Remove codespell actions job (#53)

* Remove codespell actions job

* Ignore links that cannot be checked

Author: adamltyson

.github/workflows/docs_build_and_deploy.yml

@@ -14,20 +14,16 @@ on:
   workflow_dispatch:
 
 jobs:
-  codespell:
-    name: Check for spelling errors
-    permissions:
-      contents: read
+  linting:
+    # scheduled workflows should not run on forks
+    if: (${{ github.event_name == 'schedule' }} && ${{ github.repository_owner == 'neuroinformatics-unit' }} && ${{ github.ref == 'refs/heads/main' }}) || (${{ github.event_name != 'schedule' }})
     runs-on: ubuntu-latest
     steps:
-      - name: Checkout
-        uses: actions/checkout@v3
-      - name: Codespell
-        uses: codespell-project/actions-codespell@v2
+      - uses: neuroinformatics-unit/actions/lint@v2
 
   build_sphinx_docs:
     name: Build Sphinx Docs
-    needs: codespell
+    needs: linting
     runs-on: ubuntu-latest
     steps:
       - uses: neuroinformatics-unit/actions/build_sphinx_docs@v2

README.md

@@ -2,26 +2,26 @@
 
 ![](docs/source/_static/NeuroBlueprint_logo-dark_no-text.png)
 
-`NeuroBlueprint` is a folder structure specification for (systems) neuroscience research projects. 
-It is inspired by, and based on the [BIDS specification](https://bids-specification.readthedocs.io/en/stable/), 
+`NeuroBlueprint` is a folder structure specification for (systems) neuroscience research projects.
+It is inspired by, and based on the [BIDS specification](https://bids-specification.readthedocs.io/en/stable/),
 widely used in human neuroimaging.
 
-The [NeuroBlueprint specification](https://neuroblueprint.neuroinformatics.dev/specification.html) provides 
-a set of rules and guidelines for project folder organisation, ensuring consistent data management within and 
+The [NeuroBlueprint specification](https://neuroblueprint.neuroinformatics.dev/specification.html) provides
+a set of rules and guidelines for project folder organisation, ensuring consistent data management within and
 between labs. The focus is on ensuring minimal overhead for researchers.
 
-`NeuroBlueprint` is being developed at the 
-[Sainsbury Wellcome Centre (SWC) for Neural Circuits and Behaviour](https://www.sainsburywellcome.org/) 
-by members of the [Neuroinformatics Unit (NIU)](https://neuroinformatics.dev/). 
+`NeuroBlueprint` is being developed at the
+[Sainsbury Wellcome Centre (SWC) for Neural Circuits and Behaviour](https://www.sainsburywellcome.org/)
+by members of the [Neuroinformatics Unit (NIU)](https://neuroinformatics.dev/).
 As such, it prioritizes interoperability with NIU-developed data analysis tools.
 
-That said, the specification is designed to be as general as possible, and 
-should be useful to anyone within the neuroscience field. We (the NIU) welcome feedback and contributions 
-from the wider community and commit to maintaining the specification as a living and evolving document. 
-Check out the NeuroBlueprint [Zulip chat](https://neuroinformatics.zulipchat.com/#narrow/stream/406000-NeuroBlueprint) 
-or raise a [GitHub Issue](https://github.com/neuroinformatics-unit/NeuroBlueprint/issues) to get in touch. 
-We will also collaborate with [ongoing efforts](https://github.com/INCF/neuroscience-data-structure) by 
-the [INCF](https://www.incf.org/) and [BIDS community](https://bids.neuroimaging.io/) to extend the BIDS 
+That said, the specification is designed to be as general as possible, and
+should be useful to anyone within the neuroscience field. We (the NIU) welcome feedback and contributions
+from the wider community and commit to maintaining the specification as a living and evolving document.
+Check out the NeuroBlueprint [Zulip chat](https://neuroinformatics.zulipchat.com/#narrow/stream/406000-NeuroBlueprint)
+or raise a [GitHub Issue](https://github.com/neuroinformatics-unit/NeuroBlueprint/issues) to get in touch.
+We will also collaborate with [ongoing efforts](https://github.com/INCF/neuroscience-data-structure) by
+the [INCF](https://www.incf.org/) and [BIDS community](https://bids.neuroimaging.io/) to extend the BIDS
 specification to non-human animal research.
 
 This repository hosts the source code for the [NeuroBlueprint website](https://neuroblueprint.neuroinformatics.dev).

docs/source/conf.py

@@ -137,3 +137,5 @@
     "footer_end": ["footer_end"]
 }
 
+# link-check cannot check anchors
+linkcheck_ignore = ['https://bids-specification.readthedocs.io', 'https://neuroinformatics.zulipchat.com']

docs/source/index.md

@@ -3,20 +3,20 @@
 <img src="_static/NeuroBlueprint_logo-light_no-text.png" alt="NeuroBlueprint logo" class="only-light img-responsive"/>
 <img src="_static/NeuroBlueprint_logo-dark_no-text.png" alt="NeuroBlueprint logo" class="only-dark img-responsive"/>
 
-**NeuroBlueprint** is a folder structure specification for (systems) neuroscience research projects. It is inspired by, 
+**NeuroBlueprint** is a folder structure specification for (systems) neuroscience research projects. It is inspired by,
 and based on the [BIDS specification](https://bids-specification.readthedocs.io/en/stable/), widely used in human neuroimaging.
 
-The [NeuroBlueprint specification](specification.md) provides a set of rules and guidelines for project folder organisation, 
+The [NeuroBlueprint specification](specification.md) provides a set of rules and guidelines for project folder organisation,
 ensuring consistent data management within and between labs. The focus is on ensuring minimal overhead for researchers.
 
-**NeuroBlueprint** is being developed at the [Sainsbury Wellcome Centre (SWC) for Neural Circuits and Behaviour](https://www.sainsburywellcome.org/) 
+**NeuroBlueprint** is being developed at the [Sainsbury Wellcome Centre (SWC) for Neural Circuits and Behaviour](https://www.sainsburywellcome.org/)
 by members of the [Neuroinformatics Unit (NIU)](https://neuroinformatics.dev/). As such, it prioritizes interoperability with NIU-developed data analysis tools.
 
-That said, the specification is designed to be as general as possible, and should be useful to anyone within the neuroscience field. 
-We (the NIU) welcome feedback and contributions from the wider community and commit to maintaining the specification as a living and evolving document. 
-Check out the NeuroBlueprint [Zulip chat](https://neuroinformatics.zulipchat.com/#narrow/stream/406000-NeuroBlueprint) or 
-raise a [GitHub Issue](https://github.com/neuroinformatics-unit/NeuroBlueprint/issues) to get in touch. 
-We will also collaborate with [ongoing efforts](https://github.com/INCF/neuroscience-data-structure) by the [INCF](https://www.incf.org/) 
+That said, the specification is designed to be as general as possible, and should be useful to anyone within the neuroscience field.
+We (the NIU) welcome feedback and contributions from the wider community and commit to maintaining the specification as a living and evolving document.
+Check out the NeuroBlueprint [Zulip chat](https://neuroinformatics.zulipchat.com/#narrow/stream/406000-NeuroBlueprint) or
+raise a [GitHub Issue](https://github.com/neuroinformatics-unit/NeuroBlueprint/issues) to get in touch.
+We will also collaborate with [ongoing efforts](https://github.com/INCF/neuroscience-data-structure) by the [INCF](https://www.incf.org/)
 and [BIDS community](https://bids.neuroimaging.io/) to extend the BIDS specification to non-human animal research.
 
 ```{toctree}

docs/source/specification.md

@@ -32,7 +32,7 @@ For example:
 
 * Datatype folder names *must* be one of the following : `ephys`, `behav`, `funcimg`, `anat`.
 
-* Datatype folders *must* be placed under the session level. 
+* Datatype folders *must* be placed under the session level.
 
 Below we describe each level of the `rawdata` folder hierarchy in more detail. Though we impose no absolute requirements for the folder structure within `derivatives`, it *should* match the hierarchy in `rawdata` whenever possible.