From 50e95a6fefcac8c7afd58a126006fd4f75fa28dd Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Wed, 14 Aug 2024 11:21:14 +0200
Subject: [PATCH] update readme

---
 README.md | 320 +++++++++++-------------------------------------------
 1 file changed, 66 insertions(+), 254 deletions(-)

diff --git a/README.md b/README.md
index 6dc051c..ef70e47 100644
--- a/README.md
+++ b/README.md
@@ -1,80 +1,72 @@
-[![Node Tests](https://github.com/bids-standard/bids-validator/actions/workflows/node_tests.yml/badge.svg)](https://github.com/bids-standard/bids-validator/actions/workflows/node_tests.yml)
-[![Python tests](https://github.com/bids-standard/bids-validator/actions/workflows/python_tests.yml/badge.svg)](https://github.com/bids-standard/bids-validator/actions/workflows/python_tests.yml)
-[![bids-examples tests](https://github.com/bids-standard/bids-validator/actions/workflows/test-bids-examples.yml/badge.svg)](https://github.com/bids-standard/bids-validator/actions/workflows/test-bids-examples.yml)
-[![CircleCI](https://circleci.com/gh/bids-standard/bids-validator.svg?style=shield&circle-token=:circle-token)](https://circleci.com/gh/bids-standard/bids-validator)
-[![Codecov](https://codecov.io/gh/bids-standard/bids-validator/branch/master/graph/badge.svg)](https://codecov.io/gh/bids-standard/bids-validator)
+[![.github/workflows/build-test-deploy.yml](https://github.com/bids-standard/python-validator/actions/workflows/build-test-deploy.yml/badge.svg)](https://github.com/bids-standard/python-validator/actions/workflows/build-test-deploy.yml)
+[![codecov](https://codecov.io/gh/bids-standard/python-validator/graph/badge.svg?token=5iz5rfzv93)](https://codecov.io/gh/bids-standard/python-validator)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3688707.svg)](https://doi.org/10.5281/zenodo.3688707)
+[![PyPI version](https://badge.fury.io/py/bids-validator.svg)](https://badge.fury.io/py/bids-validator)
+[![Conda version](https://img.shields.io/conda/vn/conda-forge/bids-validator)](https://anaconda.org/conda-forge/bids-validator)
+
+# Python BIDS-Validator
+
+This is a library of helper functions written in Python,
+for use with BIDS compliant applications written in this language.
+
+The main function determines if a file extension is compliant with the BIDS specification.
+
+## Installation
+
+To install with pip:
+
+```
+pip install -U bids_validator
+```
 
-# BIDS-Validator
-
-- [BIDS-Validator](#bids-validator)
-  - [Quickstart](#quickstart)
-  - [Support](#support)
-  - [Maintainers and Contributors](#maintainers-and-contributors)
-  - [Use](#use)
-    - [API](#api)
-    - [.bidsignore](#bidsignore)
-    - [Configuration](#configuration)
-    - [In the Browser](#in-the-browser)
-    - [On the Server](#on-the-server)
-    - [Through Command Line](#through-command-line)
-  - [Docker image](#docker-image)
-  - [Python Library](#python-library)
-    - [Example](#example)
-  - [Development](#development)
-    - [Running Locally in a Browser](#running-locally-in-a-browser)
-    - [Testing](#testing)
-    - [Publishing](#publishing)
-  - [Acknowledgments](#acknowledgments)
+To install with conda:
+
+```
+conda install bids-validator
+```
 
 ## Quickstart
 
-1. Web version:
-   1. Open [Google Chrome](https://www.google.com/chrome/) or
-      [Mozilla Firefox](https://mozilla.org/firefox) (currently the only
-      supported browsers)
-   1. Go to https://bids-standard.github.io/bids-validator/ and select a folder
-      with your BIDS dataset. If the validator seems to be working longer than
-      couple of minutes please open [developer tools ](https://developer.chrome.com/devtools)
-      and report the error at [https://github.com/bids-standard/bids-validator/issues](https://github.com/bids-standard/bids-validator/issues).
-1. Command line version:
-   1. Install [Node.js](https://nodejs.org) (at least version 18.0.0)
-   1. Update `npm` to be at least version 7 (`npm install --global npm@^7`)
-   1. From a terminal run `npm install -g bids-validator`
-   1. Run `bids-validator` to start validating datasets.
-1. Docker
-   1. Install Docker
-   1. From a terminal run `docker run -ti --rm -v /path/to/data:/data:ro bids/validator /data`
-      but replace the `/path/to/data` part of the command with your own path on your machine.
-1. Python Library:
-   1. Install [Python](https://www.python.org/)
-   1. Install [Pip](https://pip.pypa.io/en/stable/installing/) package manager for Python, if
-      not already installed.
-   1. From a terminal run `pip install bids_validator` to acquire the
-      [BIDS Validator PyPI package](https://pypi.org/project/bids-validator/)
-      or `conda install bids-validator` for the
-      [Conda package](https://anaconda.org/conda-forge/bids-validator).
-   1. Open a Python terminal and type: `python`
-   1. Import the BIDS Validator package `from bids_validator import BIDSValidator`
-   1. Check if a file is BIDS compatible `BIDSValidator().is_bids('/relative/path/to/a/bids/file')`
-   1. Note, the file path must be relative to the root of the BIDS dataset, and
-      a leading forward slash `/` must be added to the file path.
-
-## Support
-
-The BIDS Validator is designed to work in both the browser and in Node.js. We
-target support for the latest long term stable (LTS) release of Node.js and the
-latest version of Chrome.
-
-There is also a library of helper functions written in Python, for use with BIDS
-compliant applications written in this language.
-
-Please report any issues you experience while using these support targets via
-the [GitHub issue tracker](https://github.com/bids-standard/bids-validator/issues).
-If you experience issues outside of these supported environments and believe we
-should extend our targeted support feel free to open a new issue describing the
-issue, your support target and why you require extended support and we will
-address these issues on a case by case basis.
+1. Open a Python terminal and type: `python`
+1. Import the BIDS Validator package `from bids_validator import BIDSValidator`
+1. Check if a file is BIDS compatible `BIDSValidator().is_bids('/relative/path/to/a/bids/file')`
+1. Note, the file path must be relative to the root of the BIDS dataset, and
+  a leading forward slash `/` must be added to the file path.
+
+
+### Example
+
+```Python
+from bids_validator import BIDSValidator
+
+validator = BIDSValidator()
+
+filepaths = ["/sub-01/anat/sub-01_rec-CSD_T1w.nii.gz", "/sub-01/anat/sub-01_acq-23_rec-CSD_T1w.exe"]
+for filepath in filepaths:
+    print(validator.is_bids(filepath))  # will print True, and then False
+```
+
+Note, the file path must be relative to the root of the BIDS dataset, and a
+leading forward slash `/` must be added to the file path.
+
+## Acknowledgments
+
+Many contributions to the `bids-validator` were done by members of the
+BIDS community. See the
+[list of contributors](https://bids-specification.readthedocs.io/en/stable/99-appendices/01-contributors.html).
+
+A large part of the development of `bids-validator` is currently done by
+[Squishymedia](https://squishymedia.com/), who are in turn financed through
+different grants offered for the general development of BIDS. See the list
+below.
+
+Development and contributions were supported through the following federally
+funded projects/grants:
+
+- [BIDS Derivatives (NIMH: R24MH114705, PI: Poldrack)](https://grantome.com/grant/NIH/R24-MH114705-01)
+- [OpenNeuro (NIMH: R24MH117179, PI: Poldrack)](https://grantome.com/grant/NIH/R24-MH117179-01)
+- [Spokes: MEDIUM: WEST (NSF: 1760950, PI: Poldrack & Gorgolewski)](https://grantome.com/grant/NSF/IIS-1760950)
+- [ReproNim](http://repronim.org) [(NIH-NIBIB P41 EB019936, PI: Kennedy)](https://projectreporter.nih.gov/project_info_description.cfm?aid=8999833)
 
 ## Maintainers and Contributors
 
@@ -160,32 +152,7 @@ Please also see [Acknowledgments](#acknowledgments).
 
 <!-- ALL-CONTRIBUTORS-LIST:END -->
 
-## Use
-
-### API
-
-The BIDS Validator has one primary method that takes a directory as either a
-path to the directory (node) or the object given by selecting a directory with a
-file input (browser), an options object, and a callback.
-
-Available options include:
-
-- ignoreWarnings - (boolean - defaults to false)
-- ignoreNiftiHeaders - (boolean - defaults to false)
-
-For example:
-
-`validate.BIDS(directory, {ignoreWarnings: true}, function (issues, summary) {console.log(issues.errors, issues.warnings);});`
-
-If you would like to test individual files you can use the file specific checks
-that we expose.
-
-- validate.BIDS()
-- validate.JSON()
-- validate.TSV()
-- validate.NIFTI()
-
-Additionally you can reformat stored errors against a new config using `validate.reformat()`
+<!-- ## Use
 
 ### .bidsignore
 
@@ -329,159 +296,4 @@ bids-validator --config.ignore=99 --config.ignore=44 path/to/bids/dir
 
 This style of use puts limits on what configuration you can require, so for
 complex scenarios, we advise users to create a dedicated configuration file with
-contents as described above.
-
-### In the Browser
-
-The BIDS Validator currently works in the browser with [browserify](https://browserify.org/)
-or [webpack](https://webpack.js.org/). You can add it to a project by cloning
-the validator and requiring it with browserify syntax
-`const validate = require('bids-validator');` or an ES2015 webpack import
-`import validate from 'bids-validator'`.
-
-### On the Server
-
-The BIDS validator works like most npm packages. You can install it by running
-`npm install bids-validator`.
-
-### Through Command Line
-
-If you install the bids validator globally by using `npm install -g bids-validator`
-you will be able to use it as a command line tool. Once installed you should be
-able to run `bids-validator /path/to/your/bids/directory` and see any validation
-issues logged to the terminal. Run `bids-validator` without a directory path to
-see available options.
-
-## Docker image
-
-[![Docker Image Version (latest by date)](https://img.shields.io/docker/v/bids/validator?label=docker)](https://hub.docker.com/r/bids/validator)
-
-To use bids validator with [docker](https://www.docker.com/), you simply need to
-[install docker](https://docs.docker.com/install/) on your system.
-
-And then from a terminal run:
-
-- `docker run -ti --rm bids/validator --version` to print the version of the
-  docker image
-- `docker run -ti --rm bids/validator --help` to print the help
-- `docker run -ti --rm -v /path/to/data:/data:ro bids/validator /data`
-  to validate the dataset `/path/to/data` on your host machine
-
-See here for a brief explanation of the commands:
-
-- `docker run` is the command to tell docker to run a certain docker image,
-  usually taking the form `docker run <IMAGENAME> <COMMAND>`
-- the `-ti` flag means the inputs are accepted and outputs are printed to the
-  terminal
-- the `--rm` flag means that the state of the docker container is not saved
-  after it has run
-- the `-v` flag is adding your local data to the docker container
-  ([bind-mounts](https://docs.docker.com/storage/bind-mounts/)). Importantly,
-  the input after the `-v` flag consists of three fields separated colons: `:`
-  - the first field is the path to the directory on the host machine:
-    `/path/to/data`
-  - the second field is the path where the directory is mounted in the
-    container
-  - the third field is optional. In our case, we use `ro` to specify that the
-    mounted data is _read only_
-
-## Python Library
-
-[![PyPI version](https://badge.fury.io/py/bids-validator.svg)](https://badge.fury.io/py/bids-validator)
-[![Conda version](https://img.shields.io/conda/vn/conda-forge/bids-validator)](https://anaconda.org/conda-forge/bids-validator)
-
-There are is a limited library of helper functions written in Python. The main function
-determines if a file extension is compliant with the BIDS specification. You can find
-the available functions in the library, as well as their descriptions,
-[here](https://github.com/bids-standard/bids-validator/blob/master/bids-validator/bids_validator/bids_validator.py).
-To install, run `pip install -U bids_validator` (requires python and pip) or
-`conda install bids-validator` (requires a Conda environment).
-
-### Example
-
-```Python
-from bids_validator import BIDSValidator
-validator = BIDSValidator()
-filepaths = ["/sub-01/anat/sub-01_rec-CSD_T1w.nii.gz", "/sub-01/anat/sub-01_acq-23_rec-CSD_T1w.exe"]
-for filepath in filepaths:
-    print(validator.is_bids(filepath))  # will print True, and then False
-```
-
-Note, the file path must be relative to the root of the BIDS dataset, and a 
-leading forward slash `/` must be added to the file path.
-
-## Development
-
-To develop locally, clone the project and run `npm install` from the project
-root. This will install external dependencies. If you wish to install
-`bids-validator` globally (so that you can run it in other folders), use the
-following command to install it globally: `cd bids-validator && npm install -g` (for windows users, if in a different drive add /d, e.g. `cd /d F:\bids-validator && npm install -g`)
-
-Please see the [CONTRIBUTING.md](../CONTRIBUTING.md)
-for additional details.
-
-### Bundling
-
-bids-validator is bundled with esbuild. While developing, the script `bids-validator/bin/bids-validator` will automatically bundle the project each time it is run. To test a build without publishing it `npm -w bids-validator run build`. This will generate a bids-validator/dist directory containing the local build and `bids-validator/bin/bids-validator` will use this build. To return to automatic bundling on each run, remove the dist directory.
-
-### Running Locally in a Browser
-
-A note about OS X, the dependencies for the browser require a npm package called
-node-gyp which needs xcode to be installed in order to be compiled.
-
-1. The browser version of `bids-validator` lives in the repo subdirectory
-   `/bids-validator-web`. It is a [React.js](https://reactjs.org/) application
-   that uses the [next.js](https://nextjs.org/) framework.
-2. To develop `bids-validator` and see how it will act in the browser, simply run
-   `npm run web-dev` in the project root and navigate to `localhost:3000`.
-3. In development mode, changes to the codebase will trigger rebuilds of the application
-   automatically.
-4. Changes to the `/bids-validator` in the codebase will also be reflected in the
-   web application.
-5. Tests use the [Jest](https://jestjs.io/index.html) testing library and should be developed in `/bids-validator-web/tests`.
-   We can always use more tests, so please feel free to contribute a test that reduces the chance
-   of any bugs you fix!
-6. To ensure that the web application compiles successfully in production, run `npm run web-export`
-
-### Testing
-
-If it's your first time running tests, first use the command `git submodule update --init --depth 1` to pull the test example data. This repo contains the [bids-examples github repository](https://github.com/bids-standard/bids-examples) as a [submodule](https://git-scm.com/book/en/v2/Git-Tools-Submodules).
-
-To start the test suite run `npm run test` from the project root. `npm run test -- --watch`
-is useful to run tests while making changes. A coverage report is available with
-`npm run coverage`.
-
-To run the linter which checks code conventions run `npm run lint`.
-
-### Install globally from a development branch
-
-Global installs are not recommended for development because of the possibility of package conflicts with other Node.js projects. If you do need to test with a global install from a development tree, follow these steps to generate the NPM package without publishing it and install the package locally.
-
-1. `npm -w bids-validator run build`
-2. `npm -w bids-validator pack`
-3. `npm install -g bids-validator-*.tgz`
-
-### Publishing
-
-Publishing is done with [Lerna](https://github.com/lerna/lerna). Use the command `npx lerna publish` and follow instructions to set a new version.
-
-Using lerna publish will create a git commit with updated version information and create a version number tag for it, push the tag to GitHub, then publish to NPM and PyPI. The GitHub release is manual following that.
-
-## Acknowledgments
-
-Many contributions to the `bids-validator` were done by members of the
-BIDS community. See the
-[list of contributors](https://bids-specification.readthedocs.io/en/stable/99-appendices/01-contributors.html).
-
-A large part of the development of `bids-validator` is currently done by
-[Squishymedia](https://squishymedia.com/), who are in turn financed through
-different grants offered for the general development of BIDS. See the list
-below.
-
-Development and contributions were supported through the following federally
-funded projects/grants:
-
-- [BIDS Derivatives (NIMH: R24MH114705, PI: Poldrack)](https://grantome.com/grant/NIH/R24-MH114705-01)
-- [OpenNeuro (NIMH: R24MH117179, PI: Poldrack)](https://grantome.com/grant/NIH/R24-MH117179-01)
-- [Spokes: MEDIUM: WEST (NSF: 1760950, PI: Poldrack & Gorgolewski)](https://grantome.com/grant/NSF/IIS-1760950)
-- [ReproNim](http://repronim.org) [(NIH-NIBIB P41 EB019936, PI: Kennedy)](https://projectreporter.nih.gov/project_info_description.cfm?aid=8999833)
+contents as described above. -->