diff --git a/.github/workflows/linkcheck.yml b/.github/workflows/linkcheck.yml index 86417e5..19a3065 100644 --- a/.github/workflows/linkcheck.yml +++ b/.github/workflows/linkcheck.yml @@ -28,8 +28,16 @@ jobs: uses: actions/setup-python@v5 with: python-version: 3.12 + - name: Install MkDocs + run: pip install -r requirements.txt - - uses: tcort/github-action-markdown-link-check@v1 + - name: Build site + run: mkdocs build + + - name: Check links + uses: tcort/github-action-markdown-link-check@v1 with: use-quiet-mode: yes - # use-verbose-mode: no + config-file: .markdown-link-check.json + folder-path: site + file-extension: .html diff --git a/.markdown-link-check.json b/.markdown-link-check.json new file mode 100644 index 0000000..200c829 --- /dev/null +++ b/.markdown-link-check.json @@ -0,0 +1,11 @@ +{ + "ignorePatterns": [ + {"pattern": "^http://127\\.0\\.0\\.1:8445"}, + {"pattern": "^http://192\\.168\\.99\\.100:8445"}, + {"pattern": "biorxiv\\.org"}, + {"pattern": "doi\\.org"}, + {"pattern": "toptal\\.com"}, + {"pattern": "nbirn\\.net"}, + {"pattern": "^/"} + ] +} diff --git a/docs/apps/docker.md b/docs/apps/docker.md index 161886c..f9fff7d 100644 --- a/docs/apps/docker.md +++ b/docs/apps/docker.md @@ -292,7 +292,7 @@ Once the *Docker Engine* arguments are written, the remainder of the command line follows the interface defined by the specific *BIDS App* (for instance, [*fMRIPrep*](https://fmriprep.readthedocs.io/en/latest/usage.html) -or [*MRIQC*](https://mriqc.readthedocs.io/en/latest/running.html#command-line-interface)). +or [*MRIQC*](https://mriqc.readthedocs.io/en/latest/usage.html#a-bids-apps-command-line-interface)). The first section of a call consists of arguments specific to *Docker*, which configure the execution of the container: diff --git a/docs/apps/framework.md b/docs/apps/framework.md index 190f731..4ba14f2 100644 --- a/docs/apps/framework.md +++ b/docs/apps/framework.md @@ -5,7 +5,7 @@ brain datasets, including MRI. The common naming convention and folder structure allow researchers to easily reuse BIDS datasets, re-apply analysis protocols, and run standardized automatic data preprocessing pipelines (and particularly, BIDS Apps). The [BIDS starter-kit](https://github.com/bids-standard/bids-starter-kit) contains a wide collection of educational resources. -Validity of the structure can be assessed with the online [BIDS-Validator](https://bids-standard.github.io/bidsvalidator/). +Validity of the structure can be assessed with the online [BIDS-Validator](https://bids-standard.github.io/bids-validator/). The tree of a typical, valid (*BIDS-compliant*) dataset is shown below: ``` diff --git a/docs/apps/singularity.md b/docs/apps/singularity.md index c962983..d6e1ad7 100644 --- a/docs/apps/singularity.md +++ b/docs/apps/singularity.md @@ -72,7 +72,7 @@ $ singularity run --cleanenv fmriprep.simg \ ## Handling environment variables -Singularity by default [exposes all environment variables from the host inside the container](https://github.com/singularityware/singularity/issues/445). +Singularity by default [exposes all environment variables from the host inside the container](https://github.com/apptainer/singularity/issues/445). Because of this, your host libraries (e.g., [NiPype](https://nipype.readthedocs.io) or a Python environment) could be accidentally used instead of the ones inside the container. To avoid such a situation, we strongly **recommend** using the `--cleanenv` argument in all scenarios. For example: diff --git a/docs/assets/ORN-Workshop/index.html b/docs/assets/ORN-Workshop/index.html index a25cb50..31d3960 100644 --- a/docs/assets/ORN-Workshop/index.html +++ b/docs/assets/ORN-Workshop/index.html @@ -259,7 +259,7 @@ highlightLines: true, countIncrementalSlides: false, highlightSpans: true, - sourceUrl: 'https://raw.githubusercontent.com/nipreps/nipreps.github.io/mkdocs/docs/assets/ORN-Workshop/presentation.md', + sourceUrl: 'presentation.md', ratio: '16:9' }); diff --git a/docs/assets/ORN-Workshop/presentation.md b/docs/assets/ORN-Workshop/presentation.md index 08bf3dd..5e96826 100644 --- a/docs/assets/ORN-Workshop/presentation.md +++ b/docs/assets/ORN-Workshop/presentation.md @@ -53,7 +53,7 @@ class: section-separator

- +


@@ -77,7 +77,7 @@ layout: true

- +


@@ -125,7 +125,7 @@ template: sidebar ## The garden of forking paths

-NARPS Paper +NARPS Paper

(Botvinik-Nezer et al., 2020) @@ -139,7 +139,7 @@ Around 50% of teams used fMRIPrep'ed inputs. ### fMRIPrep produces analysis-ready data from diverse data * minimal requirements ([BIDS-compliant](https://bids-standard.github.io/bids-validator/)); * *agnostic* to downstream steps of the workflow - * produces [BIDS-Derivatives](https://bids-specification.readthedocs.io/en/derivatives/05-derivatives/01-introduction.html); + * produces [BIDS-Derivatives](https://bids-specification.readthedocs.io/en/stable/derivatives/introduction.html); * robust against inhomogeneity of data across studies ??? @@ -227,7 +227,7 @@ to fmriprep.org, which is the documentation website. ## Key aspect: credit all direct contributors

-fMRIPrep authors +fMRIPrep authors

-- diff --git a/docs/assets/bhd2020/index.html b/docs/assets/bhd2020/index.html index 4e0093b..d2ddc89 100644 --- a/docs/assets/bhd2020/index.html +++ b/docs/assets/bhd2020/index.html @@ -259,7 +259,7 @@ highlightLines: true, countIncrementalSlides: false, highlightSpans: true, - sourceUrl: 'https://raw.githubusercontent.com/nipreps/nipreps.github.io/mkdocs/docs/assets/bhd2020/presentation.md', + sourceUrl: 'presentation.md', ratio: '16:9' }); diff --git a/docs/assets/bhd2020/presentation.md b/docs/assets/bhd2020/presentation.md index 963ff75..1bc70d6 100644 --- a/docs/assets/bhd2020/presentation.md +++ b/docs/assets/bhd2020/presentation.md @@ -53,7 +53,7 @@ class: section-separator

- +


@@ -77,7 +77,7 @@ layout: true

- +


@@ -196,7 +196,7 @@ Around 50% of teams used *fMRIPrep*'ed inputs. ### fMRIPrep produces analysis-ready data from diverse data * minimal requirements ([BIDS-compliant](https://bids-standard.github.io/bids-validator/)); * *agnostic* to downstream steps of the workflow - * produces [BIDS-Derivatives](https://bids-specification.readthedocs.io/en/derivatives/05-derivatives/01-introduction.html); + * produces [BIDS-Derivatives](https://bids-specification.readthedocs.io/en/stable/derivatives/introduction.html); * robust against inhomogeneity of data across studies ??? diff --git a/docs/assets/torw2020/presentation.md b/docs/assets/torw2020/presentation.md index d4a3652..053c993 100644 --- a/docs/assets/torw2020/presentation.md +++ b/docs/assets/torw2020/presentation.md @@ -1,3 +1,4 @@ + name: title layout: true class: center @@ -103,7 +104,7 @@ template: sidebar ### fMRIPrep produces analysis-ready data from acquired (fMRI) data * minimal requirements ([BIDS-compliant](https://bids-standard.github.io/bids-validator/)); * *agnostic* to downstream steps of the workflow - * produces [BIDS-Derivatives](https://bids-specification.readthedocs.io/en/derivatives/05-derivatives/01-introduction.html); + * produces [BIDS-Derivatives](https://bids-specification.readthedocs.io/en/stable/derivatives/introduction.html); ??? @@ -1200,3 +1201,4 @@ layout: false ## Questions? ] + \ No newline at end of file diff --git a/docs/community/CONTRIBUTING.md b/docs/community/CONTRIBUTING.md index 6157c26..5825e4c 100644 --- a/docs/community/CONTRIBUTING.md +++ b/docs/community/CONTRIBUTING.md @@ -389,7 +389,7 @@ You're awesome. :wave::smiley: [link_stemmrolemodels]: https://github.com/KirstieJane/STEMMRoleModels [link_zenodo]: https://github.com/nipreps/fmriprep/blob/master/.zenodo.json [link_update_script]: https://github.com/nipreps/fmriprep/blob/master/.maint/update_authors.py -[link_devel]: https://fmriprep.readthedocs.io/en/latest/contributors.html +[link_devel]: ../devs/devenv.md [link_fmriprep]: http://fmriprep.org [link_bidsapps]: https://bids-apps.neuroimaging.io [link_mattermost]: https://mattermost.brainhack.org/brainhack/channels/fmriprep diff --git a/docs/community/features.md b/docs/community/features.md index 18ede58..51b7f55 100644 --- a/docs/community/features.md +++ b/docs/community/features.md @@ -75,7 +75,7 @@ as the *NiPreps* maintainers will consider them: > Especially when the CLI is affected, and yet another option is added, > that makes the tool more complex to use. > - > -- Alejandro ([source](https://github.com/nipreps/fmriprep/ issues/1963#issuecomment-582174814)). + > -- Alejandro ([source](https://github.com/nipreps/fmriprep/issues/1963#issuecomment-582174814)). * Does the new feature substantially **increase the internal complexity**? Maintainers and developers will attempt to consolidate tools and lower the internal diff --git a/docs/community/members.md b/docs/community/members.md index 9c70b18..e01e6f7 100644 --- a/docs/community/members.md +++ b/docs/community/members.md @@ -16,7 +16,7 @@ section. Developers are members of a wonderful team _driving the project_. Names and contacts of all developers are included in the -[`.maint/developers.json` file](https://github.com/nipreps/fmriprep/blob/master/.maint/developers.json) of each project. +[`.maint/MAINTAINERS.md` file](https://github.com/nipreps/fmriprep/blob/master/.maint/MAINTAINERS.md) of each project. Examples of steering activities that _drive the project_ are: actively participating in the follow-up meetings, leading documentation sprints, helping in the design of the tool and definition of the roadmap, providing resources (in the broad sense, including funding), code-review, etc. @@ -24,7 +24,7 @@ providing resources (in the broad sense, including funding), code-review, etc. ### Contributors Contributors enlisted in the -[`.maint/contributors.json` file](https://github.com/nipreps/fmriprep/blob/master/.maint/contributors.json) of each project +[`.maint/CONTRIBUTORS.md` file](https://github.com/nipreps/fmriprep/blob/master/.maint/CONTRIBUTORS.md) of each project actively help or have previously helped the project in a broad sense: writing code, writing documentation, benchmarking modules of the tool, proposing new features, helping improve the scientific rigor of implementations, giving out support on the different communication @@ -37,7 +37,7 @@ Before every release, unlisted contributors will be invited again to add their n Contributors who have contributed at some point to the project but were required or they wished to disconnect from the project's updates and to drop-out from publications and other dissemination activities, -are listed in the [`.maint/former.json` file](https://github.com/nipreps/fmriprep/blob/master/.maint/former.json). +are listed in the [`.maint/FORMER.md` file](https://github.com/nipreps/fmriprep/blob/master/.maint/FORMER.md). -[link_neurostars]: https://neurostars.org \ No newline at end of file +[link_neurostars]: https://neurostars.org diff --git a/docs/devs/devenv.md b/docs/devs/devenv.md index b8aeb37..25b743d 100644 --- a/docs/devs/devenv.md +++ b/docs/devs/devenv.md @@ -154,7 +154,7 @@ INFO - No authentication 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). +Now you can switch to your favorite browser and go to: `http://127.0.0.1:8445` (or `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 executable inside the docker container. diff --git a/docs/users/educational.md b/docs/users/educational.md index 760ab16..e120037 100644 --- a/docs/users/educational.md +++ b/docs/users/educational.md @@ -13,12 +13,12 @@ ## Online books -- [QC-Book, member-initiated tutorial at ISMRM 2022](../../qc-book) -- [NiPreps Book, developing processing tools for dMRI, ISBI 2021](../../nipreps-book) +- [QC-Book, member-initiated tutorial at ISMRM 2022](https://www.nipreps.org/qc-book) +- [NiPreps Book, developing processing tools for dMRI, ISBI 2021](https://www.nipreps.org/nipreps-book/) ## QC protocols and Standard Operating Procedures -- [SOPs-cookiecutter, a template repository for version-controlled SOPs](https//github.com/nipreps/sops-cookiecutter). The example template is rendered [here](/sops-cookiecutter/) +- [SOPs-cookiecutter, a template repository for version-controlled SOPs](https://github.com/nipreps/sops-cookiecutter). The example template is rendered [here](/sops-cookiecutter/) ## Presentation - [Educational Talk at OHBM 2023 - Quality Control in fMRI studies with MRIQC and fMRIPrep](../../assets/OHBM2023/QCTalkOHBM23CelineProvins.pdf)