Improve CI and some code cleanup

.github/workflows/ci.yml

@@ -17,13 +17,13 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: [3.11]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -32,12 +32,10 @@ jobs:
           python -m pip install --upgrade pip
           pip install -e .[ci]
 
-      - name: Lint with flake8
+      - name: Download executables needed for tests
+        shell: bash -l {0}
         run: |
-          # stop the build if there are Python syntax errors or undefined names
-          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-          # exit-zero treats all errors as warnings.
-          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=80 --statistics
+          python -c "import nlmod; nlmod.util.download_mfbinaries()"
 
       - name: Run tests only
         env:

.github/workflows/python-publish.yml

@@ -9,22 +9,24 @@ on:
 
 jobs:
   deploy:
-
     runs-on: ubuntu-latest
-
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
+
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.9'
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install build setuptools wheel
+
     - name: build binary wheel and a source tarball
       run: |
         python -m build --sdist --wheel --outdir dist/
+
     - name: Publish a Python distribution to PyPI
       uses: pypa/gh-action-pypi-publish@release/v1
       with:

README.md

@@ -18,9 +18,13 @@ groundwater models, makes models more reproducible and transparent.
 
 The functions in `nlmod` have four main objectives:
 
-1. Create and adapt the temporal and spatial discretization of a MODFLOW model using an xarray Dataset (`nlmod.dims`).
-2. Download and read data from external sources, project this data on the modelgrid and add this data to an xarray Dataset (`nlmod.read`).
-3. Use data in an xarray Dataset to build modflow packages for both groundwater flow and transport models using FloPy (`nlmod.sim`, `nlmod.gwf` and `nlmod.gwt` for Modflow 6 and `nlmod.modpath` for Modpath).
+1. Create and adapt the temporal and spatial discretization of a MODFLOW model using an 
+   xarray Dataset (`nlmod.dims`).
+2. Download and read data from external sources, project this data on the modelgrid and 
+   add this data to an xarray Dataset (`nlmod.read`).
+3. Use data in an xarray Dataset to build modflow packages for both groundwater flow 
+   and transport models using FloPy (`nlmod.sim`, `nlmod.gwf` and `nlmod.gwt` for 
+   Modflow 6 and `nlmod.modpath` for Modpath).
 4. Visualise modeldata in Python (`nlmod.plot`) or GIS software (`nlmod.gis`).
 
 More information can be found on the documentation-website:

docs/conf.py

@@ -10,10 +10,11 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
-from nlmod import __version__
 import os
 import sys
 
+from nlmod import __version__
+
 sys.path.insert(0, os.path.abspath("."))
 
 

docs/examples/00_model_from_scratch.ipynb

@@ -20,10 +20,9 @@
    "outputs": [],
    "source": [
     "import flopy as fp\n",
-    "import matplotlib.pyplot as plt\n",
-    "import nlmod\n",
-    "import numpy as np\n",
-    "import pandas as pd"
+    "import pandas as pd\n",
+    "\n",
+    "import nlmod"
    ]
   },
   {

docs/examples/01_basic_model.ipynb

@@ -18,12 +18,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import logging\n",
-    "import os\n",
     "\n",
-    "import flopy\n",
-    "import geopandas as gpd\n",
-    "import matplotlib.pyplot as plt\n",
     "import nlmod"
    ]
   },

docs/examples/02_surface_water.ipynb

@@ -25,8 +25,9 @@
     "import os\n",
     "\n",
     "import flopy\n",
-    "import rioxarray\n",
     "import matplotlib.pyplot as plt\n",
+    "import rioxarray\n",
+    "\n",
     "import nlmod"
    ]
   },

docs/examples/03_local_grid_refinement.ipynb

@@ -22,15 +22,12 @@
    "source": [
     "import os\n",
     "\n",
-    "import flopy\n",
-    "import numpy as np\n",
-    "import pandas as pd\n",
     "import geopandas as gpd\n",
-    "import hydropandas as hpd\n",
     "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
     "from IPython.display import HTML\n",
-    "import nlmod\n",
-    "import warnings"
+    "\n",
+    "import nlmod"
    ]
   },
   {

docs/examples/04_modifying_layermodels.ipynb

@@ -20,11 +20,11 @@
    "outputs": [],
    "source": [
     "import matplotlib.pyplot as plt\n",
-    "import nlmod\n",
     "import numpy as np\n",
-    "import pandas as pd\n",
-    "from nlmod.plot import DatasetCrossSection\n",
-    "from shapely.geometry import LineString"
+    "from shapely.geometry import LineString\n",
+    "\n",
+    "import nlmod\n",
+    "from nlmod.plot import DatasetCrossSection"
    ]
   },
   {

docs/examples/05_caching.ipynb

@@ -20,12 +20,10 @@
    "outputs": [],
    "source": [
     "import os\n",
-    "import flopy\n",
-    "import geopandas as gpd\n",
-    "import matplotlib.pyplot as plt\n",
-    "import nlmod\n",
-    "import numpy as np\n",
-    "import xarray as xr"
+    "\n",
+    "import xarray as xr\n",
+    "\n",
+    "import nlmod"
    ]
   },
   {

docs/examples/06_gridding_vector_data.ipynb

@@ -18,17 +18,15 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import nlmod\n",
+    "import geopandas as gpd\n",
+    "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
     "import xarray as xr\n",
-    "\n",
-    "import matplotlib.pyplot as plt\n",
-    "\n",
-    "import geopandas as gpd\n",
+    "from IPython.display import display\n",
     "from shapely.geometry import LineString, Point\n",
     "from shapely.geometry import Polygon as shp_polygon\n",
     "\n",
-    "from IPython.display import display"
+    "import nlmod"
    ]
   },
   {
@@ -391,8 +389,9 @@
     "    ds = ds.expand_dims({\"layer\": range(3)})\n",
     "\n",
     "# create some data arrays\n",
-    "ds[\"da1\"] = (\"layer\", \"y\", \"x\"), np.random.randint(\n",
-    "    0, 10, (ds.sizes[\"layer\"], ds.sizes[\"y\"], ds.sizes[\"x\"])\n",
+    "ds[\"da1\"] = (\n",
+    "    (\"layer\", \"y\", \"x\"),\n",
+    "    np.random.randint(0, 10, (ds.sizes[\"layer\"], ds.sizes[\"y\"], ds.sizes[\"x\"])),\n",
     ")\n",
     "ds[\"da2\"] = (\"y\", \"x\"), np.random.randint(0, 10, (ds.sizes[\"y\"], ds.sizes[\"x\"]))\n",
     "ds[\"da3\"] = (\"y\", \"x\"), np.random.randint(0, 10, (ds.sizes[\"y\"], ds.sizes[\"x\"]))\n",

docs/examples/07_resampling.ipynb

@@ -18,25 +18,17 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import nlmod\n",
-    "from nlmod import resample\n",
+    "\n",
+    "import geopandas as gpd\n",
+    "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
     "import xarray as xr\n",
-    "import flopy\n",
-    "import warnings\n",
-    "\n",
-    "\n",
     "from matplotlib.colors import Normalize\n",
-    "from matplotlib.patches import Polygon\n",
-    "from matplotlib.collections import PatchCollection\n",
-    "import matplotlib.pyplot as plt\n",
-    "\n",
-    "import geopandas as gpd\n",
-    "from shapely.geometry import LineString, Point\n",
-    "from shapely.geometry import Polygon as shp_polygon\n",
     "from scipy.interpolate import RectBivariateSpline\n",
+    "from shapely.geometry import LineString, Point\n",
     "\n",
-    "from IPython.display import display"
+    "import nlmod\n",
+    "from nlmod import resample"
    ]
   },
   {
@@ -100,7 +92,7 @@
    "outputs": [],
    "source": [
     "ds[\"data_nan\"] = ds[\"data\"].copy()\n",
-    "ds[\"data_nan\"].data[0, 1] = np.NaN\n",
+    "ds[\"data_nan\"].data[0, 1] = np.nan\n",
     "\n",
     "fig, ax = plt.subplots()\n",
     "ax.set_aspect(\"equal\")\n",
@@ -144,7 +136,7 @@
    "outputs": [],
    "source": [
     "dsv[\"data_nan\"] = dsv[\"data\"].copy()\n",
-    "dsv[\"data_nan\"][7] = np.NaN\n",
+    "dsv[\"data_nan\"][7] = np.nan\n",
     "\n",
     "fig, ax = plt.subplots()\n",
     "ax.set_aspect(\"equal\")\n",

docs/examples/08_gis.ipynb

@@ -19,14 +19,12 @@
    "outputs": [],
    "source": [
     "import os\n",
+    "\n",
     "import flopy\n",
-    "import geopandas as gpd\n",
-    "import matplotlib.pyplot as plt\n",
-    "import nlmod\n",
-    "import numpy as np\n",
     "import xarray as xr\n",
-    "from IPython.display import FileLink, FileLinks\n",
-    "from shapely.geometry import Polygon"
+    "from IPython.display import FileLink\n",
+    "\n",
+    "import nlmod"
    ]
   },
   {

docs/examples/09_schoonhoven.ipynb

@@ -18,18 +18,17 @@
    "outputs": [],
    "source": [
     "import os\n",
+    "\n",
     "import flopy\n",
+    "import geopandas as gpd\n",
     "import matplotlib\n",
     "import matplotlib.pyplot as plt\n",
-    "import nlmod\n",
     "import numpy as np\n",
-    "import xarray as xr\n",
     "import pandas as pd\n",
-    "import hydropandas as hpd\n",
-    "import geopandas as gpd\n",
-    "from nlmod.plot import DatasetCrossSection\n",
     "from shapely.geometry import LineString, Point\n",
-    "import warnings"
+    "\n",
+    "import nlmod\n",
+    "from nlmod.plot import DatasetCrossSection"
    ]
   },
   {

docs/examples/10_modpath.ipynb

@@ -28,9 +28,10 @@
     "\n",
     "import flopy\n",
     "import matplotlib.pyplot as plt\n",
-    "import nlmod\n",
     "import numpy as np\n",
-    "import xarray as xr"
+    "import xarray as xr\n",
+    "\n",
+    "import nlmod"
    ]
   },
   {
@@ -164,7 +165,7 @@
     "    marker=\"o\",\n",
     "    color=\"red\",\n",
     ")\n",
-    "ax.set_title(f\"pathlines\")\n",
+    "ax.set_title(\"pathlines\")\n",
     "ax.legend(loc=\"upper right\")"
    ]
   },
@@ -265,7 +266,7 @@
     "        marker=\"o\",\n",
     "        color=\"red\",\n",
     "    )\n",
-    "    ax.set_title(f\"pathlines\")\n",
+    "    ax.set_title(\"pathlines\")\n",
     "    ax.legend(loc=\"upper right\")\n",
     "\n",
     "    if i == 1:\n",
@@ -370,7 +371,7 @@
     "            marker=\"o\",\n",
     "            color=\"red\",\n",
     "        )\n",
-    "    ax.set_title(f\"pathlines\")\n",
+    "    ax.set_title(\"pathlines\")\n",
     "    ax.legend(loc=\"upper right\")\n",
     "\n",
     "    if i == 1:\n",
@@ -477,7 +478,7 @@
     "            marker=\"o\",\n",
     "            color=\"red\",\n",
     "        )\n",
-    "    ax.set_title(f\"pathlines\")\n",
+    "    ax.set_title(\"pathlines\")\n",
     "    ax.legend(loc=\"upper right\")\n",
     "\n",
     "    if i == 1:\n",

docs/examples/11_grid_rotation.ipynb

@@ -30,11 +30,10 @@
    "outputs": [],
    "source": [
     "import os\n",
+    "\n",
     "import matplotlib\n",
-    "import nlmod\n",
-    "import pandas as pd\n",
-    "import warnings\n",
-    "import flopy"
+    "\n",
+    "import nlmod"
    ]
   },
   {

docs/examples/12_layer_generation.ipynb

@@ -26,8 +26,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import nlmod\n",
-    "from shapely.geometry import LineString"
+    "from shapely.geometry import LineString\n",
+    "\n",
+    "import nlmod"
    ]
   },
   {