adde pre-commit hooks incl codespell

.github/workflows/docs_build_and_deploy.yml

@@ -15,8 +15,20 @@ on:
   workflow_dispatch:
 
 jobs:
+  codespell:
+    name: Check for spelling errors
+    permissions:
+      contents: read
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2
+
   build_sphinx_docs:
     name: Build Sphinx Docs
+    needs: codespell
     runs-on: ubuntu-latest
     steps:
       - uses: neuroinformatics-unit/actions/build_sphinx_docs@v2

.gitignore

@@ -81,4 +81,3 @@ venv/
 
 # written by setuptools_scm
 **/_version.py
-

.pre-commit-config.yaml

@@ -0,0 +1,19 @@
+exclude: 'conf.py'
+
+repos:
+    - repo: https://github.com/pre-commit/pre-commit-hooks
+      rev: v4.3.0
+      hooks:
+          - id: check-docstring-first
+          - id: check-executables-have-shebangs
+          - id: check-merge-conflict
+          - id: check-toml
+          - id: end-of-file-fixer
+          - id: mixed-line-ending
+            args: [--fix=lf]
+          - id: requirements-txt-fixer
+          - id: trailing-whitespace
+    - repo: https://github.com/codespell-project/codespell
+      rev: v2.2.5
+      hooks:
+      - id: codespell

CONTRIBUTING.md

@@ -15,20 +15,20 @@ To add a new guide, create a new markdown file in the appropriate section direct
 If the content you want to add is not long enough to warrant a full guide, for example a small tip or a quick solution to a common problem, you can add it to a `Troubleshooting.md` file in the appropriate section directory. For an example see `docs/source/programming/Troubleshooting.md`. Each small tip should start with a level-2 heading.
 
 > **warning**
-> 
+>
 > Since the website is already named "HowTo", please avoid starting your guides/tips with "How to ...".
 > For example, instead of "How to detach a forked repo on GitHub", use "Detach a forked repo on GitHub".
-  
+
 ## GitHub workflow
 * Clone the GitHub repository, and create your `new_branch`.
 * Edit the website and commit your changes to the `new_branch`.
 * Push the `new_branch` to GitHub and create a draft pull request. This will automatically trigger a [GitHub action](https://github.com/neuroinformatics-unit/actions/tree/main/build_sphinx_docs) that checks if the website still builds correctly.
-* If the checks pass, mark the pull request as ready to review assign someone to review your changes. 
+* If the checks pass, mark the pull request as ready to review assign someone to review your changes.
 * When the reviewer merges your changes into the `main` branch, a different [GitHub action](https://github.com/neuroinformatics-unit/actions/tree/main/deploy_sphinx_docs) will be triggered, which will build the website and publish it to the `gh-pages` branch.
 * The updated website should be available at [howto.neuroinformatics.dev](https://howto.neuroinformatics.dev)
 
 > **note**
-> 
+>
 > If you wish to view the website locally, before you push it, you can do so by running the following commands from the root of the repository.
 > ```bash
 > # First time only

docs/make.bat

@@ -1,35 +1,35 @@
-@ECHO OFF
-
-pushd %~dp0
-
-REM Command file for Sphinx documentation
-
-if "%SPHINXBUILD%" == "" (
-	set SPHINXBUILD=sphinx-build
-)
-set SOURCEDIR=source
-set BUILDDIR=build
-
-%SPHINXBUILD% >NUL 2>NUL
-if errorlevel 9009 (
-	echo.
-	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
-	echo.installed, then set the SPHINXBUILD environment variable to point
-	echo.to the full path of the 'sphinx-build' executable. Alternatively you
-	echo.may add the Sphinx directory to PATH.
-	echo.
-	echo.If you don't have Sphinx installed, grab it from
-	echo.https://www.sphinx-doc.org/
-	exit /b 1
-)
-
-if "%1" == "" goto help
-
-%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-goto end
-
-:help
-%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-
-:end
-popd
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/requirements.txt

@@ -1,7 +1,7 @@
-sphinx
-pydata-sphinx-theme
+linkify-it-py
 myst-parser
-numpydoc
 nbsphinx
-linkify-it-py
+numpydoc
+pydata-sphinx-theme
+sphinx
 sphinx-design

docs/source/_static/css/custom.css

@@ -28,4 +28,4 @@ html[data-theme=light] {
   display: flex;
   flex-wrap: wrap;
   justify-content: space-between;
-}
+}

docs/source/_templates/footer_start.html

@@ -6,4 +6,4 @@
 {{ _("Built with the") }}
 <a href="https://pydata-sphinx-theme.readthedocs.io/en/stable/index.html">PyData Sphinx Theme</a>
 {{ theme_version }}.
-</p>
+</p>

docs/source/data_analysis/index.md

@@ -6,5 +6,3 @@ Guides related to the analysis of neuroscientific data, spanning a wide range of
 :maxdepth: 1
 
 ```
-
-

docs/source/index.md

@@ -2,7 +2,7 @@
 
 On this website you can find long-form how-to guides as well as collections of small tips and tricks related to data analysis and software development in neuroscience.
 
-The webiste is maintained by members of the [Neuroinformatics Unit](https://neuroinformatics.dev). The information is primarily aimed at researchers at the [Sainsbury Wellcome Centre (SWC)](https://www.sainsburywellcome.org/web/) and [Gatsby Computational Neuroscience Unit (GCNU)](https://www.ucl.ac.uk/gatsby/gatsby-computational-neuroscience-unit), though most of it should be useful to neuroscientists in general.
+The website is maintained by members of the [Neuroinformatics Unit](https://neuroinformatics.dev). The information is primarily aimed at researchers at the [Sainsbury Wellcome Centre (SWC)](https://www.sainsburywellcome.org/web/) and [Gatsby Computational Neuroscience Unit (GCNU)](https://www.ucl.ac.uk/gatsby/gatsby-computational-neuroscience-unit), though most of it should be useful to neuroscientists in general.
 
 
 ## Main sections

docs/source/open_science/Data-sharing.md

@@ -17,15 +17,15 @@ Data is key to neuroscience, and it should be shared for maximal utility. There
 
 ## Requirements
 
-Currently, SWC does not have any specific code and data sharing requirements, but your funder or publisher may do. 
+Currently, SWC does not have any specific code and data sharing requirements, but your funder or publisher may do.
 
 **Ideally, all data and code will be shared in such a way that any other researcher could easily reproduce key figures from a publication, and build on those data and software in their own research.**
 
 
 ## Code
 Original code can be hosted in a public GitHub/GitLab repository, hosted on an organisational account (i.e. not an individual account). This could be the [SWC organisation](https://github.com/SainsburyWellcomeCentre), or that of a particular team, lab or collaboration. To enable re-use, code should include an [appropriate license](https://howto.neuroinformatics.dev/guides/Licensing.html).
 
-To ensure a permanent archive of the code associated with a publication a [DOI](https://www.doi.org/) should be created (e.g. using [Zenodo](https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content)). 
+To ensure a permanent archive of the code associated with a publication a [DOI](https://www.doi.org/) should be created (e.g. using [Zenodo](https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content)).
 
 ## Data
 ### Repository
@@ -75,4 +75,3 @@ If you have any technical questions about sharing data or code, please contact a
 | NeuroMorpho                        |https://neuromorpho.org/                           |Neuronal morphologies                                                                                |
 | Cell Image Library                 |http://ccdb.ucsd.edu/home                          |Cell images                                                                                          |
 | ModelDB                            |https://senselab.med.yale.edu/ModelDB/             |Computational neuroscience models                                                                    |
-

docs/source/open_science/Licensing.md

@@ -3,9 +3,9 @@
 ## Disclaimer
 **This document was not written by lawyers, and does not represent legal advice.**
 
-This guide was written by the [Neuroinformatics Unit](https://neuroinformatics.dev/) to help researchers at the [Sainsbury Wellcome Centre (SWC)](https://www.sainsburywellcome.org/web/) and [Gatsby Computational Neuroscience Unit (GCNU)](https://www.ucl.ac.uk/gatsby/gatsby-computational-neuroscience-unit) at [University College London (UCL)](https://www.ucl.ac.uk/) choose a license for their software. 
+This guide was written by the [Neuroinformatics Unit](https://neuroinformatics.dev/) to help researchers at the [Sainsbury Wellcome Centre (SWC)](https://www.sainsburywellcome.org/web/) and [Gatsby Computational Neuroscience Unit (GCNU)](https://www.ucl.ac.uk/gatsby/gatsby-computational-neuroscience-unit) at [University College London (UCL)](https://www.ucl.ac.uk/) choose a license for their software.
 It does not represent official guidance by SWC, GCNU or UCL.
-In particular this is not advice about intellectual property, but rather the practicalities of adding a license to your software. 
+In particular this is not advice about intellectual property, but rather the practicalities of adding a license to your software.
 For more information, SWC/GCNU researchers should consult the SWC/GCNU and UCL documentation about intellectual property or contact [UCL Business](https://www.uclb.com/) if you think your software may have commercial potential (before release).
 
 ## Summary

docs/source/open_science/index.md

@@ -7,4 +7,4 @@ A collection of long-form guides on topics related to open science.
 
 Licensing
 Data-sharing
-```
+```

docs/source/programming/Cookiecutter-cruft.md

@@ -3,7 +3,7 @@
 Ref: [original docs](https://cruft.github.io/cruft/) and [github repo](https://github.com/cruft/cruft).
 
 ## Setup: `cruft link`
-Install: `pip install cruft`.   
+Install: `pip install cruft`.
 
 If this is your first time using `cruft`, you have to set it up using the `cruft link` command. You have to specify the URL of your cookiecutter on GitHub.
 
@@ -38,6 +38,6 @@ When `cruft update` is done, you will notice that the `.cruft.json` file has bee
 `cruft check` will check if your repo is up to date with the template and just give you a boolean response.
 
 ## Commit
-Once you are satisfied, commit the changes to a new branch and open a PR to merge it into `main`. 
+Once you are satisfied, commit the changes to a new branch and open a PR to merge it into `main`.
 
 Now, check if your GitHub actions fail... 🤦🏻‍♀️ If everything is fine, you can merge the PR. 🎉 If not, you will have to fix the errors and repeat the process. 😱

docs/source/programming/Mount-ceph-ubuntu.md

@@ -9,7 +9,7 @@ The following instructions have been tested on **Ubuntu 20.04 LTS**.
 
 ## Store your SWC credentials
 First, create a file to store your SWC login credentials and save it in your home directory.
-You can do that on the terminal via `nano ~/.smb_swc`. 
+You can do that on the terminal via `nano ~/.smb_swc`.
 
 The ``.smb_swc`` file contents should look like this:
 ```bash
@@ -35,7 +35,7 @@ However, if someone gets access to your machine with your user logged in, they w
 ## Create a mount point
 Create a directory to mount the storage to. Sensible places to do this on Ubuntu would be in `/mnt` or `/media`. In the example below, we will use `/media/ceph-neuroinformatics`.
 
-```bash 
+```bash
 sudo mkdir /media/ceph-neuroinformatics
 ```
 
@@ -44,7 +44,7 @@ This will allow you to mount the storage automatically on boot. Before editing t
 ```bash
 sudo cp /etc/fstab /etc/fstab.bak
 ```
-Now, open the file with your favourite editor (e.g. `sudo nano /etc/fstab`) and add new lines at the end of the file. 
+Now, open the file with your favourite editor (e.g. `sudo nano /etc/fstab`) and add new lines at the end of the file.
 
 For example:
 ```bash

docs/source/programming/SSH-vscode.md

@@ -28,4 +28,4 @@ cd .ssh/
 touch config
 ```
 
-Connect to VPN, then use the `Open a remote window` (Remote - SSH extension) tool of vscode and connect to `remote-host`. You will be asked for your SWC and Linux passwords. 
+Connect to VPN, then use the `Open a remote window` (Remote - SSH extension) tool of vscode and connect to `remote-host`. You will be asked for your SWC and Linux passwords.

docs/source/programming/Troubleshooting.md

@@ -3,15 +3,15 @@ Small problems and their solutions.
 
 ## Ubuntu distribution update error
 This is an error that appeared when updating to a new Ubuntu distribution.
-Error msg: Software Updater - Not all updates can be installed.   
+Error msg: Software Updater - Not all updates can be installed.
 Solution: `sudo apt-get dist-upgrade`
 
 ## Terminal is not opening after installing a new Python version
-If you installed a new Python version without the use of `conda`, there might be a mismatch in the python naming in a bin file.   
+If you installed a new Python version without the use of `conda`, there might be a mismatch in the python naming in a bin file.
 If it's possible open terminal through vscode or open a virtual terminal (VT) with CTRL + ALT + F3 and run `gnome-ternimal`.
-Does it throw a Python error? If yes run `sudo nano /usr/bin/gnome-terminal` and change `#!/usr/bin/python3` to `#!/usr/bin/python3.10` if the version you're currently using is 3.10.  
+Does it throw a Python error? If yes run `sudo nano /usr/bin/gnome-terminal` and change `#!/usr/bin/python3` to `#!/usr/bin/python3.10` if the version you're currently using is 3.10.
 Exit the VT via CTRL + ALT + F2.
 
 ## Detach a forked repo on GitHub
 If you forked a repo and want to detach it from the original repo, use the [Github chatbot-virtual-assistant](https://support.github.com/contact?tags=rr-forks&subject=Detach%20Fork&flow=detach_fork).
-Follow the instructions and wait for the response.
+Follow the instructions and wait for the response.

docs/source/programming/index.md

@@ -11,4 +11,4 @@ SSH-vscode
 Mount-ceph-ubuntu
 Cookiecutter-cruft
 Troubleshooting
-```
+```