diff --git a/imod/msw/coupler_mapping.py b/imod/msw/coupler_mapping.py
index 635e4210e..351c1fe91 100644
--- a/imod/msw/coupler_mapping.py
+++ b/imod/msw/coupler_mapping.py
@@ -46,8 +46,9 @@ def _create_mod_id_rch(
         """
         mod_id = xr.full_like(svat, fill_value=0, dtype=np.int64)
         n_subunit = svat["subunit"].size
-
-        n_mod_top = idomain_top_active.sum()
+        # Sum active cells and convert to int for MyPy. This is the number of
+        # modflow cells in the top layer.
+        n_mod_top = int(idomain_top_active.sum().item())
 
         # idomain does not have a subunit dimension, so tile for n_subunits
         mod_id_1d: IntArray = np.tile(np.arange(1, n_mod_top + 1), (n_subunit, 1))
@@ -124,8 +125,9 @@ def _create_well_id(
         well_layer = well_cellid.sel(dim_cellid="layer").data
         well_row = well_cellid.sel(dim_cellid="row").data - 1
         well_column = well_cellid.sel(dim_cellid="column").data - 1
-
-        n_mod = idomain_active.sum()
+        # Sum active cells and convert to int for MyPy. This is the number of
+        # modflow cells in the top layer.
+        n_mod = int(idomain_active.sum().item())
         mod_id = xr.full_like(idomain_active, 0, dtype=np.int64)
         mod_id.data[idomain_active.data] = np.arange(1, n_mod + 1)
 
diff --git a/imod/select/cross_sections.py b/imod/select/cross_sections.py
index 90a5afa98..2fddb530d 100644
--- a/imod/select/cross_sections.py
+++ b/imod/select/cross_sections.py
@@ -274,11 +274,11 @@ def _cross_section(data, linecoords):
     else:
         ys[1:] += np.abs(dy_a).cumsum()
 
-    ixs = []
-    iys = []
-    sdxs = []
-    sdys = []
-    segments_list = []
+    ixs_ls = []
+    iys_ls = []
+    sdxs_ls = []
+    sdys_ls = []
+    segments_ls = []
 
     bounding_box = _bounding_box(xmin, xmax, ymin, ymax)
     for start, end in zip(linecoords[:-1], linecoords[1:]):
@@ -298,21 +298,21 @@ def _cross_section(data, linecoords):
             sdy = np.array([-1])
             segment_length = np.array([linestring.length])
 
-        ixs.append(i)
-        iys.append(j)
-        sdxs.append(sdx)
-        sdys.append(sdy)
-        segments_list.append(segment_length)
+        ixs_ls.append(i)
+        iys_ls.append(j)
+        sdxs_ls.append(sdx)
+        sdys_ls.append(sdy)
+        segments_ls.append(segment_length)
 
-    if len(ixs) == 0:
+    if len(ixs_ls) == 0:
         raise ValueError("Linestring does not intersect data")
 
     # Concatenate into a single array
-    ixs = np.concatenate(ixs)
-    iys = np.concatenate(iys)
-    sdxs = np.concatenate(sdxs)
-    sdys = np.concatenate(sdys)
-    segments = np.concatenate(segments_list)
+    ixs = np.concatenate(ixs_ls)
+    iys = np.concatenate(iys_ls)
+    sdxs = np.concatenate(sdxs_ls)
+    sdys = np.concatenate(sdys_ls)
+    segments = np.concatenate(segments_ls)
 
     # Flip around indexes
     if x_decreasing:
diff --git a/pixi.lock b/pixi.lock
index c5f30dc1d..3c580c54e 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -42,7 +42,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/azure-storage-blobs-cpp-12.13.0-h3cf044e_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/azure-storage-common-cpp-12.8.0-h736e048_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/azure-storage-files-datalake-cpp-12.12.0-ha633028_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/babel-2.18.0-pyhcf101f3_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/babel-2.18.0-pyhcf101f3_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/backports-1.0-pyhd8ed1ab_5.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/backports.tarfile-1.2.0-pyhcf101f3_2.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/beartype-0.22.9-pyhd8ed1ab_0.conda
@@ -62,7 +62,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/certifi-2026.2.25-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/cffi-2.0.0-py312h460c074_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/cftime-1.6.5-py312h4f23490_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.4.4-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.4.5-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/click-8.3.1-pyh8f84b5b_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/click-plugins-1.1.1.2-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/cligj-0.7.2-pyhd8ed1ab_2.conda
@@ -72,10 +72,10 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/contextily-1.7.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/contourpy-1.3.3-py312h0a2e395_4.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/coverage-7.13.4-py312h8a5da7c_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/cpython-3.12.12-py312hd8ed1ab_2.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/cpython-3.12.13-py312hd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/cryptography-46.0.5-py312ha4b625e_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/cycler-0.12.1-pyhcf101f3_2.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/cyclopts-4.5.4-pyhcf101f3_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/cyclopts-4.7.0-pyhcf101f3_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/cyrus-sasl-2.1.28-hd9c7081_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/cytoolz-1.1.0-py312h4c3975b_2.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/dask-2026.1.2-pyhcf101f3_1.conda
@@ -96,7 +96,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/execnet-2.1.2-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/expat-2.7.4-hecca717_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/ffmpeg-7.1.1-gpl_h0b79d52_704.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/filelock-3.24.3-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/filelock-3.25.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/flopy-3.9.5-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/fltk-1.3.10-hff38c0f_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/folium-0.20.0-pyhd8ed1ab_0.conda
@@ -110,7 +110,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/fonttools-4.61.1-py312h8a5da7c_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/freeglut-3.2.2-ha6d2627_3.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/freeimage-3.18.0-h3a85593_22.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/freetype-2.14.1-ha770c72_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/freetype-2.14.2-ha770c72_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/freexl-2.0.0-h9dce30a_2.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/fribidi-1.0.16-hb03c661_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/frozenlist-1.7.0-py312h447239a_0.conda
@@ -157,7 +157,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/jaraco.classes-3.4.0-pyhcf101f3_3.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/jaraco.context-6.1.0-pyhcf101f3_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/jaraco.functools-4.4.0-pyhcf101f3_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/jasper-4.2.8-he3c4edf_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/jasper-4.2.9-he3c4edf_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/jeepney-0.9.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/jinja2-3.1.6-pyhcf101f3_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/joblib-1.5.3-pyhd8ed1ab_0.conda
@@ -190,7 +190,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libbrotlienc-1.1.0-hb03c661_4.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libcap-2.77-h3ff7636_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.11.0-5_h0358290_openblas.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libclang-cpp20.1-20.1.8-default_h99862b1_12.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libclang-cpp20.1-20.1.8-default_h99862b1_13.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libclang13-21.1.0-default_h746c552_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libcrc32c-1.1.2-h9c3ff4c_0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libcups-2.3.3-hb8b1518_5.conda
@@ -206,8 +206,8 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.7.4-hecca717_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libffi-3.5.2-h3435931_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libflac-1.5.0-he200343_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libfreetype-2.14.1-ha770c72_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libfreetype6-2.14.1-h73754d4_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libfreetype-2.14.2-ha770c72_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libfreetype6-2.14.2-h73754d4_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_18.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_18.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libgd-2.3.3-h6f5c62b_11.conda
@@ -269,7 +269,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/librttopo-1.1.0-hd718a1a_18.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libsndfile-1.2.2-hc7d488a_2.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libspatialite-5.1.0-h366e088_13.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.51.2-h0c1763c_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.52.0-h0c1763c_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.1-hcf80075_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.2.0-h934c35e_18.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-15.2.0-hdf11a46_18.conda
@@ -303,7 +303,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/makefun-1.16.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/mapclassify-2.10.0-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/markdown-it-py-4.0.0-pyhd8ed1ab_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/markupsafe-3.0.3-py312h8a5da7c_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/markupsafe-3.0.3-py312h8a5da7c_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/matplotlib-3.10.8-py312h7900ff3_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/matplotlib-base-3.10.8-py312he3d6523_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/mdurl-0.1.2-pyhd8ed1ab_1.conda
@@ -325,11 +325,11 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/networkx-3.6.1-pyhcf101f3_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/nh3-0.3.3-py310h6de7dc8_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/nlohmann_json-3.12.0-h54a6638_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/numba-0.63.1-py312hd1dde6f_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/numba_celltree-0.4.1-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/numba-0.64.0-py312hd1dde6f_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/numba_celltree-0.4.2-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/numcodecs-0.16.5-py312hf79963d_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/numpy-2.3.5-py312h33ff503_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/occt-7.9.3-novtk_hac3f730_100.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/numpy-2.4.2-py312h33ff503_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/occt-7.9.3-novtk_hac3f730_101.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/ocl-icd-2.3.3-hb9d3cd8_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/opencl-headers-2025.06.13-h5888daf_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/openexr-3.3.3-hff63da0_0.conda
@@ -382,18 +382,17 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/pytest-dotenv-0.5.2-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/pytest-timeout-2.4.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/pytest-xdist-3.8.0-pyhd8ed1ab_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.12.12-hd63d673_2_cpython.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.12.13-hd63d673_0_cpython.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/python-build-1.4.0-pyh332efcf_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/python-dateutil-2.9.0.post0-pyhe01879c_2.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/python-dotenv-1.2.1-pyhcf101f3_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/python-dotenv-1.2.2-pyhcf101f3_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/python-fastjsonschema-2.21.2-pyhe01879c_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/python-gil-3.12.12-hd8ed1ab_2.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/python-gil-3.12.13-hd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/python-gmsh-4.15.0-pyh57928b3_4.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/python-graphviz-0.21-pyhbacfb6d_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/python-librt-0.8.1-py312h5253ce2_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/python_abi-3.12-8_cp312.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/pytokens-0.4.1-py312h5253ce2_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/pytz-2025.2-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/pyvista-0.47.1-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/pyyaml-6.0.3-py312h8a5da7c_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/qhull-2020.2-h434a139_5.conda
@@ -410,10 +409,10 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/rfc3986-2.0.0-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/rich-14.3.3-pyhcf101f3_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/rich-rst-1.3.2-pyhd8ed1ab_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/rioxarray-0.20.0-pyhd8ed1ab_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/rioxarray-0.22.0-pyhc364b38_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/roman-numerals-4.1.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/rpds-py-0.30.0-py312h868fb18_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/ruff-0.15.2-h40fa522_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/ruff-0.15.5-h40fa522_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/s2n-1.5.22-h96f233e_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/scikit-learn-1.8.0-np2py312h3226591_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/scipy-1.17.1-py312h54fa4ab_0.conda
@@ -440,7 +439,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-jsmath-1.0.1-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-qthelp-2.0.0-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-serializinghtml-1.1.10-pyhd8ed1ab_1.conda
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