Merge pull request #12 from metaspace2020/documentation-updates

Documentation updates

README.md

@@ -27,8 +27,9 @@ If you encounter any bugs or have suggestions for new features, please open an i
 
 Our package requires `python >= 3.9`.
 
+You can install the package directly from [PyPI](https://pypi.org/project/metaspace-converter/):
 ```bash
-pip install -U git+https://github.com/metaspace2020/metaspace-converter@master
+pip install metaspace-converter
 ```
 
 ### Import package
@@ -39,6 +40,8 @@ import metaspace_converter
 
 ## Short tutorial
 
+The full documentation for the package can be found here: [https://metaspace2020.github.io/metaspace-converter/](https://metaspace2020.github.io/metaspace-converter/)
+
 The METASPACE-converter package is using the
 [python client](https://github.com/metaspace2020/metaspace/tree/master/metaspace/python-client)
 download datasets from METASPACE.
@@ -160,6 +163,11 @@ sdata.points["maldi_points"] = sdata.transform_element_to_coordinate_system(
 
 ![Image](docs/_static/img/example_img_sd.png)
 
+## License
+
+Unless specified otherwise in file headers or LICENSE files present in subdirectories, all files are licensed under the [Apache 2.0 license](https://github.com/metaspace2020/metaspace/blob/master/LICENSE).
+
+
 [badge-docs]: https://img.shields.io/github/actions/workflow/status/metaspace2020/metaspace-converter/docs.yml?label=documentation
 [badge-pypi]: https://img.shields.io/pypi/v/metaspace-converter
 [badge-tests]: https://img.shields.io/github/actions/workflow/status/metaspace2020/metaspace-converter/tests.yml?branch=master&label=tests

docs/conf.py

@@ -18,8 +18,8 @@
 # -- Project information -----------------------------------------------------
 
 project = "METASPACE Converter"
-copyright = "2023, Tim Daniel Rose"
-author = "Tim Daniel Rose"
+copyright = "2023; Tim Daniel Rose, Andreas Eisenbarth, Theodore Alexandrov"
+author = "Tim Daniel Rose, Andreas Eisenbarth"
 
 
 # -- General configuration ---------------------------------------------------

docs/examples.rst

@@ -51,6 +51,28 @@ SquidPy
 .. image:: ./_static/img/example_img_sq.png
    :alt: Visualization with SquidPy
 
+Convert AnnData objects to ion image arrays
+-------------------------------------------
+
+If you want to work with the ion images as numpy arrays, the function `anndata_to_image_array` can
+convert previously downloaded AnnData objects to numpy arrays.
+
+.. testcode::
+
+   from metaspace_converter import metaspace_to_anndata, anndata_to_image_array
+
+   # Download data
+   adata2 = metaspace_to_anndata(dataset_id="2023-11-14_21h58m39s", fdr=0.1)
+
+   ion_images = anndata_to_image_array(adata2)
+
+   # 6 ion images of shape 61x78
+   print(ion_images.shape)
+
+.. testoutput::
+
+   (20, 130, 143)
+
 SpatialData
 -----------
 

docs/index.rst

@@ -6,10 +6,24 @@
 Welcome to METASPACE Converter's documentation!
 ===============================================
 
+|Tests badge|
+|Docs badge|
+|PyPI badge|
+
 Functions to convert `METASPACE`_ datasets to `AnnData`_ objects.
 
 This makes it easy to work with the `ScanPy`_, `SquidPy`_ and `SpatialData`_ ecosystem with METASPACE data.
 
+Installation
+------------
+You can install the package via pip:
+
+
+.. code-block::
+   
+   pip install metaspace-converter 
+
+
 .. toctree::
    :maxdepth: 2
    :caption: Contents:
@@ -22,3 +36,11 @@ This makes it easy to work with the `ScanPy`_, `SquidPy`_ and `SpatialData`_ eco
 .. _ScanPy: https://scanpy.readthedocs.io/en/stable/
 .. _SquidPy: https://squidpy.readthedocs.io/en/stable/
 .. _SpatialData: https://spatialdata.scverse.org/en/latest/
+
+
+.. |Tests badge| image:: https://img.shields.io/github/actions/workflow/status/metaspace2020/metaspace-converter/tests.yml?branch=master&label=tests
+    :target: https://github.com/metaspace2020/metaspace-converter/actions/workflows/tests.yml
+.. |Docs badge| image:: https://img.shields.io/github/actions/workflow/status/metaspace2020/metaspace-converter/docs.yml?label=documentation
+    :target: https://metaspace2020.github.io/metaspace-converter/
+.. |PyPI badge| image:: https://img.shields.io/pypi/v/metaspace-converter
+    :target: https://pypi.org/project/metaspace-converter/