diff --git a/.codespellrc b/.codespellrc new file mode 100644 index 0000000..46098bf --- /dev/null +++ b/.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 = nd +# ignore-words-list = diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml new file mode 100644 index 0000000..1f52b1e --- /dev/null +++ b/.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 diff --git a/docs/apps/singularity.md b/docs/apps/singularity.md index 399b12e..adc485b 100644 --- a/docs/apps/singularity.md +++ b/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: diff --git a/docs/assets/EPFL2023/index.html b/docs/assets/EPFL2023/index.html index 65d22df..03490e4 100644 --- a/docs/assets/EPFL2023/index.html +++ b/docs/assets/EPFL2023/index.html @@ -503,7 +503,7 @@ --- -# Why standarizing? +# Why standardizing? .boxed-content[ .distribute.large[ diff --git a/docs/assets/OHBM2022/index.html b/docs/assets/OHBM2022/index.html index 2b6d0eb..485138e 100644 --- a/docs/assets/OHBM2022/index.html +++ b/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 diff --git a/docs/assets/ORN-Workshop/presentation.md b/docs/assets/ORN-Workshop/presentation.md index 7a4a028..08bf3dd 100644 --- a/docs/assets/ORN-Workshop/presentation.md +++ b/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) diff --git a/docs/assets/fmriprep-bootcamp-geneva2024/day1-01-fmriprep-primer/index.html b/docs/assets/fmriprep-bootcamp-geneva2024/day1-01-fmriprep-primer/index.html index 03eec08..ca7b8bb 100644 --- a/docs/assets/fmriprep-bootcamp-geneva2024/day1-01-fmriprep-primer/index.html +++ b/docs/assets/fmriprep-bootcamp-geneva2024/day1-01-fmriprep-primer/index.html @@ -441,7 +441,7 @@ --- -# The neuroimaging worflow +# The neuroimaging workflow

diff --git a/docs/assets/torw2020/presentation.md b/docs/assets/torw2020/presentation.md index d999790..d4a3652 100644 --- a/docs/assets/torw2020/presentation.md +++ b/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. diff --git a/docs/community/CODE_OF_CONDUCT.md b/docs/community/CODE_OF_CONDUCT.md index f71784c..48d53c5 100644 --- a/docs/community/CODE_OF_CONDUCT.md +++ b/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 diff --git a/docs/community/CONTRIBUTING.md b/docs/community/CONTRIBUTING.md index f764886..7c23b05 100644 --- a/docs/community/CONTRIBUTING.md +++ b/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. diff --git a/docs/community/licensing.md b/docs/community/licensing.md index 8713ac8..282854c 100644 --- a/docs/community/licensing.md +++ b/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. diff --git a/docs/devs/devenv.md b/docs/devs/devenv.md index c537559..b8aeb37 100644 --- a/docs/devs/devenv.md +++ b/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