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fix(url): use modern DOI and USGS prefixes; upgrade other HTTP->HTTPS (
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2 changes: 1 addition & 1 deletion .docs/make.bat
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Expand Up @@ -21,7 +21,7 @@ if errorlevel 9009 (
echo.may add the Sphinx directory to PATH.
echo.
echo.If you don't have Sphinx installed, grab it from
echo.http://sphinx-doc.org/
echo.https://www.sphinx-doc.org/
exit /b 1
)

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2 changes: 1 addition & 1 deletion CONTRIBUTING.md
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Expand Up @@ -216,4 +216,4 @@ The footer should contain any information about **Breaking Changes** and is also

[coc]: https://github.com/modflowpy/flopy/blob/develop/CODE_OF_CONDUCT.md
[github]: https://github.com/modflowpy/flopy
[stackoverflow]: http://stackoverflow.com/questions/tagged/flopy
[stackoverflow]: https://stackoverflow.com/questions/tagged/flopy
12 changes: 6 additions & 6 deletions README.md
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Expand Up @@ -143,20 +143,20 @@ How to Cite

##### ***Citation for FloPy:***

[Bakker, Mark, Post, Vincent, Langevin, C. D., Hughes, J. D., White, J. T., Starn, J. J. and Fienen, M. N., 2016, Scripting MODFLOW Model Development Using Python and FloPy: Groundwater, v. 54, p. 733–739, doi:10.1111/gwat.12413.](http://dx.doi.org/10.1111/gwat.12413)
[Bakker, Mark, Post, Vincent, Langevin, C. D., Hughes, J. D., White, J. T., Starn, J. J. and Fienen, M. N., 2016, Scripting MODFLOW Model Development Using Python and FloPy: Groundwater, v. 54, p. 733–739, doi:10.1111/gwat.12413.](https://doi.org/10.1111/gwat.12413)

##### ***Software/Code citation for FloPy:***

[Bakker, Mark, Post, Vincent, Hughes, J. D., Langevin, C. D., White, J. T., Leaf, A. T., Paulinski, S. R., Bellino, J. C., Morway, E. D., Toews, M. W., Larsen, J. D., Fienen, M. N., Starn, J. J., and Brakenhoff, Davíd, 2022, FloPy v3.3.6 — release candidate: U.S. Geological Survey Software Release, 08 March 2022, http://dx.doi.org/10.5066/F7BK19FH](http://dx.doi.org/10.5066/F7BK19FH)
[Bakker, Mark, Post, Vincent, Hughes, J. D., Langevin, C. D., White, J. T., Leaf, A. T., Paulinski, S. R., Bellino, J. C., Morway, E. D., Toews, M. W., Larsen, J. D., Fienen, M. N., Starn, J. J., and Brakenhoff, Davíd, 2022, FloPy v3.3.6 — release candidate: U.S. Geological Survey Software Release, 08 March 2022, https://doi.org/10.5066/F7BK19FH](https://doi.org/10.5066/F7BK19FH)


MODFLOW Resources
-----------------------------------------------

+ [MODFLOW and Related Programs](http://water.usgs.gov/ogw/modflow/)
+ [Online guide for MODFLOW-2000](http://water.usgs.gov/nrp/gwsoftware/modflow2000/Guide/index.html)
+ [Online guide for MODFLOW-2005](http://water.usgs.gov/ogw/modflow/MODFLOW-2005-Guide/)
+ [Online guide for MODFLOW-NWT](http://water.usgs.gov/ogw/modflow-nwt/MODFLOW-NWT-Guide/)
+ [MODFLOW and Related Programs](https://water.usgs.gov/ogw/modflow/)
+ [Online guide for MODFLOW-2000](https://water.usgs.gov/nrp/gwsoftware/modflow2000/Guide/)
+ [Online guide for MODFLOW-2005](https://water.usgs.gov/ogw/modflow/MODFLOW-2005-Guide/)
+ [Online guide for MODFLOW-NWT](https://water.usgs.gov/ogw/modflow-nwt/MODFLOW-NWT-Guide/)


Disclaimer
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4 changes: 2 additions & 2 deletions docs/PyPI_release.md
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Expand Up @@ -26,11 +26,11 @@ How to Cite

*Citation for FloPy:*

[Bakker, Mark, Post, Vincent, Langevin, C. D., Hughes, J. D., White, J. T., Starn, J. J. and Fienen, M. N., 2016, Scripting MODFLOW Model Development Using Python and FloPy: Groundwater, v. 54, p. 733–739, doi:10.1111/gwat.12413.](http://dx.doi.org/10.1111/gwat.12413)
[Bakker, Mark, Post, Vincent, Langevin, C. D., Hughes, J. D., White, J. T., Starn, J. J. and Fienen, M. N., 2016, Scripting MODFLOW Model Development Using Python and FloPy: Groundwater, v. 54, p. 733–739, doi:10.1111/gwat.12413.](https://doi.org/10.1111/gwat.12413)

*Software/Code citation for FloPy:*

[Bakker, Mark, Post, Vincent, Hughes, J. D., Langevin, C. D., White, J. T., Leaf, A. T., Paulinski, S. R., Bellino, J. C., Morway, E. D., Toews, M. W., Larsen, J. D., Fienen, M. N., Starn, J. J., and Brakenhoff, Davíd, 2022, FloPy v3.3.6 — release candidate: U.S. Geological Survey Software Release, 08 March 2022, http://dx.doi.org/10.5066/F7BK19FH](http://dx.doi.org/10.5066/F7BK19FH)
[Bakker, Mark, Post, Vincent, Hughes, J. D., Langevin, C. D., White, J. T., Leaf, A. T., Paulinski, S. R., Bellino, J. C., Morway, E. D., Toews, M. W., Larsen, J. D., Fienen, M. N., Starn, J. J., and Brakenhoff, Davíd, 2022, FloPy v3.3.6 — release candidate: U.S. Geological Survey Software Release, 08 March 2022, https://doi.org/10.5066/F7BK19FH](https://doi.org/10.5066/F7BK19FH)


Disclaimer
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6 changes: 3 additions & 3 deletions docs/notebook_examples.md
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Expand Up @@ -45,9 +45,9 @@ The following jupyter Notebooks contain examples for using FloPy pre- and post-p

+ The [lake example](../examples/Notebooks/flopy3_lake_example.ipynb), a very simple FloPy example of steady flow in a square model with a fixed head cell in the middle (representing a lake) in a 10-layer model.

+ A variant of the [water-table example](../examples/Notebooks/flopy3_WatertableRecharge_example.ipynb), a very simple example of one-dimensional groundwater flow in an unconfined aquifer with recharge, from the MODFLOW-NWT documentation (http://pubs.usgs.gov/tm/tm6a37/). This IPython Notebook build files for MODFLOW-NWT.
+ A variant of the [water-table example](../examples/Notebooks/flopy3_WatertableRecharge_example.ipynb), a very simple example of one-dimensional groundwater flow in an unconfined aquifer with recharge, from the MODFLOW-NWT documentation (https://pubs.usgs.gov/tm/tm6a37/). This IPython Notebook build files for MODFLOW-NWT.

+ The [Zaidel discontinuous water-table example](../examples/Notebooks/flopy3_Zaidel_example.ipynb), which simulates a discontinuous water table over a stairway impervious base, from http://onlinelibrary.wiley.com/doi/10.1111/gwat.12019/abstract. This IPython Notebook build files for MODFLOW-USG. (http://pubs.usgs.gov/tm/06/a45/).
+ The [Zaidel discontinuous water-table example](../examples/Notebooks/flopy3_Zaidel_example.ipynb), which simulates a discontinuous water table over a stairway impervious base, from https://doi.org/10.1111/gwat.12019. This IPython Notebook build files for MODFLOW-USG. (https://pubs.usgs.gov/tm/06/a45/).

+ The [MT3DMS Example Problems](../examples/Notebooks/flopy3_MT3DMS_examples.ipynb), which uses to Flopy to reproduce the ten example problems described in the MT3DMS documentation report by Zheng and Wang (1999).

Expand All @@ -59,7 +59,7 @@ The following jupyter Notebooks contain examples for using FloPy pre- and post-p

+ The [Henry Problem](../examples/Notebooks/flopy3_SEAWAT_henry_problem.ipynb), a simple saltwater intrusion model developed with FloPy and run using SEAWAT.

##### ***Examples from [Bakker, M., Post, V., Langevin, C. D., Hughes, J. D., White, J. T., Starn, J. J. and Fienen, M. N., 2016, Scripting MODFLOW Model Development Using Python and FloPy: Groundwater, v. 54, p. 733–739, doi:10.1111/gwat.12413.](http://dx.doi.org/10.1111/gwat.12413)***
##### ***Examples from [Bakker, M., Post, V., Langevin, C. D., Hughes, J. D., White, J. T., Starn, J. J. and Fienen, M. N., 2016, Scripting MODFLOW Model Development Using Python and FloPy: Groundwater, v. 54, p. 733–739, doi:10.1111/gwat.12413.](https://doi.org/10.1111/gwat.12413)***

+ [A basic FloPy example](../examples/groundwater_paper/Notebooks/example_1.ipynb) Notebook.

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2 changes: 1 addition & 1 deletion docs/script_examples.md
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Expand Up @@ -3,7 +3,7 @@ Examples

### [Python Script Examples]

FloPy scripts for running and post-processing the lake example and SWI2 Examples (examples 1 to 5) that are described in [Bakker et al. (2013)](http://pubs.usgs.gov/tm/6a46/) are available:
FloPy scripts for running and post-processing the lake example and SWI2 Examples (examples 1 to 5) that are described in [Bakker et al. (2013)](https://pubs.usgs.gov/tm/6a46/) are available:

+ [Henry problem using SEAWAT version 4](../examples/scripts/flopy_henry.py)

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2 changes: 1 addition & 1 deletion examples/Notebooks/flopy3_PlotArrayExample.ipynb
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Expand Up @@ -1247,7 +1247,7 @@
"\n",
"We can also pass `matplotlib.pyplot` keywords to `.plot()` methods attached to the model input data arrays. For example you can pass a `matplotlib` colormap (`cmap=`) keyword to the `.plot()` method to plot contours of simulated heads over a color flood of hk. We can also use the `norm=LogNorm()` keyword to use a log color scale when plotting hydraulic conductivity.\n",
"\n",
"Available `matplotlib` colormaps can be found at http://matplotlib.org/examples/color/colormaps_reference.html"
"Available `matplotlib` colormaps can be found at https://matplotlib.org/stable/tutorials/colors/colormaps.html"
]
},
{
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2 changes: 1 addition & 1 deletion examples/Notebooks/flopy3_Zaidel_example.ipynb
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Expand Up @@ -10,7 +10,7 @@
"\n",
"One of the most challenging numerical cases for MODFLOW arises from drying-rewetting problems often associated with abrupt changes in the elevations of impervious base of a thin unconfined aquifer. This problem simulates a discontinuous water table configuration over a stairway impervious base and flow between constant-head boundaries in column 1 and 200. This problem is based on \n",
"\n",
"[Zaidel, J. (2013), Discontinuous Steady-State Analytical Solutions of the Boussinesq Equation and Their Numerical Representation by Modflow. Groundwater, 51: 952–959. doi: 10.1111/gwat.12019](http://onlinelibrary.wiley.com/doi/10.1111/gwat.12019/abstract)\n",
"[Zaidel, J. (2013), Discontinuous Steady-State Analytical Solutions of the Boussinesq Equation and Their Numerical Representation by Modflow. Groundwater, 51: 952–959. doi: 10.1111/gwat.12019](https://doi.org/10.1111/gwat.12019)\n",
"\n",
"The model consistes of a grid of 200 columns, 1 row, and 1 layer; a bottom altitude of ranging from 20 to 0 m; constant heads of 23 and 5 m in column 1 and 200, respectively; and a horizontal hydraulic conductivity of $1x10^{-4}$ m/d. The discretization is 5 m in the row direction for all cells.\n",
"\n",
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6 changes: 3 additions & 3 deletions examples/Notebooks/flopy3_sfrpackage_example.ipynb
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Expand Up @@ -5,7 +5,7 @@
"metadata": {},
"source": [
"## SFR package example\n",
"Demonstrates functionality of Flopy SFR module using the example documented by [Prudic and others (2004)](http://pubs.er.usgs.gov/publication/ofr20041042): \n",
"Demonstrates functionality of Flopy SFR module using the example documented by [Prudic and others (2004)](https://doi.org/10.3133/ofr20041042): \n",
"\n",
"#### Problem description:\n",
"\n",
Expand Down Expand Up @@ -190,11 +190,11 @@
"source": [
"### Read pre-prepared reach and segment data into numpy recarrays using numpy.genfromtxt()\n",
"Reach data (Item 2 in the SFR input instructions), are input and stored in a numpy record array \n",
"http://docs.scipy.org/doc/numpy/reference/generated/numpy.recarray.html \n",
"https://numpy.org/doc/stable/reference/generated/numpy.recarray.html \n",
"This allows for reach data to be indexed by their variable names, as described in the SFR input instructions.\n",
"\n",
"For more information on Item 2, see the Online Guide to MODFLOW: \n",
"<http://water.usgs.gov/nrp/gwsoftware/modflow2000/MFDOC/index.html?sfr.htm>"
"<https://water.usgs.gov/nrp/gwsoftware/modflow2000/MFDOC/sfr.html>"
]
},
{
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2 changes: 1 addition & 1 deletion examples/Notebooks/flopy3_swi2package_ex1.ipynb
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Expand Up @@ -8,7 +8,7 @@
"\n",
"### SWI2 Example 1. Rotating Interface\n",
"\n",
"This example problem is the first example problem in the SWI2 documentation (http://pubs.usgs.gov/tm/6a46/) and simulates transient movement of a freshwater\\seawater interface separating two density zones in a two-dimensional vertical plane. The problem domain is 250 m long, 40 m high, and 1 m wide. The aquifer is confined, storage changes are not considered (all MODFLOW stress periods are steady-state), and the top and bottom of the aquifer are horizontal and impermeable.\n",
"This example problem is the first example problem in the SWI2 documentation (https://pubs.usgs.gov/tm/6a46/) and simulates transient movement of a freshwater\\seawater interface separating two density zones in a two-dimensional vertical plane. The problem domain is 250 m long, 40 m high, and 1 m wide. The aquifer is confined, storage changes are not considered (all MODFLOW stress periods are steady-state), and the top and bottom of the aquifer are horizontal and impermeable.\n",
"\n",
"The domain is discretized into 50 columns, 1 row, and 1 layer, with respective cell dimensions of 5 m (`DELR`), 1 m (`DELC`), and 40 m. A constant head of 0 m is specified for column 50. The hydraulic conductivity is 2 m/d and the effective porosity (`SSZ`) is 0.2. A flow of 1 m$^3$/d of seawater is specified in column 1 and causes groundwater to flow from left to right\n",
"in the model domain.\n",
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4 changes: 2 additions & 2 deletions examples/Notebooks/flopy3_swi2package_ex4.ipynb
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Expand Up @@ -8,7 +8,7 @@
"\n",
"### SWI2 Example 4. Upconing Below a Pumping Well in a Two-Aquifer Island System\n",
"\n",
"This example problem is the fourth example problem in the SWI2 documentation (http://pubs.usgs.gov/tm/6a46/) and simulates transient movement of the freshwater-seawater interface beneath an island in response to recharge and groundwater withdrawals. The island is 2,050$\\times$2,050 m and consists of two 20-m thick aquifers that extend below sea level. The aquifers are confined, storage changes are not considered (all MODFLOW stress periods are steady-state), and the top and bottom of each aquifer is horizontal. The top of the upper aquifer and the bottom of the lower aquifer are impermeable.\n",
"This example problem is the fourth example problem in the SWI2 documentation (https://pubs.usgs.gov/tm/6a46/) and simulates transient movement of the freshwater-seawater interface beneath an island in response to recharge and groundwater withdrawals. The island is 2,050$\\times$2,050 m and consists of two 20-m thick aquifers that extend below sea level. The aquifers are confined, storage changes are not considered (all MODFLOW stress periods are steady-state), and the top and bottom of each aquifer is horizontal. The top of the upper aquifer and the bottom of the lower aquifer are impermeable.\n",
"\n",
"The domain is discretized into 61 columns, 61 rows, and 2 layers, with respective cell dimensions of 50 m (`DELR`), 50 m (`DELC`), and 20 m. A total of 230 years is simulated using three stress periods with lengths of 200, 12, and 18 years, with constant time steps of 0.2, 0.1, and 0.1 years, respectively. \n",
"\n",
Expand Down Expand Up @@ -715,7 +715,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"Recreate **Figure 9** from the SWI2 documentation (http://pubs.usgs.gov/tm/6a46/)."
"Recreate **Figure 9** from the SWI2 documentation (https://pubs.usgs.gov/tm/6a46/)."
]
},
{
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2 changes: 1 addition & 1 deletion examples/Notebooks/flopy3_uzf_example.ipynb
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Expand Up @@ -6,7 +6,7 @@
"source": [
"# FloPy\n",
"### UZF example\n",
"Demonstrates functionality of the flopy UZF module using the example from [Niswonger and others (2006)](http://pubs.usgs.gov/tm/2006/tm6a19/). This is the same as the SFR example problem from Prudic and others (2004;\n",
"Demonstrates functionality of the flopy UZF module using the example from [Niswonger and others (2006)](https://pubs.usgs.gov/tm/2006/tm6a19/). This is the same as the SFR example problem from Prudic and others (2004;\n",
"p. 13–19), except the UZF package replaces the ET and RCH packages.\n",
"\n",
"#### Problem description:\n",
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2 changes: 1 addition & 1 deletion examples/scripts/flopy_swi2_ex4.py
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Expand Up @@ -344,7 +344,7 @@ def run():
for idx in cr:
cc.append(colormap(idx))

# Recreate **Figure 9** from the SWI2 documentation (http://pubs.usgs.gov/tm/6a46/).
# Recreate **Figure 9** from the SWI2 documentation (https://pubs.usgs.gov/tm/6a46/).

plt.rcParams.update({"legend.fontsize": 6, "legend.frameon": False})
fig = plt.figure(figsize=(fwid, fhgt), facecolor="w")
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6 changes: 3 additions & 3 deletions flopy/export/metadata.py
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Expand Up @@ -22,8 +22,8 @@ class acdd:
----------
https://www.sciencebase.gov/catalog/
http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html#description-of-file-contents
http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery
https://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html#description-of-file-contents
https://wiki.esipfed.org/Attribute_Convention_for_Data_Discovery
"""

Expand Down Expand Up @@ -56,7 +56,7 @@ def __init__(self, sciencebase_id, model):
self.__dict__[k] = self.sb.get(k, None)

# highly recommended global attributes
# http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery
# https://wiki.esipfed.org/Attribute_Convention_for_Data_Discovery
self.keywords = [t["name"] for t in self.sb["tags"]]

# recommended global attributes
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2 changes: 1 addition & 1 deletion flopy/export/netcdf.py
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Expand Up @@ -627,7 +627,7 @@ def _initialize_attributes(self):
), "NetCdf._initialize_attributes() error: nc attribute already set"

self.nc_epsg_str = "epsg:4326"
self.nc_crs_longname = "http://www.opengis.net/def/crs/EPSG/0/4326"
self.nc_crs_longname = "https://www.opengis.net/def/crs/EPSG/0/4326"
self.nc_semi_major = float(6378137.0)
self.nc_inverse_flat = float(298.257223563)

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2 changes: 1 addition & 1 deletion flopy/export/shapefile_utils.py
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Expand Up @@ -737,7 +737,7 @@ def crs(self):
def grid_mapping_attribs(self):
"""
Map parameters for CF Grid Mappings
http://http://cfconventions.org/cf-conventions/cf-conventions.html,
https://cfconventions.org/cf-conventions/cf-conventions.html#appendix-grid-mappings,
Appendix F: Grid Mappings
"""
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2 changes: 0 additions & 2 deletions flopy/mfusg/mfusgcln.py
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Expand Up @@ -224,8 +224,6 @@ def __init__(
filenames=filenames,
)

self.url = "Connected_Linear_Network.htm"

self._generate_heading()

# Options
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1 change: 0 additions & 1 deletion flopy/mfusg/mfusgdisu.py
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Expand Up @@ -248,7 +248,6 @@ def __init__(
)

# Set values of all parameters
self.url = "dis.htm"
self._generate_heading()

self.nodes = nodes
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1 change: 0 additions & 1 deletion flopy/mfusg/mfusggnc.py
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Expand Up @@ -113,7 +113,6 @@ def __init__(
)

self._generate_heading()
self.url = " "

if options is None:
options = []
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2 changes: 1 addition & 1 deletion flopy/mfusg/mfusglpf.py
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Expand Up @@ -6,7 +6,7 @@
Additional information for this MODFLOW package can be found at the `Online
MODFLOW Guide
<http://water.usgs.gov/ogw/modflow/MODFLOW-2005-Guide/index.html?lpf.htm>`_.
<https://water.usgs.gov/ogw/modflow/MODFLOW-2005-Guide/lpf.html>`_.
"""
import numpy as np

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1 change: 0 additions & 1 deletion flopy/mfusg/mfusgsms.py
Original file line number Diff line number Diff line change
Expand Up @@ -290,7 +290,6 @@ def __init__(
)

self._generate_heading()
self.url = " "
self.hclose = hclose
self.hiclose = hiclose
self.mxiter = mxiter
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2 changes: 1 addition & 1 deletion flopy/mfusg/mfusgwel.py
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
Additional information for this MODFLOW package can be found at the `Online
MODFLOW Guide
<http://water.usgs.gov/ogw/modflow/MODFLOW-2005-Guide/index.html?wel.htm>`_.
<https://water.usgs.gov/ogw/modflow/MODFLOW-2005-Guide/wel.html>`_.
"""
from copy import deepcopy

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1 change: 0 additions & 1 deletion flopy/modflow/mfag.py
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Expand Up @@ -230,7 +230,6 @@ def __init__(

# set up class
self._generate_heading()
self.url = "ag.htm"

# options
self.noprint = None
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4 changes: 2 additions & 2 deletions flopy/modflow/mfbas.py
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
Additional information for this MODFLOW package can be found at the `Online
MODFLOW Guide
<http://water.usgs.gov/ogw/modflow/MODFLOW-2005-Guide/index.html?bas6.htm>`_.
<https://water.usgs.gov/ogw/modflow/MODFLOW-2005-Guide/bas6.html>`_.
"""

Expand Down Expand Up @@ -117,7 +117,7 @@ def __init__(
filenames=self._prepare_filenames(filenames),
)

self.url = "bas6.htm"
self.url = "bas6.html"

nrow, ncol, nlay, nper = self.parent.nrow_ncol_nlay_nper
self.ibound = Util3d(
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2 changes: 1 addition & 1 deletion flopy/modflow/mfbcf.py
Original file line number Diff line number Diff line change
Expand Up @@ -139,7 +139,7 @@ def __init__(
filenames=filenames[0],
)

self.url = "bcf.htm"
self.url = "bcf.html"

nrow, ncol, nlay, nper = self.parent.nrow_ncol_nlay_nper
# Set values of all parameters
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1 change: 0 additions & 1 deletion flopy/modflow/mfbct.py
Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,6 @@ def __init__(
# call base package constructor
super().__init__(model, extension, self._ftype(), unitnumber)

self.url = "bct.htm"
nrow, ncol, nlay, nper = self.parent.nrow_ncol_nlay_nper
self.itrnsp = itrnsp
self.ibctcb = ibctcb
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4 changes: 2 additions & 2 deletions flopy/modflow/mfchd.py
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
Additional information for this MODFLOW package can be found at the `Online
MODFLOW Guide
<http://water.usgs.gov/ogw/modflow-nwt/MODFLOW-NWT-Guide/chd.htm>`_.
<https://water.usgs.gov/ogw/modflow-nwt/MODFLOW-NWT-Guide/chd.html>`_.
"""

Expand Down Expand Up @@ -126,7 +126,7 @@ def __init__(
filenames=self._prepare_filenames(filenames),
)

self.url = "chd.htm"
self.url = "chd.html"
self._generate_heading()

if dtype is not None:
Expand Down
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