physiopy · me-pic · Jun 21, 2024 · Jun 21, 2024 · Jun 21, 2024 · Jun 21, 2024
diff --git a/.codespell_dict b/.codespell_dict
@@ -0,0 +1,4 @@
+file name->filename
+File name->Filename
+file names->filenames
+File names->Filenames
diff --git a/.codespellrc b/.codespellrc
@@ -0,0 +1,7 @@
+[codespell]
+skip = *.js,*.svg,*.eps,.git,node_modules,env,venv,.mypy_cache,package-lock.json,CITATION.cff,tools/new_contributors.tsv,./tools/schemacode/docs/build
+ignore-words-list = fo,te,als,Acknowledgements,acknowledgements,weill,bu,winn,manuel
+builtin = clear,rare,en-GB_to_en-US
+# this overloads default dictionaries and I have not yet figured out
+# how to have multiple https://github.com/codespell-project/codespell/issues/2727
+# dictionary = .codespell_dict
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,31 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-json
+      - id: check-ast
+      - id: check-added-large-files
+      - id: check-case-conflict
+  - repo: https://github.com/psf/black
+    rev: 24.4.2
+    hooks:
+      - id: black
+        files: ^tools/(?!schemacode)
+        args: ["--verbose"]
+      - id: black
+        name: "black bidsschematools"
+        files: tools/schemacode
+        args: ["--config", "tools/schemacode/pyproject.toml", "--verbose"]
+  - repo: https://github.com/pyCQA/flake8
+    rev: 7.1.0
+    hooks:
+      - id: flake8
+        args: [--config=tools/schemacode/setup.cfg]
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
+    hooks:
+      - id: codespell
+        args: ["--config=.codespellrc", "--dictionary=-", "--dictionary=.codespell_dict"]
diff --git a/docs/assets/images/favicon.png b/docs/assets/images/favicon.png
diff --git a/docs/assets/images/logo.png b/docs/assets/images/logo.png
diff --git a/docs/community/contributor-guide.md b/docs/community/contributor-guide.md
@@ -1,6 +1,6 @@
 # How to contribute to `physiopy`
 
-Welcome to the `physiopy` organisation! It's great news that you're
+Welcome to the `physiopy` organization! It's great news that you're
 thinking about contributing!
 
 Working with many people from many different places is great, but
@@ -20,7 +20,7 @@ in this guide? Jump to the following sections:
 
 `physiopy` is a **very** young project developed by a bunch of
 researchers from the two different sides of the Atlantic Ocean (for
-now). Our main goal is to help collect, analyse and share physiological
+now). Our main goal is to help collect, analyze and share physiological
 data, interfacing with (MRI) neuroimaging. We're trying to do so by:
 
 1. Writing packages to make a user-friendly pipeline to deal with
@@ -123,13 +123,13 @@ start!
 ## Issues and Milestones
 
 At `physiopy`, we use Issues and Milestones to keep track of and
-organise our workflow.  **Issues** describe pieces of work that need to
+organize our workflow.  **Issues** describe pieces of work that need to
 be completed to move the project forwards. We try to keep them as simple
 and clear as possible: an issue should describe a unitary, possibly
 small piece of work (unless it's about refactoring). Don't be scared of
 opening many issues at once, if it makes sense! Just check that what
 you're proposing is not listed in a previous issue (open or closed) yet
-(we don't like doubles). Issues get labelled. That helps the
+(we don't like doubles). Issues get labeled. That helps the
 contributors to know what they're about. Check the label list to know
 what types are there, and use them accordingly! Issues can also be
 **assigned**. If you want to work on an assigned issue, ask permission
@@ -154,20 +154,20 @@ right PR labels**!
 
 - ![Documentation](https://img.shields.io/badge/-Documentation-1D70CF?style=flat-square) Improvements or additions to documentation. This
   category includes (but is not limited to) docs pages, docstrings,
-  and code comments. 
+  and code comments.
 
 - ![Duplicate](https://img.shields.io/badge/-Duplicate-CFD3D7?style=flat-square) Whatever this is, it exists already! Maybe it's a closed
-  Issue/PR, that should be reopened. 
+  Issue/PR, that should be reopened.
 
 - ![Enhancement](https://img.shields.io/badge/-Enhancement-A2EEEF?style=flat-square) New features added or requested. This normally goes with a `minormod` label for PRs.
 
 - ![Outreach](https://img.shields.io/badge/-Outreach-0E8A16?style=flat-square) As part of the scientific community, we care about outreach. Check the relevant section about it, but know that this
   Issue/PR contains information or tasks about abstracts, talks,
-  demonstrations, papers. 
+  demonstrations, papers.
 
 - ![Paused](https://img.shields.io/badge/-Paused-F7C38C?style=flat-square) Issue or PR should not be worked on until the resolution of other issues or PRs.
 
-- ![released](https://img.shields.io/badge/-released-ffffff?style=flat-square) This Issue or PR has been released. 
+- ![released](https://img.shields.io/badge/-released-ffffff?style=flat-square) This Issue or PR has been released.
 
 - ![Testing](https://img.shields.io/badge/-Testing-FFB5B4?style=flat-square) This is for testing features, writing tests or producing testing code. Both user testing and CI testing!
 
@@ -182,7 +182,7 @@ right PR labels**!
 
 - ![Community](https://img.shields.io/badge/-Community-E2C7FC?style=flat-square) This issue contains information about the `physiopy`
   community (e.g. the next developer call)
- 
+
 - ![Discussion](https://img.shields.io/badge/-Discussion-1C778C?style=flat-square) Discussion of a concept or implementation. These Issues
   are prone to be open ad infinitum. Jump in the conversation if you
   want!
@@ -195,7 +195,7 @@ right PR labels**!
 
 - ![Hacktoberfest](https://img.shields.io/badge/-Hacktoberfest-FF7518?style=flat-square) Dedicated to the hacktoberfest event, so that people
   can help and feel good about it (and show it with a T-shirt!).
-  **Such commits will not be recognised in the all-contributor table,
+  **Such commits will not be recognized in the all-contributor table,
   unless otherwise specified**.
 
 - ![Help wanted](https://img.shields.io/badge/-Help%20wanted-57DB1A?style=flat-square) Extra attention is needed here! It's a good place to have a look!
@@ -207,14 +207,14 @@ right PR labels**!
 
 - ![Question](https://img.shields.io/badge/-Question-D876E3?style=flat-square) Further information is requested, from users to
   developers. Try to respond to this!
-  
+
 - ![Wontfix](https://img.shields.io/badge/-Wontfix-ffffff?style=flat-square) This will not be worked on, until further notice.
 
 ### PR-only labels
 
 #### Labels for semantic release and changelogs
 
-- ![BugFIX](https://img.shields.io/badge/-BugFIX-D73A4A?style=flat-square) These PRs close an issue labelled `Bug`. They also increase
+- ![BugFIX](https://img.shields.io/badge/-BugFIX-D73A4A?style=flat-square) These PRs close an issue labeled `Bug`. They also increase
   the semantic versioning for fixes (+0.0.1).
 
  - ![dependencies](https://img.shields.io/badge/-dependencies-0366D6?style=flat-square) Pull requests that update a dependency file
@@ -226,7 +226,7 @@ right PR labels**!
 
 - ![Minormod](https://img.shields.io/badge/-Minormod-05246D?style=flat-square) This PR generally closes an `Enhancement` issue. It increments the minor version (0.+1.0)
 
-- ![Minormod-breaking](https://img.shields.io/badge/-Minormod&ndash;breaking-05246D?style=flat-square) This label should be used during development stages (<1.0.0) only. These PRs call for a new minor release during development (0.+1.0) that **will** break backward compatibility. 
+- ![Minormod-breaking](https://img.shields.io/badge/-Minormod&ndash;breaking-05246D?style=flat-square) This label should be used during development stages (<1.0.0) only. These PRs call for a new minor release during development (0.+1.0) that **will** break backward compatibility.
 
 - ![Internal](https://img.shields.io/badge/-Internal-ffffff?style=flat-square) This PR contains changes to the internal API. It won't
   trigger a release, but it will be reported in the changelog.
@@ -419,7 +419,7 @@ 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
@@ -432,7 +432,7 @@ Before approving and/or merging PRs, be sure that:
 At `physiopy` we use the *Assignees* section of a PR to mark the
 **main reviewer** for that PR. The main reviewer is the primary person
 responsible **for the quality of the repository and its next version release**,
- as well as **for the behaviour of the other reviewers**.
+ as well as **for the behavior of the other reviewers**.
 
 ***The main reviewer takes care of the reviewing process of the PR, in particular:***
 
@@ -547,7 +547,7 @@ tests we use are:
         like we expect it to be. They are run on real or mock data, and
         call the program itself or a function.
 
-## Recognising contributors
+## Recognizing contributors
 
 We welcome and recognize [all
 contributions](https://allcontributors.org/docs/en/specification) from

diff --git a/docs/community/contributorfile.md b/docs/community/contributorfile.md
@@ -1,7 +1,7 @@
 [How to contribute to `physiopy`](#contributorfile)
 ===============================
 
-Welcome to the `physiopy` organisation! It's great news that you're
+Welcome to the `physiopy` organization! It's great news that you're
 thinking about contributing!
 
 Working with many people from many different places is great, but
@@ -37,14 +37,14 @@ in this guide? Jump to the following sections:
 -   [Reviewing PRs](#reviewing)
 -   [Style Guide](#styling)
 -   [Automatic Testing](#testing)
--   [Recognizing contributors](#recognising)
+-   [Recognizing contributors](#recognizing)
 
 [Aims of physiopy](#aims)
 ============================
 
 `physiopy` is a **very** young project developed by a bunch of
 researchers from the two different sides of the Atlantic Ocean (for
-now). Our main goal is to help collect, analyse and share physiological
+now). Our main goal is to help collect, analyze and share physiological
 data, interfacing with (MRI) neuroimaging. We're trying to do so by:
 
 1.  Writing packages to make a user-friendly pipeline to deal with
@@ -150,13 +150,13 @@ start!
 ------------------------------------------
 
 At `physiopy`, we use Issues and Milestones to keep track of and
-organise our workflow.  **Issues** describe pieces of work that need to
+organize our workflow.  **Issues** describe pieces of work that need to
 be completed to move the project forwards. We try to keep them as simple
 and clear as possible: an issue should describe a unitary, possibly
 small piece of work (unless it's about refactoring). Don't be scared of
 opening many issues at once, if it makes sense! Just check that what
 you're proposing is not listed in a previous issue (open or closed) yet
-(we don't like doubles). Issues get labelled. That helps the
+(we don't like doubles). Issues get labeled. That helps the
 contributors to know what they're about. Check the label list to know
 what types are there, and use them accordingly! Issues can also be
 **assigned**. If you want to work on an assigned issue, ask permission
@@ -214,7 +214,7 @@ right PR labels**!
     from closing them - but help newcomers closing them.
 -   Hacktoberfest: Dedicated to the hacktoberfest event, so that people
     can help and feel good about it (and show it with a T-shirt!).
-    **Such commits will not be recognised in the all-contributor table,
+    **Such commits will not be recognized in the all-contributor table,
     unless otherwise specified**.
 -   Help wanted: Extra attention is needed here! It's a good place to
     have a look!
@@ -234,7 +234,7 @@ right PR labels**!
     means that the PR is breaking backward compatibility.
 -   Minormod: These PRs call for a new minor release (0.+1.0). This
     means that the PR is **not** breaking backward compatibility.
--   BugFIX: These PRs close an issue labelled `bug`. They also increase
+-   BugFIX: These PRs close an issue labeled `bug`. They also increase
     the semantic versioning for fixes (+0.0.1).
 -   Internal: This PR contains changes to the internal API. It won\'t
     trigger a release, but it will be reported in the changelog.
@@ -427,7 +427,7 @@ 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
@@ -440,7 +440,7 @@ Before approving and/or merging PRs, be sure that:
 At `physiopy` we use the *Assignees* section of a PR to mark the
 **main reviewer** for that PR. The main reviewer is the primary person
 responsible **for the quality of the repository and its next version release**,
- as well as **for the behaviour of the other reviewers**.
+ as well as **for the behavior of the other reviewers**.
 
 ***The main reviewer takes care of the reviewing process of the PR, in particular:***
 
@@ -558,7 +558,7 @@ tests we use are:
         like we expect it to be. They are run on real or mock data, and
         call the program itself or a function.
 
-[Recognising contributors](#recognising)
+[Recognizing contributors](#recognizing)
 ------------------------
 
 We welcome and recognize [all

diff --git a/docs/community/gettingstarted.md b/docs/community/gettingstarted.md
@@ -6,7 +6,7 @@ First of all: thank you!
 Contributions can be made in different ways, not only code! As we follow
 the
 [all-contributors](https://github.com/all-contributors/all-contributors)
-specification, any contribution will be recognised accordingly.
+specification, any contribution will be recognized accordingly.
 
 Follow these steps to get started:
 

diff --git a/docs/community/other_tools.md b/docs/community/other_tools.md
@@ -1,13 +1,13 @@
 # Other Tools
 
 ### Similar projects:
-[PhysIO toolbox](https://www.nitrc.org/projects/physio/) that supports data processing, denoising, and modelling for the purpose of physiological denoising (depends on SPM and only runs on MATLAB, requiring a license). 
+[PhysIO toolbox](https://www.nitrc.org/projects/physio/) that supports data processing, denoising, and modeling for the purpose of physiological denoising (depends on SPM and only runs on MATLAB, requiring a license).
 
 PhysIO and physiopy developers have expressed interest in collaborating with each other.
 
 ### Other toolboxes with a narrower scope than physiopy’s:
-- [NeuroKit](https://neurokit2.readthedocs.io/en/latest/) which offers back-end solutions for physiological data denoising. 
-- [AFNI](https://afni.nimh.nih.gov/) and [Quantiphyse](https://quantiphyse.readthedocs.io/en/latest/) offer, among other functionalities, physiological data analysis or modelling in a complementary way to physiopy. 
+- [NeuroKit](https://neurokit2.readthedocs.io/en/latest/) which offers back-end solutions for physiological data denoising.
+- [AFNI](https://afni.nimh.nih.gov/) and [Quantiphyse](https://quantiphyse.readthedocs.io/en/latest/) offer, among other functionalities, physiological data analysis or modeling in a complementary way to physiopy.
 
 Physiopy’s developers are in contact with the developers of these software packages to collaborate on improving between-project integration.
 

diff --git a/docs/index.md b/docs/index.md
@@ -1,13 +1,13 @@
 # Home
-Welcome to the main documentation site for the physiopy community and python package! Please also check out the package's [Github Page](https://github.com/physiopy). For questions, you can always contact the project manager at [physiopy.community@gmail.com](mailto:physiopy.community@gmail.com). 
+Welcome to the main documentation site for the physiopy community and python packages! Please also check out our [Github Page](https://github.com/physiopy). For questions, you can always contact the project manager at [physiopy.community@gmail.com](mailto:physiopy.community@gmail.com).
 
 <p align="center">
 <img src="https://github.com/physiopy/phys2bids/blob/master/docs/_static/physiopy_logo_1280x640.png?raw=true" width="400">
 </p>
 
 ## Who are we?
-We are the physiopy development team consisting of an international group of volunteers. You can learn more about us by visiting the [*Community*](/community/index) page. Contributions are also very much welcomed! Check out the [*Contributors*](/community/contributor-guide) tab.
+We are the physiopy development team consisting of an international group of volunteers. You can learn more about us and how to connect with us by visiting the [*Community*](/community) page. Contributions are also very much welcomed! Check out the [*Contributor Guide*](community/contributor-guide/) tab.
 
 ## What is the importance of physiological data collection and its impact on MRI?
 
-Physiological data provides the representation of the participant with respect to extension of bodily information (i.e., heart rates, respiratory rate, skin conductance etc.). Monitoring one's physiological activity helps us understand the percerption of cognition, emotion, motivation etc. 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 [*Best Practices* section](/best-practices) 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
@@ -1,9 +1,9 @@
 # Phys2bids
 ### A python3 library to format physiological files in BIDS
-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! 
+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, The Phys2BIDS community.