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| @@ -1,102 +1,103 @@ | ||
| [](https://doi.org/10.5281/zenodo.8056010) | ||
| [](https://codeclimate.com/github/hed-standard/hed-python/maintainability) | ||
| [](https://codeclimate.com/github/hed-standard/hed-python/test_coverage) | ||
|  | ||
| [](https://hed-python.readthedocs.io/en/latest/?badge=latest) | ||
|
|
||
| # HEDTools - Python | ||
| HED (Hierarchical Event Descriptors) is a framework for systematically describing | ||
| both laboratory and real-world events as well as other experimental metadata. | ||
| HED tags are comma-separated path strings. | ||
| HED, itself, is platform-independent, extendable, and data-neutral. | ||
|
|
||
| This repository contains the underlying python tools that support validation, | ||
| summarization, and analysis of datasets using HED tags. | ||
|
|
||
| Most people will simply annotate their events by creating a spreadsheet | ||
| or a BIDS JSON sidecar that associates HED tags with event codes or the events themselves. | ||
| If you have such a spreadsheet or a JSON, | ||
| you can use the HED Online Validator currently available at | ||
| [https://hedtools.org](https://hedtools.org) to validate or transform | ||
| your files without downloading any tools. | ||
|
|
||
| A version of the online tools corresponding to the `develop` branch can be found at: | ||
| [https://hedtools.org/hed_dev](https://hedtools.org/hed_dev). | ||
|
|
||
| ### Installation | ||
| Use `pip` to install `hedtools` from PyPI: | ||
|
|
||
| ``` | ||
| pip install hedtools | ||
| ``` | ||
|
|
||
| To install directly from the | ||
| [GitHub](https://github.com/hed-standard/hed-python) repository `master` branch: | ||
|
|
||
| ``` | ||
| pip install git+https://github.com/hed-standard/hed-python/@master | ||
| ``` | ||
|
|
||
| The HEDTools in this repository require Python 3.8 or greater. | ||
|
|
||
| ### Relationship to other repositories | ||
|
|
||
| The `hed-python` repository contains the Python infrastructure for validating | ||
| and analyzing HED. This repository has several companion repositories: | ||
| - [`hed-web`](https://github.com/hed-standard/hed-web) contains the web interface | ||
| for HED as well as a deployable docker module that supports web services for HED. | ||
| - [`hed-examples`](https://github.com/hed-standard/hed-examples) contains examples of | ||
| using HED in Python and MATLAB. This repository also houses the HED resources. | ||
| See [https://www.hed-resources.org](https://www.hed-resources.org) for access to these. | ||
| - [`hed-specification`](https://github.com/hed-standard/hed-specification) contains | ||
| the HED specification documents. The `hed-python` validator is keyed to error codes | ||
| in this document. | ||
| - [`hed-schemas`](https://github.com/hed-standard/hed-schemas) contains | ||
| the official HED schemas. The tools access this repository to retrieve and cache schema versions | ||
| during execution. Starting with `hedtools 0.2.0` local copies of the most recent schema versions | ||
| are stored within the code modules for easy access. | ||
|
|
||
| #### Develop versus master versus stable branches | ||
|
|
||
| The `hed-python` repository | ||
|
|
||
| | Branch | Meaning | Synchronized with | | ||
| | ------ | -------- | ------------------ | | ||
| | stable | Officially released on PyPI as a tagged version. | `stable@hed-web`<br/>`stable@hed-specification`<br/>`stable@hed-examples` | | ||
| | latest | Most recent usable version. | `latest@hed-web`<br/>`latest@hed-specification`<br/>`latest@hed-examples` | | ||
| | develop | Experimental and evolving. | `develop@hed-web`<br/>`develop@hed-specification`<br/>`develop@hed-examples` | | ||
|
|
||
| As features are integrated, they first appear in the `develop` branches of the | ||
| repositories. | ||
| The `develop` branches of the repositories will be kept in sync as much as possible | ||
| If an interface change in `hed-python` triggers a change in `hed-web` or `hed-examples`, | ||
| every effort will be made to get the three types of branches | ||
| (`develop`, `latest`, `stable`) of the respective repositories in | ||
| sync. | ||
|
|
||
| API documentation is generated on ReadTheDocs when a new version is | ||
| pushed on any of the three branches. For example, the API documentation for the | ||
| `latest` branch can be found on [hed-python.readthedocs.io/en/latest/](hed-python.readthedocs.io/en/latest/). | ||
|
|
||
| #### To contribute | ||
|
|
||
| Contributions are welcome. | ||
| Please use the [Github issues](https://github.com/hed-standard/hed-python/issues) | ||
| for suggestions or bug reports. | ||
| The [Github pull request](https://github.com/hed-standard/hed-python/pulls) | ||
| may also be used for contributions. | ||
| These PRs should be made to the `develop` branch, not the `master` branch. | ||
|
|
||
| #### Local Settings Storage | ||
| Cached Schemas by default are stored in "home/.hedtools/" | ||
| Location of "home" directory varies by OS. | ||
|
|
||
| Use `hed.schema.set_cache_directory` to change the location. | ||
| The HED cache can be shared across processes. | ||
|
|
||
| Starting with `hedtools 0.2.0` local copies of the most recent schema versions | ||
| are stored within the code modules for easy access. | ||
|
|
||
| ### Other links of interest | ||
|
|
||
| Code climate reports: [https://codeclimate.com/github/hed-standard/hed-python](https://codeclimate.com/github/hed-standard/hed-python). | ||
| [](https://doi.org/10.5281/zenodo.8056010) | ||
| [](https://codeclimate.com/github/hed-standard/hed-python/maintainability) | ||
| [](https://codeclimate.com/github/hed-standard/hed-python/test_coverage) | ||
|  | ||
|  | ||
| [](https://hed-python.readthedocs.io/en/latest/?badge=latest) | ||
|
|
||
| # HEDTools - Python | ||
| HED (Hierarchical Event Descriptors) is a framework for systematically describing | ||
| both laboratory and real-world events as well as other experimental metadata. | ||
| HED tags are comma-separated path strings. | ||
| HED, itself, is platform-independent, extendable, and data-neutral. | ||
|
|
||
| This repository contains the underlying python tools that support validation, | ||
| summarization, and analysis of datasets using HED tags. | ||
|
|
||
| Most people will simply annotate their events by creating a spreadsheet | ||
| or a BIDS JSON sidecar that associates HED tags with event codes or the events themselves. | ||
| If you have such a spreadsheet or a JSON, | ||
| you can use the HED Online Validator currently available at | ||
| [https://hedtools.org](https://hedtools.org) to validate or transform | ||
| your files without downloading any tools. | ||
|
|
||
| A version of the online tools corresponding to the `develop` branch can be found at: | ||
| [https://hedtools.org/hed_dev](https://hedtools.org/hed_dev). | ||
|
|
||
| ### Installation | ||
| Use `pip` to install `hedtools` from PyPI: | ||
|
|
||
| ``` | ||
| pip install hedtools | ||
| ``` | ||
|
|
||
| To install directly from the | ||
| [GitHub](https://github.com/hed-standard/hed-python) repository `master` branch: | ||
|
|
||
| ``` | ||
| pip install git+https://github.com/hed-standard/hed-python/@master | ||
| ``` | ||
|
|
||
| The HEDTools in this repository require Python 3.8 or greater. | ||
|
|
||
| ### Relationship to other repositories | ||
|
|
||
| The `hed-python` repository contains the Python infrastructure for validating | ||
| and analyzing HED. This repository has several companion repositories: | ||
| - [`hed-web`](https://github.com/hed-standard/hed-web) contains the web interface | ||
| for HED as well as a deployable docker module that supports web services for HED. | ||
| - [`hed-examples`](https://github.com/hed-standard/hed-examples) contains examples of | ||
| using HED in Python and MATLAB. This repository also houses the HED resources. | ||
| See [https://www.hed-resources.org](https://www.hed-resources.org) for access to these. | ||
| - [`hed-specification`](https://github.com/hed-standard/hed-specification) contains | ||
| the HED specification documents. The `hed-python` validator is keyed to error codes | ||
| in this document. | ||
| - [`hed-schemas`](https://github.com/hed-standard/hed-schemas) contains | ||
| the official HED schemas. The tools access this repository to retrieve and cache schema versions | ||
| during execution. Starting with `hedtools 0.2.0` local copies of the most recent schema versions | ||
| are stored within the code modules for easy access. | ||
|
|
||
| #### Develop versus master versus stable branches | ||
|
|
||
| The `hed-python` repository | ||
|
|
||
| | Branch | Meaning | Synchronized with | | ||
| | ------ | -------- | ------------------ | | ||
| | stable | Officially released on PyPI as a tagged version. | `stable@hed-web`<br/>`stable@hed-specification`<br/>`stable@hed-examples` | | ||
| | latest | Most recent usable version. | `latest@hed-web`<br/>`latest@hed-specification`<br/>`latest@hed-examples` | | ||
| | develop | Experimental and evolving. | `develop@hed-web`<br/>`develop@hed-specification`<br/>`develop@hed-examples` | | ||
|
|
||
| As features are integrated, they first appear in the `develop` branches of the | ||
| repositories. | ||
| The `develop` branches of the repositories will be kept in sync as much as possible | ||
| If an interface change in `hed-python` triggers a change in `hed-web` or `hed-examples`, | ||
| every effort will be made to get the three types of branches | ||
| (`develop`, `latest`, `stable`) of the respective repositories in | ||
| sync. | ||
|
|
||
| API documentation is generated on ReadTheDocs when a new version is | ||
| pushed on any of the three branches. For example, the API documentation for the | ||
| `latest` branch can be found on [hed-python.readthedocs.io/en/latest/](hed-python.readthedocs.io/en/latest/). | ||
|
|
||
| #### To contribute | ||
|
|
||
| Contributions are welcome. | ||
| Please use the [Github issues](https://github.com/hed-standard/hed-python/issues) | ||
| for suggestions or bug reports. | ||
| The [Github pull request](https://github.com/hed-standard/hed-python/pulls) | ||
| may also be used for contributions. | ||
| These PRs should be made to the `develop` branch, not the `master` branch. | ||
|
|
||
| #### Local Settings Storage | ||
| Cached Schemas by default are stored in "home/.hedtools/" | ||
| Location of "home" directory varies by OS. | ||
|
|
||
| Use `hed.schema.set_cache_directory` to change the location. | ||
| The HED cache can be shared across processes. | ||
|
|
||
| Starting with `hedtools 0.2.0` local copies of the most recent schema versions | ||
| are stored within the code modules for easy access. | ||
|
|
||
| ### Other links of interest | ||
|
|
||
| Code climate reports: [https://codeclimate.com/github/hed-standard/hed-python](https://codeclimate.com/github/hed-standard/hed-python). |