Merge pull request #58 from jdhughes-usgs/pws_deps

more pywatershed updates

.github/workflows/ci.yml

@@ -178,19 +178,11 @@ jobs:
           cache-environment: true
           cache-downloads: true
 
-     # - name: Install miniconda
-     #    uses: conda-incubator/setup-miniconda@v3
-     #    with:
-     #      python-version: ${{ matrix.python-version }}
-     #      environment-file: "environment-pywatershed.yml"
-     #      activate-environment: "gw3099pws"
-     #      auto-activate-base: false
-
       - name: Install pywatershed
         working-directory: exercises/pywatershed
         run: |
-          git clone https://github.com/EC-USGS/pywatershed.git
-          cd pywatershed
+          git clone https://github.com/EC-USGS/pywatershed.git pywatershed_repo
+          cd pywatershed_repo
           git checkout feat_gw3099
           pip install -e .
 

.gitignore

@@ -181,11 +181,11 @@ exercises-completed/gwt/ex*/
 exercises-completed/gwe/gwe-ex0-stallman/
 exercises-completed/parallel/base/
 exercises-completed/parallel/parallel/
-exercises/pywatershed/pywatershed/
+exercises/pywatershed/pywatershed_repo
 exercises/pywatershed/step1_processes/
 exercises/pywatershed/step2_multi-process_models/
-exercises-completed/pywatershed/step1_processes/
-exercises-completed/pywatershed/step2_multi-process_models/
+exercises/pywatershed/step3_mf6_api/
+exercises/pywatershed/step4_flow_graph/
 exercises-working/
 
 # presentations

.scripts/test_notebooks.py

@@ -19,7 +19,6 @@
     pl.Path("../exercises/modflowapi/").resolve(),
     pl.Path("../exercises-completed/modflowapi/").resolve(),
     pl.Path("../exercises/parallel/").resolve(),
-    pl.Path("../exercises-completed/pywatershed/").resolve(),
     pl.Path("../exercises/netcdf/").resolve(),
     pl.Path("../exercises/PEST/notebooks").resolve(),
     pl.Path("../exercises/pywatershed").resolve(),
@@ -28,6 +27,7 @@
     "step0_netcdf_output": ("win32",),
     "step1_netcdf_input": ("win32",),
     "step2_netcdf_ncf": ("win32",),
+    "step3_mf6_api": ("win32"),
 }
 
 GIT_RESET_DIRS = (

exercises/pywatershed/helpers.py

@@ -0,0 +1,33 @@
+import pathlib as pl
+
+from IPython.core.magic import register_cell_magic
+
+
+@register_cell_magic
+def do_not_run_this_cell(line, cell):
+    return
+
+
+def read_yaml(yaml_file: pl.Path) -> dict:
+    import yaml
+
+    with pl.Path(yaml_file).open("r") as file_stream:
+        yaml_dict = yaml.load(file_stream, Loader=yaml.Loader)
+    return yaml_dict
+
+
+def write_yaml(yaml_dict: dict, yaml_file: pl.Path):
+    import yaml
+
+    with open(yaml_file, "w") as file:
+        _ = yaml.dump(yaml_dict, file)
+    return None
+
+
+def help_head(what, n=22):
+    """Equivalent to help() but we get the multiline string and just look the first n lines."""
+    import pydoc
+
+    the_help = pydoc.render_doc(what, "Help on %s")
+    print("\n".join(the_help.splitlines()[0:n]))
+    return

exercises/pywatershed/step0_intro_to_pywatershed.ipynb

@@ -84,13 +84,13 @@
     "\n",
     "```\n",
     "cd <path_to>/GW3099-2024/exercises/pywatershed\n",
-    "git clone https://github.com/EC-USGS/pywatershed.git\n",
-    "cd pywatershed\n",
+    "git clone https://github.com/EC-USGS/pywatershed.git pywatershed_repo\n",
+    "cd pywatershed_repo\n",
     "git checkout feat_gw3099\n",
     "pip install -e .\n",
     "```\n",
     "\n",
-    "When you see that version 3.0 is available at [https://github.com/EC-USGS/pywatershed/releases](https://github.com/EC-USGS/pywatershed/releases), please delete the repository at `<path_to>/GW3099-2024/exercises/pywatershed/pywatershed` and repeat the above steps but checking out `git checkout v3.0.0` instead of what is listed above. Or, at that time, you can also simply `conda install pywatershed`. \n",
+    "When you see that version 3.0 is available at [https://github.com/EC-USGS/pywatershed/releases](https://github.com/EC-USGS/pywatershed/releases), please delete the repository at `<path_to>/GW3099-2024/exercises/pywatershed/pywatershed_repo` and repeat the above steps but checking out `git checkout v3.0.0` instead of what is listed above. Or, at that time, you can also simply `conda install pywatershed`. \n",
     "\n",
     "## Learn more about pywatershed\n",
     "\n",

exercises-completed/pywatershed/step1_processes.ipynb → exercises/pywatershed/step1_processes.ipynb

@@ -12,7 +12,8 @@
     "\n",
     "![title](../../images/ClassLocation.jpg)\n",
     "\n",
-    "# Physical process models in pywatershed"
+    "# Physical process models in pywatershed\n",
+    "*(Note that this notebook follows nearly identically to the notebook in the pywatershed repository [examples/00_processes.ipynb](https://github.com/EC-USGS/pywatershed/blob/develop/examples/00_processes.ipynb))*"
    ]
   },
   {
@@ -61,14 +62,14 @@
    "outputs": [],
    "source": [
     "import pathlib as pl\n",
-    "import pydoc\n",
     "from pprint import pprint\n",
     "\n",
     "import hvplot.xarray  # noqa\n",
     "import jupyter_black\n",
     "import numpy as np\n",
     "import pywatershed as pws\n",
     "import xarray as xr\n",
+    "from helpers import help_head\n",
     "from pywatershed.utils import gis_files\n",
     "from tqdm.notebook import tqdm\n",
     "\n",
@@ -96,10 +97,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# this is equivalent to help() but we get the multiline string and just look at part of it\n",
-    "prms_gw_help = pydoc.render_doc(pws.PRMSGroundwater, \"Help on %s\")\n",
-    "# the first 22 lines of help(pws.PRMSGroundwater)\n",
-    "print(\"\\n\".join(prms_gw_help.splitlines()[0:22]))"
+    "help_head(pws.PRMSGroundwater, n=22)"
    ]
   },
   {