Fixes #737 

This PR adds a template for PRs. [Unfortunately the template only works
if it is in the default
branch](https://docs.github.com/en/communities/using-templates-to-encourage-useful-issues-and-pull-requests/about-issue-and-pull-request-templates#pull-request-templates),
(``master``) in our case, so I could not test it. I presume it works
though, [as it works for
Ribasim](https://github.com/Deltares/Ribasim/blob/main/.github/pull_request_template.md).

[Relevant
docs](https://docs.github.com/en/communities/using-templates-to-encourage-useful-issues-and-pull-requests/creating-a-pull-request-template-for-your-repository)

Fixes #767

# Description
The GitLab pipeline is no longer needed and is removed in this commit

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Fixes #774 

# Description
Build in #760 fails for
test_rasterio_ascii

``test_rasterio_ascii`` doesn't work for GDAL 3.8.3 compared to 3.7.3. 

Previously it was tested if files are exactly identical. This defeats
the purpose, more important is that GDAL can read the file and
interprets the file equal as if it were written with GDAL. Replacing
``assert_equal_content`` with the changes fixes things.

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…ightly build (#771)

Fixes #748

# Description
The unit tests and examples were failing when run against the latest
MODFLOW6 nightly. This is caused by a change on the MODFLOW6 side were
any gwf-gwt exchanges has to have an actual existing file (even though
it is emty).
The precious behaviour was that just mentioning the gwf-gwt exchanges in
the nam file was enough.

This commit adds the gwfgwt package. It uses the same logic as the
gwfgwf exchanges in terms of how it is written to disk.
Any common methods between the different type of exchanges has been
moved to the newly created ExchangeBase class

**Note**
I didn't add any unit tests for the simulation class. The reason for
this is twofold:
- I moved code around, no major functional changes
- We have to refactor they way the gwf-gwt exchanges are being created
the moment we start working on the multimodel support for gwt, making
any unit tests I add obsolete

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Fixes #779

# Description
This commit rotates the TeamCity token in the pipeline scripts

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Fixes #757

# Description
This commit adds a nightly pipeline.
The goal of the nightly pipeline is to build or repository against the
latest development branch of MODFLOW.
This will allow us to catch breaking changes early on.

The pipeline file has been refactored to prevent code duplication. This
has been accomplished by using templates.
The new nightly pipeline is added as a new subproject of the main
project

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Fixes #785

Due to a recent refactor of the pipeline a trigger is missing from the
pipeline script. As a result builds are not started automatically.
This commit restores the trigger

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Fixes #746

# Description
Fixes the slice_model function to slice transport models as well. 
Includes changes to the Advection package. The advection scheme
parameter is set by the constructors of derived types of advection.
Trying to reinitialize the derived type throws an error, as its
construction method doesn't expect arguments. As a pragmatic solution,
the constructor methods now get a ``**ignored`` argument to ignore these
kwargs.


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Fixes #783

This commit fixes all remaining MyPy errors in the mf6 module

The PR is split in several commits, each commit contains a certain file
in which the mypy errors are fixes or exist of a type of error that
crosses multiple files. I suggest reviewing this PR commit by commit.

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…tation (#794)

Fixes #793
This commit fixes all warnings and errors produced during the creation
of the documentation

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Fixes #788  and #789 

# Description
now adds split models to the solution group (ims) that the source model
belonged to.
When writing a split simulation with flow and transport, gwfgwt
exchanges are created. The models are connected based on type and
domain.

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---------

Co-authored-by: Joeri van Engelen <[email protected]>

Fixes #809

This commit updates the dependencies of the project.
There are some issues with the latest dask packag,s which isn;t playing
nice with raterio, and with the pytest package, which has issues with
pytest-cases. I've pinned both packages to a version that doesn't cause
any issue.
Further there has been an update of black which results in a new
formatting rule being applied.

Hopefully this is the last time we have to update manually as the
pipeline script to do this automatically is almost done

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…dencies to the latest version (#804)

Fixes #795

This commit adds a pipeline that periodically updates the project
dependencies.
It runs every sunday at 15:00. When changes are found a new update
branch is pushed and a PR is created.

The created PR in turn will trigger the normal build pipeline so all the
regular checks are run against this branch.
If any of the tests fail they should be fixes as part of the created PR

Reviewers are automatically assigned in this case that are @luitjansl
and @JoerivanEngelen

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…dencies to the latest version (#804)

Fixes #795

This commit adds a pipeline that periodically updates the project
dependencies.
It runs every sunday at 15:00. When changes are found a new update
branch is pushed and a PR is created.

The created PR in turn will trigger the normal build pipeline so all the
regular checks are run against this branch.
If any of the tests fail they should be fixes as part of the created PR

Reviewers are automatically assigned in this case that are @luitjansl
and @JoerivanEngelen

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Fixes #813

# Description
<!---
Thanks for opening a PR!

Please add your description here of changes made and how they are going
to
resolve the linked issue 
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Fixes #765 

# Description
creates gwtgwt exchange packages when splitting a simulation that
contains 1 or more transport models. A gwtgwt package is created per
partition boundary and per transport model. (while the geometry
constants are the same for all transport models, the options in the
gwtgwt file are specific to single transport models. However, for now,
these settings are not set; this will be the topic of #747
Also adds tests.

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---------

Co-authored-by: Joeri van Engelen <[email protected]>

Fixes #816 

This commit adds a MyPy build step to the build pipeline.
It will run as part of the regular build as well for the nightly build
Both the mypy_report as the regular mypy commands are called. The first
command produces a report that can be displayed in teamcity the same way
unit tests are. The second command will also give an output to the build
log

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Fixes #805 

# Description
Validation of concentrations was missing for the DRN, WEL, and EVT
package. This PR:
* Adds validation schemata to the DRN and EVT
* Adds ``AnyNodataSchema``
* Validate if ``Well`` has no nodata for certain variables.

I was struggling a bit with the linting/formatting it appears that we
are running both ``black `` as well as ``ruff`` which causes changes.

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Fixes #798 

When we split a simulation of both flow and transport models, the ssm
package of the transport simulation is re-generated after splitting,
because not every flow boundary will be present in every partition.


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---------

Co-authored-by: Joeri van Engelen <[email protected]>

Fixes #763

# Description
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to
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* Remove dev dependencies from pyproject.toml
* Synchronizes package versions in with pyproject.toml and pixi.toml
* Add hatchling to pixi.toml
* Updates lock file

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Fixes #747 

# Description
assigns the advection scheme and dispersion xt3d options to the gwtgwt
package. They are written into the options block of said file.

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Fixes #823 

# Description
Fixes a typo in the 1d transport model splitting test. Now that it's
fixed tolerances for the comparison could be made much stricter

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Fixes #826

This commit replaces the black linter/formatter in favor of the ruff
linter/formatter.
The ruff and black formatter are 99% compatible but they vary just
slightly.
This causes issues when calling the `pixi run format` task because they
counteract each other.

A full list of differences between black and ruff can be found at:
https://docs.astral.sh/ruff/formatter/black/

The changes to review are in the pixi.toml file. All other changes are
made by the ruff formatter.

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Fixes #1392 

# Description
Changes default to better match iMOD5. 

- Reverted the default of ``SimulationAllocationOptions.riv`` back to
what it was in the previous version, as this matches iMOD5's default
setting.
- Set ``SimulationAllocationOptions.drn`` to
``ALLOCATION_OPTION.at_elevation``, to match iMOD5's default setting.

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Fixes #1395

# Description
Use proper value for missing layers in projectfile.

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Fixes #1391 

# Description
- Add ``DISTRIBUTING_OPTION.by_corrected_thickness`` setting. 
- Move logic to compute correction factors into separate function.

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Fixes #1402

# Description
Adds known issue on literal well edge case.

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Fixes #1399

# Description
This PR sets better defaults for ``minimum_k`` and
``minimum_thickness``. See linked issue.

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Fixes #1317 and #1331

# Description
With `Numba` now also supporting python 3.13 we can also add 3.13
support to iMOD-python.
This PR adds a 3.13 environment to the pixi.toml and also adds an import
test of it to the TC pipelines.

One line of code had to be rwritten to be 3.13 compatible. The
`importlib.resources.files` no longer provides a context manager and has
to wrapped using the `importlib.resources.as_file` method

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Fixes #1207 

# Description
Exclude tests and examples from analysis

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Fixes #914

# Description
In validation messages, change tabs to four spaces and change aterisk to
dash.

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Fixes #1445

It turned out this performance issue pertained from a performance issue
where calling ``xr.DataArray().isin(pd.Series())`` was very slow for
large datasets, whereas ``pd.Series().isin(pd.Series())`` was a lot
faster.

# Description
- Fix performance issue when writing large MODFLOW6 WEL packages
- Add test which tests this performance, I had to add a small pytest
plugin for this.

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Fixes #1437 

# Description
``primod`` expects a 2D rate array or single layer array for the dummy
MODFLOW6 package, as otherwise the ``squeeze("layer")`` it does returns
an error. I think the safest for iMOD Python is to return a 2D array
with extra layer coordinate. I added some extra tests to test if this
RCH package could be clipped and regridded, as in most/all fixtures for
clipping/regridding I added packages with layer dimension. Luckily these
two extra tests turned out to be mostly for my own peace of mind, as
they ran without problems.

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Fixes #1436 

# Description
Work around Dask issue by forcing a load of idomain and svat into
memory. These grids will never be as large as the boundary condition
grids with a time axis, so I think it is acceptable. At least for the
LHM it is. I couldn't get it to work with a ``where``: numpy only
accepts 1D arrays on a boolean indexed 3D as long as the 1D array has
the length of one of the dimensions, it then does what we want to do
here. However when this is not the case, which is 95% of the time, numpy
throws an error. I therefore had to resort to loading arrays into
memory.

Furthermore I refactored ``test_coupler_mapping.py`` to be able to
reduce some code duplication and add a test case with a dask array. For
this I had to make the well package used consistent (From 2 wells to 3
wells, where the second well now lays on y=2.0 instead of y=1.0), so I
updated some of the assertions.

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Fixes #1457 

Removes ``flow`` module, it has hardly seen any use. Reduces clutter,
scope, potential hurdles to getting familiar with the code base, and
potential maintenance.

# Description
- Remove ``flow`` module
- Remove unittests for ``flow``
- Remove iMODFLOW examples
- Remove notions that iMOD Python can generate iMODFLOW models from
README
- Update changelog, so that there are no crossrefs to be removed 

I also tested generating the docs, so that there are no errors thrown.

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…aces`` (#1456)

Fixes #1454 

# Description
- Move ``imod.mf6.interfaces`` to ``imod.common.interfaces``
- Move ``imod.mf6.statusinfo.py`` to ``imod.common.statusinfo.py``

I had to move the ``statusinfo.py`` as it was imported in
``imod.common.interfaces.IModel``.

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Fixes #1465

# Description
- Move ``mask`` utilities to common utilities. 
- Move aux variable logic to ``Package.mask`` and refactor it
- Move two generic utilities from ``imod.mf6.utilities.dataset.py`` to
``imod.common.utilities.value_filters.py``
- Move generic schemata utility module to common utilities

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Fixes #1414 

# Description
- Adds ``cleanup_hfb`` function to clip barrier lines/Z polygons outside
the active domain. This unfortunately cannot deal with the edge case
where a hfb line is snapped to the outer edge of the active domain.
(These edges are filtered out when calling ``to_mf6_pkg``, but a
ValidationError is thrown when ``strict_hfb_validation`` is switched
on).
- Adds ``HorizontalFlowBarrierBase.cleanup`` method
- Moves some utility functions from ``imod.mf6.utilities`` to
``imod.prepare.hfb`` and ``imod.util.hfb``, to avoid circular imports.

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Fixes #483

# Description
Adds relevant and adapted unittests from DIS package to unittest for
DISV package

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Fixes #442 and #542

# Description
@HendrikKok asked me to clip a model for him to send it to Wageningen
and I thought this would be a trivial exercise, only I realized we still
lacked MetaSWAP clipping support. I noticed this was low-hanging fruit,
so instead of writing some special one-off script, I thought I might as
well add it to iMOD Python immediately.

This PR:

- Small refactor: Move clipping logic in ``imod.mf6.Package.clip_box``
to ``imod.common.utilities.clip`` module.
- Adds support to clip MetaSWAP packages
- Add unittests
- Boyscouting: Move clipping tests to ``test_common/test_utilities``
- Boyscouting: Move confusing name ``test_common.py`` to
``test_prepare/test_common.py``

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Fixes #1480

# Description
We are experiencing flaky builds on the TeamCity build server.

A theory is that the builds are failing due to pull collisions when the
docker images are pulled at the start of a build.
By disabling the 'explicit pull' option this might happen less frequent

With this change an image will only be pulled when its not present on
the agent. If the image is overwritten on the registry the old image has
to be manually removed from the agents
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Fixes #443 and #364

# Description

* Adds clipping method to ``imod.msw.MetaSwapModel``, this includes a
special case for ``clip_box`` method of PrecipitationMapping, and
EvapotranspirationMapping: These should not be clipped if a
``MeteoGridCopy`` instance is part of the model. Otherwise nonsensical
mappings are generated.
* Add ``imod.msw.MetaSwapModel.clip_box`` method to public API
* Override ``clip_box`` method in MeteoMapping, should clip meteo
attribute instead of dataset attribute.
* Refactor: Move time slice clipping logic to
``imod.common.utilities.clip``.
* Refactor: Make ``meteo`` class variable an attribute. This makes more
sense. I think I made it a class variable before to please mypy.
* Boyscouting: Add some extra docstring information on usecase to
``imod.msw.MeteoGridCopy``

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Fixes #492

# Description
Adds some simple logging to the simulation object. I didn't add solver
settings, these are listed in the .ims file. I also didn't add stdout of
MODFLOW6, as this is already logged in the LIST file and would require
some extra work.

Furthermore some boyscouting: fix some easy-to-fix issues raised by
Sonarcloud:

- Remove unreachable return statements
- Don't use caps in variable's name

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Fixes #1492

# Description
Replace fastcore typedispatching with plum's dispatching.
Plum is a bit stricter, which I generally think is good. When fastcore's
typedispatching didn't encounter a typedispatched fallback function for
type ``Any``, for some reason things worked, but I'm not sure what it
did. Plum is stricter so I had to explicitly had to add some fallback
functions to either raise an error or do something.

In detail, this PR
- Replaces @typedispatch with a plum Dispatcher instance, this also
limits the scope for accidentily adding typedispatched functions in
other modules
- Separate ``clip_by_grid`` method for GridDataArray into one for
xr.DataArray and xu.UgridDataArray, as plum apparently thinks this
ambiguous.
- Update some arrays in ``create_exchange_package`` to become DataArray
- Add missing fallback functions for ``enforce_dim_order`` and
``is_unstructured``
- Add function for ``enforce_dim_order`` with ``None``
- Change fallback type from ``object`` to ``Any``, to also support
``None``

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Fixes #1498 

# Description
Fix broken copy method

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---------

Co-authored-by: JoerivanEngelen <[email protected]>

Closes #305 

# Description

This throws an error when a user tries to write a model in a directory
with a space in it.

Follow-up to #1514

See my comment here:
#1514 (comment)

> Thanks for hotfixing this. FYI: This is not an immediate problem
anymore: I just talked to @TeunvanWoerkom, he moved to a drive without
spaces in the path.
> 
> I'm not sure if we should merge this, as the `wq` test bench doesn't
have the coverage of the `mf6` module. Most notably, we don't run a
model with iMOD-WQ to test if it breaks. The current `wq` module is
tried and tested in many projects, so that is sufficient to do work
with. I don't want to risk breaking it with changes.
> 
> Besides, Teun manually quoted the paths in his runfile to fix this and
then iMOD-WQ apparently also isn't able to deal with spaces in paths (at
least the version he used). It crashes upon attempting to create the
results directories.
> 
> Alternatively: We could raise an error if a user attempts to write a
`wq` model in a folder with a space in the path?


It turned out that adding quotes doesn't do the trick, as iMOD-WQ also
cannot handle spaces in paths, even when they are quoted in the runfile.
It crashes upon writing results.

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…in iMOD projectfile (#1529)

Fixes #1528 

# Description
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Fixes the issue of using relative paths for the extra MetaSWAP files in
the iMOD project file.

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---------

Co-authored-by: JoerivanEngelen <[email protected]>

Fixes #1507

# Description
- Adds validation of model options
- Add TypeSchema to validate model options, which are not DataArray or
UgridDataArray
- Clean up unused kwargs logic in ``Modflow6Model.__init__``
- Small refactor: move some logic to concatenate schemata to separate
function, force to list to allow concatenating (hidden bug that showed
up in mypy after .
- Small refactor: Add TypeAlias SchemaDict

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Fixes #1539 

# Description
Changes the following:

- Fix bug where UgridDataArrays where silently converted to regular
DataArrays (caused by the call to ``.data_vars``).
- Add unstructured grid test case to well tests where easily applicable.

# Checklist
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…abstraction rates (#1533)

Fixes #1532

# Description
Fixes a bug where surface water rates were not written to file in
absence of groundwater abstraction rates.

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…ct file. (#1543)

Fixes #1542 

# Description
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This fixes a minor bug related to unwanted case sensitivity of the
periods keyword in the iMOD project file.

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Fixes #1536

# Description
- Remove unnecessary calls to ``.values``
- Fix bug in ``_skip_if_datarray`` where the spatial dimension of
unstructured grids was hardcoded
- Refactor exchange creation logic to use
``xr.Dataset().to_dataframe()``, this to carefully merge variables into
a dataset with matching dimensions, then convert to pandas dataframe.

I can't verify yet if this improves things with Teun's example as I do
not have his scripts, but this fixes a bug and will improve performance
somewhat when using dask (as it reduces unnecessary loads into memory)

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Fixes #1525

# Description
Add support to directly provide repeat_stresses as dictionary. As issue
states: Simplifies API for users a lot, as they don't need to search for
the obscure utility function ``get_period_stess``.

# Checklist
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