[Docs] Fix and update docs

docs/api.md

@@ -25,10 +25,12 @@
     transform_shapes
 ```
 
-<!-- ## Plotting
+## Write
 
 ```{eval-rst}
-.. module:: dvpio.pl
-.. currentmodule:: dvpio
+.. currentmodule:: dvpio.write
+.. autosummary::
+    :toctree: generated
 
-``` -->
+    write_lmd
+```

src/dvpio/read/image/czi.py

@@ -146,14 +146,14 @@ def read_czi(
         Path to file
     chunk_size
         Size of the individual regions that are read into memory during the process
-    kwargs
-        Keyword arguments passed to Image2DModel.parse
     channels
         If multiple channels are available, select these channels
     timepoint
         If timeseries, select the given index (defaults to 0 [first])
     z_stack
         If z_stack, defaults to the given stack/index (defaults to 0 [first])
+    kwargs
+        Keyword arguments passed to :meth:`spatialdata.models.Image2DModel.parse`
 
     Returns
     -------

src/dvpio/read/shapes/lmd_reader.py

@@ -32,14 +32,14 @@ def transform_shapes(
 
     Returns
     -------
-    `class`::`spatialdata.models.ShapesModel`
+    :class:`spatialdata.models.ShapesModel`
         Transformed shapes in target coordinate system
 
     Object has special attributes
 
     - `ShapesModel.attrs.transformation`
-        - global: (image coordinates)
-        - leica_micro_dissection: Leica coordinate system transformation
+        - `global`: (image coordinates)
+        - `to_lmd`: Leica coordinate system transformation
 
     Raises
     ------
@@ -104,7 +104,7 @@ def read_lmd(path: str, calibration_points_image: PointsModel, switch_orientatio
 
     Returns
     -------
-    `class`::`spatialdata.models.ShapesModel`
+    :class:`spatialdata.models.ShapesModel`
         Transformed shapes in image coordinates.
 
         Object has special attributes

src/dvpio/write/lmd_writer.py

@@ -23,23 +23,21 @@ def write_lmd(
     ----------
     path:
         Export path for .xml
-    sdata
-        Spatialdata
     annotation
         Shapes to export with pyLMD
     calibration_points
-        Calibration points in the image.
+        Calibration points in image coordinates
     affine_transformation
-        Optional. Affine transformation to apply to the data to recover Leica coordinate system. If None,
-        tries to recover the `leica_micro_dissection` coordinate transformation from the `annotation`
-        `class`::`spatialdata.models.ShapesModel` object
+        Optional. Affine transformation to apply to the data to recover Leica coordinate system. If `None`,
+        tries to recover the `to_lmd` coordinate transformation from the `annotation`
+        :class:`spatialdata.models.ShapesModel` object
     annotation_name_column
         Optional. Provide column that specifies a (unique) cell name in `annotation`
-        `class`::`spatialdata.models.ShapesModel` object. Will be stored in as the tag of
+        :class:`spatialdata.models.ShapesModel` object. Will be stored as the tag of
         the Shape.
     annotation_well_column
         Optional. Provide column that specifies a well in the `annotation`
-        `class`::`spatialdata.models.ShapesModel` object. Will be stored in as the `CapID` attribute of
+        :class:`spatialdata.models.ShapesModel` object. Will be stored in as the `CapID` attribute of
         the Shape.
     overwrite
         Default `True`. Whether to overwrite existing data.
@@ -51,6 +49,7 @@ def write_lmd(
     Example
     -------
     .. code-block:: python
+
         from spatialdata.models import ShapesModel, PointsModel
         from tempfile import mkdtemp
         from dvpio.write import write_lmd