Add codespell support (config, workflow to detect/not fix) and make i…

…t fix few typos (#43)

* Add github action to codespell mkdocs on push and PRs

* Add rudimentary codespell config

* Some ignores for codespell

* [DATALAD RUNCMD] run codespell throughout fixing typos automagically

=== Do not change lines below ===
{
 "chain": [],
 "cmd": "codespell -w",
 "exit": 0,
 "extra_inputs": [],
 "inputs": [],
 "outputs": [],
 "pwd": "."
}
^^^ Do not change lines above ^^^

.codespellrc

@@ -0,0 +1,6 @@
+[codespell]
+# Ref: https://github.com/codespell-project/codespell#using-a-config-file
+skip = .git*,*.pdf,*.svg,*.css,*.min.*,.codespellrc,*.js,*.cast
+check-hidden = true
+ignore-regex = <sup>nd</sup>
+# ignore-words-list =

.github/workflows/codespell.yml

@@ -0,0 +1,25 @@
+# Codespell configuration is within .codespellrc
+---
+name: Codespell
+
+on:
+  push:
+    branches: [mkdocs]
+  pull_request:
+    branches: [mkdocs]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Annotate locations with typos
+        uses: codespell-project/codespell-problem-matcher@v1
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

docs/apps/singularity.md

@@ -246,7 +246,7 @@ endpoints), then you can try the following:
 
 * `requests.exceptions.SSLError: HTTPSConnectionPool ...`. In this case,
   your container seems to be able to reach the Internet, but unable to use
-  SSL encription. There are two potential solutions to the issue. The
+  SSL encryption. There are two potential solutions to the issue. The
   [recommended one](https://neurostars.org/t/problems-using-pediatric-template-from-templateflow/4566/17)
   is setting `REQUESTS_CA_BUNDLE` to the appropriate path, and/or binding
   the appropriate filesystem:

docs/assets/EPFL2023/index.html

@@ -503,7 +503,7 @@
 
 ---
 
-# Why standarizing?
+# Why standardizing?
 
 .boxed-content[
 .distribute.large[

docs/assets/OHBM2022/index.html

@@ -554,7 +554,7 @@
 *(... or the lack thereof)*
 
 * *fMRIPrep* does not guarantee full run reproducibility with `--omp-nthreads` larger than 1
-    * Which means, **disabling within-node paralellization**.
+    * Which means, **disabling within-node parallelization**.
 
 * *fMRIPrep* writes out a config file
     * stores **seeds** for all random number generators it has access to

docs/assets/ORN-Workshop/presentation.md

@@ -290,7 +290,7 @@ Therefore, it is better to keep things that way (although some minimal efforts t
 
 ## The *dMRIPrep* story
 
-After the success of *fMRIPrep*, some neuroimagers asked "*when a diffussion MRI fMRIPrep?*"
+After the success of *fMRIPrep*, some neuroimagers asked "*when a diffusion MRI fMRIPrep?*"
 
 ## NeuroStars.org
 (please note this down)

docs/assets/fmriprep-bootcamp-geneva2024/day1-01-fmriprep-primer/index.html

@@ -441,7 +441,7 @@
 
 ---
 
-# The neuroimaging worflow
+# The neuroimaging workflow
 
 <br />
 <br />

docs/assets/torw2020/presentation.md

@@ -1072,7 +1072,7 @@ Such is the case of the quality control tools.
 
 MRIQC produces visual reports for the efficient screening of acquired (meaning, unprocessed) data - in particular anatomical and functional MRI of the human brain.
 
-CrowdMRI is an internet service where anonimized quality control metrics are uploaded automatically as they are computed by MRIQC.
+CrowdMRI is an internet service where anonymized quality control metrics are uploaded automatically as they are computed by MRIQC.
 
 The endgoal is to gather enough data to describe the normative distribution of these metrics across image parameters and scanning devices and sites.
 

docs/community/CODE_OF_CONDUCT.md

@@ -6,7 +6,7 @@ In the interest of fostering an open and welcoming environment, we as
 contributors and maintainers pledge to making participation in our project and
 our community a harassment-free experience for everyone, regardless of age, body
 size, disability, ethnicity, sex characteristics, gender identity and expression,
-level of experience, education, socio-economic status, nationality, personal
+level of experience, education, socioeconomic status, nationality, personal
 appearance, race, religion, or sexual identity and orientation.
 
 ## Our Standards

docs/community/CONTRIBUTING.md

@@ -232,7 +232,7 @@ but those accepted fastest will follow a workflow similar to the following:
      * `DOC`: new or updated documentation ([example][doc_ex])
      * `STY`: style changes ([example][sty_ex])
      * `REF`: refactoring existing code ([example][ref_ex])
-     * `CI`: updates to continous integration infrastructure ([example][ci_ex])
+     * `CI`: updates to continuous integration infrastructure ([example][ci_ex])
      * `MAINT`: general maintenance ([example][maint_ex])
      * For works-in-progress, add the `WIP` tag in addition to the descriptive prefix.
        Pull-requests tagged with `WIP:` will not be merged until the tag is removed.

docs/community/licensing.md

@@ -33,7 +33,7 @@ Containerized Images bundling *NiPreps* components and their dependencies can be
 distributed under a free and open-source license without copyleft, such as the
 [MIT License](https://choosealicense.com/licenses/mit/).
 In such a case, the attribution notice of the MIT license must be present in the
-header comment of the container image bootstraping file (for instance, the so-called
+header comment of the container image bootstrapping file (for instance, the so-called
 `Dockerfile`).
 This different licensing must be also indicated in the `NOTICE` file of the corresponding
 *NiPreps* components bundled within the image.

docs/devs/devenv.md

@@ -157,7 +157,7 @@ INFO    - Not serving HTTPS
 Now you can switch to your favorite browser and go to: [127.0.0.1:8445](http://127.0.0.1:8445) (or [192.168.99.100:8445](http://192.168.99.100:8445) for Docker Toolbox).
 
 **3. Copy `fmriprep.egg-info` into your `fmriprep/` project directory**
-`fmriprep.egg-info` makes the package exacutable inside the docker container.
+`fmriprep.egg-info` makes the package executable inside the docker container.
 Open a terminal in vscode and type the following:
 
 ```shell