Nipype 2.0: building new ecosystem around Pydra

Project info

Title: Nipype 2.0: building new ecosystem around Pydra

Project lead: Dorota Jarecka, @djarecka Christopher Markiewicz: @effigies Hao-Ting Wang: @htwangtw Jeffrey Wigger: @jw-96 Satra Ghosh @satra

Timezone:

afternoon/evening Europe & morning/afternoon East Coast we will start around noon UTC and finish around 7/8 PM UTC

Description: We are creating Nipype 2.0 ecosystem around Pydra package. Pydra is a new dataflow engine, coordinating the movement of data from the output of one computational node to the input of another node. A workflow is represented as a graph, and each node is a Task object, which may be a Python function or an interface to an external tool.

During this hackathon we want to work on the core package, but also prepare converters for Nipype 1.0 interfaces. We are also planning to improve documentation and tutorials.

Pyrda is a lightweight, Py3.7+ dataflow engine for computational graph construction, manipulation, and distributed execution.

Link to project: any repo from the nipype organization: https://github.com/nipype

Mattermost handle: dorota, markiewicz, haoting, jeffrey

Goals for the OHBM Brainhack

working on pydra - dataflow engine
converting Nipype interfaces
adding better support for boutiques
improving documentation and tutorial full list could be found (and edited) here: https://docs.google.com/document/d/1ZuMD-hagnUQPZvud8k1jXdAPE55RpWGMYXcVBcsw6S8/edit?usp=sharing

Good first issues:

exploring tutorial: https://github.com/nipype/pydra-tutorial
improving documentation: https://github.com/nipype/pydra/issues?q=is%3Aissue+is%3Aopen+label%3A%22good+first+issue%22

Skills:

some python
nipype experience (optional)
experience with any software supported by nipype (FSL, ANTs, SPM, etc.; optional)
distributed execution (optional)

Chat channel:

nipype

https://mattermost.brainhack.org/brainhack/channels/nipype

Video channel:

we will be using either the main platform or jitsi. Please check the mattermost

Image for the OHBM brainhack website

pydra_logo

Project submission

Submission checklist

Once the issue is submitted, please check items in this list as you add under 'Additional project info'

Please include the following above (all required):

[x] Link to your project: could be a code repository, a shared document, etc. See here
[x] Include your Mattermost handle (i.e. your username). If you do not have an account, please sign up here.
[x] Goals for the OHBM Brainhack: describe what you want to achieve during this brainhack. See here.
[x] Flesh out at least 2 "good first issues": those are tasks that do not require any prior knowledge about your project, could be defined as issues in a GitHub repository, or in a shared document, cf here.
[x] Skills: list skills that would be particularly suitable for your project. We ask you to include at least one non-coding skill, cf. here.
[x] Chat channel: A link to a chat channel that will be used during the OHBM Brainhack. This can be an existing channel or a new one. We recommend using the Brainhack space on mattermost, cf. here.
[x] Provide an image of your project for the OHBM brainhack website

You can also include information about (all optional):

[ ] Someone co-leading the project in the timeslot you have not selected to provide additional visibility.
[ ] Number of participants, cf. here
[ ] Twitter-size summary of your project pitch, cf. here
[ ] Set up a kanban board on your repository to better divide the work and keep track of things, cf here
[ ] Project snippet for the OHBM Brainhack website, cf. here

We would like to think about how you will credit and onboard new members to your project. We recommend reading references from this section. If you'd like to share your thoughts with future project participants, you can include information about (recommended):

[ ] Specify how will you acknowledge contributions (e.g. listing members on a contributing page).
[ ] Provide links to onboarding documents if you have some.

QMENTA has agreed to sponsor the event and provide computational resources through their platform.

[ ] Get in touch with QMENTA through their Brain Innovation Hub Slack space, if you think your project would benefit from their support.

ohbm / hackathon2021