From 52dd8f78a65210153cce3207a21e38b0e8416494 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Thu, 19 Dec 2024 12:49:34 -0500 Subject: [PATCH 1/4] Add github action to codespell main on push and PRs --- .github/workflows/codespell.yml | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 .github/workflows/codespell.yml diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml new file mode 100644 index 0000000..c59e047 --- /dev/null +++ b/.github/workflows/codespell.yml @@ -0,0 +1,25 @@ +# Codespell configuration is within .codespellrc +--- +name: Codespell + +on: + push: + branches: [main] + pull_request: + branches: [main] + +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 From cba8dbadf6e1898446460720603ebb8d48ae5e54 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Thu, 19 Dec 2024 12:49:34 -0500 Subject: [PATCH 2/4] Add rudimentary codespell config --- .codespellrc | 6 ++++++ 1 file changed, 6 insertions(+) create mode 100644 .codespellrc diff --git a/.codespellrc b/.codespellrc new file mode 100644 index 0000000..076a2e1 --- /dev/null +++ b/.codespellrc @@ -0,0 +1,6 @@ +[codespell] +# Ref: https://github.com/codespell-project/codespell#using-a-config-file +skip = .git*,go.sum,i18n,*.css,.codespellrc +check-hidden = true +# ignore-regex = +# ignore-words-list = From 4764619b5ed6c8765785194a34ec73b1a34f4e16 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Thu, 19 Dec 2024 12:51:18 -0500 Subject: [PATCH 3/4] ignore lines with names --- .codespellrc | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.codespellrc b/.codespellrc index 076a2e1..241d33c 100644 --- a/.codespellrc +++ b/.codespellrc @@ -2,5 +2,6 @@ # Ref: https://github.com/codespell-project/codespell#using-a-config-file skip = .git*,go.sum,i18n,*.css,.codespellrc check-hidden = true -# ignore-regex = +# lines with names in publications +ignore-regex = (^- (name|.*\bdoi):.*|fnndsc\.childrens\.harvard\.edu) # ignore-words-list = From 7e4e1ebda6dcb7225d7f1059de049248bffe6a71 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Thu, 19 Dec 2024 12:52:13 -0500 Subject: [PATCH 4/4] [DATALAD RUNCMD] run codespell throughout fixing few left typos automagically === Do not change lines below === { "chain": [], "cmd": "codespell -w", "exit": 0, "extra_inputs": [], "inputs": [], "outputs": [], "pwd": "." } ^^^ Do not change lines above ^^^ --- code-of-conduct.md | 4 ++-- content/resources/tutorials/data-management-and-sharing.md | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/code-of-conduct.md b/code-of-conduct.md index b540ad9..1ee95b6 100644 --- a/code-of-conduct.md +++ b/code-of-conduct.md @@ -1,11 +1,11 @@ # Code of Conduct -The ReproNIM orginization is dedicated to providing an environment where people are kind and respectful to each other, a harassment-free learning experience for everyone, regardless of gender, gender identity and expression, sexual orientation, disability, physical appearance, body size, race, age or religion. +The ReproNIM organization is dedicated to providing an environment where people are kind and respectful to each other, a harassment-free learning experience for everyone, regardless of gender, gender identity and expression, sexual orientation, disability, physical appearance, body size, race, age or religion. We do not tolerate harassment in any form. Sexual language and imagery is not appropriate for any ReproNIM event, including meetings, workshops, and online forums. Participants violating these rules may be sanctioned or expelled from participation in the group at the discretion of the organizers. -### Harrassment +### Harassment ⛔ Harassment includes, but _is not limited to_: diff --git a/content/resources/tutorials/data-management-and-sharing.md b/content/resources/tutorials/data-management-and-sharing.md index 0a4bd92..7e15d36 100644 --- a/content/resources/tutorials/data-management-and-sharing.md +++ b/content/resources/tutorials/data-management-and-sharing.md @@ -34,7 +34,7 @@ We also provide some guidance on preparing a DMSP budget for implementing the pl 3. **Metadata, other relevant data, and associated documentation:** * **Study protocols**: We recommend pre-registering the study protocol using a platform such as the Open Science Framework (osf.io). Pre-registering your study design, including planned outcome measures, increases transparency and accountability. -* **Associate relevant metadata with both imaging and behavioral raw data**. Using BIDS and NIDM provides the means to associate metadata with imaging raw data. Use ReproSchema to prospectively create a re-usable schema for structured behavioral data capture. Use NeuroBagel to annotate behavioral data retrospectively. +* **Associate relevant metadata with both imaging and behavioral raw data**. Using BIDS and NIDM provides the means to associate metadata with imaging raw data. Use ReproSchema to prospectively create a reusable schema for structured behavioral data capture. Use NeuroBagel to annotate behavioral data retrospectively. * **Data dictionary:** * **Good**: Create a data dictionary to define your variables. (provide a link to examples) * **Best:** Use NIDM to create or map the data dictionary to standard variable names and value sets. NIDM also provides additional semantics, i.e., the necessary human knowledge for both humans and machines to interpret and relate data elements. NIDM utilizes community ontologies to provide this knowledge in the form of a common vocabulary and relationships between terms, e.g., Freesurfer variable *caudate\_left\_volume* maps to the term “caudate nucleus” in the UBERON anatomical ontology. Caudate nucleus is part of the striatum and telencephalon.