Merge pull request #2452 from modflowpy/post-release-3.9.2-reset

Post release 3.9.2 reset
modflowpy · Feb 12, 2025 · f6e69e9 · f6e69e9
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diff --git a/.docs/md/version_changes.md b/.docs/md/version_changes.md
@@ -1,4 +1,31 @@
 # Changelog
+### Version 3.9.2
+
+#### New features
+
+* [feat(mf2005,mf2k)](https://github.com/modflowpy/flopy/commit/f058122a51404aadb5d28d23548ec96eff82ec8a): Allow loading custom flopy packages (#2404). Committed by Davíd Brakenhoff on 2025-01-10.
+* [feat(generate_classes.py)](https://github.com/modflowpy/flopy/commit/48ec3b2f2cfa0287c94fb6d62a596196294cfc2d): Allow excluding components (#2447). Committed by wpbonelli on 2025-02-11.
+
+#### Bug fixes
+
+* [fix(mp7particledata)](https://github.com/modflowpy/flopy/commit/942a4cd0eadec1201b430867f84412a03751747e): Add global_xy option for to_coords/to_prp (#2405). Committed by Davíd Brakenhoff on 2024-12-23.
+* [fix(resolve_exe)](https://github.com/modflowpy/flopy/commit/4deabe1d34b3476d9134bf0b64614ef0779634bb): Allow shutil.which() to find exe without suffix in Windows (#2408). Committed by martclanor on 2025-01-10.
+* [fix(cvfdutil)](https://github.com/modflowpy/flopy/commit/f9da244347f6e076e8e5d65562efc06640b07677): Fix skip_hanging_node_check (#2423). Committed by Oscar  Sanchez on 2025-01-21.
+* [fix(Mf6Splitter)](https://github.com/modflowpy/flopy/commit/25ec5cd4ce32e8862760ef672ef709fbb870d19f): Multiple bug fixes and added support (#2418). Committed by Joshua Larsen on 2025-01-30.
+* [fix(mp7particledata.py)](https://github.com/modflowpy/flopy/commit/9385daac51d064b34ca72117a27d5ec741a640c7): Avoid attribute error (#2441). Committed by wpbonelli on 2025-02-08.
+
+#### Perf
+
+* [perf(tutorials)](https://github.com/modflowpy/flopy/commit/8fd63758606091b323b01b1b77d39be964650cdd): Skip some writes in export_vtk_tutorial.py (#2432). Committed by wpbonelli on 2025-02-03.
+
+#### Refactoring
+
+* [refactor(model_splitter)](https://github.com/modflowpy/flopy/commit/bb587c3e46d934799e1e1060681dd10073ad935e): Add timeseries support (#2403). Committed by Joshua Larsen on 2025-01-03.
+* [refactor(FlopyBinaryData)](https://github.com/modflowpy/flopy/commit/ef5ca6a6361bab020f9e198563c18d7242f12e28): Make properties readonly, deprecate set_float() (#2421). Committed by wpbonelli on 2025-01-20.
+* [refactor(get-modflow)](https://github.com/modflowpy/flopy/commit/6a8f313df441c73673f8780a203a7233ae4f3ecc): Don't hard-code available os tags (#2426). Committed by wpbonelli on 2025-01-26.
+* [refactor(mf6)](https://github.com/modflowpy/flopy/commit/816ff8108f6985e0b2ead549a13f6446639d8f61): Allow using existing dfn files in generate_classes.py (#2431). Committed by wpbonelli on 2025-02-03.
+* [refactor(ModelTime)](https://github.com/modflowpy/flopy/commit/069d5430760fd0a9eb5eff6e8f36ce39974e25d3): Refactor ModelTime and add new features (#2367). Committed by Joshua Larsen on 2025-02-05.
+
 ### Version 3.9.1
 
 #### Mf6

diff --git a/CITATION.cff b/CITATION.cff
@@ -3,8 +3,8 @@ message: If you use this software, please cite both the article from preferred-c
   references, and the software itself.
 type: software
 title: FloPy
-version: 3.10.0.dev1
-date-released: '2024-12-20'
+version: 3.10.0.dev2
+date-released: '2025-02-12'
 doi: 10.5066/F7BK19FH
 abstract: A Python package to create, run, and post-process MODFLOW-based models.
 repository-artifact: https://pypi.org/project/flopy

diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
 
 <img src="https://raw.githubusercontent.com/modflowpy/flopy/master/examples/images/flopy3.png" alt="flopy3" style="width:50;height:20">
 
-### Version 3.10.0.dev1
+### Version 3.10.0.dev2
 [![flopy continuous integration](https://github.com/modflowpy/flopy/actions/workflows/commit.yml/badge.svg?branch=develop)](https://github.com/modflowpy/flopy/actions/workflows/commit.yml)
 [![Read the Docs](https://github.com/modflowpy/flopy/actions/workflows/rtd.yml/badge.svg?branch=develop)](https://github.com/modflowpy/flopy/actions/workflows/rtd.yml)
 
@@ -150,7 +150,7 @@ How to Cite
 
 ##### ***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., Brakenhoff, D. A., and Bonelli, W. P., 2024, FloPy v3.10.0.dev1: U.S. Geological Survey Software Release, 20 December 2024, https://doi.org/10.5066/F7BK19FH](https://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., Brakenhoff, D. A., and Bonelli, W. P., 2025, FloPy v3.10.0.dev2: U.S. Geological Survey Software Release, 12 February 2025, https://doi.org/10.5066/F7BK19FH](https://doi.org/10.5066/F7BK19FH)
 
 
 Additional FloPy Related Publications

diff --git a/docs/PyPI_release.md b/docs/PyPI_release.md
@@ -30,4 +30,4 @@ How to Cite
 
 *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., Brakenhoff, D. A., and Bonelli, W. P., 2024, FloPy v3.10.0.dev1: U.S. Geological Survey Software Release, 20 December 2024, https://doi.org/10.5066/F7BK19FH](https://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., Brakenhoff, D. A., and Bonelli, W. P., 2025, FloPy v3.10.0.dev2: U.S. Geological Survey Software Release, 12 February 2025, https://doi.org/10.5066/F7BK19FH](https://doi.org/10.5066/F7BK19FH)
diff --git a/flopy/mf6/data/dfn/gwe-adv.dfn b/flopy/mf6/data/dfn/gwe-adv.dfn
@@ -9,3 +9,11 @@ optional true
 longname advective scheme
 description scheme used to solve the advection term.  Can be upstream, central, or TVD.  If not specified, upstream weighting is the default weighting scheme.
 
+
+block options
+name ats_percel
+type double precision
+reader urword
+optional true
+longname fractional cell distance used for time step calculation
+description fractional cell distance submitted by the ADV Package to the adaptive time stepping (ATS) package.  If ATS\_PERCEL is specified and the ATS Package is active, a time step calculation will be made for each cell based on flow through the cell and cell properties.  The largest time step will be calculated such that the advective fractional cell distance (ATS\_PERCEL) is not exceeded for any active cell in the grid.  This time-step constraint will be submitted to the ATS Package, perhaps with constraints submitted by other packages, in the calculation of the time step.  ATS\_PERCEL must be greater than zero.  If a value of zero is specified for ATS\_PERCEL the program will automatically reset it to an internal no data value to indicate that time steps should not be subject to this constraint.
diff --git a/flopy/mf6/data/dfn/gwe-est.dfn b/flopy/mf6/data/dfn/gwe-est.dfn
@@ -9,12 +9,20 @@ longname save calculated flows to budget file
 description REPLACE save_flows {'{#1}': 'EST'}
 
 block options
-name zero_order_decay
+name zero_order_decay_water
 type keyword
 reader urword
 optional true
-longname activate zero-order decay
-description is a text keyword to indicate that zero-order decay will occur.  Use of this keyword requires that DECAY is specified in the GRIDDATA block.
+longname activate zero-order decay in aqueous phase
+description is a text keyword to indicate that zero-order decay will occur in the aqueous phase. That is, decay occurs in the water and is a rate per volume of water only, not per volume of aquifer (i.e., grid cell).  Use of this keyword requires that DECAY\_WATER is specified in the GRIDDATA block.
+
+block options
+name zero_order_decay_solid
+type keyword
+reader urword
+optional true
+longname activate zero-order decay in solid phase
+description is a text keyword to indicate that zero-order decay will occur in the solid phase. That is, decay occurs in the solid and is a rate per mass (not volume) of solid only.  Use of this keyword requires that DECAY\_SOLID is specified in the GRIDDATA block.
 
 block options
 name density_water
@@ -58,14 +66,24 @@ longname porosity
 description is the mobile domain porosity, defined as the mobile domain pore volume per mobile domain volume.  The GWE model does not support the concept of an immobile domain in the context of heat transport. 
 
 block griddata
-name decay
+name decay_water
 type double precision
 shape (nodes)
 reader readarray
 layered true
 optional true
 longname aqueous phase decay rate coefficient
-description is the rate coefficient for zero-order decay for the aqueous phase of the mobile domain.  A negative value indicates heat (energy) production.  The dimensions of decay for zero-order decay is energy per length cubed per time.  Zero-order decay will have no effect on simulation results unless zero-order decay is specified in the options block.
+description is the rate coefficient for zero-order decay for the aqueous phase of the mobile domain.  A negative value indicates heat (energy) production.  The dimensions of zero-order decay in the aqueous phase are energy per length cubed (volume of water) per time.  Zero-order decay in the aqueous phase will have no effect on simulation results unless ZERO\_ORDER\_DECAY\_WATER is specified in the options block.
+
+block griddata
+name decay_solid
+type double precision
+shape (nodes)
+reader readarray
+layered true
+optional true
+longname solid phase decay rate coefficient
+description is the rate coefficient for zero-order decay for the solid phase.  A negative value indicates heat (energy) production. The dimensions of zero-order decay in the solid phase are energy per mass of solid per time. Zero-order decay in the solid phase will have no effect on simulation results unless ZERO\_ORDER\_DECAY\_SOLID is specified in the options block.
 
 block griddata
 name heat_capacity_solid

diff --git a/flopy/mf6/data/dfn/gwe-fmi.dfn b/flopy/mf6/data/dfn/gwe-fmi.dfn
@@ -33,7 +33,7 @@ type string
 tagged false
 reader urword
 longname flow type
-description is the word GWFBUDGET, GWFHEAD, GWFMOVER or the name of an advanced GWF stress package.  If GWFBUDGET is specified, then the corresponding file must be a budget file from a previous GWF Model run.  If an advanced GWF stress package name appears then the corresponding file must be the budget file saved by a LAK, SFR, MAW or UZF Package.
+description is the word GWFBUDGET, GWFHEAD, GWFGRID, GWFMOVER or the name of an advanced GWF stress package from a previous model run.  If GWFBUDGET is specified, then the corresponding file must be a budget file.  If GWFHEAD is specified, the file must be a head file.  If GWFGRID is specified, the file must be a binary grid file. If GWFMOVER is specified, the file must be a mover file.  If an advanced GWF stress package name appears then the corresponding file must be the budget file saved by a LAK, SFR, MAW or UZF Package.
 
 block packagedata
 name filein

diff --git a/flopy/mf6/data/dfn/gwe-lke.dfn b/flopy/mf6/data/dfn/gwe-lke.dfn
@@ -294,7 +294,7 @@ tagged false
 in_record true
 reader urword
 longname boundary thermal conductivity
-description is the thermal conductivity of the of the interface between the aquifer cell and the lake.  
+description is the thermal conductivity of the material between the aquifer cell and the lake. The thickness of the material is defined by the variable RBTHCND.
 
 block packagedata
 name rbthcnd

diff --git a/flopy/mf6/data/dfn/gwe-mwe.dfn b/flopy/mf6/data/dfn/gwe-mwe.dfn
@@ -294,7 +294,7 @@ tagged false
 in_record true
 reader urword
 longname thermal conductivity of the feature
-description is the thermal conductivity of the interface between the aquifer cell and the feature.
+description is the thermal conductivity of the material between the aquifer cell and the feature. The thickness of the material is defined by the variable FTHK.
 
 block packagedata
 name fthk
@@ -404,7 +404,7 @@ in_record true
 reader urword
 time_series true
 longname well injection temperature
-description real or character value that defines the injection temperature $(e.g., ^{\circ}C or ^{\circ}F)$ for the well. If the Options block includes a TIMESERIESFILE entry (see the ``Time-Variable Input'' section), values can be obtained from a time series by entering the time-series name in place of a numeric value.
+description real or character value that defines the injection temperature $(e.g.,\:^{\circ}C\:or\:^{\circ}F)$ for the well. If the Options block includes a TIMESERIESFILE entry (see the ``Time-Variable Input'' section), values can be obtained from a time series by entering the time-series name in place of a numeric value.
 
 block period
 name auxiliaryrecord

diff --git a/flopy/mf6/data/dfn/gwe-sfe.dfn b/flopy/mf6/data/dfn/gwe-sfe.dfn
@@ -294,7 +294,7 @@ tagged false
 in_record true
 reader urword
 longname boundary thermal conductivity
-description is the thermal conductivity of the of the interface between the aquifer cell and the stream reach.  
+description is the thermal conductivity of the material between the aquifer cell and the stream reach. The thickness of the material is defined by the variable RBTHCND.
 
 block packagedata
 name rbthcnd
@@ -404,7 +404,7 @@ in_record true
 reader urword
 time_series true
 longname rainfall temperature
-description real or character value that defines the rainfall temperature $(e.g., ^{\circ}C or ^{\circ}F)$ for the reach. If the Options block includes a TIMESERIESFILE entry (see the ``Time-Variable Input'' section), values can be obtained from a time series by entering the time-series name in place of a numeric value.
+description real or character value that defines the rainfall temperature $(e.g.,\:^{\circ}C\:or\:^{\circ}F)$ for the reach. If the Options block includes a TIMESERIESFILE entry (see the ``Time-Variable Input'' section), values can be obtained from a time series by entering the time-series name in place of a numeric value.
 
 block period
 name evaporation
@@ -426,7 +426,7 @@ in_record true
 reader urword
 time_series true
 longname runoff temperature
-description real or character value that defines the temperature of runoff $(e.g., ^{\circ}C or ^{\circ}F)$ for the reach.  Users are free to use whatever temperature scale they want, which might include negative temperatures.  If the Options block includes a TIMESERIESFILE entry (see the ``Time-Variable Input'' section), values can be obtained from a time series by entering the time-series name in place of a numeric value.
+description real or character value that defines the temperature of runoff $(e.g.,\:^{\circ}C\:or\:^{\circ}F)$ for the reach.  Users are free to use whatever temperature scale they want, which might include negative temperatures.  If the Options block includes a TIMESERIESFILE entry (see the ``Time-Variable Input'' section), values can be obtained from a time series by entering the time-series name in place of a numeric value.
 
 block period
 name inflow
@@ -437,7 +437,7 @@ in_record true
 reader urword
 time_series true
 longname inflow temperature
-description real or character value that defines the temperature of inflow $(e.g., ^{\circ}C or ^{\circ}F)$ for the reach. Users are free to use whatever temperature scale they want, which might include negative temperatures.  If the Options block includes a TIMESERIESFILE entry (see the ``Time-Variable Input'' section), values can be obtained from a time series by entering the time-series name in place of a numeric value.
+description real or character value that defines the temperature of inflow $(e.g.,\:^{\circ}C\:or\:^{\circ}F)$ for the reach. Users are free to use whatever temperature scale they want, which might include negative temperatures.  If the Options block includes a TIMESERIESFILE entry (see the ``Time-Variable Input'' section), values can be obtained from a time series by entering the time-series name in place of a numeric value.
 
 block period
 name auxiliaryrecord

diff --git a/flopy/mf6/data/dfn/gwe-uze.dfn b/flopy/mf6/data/dfn/gwe-uze.dfn
@@ -384,7 +384,7 @@ in_record true
 reader urword
 time_series true
 longname infiltration temperature
-description real or character value that defines the temperature of the infiltration $(e.g., ^{\circ}C or ^{\circ}F)$ for the UZF cell. If the Options block includes a TIMESERIESFILE entry (see the ``Time-Variable Input'' section), values can be obtained from a time series by entering the time-series name in place of a numeric value.
+description real or character value that defines the temperature of the infiltration $(e.g.,\:^{\circ}C\:or\:^{\circ}F)$ for the UZF cell. If the Options block includes a TIMESERIESFILE entry (see the ``Time-Variable Input'' section), values can be obtained from a time series by entering the time-series name in place of a numeric value.
 
 block period
 name uzet

diff --git a/flopy/mf6/data/dfn/gwt-fmi.dfn b/flopy/mf6/data/dfn/gwt-fmi.dfn
@@ -33,7 +33,7 @@ type string
 tagged false
 reader urword
 longname flow type
-description is the word GWFBUDGET, GWFHEAD, GWFMOVER or the name of an advanced GWF stress package.  If GWFBUDGET is specified, then the corresponding file must be a budget file from a previous GWF Model run.  If an advanced GWF stress package name appears then the corresponding file must be the budget file saved by a LAK, SFR, MAW or UZF Package.
+description is the word GWFBUDGET, GWFHEAD, GWFMOVER or the name of an advanced GWF stress package.  If GWFBUDGET is specified, then the corresponding file must be a budget file. If GWFHEAD is specified, the file must be a head file.  If GWFGRID is specified, the file must be a binary grid file.  If an advanced GWF stress package name appears then the corresponding file must be the budget file saved by a LAK, SFR, MAW or UZF Package.
 
 block packagedata
 name filein

diff --git a/flopy/mf6/data/dfn/gwt-ist.dfn b/flopy/mf6/data/dfn/gwt-ist.dfn
@@ -92,7 +92,7 @@ valid linear freundlich langmuir
 reader urword
 optional true
 longname activate sorption
-description is a text keyword to indicate that sorption will be activated.  Valid sorption options include LINEAR, FREUNDLICH, and LANGMUIR.  Use of this keyword requires that BULK\_DENSITY and DISTCOEF are specified in the GRIDDATA block.  If sorption is specified as FREUNDLICH or LANGMUIR then SP2 is also required in the GRIDDATA block.
+description is a text keyword to indicate that sorption will be activated.  Valid sorption options include LINEAR, FREUNDLICH, and LANGMUIR.  Use of this keyword requires that BULK\_DENSITY and DISTCOEF are specified in the GRIDDATA block.  If sorption is specified as FREUNDLICH or LANGMUIR then SP2 is also required in the GRIDDATA block.  The sorption option must be consistent with the sorption option specified in the MST Package or the program will terminate with an error.
 
 block options
 name first_order_decay

diff --git a/flopy/mf6/data/dfn/prt-fmi.dfn b/flopy/mf6/data/dfn/prt-fmi.dfn
@@ -25,7 +25,7 @@ type string
 tagged false
 reader urword
 longname flow type
-description is the word GWFBUDGET or GWFHEAD.  If GWFBUDGET is specified, then the corresponding file must be a budget file from a previous GWF Model run.
+description is the word GWFBUDGET, GWFHEAD, or GWFGRID.  If GWFBUDGET is specified, then the corresponding file must be a budget file.  If GWFHEAD is specified, the file must be a head file.  If GWFGRID is specified, the file must be a binary grid file.
 
 block packagedata
 name filein
Original file line number	Diff line number	Diff line change
Expand Up		@@ -30,4 +30,4 @@ How to Cite

		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., Brakenhoff, D. A., and Bonelli, W. P., 2024, FloPy v3.10.0.dev1: U.S. Geological Survey Software Release, 20 December 2024, https://doi.org/10.5066/F7BK19FH](https://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., Brakenhoff, D. A., and Bonelli, W. P., 2025, FloPy v3.10.0.dev2: U.S. Geological Survey Software Release, 12 February 2025, https://doi.org/10.5066/F7BK19FH](https://doi.org/10.5066/F7BK19FH)