Aerts", email = "[email protected]" },
+    { name = "Ron Bruijns", email = "[email protected]" },
 ]
 license = { text = "MIT" }
 
 requires-python = ">=3.10"
-dependencies = [
-    "geopandas",
-	"numpy",
-	"pandas",
-	"pydantic",
-	"shapely",
-	"tqdm",
-]
+dependencies = ["geopandas", "numpy", "pandas", "pydantic", "shapely", "tqdm"]
 dynamic = ["version"]
 
 [project.optional-dependencies]
 tests = ["pytest"]
 
-[tool.setuptools]
-zip-safe = true
-
-[tool.setuptools.dynamic]
-version = { attr = "peilbeheerst_model.__version__" }
-
-[tool.setuptools.packages.find]
-include = ["peilbeheerst_model"]
-
+[tool.hatch.version]
+path = "peilbeheerst_model/__init__.py"
 
 [project.urls]
 Documentation = "https://deltares.github.io/Ribasim-NL/Peilbeheerst-model"

src/ribasim_lumping/.gitignore

@@ -0,0 +1,136 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# PyCharm .idea-folder
+.idea/*
+
+# Windows command-files
+*.cmd
+*.bat

src/ribasim_lumping/README.md

@@ -0,0 +1,29 @@
+# ribasim-lumping
+
+This python package is used to develop an aggregated Ribasim network (Deltares, https://github.com/Deltares/Ribasim). Documentation: https://deltares.github.io/Ribasim/
+
+This code was integrated into the Ribasim-NL repository after development in https://github.com/harm-nomden-sweco/ribasim_lumping.
+
+### Objective
+This python-package provides functions to translate a D-Hydro or a HyDAMO network into a simplified (aggregated/lumped) Ribasim-network: 
+- The user provides a list of locations where the network should be split, resulting into sub-networks which are called 'basins'';
+- For these basins relations regarding waterlevel-watersurface-watervolume are calculated;
+- Exchange of watervolume (flow) between basins takes place via these split locations. 
+- Stage-discharge relations are generated to define flow-rates between basins.
+
+### Dependencies
+Most important dependencies:
+- NETWORKX (https://networkx.org/, Hagberg et al., 2008)
+- UGRID (https://github.com/Deltares/UGridPy)
+- XUGRID (https://github.com/Deltares/xugrid)
+
+### Installation
+We will make this package accessible via pypi. It is recommended to clone this repository because it is under development and it includes some example notebooks. We are still working on tests and test data, etc.
+
+### Development, contributions and licences
+This package is developed by Sweco (contributors: Harm Nomden and Tessa Andringa) when working on a TKI-project (top consortia for knowledge and innovation) within the NHI programme (Dutch Hydrological Instruments programme). This focuses on the development, testing and application of the new Ribasim-model (https://tkideltatechnologie.nl/project/oppervlaktewatermodule-nhi/). 
+It is possible to contribute, create issues, start discussions. We will respond as soon as possible.
+This package is developed under the MIT license. Reference to this package: Ribasim-Lumping (Sweco, 2023).
+
+### References:
+Aric A. Hagberg, Daniel A. Schult and Pieter J. Swart, “Exploring network structure, dynamics, and function using NetworkX”, in Proceedings of the 7th Python in Science Conference (SciPy2008), Gäel Varoquaux, Travis Vaught, and Jarrod Millman (Eds), (Pasadena, CA USA), pp. 11–15, Aug 2008

src/ribasim_lumping/pyproject.toml

@@ -0,0 +1,32 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "ribasim_lumping"
+description = "Aggregate a HyDAMO or D-Hydro network into a simplified Ribasim network"
+readme = "README.md"
+authors = [
+    { name = "Harm Nomden", email = "[email protected]" },
+    { name = "Tessa Andringa", email = "[email protected]" },
+]
+license = { text = "MIT" }
+
+requires-python = ">=3.10"
+dependencies = [
+    "contextily",
+    "geopandas",
+    "matplotlib",
+    "networkx",
+    "numpy",
+    "pandas",
+    "pydantic",
+    "ribasim",
+    "shapely",
+    "xarray",
+    "xugrid",
+]
+dynamic = ["version"]
+
+[tool.hatch.version]
+path = "ribasim_lumping/__init__.py"

scripts/ribasim_lumping/__init__.py → src/ribasim_lumping/ribasim_lumping/__init__.py

@@ -1,3 +1,5 @@
+__version__ = "0.1.0"
+
 from ribasim_lumping.ribasim_lumping import create_ribasim_lumping_network
 
 __all__ = ["create_ribasim_lumping_network"]

src/ribasim_nl/pyproject.toml

@@ -1,14 +1,14 @@
 [build-system]
-requires = ["setuptools>=61"]
-build-backend = "setuptools.build_meta"
+requires = ["hatchling"]
+build-backend = "hatchling.build"
 
 [project]
 name = "ribasim_nl"
 description = "functions to work with python classes you typically find in hydro-datasets"
 readme = "README.md"
 authors = [
     { name = "Daniel Tollenaar", email = "[email protected]" },
-	{ name = "Martijn Visser", email = "[email protected]" }
+    { name = "Martijn Visser", email = "[email protected]" }
 ]
 license = { text = "MIT" }
 
@@ -21,15 +21,8 @@ dynamic = ["version"]
 [project.optional-dependencies]
 tests = ["pytest"]
 
-[tool.setuptools]
-zip-safe = true
-
-[tool.setuptools.dynamic]
-version = { attr = "ribasim_nl.__version__" }
-
-[tool.setuptools.packages.find]
-include = ["ribasim_nl"]
-
+[tool.hatch.version]
+path = "ribasim_nl/__init__.py"
 
 [project.urls]
 Documentation = "https://deltares.github.io/Ribasim-NL"

src/ribasim_nl/ribasim_nl/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.0.1"
+__version__ = "0.1.0"
 
 from ribasim_nl.cloud import CloudStorage
 from ribasim_nl.model import Model