incf-nidash / nidmresults

Read/Write NIDM-Results in Python

nidmresults

A Python library to read and write NIDM-Results packs.

specification: http://nidm.nidash.org/specs/nidm-results.html manuscript: https://dx.doi.org/10.1038/sdata.2016.102

You are free to copy, modify, and distribute nidmresults with attribution under the terms of the MIT license. See the LICENSE file for details.

Install

nidmresults is distributed with PyPI, to install the latest release you can use:

pip install nidmresults

To work with the current development version we recommend cloning this repository locally and then install using

python setup.py install

Example of usage

Examples are available in the examples folder.

Contributing

Thanks for your interest in contributing to nidmresults. All contributions are very welcome! If you experience difficulties using the library, please open an issue describing the problem. See the list of current issues.

nidmresults's Issues

Move TestResultDataModel.py from main nidm repository

The python file https://github.com/incf-nidash/nidm/blob/master/nidm/nidm-results/test/TestResultDataModel.py should be moved over here as all the NIDM-Results exporter repositories now depend on the nidmresults module.

Example of how to read a NIDM-Results pack

nidmresults lacks documentation. It would be great to create an examples folder containing jupyter notebooks.

The first example could be a demonstration of how to read a NIDM pack and retrieve the statistic map (example datasets are available at: https://neurovault.org/collections/1425/).

Delete temporary nidm folder if error

Just discussed with @nicholst: when an error is thrown (e.g. no number of subjects for a group analysis), the created temporary nidm folder should be deleted before returning.

Mandatory arguments should be consistent with SPARQL query

MKDA exported coordinates should be sorted

(so that we can version control differences in exported files)

Test should use NIDM version in config file

(instead of nidm version in the exported document).

Faster reading and testing

Reading is quite slow... is there anything we can do to have read faster. Maybe by updating the queries / checking which query if run when / relying on the JSON when available.

clean up roadmap

• move testing to GHA
• update to avoid any failing or flaky test
• update packaging (setup.py + setuptools -> pyproject.toml + hatchling)
• use pytest for testing and get coverage
• enforce code style: black + flake8 + precommit
• upgrade code to use more modern python features: https://github.com/asottile/pyupgrade
• incorporate refactoring from sourcery: Remi-Gau#1

Modification of string cast in owl_reader.py

I would like to suggest a modification to owl_reader.py. Right now any modifications to the nidm-experiment owl or import files fails due to the string cast here. The files pass the Travis checking if the cast to string is removed. This was discussed awhile ago, but it was never changed. IIRC the reason for the cast was not clear at the time. @cmaumet is there any reason not to make this modification?

Some examples of code that could be replaced by nidmresults functions

After discussion at NIDM sprint we decided to implement easy to use functions for common NIDM Results queries. This should lower the access barrier for new developer. Those functions can live in the nidmresults package. They could immediately replace some sparql queries in NeuroVault and nidmviewer (maintained by @vsoch).

get_statmaps() https://github.com/NeuroVault/NeuroVault/blob/0ba7f42a11d703ee608317fe7f0c24fd62d48fc5/neurovault/apps/statmaps/nidm_results.py#L64
as well as https://github.com/vsoch/nidmviewer/blob/882f5201354135ff4dc6ec8739621a94341d0fef/nidmviewer/sparql.py#L43
(this could be split into more functions if that makes sense)

get_coordinates()
https://github.com/vsoch/nidmviewer/blob/882f5201354135ff4dc6ec8739621a94341d0fef/nidmviewer/sparql.py#L28

Refactoring: bundle class should be in objects module

Inject an ID namespace in the NIDM context when using external ID mapping

As discussed with @mih at cmaumet#2 (comment), we need to implement "how to properly inject an ID namespace in the NIDM context. But for now search&replace is good enough."

Inconsistent API

get_excursion_set_maps() returns a dictionary and get_statistic_maps() returns a list

Embed nidm-results.owl

nidm-results.owl (released versions) should be included in the nidmresults library so that we can look up labels and avoid dependency on nidm repository.

Run FSL's testing suite when submitting a PR?

Check if whenever we create a new PR in this repo we could run the FSL's exporter tests to check that both modules are still compatible.

Remove provn serialisation

As agreed in incf-nidash/nidm-specs#378, provn serialisation should be removed.

Minimal contributing documentation

Let's make our project more welcoming!

First steps, adding:

• Open source license --> #47
• README
• Contributing guidelines
• Code of conduct

Some resources: Open source guide, Mozilla open leadership training: write a great project readme and README checklist.