|
1 | | -[](https://doi.org/10.5281/zenodo.8056010) |
2 | | -[](https://codeclimate.com/github/hed-standard/hed-python/maintainability) |
3 | | -[](https://codeclimate.com/github/hed-standard/hed-python/test_coverage) |
4 | | - |
5 | | -[](https://hed-python.readthedocs.io/en/latest/?badge=latest) |
6 | | - |
7 | | -# HEDTools - Python |
8 | | -HED (Hierarchical Event Descriptors) is a framework for systematically describing |
9 | | -both laboratory and real-world events as well as other experimental metadata. |
10 | | -HED tags are comma-separated path strings. |
11 | | -HED, itself, is platform-independent, extendable, and data-neutral. |
12 | | - |
13 | | -This repository contains the underlying python tools that support validation, |
14 | | -summarization, and analysis of datasets using HED tags. |
15 | | - |
16 | | -Most people will simply annotate their events by creating a spreadsheet |
17 | | -or a BIDS JSON sidecar that associates HED tags with event codes or the events themselves. |
18 | | -If you have such a spreadsheet or a JSON, |
19 | | -you can use the HED Online Validator currently available at |
20 | | -[https://hedtools.org](https://hedtools.org) to validate or transform |
21 | | -your files without downloading any tools. |
22 | | - |
23 | | -A version of the online tools corresponding to the `develop` branch can be found at: |
24 | | -[https://hedtools.org/hed_dev](https://hedtools.org/hed_dev). |
25 | | - |
26 | | -### Installation |
27 | | -Use `pip` to install `hedtools` from PyPI: |
28 | | - |
29 | | - ``` |
30 | | - pip install hedtools |
31 | | - ``` |
32 | | - |
33 | | -To install directly from the |
34 | | -[GitHub](https://github.com/hed-standard/hed-python) repository `master` branch: |
35 | | - |
36 | | - ``` |
37 | | - pip install git+https://github.com/hed-standard/hed-python/@master |
38 | | - ``` |
39 | | - |
40 | | -The HEDTools in this repository require Python 3.8 or greater. |
41 | | - |
42 | | -### Relationship to other repositories |
43 | | - |
44 | | -The `hed-python` repository contains the Python infrastructure for validating |
45 | | -and analyzing HED. This repository has several companion repositories: |
46 | | -- [`hed-web`](https://github.com/hed-standard/hed-web) contains the web interface |
47 | | -for HED as well as a deployable docker module that supports web services for HED. |
48 | | -- [`hed-examples`](https://github.com/hed-standard/hed-examples) contains examples of |
49 | | -using HED in Python and MATLAB. This repository also houses the HED resources. |
50 | | -See [https://www.hed-resources.org](https://www.hed-resources.org) for access to these. |
51 | | -- [`hed-specification`](https://github.com/hed-standard/hed-specification) contains |
52 | | -the HED specification documents. The `hed-python` validator is keyed to error codes |
53 | | -in this document. |
54 | | -- [`hed-schemas`](https://github.com/hed-standard/hed-schemas) contains |
55 | | -the official HED schemas. The tools access this repository to retrieve and cache schema versions |
56 | | -during execution. Starting with `hedtools 0.2.0` local copies of the most recent schema versions |
57 | | -are stored within the code modules for easy access. |
58 | | - |
59 | | -#### Develop versus master versus stable branches |
60 | | - |
61 | | -The `hed-python` repository |
62 | | - |
63 | | -| Branch | Meaning | Synchronized with | |
64 | | -| ------ | -------- | ------------------ | |
65 | | -| stable | Officially released on PyPI as a tagged version. | `stable@hed-web`<br/>`stable@hed-specification`<br/>`stable@hed-examples` | |
66 | | -| latest | Most recent usable version. | `latest@hed-web`<br/>`latest@hed-specification`<br/>`latest@hed-examples` | |
67 | | -| develop | Experimental and evolving. | `develop@hed-web`<br/>`develop@hed-specification`<br/>`develop@hed-examples` | |
68 | | - |
69 | | -As features are integrated, they first appear in the `develop` branches of the |
70 | | -repositories. |
71 | | -The `develop` branches of the repositories will be kept in sync as much as possible |
72 | | -If an interface change in `hed-python` triggers a change in `hed-web` or `hed-examples`, |
73 | | -every effort will be made to get the three types of branches |
74 | | -(`develop`, `latest`, `stable`) of the respective repositories in |
75 | | -sync. |
76 | | - |
77 | | -API documentation is generated on ReadTheDocs when a new version is |
78 | | -pushed on any of the three branches. For example, the API documentation for the |
79 | | -`latest` branch can be found on [hed-python.readthedocs.io/en/latest/](hed-python.readthedocs.io/en/latest/). |
80 | | - |
81 | | -#### To contribute |
82 | | - |
83 | | -Contributions are welcome. |
84 | | -Please use the [Github issues](https://github.com/hed-standard/hed-python/issues) |
85 | | -for suggestions or bug reports. |
86 | | -The [Github pull request](https://github.com/hed-standard/hed-python/pulls) |
87 | | -may also be used for contributions. |
88 | | -These PRs should be made to the `develop` branch, not the `master` branch. |
89 | | - |
90 | | -#### Local Settings Storage |
91 | | -Cached Schemas by default are stored in "home/.hedtools/" |
92 | | -Location of "home" directory varies by OS. |
93 | | - |
94 | | -Use `hed.schema.set_cache_directory` to change the location. |
95 | | -The HED cache can be shared across processes. |
96 | | - |
97 | | -Starting with `hedtools 0.2.0` local copies of the most recent schema versions |
98 | | -are stored within the code modules for easy access. |
99 | | - |
100 | | -### Other links of interest |
101 | | - |
102 | | -Code climate reports: [https://codeclimate.com/github/hed-standard/hed-python](https://codeclimate.com/github/hed-standard/hed-python). |
| 1 | +[](https://doi.org/10.5281/zenodo.8056010) |
| 2 | +[](https://codeclimate.com/github/hed-standard/hed-python/maintainability) |
| 3 | +[](https://codeclimate.com/github/hed-standard/hed-python/test_coverage) |
| 4 | + |
| 5 | + |
| 6 | +[](https://hed-python.readthedocs.io/en/latest/?badge=latest) |
| 7 | + |
| 8 | +# HEDTools - Python |
| 9 | +HED (Hierarchical Event Descriptors) is a framework for systematically describing |
| 10 | +both laboratory and real-world events as well as other experimental metadata. |
| 11 | +HED tags are comma-separated path strings. |
| 12 | +HED, itself, is platform-independent, extendable, and data-neutral. |
| 13 | + |
| 14 | +This repository contains the underlying python tools that support validation, |
| 15 | +summarization, and analysis of datasets using HED tags. |
| 16 | + |
| 17 | +Most people will simply annotate their events by creating a spreadsheet |
| 18 | +or a BIDS JSON sidecar that associates HED tags with event codes or the events themselves. |
| 19 | +If you have such a spreadsheet or a JSON, |
| 20 | +you can use the HED Online Validator currently available at |
| 21 | +[https://hedtools.org](https://hedtools.org) to validate or transform |
| 22 | +your files without downloading any tools. |
| 23 | + |
| 24 | +A version of the online tools corresponding to the `develop` branch can be found at: |
| 25 | +[https://hedtools.org/hed_dev](https://hedtools.org/hed_dev). |
| 26 | + |
| 27 | +### Installation |
| 28 | +Use `pip` to install `hedtools` from PyPI: |
| 29 | + |
| 30 | + ``` |
| 31 | + pip install hedtools |
| 32 | + ``` |
| 33 | + |
| 34 | +To install directly from the |
| 35 | +[GitHub](https://github.com/hed-standard/hed-python) repository `master` branch: |
| 36 | + |
| 37 | + ``` |
| 38 | + pip install git+https://github.com/hed-standard/hed-python/@master |
| 39 | + ``` |
| 40 | + |
| 41 | +The HEDTools in this repository require Python 3.8 or greater. |
| 42 | + |
| 43 | +### Relationship to other repositories |
| 44 | + |
| 45 | +The `hed-python` repository contains the Python infrastructure for validating |
| 46 | +and analyzing HED. This repository has several companion repositories: |
| 47 | +- [`hed-web`](https://github.com/hed-standard/hed-web) contains the web interface |
| 48 | +for HED as well as a deployable docker module that supports web services for HED. |
| 49 | +- [`hed-examples`](https://github.com/hed-standard/hed-examples) contains examples of |
| 50 | +using HED in Python and MATLAB. This repository also houses the HED resources. |
| 51 | +See [https://www.hed-resources.org](https://www.hed-resources.org) for access to these. |
| 52 | +- [`hed-specification`](https://github.com/hed-standard/hed-specification) contains |
| 53 | +the HED specification documents. The `hed-python` validator is keyed to error codes |
| 54 | +in this document. |
| 55 | +- [`hed-schemas`](https://github.com/hed-standard/hed-schemas) contains |
| 56 | +the official HED schemas. The tools access this repository to retrieve and cache schema versions |
| 57 | +during execution. Starting with `hedtools 0.2.0` local copies of the most recent schema versions |
| 58 | +are stored within the code modules for easy access. |
| 59 | + |
| 60 | +#### Develop versus master versus stable branches |
| 61 | + |
| 62 | +The `hed-python` repository |
| 63 | + |
| 64 | +| Branch | Meaning | Synchronized with | |
| 65 | +| ------ | -------- | ------------------ | |
| 66 | +| stable | Officially released on PyPI as a tagged version. | `stable@hed-web`<br/>`stable@hed-specification`<br/>`stable@hed-examples` | |
| 67 | +| latest | Most recent usable version. | `latest@hed-web`<br/>`latest@hed-specification`<br/>`latest@hed-examples` | |
| 68 | +| develop | Experimental and evolving. | `develop@hed-web`<br/>`develop@hed-specification`<br/>`develop@hed-examples` | |
| 69 | + |
| 70 | +As features are integrated, they first appear in the `develop` branches of the |
| 71 | +repositories. |
| 72 | +The `develop` branches of the repositories will be kept in sync as much as possible |
| 73 | +If an interface change in `hed-python` triggers a change in `hed-web` or `hed-examples`, |
| 74 | +every effort will be made to get the three types of branches |
| 75 | +(`develop`, `latest`, `stable`) of the respective repositories in |
| 76 | +sync. |
| 77 | + |
| 78 | +API documentation is generated on ReadTheDocs when a new version is |
| 79 | +pushed on any of the three branches. For example, the API documentation for the |
| 80 | +`latest` branch can be found on [hed-python.readthedocs.io/en/latest/](hed-python.readthedocs.io/en/latest/). |
| 81 | + |
| 82 | +#### To contribute |
| 83 | + |
| 84 | +Contributions are welcome. |
| 85 | +Please use the [Github issues](https://github.com/hed-standard/hed-python/issues) |
| 86 | +for suggestions or bug reports. |
| 87 | +The [Github pull request](https://github.com/hed-standard/hed-python/pulls) |
| 88 | +may also be used for contributions. |
| 89 | +These PRs should be made to the `develop` branch, not the `master` branch. |
| 90 | + |
| 91 | +#### Local Settings Storage |
| 92 | +Cached Schemas by default are stored in "home/.hedtools/" |
| 93 | +Location of "home" directory varies by OS. |
| 94 | + |
| 95 | +Use `hed.schema.set_cache_directory` to change the location. |
| 96 | +The HED cache can be shared across processes. |
| 97 | + |
| 98 | +Starting with `hedtools 0.2.0` local copies of the most recent schema versions |
| 99 | +are stored within the code modules for easy access. |
| 100 | + |
| 101 | +### Other links of interest |
| 102 | + |
| 103 | +Code climate reports: [https://codeclimate.com/github/hed-standard/hed-python](https://codeclimate.com/github/hed-standard/hed-python). |
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