Updating the documentation (#679)

* Change text for shift from setup.py to pyproject.toml

* Adding doi badge

* Update README.md text

Author: IFenton

README.md

@@ -7,34 +7,39 @@
 [![PyPI badge](https://img.shields.io/pypi/v/scivision)](https://pypi.org/project/scivision/)
 [![All Contributors](https://img.shields.io/github/all-contributors/alan-turing-institute/scivision?color=ee8449)](#contributors)
 [![Licence badge (BSD 3 Clause)](https://img.shields.io/badge/License-BSD_3--Clause-blue.svg)](https://github.com/alan-turing-institute/scivision/blob/main/LICENSE)
+[![DOI](https://zenodo.org/badge/367023884.svg)](https://zenodo.org/doi/10.5281/zenodo.10792860)
 
 If you are new to Scivision, start with the [website](https://sci.vision/).
 
 The Scivision project is building:
 
-- Some things hosted in [this GitHub repository](https://github.com/alan-turing-institute/scivision):
-  - A **catalog** of community-curated computer vision [models](https://sci.vision/#/model-grid) and [datasets](https://sci.vision/#/datasource-grid) from the sciences and humanities
-  - A **Python package**, for conveniently downloading and using these models and datasets from Python ([scivision on PyPI](https://pypi.org/project/scivision/))
-  - **Documentation** for the above ([documentation website](https://scivision.readthedocs.io/en/latest/))
-- A [**gallery of notebooks**](https://github.com/scivision-gallery) using Scivision models and datasets
-- a **community** of computer vision practitioners in the sciences and humanities
-   ([mailing list](https://scivision.substack.com/), [get Slack invitation](https://docs.google.com/forms/d/e/1FAIpQLSfDPbsb_CWApnodHlNyOQMQdKhKA9meJi_SAuh8K8dVpbIiDA/viewform))
-- A (nascent) **ecosystem of computer vision tools and utilities**
+- A **community** of computer vision practitioners in the sciences and humanities
+   ([get a Slack invitation](https://docs.google.com/forms/d/e/1FAIpQLSfDPbsb_CWApnodHlNyOQMQdKhKA9meJi_SAuh8K8dVpbIiDA/viewform), [join the mailing list](https://scivision.substack.com/))
+- A **catalog** of community-curated computer vision [models](https://sci.vision/#/model-grid) and [datasets](https://sci.vision/#/datasource-grid) from the sciences and humanities
+- A software **ecosystem of interoperable tools** and utilities for working with computer vision models and data, including:
+  - **Scivision.Py**, a Python package for conveniently downloading and using the computer vision models and datasets from Python ([scivision on PyPI](https://pypi.org/project/scivision/))
+  - **[Pixelflow](https://github.com/alan-turing-institute/pixelflow)**, a tool for extracting information about the characteristics of objects in images
 
-Submit a bug or feature request [here](https://github.com/alan-turing-institute/scivision/issues).
-
-If you would like a link to a model or datasource to be listed in the catalog, such a contribution would be gratefully received. See the [Contributing Guide](https://scivision.readthedocs.io/en/latest/contributing.html) for how to set up and submit a new entry.  Pull requests for code changes are also welcome.
+  Example use cases for these tools can be found in the [**gallery of notebooks**](https://github.com/scivision-gallery) using Scivision models and datasets 
 
-The Scivision project is funded by the Alan Turing Institute.
+The Scivision project is funded by [the Alan Turing Institute](https://www.turing.ac.uk/).
 
 ## Repository contents
 
-The main [project repository on GitHub](https://github.com/alan-turing-institute/scivision) hosts
+This main [project repository on GitHub](https://github.com/alan-turing-institute/scivision) hosts
   - development of the Python package (in the root directory)
   - development of the website (in `frontend`)
   - the documentation sources (in `docs`)
 
-## Getting Started
+## Get involved
+Submit a bug or feature request [here](https://github.com/alan-turing-institute/scivision/issues).
+
+If you would like a link to a model or datasource to be listed in the catalog, such a contribution would be gratefully received. These can be submitted through the [scivision website](https://sci.vision/#/contribute). See the [Contributing Guide](https://scivision.readthedocs.io/en/latest/contributing.html) for more details on how to format your model / data.  
+
+Pull requests for code changes are also welcome.
+
+
+## Getting Started with Scivision.Py
 
 A quick overview of using the Scivision.Py python package.
 
@@ -91,7 +96,7 @@ plt.imshow(test_image)
 
 ![Image showing test_image (a picture of a Koala)](https://upload.wikimedia.org/wikipedia/commons/thumb/2/21/Cutest_Koala.jpg/262px-Cutest_Koala.jpg)
 
-- [More about datasources](https://scivision.readthedocs.io/en/latest/datasource_repository_template.html)
+- [More about datasources](https://scivision.readthedocs.io/en/latest/data_repository_template.html)
 
 ### Run a Scivision model
 
@@ -122,8 +127,7 @@ Output:
 |  ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ |
 
 
-- [Contributing an entry to the catalog](https://scivision.readthedocs.io/en/latest/contributing.html#extending-the-scivision-catalog)
-- The catalogs are browsable online:
+The catalogs are browsable online:
   - [model catalog](https://sci.vision/#/model-grid)
   - [datasource catalog](https://sci.vision/#/datasource-grid)
 

docs/maintainers.md

@@ -15,15 +15,15 @@ If you are new to the `scivision` project and wish to become a maintainer for ei
 
 A new release of the scivision package will be uploaded to PyPI each time a tagged commit is pushed to the main branch of the [scivision GitHub repo](https://github.com/alan-turing-institute/scivision). In order to trigger this automated process, do the following:
 
-1. On a new branch of the `scivision` repo, containing your changes to be included in the release, increment the `version` in `setup.py` and any other metadata that differs for the new release.
+1. On a new branch of the `scivision` repo, containing your changes to be included in the release, increment the `version` in `pyproject.toml` and any other metadata that differs for the new release.
 
 2. Create a pull request and merge to the `main` branch.
 
-3. At the main repo page on GitHub, click the following `Releases -> Draft a new release`. Click `Choose a tag` and create a new tag named as the `version` number. Fill in the descriptive fields and publish the release. After a few moments, the new version should show up at https://pypi.org/project/scivision/
+3. At the main repo page on GitHub, click the following `Releases -> Draft a new release`. Click `Choose a tag` and create a new tag named as the `version` number. Fill in the descriptive fields and publish the release. (You don't need to upload the binaries as these are automatically generated). After a few moments, the new version should show up at https://pypi.org/project/scivision/
 
 Alternatively, developers of `scivision` with maintainer access to https://github.com/alan-turing-institute/scivision & https://pypi.org/project/scivision can manually release a new version of the package with the following steps:
 
-1. On a new branch of the `scivision` repo, containing your changes to be included in the release, increment the `version` in `setup.py` and any other metadata that differs for the new release.
+1. On a new branch of the `scivision` repo, containing your changes to be included in the release, increment the `version` in `pyproject.toml` and any other metadata that differs for the new release.
 
 2. Make sure you have a working python 3 installation. Check your version with:
 
@@ -46,7 +46,7 @@ Alternatively, developers of `scivision` with maintainer access to https://githu
    python -m twine upload dist/<version>*
    ```
     * Note: You'll need to provide your PyPI username and password
-6. Commit changes to `setup.py` and pull request to the `main` branch of https://github.com/alan-turing-institute/scivision
+6. Commit changes to `pyproject.toml` and pull request to the `main` branch of https://github.com/alan-turing-institute/scivision
 
 .. _building:
 
@@ -81,4 +81,4 @@ Maintainers of this `readthedocs` site can build and view the docs by doing the
 5. Push the updates to the readthedocs site:
   * Create a pull request with your changes
   * A build of the docs should be triggered
-  * You can also log into the https://readthedocs.org/projects/scivision/ dashboard as a maintainer and click `Builds->Build Version`
+  * You can also log into the https://readthedocs.org/projects/scivision/ dashboard as a maintainer and click `Builds->Build Version`