Merge branch 'main' into fm-isel-no-sort

.github/workflows/build_docs.yml

@@ -18,6 +18,7 @@ jobs:
 
     - name: Install MIKE IO
       run: |
+        pip install quartodoc@git+https://github.com/machow/quartodoc#d4140b4f804ebc6ec249699d52e3efa62cf53127
         pip install .[dev]
     
     - name: Build documentation

.github/workflows/docs.yml

@@ -21,6 +21,7 @@ jobs:
         
     - name: Install mikeio
       run: |
+        pip install quartodoc@git+https://github.com/machow/quartodoc#d4140b4f804ebc6ec249699d52e3efa62cf53127
         pip install .[dev]
     
     - name: Build documentation

docs/_quarto.yml

@@ -76,7 +76,7 @@ interlinks:
       pandas: 
         url: https://pandas.pydata.org/docs/
       scipy: 
-        url: https://docs.scipy.org/doc/scipy/reference/
+        url: https://docs.scipy.org/doc/scipy/
 
 quartodoc:
   style: pkgdown

docs/examples/Dfsu-2D-interpolation.qmd

@@ -163,7 +163,7 @@ Let's first try the approx for a single element:
 * Interpolate
 
 ```{python}
-dist = dist_in_meters(scatter[:,:2], dfs.element_coordinates[0,:2])
+dist = dist_in_meters(scatter[:,:2], dfs.geometry.element_coordinates[0,:2])
 dist
 ```
 
@@ -179,11 +179,11 @@ np.dot(scatter[:,2], w) # interpolated value in element 0
 Let's do the same for all points in the mesh and plot in the end
 
 ```{python}
-dati = np.zeros((1,dfs.n_elements))
-for j in range(dfs.n_elements):
-    dist = dist_in_meters(scatter[:,:2], dfs.element_coordinates[j,:2])
+dati = np.zeros((1, dfs.geometry.n_elements))
+for j in range(dfs.geometry.n_elements):
+    dist = dist_in_meters(scatter[:, :2], dfs.geometry.element_coordinates[j, :2])
     w = get_idw_interpolant(dist, p=2)
-    dati[0,j] = np.dot(scatter[:,2], w)
+    dati[0, j] = np.dot(scatter[:, 2], w)
 ```
 
 ```{python}

docs/user-guide/dataarray.qmd

@@ -92,16 +92,14 @@ See details in the [API specification](`mikeio.dataset._data_plot._DataArrayPlot
 
 The DataArray has several properties:
 
-* n_items - Number of items
-* n_timesteps - Number of timesteps
-* n_elements - Number of elements
-* start_time - First time instance (as datetime)
-* end_time - Last time instance (as datetime)
-* is_equidistant - Is the time series equidistant in time
-* timestep - Time step in seconds (if is_equidistant)
-* shape - Shape of each item
+* time - Time index
+* geometry - geometry of the data (e.g. `spatial.GeometryFM2D`)
+* shape - Shape of the data
 * deletevalue - File delete value (NaN value)
 
+```{python}
+da.geometry
+```
 
 
 ## Methods

docs/user-guide/dataset.qmd

@@ -14,19 +14,10 @@ The Dataset has the following primary properties:
 Use Dataset's string representation to get an overview of the Dataset
 
 
-```python
->>> import mikeio
->>> ds = mikeio.read("testdata/HD2D.dfsu")
->>> ds
-<mikeio.Dataset>
-dims: (time:9, element:884)
-time: 1985-08-06 07:00:00 - 1985-08-07 03:00:00 (9 records)
-geometry: Dfsu2D (884 elements, 529 nodes)
-items:
-  0:  Surface elevation <Surface Elevation> (meter)
-  1:  U velocity <u velocity component> (meter per sec)
-  2:  V velocity <v velocity component> (meter per sec)
-  3:  Current speed <Current Speed> (meter per sec)
+```{python}
+import mikeio
+ds = mikeio.read("../data/HD2D.dfsu")
+ds
 ```
 
 ## {{< fa filter >}} Selecting items
@@ -41,13 +32,8 @@ Selecting a specific item "itemA" (at position 0) from a Dataset ds can be done
 
 We recommend the use *named* items for readability. 
 
-```
->>> ds.Surface_elevation
-<mikeio.DataArray>
-name: Surface elevation
-dims: (time:9, element:884)
-time: 1985-08-06 07:00:00 - 1985-08-07 03:00:00 (9 records)
-geometry: Dfsu2D (884 elements, 529 nodes)
+```{python}
+ds.Surface_elevation
 ```
 
 Negative index e.g. ds[-1] can also be used to select from the end. 
@@ -63,46 +49,20 @@ Note that this behavior is similar to pandas and xarray.
 
 A time slice of a Dataset can be selected in several different ways. 
 
-```python
->>> ds.sel(time="1985-08-06 12:00")
-<mikeio.Dataset>
-dims: (element:884)
-time: 1985-08-06 12:00:00 (time-invariant)
-geometry: Dfsu2D (884 elements, 529 nodes)
-items:
-  0:  Surface elevation <Surface Elevation> (meter)
-  1:  U velocity <u velocity component> (meter per sec)
-  2:  V velocity <v velocity component> (meter per sec)
-  3:  Current speed <Current Speed> (meter per sec)
-
->>> ds["1985-8-7":]
-<mikeio.Dataset>
-dims: (time:2, element:884)
-time: 1985-08-07 00:30:00 - 1985-08-07 03:00:00 (2 records)
-geometry: Dfsu2D (884 elements, 529 nodes)
-items:
-  0:  Surface elevation <Surface Elevation> (meter)
-  1:  U velocity <u velocity component> (meter per sec)
-  2:  V velocity <v velocity component> (meter per sec)
-  3:  Current speed <Current Speed> (meter per sec)
+```{python}
+ds.sel(time="1985-08-06 12:00")
+```
 
+```{python}
+ds["1985-8-7":]
 ```
 
 ## {{< fa map >}} Spatial selection
 
-The `sel` method finds the nearest element.
-
-```python
->>> ds.sel(x=607002, y=6906734)
-<mikeio.Dataset>
-dims: (time:9)
-time: 1985-08-06 07:00:00 - 1985-08-07 03:00:00 (9 records)
-geometry: GeometryPoint2D(x=607002.7094112666, y=6906734.833048992)
-items:
-  0:  Surface elevation <Surface Elevation> (meter)
-  1:  U velocity <u velocity component> (meter per sec)
-  2:  V velocity <v velocity component> (meter per sec)
-  3:  Current speed <Current Speed> (meter per sec)
+The `sel` method finds a single element.
+
+```{python}
+ds.sel(x=607002, y=6906734)
 ```
 
 
@@ -129,8 +89,6 @@ The Dataset (and DataArray) has several properties:
 * shape - Shape of each item
 * deletevalue - File delete value (NaN value)
 
-
-
 ## Methods
 
 Dataset (and DataArray) has several useful methods for working with data, 

docs/user-guide/dfsu.qmd

@@ -31,7 +31,7 @@ In MIKE Zero, node ids, element ids and layer ids are 1-based.  In MIKE IO, all
 
 ## MIKE IO Flexible Mesh Geometry 
 
-MIKE IO has a Flexible Mesh Geometry class, [`GeometryFM`](`mikeio.spatial.GeometryFM2D`), containing the list of node coordinates and the element table which defines the mesh, as well as a number of derived properties (e.g. element coordinates) and methods making it convenient to work with the mesh. 
+MIKE IO has Flexible Mesh Geometry classes, e.g. [`GeometryFM2D`](`mikeio.spatial.GeometryFM2D`), containing the list of node coordinates and the element table which defines the mesh, as well as a number of derived properties (e.g. element coordinates) and methods making it convenient to work with the mesh. 
 
 | Property  |      Description     |
 |----------|--------------|

mikeio/__init__.py

@@ -21,7 +21,7 @@
 # 'X.Y.dev0' is the canonical version of 'X.Y.dev'
 #
 
-__version__ = "2.0.dev0"  # TODO use git hash instead for dev version?
+__version__ = "2.0.b0"  # TODO use git hash instead for dev version?
 # __version__ = "1.5.0"
 __dfs_version__: int = 200
 

mikeio/dataset/_dataset.py

@@ -573,8 +573,6 @@ def remove(self, key: int | str) -> None:
         --------
         pop
         """
-        # deprecated
-        warnings.warn("Dataset.remove is deprecated", FutureWarning)
         self.__delitem__(key)
 
     def rename(self, mapper: Mapping[str, str], inplace: bool = False) -> "Dataset":

mikeio/spatial/_utils.py

@@ -1,3 +1,4 @@
+from __future__ import annotations
 import numpy as np
 
 from ._geometry import BoundingBox

pyproject.toml

@@ -10,7 +10,7 @@ allow-direct-references = true
 
 [project]
 name="mikeio"
-version="2.0.dev0"
+version="2.0.b0"
 dependencies = [
     "mikecore>=0.2.1",
     "numpy>=1.22.0",
@@ -48,7 +48,7 @@ classifiers = [
 dev = ["pytest",
        "black==22.3.0",
        "quarto-cli",
-       "quartodoc@git+https://github.com/machow/quartodoc#d4140b4f804ebc6ec249699d52e3efa62cf53127",
+       "quartodoc",
        "shapely",
        "pyproj",
        "xarray",