Merge pull request #128 from aleaf/main

Peer review revisions; fix some markdown headers for the doc menus; clear output in all notebooks except 10: MODPATH
DOI-USGS · Mar 18, 2024 · f658558 · f658558
2 parents 79537e6 + d364b6d
commit f658558
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diff --git a/docs/docs-environment.yml b/docs/docs-environment.yml
@@ -30,12 +30,14 @@ dependencies:
   - geos
   - geojson
   - geopandas
-  - vtk
   - xarray
   - rioxarray
   - uxarray
   - pyyaml
   - rtree
+  - pyvista
+  - vtk
+  - imageio
   - requests
   - pytest
   - statsmodels

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -267,16 +267,19 @@
     source_path / 'part0_python_intro/solutions/07a_Theis-exercise-solution.ipynb',
     source_path / 'part0_python_intro/07b_VSCode.md',
     source_path / 'part0_python_intro/solutions/08_pandas.ipynb',
-    source_path / 'part0_python_intro/data/pandas',
+    source_path / 'part0_python_intro/data/',
     source_path / 'part0_python_intro/09_Geopandas.ipynb',
     source_path / 'part0_python_intro/data/geopandas',
     source_path / 'part0_python_intro/solutions/09_Geopandas__solutions.ipynb',
     source_path / 'part0_python_intro/10_Rasterio.ipynb',
     source_path / 'part0_python_intro/11_xarray_mt_rainier_precip.ipynb',
     source_path / 'part1_flopy/solutions/02-Building-Post-Processing-MODFLOW6__solutions.ipynb',
+    source_path / 'part1_flopy/data/',
+    source_path / 'part1_flopy/data_project/',
     source_path / 'part1_flopy/solutions/03_Loading_and_visualizing_models-solutions.ipynb',
     source_path / 'part1_flopy/solutions/04_Modelgrid_and_intersection_solution.ipynb',
     source_path / 'part1_flopy/05-unstructured-grids.ipynb',
+    source_path / 'part1_flopy/basin.py',
     source_path / 'part1_flopy/solutions/06-Project-quadtree.ipynb',
     source_path / 'part1_flopy/solutions/06-Project-structured_completed.ipynb',
     source_path / 'part1_flopy/solutions/06-Project-voronoi.ipynb',
@@ -292,7 +295,7 @@
     dest_f = dest_path / f.relative_to(source_path)
     dest_f.parent.mkdir(exist_ok=True, parents=True)
     if f.is_dir():
-        shutil.copytree(f, dest_f)
+        shutil.copytree(f, dest_f, dirs_exist_ok=True)
     else:
         shutil.copy(f, dest_f)
     print(f"copied {f} to {dest_f}")

diff --git a/installation/environment.yml b/installation/environment.yml
@@ -30,7 +30,6 @@ dependencies:
   - geos
   - geojson
   - geopandas
-  - vtk
   - xarray
   - rioxarray
   - uxarray
@@ -46,6 +45,5 @@ dependencies:
   - flopy
   - gis-utils
   - sfrmaker
-  - imageio
   - modflow-export
   - modflow-setup
diff --git a/notebooks/clear_all_notebooks.py b/notebooks/clear_all_notebooks.py
@@ -7,14 +7,14 @@
 # all solutions are still not being cleared
 
 skip_notebooks = [
-    '10_Rasterio.ipynb',
-    '11_xarray_mt_rainier_precip.ipynb',
-    '09_Geopandas_ABQ.ipynb',
+    #'10_Rasterio.ipynb',
+    #'11_xarray_mt_rainier_precip.ipynb',
+    #'09_Geopandas_ABQ.ipynb',
     #'03_Loading_and_visualizing_models-solutions.ipynb',
-    '05-unstructured-grids.ipynb',
-    '07-stream_capture_voronoi.ipynb',
-    '08_Modflow-setup-demo.ipynb',
-    '09-gwt-voronoi-demo.ipynb',
+    #'05-unstructured-grids.ipynb',
+    #'07-stream_capture_voronoi.ipynb',
+    #'08_Modflow-setup-demo.ipynb',
+    #'09-gwt-voronoi-demo.ipynb',
     '10_modpath-demo.ipynb'
     ]
 

diff --git a/notebooks/part0_python_intro/03_useful-std-library-modules.ipynb b/notebooks/part0_python_intro/03_useful-std-library-modules.ipynb
@@ -11,24 +11,24 @@
     "\n",
     "\n",
     "#### Topics covered:\n",
-    "* **``pathlib``**:\n",
+    "* **pathlib**:\n",
     "    * listing files\n",
     "    * creating, moving and deleting files\n",
     "    * absolute vs relative paths\n",
     "    * useful path object attributes\n",
-    "* **``shutil``**: \n",
+    "* **shutil**: \n",
     "    * copying, moving and deleting files AND folders\n",
-    "* **``sys``**: \n",
+    "* **sys**: \n",
     "    * python and platform information\n",
     "    * command line arguments\n",
     "    * modifying the python path to import code from other locations\n",
-    "* **``os``**:\n",
+    "* **os**:\n",
     "    * changing the working directory\n",
     "    * recursive iteration through folder structures\n",
     "    * accessing environmental variables\n",
-    "* **``subprocess``**: \n",
+    "* **subprocess**: \n",
     "    * running system commands and checking the results\n",
-    "* **``zipfile``**:\n",
+    "* **zipfile**:\n",
     "    * creating and extracting from zip archives"
    ]
   },
@@ -528,7 +528,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Delete the file"
+    "Move the file"
    ]
   },
   {
@@ -537,7 +537,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fname.unlink()"
+    "fname2 = Path('new_file2.txt')\n",
+    "fname.rename(fname2)"
    ]
   },
   {
@@ -549,6 +550,31 @@
     "fname.exists()"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Delete the file"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "fname2.unlink()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "fname2.exists()"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -920,6 +946,22 @@
     "print(subprocess.run(['ls', '-l'], shell=True))"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "With the `cwd` argument, we can control the working directory for the command. Here we list the files in the parent directory."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "print(subprocess.run(['ls', '-l'], shell=True, cwd='..'))"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -1206,8 +1248,22 @@
   }
  ],
  "metadata": {
+  "kernelspec": {
+   "display_name": "pyclass",
+   "language": "python",
+   "name": "python3"
+  },
   "language_info": {
-   "name": "python"
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.7"
   }
  },
  "nbformat": 4,

diff --git a/notebooks/part0_python_intro/09_Geopandas_ABQ.ipynb b/notebooks/part0_python_intro/09_Geopandas_ABQ.ipynb
diff --git a/notebooks/part0_python_intro/10_Rasterio.ipynb b/notebooks/part0_python_intro/10_Rasterio.ipynb
diff --git a/notebooks/part0_python_intro/11_xarray_mt_rainier_precip.ipynb b/notebooks/part0_python_intro/11_xarray_mt_rainier_precip.ipynb
diff --git a/notebooks/part0_python_intro/solutions/03_useful-std-library-modules-solutions.ipynb b/notebooks/part0_python_intro/solutions/03_useful-std-library-modules-solutions.ipynb
@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## 03: Solutions to Useful standard library modules exercises"
+    "# 03: Solutions to Useful standard library modules exercises"
    ]
   },
   {

diff --git a/notebooks/part0_python_intro/solutions/07a_Theis-exercise-solution.ipynb b/notebooks/part0_python_intro/solutions/07a_Theis-exercise-solution.ipynb
diff --git a/notebooks/part1_flopy/02-Building-Post-Processing-MODFLOW6.ipynb b/notebooks/part1_flopy/02-Building-Post-Processing-MODFLOW6.ipynb
@@ -1,17 +1,5 @@
 {
  "cells": [
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import numpy as np\n",
-    "import matplotlib.pyplot as plt\n",
-    "import flopy\n",
-    "from flopy.plot import styles"
-   ]
-  },
   {
    "attachments": {
     "ex01a.png": {
@@ -28,12 +16,29 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Building and post-processing a MODFLOW 6 model\n",
+    "# 02: Building and post-processing a MODFLOW 6 model\n",
     "\n",
     "A MODFLOW 6 model will be developed of the domain shown above. This model simulation is based on example 1 in [Pollock, D.W., 2016, User guide for MODPATH Version 7—A particle-tracking model for MODFLOW: U.S. Geological Survey Open-File Report 2016–1086, 35 p., http://dx.doi.org/10.3133/ofr20161086](https://doi.org/10.3133/ofr20161086).\n",
     "\n",
-    "The model domain will be discretized into 3 layers, 21 rows, and 20 columns. A constant value of 500. will `delr` and `delc`. The top of the model should be set to 400 and the bottom of the three layers should be set to 220, 200, and 0. The model has one steady-state stress period. \n",
-    "\n",
+    "The model domain will be discretized into 3 layers, 21 rows, and 20 columns. A constant value of 500. will `delr` and `delc`. The top of the model should be set to 400 and the bottom of the three layers should be set to 220, 200, and 0. The model has one steady-state stress period. "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "import matplotlib.pyplot as plt\n",
+    "import flopy\n",
+    "from flopy.plot import styles"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
     "Create a simulation object, a time discretization object, and a iterative model solution object using `flopy.mf6.MFSimulation()`, `flopy.mf6.ModflowTdis()`, and `flopy.mf6.ModflowIms()`, respectively. Use default values for all iterative model solution variables.\n",
     "\n",
     "Before creating the simulation object you should define the simulation workspace (`sim_ws`) where the model files are, the simulation name (`name`), and the name and path of the model executable (`exe_name`).  The `sim_ws` should be set to `'data/ex01b'`, `name` should be set to `ex01b`, and `exe_name` should be set to `bin/mf6`."
@@ -45,7 +50,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ws = \"./temp/ex01b\"\n",
+    "ws = \"./temp/ex01b\" \n",
     "name = \"ex01b\"\n",
     "exe_name = \"mf6\""
    ]