From b5c5fb692822112a690c08e9110c9b2bbabb769b Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Fri, 12 Jan 2024 12:18:11 -0500 Subject: [PATCH 1/5] Add github action to codespell master 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..daa4072 --- /dev/null +++ b/.github/workflows/codespell.yml @@ -0,0 +1,23 @@ +# Codespell configuration is within .codespellrc +--- +name: Codespell + +on: + push: + branches: [master] + pull_request: + branches: [master] + +permissions: + contents: read + +jobs: + codespell: + name: Check for spelling errors + runs-on: ubuntu-latest + + steps: + - name: Checkout + uses: actions/checkout@v3 + - name: Codespell + uses: codespell-project/actions-codespell@v2 From 0d3e939f36872b08c51f82ce4fb9439c2e10076e Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Fri, 12 Jan 2024 12:18:11 -0500 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..e641818 --- /dev/null +++ b/.codespellrc @@ -0,0 +1,6 @@ +# Ref: https://github.com/codespell-project/codespell#using-a-config-file +[codespell] +skip = .git,*.pdf,*.svg,go.sum,*.css,*.min.*,.codespellrc +check-hidden = true +# ignore-regex = +# ignore-words-list = From 96cacba753e75f4800256f041a6fa07bdf1fb7da Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Fri, 12 Jan 2024 12:19:05 -0500 Subject: [PATCH 3/5] ignore some words from codespell --- .codespellrc | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.codespellrc b/.codespellrc index e641818..674445b 100644 --- a/.codespellrc +++ b/.codespellrc @@ -2,5 +2,5 @@ [codespell] skip = .git,*.pdf,*.svg,go.sum,*.css,*.min.*,.codespellrc check-hidden = true -# ignore-regex = +ignore-regex = \b(TE|currentY|Lew)\b # ignore-words-list = From e4a9d11c1aee705316e4e0e518603f4b3faccf8d Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Fri, 12 Jan 2024 12:19:16 -0500 Subject: [PATCH 4/5] [DATALAD RUNCMD] run codespell throughout but ignore fail === Do not change lines below === { "chain": [], "cmd": "codespell -w || :", "exit": 0, "extra_inputs": [], "inputs": [], "outputs": [], "pwd": "." } ^^^ Do not change lines above ^^^ --- 5Steps/acquisition.html | 2 +- do.html | 4 ++-- news_archive.html | 2 +- teach.html | 2 +- webinar-series.html | 2 +- 5 files changed, 6 insertions(+), 6 deletions(-) diff --git a/5Steps/acquisition.html b/5Steps/acquisition.html index d9e5a1f..0e79a3b 100644 --- a/5Steps/acquisition.html +++ b/5Steps/acquisition.html @@ -82,7 +82,7 @@

Data Acquisition Considerations for More Rep
  • Use ReproIn to automate conversion of your imaging data to BIDS.
  • Annotate your metadata (all experimental details) as you collect it.
      -
    • There are a number of ways to annotate your data. The idea with annotations are to provide unambigous markup of your data, whether it be imaging, behavioral, clinical, etc. One strategy is to annotate the variables you intend to collect during the study design process. This can occur by choosing data structures that are publically available and already annotated (e.g. NDAR) or by using the tools below. Regardless of the approach, the important aspect is to unambigously describe what the variables collected mean, their ranges, min/max, units, etc. For more information on the desired properties for annotations, see: Federated Data Elements +
    • There are a number of ways to annotate your data. The idea with annotations are to provide unambiguous markup of your data, whether it be imaging, behavioral, clinical, etc. One strategy is to annotate the variables you intend to collect during the study design process. This can occur by choosing data structures that are publicly available and already annotated (e.g. NDAR) or by using the tools below. Regardless of the approach, the important aspect is to unambiguously describe what the variables collected mean, their ranges, min/max, units, etc. For more information on the desired properties for annotations, see: Federated Data Elements
      • BrainVerse is a tool being developed which can help to annotate your variables by directly incorporating data structures from NDAR.
      • PyNIDM is both a Python library for creating metadata documents using the Neuroimaging Data Model (NIDM) but also contains tools such as "bidsmri2nidm" and "csv2nidm" which can be used to interactively annotate both BIDS datasets (via participants.csv file) and general CSV-formatted data files containinga header row of variables which require annotation. The annotation process requires you to have a SciCrunch account and API-access key which are freely available on the site. The tools iteratve over your variables and query the InterLex information resource looking for terms that match your variables. If no term is found you are asked to contribute a new term definition which will be used in the InterLex and thus provide persistent annotations. diff --git a/do.html b/do.html index 455f60d..99c9114 100644 --- a/do.html +++ b/do.html @@ -92,7 +92,7 @@

        What are you waiting for?
        Just Do

        We strongly believe in the benefits of modular design, - collaboration, and re-use. That is why, instead of developing a + collaboration, and reuse. That is why, instead of developing a single monolithic platform to "solve all the problems", we are reusing and contributing to existing projects as much as possible. To that end, in the scope of this project, we actively maintain @@ -195,7 +195,7 @@

        YODA Principles

        cover the entire life-span of a research project with reliable, non-ambiguous tracking and orchestration of all digital products of a study (e.g., inputs, code, outputs). Modularization facilitates - the independent re-use of parts (e.g., the same data used across + the independent reuse of parts (e.g., the same data used across multiple studies, versions of a software library used repeatedly) in a manner that scales to dataset sizes found in cutting edge high-resolution neuroimaging research.

        diff --git a/news_archive.html b/news_archive.html index 1f3f438..adbaa58 100644 --- a/news_archive.html +++ b/news_archive.html @@ -113,7 +113,7 @@

        Past Events and Activities

      • Although the course is now completed, all lectures and course materials continue to be publicly available online: diff --git a/teach.html b/teach.html index 59908e3..4f2b06a 100644 --- a/teach.html +++ b/teach.html @@ -114,7 +114,7 @@

        Reproducibility Basics

        FAIR Data

        -

        FAIR is a collection of guiding principles to make data Findable, Accessible, Interoperable, and Re-usable. We look at ways to ensure that a researcher’s data is properly managed and published in support of reproducible research.

        +

        FAIR is a collection of guiding principles to make data Findable, Accessible, Interoperable, and Reusable. We look at ways to ensure that a researcher’s data is properly managed and published in support of reproducible research.

        Go to module.

        diff --git a/webinar-series.html b/webinar-series.html index 782dac4..8a1ee67 100644 --- a/webinar-series.html +++ b/webinar-series.html @@ -315,7 +315,7 @@

        Webinar Presentations to Date

      • Friday, February 5, 2021 at 2pm EST
          -
        • ReproNim investigators Jeffrey Grethe, David Keator, and Albert Crowley discuss how to create and utilize local metadata storage in "How to Build Your Own ReproPond," including various aspects of setup, local installation of BlazeGraph, and usage pointers. +
        • ReproNim investigators Jeffrey Grethe, David Keator, and Albert Crowley discuss how to create and utilize local metadata storage in "How to Build Your Own ReproPond," including various aspects of setup, local installation of BlazeGraph, and usage pointers.
        • Video Presentation and Slides are available.
        From 9c00d34a68e1ff24296c831bb90ef03c603d7f69 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Fri, 12 Jan 2024 12:22:22 -0500 Subject: [PATCH 5/5] ignore mistyped URL fnndsc.childrens.harvard.edu --- .codespellrc | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.codespellrc b/.codespellrc index 674445b..bd53e84 100644 --- a/.codespellrc +++ b/.codespellrc @@ -2,5 +2,5 @@ [codespell] skip = .git,*.pdf,*.svg,go.sum,*.css,*.min.*,.codespellrc check-hidden = true -ignore-regex = \b(TE|currentY|Lew)\b +ignore-regex = \b(TE|currentY|Lew|fnndsc.childrens.harvard.edu)\b # ignore-words-list =