Move to pyproject.toml

.github/workflows/ci.yml

@@ -30,12 +30,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install flake8 pytest
-          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-          pip install pytest-cov
-          pip install pytest-dependency
-          pip install codacy-coverage
-          pip install -e .
+          pip install -e .[ci]
 
       - name: Lint with flake8
         run: |

.readthedocs.yml

@@ -20,7 +20,11 @@ sphinx:
 
 # Optionally declare the Python requirements required to build your docs
 python:
+  system_packages: true
   install:
-    - requirements: docs/requirements.txt
-    - method: setuptools
+    - method: pip
       path: .
+      extra_requirements:
+        - nbtest
+        - rtd
+

docs/examples/00_model_from_scratch.ipynb

@@ -1,6 +1,7 @@
 {
  "cells": [
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -35,6 +36,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -53,6 +55,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -78,6 +81,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -105,6 +109,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -121,6 +126,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -144,6 +150,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -173,6 +180,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -215,6 +223,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -231,6 +240,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -247,6 +257,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -276,6 +287,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [

docs/examples/01_basic_model.ipynb

@@ -39,6 +39,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -49,7 +50,7 @@
     "- a structured grid based on the subsurface models [Regis](https://www.dinoloket.nl/regis-ii-het-hydrogeologische-model) and [Geotop](https://www.dinoloket.nl/detaillering-van-de-bovenste-lagen-met-geotop). The Regis layers that are not present within the extent are removed. In this case we use 'MSz1' as the bottom layer of the model. Use `nlmod.read.regis.get_layer_names()` to get all the layer names of Regis. All Regis layers below this layer are not used in the model. Geotop is used to replace the holoceen layer in Regis because there is no kh or kv defined for the holoceen in Regis. Part of the model is in the North sea. Regis and Geotop have no data there. Therefore the Regis and Geotop layers are extrapolated from the shore and the seabed is added using bathymetry data from [Jarkus](https://www.openearth.nl/rws-bathymetry/2018.html).\n",
     "- starting heads of 1 in every cell.\n",
     "- the model is a steady state model of a single time step.\n",
-    "- big surface water bodies (Northsea, IJsselmeer, Markermeer, Noordzeekanaal) within the extent are added as a general head boundary. The surface water bodies are obtained from a [shapefile](..\\data\\opp_water.shp).\n",
+    "- big surface water bodies (Northsea, IJsselmeer, Markermeer, Noordzeekanaal) within the extent are added as a general head boundary. The surface water bodies are obtained from a [shapefile](..\\data\\shapes\\opp_water.shp).\n",
     "- surface drainage is added using [ahn](https://www.ahn.nl) data and a default conductance of $1000 m^2/d$\n",
     "- recharge is added using data from the [knmi](https://www.knmi.nl/nederland-nu/klimatologie/daggegevens) using the following steps:~~\n",
     "    1. Check for each cell which KNMI weather and/or rainfall station is closest.\n",

docs/examples/03_local_grid_refinement.ipynb

@@ -399,22 +399,8 @@
   }
  ],
  "metadata": {
-  "kernelspec": {
-   "display_name": "artesia",
-   "language": "python",
-   "name": "python3"
-  },
   "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.9.7"
+   "name": "python"
   }
  },
  "nbformat": 4,

docs/examples/11_grid_rotation.ipynb

@@ -358,22 +358,8 @@
   }
  ],
  "metadata": {
-  "kernelspec": {
-   "display_name": "artesia",
-   "language": "python",
-   "name": "python3"
-  },
   "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.9.7"
+   "name": "python"
   }
  },
  "nbformat": 4,

docs/examples/16_groundwater_transport.ipynb

@@ -553,22 +553,8 @@
   }
  ],
  "metadata": {
-  "kernelspec": {
-   "display_name": "artesia",
-   "language": "python",
-   "name": "python3"
-  },
   "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.9.7"
+   "name": "python"
   }
  },
  "nbformat": 4,

nlmod/dcs.py

@@ -230,7 +230,7 @@ def plot_grid(
         horizontal=True,
         vertical=True,
         ilayers=None,
-        **kwargs
+        **kwargs,
     ):
         lines = []
         if ilayers is None:

nlmod/dims/grid.py

@@ -9,7 +9,7 @@
 import logging
 import os
 import warnings
-import os
+
 import flopy
 import geopandas as gpd
 import numpy as np

nlmod/read/geotop.py

@@ -196,7 +196,7 @@ def convert_geotop_to_ml_layers(
     lay = 0
     logger.info("creating top and bot per geo eenheid")
     for geo_eenheid in geo_eenheden:
-        logger.debug(geo_eenheid)
+        logger.debug(int(geo_eenheid))
 
         mask = geotop_ds_raw.strat == geo_eenheid
         geo_z = xr.where(mask, geotop_ds_raw.z, np.NaN)

nlmod/read/knmi.py

@@ -2,9 +2,9 @@
 import logging
 
 import hydropandas as hpd
-from hydropandas.io import knmi as hpd_knmi
 import numpy as np
 import pandas as pd
+from hydropandas.io import knmi as hpd_knmi
 
 from .. import cache, util
 from ..dims.layers import get_first_active_layer

nlmod/read/meteobase.py

@@ -108,7 +108,7 @@ def read_ascii(fo: FileIO) -> Union[np.ndarray, dict]:
     line_cnt = 0
     for line in lines:
         linestr = str(line, encoding="utf-8").lower()
-        if not any([x for x in ascii_header_keys if x in str(linestr)]):
+        if not any((x for x in ascii_header_keys if x in str(linestr))):
             break
         l1, l2 = linestr.split()
         if l1.lower() in ("ncols", "nrows", "nodata_value"):

nlmod/read/rws.py

@@ -31,7 +31,7 @@ def get_gdf_surface_water(ds):
         surface water geodataframe.
     """
     # laad bestanden in
-    fname = os.path.join(nlmod.NLMOD_DATADIR, "opp_water.shp")
+    fname = os.path.join(nlmod.NLMOD_DATADIR, "shapes", "opp_water.shp")
     gdf_swater = gpd.read_file(fname)
     extent = dims.get_extent(ds)
     gdf_swater = util.gdf_within_extent(gdf_swater, extent)
@@ -135,9 +135,9 @@ def get_northsea(ds, da_name="northsea"):
 def add_northsea(ds, cachedir=None):
     """Add datavariable bathymetry to model dataset.
 
-    Performs the following steps:     
+    Performs the following steps:
 
-    a) get cells from modelgrid that are within the northsea, add data 
+    a) get cells from modelgrid that are within the northsea, add data
        variable 'northsea' to ds
     b) fill top, bot, kh and kv add northsea cell by extrapolation
     c) get bathymetry (northsea depth) from jarkus.

nlmod/read/webservices.py

@@ -1,6 +1,7 @@
 import logging
 import xml.etree.ElementTree as ET
 from io import BytesIO
+
 import geopandas as gpd
 import numpy as np
 import pandas as pd

pyproject.toml

@@ -0,0 +1,88 @@
+[build-system]
+requires = ["setuptools>=64.0.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+
+[project]
+name = "nlmod"
+dynamic = ["version"]
+description = "nlmod is an open-source Python package for building Modflow 6 groundwater models from online data sources in The Netherlands"
+license = { file = "LICENSE" }
+readme = "README.md"
+authors = [
+    { name = "O. Ebbens" },
+    { name = "R. Caljé" },
+    { name = "D.A. Brakenhoff" },
+]
+maintainers = [
+    { name = "O. Ebbens", email = "o.ebbens@artesia-water.nl" },
+    { name = "R. Calje", email = "r.calje@artesia-water.nl" },
+    { name = "D.A. Brakenhoff", email = "d.brakenhoff@artesia-water.nl" },
+]
+requires-python = ">= 3.8"
+dependencies = [
+    "flopy>=3.3.6",
+    "xarray>=0.16.1",
+    "netcdf4>=1.5.7",
+    "rasterio>=1.1.0",
+    "rioxarray",
+    "affine>=0.3.1",
+    "geopandas",
+    "owslib>=0.24.1",
+    "hydropandas>=0.7.1",
+    "shapely>=2.0.0",
+    "pyshp>=2.1.3",
+    "matplotlib",
+    "dask",
+    "colorama",
+]
+keywords = ["hydrology", "groundwater", "modeling", "Modflow 6", "flopy"]
+classifiers = [
+    'Development Status :: 4 - Beta',
+    'Intended Audience :: Science/Research',
+    'Intended Audience :: Other Audience',
+    'License :: OSI Approved :: MIT License',
+    'Programming Language :: Python :: 3 :: Only',
+    'Programming Language :: Python :: 3.8',
+    'Programming Language :: Python :: 3.9',
+    'Programming Language :: Python :: 3.10',
+    'Topic :: Scientific/Engineering :: Hydrology',
+]
+
+[project.urls]
+homepage = "https://github.com/ArtesiaWater/nlmod"
+repository = "https://github.com/ArtesiaWater/nlmod"
+documentation = "https://nlmod.readthedocs.io/en/latest/"
+
+[project.optional-dependencies]
+full = ["gdown", "geocube", "gdown", "bottleneck", "contextily"]
+test = ["pytest>=7", "pytest-cov", "pytest-dependency"]
+nbtest = ["nbformat", "nbconvert>6.4.5"]
+lint = ["flake8", "isort", "black[jupyter]"]
+ci = ["nlmod[full,lint,test,nbtest]", "netCDF4==1.5.7"]
+rtd = ["ipython", "ipykernel", "nbsphinx", "nbconvert>6.4.5"]
+
+[tool.setuptools.dynamic]
+version = { attr = "nlmod.version.__version__" }
+
+[tool.setuptools.packages.find]
+where = ["."]
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.package-data]
+"nlmod.data" = ["*.gleg"]
+"nlmod.data.geotop" = ["*.csv"]
+"nlmod.data.shapes" = ["*"]
+
+[tool.black]
+line-length = 88
+
+[tool.isort]
+profile = "black"
+
+[tool.pytest.ini_options]
+addopts = "--strict-markers --durations=0"
+markers = ["notebooks: run notebooks"]
+