Merge pull request #1087 from mnoergaard/martin

[ENH] Update BEP009 with newest version of validator #1085

.github/workflows/python_tests 2.yml

@@ -0,0 +1,60 @@
+name: Python tests
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+    strategy:
+      fail-fast: false
+      matrix:
+        platform: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: [3.7]
+
+    runs-on: ${{ matrix.platform }}
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: goanpeca/setup-miniconda@v1
+      with:
+        auto-update-conda: true
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install git-annex ubuntu
+      if: matrix.platform == 'ubuntu-latest'
+      shell: bash -l {0}
+      run: conda install -c conda-forge git-annex
+
+    - name: Install git-annex macos
+      if: matrix.platform == 'macos-latest'
+      shell: bash -l {0}
+      run: brew install git-annex
+
+    - name: Install git-annex windows
+      if: matrix.platform == 'windows-latest'
+      uses: crazy-max/ghaction-chocolatey@v1
+      with:
+        args: install git-annex --yes --ignore-checksums
+
+    - name: Install remaining dependencies
+      shell: bash -l {0}
+      run: |
+        which python
+        pip install datalad
+        pip install pytest pytest-sugar flake8 pydocstyle
+        pip install -e ./bids-validator
+
+    - name: Check formatting
+      shell: bash -l {0}
+      run: |
+        flake8 bids-validator/bids_validator
+        pydocstyle bids-validator/bids_validator/bids_validator.py
+
+    - name: Test with pytest
+      shell: bash -l {0}
+      run: |
+        pytest --doctest-modules bids-validator/bids_validator --verbose

CODE_OF_CONDUCT.md

@@ -34,11 +34,11 @@ This Code of Conduct applies both within project spaces and in public spaces whe
 
 ## Enforcement
 
-Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team at ffein@stanford.edu. The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team at krzysztof.gorgolewski@gmail.com. The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
 
 Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
 
-## Attribution
+## Attribution 
 
 This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [http://contributor-covenant.org/version/1/4][version]
 

bids-validator-web/package.json

@@ -1,6 +1,6 @@
 {
   "name": "bids-validator-web",
-  "version": "1.5.5-dev.0",
+  "version": "1.4.0",
   "description": "web client for bids-validator",
   "main": "index.js",
   "license": "MIT",
@@ -9,9 +9,9 @@
     "@zeit/next-sass": "^1.0.1",
     "bootstrap": "^4.3.0",
     "bowser": "^1.0.0",
-    "next": "^9.3.2",
+    "next": "^8.0.0",
     "next-transpile-modules": "^2.3.1",
-    "node-sass": "4.13.1",
+    "node-sass": "^4.11.0",
     "react": "^16.8.1",
     "react-bootstrap": "^1.0.0-beta.5",
     "react-dom": "^16.8.1"

bids-validator/README.md

@@ -1,31 +1,8 @@
-[![CircleCI](https://circleci.com/gh/bids-standard/bids-validator.svg?style=shield&circle-token=:circle-token)](https://circleci.com/gh/bids-standard/bids-validator)
-[![Gitlab pipeline status](https://img.shields.io/gitlab/pipeline/bids-standard/bids-validator?logo=GitLab)](https://gitlab.com/bids-standard/bids-validator/pipelines)
-[![Codecov](https://codecov.io/gh/bids-standard/bids-validator/branch/master/graph/badge.svg)](https://codecov.io/gh/bids-standard/bids-validator)
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3688707.svg)](https://doi.org/10.5281/zenodo.3688707)
-
+![](https://circleci.com/gh/bids-standard/bids-validator.svg?style=shield&circle-token=:circle-token)
+![](https://codecov.io/gh/bids-standard/bids-validator/branch/master/graph/badge.svg)
 
 # 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)
-
 ## Quickstart
 
 1. Web version:
@@ -43,7 +20,6 @@
 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/) (works with python2 and python3)
    1. Install [Pip](https://pip.pypa.io/en/stable/installing/) package manager for python, if
@@ -78,11 +54,9 @@ Some of our awesome contributors include:
 
 [![](https://sourcerer.io/fame/chrisfilo/bids-standard/bids-validator/images/0)](https://sourcerer.io/fame/chrisfilo/bids-standard/bids-validator/links/0)[![](https://sourcerer.io/fame/chrisfilo/bids-standard/bids-validator/images/1)](https://sourcerer.io/fame/chrisfilo/bids-standard/bids-validator/links/1)[![](https://sourcerer.io/fame/chrisfilo/bids-standard/bids-validator/images/2)](https://sourcerer.io/fame/chrisfilo/bids-standard/bids-validator/links/2)[![](https://sourcerer.io/fame/chrisfilo/bids-standard/bids-validator/images/3)](https://sourcerer.io/fame/chrisfilo/bids-standard/bids-validator/links/3)[![](https://sourcerer.io/fame/chrisfilo/bids-standard/bids-validator/images/4)](https://sourcerer.io/fame/chrisfilo/bids-standard/bids-validator/links/4)[![](https://sourcerer.io/fame/chrisfilo/bids-standard/bids-validator/images/5)](https://sourcerer.io/fame/chrisfilo/bids-standard/bids-validator/links/5)[![](https://sourcerer.io/fame/chrisfilo/bids-standard/bids-validator/images/6)](https://sourcerer.io/fame/chrisfilo/bids-standard/bids-validator/links/6)[![](https://sourcerer.io/fame/chrisfilo/bids-standard/bids-validator/images/7)](https://sourcerer.io/fame/chrisfilo/bids-standard/bids-validator/links/7)
 
-Please also see [Acknowledgments](#acknowledgments).
-
 ## Use
 
-### API
+#### 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
@@ -107,7 +81,7 @@ that we expose.
 
 Additionally you can reformat stored errors against a new config using `validate.reformat()`
 
-### .bidsignore
+#### .bidsignore
 
 Optionally one can include a `.bidsignore` file in the root of the dataset. This
 file lists patterns (compatible with the [.gitignore syntax](https://git-scm.com/docs/gitignore))
@@ -120,7 +94,7 @@ specification.
 extra_data/
 ```
 
-### Configuration
+#### Configuration
 
 You can configure the severity of errors by passing a json configuration file
 with a `-c` or `--config` flag to the command line interface or by defining a
@@ -252,77 +226,45 @@ 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
+#### In the Browser
 
 The BIDS Validator currently works in the browser with [browserify](http://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
 `var validate = require('bids-validator');` or an ES2015 webpack import
 `import validate from 'bids-validator'`.
 
-### On the Server
+#### On the Server
 
 The BIDS validator works like most npm packages. You can install it by running
 `npm install bids-validator`.
 
-### Through Command Line
+#### 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)
-
 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).
+To install, run `pip install bids_validator` (requires python and pip).
 
-### Example
+#### 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
+```
+>>> 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) )
+True
+False
 ```
 
 ## Development
@@ -332,10 +274,7 @@ 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`
 
-Please see the [CONTRIBUTING.md](../CONTRIBUTING.md)
-for additional details.
-
-### Running Locally in a Browser
+#### 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.
@@ -354,7 +293,7 @@ node-gyp which needs xcode to be installed in order to be compiled.
 	of any bugs you fix!
 6. To ensure that the web application compiles successfully in production, run `yarn web-export`
 
-### Testing
+#### 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).
 
@@ -364,7 +303,7 @@ is useful to run tests while making changes. A coverage report is available with
 
 To run the linter which checks code conventions run `npm run lint`.
 
-### Publishing
+#### Publishing
 
 Publishing is done with [Lerna](https://github.com/lerna/lerna). Use the command `yarn lerna publish` and follow instructions to set a new version.
 
@@ -373,8 +312,7 @@ Using lerna publish will create a git commit with updated version information an
 ## 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).
+BIDS community. See the [list of contributors](https://github.com/bids-standard/bids-validator/graphs/contributors).
 
 A large part of the development of `bids-validator` is currently done by
 [Squishymedia](https://squishymedia.com/), who are in turn financed through