use pooch for a few more examples

MODFLOW-USGS · Jan 11, 2024 · 8187830 · 8187830
1 parent 84a1e97
commit 8187830
Show file tree

Hide file tree

Showing 10 changed files with 71 additions and 65 deletions.
diff --git a/scripts/ex-gwf-advtidal.py b/scripts/ex-gwf-advtidal.py
@@ -19,11 +19,11 @@
 import flopy
 import matplotlib.pyplot as plt
 import numpy as np
+import pooch
 from flopy.plot.styles import styles
 from flopy.utils.gridintersect import GridIntersect
 from modflow_devtools.misc import timed
 from shapely.geometry import Polygon
-import pooch
 
 # Simulation name and workspace
 
@@ -191,7 +191,7 @@ def build_model():
     ghb_spd = {0: ghb_spd}
     fname = pooch.retrieve(
         url=f"https://github.com/MODFLOW-USGS/modflow6-examples/raw/master/data/{sim_name}/tides.csv",
-        known_hash="md5:425337a0bf24fa72c9e40f4e3d9f698a"
+        known_hash="md5:425337a0bf24fa72c9e40f4e3d9f698a",
     )
     tsdict = get_timeseries(fname, "tides", "linear")
     ghbobs_dict = {}
@@ -230,7 +230,7 @@ def build_model():
     ]
     fname = pooch.retrieve(
         url=f"https://github.com/MODFLOW-USGS/modflow6-examples/raw/master/data/{sim_name}/wellrates.csv",
-        known_hash="md5:6ca7366be279d679b14e8338a195422f"
+        known_hash="md5:6ca7366be279d679b14e8338a195422f",
     )
     tsdict = get_timeseries(
         fname,
@@ -263,7 +263,7 @@ def build_model():
     riv_spd = list(zip(rivlay, rivrow, rivcol, rivstg, rivcnd, rivrbt, rivbnd))
     fname = pooch.retrieve(
         url=f"https://github.com/MODFLOW-USGS/modflow6-examples/raw/master/data/{sim_name}/riverstage.csv",
-        known_hash="md5:83f8b526ec6e6978b1d9dbd6fde231ef"
+        known_hash="md5:83f8b526ec6e6978b1d9dbd6fde231ef",
     )
     tsdict = get_timeseries(
         fname,
@@ -281,7 +281,7 @@ def build_model():
     hashes = [
         "f8b9b26a3403101f3568cd42f759554f",
         "c1ea7ded8edf33d6d70a1daf2524584a",
-        "9ca294d3260c9d3c3487f8db498a0aa6"
+        "9ca294d3260c9d3c3487f8db498a0aa6",
     ]
     for ipak, p in enumerate([recharge_zone_1, recharge_zone_2, recharge_zone_3]):
         ix = GridIntersect(gwf.modelgrid, method="vertex", rtree=True)
@@ -298,7 +298,7 @@ def build_model():
             )
         fname = pooch.retrieve(
             url=f"https://github.com/MODFLOW-USGS/modflow6-examples/raw/master/data/{sim_name}/recharge{ipak + 1}.csv",
-            known_hash=f"md5:{hashes[ipak]}"
+            known_hash=f"md5:{hashes[ipak]}",
         )
         tsdict = get_timeseries(
             fname,

diff --git a/scripts/ex-gwf-bcf2ss.py b/scripts/ex-gwf-bcf2ss.py
@@ -17,14 +17,14 @@
 import matplotlib as mpl
 import matplotlib.pyplot as plt
 import numpy as np
+import pooch
 from flopy.plot.styles import styles
 from modflow_devtools.misc import timed
 
 # Simulation name and workspace
 
 sim_name = "ex-gwf-bcf2ss"
 ws = pl.Path("../examples")
-data_ws = pl.Path("../data")
 
 # Configuration
 
@@ -43,7 +43,10 @@
 
 # Load the wetdry array for layer 1
 
-pth = data_ws / sim_name / "wetdry01.txt"
+pth = pooch.retrieve(
+    url=f"https://github.com/MODFLOW-USGS/modflow6-examples/raw/master/data/{sim_name}/wetdry01.txt",
+    known_hash="md5:3a4b357b7d2cd5175a205f3347ab973d",
+)
 wetdry_layer0 = np.loadtxt(
     pth,
 )

diff --git a/scripts/ex-gwf-capture.py b/scripts/ex-gwf-capture.py
@@ -23,6 +23,7 @@
 import matplotlib.pyplot as plt
 import modflowapi
 import numpy as np
+import pooch
 from flopy.plot.styles import styles
 from modflow_devtools.misc import timed
 
@@ -48,16 +49,21 @@
 
 # Load the bottom, hydraulic conductivity, and idomain arrays
 
-bottom = np.loadtxt(
-    os.path.join("..", "data", sim_name, "bottom.txt"),
+pth = pooch.retrieve(
+    url=f"https://github.com/MODFLOW-USGS/modflow6-examples/raw/master/data/{sim_name}/bottom.txt",
+    known_hash="md5:201758a5b7febb0390b8b52e634be27f",
 )
-k11 = np.loadtxt(
-    os.path.join("..", "data", sim_name, "hydraulic_conductivity.txt"),
+bottom = np.loadtxt(pth)
+pth = pooch.retrieve(
+    url=f"https://github.com/MODFLOW-USGS/modflow6-examples/raw/master/data/{sim_name}/hydraulic_conductivity.txt",
+    known_hash="md5:6c78564ba92e850d7d51d6e957b8a3ff",
 )
-idomain = np.loadtxt(
-    os.path.join("..", "data", sim_name, "idomain.txt"),
-    dtype=np.int32,
+k11 = np.loadtxt(pth)
+pth = pooch.retrieve(
+    url=f"https://github.com/MODFLOW-USGS/modflow6-examples/raw/master/data/{sim_name}/idomain.txt",
+    known_hash="md5:435d4490adff7a35d1d4928661e45d81",
 )
+idomain = np.loadtxt(pth, dtype=np.int32)
 
 
 # Table Capture Fraction Model Parameters

diff --git a/scripts/ex-gwf-csub-p01.py b/scripts/ex-gwf-csub-p01.py
@@ -19,14 +19,14 @@
 import matplotlib as mpl
 import matplotlib.pyplot as plt
 import numpy as np
+import pooch
 from flopy.plot.styles import styles
 from modflow_devtools.misc import timed
 
 # Simulation name and workspace
 
 sim_name = "ex-gwf-csub-p01"
 ws = pl.Path("../examples")
-data_ws = pl.Path("../data")
 
 # Configuration
 
@@ -82,7 +82,10 @@
 
 # Load the aquifer load time series
 
-pth = data_ws / sim_name / "train_load_193704231304.csv"
+pth = pooch.retrieve(
+    url=f"https://github.com/MODFLOW-USGS/modflow6-examples/raw/master/data/{sim_name}/train_load_193704231304.csv",
+    known_hash="md5:32dc8e7b7e39876374af43605e264725",
+)
 csv_load = np.genfromtxt(pth, names=True, delimiter=",")
 
 # Reformat csv data into format for MODFLOW 6 timeseries file

diff --git a/scripts/ex-gwf-csub-p02.py b/scripts/ex-gwf-csub-p02.py
@@ -35,7 +35,6 @@
 
 sim_name = "ex-gwf-csub-p02"
 ws = pl.Path("../examples")
-data_ws = pl.Path("../data")
 
 # Scenario parameters
 

diff --git a/scripts/ex-gwf-csub-p03.py b/scripts/ex-gwf-csub-p03.py
@@ -34,7 +34,6 @@
 
 sim_name = "ex-gwf-csub-p03"
 ws = pl.Path("../examples")
-data_ws = pl.Path("../data")
 
 # Configuration
 

diff --git a/scripts/ex-gwf-csub-p04.py b/scripts/ex-gwf-csub-p04.py
@@ -25,7 +25,6 @@
 
 sim_name = "ex-gwf-csub-p03"
 ws = pl.Path("../examples")
-data_ws = pl.Path("../data")
 
 # Configuration
 

diff --git a/scripts/ex-gwf-disvmesh.py b/scripts/ex-gwf-disvmesh.py
@@ -19,6 +19,7 @@
 import flopy.utils.cvfdutil
 import matplotlib.pyplot as plt
 import numpy as np
+import pooch
 from flopy.plot.styles import styles
 from flopy.utils.geometry import get_polygon_area
 from flopy.utils.gridintersect import GridIntersect
@@ -32,7 +33,6 @@
 # Simulation name and workspace
 sim_name = "ex-gwf-disvmesh"
 ws = pl.Path("../examples")
-data_ws = pl.Path("../data")
 
 # Configuration
 
@@ -110,7 +110,10 @@ def from_argus_export(fname):
 
 # Load argus mesh and get disv grid properties
 
-fname = os.path.join(data_ws, "ex-gwf-disvmesh", "argus.exp")
+fname = pooch.retrieve(
+    url=f"https://github.com/MODFLOW-USGS/modflow6-examples/raw/master/data/ex-gwf-disvmesh/argus.exp",
+    known_hash="md5:072a758ca3d35831acb7e1e27e7b8524",
+)
 verts, iverts = from_argus_export(fname)
 gridprops = flopy.utils.cvfdutil.get_disv_gridprops(verts, iverts)
 cell_areas = []

diff --git a/scripts/ex-gwf-drn-p01.py b/scripts/ex-gwf-drn-p01.py
@@ -16,6 +16,7 @@
 import flopy
 import matplotlib.pyplot as plt
 import numpy as np
+import pooch
 from flopy.plot.styles import styles
 from modflow_devtools.latex import (build_table, exp_format, float_format,
                                     int_format)
@@ -30,7 +31,6 @@
 
 sim_name = "ex-gwf-drn-p01"
 ws = pl.Path("../examples")
-data_ws = pl.Path("../data")
 
 # Configuration
 
@@ -92,20 +92,36 @@
 
 # Load the idomain, top, bottom, and uzf/mvr arrays
 
-data_pth = data_ws / "ex-gwf-sfr-p01"
-fpth = os.path.join(data_pth, "idomain.txt")
+fpth = pooch.retrieve(
+    url=f"https://github.com/MODFLOW-USGS/modflow6-examples/raw/master/data/ex-gwf-sfr-p01/idomain.txt",
+    known_hash="md5:a0b12472b8624aecdc79e5c19c97040c",
+)
 idomain = np.loadtxt(fpth, dtype=int)
-fpth = os.path.join(data_pth, "bottom.txt")
+fpth = pooch.retrieve(
+    url=f"https://github.com/MODFLOW-USGS/modflow6-examples/raw/master/data/ex-gwf-sfr-p01/bottom.txt",
+    known_hash="md5:fa5fe276f4f58a01eabfe88516cc90af",
+)
 botm = np.loadtxt(fpth, dtype=float)
 
-data_pth = data_ws / sim_name
-fpth = os.path.join(data_pth, "top.txt")
+fpth = pooch.retrieve(
+    url=f"https://github.com/MODFLOW-USGS/modflow6-examples/raw/master/data/{sim_name}/top.txt",
+    known_hash="md5:88cc15f87824ebfd35ed5b4be7f68387",
+)
 top = np.loadtxt(fpth, dtype=float)
-fpth = os.path.join(data_pth, "infilt_mult.txt")
+fpth = pooch.retrieve(
+    url=f"https://github.com/MODFLOW-USGS/modflow6-examples/raw/master/data/{sim_name}/infilt_mult.txt",
+    known_hash="md5:8bf0a48d604263cb35151587a9d8ca29",
+)
 infilt_mult = np.loadtxt(fpth, dtype=float)
-fpth = os.path.join(data_pth, "extwc_mult.txt")
+fpth = pooch.retrieve(
+    url=f"https://github.com/MODFLOW-USGS/modflow6-examples/raw/master/data/{sim_name}/extwc_mult.txt",
+    known_hash="md5:6e289692a2b55b7bafb8bd9d71b0a2cb",
+)
 extwc_mult = np.loadtxt(fpth, dtype=float)
-fpth = os.path.join(data_pth, "routing_map.txt")
+fpth = pooch.retrieve(
+    url=f"https://github.com/MODFLOW-USGS/modflow6-examples/raw/master/data/{sim_name}/routing_map.txt",
+    known_hash="md5:1bf9a6bb3513a184aa5093485e622f5b",
+)
 routing_map = np.loadtxt(fpth, dtype=int)
 
 # convert routing map to zero-based reach numbers

diff --git a/scripts/process-scripts.py b/scripts/process-scripts.py
@@ -50,25 +50,20 @@
     >>> process-scripts.py -k *-maw-*  # process all MAW example problems.
 """
 import ast
+import fnmatch
 import os
 import re
 import sys
-import fnmatch
 
 import flopy
-
-from modflow_devtools.latex import get_header, get_footer
+from modflow_devtools.latex import get_footer, get_header
 
 # path to the example files
 ex_pth = os.path.join("..", "examples")
 
 # only process python files starting with ex_
 files = sorted(
-    [
-        file
-        for file in os.listdir()
-        if file.endswith(".py") and file.startswith("ex-")
-    ]
+    [file for file in os.listdir() if file.endswith(".py") and file.startswith("ex-")]
 )
 
 only_process_ex = []
@@ -89,9 +84,7 @@ def table_standard_header(caption, label):
         "Parameter",
         "Value",
     )
-    return get_header(
-        caption, label, headings, col_widths=col_widths, center=False
-    )
+    return get_header(caption, label, headings, col_widths=col_widths, center=False)
 
 
 def table_scenario_header(caption, label):
@@ -107,9 +100,7 @@ def table_scenario_header(caption, label):
         "Parameter",
         "Value",
     )
-    return get_header(
-        caption, label, headings, col_widths=col_widths, center=False
-    )
+    return get_header(caption, label, headings, col_widths=col_widths, center=False)
 
 
 def table_footer():
@@ -123,9 +114,7 @@ def make_tables():
 
     for file in files:
         print(f"processing...'{file}'")
-        basename = os.path.splitext(os.path.basename(file))[0].replace(
-            "_", "-"
-        )
+        basename = os.path.splitext(os.path.basename(file))[0].replace("_", "-")
         # do a little processing
         with open(file) as f:
             txt = f.read()
@@ -183,9 +172,7 @@ def make_tables():
                         except:
                             units = " (unknown)"
                     if len(table_line) > 0:
-                        table_line += "\t{}{} & {}".format(
-                            text_to_write, units, value
-                        )
+                        table_line += "\t{}{} & {}".format(text_to_write, units, value)
                     else:
                         table_line = "\t& & {}{} & {}".format(
                             text_to_write, units, value
@@ -338,14 +325,11 @@ def get_examples_dict(verbose=False):
                 if file_name.lower() == "mfsim.nam":
                     if verbose:
                         msg = (
-                            "  Found MODFLOW 6 simulation "
-                            + f"name file: {file_name}"
+                            "  Found MODFLOW 6 simulation " + f"name file: {file_name}"
                         )
                         print(msg)
                     print(f"Using flopy to load {dirName}")
-                    sim = flopy.mf6.MFSimulation.load(
-                        sim_ws=dirName, verbosity_level=0
-                    )
+                    sim = flopy.mf6.MFSimulation.load(sim_ws=dirName, verbosity_level=0)
                     sim_paks = []
                     for pak in sim.sim_package_list:
                         pak_type = pak.package_abbr
@@ -402,9 +386,7 @@ def build_md_tables(ex_dict):
     for ex_name in ex_paks.keys():
         for ex_root in ex_order:
             if ex_root in ex_name:
-                pak_link[ex_name] = "[{}](_examples/{}.html)".format(
-                    ex_name, ex_root
-                )
+                pak_link[ex_name] = "[{}](_examples/{}.html)".format(ex_name, ex_root)
                 break
         if ex_name not in list(pak_link.keys()):
             pak_link[ex_name] = ex_name
@@ -587,9 +569,7 @@ def build_tex_tables(ex_dict):
     for idx, ex in enumerate(ex_order):
         for key, d in ex_dict.items():
             if ex in key:
-                ex_number = [idx + 1] + [
-                    " " for i in range(len(d["paks"]) - 1)
-                ]
+                ex_number = [idx + 1] + [" " for i in range(len(d["paks"]) - 1)]
                 d["ex_number"] = ex_number
                 ex_tex[key] = d
 
@@ -611,9 +591,7 @@ def build_tex_tables(ex_dict):
     caption = "List of example problems and simulation characteristics."
     label = "tab:ex-table"
 
-    lines = get_header(
-        caption, label, headings, col_widths=col_widths, firsthead=True
-    )
+    lines = get_header(caption, label, headings, col_widths=col_widths, firsthead=True)
 
     on_ex = 0
     for idx, (key, sim_dict) in enumerate(ex_tex.items()):