multielectrode_grasp/code/python-odml

odML (Open metaData Markup Language) core library

The open metadata Markup Language is a file based format (XML, JSON, YAML) for storing metadata in an organised human- and machine-readable way. odML is an initiative to define and establish an open, flexible, and easy-to-use format to transport metadata.

The Python-odML library can be easily installed via pip. The source code is freely available on GitHub. If you are not familiar with the version control system git, but still want to use it, have a look at the documentation available on the git-scm website.

odML Project page

More information about the project including related projects as well as tutorials and examples can be found at our odML project page.

Getting started

Installation

python-odml is most conveniently installed via pip.

pip install odml

To install the latest development version of odml you can use the git installation option of pip:

pip install git+https://github.com/G-Node/python-odml

Please note that this version might not be stable.

Tutorial and examples

• We have assembled a set of tutorials.

Python convenience scripts

The Python installation features multiple convenience commandline scripts.

• odmlconvert: Converts odML files of previous file versions into the current one.
• odmltordf: Converts odML files to the supported RDF version of odML.
• odmlview: Render and browse local XML odML files in the webbrowser.

All scripts provide detailed usage descriptions by adding the help flag to the command.

odmlconvert -h
odmltordf -h
odmlview -h

Breaking changes

odML Version 1.4 introduced breaking format and API changes compared to the previous versions of odML. Files saved in the previous format versions can be converted to a 1.4 compatible format using the version converter from the odml/tools package.

Be aware that the value dtype binary has been removed. Incorporating actual binary data into odML files is discouraged, provide references to the original files using the

For details regarding the introduced changes please check the [github
release notes](https://github.com/G-Node/python-odml/releases).


# Dependencies

* Python 3.6+
* Python packages:

  * lxml (version 3.7.2)
  * yaml (version >= 5.1)
  * rdflib (version >=4.2.2)

* These packages will be downloaded and installed automatically if the ```pip```
  method is used to install odML. Alternatively, they can be installed from the OS
  package manager. On Ubuntu, they are available as:

  * python-lxml
  * python-yaml
  * python-rdflib

* If you prefer installing using the Python package manager, the following packages are
  required to build the lxml Python package on Ubuntu 14.04:

  * libxml2-dev
  * libxslt1-dev
  * lib32z1-dev

## Previous Python versions

Python 2 has reached end of life. We will not keep any future versions of odml Python 2 compatible and will completely drop support for Python 2 with August 2020. We also recommend using a Python version >= 3.6. If a Python version < 3.6 is a requirement, the following dependency needs to be installed as well:

* pip install
  * enum34 (version 0.4.4)
* apt install
  * python-enum

# Building from source

To download the Python-odML library please either use git and clone
the repository from GitHub:

$ git clone https://github.com/G-Node/python-odml.git

If you don't want to use git download the ZIP file also provided on
GitHub to your computer (e.g. as above on your home directory under a "toolbox"
folder).

To install the Python-odML library, enter the corresponding directory and run:

$ cd python-odml $ python setup.py install ```

Note The master branch is our current development branch, not all features might be working as expected. Use the release tags instead.

Contributing and Governance

See the CONTRIBUTING document for more information on this.

Bugs & Questions

Should you find a behaviour that is likely a bug, please file a bug report at the github bug tracker.

If you have questions regarding the use of the library, feel free to join the #gnode IRC channel on freenode.