Merging of bg-atlasapi and bg-atlasgen (#150)

* Write blog post

* bg-atlasapi -> brainglobe-atlasapi

* bg_atlasapi -> brainglobe_atlasapi

* Update atlasgen references

* Link checker

* More link chckers

docs/source/about.md

@@ -23,7 +23,7 @@ We aim to facilitate the access to available datasets, and have developed severa
 download gene expression and mesoscale connectomics data for the mouse brain from the Allen institute.
 
 A core step towards facilitating the usage of atlas data was also taken by developing the 
-[BrainGlobe AtlasAPI](/documentation/bg-atlasapi/index). This tool provides a 
+[BrainGlobe AtlasAPI](/documentation/brainglobe-atlasapi/index). This tool provides a 
 simple and unified interface for downloading and using data from a number of available atlases. Additionally, new atlases 
 can easily be added to the API. With this tool we address a major obstacle when developing software for neuroanatomy:
 few of the available atlases provide programmatic access to their data, and the APIs used to access the data vary 

docs/source/blog/atlasapi-atlasgen-merge.md

@@ -0,0 +1,42 @@
+---
+blogpost: true
+date: Feb 14, 2024
+author: Will Graham
+location: London, England
+category: brainglobe
+language: English
+---
+
+# `bg-atlasapi` and `bg-atlasgen` have merged under a new name
+
+`bg-atlasapi` and `bg-atlasgen` have merged into a single package, now called `brainglobe-atlasapi`.
+`brainglobe-atlasapi` now provides the same API that `bg-atlasapi` provided, in exactly the same way - all that needs to happen is a name change in your scripts.
+
+`bg-atlasgen` used to provide the developer code for adding a new atlas to the collection of BrainGlobe atlases that are available for download.
+This code was exclusively used by developers, however it hinges on the functionality of `bg-atlasapi` to complete the generation and upload process.
+As such, it has now been moved into a submodule, `brainglobe_atlasapi.atlas_generation`, but again the way one interacts with this submodule is the same as they would have with `bg-atlasgen`.
+
+## What do I need to do?
+
+If you are using an install of `bg-atlasapi` that you got through `pip install brainglobe`, then all you need to do is update `brainglobe` to the latest version with
+
+```bash
+pip install --update brainglobe
+```
+
+This will remove the old packages from your environment, install `brainglobe-atlasapi`, and also update all your other BrainGlobe tools to use the new package rather than the old `bg-atlasapi`.
+
+If you were previously using a standalone install of `bg-atlasapi`, to continue receiving updates you should perform the following changes to your environment:
+
+- Uninstall `bg-atlasapi` (and `bg-atlasgen` if you have it).
+- Install the latest version of `brainglobe-atlasapi`.
+- Update all of the following BrainGlobe tools that you also have in your environment:
+  - `brainrender-napari`
+  - `brainglobe-utils`
+  - `brainglobe-segmentation`
+  - `brainreg`
+  - `brainglobe-napari-io`
+  - `cellfinder`
+  - `morphapi`
+  - `brainrender`
+  - `brainglobe-heatmap`

docs/source/community/developers/index.md

@@ -19,7 +19,7 @@ You can view these repositories and the relevant information by heading to the [
 
 ## To contribute a new atlas
 
-To add a new BrainGlobe atlas, please see the guide [here](/documentation/bg-atlasapi/adding-a-new-atlas).
+To add a new BrainGlobe atlas, please see the guide [here](/documentation/brainglobe-atlasapi/adding-a-new-atlas).
 
 ## To contribute code
 

docs/source/community/developers/intro_to_codebase.md

@@ -36,7 +36,7 @@ Code providing functionality related to a specific analysis or visualisation ste
 Each BrainGlobe tool has its own Github repository on the BrainGlobe organisation. 
 
 Currently stable tools are:
-- [`brainglobe-atlasapi`](https://github.com/brainglobe/bg-atlasapi)
+- [`brainglobe-atlasapi`](https://github.com/brainglobe/brainglobe-atlasapi)
 - [`brainglobe-heatmap`](https://github.com/brainglobe/brainglobe-heatmap)
 - [`brainglobe-segmentation`](https://github.com/brainglobe/brainglobe-segmentation)
 - [`brainreg`](https://github.com/brainglobe/brainreg)

docs/source/community/developers/repositories/brainglobe-utils/index.md

@@ -29,7 +29,7 @@ The `citation` submodule itself breaks down further to accommodate the steps of
 
 `cite-brainglobe` is only aware of the repositories that we tell it about - and any such repository must have a CITATION.cff (or equivalent metadata file) present in it that we can fetch.
 
-To make `cite-brainglobe` aware of a new BrainGlobe tool, add a static `Repository` instance to the `citation.repositories` submodule [as detailed here](#citationrepositories), specifying the required information.
+To make `cite-brainglobe` aware of a new BrainGlobe tool, add a static `Repository` instance to the `citation.repositories` submodule as detailed in the `citation.repositories` section, specifying the required information.
 
 ### Adding a new supported citation format
 

docs/source/community/external-tools.md

@@ -1,6 +1,6 @@
 # Software built by the community
 
-Tools like the [BrainGlobe Atlas API](/documentation/bg-atlasapi/index) were developed to help establish a community of 
+Tools like the [BrainGlobe Atlas API](/documentation/brainglobe-atlasapi/index) were developed to help establish a community of 
 developers creating interoperable tools. The BrainGlobe core developers have created a number of such tools
 ([cellfinder](/documentation/cellfinder/index), [brainreg](/documentation/brainreg/index), 
 [brainrender](/documentation/brainrender/index) etc.). More recently, members of the community have built their own