From 394c53153b4b00d5a2b7f24c62199c9563ad7b94 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Mon, 10 Nov 2025 10:33:50 -0500 Subject: [PATCH 1/3] Add github action to codespell mkdocs 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..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 From 83cc1274cd6776a2e9a4ebd02ebe916f0b34f90f Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Mon, 10 Nov 2025 10:33:50 -0500 Subject: [PATCH 2/3] 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..1cd4cac --- /dev/null +++ b/.codespellrc @@ -0,0 +1,6 @@ +[codespell] +# Ref: https://github.com/codespell-project/codespell#using-a-config-file +skip = .git*,.codespellrc +check-hidden = true +# ignore-regex = +# ignore-words-list = From 806906daf1e41ecf2e9872d1aebc49791d05822d Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Mon, 10 Nov 2025 10:33:50 -0500 Subject: [PATCH 3/3] [DATALAD RUNCMD] chore: 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 ^^^ --- docs/contributors-guide/codebase/reviewing-prs.md | 2 +- docs/index.md | 2 +- docs/libraries/phys2bids.md | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/contributors-guide/codebase/reviewing-prs.md b/docs/contributors-guide/codebase/reviewing-prs.md index af831bb..6d1e1b4 100644 --- a/docs/contributors-guide/codebase/reviewing-prs.md +++ b/docs/contributors-guide/codebase/reviewing-prs.md @@ -56,7 +56,7 @@ reviewing PRs: Before approving and/or merging PRs, be sure that: - All the tests in CircleCI/Azure pass without errors. -- Prefereably, codecov checks pass as well. If they don't, discuss +- Preferably, codecov checks pass as well. If they don't, discuss what to do. - The title describes the content of the PR clearly enough to be meaningful on its own - remember that it will appear in the version diff --git a/docs/index.md b/docs/index.md index 9766aa5..438119b 100644 --- a/docs/index.md +++ b/docs/index.md @@ -10,4 +10,4 @@ We are the physiopy development team consisting of an international group of vol ## What is the importance of physiological data collection and its impact on MRI? -Physiological data provides a rich representation of a research subject with respect to their bodily information (i.e., heart rate, respiratory rate and depth of breathing, skin conductance, etc.). Examining physiological activity helps us to understand the perception and embodied experience of cognition, emotion, motivation, and more. Additionaly, physiological data is a key component in understanding physiological sources of signal variance in fMRI data. Collecting these data helps to provide more accurate models of fMRI time-series. It also provides a real-time method to monitor subjects during scanning. See the [*Community Practices* documentation](https://physiopy-community-guidelines.readthedocs.io/en/latest/index.html) for recommendations from key personnel in the field on physiological data collection and analysis. +Physiological data provides a rich representation of a research subject with respect to their bodily information (i.e., heart rate, respiratory rate and depth of breathing, skin conductance, etc.). Examining physiological activity helps us to understand the perception and embodied experience of cognition, emotion, motivation, and more. Additionally, physiological data is a key component in understanding physiological sources of signal variance in fMRI data. Collecting these data helps to provide more accurate models of fMRI time-series. It also provides a real-time method to monitor subjects during scanning. See the [*Community Practices* documentation](https://physiopy-community-guidelines.readthedocs.io/en/latest/index.html) for recommendations from key personnel in the field on physiological data collection and analysis. diff --git a/docs/libraries/phys2bids.md b/docs/libraries/phys2bids.md index c21000e..0a57a42 100644 --- a/docs/libraries/phys2bids.md +++ b/docs/libraries/phys2bids.md @@ -4,7 +4,7 @@ It was born for AcqKnowledge files (BIOPAC), and at the moment it supports `.acq` files as well as `.txt` files obtained by labchart (ADInstruments). We're also adding support for MRI-produced files, let us know if you're interested in collaborating to implement support! ### Overview -The Brain Imaging Data Standard (BIDS) is the most commonly used standard for organizing neuroimaging data. `Phys2bids` was origianlly developed by neuroscientists who wanted to standarize the ability to examine the relationship between physiology and brain function as there are many different data formats. Follow the links for more information on how to [install](https://phys2bids.readthedocs.io/en/latest/installation.html) and [use](https://phys2bids.readthedocs.io/en/latest/howto.html) `phys2bids`, as well as the importance of [standarization to BIDS](https://phys2bids.readthedocs.io/en/latest/bids.html) format and [more](https://phys2bids.readthedocs.io/en/latest/index.html). +The Brain Imaging Data Standard (BIDS) is the most commonly used standard for organizing neuroimaging data. `Phys2bids` was originally developed by neuroscientists who wanted to standardize the ability to examine the relationship between physiology and brain function as there are many different data formats. Follow the links for more information on how to [install](https://phys2bids.readthedocs.io/en/latest/installation.html) and [use](https://phys2bids.readthedocs.io/en/latest/howto.html) `phys2bids`, as well as the importance of [standardization to BIDS](https://phys2bids.readthedocs.io/en/latest/bids.html) format and [more](https://phys2bids.readthedocs.io/en/latest/index.html). ### License Information Copyright 2019-2025, The Physiopy community.