pax_global_header00006660000000000000000000000064135205640410014512gustar00rootroot0000000000000052 comment=e7eb3c9b34b0fa2e060ba67a05a2179d64f50370 python-bids-validator-1.2.4/000077500000000000000000000000001352056404100157415ustar00rootroot00000000000000python-bids-validator-1.2.4/MANIFEST.in000066400000000000000000000001171352056404100174760ustar00rootroot00000000000000include CODE_OF_CONDUCT.md LICENSE MANIFEST.in README.md include versioneer.py python-bids-validator-1.2.4/PKG-INFO000066400000000000000000000344471352056404100170520ustar00rootroot00000000000000Metadata-Version: 2.1 Name: bids-validator Version: 1.2.4 Summary: Validator for the Brain Imaging Data Structure Home-page: https://github.com/bids-standard/bids-validator Author: PyBIDS developers Author-email: bids-discussion@googlegroups.com Maintainer: BIDS Developers Maintainer-email: bids-discussion@googlegroups.com License: MIT Description: ![](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 ## 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 http://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 8.0) 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` 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 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/) 1. Open a Python terminal `python` 1. Import the BIDS Validator package `from bids_validator import BIDSValidator` 1. Check if a file is BIDS compatible `BIDSValidator().is_bids('path/to/a/bids/file')` ## 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. 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. ## Maintainers and Contributors This package is maintained by [@rwblair](https://github.com/rwblair/). 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) ## 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()` #### .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)) defining files that should be ignored by the validator. This option is useful when the validated dataset includes file types not yet supported by BIDS specification. ```Text *_not_bids.txt extra_data/ ``` #### 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 config object on the options object passed during javascript usage. The basic configuration format is outlined below. All configuration is optional. ```JSON { "ignore": [], "warn": [], "error": [], "ignoredFiles": [] } ``` `ignoredFiles` takes a list of file paths or glob patterns you'd like to ignore. Lets say we want to ignore all files and sub-directory under `/derivatives/`. **This is not the same syntax as used in the .bidsignore file** ```JSON { "ignoredFiles": ["/derivatives/**"] } ``` Note that adding two stars `**` in path makes validator recognize all files and sub-dir to be ignored. `ignore`, `warn`, and `error` take lists of issue codes or issue keys and change the severity of those issues so they are either ignored or reported as warnings or errors. You can find a list of all available issues at [utils/issues/list](https://github.com/bids-standard/bids-validator/tree/master/utils/issues/list.js). Some issues may be ignored by default, but can be elevated to warnings or errors. These provide a way to check for common things that are more specific than BIDS compatibility. An example is a check for the presence of a T1w modality. The following would raise an error if no T1W image was found in a dataset. ```JSON { "error": ["NO_T1W"] } ``` In addition to issue codes and keys these lists can also contain objects with and "and" or "or" properties set to arrays of codes or keys. These allow some level of conditional logic when configuring issues. For example: ```JSON { "ignore": [ { "and": [ "ECHO_TIME_GREATER_THAN", "ECHO_TIME_NOT_DEFINED" ] } ] } ``` In the above example the two issues will only be ignored if both of them are triggered during validation. ```JSON { "ignore": [ { "and": [ "ECHO_TIME_GREATER_THAN", "ECHO_TIME_NOT_DEFINED" { "or": [ "ECHO_TIME1-2_NOT_DEFINED", "ECHO_TIME_MUST_DEFINE" ] } ] } ] } ``` And in this example the listed issues will only be ignored if `ECHO_TIME_GREATER_THAN`, `ECHO_TIME_NOT_DEFINED` and either `ECHO_TIME1-2_NOT_DEFINED` or `ECHO_TIME_MUST_DEFINE` are triggered during validation. "or" arrays are not supported at the lowest level because it wouldn't add any functionality. For example the following is not supported. ```JSON { "ignore": [ { "or": [ "ECHO_TIME_GREATER_THAN", "ECHO_TIME_NOT_DEFINED" ] } ] } ``` because it would be functionally the same as this: ```JSON { "ignore": [ "ECHO_TIME_GREATER_THAN", "ECHO_TIME_NOT_DEFINED" ] } ``` For passing a configuration while using the bids-validator on the command line, note that you **have to specify at least two configurations of a given type**, because an array is expected. For example, the following code will ignore empty file errors (99) and files that cannot be read (44): ``` 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](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 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. ## Python Library 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 bids_validator` (requires python and pip). #### Example ``` >>> 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 To develop locally, clone the project and run `yarn` 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` #### 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 `yarn 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 `yarn web-export` #### Testing To start the test suite run `npm test` from the project root. `npm 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`. Platform: UNKNOWN Classifier: Development Status :: 3 - Alpha Classifier: Environment :: Console Classifier: Intended Audience :: Science/Research Classifier: License :: OSI Approved :: MIT License Classifier: Operating System :: OS Independent Classifier: Programming Language :: Python Classifier: Topic :: Scientific/Engineering Description-Content-Type: text/markdown python-bids-validator-1.2.4/README.md000066400000000000000000000263731352056404100172330ustar00rootroot00000000000000![](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 ## 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 http://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 8.0) 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` 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 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/) 1. Open a Python terminal `python` 1. Import the BIDS Validator package `from bids_validator import BIDSValidator` 1. Check if a file is BIDS compatible `BIDSValidator().is_bids('path/to/a/bids/file')` ## 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. 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. ## Maintainers and Contributors This package is maintained by [@rwblair](https://github.com/rwblair/). 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) ## 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()` #### .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)) defining files that should be ignored by the validator. This option is useful when the validated dataset includes file types not yet supported by BIDS specification. ```Text *_not_bids.txt extra_data/ ``` #### 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 config object on the options object passed during javascript usage. The basic configuration format is outlined below. All configuration is optional. ```JSON { "ignore": [], "warn": [], "error": [], "ignoredFiles": [] } ``` `ignoredFiles` takes a list of file paths or glob patterns you'd like to ignore. Lets say we want to ignore all files and sub-directory under `/derivatives/`. **This is not the same syntax as used in the .bidsignore file** ```JSON { "ignoredFiles": ["/derivatives/**"] } ``` Note that adding two stars `**` in path makes validator recognize all files and sub-dir to be ignored. `ignore`, `warn`, and `error` take lists of issue codes or issue keys and change the severity of those issues so they are either ignored or reported as warnings or errors. You can find a list of all available issues at [utils/issues/list](https://github.com/bids-standard/bids-validator/tree/master/utils/issues/list.js). Some issues may be ignored by default, but can be elevated to warnings or errors. These provide a way to check for common things that are more specific than BIDS compatibility. An example is a check for the presence of a T1w modality. The following would raise an error if no T1W image was found in a dataset. ```JSON { "error": ["NO_T1W"] } ``` In addition to issue codes and keys these lists can also contain objects with and "and" or "or" properties set to arrays of codes or keys. These allow some level of conditional logic when configuring issues. For example: ```JSON { "ignore": [ { "and": [ "ECHO_TIME_GREATER_THAN", "ECHO_TIME_NOT_DEFINED" ] } ] } ``` In the above example the two issues will only be ignored if both of them are triggered during validation. ```JSON { "ignore": [ { "and": [ "ECHO_TIME_GREATER_THAN", "ECHO_TIME_NOT_DEFINED" { "or": [ "ECHO_TIME1-2_NOT_DEFINED", "ECHO_TIME_MUST_DEFINE" ] } ] } ] } ``` And in this example the listed issues will only be ignored if `ECHO_TIME_GREATER_THAN`, `ECHO_TIME_NOT_DEFINED` and either `ECHO_TIME1-2_NOT_DEFINED` or `ECHO_TIME_MUST_DEFINE` are triggered during validation. "or" arrays are not supported at the lowest level because it wouldn't add any functionality. For example the following is not supported. ```JSON { "ignore": [ { "or": [ "ECHO_TIME_GREATER_THAN", "ECHO_TIME_NOT_DEFINED" ] } ] } ``` because it would be functionally the same as this: ```JSON { "ignore": [ "ECHO_TIME_GREATER_THAN", "ECHO_TIME_NOT_DEFINED" ] } ``` For passing a configuration while using the bids-validator on the command line, note that you **have to specify at least two configurations of a given type**, because an array is expected. For example, the following code will ignore empty file errors (99) and files that cannot be read (44): ``` 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](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 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. ## Python Library 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 bids_validator` (requires python and pip). #### Example ``` >>> 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 To develop locally, clone the project and run `yarn` 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` #### 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 `yarn 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 `yarn web-export` #### Testing To start the test suite run `npm test` from the project root. `npm 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`. python-bids-validator-1.2.4/bids_validator.egg-info/000077500000000000000000000000001352056404100224215ustar00rootroot00000000000000python-bids-validator-1.2.4/bids_validator.egg-info/PKG-INFO000066400000000000000000000344471352056404100235320ustar00rootroot00000000000000Metadata-Version: 2.1 Name: bids-validator Version: 1.2.4 Summary: Validator for the Brain Imaging Data Structure Home-page: https://github.com/bids-standard/bids-validator Author: PyBIDS developers Author-email: bids-discussion@googlegroups.com Maintainer: BIDS Developers Maintainer-email: bids-discussion@googlegroups.com License: MIT Description: ![](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 ## 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 http://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 8.0) 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` 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 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/) 1. Open a Python terminal `python` 1. Import the BIDS Validator package `from bids_validator import BIDSValidator` 1. Check if a file is BIDS compatible `BIDSValidator().is_bids('path/to/a/bids/file')` ## 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. 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. ## Maintainers and Contributors This package is maintained by [@rwblair](https://github.com/rwblair/). 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) ## 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()` #### .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)) defining files that should be ignored by the validator. This option is useful when the validated dataset includes file types not yet supported by BIDS specification. ```Text *_not_bids.txt extra_data/ ``` #### 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 config object on the options object passed during javascript usage. The basic configuration format is outlined below. All configuration is optional. ```JSON { "ignore": [], "warn": [], "error": [], "ignoredFiles": [] } ``` `ignoredFiles` takes a list of file paths or glob patterns you'd like to ignore. Lets say we want to ignore all files and sub-directory under `/derivatives/`. **This is not the same syntax as used in the .bidsignore file** ```JSON { "ignoredFiles": ["/derivatives/**"] } ``` Note that adding two stars `**` in path makes validator recognize all files and sub-dir to be ignored. `ignore`, `warn`, and `error` take lists of issue codes or issue keys and change the severity of those issues so they are either ignored or reported as warnings or errors. You can find a list of all available issues at [utils/issues/list](https://github.com/bids-standard/bids-validator/tree/master/utils/issues/list.js). Some issues may be ignored by default, but can be elevated to warnings or errors. These provide a way to check for common things that are more specific than BIDS compatibility. An example is a check for the presence of a T1w modality. The following would raise an error if no T1W image was found in a dataset. ```JSON { "error": ["NO_T1W"] } ``` In addition to issue codes and keys these lists can also contain objects with and "and" or "or" properties set to arrays of codes or keys. These allow some level of conditional logic when configuring issues. For example: ```JSON { "ignore": [ { "and": [ "ECHO_TIME_GREATER_THAN", "ECHO_TIME_NOT_DEFINED" ] } ] } ``` In the above example the two issues will only be ignored if both of them are triggered during validation. ```JSON { "ignore": [ { "and": [ "ECHO_TIME_GREATER_THAN", "ECHO_TIME_NOT_DEFINED" { "or": [ "ECHO_TIME1-2_NOT_DEFINED", "ECHO_TIME_MUST_DEFINE" ] } ] } ] } ``` And in this example the listed issues will only be ignored if `ECHO_TIME_GREATER_THAN`, `ECHO_TIME_NOT_DEFINED` and either `ECHO_TIME1-2_NOT_DEFINED` or `ECHO_TIME_MUST_DEFINE` are triggered during validation. "or" arrays are not supported at the lowest level because it wouldn't add any functionality. For example the following is not supported. ```JSON { "ignore": [ { "or": [ "ECHO_TIME_GREATER_THAN", "ECHO_TIME_NOT_DEFINED" ] } ] } ``` because it would be functionally the same as this: ```JSON { "ignore": [ "ECHO_TIME_GREATER_THAN", "ECHO_TIME_NOT_DEFINED" ] } ``` For passing a configuration while using the bids-validator on the command line, note that you **have to specify at least two configurations of a given type**, because an array is expected. For example, the following code will ignore empty file errors (99) and files that cannot be read (44): ``` 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](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 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. ## Python Library 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 bids_validator` (requires python and pip). #### Example ``` >>> 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 To develop locally, clone the project and run `yarn` 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` #### 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 `yarn 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 `yarn web-export` #### Testing To start the test suite run `npm test` from the project root. `npm 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`. Platform: UNKNOWN Classifier: Development Status :: 3 - Alpha Classifier: Environment :: Console Classifier: Intended Audience :: Science/Research Classifier: License :: OSI Approved :: MIT License Classifier: Operating System :: OS Independent Classifier: Programming Language :: Python Classifier: Topic :: Scientific/Engineering Description-Content-Type: text/markdown python-bids-validator-1.2.4/bids_validator.egg-info/SOURCES.txt000066400000000000000000000012531352056404100243060ustar00rootroot00000000000000MANIFEST.in README.md setup.cfg setup.py versioneer.py bids_validator/__init__.py bids_validator/_version.py bids_validator/bids_validator.py bids_validator.egg-info/PKG-INFO bids_validator.egg-info/SOURCES.txt bids_validator.egg-info/dependency_links.txt bids_validator.egg-info/top_level.txt bids_validator/rules/associated_data_rules.json bids_validator/rules/file_level_rules.json bids_validator/rules/fixed_top_level_names.json bids_validator/rules/path.json bids_validator/rules/phenotypic_rules.json bids_validator/rules/session_level_rules.json bids_validator/rules/subject_level_rules.json bids_validator/rules/top_level_rules.json bids_validator/tsv/non_custom_columns.jsonpython-bids-validator-1.2.4/bids_validator.egg-info/dependency_links.txt000066400000000000000000000000011352056404100264670ustar00rootroot00000000000000 python-bids-validator-1.2.4/bids_validator.egg-info/top_level.txt000066400000000000000000000000171352056404100251510ustar00rootroot00000000000000bids_validator python-bids-validator-1.2.4/bids_validator/000077500000000000000000000000001352056404100207275ustar00rootroot00000000000000python-bids-validator-1.2.4/bids_validator/__init__.py000066400000000000000000000003161352056404100230400ustar00rootroot00000000000000"""BIDS validator common Python package.""" from ._version import get_versions from .bids_validator import BIDSValidator __version__ = get_versions()['version'] __all__ = ['BIDSValidator'] del get_versions python-bids-validator-1.2.4/bids_validator/_version.py000066400000000000000000000007611352056404100231310ustar00rootroot00000000000000 # This file was generated by 'versioneer.py' (0.18) from # revision-control system data, or from the parent directory name of an # unpacked source archive. Distribution tarballs contain a pre-generated copy # of this file. import json version_json = ''' { "date": "2019-05-31T10:22:43-0700", "dirty": false, "error": null, "full-revisionid": "fa00fd70c8931fa8477b2157bdea219a4564f0da", "version": "1.2.4" } ''' # END VERSION_JSON def get_versions(): return json.loads(version_json) python-bids-validator-1.2.4/bids_validator/bids_validator.py000066400000000000000000000135471352056404100243010ustar00rootroot00000000000000"""Validation class for BIDS projects.""" import re import os import json class BIDSValidator(): """An object for BIDS (Brain Imaging Data Structure) verification in a data. The main method of this class is `is_bids()`. You should use it for checking whether a file path compatible with BIDS. Parameters ---------- index_associated : bool, default: True Specifies if an associated data should be checked. If it is true then any file paths in directories `code/`, `derivatives/`, `sourcedata/` and `stimuli/` will pass the validation, else they won't. Examples -------- >>> from bids.grabbids 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", #wrong extension >>> "/participants.tsv"] >>> for filepath in filepaths: >>> print( validator.is_bids(filepath) ) True False True """ def __init__(self, index_associated=True): self.dir_rules=os.path.join(os.path.dirname(__file__)) + "/rules/" self.index_associated = index_associated def is_bids(self, path): """Checks if a file path appropriate for BIDS. Main method of the validator. uses other class methods for checking different aspects of the file path. Parameters ---------- path: string A path of a file you want to check. Examples -------- >>> from bids.grabbids import BIDSValidator >>> validator = BIDSValidator() >>> validator.is_bids("/sub-01/ses-test/anat/sub-01_ses-test_rec-CSD_run-23_T1w.nii.gz") True >>> validator.is_bids("/sub-01/ses-test/sub-01_run-01_dwi.bvec") # missed session in the filename False """ conditions = [] conditions.append(self.is_top_level(path)) conditions.append(self.is_associated_data(path)) conditions.append(self.is_session_level(path)) conditions.append(self.is_subject_level(path)) conditions.append(self.is_phenotypic(path)) conditions.append(self.is_file(path)) return (any(conditions)) def is_top_level(self, path): ''' Check if the file has appropriate name for a top-level file. ''' with open(self.dir_rules + 'fixed_top_level_names.json', 'r') as f: fixed_top_level_json = json.load(f) fixed_top_level_names = fixed_top_level_json['fixed_top_level_names'] regexps = self.get_regular_expressions(self.dir_rules + 'top_level_rules.json') conditions = [False if re.compile(x).search(path) is None else True for x in regexps] conditions.append(path in fixed_top_level_names) return (any(conditions)) def is_associated_data(self, path): ''' Check if file is appropriate associated data. ''' if not self.index_associated: return False regexps = self.get_regular_expressions(self.dir_rules + 'associated_data_rules.json') conditions = [(re.compile(x).search(path) is not None) for x in regexps] return any(conditions) def is_session_level(self, path): ''' Check if the file has appropriate name for a session level. ''' regexps = self.get_regular_expressions(self.dir_rules + 'session_level_rules.json') conditions = [self.conditional_match(x, path) for x in regexps] return (any(conditions)) def is_subject_level(self, path): ''' Check if the file has appropriate name for a subject level. ''' regexps = self.get_regular_expressions(self.dir_rules + 'subject_level_rules.json') conditions = [(re.compile(x).search(path) is not None) for x in regexps] return (any(conditions)) def is_phenotypic(self, path): ''' Check if file is phenotypic data. ''' regexps = self.get_regular_expressions(self.dir_rules + 'phenotypic_rules.json') conditions = [(re.compile(x).search(path) is not None) for x in regexps] return (any(conditions)) def is_file(self, path): ''' Check if file is phenotypic data. ''' regexps = self.get_regular_expressions(self.dir_rules + 'file_level_rules.json') conditions = [(re.compile(x).search(path) is not None) for x in regexps] return (any(conditions)) def get_regular_expressions(self, fileName): regexps = [] with open(fileName, 'r') as f: rules = json.load(f) for key in list(rules.keys()): rule = rules[key] regexp = rule["regexp"] if "tokens" in rule: tokens = rule["tokens"] for token in list(tokens): regexp = regexp.replace(token, "|".join(tokens[token])) regexps.append(regexp) return regexps def get_path_values(self, path): ''' Takes a file path and returns values found for the following path keys: sub- ses- ''' values = {} regexps = self.get_regular_expressions(self.dir_rules + 'path.json') # capture subject for paths in ['sub', 'ses']: match = re.compile(regexps[paths]).findall(path) values[paths] = match[1] if match & match[1] else None return values def conditional_match(self, expression, path): match = re.compile(expression).findall(path) match = match[0] if len(match) >= 1 else False # adapted from JS code and JS does not support conditional groups if (match): if ((match[1] == match[2][1:]) | (not match[1])): return True else: return False else: return False python-bids-validator-1.2.4/bids_validator/rules/000077500000000000000000000000001352056404100220615ustar00rootroot00000000000000python-bids-validator-1.2.4/bids_validator/rules/associated_data_rules.json000066400000000000000000000003641352056404100273010ustar00rootroot00000000000000{ "associated_data": { "regexp": "^\\/(?:@@@_associated_data_type_@@@)\\/(?:.*)$", "tokens": { "@@@_associated_data_type_@@@": [ "code", "derivatives", "sourcedata", "stimuli" ] } } } python-bids-validator-1.2.4/bids_validator/rules/file_level_rules.json000066400000000000000000000150301352056404100262730ustar00rootroot00000000000000{ "anat": { "regexp": "^\\/(sub-[a-zA-Z0-9]+)\\/(?:(ses-[a-zA-Z0-9]+)\\/)?anat\\/\\1(_\\2)?(?:_acq-[a-zA-Z0-9]+)?(?:_ce-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?_(?:@@@_anat_suffixes_@@@)\\.(@@@_anat_ext_@@@)$", "tokens": { "@@@_anat_suffixes_@@@": [ "T1w", "T2w", "T1map", "T2map", "T1rho", "FLAIR", "PD", "PDT2", "inplaneT1", "inplaneT2", "angio", "SWImagandphase", "T2star", "FLASH", "PDmap", "photo" ], "@@@_anat_ext_@@@": ["nii\\.gz", "nii", "json"] } }, "anat_defacemask": { "regexp": "^\\/(sub-[a-zA-Z0-9]+)\\/(?:(ses-[a-zA-Z0-9]+)\\/)?anat\\/\\1(_\\2)?(?:_acq-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(?:_mod-(?:@@@_anat_suffixes_@@@))?_defacemask\\.(@@@_anat_ext_@@@)$", "tokens": { "@@@_anat_suffixes_@@@": [ "T1w", "T2w", "T1map", "T2map", "T1rho", "FLAIR", "PD", "PDT2", "inplaneT1", "inplaneT2", "angio", "SWImagandphase", "T2star", "FLASH", "PDmap", "photo" ], "@@@_anat_ext_@@@": ["nii.gz", "nii"] } }, "behavioral": { "regexp": "^\\/(sub-[a-zA-Z0-9]+)\\/(?:(ses-[a-zA-Z0-9]+)\\/)?beh\\/\\1(_\\2)?_task-[a-zA-Z0-9]+(?:_acq-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(?:@@@_behavioral_ext_@@@)$", "tokens": { "@@@_behavioral_ext_@@@": [ "_beh\\.json", "_beh\\.tsv", "_events\\.json", "_events\\.tsv", "_physio\\.tsv\\.gz", "_stim\\.tsv\\.gz", "_physio\\.json", "_stim\\.json" ] } }, "cont": { "regexp": "^\\/(sub-[a-zA-Z0-9]+)\\/(?:(ses-[a-zA-Z0-9]+)\\/)?(?:func|beh)\\/\\1(_\\2)?_task-[a-zA-Z0-9]+(?:_acq-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(?:_recording-[a-zA-Z0-9]+)?(?:@@@_cont_ext_@@@)$", "tokens": { "@@@_cont_ext_@@@": [ "_physio\\.tsv\\.gz", "_stim\\.tsv\\.gz", "_physio\\.json", "_stim\\.json" ] } }, "dwi": { "regexp": "^\\/(sub-[a-zA-Z0-9]+)\\/(?:(ses-[a-zA-Z0-9]+)\\/)?dwi\\/\\1(_\\2)?(?:_acq-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_dir-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?_(?:@@@_dwi_type_@@@)\\.(@@@_dwi_ext_@@@)$", "tokens": { "@@@_dwi_ext_@@@": ["nii\\.gz", "nii", "json", "bvec", "bval"], "@@@_dwi_type_@@@": ["dwi", "sbref"] } }, "eeg": { "regexp": "^\\/(sub-[a-zA-Z0-9]+)\\/(?:(ses-[a-zA-Z0-9]+)\\/)?eeg\\/\\1(_\\2)?(?:_task-[a-zA-Z0-9]+)?(?:_acq-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(?:_proc-[a-zA-Z0-9]+)?(?:_part-[0-9]+)?(_eeg\\.(@@@_eeg_type_@@@)|(@@@_eeg_ext_@@@))$", "tokens": { "@@@_eeg_type_@@@": ["vhdr", "vmrk", "eeg", "edf", "bdf", "set", "fdt"], "@@@_eeg_ext_@@@": [ "_events\\.json", "_events\\.tsv", "_electrodes\\.json", "_electrodes\\.tsv", "_channels\\.json", "_channels\\.tsv", "_eeg\\.json", "_coordsystem\\.json", "_photo\\.jpg" ] } }, "field_map": { "regexp": "^\\/(sub-[a-zA-Z0-9]+)\\/(?:(ses-[a-zA-Z0-9]+)\\/)?fmap\\/\\1(_\\2)?(?:_acq-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_dir-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?_(?:@@@_field_map_type_@@@)\\.(@@@_field_map_ext_@@@)$", "tokens": { "@@@_field_map_type_@@@": [ "phasediff", "phase1", "phase2", "magnitude1", "magnitude2", "magnitude", "fieldmap", "epi" ], "@@@_field_map_ext_@@@": ["nii\\.gz", "nii", "json"] } }, "field_map_main_nii": { "regexp": "^\\/(sub-[a-zA-Z0-9]+)\\/(?:(ses-[a-zA-Z0-9]+)\\/)?fmap\\/\\1(_\\2)?(?:_acq-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_dir-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?_(?:@@@_field_map_type_@@@)\\.(@@@_field_map_ext_@@@)$", "tokens": { "@@@_field_map_type_@@@": [ "phasediff", "phase1", "phase2", "fieldmap", "epi" ], "@@@_field_map_ext_@@@": ["nii\\.gz", "nii"] } }, "func": { "regexp": "^\\/(sub-[a-zA-Z0-9]+)\\/(?:(ses-[a-zA-Z0-9]+)\\/)?func\\/\\1(_\\2)?_task-[a-zA-Z0-9]+(?:_acq-[a-zA-Z0-9]+)?(?:_ce-[a-zA-Z0-9]+)?(?:_dir-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(?:_echo-[0-9]+)?(?:@@@_func_ext_@@@)$", "tokens": { "@@@_func_ext_@@@": [ "_bold\\.nii\\.gz", "_bold\\.nii", "_bold\\.json", "_cbv\\.nii\\.gz", "_cbv\\.nii", "_cbv\\.json", "_sbref\\.nii\\.gz", "_sbref\\.json", "_events\\.json", "_events\\.tsv", "_physio\\.tsv\\.gz", "_stim\\.tsv\\.gz", "_physio\\.json", "_stim\\.json", "_defacemask\\.nii\\.gz", "_defacemask\\.nii" ] } }, "func_bold": { "regexp": "^\\/(sub-[a-zA-Z0-9]+)\\/(?:(ses-[a-zA-Z0-9]+)\\/)?func\\/\\1(_\\2)?_task-[a-zA-Z0-9]+(?:_acq-[a-zA-Z0-9]+)?(?:_ce-[a-zA-Z0-9]+)?(?:_dir-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(?:_echo-[0-9]+)?(?:@@@_func_bold_ext_@@@)$", "tokens": { "@@@_func_bold_ext_@@@": [ "_bold\\.nii\\.gz", "_bold\\.nii", "_sbref\\.nii\\.gz", "_sbref\\.nii" ] } }, "ieeg": { "regexp": "^\\/(sub-[a-zA-Z0-9]+)\\/(?:(ses-[a-zA-Z0-9]+)\\/)?ieeg\\/\\1(_\\2)?(?:_task-[a-zA-Z0-9]+)?(?:_acq-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(?:_proc-[a-zA-Z0-9]+)?(?:_part-[0-9]+)?(?:_space-[a-zA-Z0-9]+)?(_ieeg\\.(@@@_ieeg_type_@@@)|(@@@_ieeg_ext_@@@))$", "tokens": { "@@@_ieeg_type_@@@": [ "edf", "vhdr", "vmrk", "eeg", "set", "fdt", "nwb", "mef" ], "@@@_ieeg_ext_@@@": [ "_events\\.json", "_events\\.tsv", "_electrodes\\.json", "_electrodes\\.tsv", "_channels\\.json", "_channels\\.tsv", "_ieeg\\.json", "_coordsystem\\.json", "_photo\\.jpg" ] } }, "meg": { "regexp": "^\\/(sub-[a-zA-Z0-9]+)\\/(?:(ses-[a-zA-Z0-9]+)\\/)?meg\\/\\1(_\\2)?(?:_task-[a-zA-Z0-9]+)?(?:_acq-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(?:_proc-[a-zA-Z0-9]+)?(?:_part-[0-9]+)?(_meg(@@@_meg_type_@@@\\/.*|\\/.*)|(@@@_meg_ext_@@@))$", "tokens": { "@@@_meg_type_@@@": ["\\.fif", "\\.ds"], "@@@_meg_ext_@@@": [ "_events\\.json", "_events\\.tsv", "_channels\\.json", "_channels\\.tsv", "_meg\\.json", "_coordsystem\\.json", "_photo\\.jpg", "_headshape\\.pos" ] } }, "stimuli": { "regexp": "^\\/(?:stimuli)\\/(?:.*)$" } } python-bids-validator-1.2.4/bids_validator/rules/fixed_top_level_names.json000066400000000000000000000003541352056404100273110ustar00rootroot00000000000000{ "fixed_top_level_names": [ "/README", "/CHANGES", "/dataset_description.json", "/participants.tsv", "/participants.json", "/phasediff.json", "/phase1.json", "/phase2.json", "/fieldmap.json" ] } python-bids-validator-1.2.4/bids_validator/rules/path.json000066400000000000000000000001571352056404100237130ustar00rootroot00000000000000{ "path": { "sub": "/^/sub-([a-zA-Z0-9]+)/)", "ses": "/^/sub-[a-zA-Z0-9]+/ses-([a-zA-Z0-9]+)/" } } python-bids-validator-1.2.4/bids_validator/rules/phenotypic_rules.json000066400000000000000000000001331352056404100263450ustar00rootroot00000000000000{ "phenotypic_data": { "regexp": "^\\/(?:phenotype)\\/(?:.*\\.tsv|.*\\.json)$" } } python-bids-validator-1.2.4/bids_validator/rules/session_level_rules.json000066400000000000000000000050441352056404100270430ustar00rootroot00000000000000{ "scans": { "regexp": "^\\/(sub-[a-zA-Z0-9]+)\\/(?:(ses-[a-zA-Z0-9]+)\\/)?\\1(_\\2)?(@@@_scat_ext_@@@)$", "tokens": { "@@@_scat_ext_@@@": ["_scans.tsv", "_scans.json"] } }, "func_ses": { "regexp": "^\\/(sub-[a-zA-Z0-9]+)\\/(?:(ses-[a-zA-Z0-9]+)\\/)?\\1(_\\2)?task-[a-zA-Z0-9]+(?:_acq-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(?:_echo-[0-9]+)?(@@@_func_ses_ext_@@@)$", "tokens": { "@@@_func_ses_ext_@@@": [ "_bold.json", "_sbref.json", "_events.json", "_events.tsv", "_physio.json", "_stim.json" ] } }, "anat_ses": { "regexp": "^\\/(sub-[a-zA-Z0-9]+)\\/(?:(ses-[a-zA-Z0-9]+)\\/)?\\1(_\\2)?(?:_acq-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_run-[0-9]+_)?(@@@_anat_ses_type_@@@).json$", "tokens": { "@@@_anat_ses_type_@@@": [ "T1w", "T2w", "T1map", "T2map", "T1rho", "FLAIR", "PD", "PDT2", "inplaneT1", "inplaneT2", "angio", "defacemask", "SWImagandphase" ] } }, "dwi_ses": { "regexp": "^\\/(sub-[a-zA-Z0-9]+)\\/(?:(ses-[a-zA-Z0-9]+)\\/)?\\1(_\\2)?(?:_acq-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(?:_)?dwi.(?:@@@_dwi_ses_ext_@@@)$", "tokens": { "@@@_dwi_ses_ext_@@@": ["json", "bval", "bvec"] } }, "meg_ses": { "regexp": "^\\/(sub-[a-zA-Z0-9]+)\\/(?:(ses-[a-zA-Z0-9]+)\\/)?\\1(_\\2)?(?:_task-[a-zA-Z0-9]+)?(?:_acq-[a-zA-Z0-9]+)?(?:_proc-[a-zA-Z0-9]+)?(@@@_meg_ses_type_@@@)$", "tokens": { "@@@_meg_ses_type_@@@": [ "_events.tsv", "_channels.tsv", "_meg.json", "_coordsystem.json", "_photo.jpg", "_headshape.pos" ] } }, "eeg_ses": { "regexp": "^\\/(sub-[a-zA-Z0-9]+)\\/(?:(ses-[a-zA-Z0-9]+)\\/)?\\1(_\\2)?(?:_task-[a-zA-Z0-9]+)?(?:_acq-[a-zA-Z0-9]+)?(?:_proc-[a-zA-Z0-9]+)?(@@@_eeg_ses_type_@@@)$", "tokens": { "@@@_eeg_ses_type_@@@": [ "_events.tsv", "_channels.tsv", "_electrodes.tsv", "_eeg.json", "_coordsystem.json", "_photo.jpg" ] } }, "ieeg_ses": { "regexp": "^\\/(sub-[a-zA-Z0-9]+)\\/(?:(ses-[a-zA-Z0-9]+)\\/)?\\1(_\\2)?(?:_task-[a-zA-Z0-9]+)?(?:_acq-[a-zA-Z0-9]+)?(?:_proc-[a-zA-Z0-9]+)?(?:_space-[a-zA-Z0-9]+)?(@@@_ieeg_ses_type_@@@)$", "tokens": { "@@@_ieeg_ses_type_@@@": [ "_events.tsv", "_channels.tsv", "_electrodes.tsv", "_ieeg.json", "_coordsystem.json", "_photo.jpg" ] } } } python-bids-validator-1.2.4/bids_validator/rules/subject_level_rules.json000066400000000000000000000003101352056404100270060ustar00rootroot00000000000000{ "subject_level": { "regexp": "^\\/(sub-[a-zA-Z0-9]+)\\/\\1(@@@_subject_level_ext_@@@)$", "tokens": { "@@@_subject_level_ext_@@@": ["_sessions\\.tsv", "_sessions\\.json"] } } } python-bids-validator-1.2.4/bids_validator/rules/top_level_rules.json000066400000000000000000000050461352056404100261640ustar00rootroot00000000000000{ "func_top": { "regexp": "^\\/(?:ses-[a-zA-Z0-9]+_)?(?:recording-[a-zA-Z0-9]+_)?task-[a-zA-Z0-9]+(?:_acq-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(?:_echo-[0-9]+)?(@@@_func_top_ext_@@@)$", "tokens": { "@@@_func_top_ext_@@@": [ "_bold\\.json", "_sbref\\.json", "_events\\.json", "_events\\.tsv", "_physio\\.json", "_stim\\.json", "_beh\\.json" ] } }, "anat_top": { "regexp": "^\\/(?:ses-[a-zA-Z0-9]+_)?(?:acq-[a-zA-Z0-9]+_)?(?:rec-[a-zA-Z0-9]+_)?(?:run-[0-9]+_)?(@@@_anat_suffixes_@@@)\\.json$", "tokens": { "@@@_anat_suffixes_@@@": [ "T1w", "T2w", "T1map", "T2map", "T1rho", "FLAIR", "PD", "PDT2", "inplaneT1", "inplaneT2", "angio", "SWImagandphase", "T2star", "FLASH", "PDmap", "photo" ] } }, "dwi_top": { "regexp": "^\\/(?:ses-[a-zA-Z0-9]+_)?(?:acq-[a-zA-Z0-9]+_)?(?:rec-[a-zA-Z0-9]+_)?(?:run-[0-9]+_)?dwi\\.(?:@@@_dwi_top_ext_@@@)$", "tokens": { "@@@_dwi_top_ext_@@@": ["json", "bval", "bvec"] } }, "eeg_top": { "regexp": "^\\/(?:ses-[a-zA-Z0-9]+_)?task-[a-zA-Z0-9]+(?:_acq-[a-zA-Z0-9]+)?(?:_proc-[a-zA-Z0-9]+)?(?:@@@_eeg_top_ext_@@@)$", "tokens": { "@@@_eeg_top_ext_@@@": [ "_eeg\\.json", "_channels\\.tsv", "_electrodes\\.tsv", "_photo\\.jpg", "_coordsystem\\.json" ] } }, "ieeg_top": { "regexp": "^\\/(?:ses-[a-zA-Z0-9]+_)?task-[a-zA-Z0-9]+(?:_acq-[a-zA-Z0-9]+)?(?:_proc-[a-zA-Z0-9]+)?(?:@@@_ieeg_top_ext_@@@)$", "tokens": { "@@@_ieeg_top_ext_@@@": [ "_ieeg\\.json", "_channels\\.tsv", "_electrodes\\.tsv", "_photo\\.jpg", "_coordsystem\\.json" ] } }, "meg_top": { "regexp": "^\\/(?:ses-[a-zA-Z0-9]+_)?task-[a-zA-Z0-9]+(?:_acq-[a-zA-Z0-9]+)?(?:_proc-[a-zA-Z0-9]+)?(?:@@@_meg_top_ext_@@@)$", "tokens": { "@@@_meg_top_ext_@@@": [ "_meg\\.json", "_channels\\.tsv", "_photo\\.jpg", "_coordsystem\\.json" ] } }, "multi_dir_fieldmap": { "regexp": "^\\/(?:acq-[a-zA-Z0-9]+_)?(?:dir-[a-zA-Z0-9]+_)epi\\.json$" }, "other_top_files": { "regexp": "^\\/(?:ses-[a-zA-Z0-9]+_)?(?:recording-[a-zA-Z0-9]+_)?(?:task-[a-zA-Z0-9]+_)?(?:acq-[a-zA-Z0-9]+_)?(?:rec-[a-zA-Z0-9]+_)?(?:run-[0-9]+_)?(@@@_other_top_files_ext_@@@)$", "tokens": { "@@@_other_top_files_ext_@@@": ["physio\\.json", "stim\\.json"] } } } python-bids-validator-1.2.4/bids_validator/tsv/000077500000000000000000000000001352056404100215435ustar00rootroot00000000000000python-bids-validator-1.2.4/bids_validator/tsv/non_custom_columns.json000066400000000000000000000013461352056404100263660ustar00rootroot00000000000000{ "channels": [ "description", "high_cutoff", "low_cutoff", "name", "notch", "sampling_frequency", "software_filters", "status", "status_description", "type", "units", "reference", "group" ], "electrodes": [ "name", "x", "y", "z", "size", "material", "manufacturer", "group", "hemisphere", "type", "impedance", "dimension" ], "events": [ "duration", "HED", "onset", "trial_type", "response_time", "stim_file", "sample", "value" ], "misc": [], "participants": ["participant_id"], "phenotype": ["participant_id"], "scans": ["acq_time", "filename"], "sessions": ["acq_time", "session_id"] } python-bids-validator-1.2.4/setup.cfg000066400000000000000000000017261352056404100175700ustar00rootroot00000000000000[metadata] name = bids-validator url = https://github.com/bids-standard/bids-validator author = PyBIDS developers author_email = bids-discussion@googlegroups.com maintainer = BIDS Developers maintainer_email = bids-discussion@googlegroups.com description = Validator for the Brain Imaging Data Structure long_description = file:README.md long_description_content_type = text/markdown license = MIT classifiers = Development Status :: 3 - Alpha Environment :: Console Intended Audience :: Science/Research License :: OSI Approved :: MIT License Operating System :: OS Independent Programming Language :: Python Topic :: Scientific/Engineering [options] packages = find: [options.package_data] bids_validator = rules/*.json tsv/*.json [bdist_wheel] universal = 1 [versioneer] vcs = git style = pep440 versionfile_source = bids_validator/_version.py versionfile_build = bids_validator/_version.py tag_prefix = parentdir_prefix = [egg_info] tag_build = tag_date = 0 python-bids-validator-1.2.4/setup.py000066400000000000000000000002301352056404100174460ustar00rootroot00000000000000#!/usr/bin/env python from setuptools import setup import versioneer setup(version=versioneer.get_version(), cmdclass=versioneer.get_cmdclass()) python-bids-validator-1.2.4/versioneer.py000066400000000000000000002060031352056404100204750ustar00rootroot00000000000000 # Version: 0.18 """The Versioneer - like a rocketeer, but for versions. The Versioneer ============== * like a rocketeer, but for versions! * https://github.com/warner/python-versioneer * Brian Warner * License: Public Domain * Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, 3.5, 3.6, and pypy * [![Latest Version] (https://pypip.in/version/versioneer/badge.svg?style=flat) ](https://pypi.python.org/pypi/versioneer/) * [![Build Status] (https://travis-ci.org/warner/python-versioneer.png?branch=master) ](https://travis-ci.org/warner/python-versioneer) This is a tool for managing a recorded version number in distutils-based python projects. The goal is to remove the tedious and error-prone "update the embedded version string" step from your release process. Making a new release should be as easy as recording a new tag in your version-control system, and maybe making new tarballs. ## Quick Install * `pip install versioneer` to somewhere to your $PATH * add a `[versioneer]` section to your setup.cfg (see below) * run `versioneer install` in your source tree, commit the results ## Version Identifiers Source trees come from a variety of places: * a version-control system checkout (mostly used by developers) * a nightly tarball, produced by build automation * a snapshot tarball, produced by a web-based VCS browser, like github's "tarball from tag" feature * a release tarball, produced by "setup.py sdist", distributed through PyPI Within each source tree, the version identifier (either a string or a number, this tool is format-agnostic) can come from a variety of places: * ask the VCS tool itself, e.g. "git describe" (for checkouts), which knows about recent "tags" and an absolute revision-id * the name of the directory into which the tarball was unpacked * an expanded VCS keyword ($Id$, etc) * a `_version.py` created by some earlier build step For released software, the version identifier is closely related to a VCS tag. Some projects use tag names that include more than just the version string (e.g. "myproject-1.2" instead of just "1.2"), in which case the tool needs to strip the tag prefix to extract the version identifier. For unreleased software (between tags), the version identifier should provide enough information to help developers recreate the same tree, while also giving them an idea of roughly how old the tree is (after version 1.2, before version 1.3). Many VCS systems can report a description that captures this, for example `git describe --tags --dirty --always` reports things like "0.7-1-g574ab98-dirty" to indicate that the checkout is one revision past the 0.7 tag, has a unique revision id of "574ab98", and is "dirty" (it has uncommitted changes. The version identifier is used for multiple purposes: * to allow the module to self-identify its version: `myproject.__version__` * to choose a name and prefix for a 'setup.py sdist' tarball ## Theory of Operation Versioneer works by adding a special `_version.py` file into your source tree, where your `__init__.py` can import it. This `_version.py` knows how to dynamically ask the VCS tool for version information at import time. `_version.py` also contains `$Revision$` markers, and the installation process marks `_version.py` to have this marker rewritten with a tag name during the `git archive` command. As a result, generated tarballs will contain enough information to get the proper version. To allow `setup.py` to compute a version too, a `versioneer.py` is added to the top level of your source tree, next to `setup.py` and the `setup.cfg` that configures it. This overrides several distutils/setuptools commands to compute the version when invoked, and changes `setup.py build` and `setup.py sdist` to replace `_version.py` with a small static file that contains just the generated version data. ## Installation See [INSTALL.md](./INSTALL.md) for detailed installation instructions. ## Version-String Flavors Code which uses Versioneer can learn about its version string at runtime by importing `_version` from your main `__init__.py` file and running the `get_versions()` function. From the "outside" (e.g. in `setup.py`), you can import the top-level `versioneer.py` and run `get_versions()`. Both functions return a dictionary with different flavors of version information: * `['version']`: A condensed version string, rendered using the selected style. This is the most commonly used value for the project's version string. The default "pep440" style yields strings like `0.11`, `0.11+2.g1076c97`, or `0.11+2.g1076c97.dirty`. See the "Styles" section below for alternative styles. * `['full-revisionid']`: detailed revision identifier. For Git, this is the full SHA1 commit id, e.g. "1076c978a8d3cfc70f408fe5974aa6c092c949ac". * `['date']`: Date and time of the latest `HEAD` commit. For Git, it is the commit date in ISO 8601 format. This will be None if the date is not available. * `['dirty']`: a boolean, True if the tree has uncommitted changes. Note that this is only accurate if run in a VCS checkout, otherwise it is likely to be False or None * `['error']`: if the version string could not be computed, this will be set to a string describing the problem, otherwise it will be None. It may be useful to throw an exception in setup.py if this is set, to avoid e.g. creating tarballs with a version string of "unknown". Some variants are more useful than others. Including `full-revisionid` in a bug report should allow developers to reconstruct the exact code being tested (or indicate the presence of local changes that should be shared with the developers). `version` is suitable for display in an "about" box or a CLI `--version` output: it can be easily compared against release notes and lists of bugs fixed in various releases. The installer adds the following text to your `__init__.py` to place a basic version in `YOURPROJECT.__version__`: from ._version import get_versions __version__ = get_versions()['version'] del get_versions ## Styles The setup.cfg `style=` configuration controls how the VCS information is rendered into a version string. The default style, "pep440", produces a PEP440-compliant string, equal to the un-prefixed tag name for actual releases, and containing an additional "local version" section with more detail for in-between builds. For Git, this is TAG[+DISTANCE.gHEX[.dirty]] , using information from `git describe --tags --dirty --always`. For example "0.11+2.g1076c97.dirty" indicates that the tree is like the "1076c97" commit but has uncommitted changes (".dirty"), and that this commit is two revisions ("+2") beyond the "0.11" tag. For released software (exactly equal to a known tag), the identifier will only contain the stripped tag, e.g. "0.11". Other styles are available. See [details.md](details.md) in the Versioneer source tree for descriptions. ## Debugging Versioneer tries to avoid fatal errors: if something goes wrong, it will tend to return a version of "0+unknown". To investigate the problem, run `setup.py version`, which will run the version-lookup code in a verbose mode, and will display the full contents of `get_versions()` (including the `error` string, which may help identify what went wrong). ## Known Limitations Some situations are known to cause problems for Versioneer. This details the most significant ones. More can be found on Github [issues page](https://github.com/warner/python-versioneer/issues). ### Subprojects Versioneer has limited support for source trees in which `setup.py` is not in the root directory (e.g. `setup.py` and `.git/` are *not* siblings). The are two common reasons why `setup.py` might not be in the root: * Source trees which contain multiple subprojects, such as [Buildbot](https://github.com/buildbot/buildbot), which contains both "master" and "slave" subprojects, each with their own `setup.py`, `setup.cfg`, and `tox.ini`. Projects like these produce multiple PyPI distributions (and upload multiple independently-installable tarballs). * Source trees whose main purpose is to contain a C library, but which also provide bindings to Python (and perhaps other langauges) in subdirectories. Versioneer will look for `.git` in parent directories, and most operations should get the right version string. However `pip` and `setuptools` have bugs and implementation details which frequently cause `pip install .` from a subproject directory to fail to find a correct version string (so it usually defaults to `0+unknown`). `pip install --editable .` should work correctly. `setup.py install` might work too. Pip-8.1.1 is known to have this problem, but hopefully it will get fixed in some later version. [Bug #38](https://github.com/warner/python-versioneer/issues/38) is tracking this issue. The discussion in [PR #61](https://github.com/warner/python-versioneer/pull/61) describes the issue from the Versioneer side in more detail. [pip PR#3176](https://github.com/pypa/pip/pull/3176) and [pip PR#3615](https://github.com/pypa/pip/pull/3615) contain work to improve pip to let Versioneer work correctly. Versioneer-0.16 and earlier only looked for a `.git` directory next to the `setup.cfg`, so subprojects were completely unsupported with those releases. ### Editable installs with setuptools <= 18.5 `setup.py develop` and `pip install --editable .` allow you to install a project into a virtualenv once, then continue editing the source code (and test) without re-installing after every change. "Entry-point scripts" (`setup(entry_points={"console_scripts": ..})`) are a convenient way to specify executable scripts that should be installed along with the python package. These both work as expected when using modern setuptools. When using setuptools-18.5 or earlier, however, certain operations will cause `pkg_resources.DistributionNotFound` errors when running the entrypoint script, which must be resolved by re-installing the package. This happens when the install happens with one version, then the egg_info data is regenerated while a different version is checked out. Many setup.py commands cause egg_info to be rebuilt (including `sdist`, `wheel`, and installing into a different virtualenv), so this can be surprising. [Bug #83](https://github.com/warner/python-versioneer/issues/83) describes this one, but upgrading to a newer version of setuptools should probably resolve it. ### Unicode version strings While Versioneer works (and is continually tested) with both Python 2 and Python 3, it is not entirely consistent with bytes-vs-unicode distinctions. Newer releases probably generate unicode version strings on py2. It's not clear that this is wrong, but it may be surprising for applications when then write these strings to a network connection or include them in bytes-oriented APIs like cryptographic checksums. [Bug #71](https://github.com/warner/python-versioneer/issues/71) investigates this question. ## Updating Versioneer To upgrade your project to a new release of Versioneer, do the following: * install the new Versioneer (`pip install -U versioneer` or equivalent) * edit `setup.cfg`, if necessary, to include any new configuration settings indicated by the release notes. See [UPGRADING](./UPGRADING.md) for details. * re-run `versioneer install` in your source tree, to replace `SRC/_version.py` * commit any changed files ## Future Directions This tool is designed to make it easily extended to other version-control systems: all VCS-specific components are in separate directories like src/git/ . The top-level `versioneer.py` script is assembled from these components by running make-versioneer.py . In the future, make-versioneer.py will take a VCS name as an argument, and will construct a version of `versioneer.py` that is specific to the given VCS. It might also take the configuration arguments that are currently provided manually during installation by editing setup.py . Alternatively, it might go the other direction and include code from all supported VCS systems, reducing the number of intermediate scripts. ## License To make Versioneer easier to embed, all its code is dedicated to the public domain. The `_version.py` that it creates is also in the public domain. Specifically, both are released under the Creative Commons "Public Domain Dedication" license (CC0-1.0), as described in https://creativecommons.org/publicdomain/zero/1.0/ . """ from __future__ import print_function try: import configparser except ImportError: import ConfigParser as configparser import errno import json import os import re import subprocess import sys class VersioneerConfig: """Container for Versioneer configuration parameters.""" def get_root(): """Get the project root directory. We require that all commands are run from the project root, i.e. the directory that contains setup.py, setup.cfg, and versioneer.py . """ root = os.path.realpath(os.path.abspath(os.getcwd())) setup_py = os.path.join(root, "setup.py") versioneer_py = os.path.join(root, "versioneer.py") if not (os.path.exists(setup_py) or os.path.exists(versioneer_py)): # allow 'python path/to/setup.py COMMAND' root = os.path.dirname(os.path.realpath(os.path.abspath(sys.argv[0]))) setup_py = os.path.join(root, "setup.py") versioneer_py = os.path.join(root, "versioneer.py") if not (os.path.exists(setup_py) or os.path.exists(versioneer_py)): err = ("Versioneer was unable to run the project root directory. " "Versioneer requires setup.py to be executed from " "its immediate directory (like 'python setup.py COMMAND'), " "or in a way that lets it use sys.argv[0] to find the root " "(like 'python path/to/setup.py COMMAND').") raise VersioneerBadRootError(err) try: # Certain runtime workflows (setup.py install/develop in a setuptools # tree) execute all dependencies in a single python process, so # "versioneer" may be imported multiple times, and python's shared # module-import table will cache the first one. So we can't use # os.path.dirname(__file__), as that will find whichever # versioneer.py was first imported, even in later projects. me = os.path.realpath(os.path.abspath(__file__)) me_dir = os.path.normcase(os.path.splitext(me)[0]) vsr_dir = os.path.normcase(os.path.splitext(versioneer_py)[0]) if me_dir != vsr_dir: print("Warning: build in %s is using versioneer.py from %s" % (os.path.dirname(me), versioneer_py)) except NameError: pass return root def get_config_from_root(root): """Read the project setup.cfg file to determine Versioneer config.""" # This might raise EnvironmentError (if setup.cfg is missing), or # configparser.NoSectionError (if it lacks a [versioneer] section), or # configparser.NoOptionError (if it lacks "VCS="). See the docstring at # the top of versioneer.py for instructions on writing your setup.cfg . setup_cfg = os.path.join(root, "setup.cfg") parser = configparser.SafeConfigParser() with open(setup_cfg, "r") as f: parser.readfp(f) VCS = parser.get("versioneer", "VCS") # mandatory def get(parser, name): if parser.has_option("versioneer", name): return parser.get("versioneer", name) return None cfg = VersioneerConfig() cfg.VCS = VCS cfg.style = get(parser, "style") or "" cfg.versionfile_source = get(parser, "versionfile_source") cfg.versionfile_build = get(parser, "versionfile_build") cfg.tag_prefix = get(parser, "tag_prefix") if cfg.tag_prefix in ("''", '""'): cfg.tag_prefix = "" cfg.parentdir_prefix = get(parser, "parentdir_prefix") cfg.verbose = get(parser, "verbose") return cfg class NotThisMethod(Exception): """Exception raised if a method is not valid for the current scenario.""" # these dictionaries contain VCS-specific tools LONG_VERSION_PY = {} HANDLERS = {} def register_vcs_handler(vcs, method): # decorator """Decorator to mark a method as the handler for a particular VCS.""" def decorate(f): """Store f in HANDLERS[vcs][method].""" if vcs not in HANDLERS: HANDLERS[vcs] = {} HANDLERS[vcs][method] = f return f return decorate def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=None): """Call the given command(s).""" assert isinstance(commands, list) p = None for c in commands: try: dispcmd = str([c] + args) # remember shell=False, so use git.cmd on windows, not just git p = subprocess.Popen([c] + args, cwd=cwd, env=env, stdout=subprocess.PIPE, stderr=(subprocess.PIPE if hide_stderr else None)) break except EnvironmentError: e = sys.exc_info()[1] if e.errno == errno.ENOENT: continue if verbose: print("unable to run %s" % dispcmd) print(e) return None, None else: if verbose: print("unable to find command, tried %s" % (commands,)) return None, None stdout = p.communicate()[0].strip() if sys.version_info[0] >= 3: stdout = stdout.decode() if p.returncode != 0: if verbose: print("unable to run %s (error)" % dispcmd) print("stdout was %s" % stdout) return None, p.returncode return stdout, p.returncode LONG_VERSION_PY['git'] = ''' # This file helps to compute a version number in source trees obtained from # git-archive tarball (such as those provided by githubs download-from-tag # feature). Distribution tarballs (built by setup.py sdist) and build # directories (produced by setup.py build) will contain a much shorter file # that just contains the computed version number. # This file is released into the public domain. Generated by # versioneer-0.18 (https://github.com/warner/python-versioneer) """Git implementation of _version.py.""" import errno import os import re import subprocess import sys def get_keywords(): """Get the keywords needed to look up the version information.""" # these strings will be replaced by git during git-archive. # setup.py/versioneer.py will grep for the variable names, so they must # each be defined on a line of their own. _version.py will just call # get_keywords(). git_refnames = "%(DOLLAR)sFormat:%%d%(DOLLAR)s" git_full = "%(DOLLAR)sFormat:%%H%(DOLLAR)s" git_date = "%(DOLLAR)sFormat:%%ci%(DOLLAR)s" keywords = {"refnames": git_refnames, "full": git_full, "date": git_date} return keywords class VersioneerConfig: """Container for Versioneer configuration parameters.""" def get_config(): """Create, populate and return the VersioneerConfig() object.""" # these strings are filled in when 'setup.py versioneer' creates # _version.py cfg = VersioneerConfig() cfg.VCS = "git" cfg.style = "%(STYLE)s" cfg.tag_prefix = "%(TAG_PREFIX)s" cfg.parentdir_prefix = "%(PARENTDIR_PREFIX)s" cfg.versionfile_source = "%(VERSIONFILE_SOURCE)s" cfg.verbose = False return cfg class NotThisMethod(Exception): """Exception raised if a method is not valid for the current scenario.""" LONG_VERSION_PY = {} HANDLERS = {} def register_vcs_handler(vcs, method): # decorator """Decorator to mark a method as the handler for a particular VCS.""" def decorate(f): """Store f in HANDLERS[vcs][method].""" if vcs not in HANDLERS: HANDLERS[vcs] = {} HANDLERS[vcs][method] = f return f return decorate def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=None): """Call the given command(s).""" assert isinstance(commands, list) p = None for c in commands: try: dispcmd = str([c] + args) # remember shell=False, so use git.cmd on windows, not just git p = subprocess.Popen([c] + args, cwd=cwd, env=env, stdout=subprocess.PIPE, stderr=(subprocess.PIPE if hide_stderr else None)) break except EnvironmentError: e = sys.exc_info()[1] if e.errno == errno.ENOENT: continue if verbose: print("unable to run %%s" %% dispcmd) print(e) return None, None else: if verbose: print("unable to find command, tried %%s" %% (commands,)) return None, None stdout = p.communicate()[0].strip() if sys.version_info[0] >= 3: stdout = stdout.decode() if p.returncode != 0: if verbose: print("unable to run %%s (error)" %% dispcmd) print("stdout was %%s" %% stdout) return None, p.returncode return stdout, p.returncode def versions_from_parentdir(parentdir_prefix, root, verbose): """Try to determine the version from the parent directory name. Source tarballs conventionally unpack into a directory that includes both the project name and a version string. We will also support searching up two directory levels for an appropriately named parent directory """ rootdirs = [] for i in range(3): dirname = os.path.basename(root) if dirname.startswith(parentdir_prefix): return {"version": dirname[len(parentdir_prefix):], "full-revisionid": None, "dirty": False, "error": None, "date": None} else: rootdirs.append(root) root = os.path.dirname(root) # up a level if verbose: print("Tried directories %%s but none started with prefix %%s" %% (str(rootdirs), parentdir_prefix)) raise NotThisMethod("rootdir doesn't start with parentdir_prefix") @register_vcs_handler("git", "get_keywords") def git_get_keywords(versionfile_abs): """Extract version information from the given file.""" # the code embedded in _version.py can just fetch the value of these # keywords. When used from setup.py, we don't want to import _version.py, # so we do it with a regexp instead. This function is not used from # _version.py. keywords = {} try: f = open(versionfile_abs, "r") for line in f.readlines(): if line.strip().startswith("git_refnames ="): mo = re.search(r'=\s*"(.*)"', line) if mo: keywords["refnames"] = mo.group(1) if line.strip().startswith("git_full ="): mo = re.search(r'=\s*"(.*)"', line) if mo: keywords["full"] = mo.group(1) if line.strip().startswith("git_date ="): mo = re.search(r'=\s*"(.*)"', line) if mo: keywords["date"] = mo.group(1) f.close() except EnvironmentError: pass return keywords @register_vcs_handler("git", "keywords") def git_versions_from_keywords(keywords, tag_prefix, verbose): """Get version information from git keywords.""" if not keywords: raise NotThisMethod("no keywords at all, weird") date = keywords.get("date") if date is not None: # git-2.2.0 added "%%cI", which expands to an ISO-8601 -compliant # datestamp. However we prefer "%%ci" (which expands to an "ISO-8601 # -like" string, which we must then edit to make compliant), because # it's been around since git-1.5.3, and it's too difficult to # discover which version we're using, or to work around using an # older one. date = date.strip().replace(" ", "T", 1).replace(" ", "", 1) refnames = keywords["refnames"].strip() if refnames.startswith("$Format"): if verbose: print("keywords are unexpanded, not using") raise NotThisMethod("unexpanded keywords, not a git-archive tarball") refs = set([r.strip() for r in refnames.strip("()").split(",")]) # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of # just "foo-1.0". If we see a "tag: " prefix, prefer those. TAG = "tag: " tags = set([r[len(TAG):] for r in refs if r.startswith(TAG)]) if not tags: # Either we're using git < 1.8.3, or there really are no tags. We use # a heuristic: assume all version tags have a digit. The old git %%d # expansion behaves like git log --decorate=short and strips out the # refs/heads/ and refs/tags/ prefixes that would let us distinguish # between branches and tags. By ignoring refnames without digits, we # filter out many common branch names like "release" and # "stabilization", as well as "HEAD" and "master". tags = set([r for r in refs if re.search(r'\d', r)]) if verbose: print("discarding '%%s', no digits" %% ",".join(refs - tags)) if verbose: print("likely tags: %%s" %% ",".join(sorted(tags))) for ref in sorted(tags): # sorting will prefer e.g. "2.0" over "2.0rc1" if ref.startswith(tag_prefix): r = ref[len(tag_prefix):] if verbose: print("picking %%s" %% r) return {"version": r, "full-revisionid": keywords["full"].strip(), "dirty": False, "error": None, "date": date} # no suitable tags, so version is "0+unknown", but full hex is still there if verbose: print("no suitable tags, using unknown + full revision id") return {"version": "0+unknown", "full-revisionid": keywords["full"].strip(), "dirty": False, "error": "no suitable tags", "date": None} @register_vcs_handler("git", "pieces_from_vcs") def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): """Get version from 'git describe' in the root of the source tree. This only gets called if the git-archive 'subst' keywords were *not* expanded, and _version.py hasn't already been rewritten with a short version string, meaning we're inside a checked out source tree. """ GITS = ["git"] if sys.platform == "win32": GITS = ["git.cmd", "git.exe"] out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root, hide_stderr=True) if rc != 0: if verbose: print("Directory %%s not under git control" %% root) raise NotThisMethod("'git rev-parse --git-dir' returned error") # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] # if there isn't one, this yields HEX[-dirty] (no NUM) describe_out, rc = run_command(GITS, ["describe", "--tags", "--dirty", "--always", "--long", "--match", "%%s*" %% tag_prefix], cwd=root) # --long was added in git-1.5.5 if describe_out is None: raise NotThisMethod("'git describe' failed") describe_out = describe_out.strip() full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root) if full_out is None: raise NotThisMethod("'git rev-parse' failed") full_out = full_out.strip() pieces = {} pieces["long"] = full_out pieces["short"] = full_out[:7] # maybe improved later pieces["error"] = None # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty] # TAG might have hyphens. git_describe = describe_out # look for -dirty suffix dirty = git_describe.endswith("-dirty") pieces["dirty"] = dirty if dirty: git_describe = git_describe[:git_describe.rindex("-dirty")] # now we have TAG-NUM-gHEX or HEX if "-" in git_describe: # TAG-NUM-gHEX mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe) if not mo: # unparseable. Maybe git-describe is misbehaving? pieces["error"] = ("unable to parse git-describe output: '%%s'" %% describe_out) return pieces # tag full_tag = mo.group(1) if not full_tag.startswith(tag_prefix): if verbose: fmt = "tag '%%s' doesn't start with prefix '%%s'" print(fmt %% (full_tag, tag_prefix)) pieces["error"] = ("tag '%%s' doesn't start with prefix '%%s'" %% (full_tag, tag_prefix)) return pieces pieces["closest-tag"] = full_tag[len(tag_prefix):] # distance: number of commits since tag pieces["distance"] = int(mo.group(2)) # commit: short hex revision ID pieces["short"] = mo.group(3) else: # HEX: no tags pieces["closest-tag"] = None count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"], cwd=root) pieces["distance"] = int(count_out) # total number of commits # commit date: see ISO-8601 comment in git_versions_from_keywords() date = run_command(GITS, ["show", "-s", "--format=%%ci", "HEAD"], cwd=root)[0].strip() pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) return pieces def plus_or_dot(pieces): """Return a + if we don't already have one, else return a .""" if "+" in pieces.get("closest-tag", ""): return "." return "+" def render_pep440(pieces): """Build up version string, with post-release "local version identifier". Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty Exceptions: 1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty] """ if pieces["closest-tag"]: rendered = pieces["closest-tag"] if pieces["distance"] or pieces["dirty"]: rendered += plus_or_dot(pieces) rendered += "%%d.g%%s" %% (pieces["distance"], pieces["short"]) if pieces["dirty"]: rendered += ".dirty" else: # exception #1 rendered = "0+untagged.%%d.g%%s" %% (pieces["distance"], pieces["short"]) if pieces["dirty"]: rendered += ".dirty" return rendered def render_pep440_pre(pieces): """TAG[.post.devDISTANCE] -- No -dirty. Exceptions: 1: no tags. 0.post.devDISTANCE """ if pieces["closest-tag"]: rendered = pieces["closest-tag"] if pieces["distance"]: rendered += ".post.dev%%d" %% pieces["distance"] else: # exception #1 rendered = "0.post.dev%%d" %% pieces["distance"] return rendered def render_pep440_post(pieces): """TAG[.postDISTANCE[.dev0]+gHEX] . The ".dev0" means dirty. Note that .dev0 sorts backwards (a dirty tree will appear "older" than the corresponding clean one), but you shouldn't be releasing software with -dirty anyways. Exceptions: 1: no tags. 0.postDISTANCE[.dev0] """ if pieces["closest-tag"]: rendered = pieces["closest-tag"] if pieces["distance"] or pieces["dirty"]: rendered += ".post%%d" %% pieces["distance"] if pieces["dirty"]: rendered += ".dev0" rendered += plus_or_dot(pieces) rendered += "g%%s" %% pieces["short"] else: # exception #1 rendered = "0.post%%d" %% pieces["distance"] if pieces["dirty"]: rendered += ".dev0" rendered += "+g%%s" %% pieces["short"] return rendered def render_pep440_old(pieces): """TAG[.postDISTANCE[.dev0]] . The ".dev0" means dirty. Eexceptions: 1: no tags. 0.postDISTANCE[.dev0] """ if pieces["closest-tag"]: rendered = pieces["closest-tag"] if pieces["distance"] or pieces["dirty"]: rendered += ".post%%d" %% pieces["distance"] if pieces["dirty"]: rendered += ".dev0" else: # exception #1 rendered = "0.post%%d" %% pieces["distance"] if pieces["dirty"]: rendered += ".dev0" return rendered def render_git_describe(pieces): """TAG[-DISTANCE-gHEX][-dirty]. Like 'git describe --tags --dirty --always'. Exceptions: 1: no tags. HEX[-dirty] (note: no 'g' prefix) """ if pieces["closest-tag"]: rendered = pieces["closest-tag"] if pieces["distance"]: rendered += "-%%d-g%%s" %% (pieces["distance"], pieces["short"]) else: # exception #1 rendered = pieces["short"] if pieces["dirty"]: rendered += "-dirty" return rendered def render_git_describe_long(pieces): """TAG-DISTANCE-gHEX[-dirty]. Like 'git describe --tags --dirty --always -long'. The distance/hash is unconditional. Exceptions: 1: no tags. HEX[-dirty] (note: no 'g' prefix) """ if pieces["closest-tag"]: rendered = pieces["closest-tag"] rendered += "-%%d-g%%s" %% (pieces["distance"], pieces["short"]) else: # exception #1 rendered = pieces["short"] if pieces["dirty"]: rendered += "-dirty" return rendered def render(pieces, style): """Render the given version pieces into the requested style.""" if pieces["error"]: return {"version": "unknown", "full-revisionid": pieces.get("long"), "dirty": None, "error": pieces["error"], "date": None} if not style or style == "default": style = "pep440" # the default if style == "pep440": rendered = render_pep440(pieces) elif style == "pep440-pre": rendered = render_pep440_pre(pieces) elif style == "pep440-post": rendered = render_pep440_post(pieces) elif style == "pep440-old": rendered = render_pep440_old(pieces) elif style == "git-describe": rendered = render_git_describe(pieces) elif style == "git-describe-long": rendered = render_git_describe_long(pieces) else: raise ValueError("unknown style '%%s'" %% style) return {"version": rendered, "full-revisionid": pieces["long"], "dirty": pieces["dirty"], "error": None, "date": pieces.get("date")} def get_versions(): """Get version information or return default if unable to do so.""" # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have # __file__, we can work backwards from there to the root. Some # py2exe/bbfreeze/non-CPython implementations don't do __file__, in which # case we can only use expanded keywords. cfg = get_config() verbose = cfg.verbose try: return git_versions_from_keywords(get_keywords(), cfg.tag_prefix, verbose) except NotThisMethod: pass try: root = os.path.realpath(__file__) # versionfile_source is the relative path from the top of the source # tree (where the .git directory might live) to this file. Invert # this to find the root from __file__. for i in cfg.versionfile_source.split('/'): root = os.path.dirname(root) except NameError: return {"version": "0+unknown", "full-revisionid": None, "dirty": None, "error": "unable to find root of source tree", "date": None} try: pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose) return render(pieces, cfg.style) except NotThisMethod: pass try: if cfg.parentdir_prefix: return versions_from_parentdir(cfg.parentdir_prefix, root, verbose) except NotThisMethod: pass return {"version": "0+unknown", "full-revisionid": None, "dirty": None, "error": "unable to compute version", "date": None} ''' @register_vcs_handler("git", "get_keywords") def git_get_keywords(versionfile_abs): """Extract version information from the given file.""" # the code embedded in _version.py can just fetch the value of these # keywords. When used from setup.py, we don't want to import _version.py, # so we do it with a regexp instead. This function is not used from # _version.py. keywords = {} try: f = open(versionfile_abs, "r") for line in f.readlines(): if line.strip().startswith("git_refnames ="): mo = re.search(r'=\s*"(.*)"', line) if mo: keywords["refnames"] = mo.group(1) if line.strip().startswith("git_full ="): mo = re.search(r'=\s*"(.*)"', line) if mo: keywords["full"] = mo.group(1) if line.strip().startswith("git_date ="): mo = re.search(r'=\s*"(.*)"', line) if mo: keywords["date"] = mo.group(1) f.close() except EnvironmentError: pass return keywords @register_vcs_handler("git", "keywords") def git_versions_from_keywords(keywords, tag_prefix, verbose): """Get version information from git keywords.""" if not keywords: raise NotThisMethod("no keywords at all, weird") date = keywords.get("date") if date is not None: # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant # datestamp. However we prefer "%ci" (which expands to an "ISO-8601 # -like" string, which we must then edit to make compliant), because # it's been around since git-1.5.3, and it's too difficult to # discover which version we're using, or to work around using an # older one. date = date.strip().replace(" ", "T", 1).replace(" ", "", 1) refnames = keywords["refnames"].strip() if refnames.startswith("$Format"): if verbose: print("keywords are unexpanded, not using") raise NotThisMethod("unexpanded keywords, not a git-archive tarball") refs = set([r.strip() for r in refnames.strip("()").split(",")]) # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of # just "foo-1.0". If we see a "tag: " prefix, prefer those. TAG = "tag: " tags = set([r[len(TAG):] for r in refs if r.startswith(TAG)]) if not tags: # Either we're using git < 1.8.3, or there really are no tags. We use # a heuristic: assume all version tags have a digit. The old git %d # expansion behaves like git log --decorate=short and strips out the # refs/heads/ and refs/tags/ prefixes that would let us distinguish # between branches and tags. By ignoring refnames without digits, we # filter out many common branch names like "release" and # "stabilization", as well as "HEAD" and "master". tags = set([r for r in refs if re.search(r'\d', r)]) if verbose: print("discarding '%s', no digits" % ",".join(refs - tags)) if verbose: print("likely tags: %s" % ",".join(sorted(tags))) for ref in sorted(tags): # sorting will prefer e.g. "2.0" over "2.0rc1" if ref.startswith(tag_prefix): r = ref[len(tag_prefix):] if verbose: print("picking %s" % r) return {"version": r, "full-revisionid": keywords["full"].strip(), "dirty": False, "error": None, "date": date} # no suitable tags, so version is "0+unknown", but full hex is still there if verbose: print("no suitable tags, using unknown + full revision id") return {"version": "0+unknown", "full-revisionid": keywords["full"].strip(), "dirty": False, "error": "no suitable tags", "date": None} @register_vcs_handler("git", "pieces_from_vcs") def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): """Get version from 'git describe' in the root of the source tree. This only gets called if the git-archive 'subst' keywords were *not* expanded, and _version.py hasn't already been rewritten with a short version string, meaning we're inside a checked out source tree. """ GITS = ["git"] if sys.platform == "win32": GITS = ["git.cmd", "git.exe"] out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root, hide_stderr=True) if rc != 0: if verbose: print("Directory %s not under git control" % root) raise NotThisMethod("'git rev-parse --git-dir' returned error") # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] # if there isn't one, this yields HEX[-dirty] (no NUM) describe_out, rc = run_command(GITS, ["describe", "--tags", "--dirty", "--always", "--long", "--match", "%s*" % tag_prefix], cwd=root) # --long was added in git-1.5.5 if describe_out is None: raise NotThisMethod("'git describe' failed") describe_out = describe_out.strip() full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root) if full_out is None: raise NotThisMethod("'git rev-parse' failed") full_out = full_out.strip() pieces = {} pieces["long"] = full_out pieces["short"] = full_out[:7] # maybe improved later pieces["error"] = None # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty] # TAG might have hyphens. git_describe = describe_out # look for -dirty suffix dirty = git_describe.endswith("-dirty") pieces["dirty"] = dirty if dirty: git_describe = git_describe[:git_describe.rindex("-dirty")] # now we have TAG-NUM-gHEX or HEX if "-" in git_describe: # TAG-NUM-gHEX mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe) if not mo: # unparseable. Maybe git-describe is misbehaving? pieces["error"] = ("unable to parse git-describe output: '%s'" % describe_out) return pieces # tag full_tag = mo.group(1) if not full_tag.startswith(tag_prefix): if verbose: fmt = "tag '%s' doesn't start with prefix '%s'" print(fmt % (full_tag, tag_prefix)) pieces["error"] = ("tag '%s' doesn't start with prefix '%s'" % (full_tag, tag_prefix)) return pieces pieces["closest-tag"] = full_tag[len(tag_prefix):] # distance: number of commits since tag pieces["distance"] = int(mo.group(2)) # commit: short hex revision ID pieces["short"] = mo.group(3) else: # HEX: no tags pieces["closest-tag"] = None count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"], cwd=root) pieces["distance"] = int(count_out) # total number of commits # commit date: see ISO-8601 comment in git_versions_from_keywords() date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[0].strip() pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) return pieces def do_vcs_install(manifest_in, versionfile_source, ipy): """Git-specific installation logic for Versioneer. For Git, this means creating/changing .gitattributes to mark _version.py for export-subst keyword substitution. """ GITS = ["git"] if sys.platform == "win32": GITS = ["git.cmd", "git.exe"] files = [manifest_in, versionfile_source] if ipy: files.append(ipy) try: me = __file__ if me.endswith(".pyc") or me.endswith(".pyo"): me = os.path.splitext(me)[0] + ".py" versioneer_file = os.path.relpath(me) except NameError: versioneer_file = "versioneer.py" files.append(versioneer_file) present = False try: f = open(".gitattributes", "r") for line in f.readlines(): if line.strip().startswith(versionfile_source): if "export-subst" in line.strip().split()[1:]: present = True f.close() except EnvironmentError: pass if not present: f = open(".gitattributes", "a+") f.write("%s export-subst\n" % versionfile_source) f.close() files.append(".gitattributes") run_command(GITS, ["add", "--"] + files) def versions_from_parentdir(parentdir_prefix, root, verbose): """Try to determine the version from the parent directory name. Source tarballs conventionally unpack into a directory that includes both the project name and a version string. We will also support searching up two directory levels for an appropriately named parent directory """ rootdirs = [] for i in range(3): dirname = os.path.basename(root) if dirname.startswith(parentdir_prefix): return {"version": dirname[len(parentdir_prefix):], "full-revisionid": None, "dirty": False, "error": None, "date": None} else: rootdirs.append(root) root = os.path.dirname(root) # up a level if verbose: print("Tried directories %s but none started with prefix %s" % (str(rootdirs), parentdir_prefix)) raise NotThisMethod("rootdir doesn't start with parentdir_prefix") SHORT_VERSION_PY = """ # This file was generated by 'versioneer.py' (0.18) from # revision-control system data, or from the parent directory name of an # unpacked source archive. Distribution tarballs contain a pre-generated copy # of this file. import json version_json = ''' %s ''' # END VERSION_JSON def get_versions(): return json.loads(version_json) """ def versions_from_file(filename): """Try to determine the version from _version.py if present.""" try: with open(filename) as f: contents = f.read() except EnvironmentError: raise NotThisMethod("unable to read _version.py") mo = re.search(r"version_json = '''\n(.*)''' # END VERSION_JSON", contents, re.M | re.S) if not mo: mo = re.search(r"version_json = '''\r\n(.*)''' # END VERSION_JSON", contents, re.M | re.S) if not mo: raise NotThisMethod("no version_json in _version.py") return json.loads(mo.group(1)) def write_to_version_file(filename, versions): """Write the given version number to the given _version.py file.""" os.unlink(filename) contents = json.dumps(versions, sort_keys=True, indent=1, separators=(",", ": ")) with open(filename, "w") as f: f.write(SHORT_VERSION_PY % contents) print("set %s to '%s'" % (filename, versions["version"])) def plus_or_dot(pieces): """Return a + if we don't already have one, else return a .""" if "+" in pieces.get("closest-tag", ""): return "." return "+" def render_pep440(pieces): """Build up version string, with post-release "local version identifier". Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty Exceptions: 1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty] """ if pieces["closest-tag"]: rendered = pieces["closest-tag"] if pieces["distance"] or pieces["dirty"]: rendered += plus_or_dot(pieces) rendered += "%d.g%s" % (pieces["distance"], pieces["short"]) if pieces["dirty"]: rendered += ".dirty" else: # exception #1 rendered = "0+untagged.%d.g%s" % (pieces["distance"], pieces["short"]) if pieces["dirty"]: rendered += ".dirty" return rendered def render_pep440_pre(pieces): """TAG[.post.devDISTANCE] -- No -dirty. Exceptions: 1: no tags. 0.post.devDISTANCE """ if pieces["closest-tag"]: rendered = pieces["closest-tag"] if pieces["distance"]: rendered += ".post.dev%d" % pieces["distance"] else: # exception #1 rendered = "0.post.dev%d" % pieces["distance"] return rendered def render_pep440_post(pieces): """TAG[.postDISTANCE[.dev0]+gHEX] . The ".dev0" means dirty. Note that .dev0 sorts backwards (a dirty tree will appear "older" than the corresponding clean one), but you shouldn't be releasing software with -dirty anyways. Exceptions: 1: no tags. 0.postDISTANCE[.dev0] """ if pieces["closest-tag"]: rendered = pieces["closest-tag"] if pieces["distance"] or pieces["dirty"]: rendered += ".post%d" % pieces["distance"] if pieces["dirty"]: rendered += ".dev0" rendered += plus_or_dot(pieces) rendered += "g%s" % pieces["short"] else: # exception #1 rendered = "0.post%d" % pieces["distance"] if pieces["dirty"]: rendered += ".dev0" rendered += "+g%s" % pieces["short"] return rendered def render_pep440_old(pieces): """TAG[.postDISTANCE[.dev0]] . The ".dev0" means dirty. Eexceptions: 1: no tags. 0.postDISTANCE[.dev0] """ if pieces["closest-tag"]: rendered = pieces["closest-tag"] if pieces["distance"] or pieces["dirty"]: rendered += ".post%d" % pieces["distance"] if pieces["dirty"]: rendered += ".dev0" else: # exception #1 rendered = "0.post%d" % pieces["distance"] if pieces["dirty"]: rendered += ".dev0" return rendered def render_git_describe(pieces): """TAG[-DISTANCE-gHEX][-dirty]. Like 'git describe --tags --dirty --always'. Exceptions: 1: no tags. HEX[-dirty] (note: no 'g' prefix) """ if pieces["closest-tag"]: rendered = pieces["closest-tag"] if pieces["distance"]: rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) else: # exception #1 rendered = pieces["short"] if pieces["dirty"]: rendered += "-dirty" return rendered def render_git_describe_long(pieces): """TAG-DISTANCE-gHEX[-dirty]. Like 'git describe --tags --dirty --always -long'. The distance/hash is unconditional. Exceptions: 1: no tags. HEX[-dirty] (note: no 'g' prefix) """ if pieces["closest-tag"]: rendered = pieces["closest-tag"] rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) else: # exception #1 rendered = pieces["short"] if pieces["dirty"]: rendered += "-dirty" return rendered def render(pieces, style): """Render the given version pieces into the requested style.""" if pieces["error"]: return {"version": "unknown", "full-revisionid": pieces.get("long"), "dirty": None, "error": pieces["error"], "date": None} if not style or style == "default": style = "pep440" # the default if style == "pep440": rendered = render_pep440(pieces) elif style == "pep440-pre": rendered = render_pep440_pre(pieces) elif style == "pep440-post": rendered = render_pep440_post(pieces) elif style == "pep440-old": rendered = render_pep440_old(pieces) elif style == "git-describe": rendered = render_git_describe(pieces) elif style == "git-describe-long": rendered = render_git_describe_long(pieces) else: raise ValueError("unknown style '%s'" % style) return {"version": rendered, "full-revisionid": pieces["long"], "dirty": pieces["dirty"], "error": None, "date": pieces.get("date")} class VersioneerBadRootError(Exception): """The project root directory is unknown or missing key files.""" def get_versions(verbose=False): """Get the project version from whatever source is available. Returns dict with two keys: 'version' and 'full'. """ if "versioneer" in sys.modules: # see the discussion in cmdclass.py:get_cmdclass() del sys.modules["versioneer"] root = get_root() cfg = get_config_from_root(root) assert cfg.VCS is not None, "please set [versioneer]VCS= in setup.cfg" handlers = HANDLERS.get(cfg.VCS) assert handlers, "unrecognized VCS '%s'" % cfg.VCS verbose = verbose or cfg.verbose assert cfg.versionfile_source is not None, \ "please set versioneer.versionfile_source" assert cfg.tag_prefix is not None, "please set versioneer.tag_prefix" versionfile_abs = os.path.join(root, cfg.versionfile_source) # extract version from first of: _version.py, VCS command (e.g. 'git # describe'), parentdir. This is meant to work for developers using a # source checkout, for users of a tarball created by 'setup.py sdist', # and for users of a tarball/zipball created by 'git archive' or github's # download-from-tag feature or the equivalent in other VCSes. get_keywords_f = handlers.get("get_keywords") from_keywords_f = handlers.get("keywords") if get_keywords_f and from_keywords_f: try: keywords = get_keywords_f(versionfile_abs) ver = from_keywords_f(keywords, cfg.tag_prefix, verbose) if verbose: print("got version from expanded keyword %s" % ver) return ver except NotThisMethod: pass try: ver = versions_from_file(versionfile_abs) if verbose: print("got version from file %s %s" % (versionfile_abs, ver)) return ver except NotThisMethod: pass from_vcs_f = handlers.get("pieces_from_vcs") if from_vcs_f: try: pieces = from_vcs_f(cfg.tag_prefix, root, verbose) ver = render(pieces, cfg.style) if verbose: print("got version from VCS %s" % ver) return ver except NotThisMethod: pass try: if cfg.parentdir_prefix: ver = versions_from_parentdir(cfg.parentdir_prefix, root, verbose) if verbose: print("got version from parentdir %s" % ver) return ver except NotThisMethod: pass if verbose: print("unable to compute version") return {"version": "0+unknown", "full-revisionid": None, "dirty": None, "error": "unable to compute version", "date": None} def get_version(): """Get the short version string for this project.""" return get_versions()["version"] def get_cmdclass(): """Get the custom setuptools/distutils subclasses used by Versioneer.""" if "versioneer" in sys.modules: del sys.modules["versioneer"] # this fixes the "python setup.py develop" case (also 'install' and # 'easy_install .'), in which subdependencies of the main project are # built (using setup.py bdist_egg) in the same python process. Assume # a main project A and a dependency B, which use different versions # of Versioneer. A's setup.py imports A's Versioneer, leaving it in # sys.modules by the time B's setup.py is executed, causing B to run # with the wrong versioneer. Setuptools wraps the sub-dep builds in a # sandbox that restores sys.modules to it's pre-build state, so the # parent is protected against the child's "import versioneer". By # removing ourselves from sys.modules here, before the child build # happens, we protect the child from the parent's versioneer too. # Also see https://github.com/warner/python-versioneer/issues/52 cmds = {} # we add "version" to both distutils and setuptools from distutils.core import Command class cmd_version(Command): description = "report generated version string" user_options = [] boolean_options = [] def initialize_options(self): pass def finalize_options(self): pass def run(self): vers = get_versions(verbose=True) print("Version: %s" % vers["version"]) print(" full-revisionid: %s" % vers.get("full-revisionid")) print(" dirty: %s" % vers.get("dirty")) print(" date: %s" % vers.get("date")) if vers["error"]: print(" error: %s" % vers["error"]) cmds["version"] = cmd_version # we override "build_py" in both distutils and setuptools # # most invocation pathways end up running build_py: # distutils/build -> build_py # distutils/install -> distutils/build ->.. # setuptools/bdist_wheel -> distutils/install ->.. # setuptools/bdist_egg -> distutils/install_lib -> build_py # setuptools/install -> bdist_egg ->.. # setuptools/develop -> ? # pip install: # copies source tree to a tempdir before running egg_info/etc # if .git isn't copied too, 'git describe' will fail # then does setup.py bdist_wheel, or sometimes setup.py install # setup.py egg_info -> ? # we override different "build_py" commands for both environments if "setuptools" in sys.modules: from setuptools.command.build_py import build_py as _build_py else: from distutils.command.build_py import build_py as _build_py class cmd_build_py(_build_py): def run(self): root = get_root() cfg = get_config_from_root(root) versions = get_versions() _build_py.run(self) # now locate _version.py in the new build/ directory and replace # it with an updated value if cfg.versionfile_build: target_versionfile = os.path.join(self.build_lib, cfg.versionfile_build) print("UPDATING %s" % target_versionfile) write_to_version_file(target_versionfile, versions) cmds["build_py"] = cmd_build_py if "cx_Freeze" in sys.modules: # cx_freeze enabled? from cx_Freeze.dist import build_exe as _build_exe # nczeczulin reports that py2exe won't like the pep440-style string # as FILEVERSION, but it can be used for PRODUCTVERSION, e.g. # setup(console=[{ # "version": versioneer.get_version().split("+", 1)[0], # FILEVERSION # "product_version": versioneer.get_version(), # ... class cmd_build_exe(_build_exe): def run(self): root = get_root() cfg = get_config_from_root(root) versions = get_versions() target_versionfile = cfg.versionfile_source print("UPDATING %s" % target_versionfile) write_to_version_file(target_versionfile, versions) _build_exe.run(self) os.unlink(target_versionfile) with open(cfg.versionfile_source, "w") as f: LONG = LONG_VERSION_PY[cfg.VCS] f.write(LONG % {"DOLLAR": "$", "STYLE": cfg.style, "TAG_PREFIX": cfg.tag_prefix, "PARENTDIR_PREFIX": cfg.parentdir_prefix, "VERSIONFILE_SOURCE": cfg.versionfile_source, }) cmds["build_exe"] = cmd_build_exe del cmds["build_py"] if 'py2exe' in sys.modules: # py2exe enabled? try: from py2exe.distutils_buildexe import py2exe as _py2exe # py3 except ImportError: from py2exe.build_exe import py2exe as _py2exe # py2 class cmd_py2exe(_py2exe): def run(self): root = get_root() cfg = get_config_from_root(root) versions = get_versions() target_versionfile = cfg.versionfile_source print("UPDATING %s" % target_versionfile) write_to_version_file(target_versionfile, versions) _py2exe.run(self) os.unlink(target_versionfile) with open(cfg.versionfile_source, "w") as f: LONG = LONG_VERSION_PY[cfg.VCS] f.write(LONG % {"DOLLAR": "$", "STYLE": cfg.style, "TAG_PREFIX": cfg.tag_prefix, "PARENTDIR_PREFIX": cfg.parentdir_prefix, "VERSIONFILE_SOURCE": cfg.versionfile_source, }) cmds["py2exe"] = cmd_py2exe # we override different "sdist" commands for both environments if "setuptools" in sys.modules: from setuptools.command.sdist import sdist as _sdist else: from distutils.command.sdist import sdist as _sdist class cmd_sdist(_sdist): def run(self): versions = get_versions() self._versioneer_generated_versions = versions # unless we update this, the command will keep using the old # version self.distribution.metadata.version = versions["version"] return _sdist.run(self) def make_release_tree(self, base_dir, files): root = get_root() cfg = get_config_from_root(root) _sdist.make_release_tree(self, base_dir, files) # now locate _version.py in the new base_dir directory # (remembering that it may be a hardlink) and replace it with an # updated value target_versionfile = os.path.join(base_dir, cfg.versionfile_source) print("UPDATING %s" % target_versionfile) write_to_version_file(target_versionfile, self._versioneer_generated_versions) cmds["sdist"] = cmd_sdist return cmds CONFIG_ERROR = """ setup.cfg is missing the necessary Versioneer configuration. You need a section like: [versioneer] VCS = git style = pep440 versionfile_source = src/myproject/_version.py versionfile_build = myproject/_version.py tag_prefix = parentdir_prefix = myproject- You will also need to edit your setup.py to use the results: import versioneer setup(version=versioneer.get_version(), cmdclass=versioneer.get_cmdclass(), ...) Please read the docstring in ./versioneer.py for configuration instructions, edit setup.cfg, and re-run the installer or 'python versioneer.py setup'. """ SAMPLE_CONFIG = """ # See the docstring in versioneer.py for instructions. Note that you must # re-run 'versioneer.py setup' after changing this section, and commit the # resulting files. [versioneer] #VCS = git #style = pep440 #versionfile_source = #versionfile_build = #tag_prefix = #parentdir_prefix = """ INIT_PY_SNIPPET = """ from ._version import get_versions __version__ = get_versions()['version'] del get_versions """ def do_setup(): """Main VCS-independent setup function for installing Versioneer.""" root = get_root() try: cfg = get_config_from_root(root) except (EnvironmentError, configparser.NoSectionError, configparser.NoOptionError) as e: if isinstance(e, (EnvironmentError, configparser.NoSectionError)): print("Adding sample versioneer config to setup.cfg", file=sys.stderr) with open(os.path.join(root, "setup.cfg"), "a") as f: f.write(SAMPLE_CONFIG) print(CONFIG_ERROR, file=sys.stderr) return 1 print(" creating %s" % cfg.versionfile_source) with open(cfg.versionfile_source, "w") as f: LONG = LONG_VERSION_PY[cfg.VCS] f.write(LONG % {"DOLLAR": "$", "STYLE": cfg.style, "TAG_PREFIX": cfg.tag_prefix, "PARENTDIR_PREFIX": cfg.parentdir_prefix, "VERSIONFILE_SOURCE": cfg.versionfile_source, }) ipy = os.path.join(os.path.dirname(cfg.versionfile_source), "__init__.py") if os.path.exists(ipy): try: with open(ipy, "r") as f: old = f.read() except EnvironmentError: old = "" if INIT_PY_SNIPPET not in old: print(" appending to %s" % ipy) with open(ipy, "a") as f: f.write(INIT_PY_SNIPPET) else: print(" %s unmodified" % ipy) else: print(" %s doesn't exist, ok" % ipy) ipy = None # Make sure both the top-level "versioneer.py" and versionfile_source # (PKG/_version.py, used by runtime code) are in MANIFEST.in, so # they'll be copied into source distributions. Pip won't be able to # install the package without this. manifest_in = os.path.join(root, "MANIFEST.in") simple_includes = set() try: with open(manifest_in, "r") as f: for line in f: if line.startswith("include "): for include in line.split()[1:]: simple_includes.add(include) except EnvironmentError: pass # That doesn't cover everything MANIFEST.in can do # (http://docs.python.org/2/distutils/sourcedist.html#commands), so # it might give some false negatives. Appending redundant 'include' # lines is safe, though. if "versioneer.py" not in simple_includes: print(" appending 'versioneer.py' to MANIFEST.in") with open(manifest_in, "a") as f: f.write("include versioneer.py\n") else: print(" 'versioneer.py' already in MANIFEST.in") if cfg.versionfile_source not in simple_includes: print(" appending versionfile_source ('%s') to MANIFEST.in" % cfg.versionfile_source) with open(manifest_in, "a") as f: f.write("include %s\n" % cfg.versionfile_source) else: print(" versionfile_source already in MANIFEST.in") # Make VCS-specific changes. For git, this means creating/changing # .gitattributes to mark _version.py for export-subst keyword # substitution. do_vcs_install(manifest_in, cfg.versionfile_source, ipy) return 0 def scan_setup_py(): """Validate the contents of setup.py against Versioneer's expectations.""" found = set() setters = False errors = 0 with open("setup.py", "r") as f: for line in f.readlines(): if "import versioneer" in line: found.add("import") if "versioneer.get_cmdclass()" in line: found.add("cmdclass") if "versioneer.get_version()" in line: found.add("get_version") if "versioneer.VCS" in line: setters = True if "versioneer.versionfile_source" in line: setters = True if len(found) != 3: print("") print("Your setup.py appears to be missing some important items") print("(but I might be wrong). Please make sure it has something") print("roughly like the following:") print("") print(" import versioneer") print(" setup( version=versioneer.get_version(),") print(" cmdclass=versioneer.get_cmdclass(), ...)") print("") errors += 1 if setters: print("You should remove lines like 'versioneer.VCS = ' and") print("'versioneer.versionfile_source = ' . This configuration") print("now lives in setup.cfg, and should be removed from setup.py") print("") errors += 1 return errors if __name__ == "__main__": cmd = sys.argv[1] if cmd == "setup": errors = do_setup() errors += scan_setup_py() if errors: sys.exit(1)