Package: neurodatapub
NeuroDataPub: NCCR-SYNAPSY Neuroimaging Dataset Publishing ToolThis tool is developed by theConnectomics
Labat the University Hospital of
Lausanne (CHUV) for use within the lab and within theNational Centre
of Competence in Research (NCCR) "SYNAPSY – Synaptic Bases of Mental
Diseases" NCCR-SYNAPSY, as well as for
open-source software distribution.OverviewNeuroDataPubis an open-source neuroimaging dataset publishing tool written in Python and built on top of
Datalad and git-annex. It aims to lower the barriers, for the NCCR-SYNAPSY members,
to manage and publish, privately or publicly, their dataset repositories on GitHub and the annexed files on
their SSH data server, in order to fully fulfill the implemented Neuroimaging Data Management Plan.Sincev0.3, you can use either (1) a server accessible viasshor (2) the Open Science Foundation (OSF)
platform, as a git-annex special remote, to host your annexed files.Sincev0.4,NeuroDataPubcan handle datasets that do and do not follow theBrain Imaging Data Structurestandard.NeuroDataPubcomes with its graphical user interface, aka theNeuroDataPub Assistant,
created to facilitate:the configuration of the siblings,the creation of the JSON configuration files, as well asthe execution of NeuroDataPub in three different modes:creation and publication of a datalad dataset,creation of a datalad dataset only,publication of an existing datalad dataset only,the creation of a Linux shell script for later execution where all commands are recorded.NeuroDataPubis a Python 3.8 package that can be easily installed withpipas follows:pipinstallneurodatapubDocumentationhttps://neurodatapub.readthedocs.io/UsageNeuroDataPubhas the following commandline arguments:usage: neurodatapub [-h] --mode {all,create-only,publish-only}--dataset_dir DATASET_DIR [--is_not_bids]--datalad_dir DATALAD_DIR--github_sibling_config GITHUB_SIBLING_CONFIG(--git_annex_ssh_special_sibling_config GIT_ANNEX_SSH_SPECIAL_SIBLING_CONFIG | --osf_sibling_config OSF_SIBLING_CONFIG)[--gui] [--generate_script] [-v]Command-line argument parser of `NeuroDataPub` (v0.4)optional arguments:-h, --help            show this help message and exit.--mode {all,create-only,publish-only}Mode in which ``neurodatapub`` is run: ``"create-only"`` createthe datalad dataset only, ``"publish-only"`` publish the dataladdataset only, ``"all"` create and publish the datalad dataset.--dataset_dir DATASET_DIRThe directory with the input dataset formatted accordingto the BIDS standard. Specify if the directory with the inputdataset is not formatted according to the BIDS standard.--is_not_bids         Specify if the directory with the input dataset is not formattedaccording to the BIDS standard.--datalad_dir DATALAD_DIRThe local directory where the Datalad dataset should be.--github_sibling_config GITHUB_SIBLING_CONFIGPath to a JSON file containing configuration parameters forthe GitHub dataset repository sibling.--git_annex_ssh_special_sibling_config GIT_ANNEX_SSH_SPECIAL_SIBLING_CONFIGPath to a JSON file containing configuration parameters forthe git-annex SSH special remote dataset sibling.--osf_sibling_config OSF_SIBLING_CONFIGPath to a JSON file containing configuration parameters forthe git-annex OSF special remote dataset sibling.--gui                 Run NeuroDataPub in GUI mode.--generate_script     Dry run that generates a bash script called`neurodatapub_DD-MM-YYYY_hh:mm:ss.sh` in the `code/` folderof the input dataset that records all commands for later execution.-v, --version         show program's version number and exit.AcknowledgmentIf your are usingNeuroDataPubin your work, please acknowledge this
software and its dependencies:Tourbier S, Hagmann P., (2021). NCCR-SYNAPSY/neurodatapub: NCCR-SYNAPSY Neuroimaging Dataset Publishing Tool (Version 0.1). Zenodo.Halchenko et al., (2021). DataLad: distributed system for joint management of code, data, and their relationship. Journal of Open Source Software, 6(63), 3262,https://doi.org/10.21105/joss.03262.License informationThis software is distributed under the open-source Apache 2.0 license.
Seelicensefor more details.All trademarks referenced herein are property of their respective
holders.Help/QuestionsIf you run into any problems or have any code bugs or questions, please
create a newGitHub Issue.FundingSupported by the National Centre of Competence in Research (NCCR)
"SYNAPSY – Synaptic Bases of Mental Diseases"
(NCCR-SYNAPSY website/NCCR-SYNAPSY Swiss National Science Foundation page) supported bySNF-185897 grant.Contributors ✨Thanks goes to these wonderful people (emoji key):Sébastien Tourbier💻📖🎨🤔🚇🚧🧑‍🏫📆💬👀Patric Hagmann🔍This project follows theall-contributorsspecification. Contributions of any kind welcome!