Merge pull request #195 from aleaf/main

pandas 3 support, flopy fixes and PRT demo fix + update

Author: mnfienen

.github/workflows/build_docs.yaml

@@ -39,6 +39,7 @@ jobs:
       with:
         path: ~/.local/bin
         github_token: ${{ secrets.GITHUB_TOKEN }}
+        repo: modflow6
     - name: Modflow version
       shell: bash -l {0}
       run: mf6 --version

.github/workflows/test.yaml

@@ -11,13 +11,15 @@ on:
 
 jobs:
   build:
-    name: ${{ matrix.python-version }}, ${{ matrix.os }}
+    name: ${{ matrix.env }}, ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         os: [ ubuntu-latest, macos-latest, windows-latest ]
-        python-version: ['3.12']
+        env:
+          - installation/environment.yml
+          - ci/pandas2_env.yml
 
     steps:
     - name: Checkout source
@@ -31,7 +33,7 @@ jobs:
     - name: Setup Micromamba
       uses: mamba-org/setup-micromamba@v2
       with:
-        environment-file: installation/environment.yml
+        environment-file: ${{ matrix.env }}
         cache-environment: false
         cache-downloads: false
         # persist on the same day.
@@ -52,6 +54,8 @@ jobs:
       with:
         path: ~/.local/bin
         github_token: ${{ secrets.GITHUB_TOKEN }}
+        repo: modflow6
+        cache: false
     - name: Modflow version
       shell: bash -l {0}
       run: mf6 --version
@@ -76,6 +80,6 @@ jobs:
     - name: Run tests
       shell: bash -l {0}
       run: |
-        pytest tests/test_notebooks.py -v
+        pytest tests/test_notebooks.py
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

AGENDA.md

@@ -57,6 +57,6 @@ Monday
 - 1500-1515: break
 - 1515-1545: 08 Modflow-setup demo (Andy) 
 - 1545-1600: break
-- 1600-1630: 09 Run and process MF6T (Kalle) 
+- 1600-1630: 09 Run and process MF6 GWT (Kalle) 
 - 1630-1700: 10 Run and process MODPATH/MF6-PRT models (Andy) 
 - 1700: Wrap up

ci/pandas2_env.yml

@@ -0,0 +1,52 @@
+name: pyclass
+channels:
+  - conda-forge
+  - nodefaults
+dependencies:
+  # required
+  - python=3.14
+  - pip
+
+  - numpy
+  - matplotlib
+
+  - jupyter
+  - jupytext
+  - jupyterlab
+  - git
+  - python-dateutil
+  - affine
+  - scipy
+  - openpyxl
+  - xlrd
+  - pandas<3
+  - netcdf4
+  - pyshp
+  - rasterio
+  - rasterstats
+  - fiona
+  - descartes
+  - pyproj
+  - shapely
+  - geos
+  - geojson
+  - geopandas
+  - xarray
+  - rioxarray
+  - uxarray
+  - pyyaml
+  - rtree
+  - pyvista
+  - vtk
+  - imageio
+  - requests
+  - pytest
+  - statsmodels
+  - dataretrieval
+  - flopy=3.9
+  - gis-utils
+  - sfrmaker
+  - contextily
+  - cartopy
+  - modflow-export
+  - modflow-setup

docs/docs-environment.yml

@@ -3,7 +3,7 @@ channels:
   - conda-forge
 dependencies:
   # required
-  - python=3.11
+  - python=3.14
   - pip
 
   - numpy

installation/environment.yml

@@ -43,7 +43,7 @@ dependencies:
   - pytest
   - statsmodels
   - dataretrieval
-  - flopy>=3.7
+  - flopy=3.9
   - gis-utils
   - sfrmaker
   - contextily

notebooks/part1_flopy/03_Loading_and_visualizing_models.ipynb

@@ -183,22 +183,6 @@
     "ax.set_ylabel(f'{modelgrid.units.capitalize()} northing, {modelgrid.crs.name}')"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "### Exporting the model grid to a shapefile"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "modelgrid.write_shapefile(str(output_folder / 'pleasant_grid.shp'))"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -213,41 +197,15 @@
    "outputs": [],
    "source": [
     "modelgrid = model.modelgrid\n",
-    "modelgrid_gdf = modelgrid.geo_dataframe"
+    "modelgrid_gdf = modelgrid.geo_dataframe\n",
+    "modelgrid_gdf"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "#### Add row, column information to model grid `GeoDataFrame`"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "modelgrid.shape"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "modelgrid_gdf.index[-1] // modelgrid.ncol"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "1 // modelgrid.ncol"
+    "### Exporting the model grid to a shapefile"
    ]
   },
   {
@@ -256,9 +214,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "modelgrid_gdf['i'] = modelgrid_gdf.index // modelgrid.ncol\n",
-    "modelgrid_gdf['j'] = modelgrid_gdf.index % modelgrid.ncol\n",
-    "modelgrid_gdf.head()"
+    "modelgrid_gdf.to_file(output_folder / 'pleasant_grid.shp')"
    ]
   },
   {
@@ -1100,13 +1056,24 @@
     "fig, ax = plt.subplots(figsize=(10, 5))\n",
     "in_cols = ['STO-SS_IN', 'STO-SY_IN', 'WEL_IN', 'RCHA_IN', 'CHD_IN', 'SFR_IN', 'LAK_IN']\n",
     "out_cols = [c.replace('_IN', '_OUT') for c in in_cols]\n",
+    "# as of pandas 3.0.1, \n",
+    "# the datatime index of the flux dataframe produced by Flopy produces an error with .plot.bar();\n",
+    "# switch the index to a categorical (date string) index instead\n",
+    "flux.index = flux.index.strftime('%Y-%m-%d')\n",
     "flux[in_cols].plot.bar(stacked=True, ax=ax)\n",
     "(-flux[out_cols]).plot.bar(stacked=True, ax=ax)\n",
     "ax.legend(loc='lower left', bbox_to_anchor=(1, 0))\n",
     "ax.axhline(0, lw=0.5, c='k')\n",
     "ax.set_ylabel('Simulated Flux, in $m^3/d$')"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -1142,7 +1109,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.11"
+   "version": "3.14.3"
   }
  },
  "nbformat": 4,

notebooks/part1_flopy/04_Modelgrid_and_intersection.ipynb

@@ -1202,7 +1202,7 @@
    "outputs": [],
    "source": [
     "main_stem = []\n",
-    "gx = GridIntersect(modelgrid, method=\"vertex\")\n",
+    "gx = GridIntersect(modelgrid)\n",
     "for iloc, row in flw_main.iterrows():\n",
     "    results = gx.intersect(row.geometry)\n",
     "    main_stem.extend(results.cellids)\n",

notebooks/part1_flopy/05_Unstructured_Grid_generation.ipynb

@@ -399,7 +399,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ix = GridIntersect(sgrid, method=\"vertex\")\n",
+    "ix = GridIntersect(sgrid)\n",
     "result = ix.intersect(basindf.geometry.values[0], contains_centroid=True)\n",
     "rowcol = result[\"cellids\"]"
    ]
@@ -550,7 +550,7 @@
    "outputs": [],
    "source": [
     "rowcols = []\n",
-    "ix = GridIntersect(sgrid, method=\"vertex\")\n",
+    "ix = GridIntersect(sgrid)\n",
     "for geom in nhddf.geometry.values:\n",
     "    rcs = ix.intersects(geom)[\"cellids\"]\n",
     "    rowcols.extend(list(rcs))"
@@ -673,7 +673,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ix = GridIntersect(rfgrid, method=\"vertex\")\n",
+    "ix = GridIntersect(rfgrid)\n",
     "result = ix.intersect(basindf.geometry.values[0], contains_centroid=True)\n",
     "rowcol = result[\"cellids\"]\n",
     "\n",
@@ -849,7 +849,7 @@
     "# live code this/give it as an activity\n",
     "idomainp = np.ones(sgrid.idomain.shape, dtype=int)\n",
     "\n",
-    "gix = GridIntersect(sgrid, method=\"vertex\")\n",
+    "gix = GridIntersect(sgrid)\n",
     "result = gix.intersect(lgr_gdf.geometry.values[0])\n",
     "cid = result[\"cellids\"]\n",
     "\n",
@@ -959,7 +959,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ix = GridIntersect(childgrid, method=\"vertex\")\n",
+    "ix = GridIntersect(childgrid)\n",
     "cstrmcells = []\n",
     "for geom in nhddf.geometry.values:\n",
     "    rcs = ix.intersects(geom)[\"cellids\"]\n",
@@ -1120,7 +1120,7 @@
    "source": [
     "# create the idomain array\n",
     "idomain = np.zeros(quadgrid.shape, dtype=int)\n",
-    "ix = GridIntersect(quadgrid, method=\"vertex\")\n",
+    "ix = GridIntersect(quadgrid)\n",
     "nodes = ix.intersect(basindf.geometry.values[0], contains_centroid=True)[\"cellids\"]\n",
     "\n",
     "idomain[:, list(nodes)] = 1\n",
@@ -1136,7 +1136,7 @@
    "source": [
     "# create an array of stream cells\n",
     "qstr = []\n",
-    "ix = GridIntersect(quadgrid, method=\"vertex\")\n",
+    "ix = GridIntersect(quadgrid)\n",
     "for geom in nhddf.geometry.values:\n",
     "    nodes = ix.intersects(geom)[\"cellids\"]\n",
     "    qstr.extend(list(nodes))"
@@ -1383,7 +1383,7 @@
    "outputs": [],
    "source": [
     "tristr = []\n",
-    "ix = GridIntersect(trigrid, method=\"vertex\")\n",
+    "ix = GridIntersect(trigrid)\n",
     "for geom in nhddf.geometry.values:\n",
     "    nodes = ix.intersects(geom)[\"cellids\"]\n",
     "    tristr.extend(list(nodes))\n",
@@ -1519,7 +1519,7 @@
    "outputs": [],
    "source": [
     "vorst = []\n",
-    "ix = GridIntersect(vorgrid, method=\"vertex\")\n",
+    "ix = GridIntersect(vorgrid)\n",
     "for geom in nhddf.geometry.values:\n",
     "    nodes = ix.intersects(geom)[\"cellids\"]\n",
     "    vorst.extend(list(nodes))\n",

notebooks/part1_flopy/06-Project-structured.ipynb

@@ -143,7 +143,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ix = GridIntersect(base_grid, method=\"vertex\", rtree=True)"
+    "ix = GridIntersect(base_grid, rtree=True)"
    ]
   },
   {