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Work on comments, add linting workflow
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@dannbuckley
dannbuckley committed Jan 13, 2024
1 parent b2d09c4 commit 82cf627
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31 changes: 31 additions & 0 deletions .github/workflows/linting.yml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,31 @@
name: linting

on:
push:
branches: ["main"]
pull_request:
branches: ["main"]

jobs:
linting:
name: py${{ matrix.python-version }} on ${{ matrix.os }}
runs-on: ${{ matrix.os }}
strategy:
fail-fast: false
matrix:
os: ["ubuntu-latest"]
python-version: ["3.11"]
steps:
- uses: actions/checkout@v4
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
- name: Upgrade pip, setuptools, wheel
run: python3 -m pip install -U pip setuptools wheel
- name: Install flopy_mf6_work with runtime dependencies
run: python3 -m pip install .
- name: Install flopy_mf6_work with development dependencies
run: python3 -m pip install .[testing]
- name: Lint Python files
run: python3 -m pylint src/flopy_mf6_work/*
150 changes: 129 additions & 21 deletions src/flopy_mf6_work/gwf/twri01.py
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Original file line number Diff line number Diff line change
Expand Up @@ -89,9 +89,9 @@ def plot_mapview_unconfined(self):
-------
fig : matplotlib.figure.Figure
"""
fig, ax = plt.subplots()
ax.set_title("Map View of Unconfined Aquifer Layer", fontweight="bold")
mapview = fp.plot.PlotMapView(model=self._model, ax=ax)
fig, axes = plt.subplots()
axes.set_title("Map View of Unconfined Aquifer Layer", fontweight="bold")
mapview = fp.plot.PlotMapView(model=self._model, ax=axes)
mapview.plot_ibound()
mapview.plot_grid()

Expand All @@ -113,9 +113,9 @@ def plot_mapview_middle_confined(self):
-------
fig : matplotlib.figure.Figure
"""
fig, ax = plt.subplots()
ax.set_title("Map View of Middle Confined Aquifer Layer", fontweight="bold")
mapview = fp.plot.PlotMapView(model=self._model, ax=ax, layer=2)
fig, axes = plt.subplots()
axes.set_title("Map View of Middle Confined Aquifer Layer", fontweight="bold")
mapview = fp.plot.PlotMapView(model=self._model, ax=axes, layer=2)
mapview.plot_ibound()
mapview.plot_grid()

Expand All @@ -135,9 +135,9 @@ def plot_mapview_lower_confined(self):
-------
fig : matplotlib.figure.Figure
"""
fig, ax = plt.subplots()
ax.set_title("Map View of Lower Confined Aquifer Layer", fontweight="bold")
mapview = fp.plot.PlotMapView(model=self._model, ax=ax, layer=4)
fig, axes = plt.subplots()
axes.set_title("Map View of Lower Confined Aquifer Layer", fontweight="bold")
mapview = fp.plot.PlotMapView(model=self._model, ax=axes, layer=4)
mapview.plot_ibound()
mapview.plot_grid()

Expand All @@ -148,7 +148,11 @@ def plot_mapview_lower_confined(self):
return fig

def _add_sim_tdis(self):
"""Add Temporal Discretization (TDIS) packge to simulation."""
"""Add Temporal Discretization (TDIS) packge to simulation.
A single steady-stress period with a total length of 86,400 seconds
(1 day) is simulated.
"""
try:
fp.mf6.ModflowTdis(
simulation=getattr(self, "_simulation"),
Expand Down Expand Up @@ -180,7 +184,15 @@ def _add_sim_ims(self):
pass

def _add_model_dis(self):
"""Add Structured Discretization (DIS) to model."""
"""Add Structured Discretization (DIS) to model.
There are three simulated aquifers, which are separated from each other by confining layers.
The confining beds are 50 ft thick and are explicitly simulated as
model layers 2 and 4, respectively.
Each layer is a square 75,000 ft on a side and is divided into a
grid with 15 rows and 15 columns,
which forms squares 5,000 ft on a side.
"""
try:
fp.mf6.ModflowGwfdis(
model=getattr(self, "_model"),
Expand All @@ -190,8 +202,20 @@ def _add_model_dis(self):
ncol=15,
delr=5000.0,
delc=5000.0,
# top of unconfined aquifer
top=200.0,
botm=[-150.0, -200.0, -300.0, -350.0, -450.0],
botm=[
# bottom of unconfined aquifer
-150.0,
# bottom of first confining unit
-200.0,
# bottom of middle confined aquifer
-300.0,
# bottom of second confining unit
-350.0,
# bottom of lower confined aquifer
-450.0,
],
filename=f"{self.sim_name}.dis",
pname="dis",
)
Expand All @@ -200,15 +224,50 @@ def _add_model_dis(self):
pass

def _add_model_npf(self):
"""Add Node Property Flow (NPF) package to model."""
"""Add Node Property Flow (NPF) package to model.
The transmissivity of the middle and lower aquifers was converted to
a horizontal hydraulic conductivity using the layer thickness. The
vertical hydraulic conductivity in the aquifers was set equal to the
horizontal hydraulic conductivity. The vertical hydraulic conductivity
of the confining units was calculated from the vertical conductance
of the confining beds defined in the original problem and the
confining unit thickness; the horizontal hydraulic conductivity of
the confining bed was set to the vertical hydraulic conductivity
and results in vertical flow in the confining unit.
"""
try:
k = [0.001, 1e-8, 0.0001, 5e-7, 0.0002]
k = [
# unconfined aquifer
0.001,
# first confining unit
1e-8,
# middle confined aquifer
0.0001,
# second confining unit
5e-7,
# lower confined aquifer
0.0002,
]
fp.mf6.ModflowGwfnpf(
model=getattr(self, "_model"),
cvoptions=[(True, "DEWATERED")],
# when a cell is overlying a dewatered convertible cell, the head difference
# used in Darcy's Law is equal to the head in the overlying cell minus
# the bottom elevation of the overlying cell
perched=True,
save_specific_discharge=True,
icelltype=[1, 0, 0, 0, 0],
icelltype=[
# first layer: saturated thickness varies with computed head when
# head is below the cell top
# (i.e., first layer is unconfined)
1,
# remaining layers: saturated thickness is held constant
0,
0,
0,
0,
],
k=k,
k33=k,
filename=f"{self.sim_name}.npf",
Expand All @@ -219,10 +278,16 @@ def _add_model_npf(self):
pass

def _add_model_ic(self):
"""Add Initial Conditions (IC) package to model."""
"""Add Initial Conditions (IC) package to model.
An initial head of zero ft was specified in all model layers.
Any initial head exceeding the bottom of model layer 1 (-150 ft)
could be specified since the model is steady-state.
"""
try:
fp.mf6.ModflowGwfic(
model=getattr(self, "_model"),
# initial (starting) head
strt=0.0,
filename=f"{self.sim_name}.ic",
pname="ic",
Expand All @@ -232,7 +297,11 @@ def _add_model_ic(self):
pass

def _add_model_chd(self):
"""Add Constant-Head (CHD) package to model."""
"""Add Constant-Head (CHD) package to model.
Flow out of the model is partly from a lake represented by
constant head (CHD) package cells in the unconfined and middle aquifers.
"""

def _make_chd_iter() -> Iterator[tuple[tuple[int, int, int], float]]:
"""Generate constant-head data for model.
Expand All @@ -243,13 +312,21 @@ def _make_chd_iter() -> Iterator[tuple[tuple[int, int, int], float]]:
((layer, row, column), head)
"""
for layer in [0, 2]:
# layer = 0: unconfined aquifer
# layer = 2: middle confined aquifer
for row in range(15):
# apply constant-head to entire first column
yield ((layer, row, 0), 0.0)

try:
fp.mf6.ModflowGwfchd(
model=getattr(self, "_model"),
# maximum number of constant-head cells that will be specified
# for use during any stress period
maxbound=30,
# list of (cellid, head)
# cellid: (layer, row, column)
# head: 0
stress_period_data=list(_make_chd_iter()),
filename=f"{self.sim_name}.chd",
pname="chd_0",
Expand All @@ -259,7 +336,11 @@ def _make_chd_iter() -> Iterator[tuple[tuple[int, int, int], float]]:
pass

def _add_model_drn(self):
"""Add Drain (DRN) package to model."""
"""Add Drain (DRN) package to model.
Flow out of the model is partly from buried drain tubes represented by
drain (DRN) pacakge cells in model layer 1.
"""

def _make_drn_iter() -> Iterator[tuple[tuple[int, int, int], float, float]]:
"""Generate drain data for model.
Expand All @@ -275,7 +356,14 @@ def _make_drn_iter() -> Iterator[tuple[tuple[int, int, int], float, float]]:
try:
fp.mf6.ModflowGwfdrn(
model=getattr(self, "_model"),
# maximum number of drain cells that will be specified
# for use during any stress period
maxbound=9,
# list of (cellid, elev, cond)
# cellid: (layer, row, column)
# elev: elevation of the drain
# cond: hydraulic conductance of the interface between the aquifer
# and the drain
stress_period_data=list(_make_drn_iter()),
filename=f"{self.sim_name}.drn",
pname="drn_0",
Expand All @@ -285,7 +373,11 @@ def _make_drn_iter() -> Iterator[tuple[tuple[int, int, int], float, float]]:
pass

def _add_model_wel(self):
"""Add Well (WEL) package to model."""
"""Add Well (WEL) package to model.
Flow out of the model is partly from discharging wells represented by
well (WEL) package cells in all three aquifers.
"""

def _make_wel_iter() -> Iterator[tuple[tuple[int, int, int], float]]:
"""Generate well data for model.
Expand All @@ -297,6 +389,7 @@ def _make_wel_iter() -> Iterator[tuple[tuple[int, int, int], float]]:
# wells in unconfined aquifer
for row in range(8, 13, 2):
for col in range(7, 14, 2):
# negative well rate indicates discharge (extraction)
yield ((0, row, col), -5.0)

# wells in middle confined aquifer
Expand All @@ -309,7 +402,12 @@ def _make_wel_iter() -> Iterator[tuple[tuple[int, int, int], float]]:
try:
fp.mf6.ModflowGwfwel(
model=getattr(self, "_model"),
# maximum number of well cells that will be specified
# for use during any stress period
maxbound=15,
# list of (cellid, q)
# cellid: (layer, row, column)
# q: volumetric well rate
stress_period_data=list(_make_wel_iter()),
filename=f"{self.sim_name}.wel",
pname="wel_0",
Expand All @@ -319,10 +417,16 @@ def _make_wel_iter() -> Iterator[tuple[tuple[int, int, int], float]]:
pass

def _add_model_rcha(self):
"""Add Recharge (RCH) package to model (array-based version)."""
"""Add Recharge (RCH) package to model (array-based version).
Flow into the system is from infiltration from precipitation and was
represented using the recharge (RCH) package. A constant recharge rate
was specified for every cell in model layer 1.
"""
try:
fp.mf6.ModflowGwfrcha(
model=getattr(self, "_model"),
# recharge flux rate (L / T)
recharge=3e-8,
filename=f"{self.sim_name}.rcha",
pname="rcha_0",
Expand All @@ -336,10 +440,14 @@ def _add_model_oc(self):
try:
fp.mf6.ModflowGwfoc(
model=getattr(self, "_model"),
# output file for budget info
budget_filerecord=[f"{self.sim_name}.cbc"],
# output file for head info
head_filerecord=[f"{self.sim_name}.hds"],
# list of (rtype, ocsetting)
# rtype: type of info
# ocsetting: which steps
saverecord=[("head", "all"), ("budget", "all")],
# printrecord=None,
filename=f"{self.sim_name}.oc",
pname="oc",
)
Expand Down

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