From f94695875f36a8f66d9fd6054800cc0ac03da4b9 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Fri, 19 Apr 2024 15:17:48 -0400 Subject: [PATCH 1/5] Add github action to codespell main on push and PRs --- .github/workflows/codespell.yml | 23 +++++++++++++++++++++++ 1 file changed, 23 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..7c9eafb --- /dev/null +++ b/.github/workflows/codespell.yml @@ -0,0 +1,23 @@ +# 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: Codespell + uses: codespell-project/actions-codespell@v2 From 33747e4705ee310c996fa7d05d7decf915fa33f6 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Fri, 19 Apr 2024 15:17:48 -0400 Subject: [PATCH 2/5] 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..91b971c --- /dev/null +++ b/.codespellrc @@ -0,0 +1,6 @@ +[codespell] +# Ref: https://github.com/codespell-project/codespell#using-a-config-file +skip = .git*,*.pdf,*.css,*.min.*,.codespellrc +check-hidden = true +# ignore-regex = +# ignore-words-list = From e0706d003d86096618bcb3baad091ba1b9d8b70a Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Fri, 19 Apr 2024 15:20:53 -0400 Subject: [PATCH 3/5] ambigous typo --- labguide/research/statistical_methods.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/labguide/research/statistical_methods.md b/labguide/research/statistical_methods.md index 8300d5d..02fd3a0 100644 --- a/labguide/research/statistical_methods.md +++ b/labguide/research/statistical_methods.md @@ -12,7 +12,7 @@ the preregistration document. - The nature of grouping for multiple testing corrections (e.g., parameter within single models, - sets ot models, etc) should be pre-specified. + sets of models, etc) should be pre-specified. - For fMRI data, if using cluster-based thresholding the cluster forming threshold must be Z ≥ 3.1 if using parametric thresholding. There are no restrictions on From 83d923b03d78f4d52b0953cbc72e23953176e849 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Fri, 19 Apr 2024 15:23:05 -0400 Subject: [PATCH 4/5] custom excludes on indexed metadata and generated files --- .codespellrc | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.codespellrc b/.codespellrc index 91b971c..f56cd04 100644 --- a/.codespellrc +++ b/.codespellrc @@ -1,6 +1,7 @@ [codespell] # Ref: https://github.com/codespell-project/codespell#using-a-config-file -skip = .git*,*.pdf,*.css,*.min.*,.codespellrc +# ./labguide/research is generated from .md +skip = .git*,*.pdf,*.css,*.min.*,.codespellrc,site_libs,search.json,publications.html,additional_pubs.csv,./docs/labguide/*/*.html,./academicdb/*.csv check-hidden = true -# ignore-regex = +ignore-regex = \bNichols TE\b # ignore-words-list = From 1bf5909872c49ff4f9c6093f0b6d0304377a69b1 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Fri, 19 Apr 2024 15:23:08 -0400 Subject: [PATCH 5/5] [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 ^^^ --- labguide/environment/code_of_conduct.md | 2 +- labguide/research/intellectual_property.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/labguide/environment/code_of_conduct.md b/labguide/environment/code_of_conduct.md index eeaba84..3b11bf3 100644 --- a/labguide/environment/code_of_conduct.md +++ b/labguide/environment/code_of_conduct.md @@ -12,7 +12,7 @@ Conduct](https://adminguide.stanford.edu/chapter-1/subchapter-1/policy-1-1-1). For definitions of an act of intolerance & hate crime escalation policy please see this page on University [AOI](https://deanofstudents.stanford.edu/acts-intolerance-protocol/overview/definitions). If you wish to speak with someone outside of the lab regarding an -incident that occured in or outside of the lab, the university has +incident that occurred in or outside of the lab, the university has this[ list of resources.](https://deanofstudents.stanford.edu/acts-intolerance-protocol/talk-someone) diff --git a/labguide/research/intellectual_property.md b/labguide/research/intellectual_property.md index 72b65a2..38d2e9a 100644 --- a/labguide/research/intellectual_property.md +++ b/labguide/research/intellectual_property.md @@ -4,7 +4,7 @@ All products of research at Stanford (including data and code) are the property As discussed in the section on [data management and sharing](https://poldracklab.github.io/research/data_management.html), all data collected within our laboratory is meant to be shared upon submission of the related paper. In cases where these data can be deidentified they will be shared under a public domain dedication (CC0), which places no restrictions on their use by other researchers. Thus, any researcher can continue to use those data once they leave the lab. In other cases it may be necessary to restrict data sharing (e.g. when the data cannot be deidentified), in which case researchers will need to obtain a data use agreement from Stanford in order to access those data at their new institution. Dr. Poldrack commits to supporting any such requests, unless they violate other obligations of his or the University. -In many cases we use data within the lab under Data Use Agreements (such as the ABCD or HCP datasets), and any researcher wishing to use such datasets must be explcitly listed on the DUA. Once a researcher is no longer included in the Stanford DUA for a particular dataset, they must no longer access the dataset via Stanford computer systems. +In many cases we use data within the lab under Data Use Agreements (such as the ABCD or HCP datasets), and any researcher wishing to use such datasets must be explicitly listed on the DUA. Once a researcher is no longer included in the Stanford DUA for a particular dataset, they must no longer access the dataset via Stanford computer systems. ## Research ideas