neurodatapub - NeuroDataPub v0.4

NeuroDataPub is an open-source neuroimaging dataset publication tool, built on top of Datalad , designed to helpsNCCR-Synapsy members in the task of managing their dataset with Datalad, and referencing them to the NCCR-SYNAPSY GitHub organization.

This corresponds to the fourth beta release of NeuroDataPub.

What's changed?

New Features

• Create a bash script that records all commands generated by NeuroDataPub for later execution.

• Give the option to handle datasets that do not follow BIDS standard. This can be configured either via the new is_not_bids option flag of the commandline interface, or by disabling the "Dataset is bids" option in the "Configuration of Directories" tab.

• Ignore existing files during the copy of dataset files with rsync.

Minor changes

• Copyright year has been updated in all files.

• --bids_dir argument of the commandline interface has been changed to --dataset_dir.

• The attribute input_bids_dir of NeuroDataPubProject has been changed to input_dataset_dir.

• Suppress QXcbConnection: XCB error message during execution of NeuroDataPub.

Bug Fixes

• Correct the pattern employed during the check of the schema of the JSON configurations for the "github_login" and "github_token" fields.

• Do not reload datalap.api and do not reset osf credentials in authenticate_osf().

Documentation

• Update documentation for the creation of the bash script using NeuroDataPub Assistant.

• Add details about the new option to handle non BIDS datasets.

More...

Please check the main release pull request PR #38.

- Python
Published by sebastientourbier about 4 years ago

neurodatapub - NeuroDataPub v0.3

Third beta release of NeuroDataPub that includes in particular the following changes.

New Features

• Publish dataset (no annex) to GitHub and the annexed files to OSF. (See PR#35)
• Improve automation of GitHub authentication and add github_organization to the config file. (See PR#36)

Documentation

• Update documentation for the publication to OSF and update the image for the configuration of the siblings using NeuroDataPub Assistant. (See PR#37)

More...

Please check the main release pull request PR#32.

- Python
Published by sebastientourbier over 4 years ago

neurodatapub - NeuroDataPub v0.2

Second beta release of NeuroDataPub that includes in particular the following changes since v0.1.

New Features

• Update automatically the SSH config with an entry for the remote SSH server to configure the user login used by default by ssh. (PR#25)

Documentation

• Add documentation page to give instructions for the remote data server setup. (PR#28)
• Update documentation for the creation of the conda environment and the installation of git-annex on Linux and MacOSX (PR#23)

Bug Fixes

• Replace old datalad.api.publish() with new datalad.api.push(). (PR#22)

Misc

• Add conda/environment_macosx.yml, a conda environment file specific to MacOSX where git-annex is not included. (PR#23)
• Use content of README as long_description in setup.py for publication to PyPI. (PR#26)

More...

Please check PR#24, the main release pull request.

- Python
Published by sebastientourbier over 4 years ago

neurodatapub - NeuroDataPub v0.1

Beta release of NeuroDataPub which provides a first working prototype.

Features

• Provide a commandline interface (CLI) to create and publish neuroimaging datasets to GitHub NCCR-SYNAPSY, with files annexed in a host institution, accessible via ssh.
• Adopt a traits/traitsui model that extends the CLI with a graphical user interface, aka the NeuroDataPub Assistant, to improve its accessibility by non IT experts.
• Provide a Conda environment.yml to support the installation of Python with all dependencies.
• Provide a setup.py to make installation of the neurodatapub package easy with pip install.
• Adopt CircleCI for continuous integration testing. CircleCI project page: https://app.circleci.com/pipelines/github/NCCR-SYNAPSY/neurodatapub
• Use Codacy to support code reviews and monitor code quality over time. Codacy project page: https://app.codacy.com/gh/NCCR-SYNAPSY/neurodatapub/dashboard

More...

For more change details and development discussions, please check:

• PR #1: Main PR with the core API.
• PR #7, PR #16, PR #17, PR #18, PR #19: PRs that adds the read-the-docs documentation source code and images.
• PR #8: PR that adds the use of CircleCI for testing the installation and deploying the package to PyPI.
• PR #9: PR that adopts Codacy, correct code style issues, and update the README.
• PR #12: PR that refines the setup.py (project status set to BETA) before deployment to PyPI .
• PR #13, PR #21: PRs that refines changes.rst. PR #21 updates tool intro in index.rst and README.md before deployment to PyPI.
• PR #20: PR that makes all options not required when executing with --gui.

GitHub Repo

• https://github.com/NCCR-SYNAPSY/neurodatapub

- Python
Published by sebastientourbier over 4 years ago