Fix user-guide

docs/user-guide/dataset.qmd

@@ -6,7 +6,7 @@ The [](`mikeio.read`) methods returns a Dataset as a container of [DataArray](`m
 
 The Dataset has the following primary properties: 
 
-* **items** - a list of [](`mikeio.eum.ItemInfo`) items for each dataarray
+* **items** - a list of [](`mikeio.ItemInfo`) items for each dataarray
 * **time** - a [](`pandas.DatetimeIndex`) with the time instances of the data
 * **geometry** - a Geometry object with the spatial description of the data
 

docs/user-guide/mesh.qmd

@@ -63,7 +63,6 @@ coastalzone
 Find if points are inside the domain
 
 ```{python}
-#| tags: []
 from shapely.geometry import Point
 
 p1 = Point(216000, 6162000)
@@ -72,11 +71,11 @@ print(mp.contains(p1))
 print(mp.contains(p2))
 ```
 
-## Mesh class can also check if a mesh contains points 
+We can get similar functionality from the `.geometry` attribute of the mesh object.
 
 ```{python}
 p1p2 = [[216000, 6162000], [220000, 6156000]]
-msh.contains(p1p2)
+msh.geometry.contains(p1p2)
 ```
 
 ```{python}
@@ -91,23 +90,34 @@ ax.legend();
 Assume that we want to have a minimum depth of 2 meters and change the open boundary (code 2) to a closed one (code 1). 
 
 ```{python}
-print(f'max z before: {msh.node_coordinates[:,2].max()}')
-zc = msh.node_coordinates[:,2]
+g = msh.geometry
+print(f'max z before: {g.node_coordinates[:,2].max()}')
+zc = g.node_coordinates[:,2]
 zc[zc>-2] = -2
-msh.zn = zc
-print(f'max z after: {msh.node_coordinates[:,2].max()}')
+g.node_coordinates[:,2] = zc
+print(f'max z after: {g.node_coordinates[:,2].max()}')
 ```
 
+
 ```{python}
-print(f'valid codes before: {msh.valid_codes}')
-c = msh.geometry.codes
+c = g.codes
 c[c==2] = 1
-msh.codes = c
-print(f'valid codes after: {msh.valid_codes}')
+g.codes = c
 ```
 
+Save the modfied geometry to a new mesh file
+
 ```{python}
-msh.plot()
+g.to_mesh("new_mesh.mesh")
 ```
 
+Cleanup
+
+```{python}
+import os
+
+os.remove("new_mesh.mesh")
+```
+
+
 

docs/user-guide/pfs.qmd

@@ -41,20 +41,20 @@ pfs
 
 ### PfsDocument
 
-The [](`-mikeio.PfsDocument`) is the MIKE IO equivalent to a PFS file. Its targets can be accessed by their name (as properties), like this:  
+The [](`mikeio.PfsDocument`) is the MIKE IO equivalent to a PFS file. Its targets can be accessed by their name (as properties), like this:  
 
 ```{python}
 pfs.txconc
 ```
 
 Or by the `pfs.targets` object (which is a list of PfsSections). Each of the targets is a `PfsSection` object consisting of key-value pairs (keyword-parameter) and other PfsSections. 
 
-The [](`-mikeio.PfsDocument`) object is similar to a dictionary. You can loop over its contents with `items()`, `keys()` and `values()` like a dictionary. 
+The [](`mikeio.PfsDocument`) object is similar to a dictionary. You can loop over its contents with `items()`, `keys()` and `values()` like a dictionary. 
 
 
 ### PfsSection
 
-The [](`-mikeio.PfsSection`) object is also similar to a dictionary. You can loop over its contents with `items()`, `keys()` and `values()` like a dictionary. 
+The [](`mikeio.PfsSection`) object is also similar to a dictionary. You can loop over its contents with `items()`, `keys()` and `values()` like a dictionary. 
 
 ```{python}
 pfs.txconc.keys()
@@ -88,7 +88,7 @@ pfs.txconc.Setup.to_dataframe(prefix="File_")
 
 ### Unique or non-unique keywords
 
-Depending on the engine intended for reading the PFS file it may or may not make sense to have multiple identical keywords in the same PfsSection. MIKE 21/3 and the marine tools does *not* support non-unique keywords---if non-unique keywords are present, only the first will be read and the presence is most likely a mistake made by hand-editing the file. In other tools, e.g. MIKE Plot Composer, non-unique keywords are used a lot. How MIKE IO shall deal with non-unique keywords can be specified using the `unique_keywords` argument in the [](`-mikeio.read_pfs`) function: 
+Depending on the engine intended for reading the PFS file it may or may not make sense to have multiple identical keywords in the same PfsSection. MIKE 21/3 and the marine tools does *not* support non-unique keywords---if non-unique keywords are present, only the first will be read and the presence is most likely a mistake made by hand-editing the file. In other tools, e.g. MIKE Plot Composer, non-unique keywords are used a lot. How MIKE IO shall deal with non-unique keywords can be specified using the `unique_keywords` argument in the [](`mikeio.read_pfs`) function: 
 
 ```python
 pfs = mikeio.read_pfs("myplot.plt", unique_keywords=False)