Updating the readthedocs text

docs/contributing.md

@@ -35,13 +35,13 @@ The Scivision project is fully open-source and invites contributions from anyone
 
 Adding a model or dataset to the catalog makes it discoverable by other Scivision users.
 
-See :ref:`contributing-to-the-scivision-catalog`.
+See :ref:`contributing-a-model` or :ref:`contributing-a-datasource`.
 
 #### Project pages
 
 Adding a project page allows you to describe in more detail how your models / data in the Scivision catalog have been used. This can contain details of the project and links to example notebooks or papers that use them. 
 
-See :ref:`contributing-to-the-scivision-catalog`.
+See :ref:`contributing-a-project`.
 
 #### Bug reports
 
@@ -94,9 +94,9 @@ There are three ways in which you can contribute to the Scivision catalog: model
 
 #### Preparing a model for inclusion in the catalog
 
-In order to submit a model to the Scivision catalog, it must be publically available from a source repository or on a package server, so that it can installed using pip. The model must include everything needed to run it, including any weights and parameters.
+In order to submit a model to the Scivision catalog, it must be publically available from a source repository or on a package server, so that it can installed using pip. The model must include everything needed to run it, including any weights and parameters. More details can be found in the :ref:`model-repo-template`. 
 
-Additionally, if you would like to be able to load your model using the Scivision API and run it on matching datasets present in the catalog, you must first set up the GitHub repository containing the model as per the :ref:`model-repo-template`.
+Additionally, if you would like to be able to load your model using the Scivision API and run it on matching datasets present in the catalog, you must first set up the GitHub repository containing the model as explained [here](https://scivision.readthedocs.io/en/latest/model_repository_template.html#requirements-for-the-scivision-api).
 
 #### Submitting your model to the catalog
 
@@ -120,9 +120,9 @@ After you are done, create a pull request with the changes. A Scivision maintain
 
 #### Preparing a dataset for inclusion in the catalog
 
-In order to submit a dataset to the Scivision catalog, your data must be in a publicly accessible location (for example, on [Zenodo](https://zenodo.org/)).
+In order to submit a dataset to the Scivision catalog, your data must be in a publicly accessible location (for example, on [Zenodo](https://zenodo.org/)). More details can be found in the :ref:`data-repo-template`. 
 
-Additionally if you would like to be able to load your dataset via the Scivision API and run matching models from catalog on it, you must first set up a GitHub repository containing important metadata as per the :ref:`data-repo-template`.
+Additionally if you would like to be able to load your dataset via the Scivision API and run matching models from catalog on it, you must first set up a GitHub repository containing important metadata as as explained [here](https://scivision.readthedocs.io/en/latest/data_repository_template.html#requirements-for-the-scivision-api).
 
 
 #### Adding a new dataset to the catalog
@@ -149,7 +149,7 @@ After you are done, create a pull request to the original repo with the changes.
 Once you have submitted your model / datasource for inclusion in the catalog, you might want to also consider submitting a project to provide some more details about how they have been used in your research. 
 
 #### Adding a new project to the catalog
-To submit a project, enter the relevant details about it [here](https://sci.vision/new-project). This will create a .json file in the correct format. Open a [new issue on GitHub](https://github.com/alan-turing-institute/scivision/issues/new?assignees=&labels=catalog%2Cdata&projects=&template=new-datasource.md&title=%5BPROJECT%5D), attaching the .json file and an appropriate thumbnail (a 256x256 .png or .jpg file with the same name as the datasource). You will need a GitHub account. 
+To submit a project, enter the relevant details about it [here](https://sci.vision/new-project). This will create a .json file in the correct format. Open a [new issue on GitHub](https://github.com/alan-turing-institute/scivision/issues/new?assignees=&labels=catalog%2Cproject&projects=&template=new-project.md&title=%5BPROJECT%5D), attaching the .json file and an appropriate thumbnail (a 256x256 .png or .jpg file with the same name as the datasource). You will need a GitHub account. 
 
 Once your submission is accepted, the project will become visible to other users of Scivision, and it will appear on the [website](https://sci.vision/project-grid).
 
@@ -160,6 +160,6 @@ This section describes how to add a catalog entry by hand.  These steps are an a
 
 Fork the [Scivision repository](https://github.com/alan-turing-institute/scivision). Fill in [the form](https://sci.vision/new-project) on the scivision website to get the details for your project in to the correct format.  On your new branch, add this information to the end of `projects.json` (found in `scivision/src/scivision/catalog/projects/`), under `"entries"`.
 
-Additionally, upload a suitable thumbnail to the [thumbnail datasources folder](https://github.com/alan-turing-institute/scivision/tree/main/src/scivision/catalog/data/thumbnails/datasources). This must be a 256x256 .png or .jpg file with the same name as the datasource.
+Additionally, upload a suitable thumbnail to the [thumbnail project folder](https://github.com/alan-turing-institute/scivision/tree/main/src/scivision/catalog/data/thumbnails/projects). This must be a 256x256 .png or .jpg file with the same name as the datasource.
 
 After you are done, create a pull request to the original repo with the changes. A Scivision maintainer will approve the addition, and it will appear on the [website](https://sci.vision/project-grid).

docs/data_repository_template.md

@@ -6,55 +6,55 @@ In order to include a dataset in the Scivision catalog, it must be hosted in a p
 
 This guide explains how to ensure your datasets are compatible with Scivision. The basic requirements for addition to the Scivision catalog are described first. There are then details on the additional requirements to enable the dataset to be loaded / run through the scivision API.
 
-These instructions will enable you to get your dataset into the correct format for adding to the Scivision "catalog". Once you have set up your dataset as per this guide, consult the [contributor page](./contributing.html#gift-contributing-to-the-scivision-catalog) for details of how to submit it.  
+These instructions will enable you to get your dataset into the correct format for adding to the Scivision "catalog". Once you have set up your dataset as per this guide, consult the [contributor page](https://scivision.readthedocs.io/en/latest/contributing.html#contributing-a-datasource) for details of how to submit it.  
 
 
 📚 **Contents:**
 
-- :ref:`catalog`
+- :ref:`data-catalog`
   - :ref:`documentation`
   - :ref:`data-license`
   - :ref:`data-thumbnail`
-- :ref:`api`
+- :ref:`data-api`
   - :ref:`data-repo-structure`
   - :ref:`data-config-file`
 
 <!-- - :ref:`example-data-repos` -->
 
-.. _catalog:
+.. _data-catalog:
 
 ## 📁 Requirements for the Scivision catalog
 
 .. _documentation:
 
-### 📄 Documentation
+#### 📄 Documentation
 
 Helpful information on the dataset and its origin should be included with the dataset, for example a `README` file. Without this, your dataset may not be accepted for inclusion in the Scivision catalog.
 
 .. _data-license:
 
-### 📜 Data license
+#### 📜 Data license
 
 You should include a `LICENSE` file, so that Scivision users who come across it can understand the conditions of the data's usage. For help deciding which license to include, check out the section on [data licenses](https://the-turing-way.netlify.app/reproducible-research/licensing/licensing-data.html) in The Turing Way online handbook.
 
 .. _data-thumbnail:
 
-### 🎆 Data Thumbnail
+#### 🎆 Data Thumbnail
 
 When viewing the dataset in [sci.vision](https://sci.vision/#/datasource-grid) a dataset thumbnail is required. The thumbnail can be an interesting image or slice of the dataset that catches the attention of the Scivision user (creativity encouraged!). 
 
 - It must be a 256x256 PNG or JPEG file
 - The file name should be the name of the dataset as in the catalog
 
-.. _api:
+.. _data-api:
 
 ## ✨ Requirements for the Scivision API
 
-.. _data-repo-structure:
-
 For your data(s) to be loadable by the Scivision API, it is necessary to create a GitHub repo structure in a particular structure, and include a data config file. 
 
-### 🧱 Data repo structure
+.. _data-repo-structure:
+
+#### 🧱 Data repo structure
 
 We recommend to set up a data repo for Scivision with the following structure, with the default name for the config file that the Scivision API will recognise being `.scivision/data.yml`:
 
@@ -69,7 +69,7 @@ exampleuser/data_repo
 
 .. _data-config-file:
 
-### 🖋️ Data config file
+#### 🖋️ Data config file
 
 The `scivision` python API relies upon another open source python tool called `intake` for loading datasets. We recommend creating a YAML format "intake catalog" (config file), to enable Scivision users who discover your dataset to easily load it via the API.
 

docs/model_repository_template.md

@@ -6,7 +6,7 @@ In order to include a computer vision (CV) model in the Scivision catalog, a Git
 
 This guide explains how to set up a GitHub repository for your CV model(s) compatible with Scivision. The basic requirements for addition to the Scivision catalog are described first. There are then details on the additional requirements to enable a model to be loaded / run through the scivision API. Followed by some features that are optional, but good to have. 
 
-These instructions will enable you to get your model into the correct format for adding to the Scivision "catalog". Once you have set up your model as per this guide, consult the [contributor page](./contributing.html#gift-contributing-to-the-scivision-catalog) for details of how to submit it. 
+These instructions will enable you to get your model into the correct format for adding to the Scivision "catalog". Once you have set up your model as per this guide, consult the [contributor page](https://scivision.readthedocs.io/en/latest/contributing.html#contributing-a-model) for details of how to submit it. 
 
 📚 **Contents:**
 
@@ -66,19 +66,19 @@ The essential components of a Scivision model repo include everything required f
 
 .. _installations:
 
-### 📄 Installation documentation
+#### 📄 Installation documentation
 
 A `README`, which includes detailed instructions on how the model can be installed. Without this, your model(s) will not be accepted for inclusion in the Scivision catalog.
 
 .. _software-licence:
 
-### 📜 Software license
+#### 📜 Software license
 
 You should include a `LICENSE` file in the repository, so that Scivision users who come across it can understand the conditions of its usage. For help deciding which license to include, see www.choosealicense.com or check out the section on [software licenses](https://book.the-turing-way.org/reproducible-research/licensing.html?highlight=license) in The Turing Way online handbook.
 
 .. _model-thumbnail:
 
-### 🎆 Model Thumbnail
+#### 🎆 Model Thumbnail
 
 When viewing the model in [sci.vision](https://sci.vision/#/model-grid) a model thumbnail is required. The thumbnail can be an interesting image explaining the model and that catches the attention of the Scivision user (creativity encouraged!).
 
@@ -95,7 +95,7 @@ For your model(s) to be loadable by the Scivision API, we additionally insist th
 
 .. _model-code:
 
-### 🏗️ Model code
+#### 🏗️ Model code
 
 The script called `model.py` must either contain the model itself (i.e. code that both trains and runs the model), or import a pre-trained model from elsewhere.
 
@@ -105,7 +105,7 @@ For examples, check out the [example model repos](#example-repos) section.
 
 .. _config:
 
-### 🖋️ Model config file
+#### 🖋️ Model config file
 
 The default name for the config file included in your repo should be `model.yml`, and should be kept in the `.scivision` directory. Take a look at this config from one of our example model repositories: [alan-turing-institute/plankton-cefas-scivision](https://github.com/alan-turing-institute/plankton-cefas-scivision):
 
@@ -140,7 +140,7 @@ It's also possible to specify multiple models from the same model repository. Fo
 
 .. _pip:
 
-### 🐍 Installability with pip
+#### 🐍 Installability with pip
 
 You can include a `setup.py` to enable the model(s) to be installed via pip, which is necessary for the Scivision API to be able to load the model(s). For an explanation of how this works, see this [packaging guide](https://packaging.python.org/en/latest/tutorials/packaging-projects/#configuring-metadata) for Python. By additionally including a `requirements.txt` with the required packages for your model, you can make it so these are installed along with the model code.
 
@@ -178,15 +178,15 @@ Some other components of a Scivision model repository that we recommend, but whi
 
 .. _tests:
 
-### 🧪 Tests
+#### 🧪 Tests
 
 Effective testing of code is vitally important to ensure the reliability of software, and in the context of scientific research code, the reproducibility of analyses and results.
 
 We recommend that models repos submitted to the Scivision catalog are thoroughly tested. For more information of testing for research code, check out [The Turing Way](https://the-turing-way.netlify.app/reproducible-research/testing.html) online handbook.
 
 .. _example-data:
 
-### 📊 Example data
+#### 📊 Example data
 
 We recommend including a directory with a small amount of test image data, in a format that can be used by the model(s) in the repo. This will be useful for Scivision users who wish to try running your model(s).