Deltares · Manangka · Jan 31, 2024 · Jan 31, 2024
diff --git a/docs/api/changelog.rst b/docs/api/changelog.rst
@@ -15,7 +15,7 @@ Fixed
 - Fixed bugs with clipping :class:`imod.mf6.HorizontalFlowBarrier` for
   structured grids
 - Improved performance for merging structured multimodel Modflow 6 output
-- Bug where :function:`imod.formats.idf.open_subdomains` did not properly support custom
+- Bug where :func:`imod.formats.idf.open_subdomains` did not properly support custom
   patterns
 
 Changed
@@ -47,7 +47,7 @@ Fixed
 - Fixed bug where simulations with :class:`imod.mf6.Well` were not partitioned
   into multiple models.
 - Fixed erroneous default value for the ``out_of_bounds`` in
-  :function:`imod.select.points.point_values`
+  :func:`imod.select.points.point_values`
 - Fixed bug where :class:`imod.mf6.Well` could not be assigned to the first cell
   of an unstructured grid.
 - HorizontalFlowBarrier package now dropped if completely outside partition in a
@@ -88,8 +88,8 @@ Fixed
   default tile provider being used was Stamen. However Stamen is no longer free
   which caused Contextily to fail. The default tile provider has been changed to
   OpenStreetMap to resolve this issue.
-- :function:`imod.mf6.open_cbc` now reads saved cell saturations and specific discharges.
-- :function:`imod.mf6.open_cbc` failed to read unstructured budgets stored
+- :func:`imod.mf6.open_cbc` now reads saved cell saturations and specific discharges.
+- :func:`imod.mf6.open_cbc` failed to read unstructured budgets stored
   following IMETH1, most importantly the storage fluxes.
 - Fixed support of Python 3.11 by dropping the obsolete ``qgs`` module.
 - Bug in :class:`imod.mf6.SourceSinkMixing` where, in case of multiple active
@@ -121,11 +121,11 @@ Added
 - The unit tests results are now published on GitLab
 - A ``save_saturation`` option to :class:`imod.mf6.NodePropertyFlow` which saves
   cell saturations for unconfined flow.
-- Functions :function:`imod.prepare.layer.get_upper_active_layer_number` and
-  :function:`imod.prepare.layer.get_lower_active_layer_number` to return planar
+- Functions :func:`imod.prepare.layer.get_upper_active_layer_number` and
+  :func:`imod.prepare.layer.get_lower_active_layer_number` to return planar
   grids with numbers of the highest and lowest active cells respectively.
-- Functions :function:`imod.prepare.layer.get_upper_active_grid_cells` and
-  :function:`imod.prepare.layer.get_lower_active_grid_cells` to return boolean
+- Functions :func:`imod.prepare.layer.get_upper_active_grid_cells` and
+  :func:`imod.prepare.layer.get_lower_active_grid_cells` to return boolean
   grids designating respectively the highest and lowest active cells in a grid.
 - validation of ``transient`` argument in :class:`imod.mf6.StorageCoefficient`
   and :class:`imod.mf6.SpecificStorage`.
@@ -142,7 +142,7 @@ Added
   connect the submodels. At the moment auxiliary variables ``cdist`` and
   ``angldegx`` are only computed for structured grids. 
 - The label array can be generated through a convenience function
-  :function:`imod.mf6.partition_generator.get_label_array`
+  :func:`imod.mf6.partition_generator.get_label_array`
 - Once a split simulation has been executed by MF6, we find head and balance
   results in each of the partition models. These can now be merged into head and
   balance datasets for the original domain using

diff --git a/docs/api/metamod.rst b/docs/api/metamod.rst
@@ -7,6 +7,3 @@ MetaMod
     :toctree: generated/metamod
 
     MetaMod
-    NodeSvatMapping
-    RechargeSvatMapping
-    WellSvatMapping
diff --git a/docs/api/prepare.rst b/docs/api/prepare.rst
@@ -27,7 +27,7 @@ Prepare model input
 
     assign_wells
 
-    get_lower_active_grid_cells,
-    get_lower_active_layer_number,
-    get_upper_active_grid_cells,
-    get_upper_active_layer_number,
+    get_lower_active_grid_cells
+    get_lower_active_layer_number
+    get_upper_active_grid_cells
+    get_upper_active_layer_number
diff --git a/docs/faq/python.rst b/docs/faq/python.rst
@@ -144,45 +144,29 @@ Setting up an environment
 At some point you will run into a dependency issue. Sometimes the dependency
 requirements of two packages are straight out unsatisfiable. In other cases,
 you'd like to use the latest version, but this would break other packages.
-The solution conda offers is easy switching between different Python
-installations. A conda environment is simply a complete Python installation
-with all necessary dependencies. Creating a new environment will result in a
-new Python installation, without sharing of dependencies with other
+The solution used by imod-python is using Pixi. Pixi creates a complete Python
+installation with all necessary dependencies. Creating a new environment will
+result in a new Python installation, without sharing of dependencies with other
 environments. (This is hardly the most efficient use of your hard disk space
 from a theoretical perspective, but it greatly simplifies matters in the
 practical sense.)
 
-Below is the specification for an environment that should provide you with
-all the dependencies and requirements you need to build groundwater models
-with iMOD Python, and then some (for testing/development).
+To create a Pixi environment open a command prompt and ``cd`` to the imod folder.
+In the imod folder use the following command::
 
-.. literalinclude:: ../../imod-environment.yml
-   :language: yaml
-   :caption: imod-environment.yml
+    pixi run install
 
-Save this text into a file called ``imod-environment.yml``, location doesn't
-really matter. In your command prompt, ``cd`` to this location and run::
+This will create a conda environment inside the imod folder. To activate the environment run::
 
-    mamba env create -f imod-environment.yml
+    pixi shell
 
-This will create a conda environment named ``imod`` as it is specified in the
-file.
 
-Environments can be "activated" by running::
-
-    conda activate {name of environment}
-
-Active the just installed environment by running:: 
-
-    conda activate imod
-
 This essentially temporarily updates your `PATH variable`_, which is the set
-of directories where executable programs are located. After deactivating the
-conda environment, either via ``conda deactivate`` or by closing the command
-prompt, these directories are removed from PATH again so that the Python
-installation is properly isolated.
+of directories where executable programs are located. closing the command prompt,
+these directories are removed from PATH again so that the Python installation is
+properly isolated.
 
-Read more at the full `conda docs`_.
+Read more at the full `pixi docs`_.
 
 
 Installing a newer or old version
@@ -219,5 +203,5 @@ Past versions can also be found on the iMOD Python `releases page`_.
 .. _Terms of Service: https://www.anaconda.com/terms-of-service
 .. _conda-forge: https://conda-forge.org/
 .. _PATH variable: https://en.wikipedia.org/wiki/PATH_(variable)
-.. _conda docs: https://conda.io/projects/conda/en/latest
+.. _pixi docs: https://pixi.sh/
 .. _releases page: https://github.com/Deltares/imod-python/releases
diff --git a/examples/imod-wq/Henry.py → examples/imod-wq/Henry-wq.py b/examples/imod-wq/Henry.py → examples/imod-wq/Henry-wq.py
diff --git a/examples/mf6/circle_partitioned.py b/examples/mf6/circle_partitioned.py
@@ -1,4 +1,7 @@
 """
+Circle partitioned
+==================
+
 This example illustrates a circular model that is split into 3 submodels.
 The split method returns a simulation object that can be run as is. In this
 case the 3 submodels are roughly equal sized partitions that have the shape