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WIP: Update to automatically work with our current pyAFQ outputs #3

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WIP: Update to automatically work with our current pyAFQ outputs #3

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898ec99
DOC: Update front page with the full citation to our paper.
arokem Aug 20, 2024
3aa6dd6
Some linting, use modern python version for pypi upload.
arokem Sep 11, 2024
0b6ef5d
Newer version of this action.
arokem Sep 11, 2024
0b44229
Two-digit minor versions are so special.
arokem Sep 11, 2024
b7f6acc
Upgrade upload artifact action version.
arokem Sep 11, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/docs.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@ jobs:
cd docs
make html
- name: Upload docs
uses: actions/upload-artifact@v1
uses: actions/upload-artifact@v4
with:
name: docs
path: docs/_build/html
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6 changes: 3 additions & 3 deletions .github/workflows/publish-to-test-pypi.yml
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Expand Up @@ -13,10 +13,10 @@ jobs:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Set up Python 3.7
uses: actions/setup-python@v1
- name: Set up Python 3.10
uses: actions/setup-python@v5
with:
python-version: 3.7
python-version: "3.10"
- name: Install pep517
run: >-
python -m
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5 changes: 3 additions & 2 deletions afqbrowser/browser.py
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Expand Up @@ -76,7 +76,8 @@ def _extract_params(afq):

def _create_metadata(subject_ids, meta_fname):
"""Helper function to create a minimal metadata file."""
meta_df = pd.DataFrame({"subjectID": subject_ids}, index=range(len(subject_ids)))
meta_df = pd.DataFrame({"subjectID": subject_ids},
index=range(len(subject_ids)))
meta_df.to_csv(meta_fname)


Expand Down Expand Up @@ -176,7 +177,7 @@ def _validate(nodes_fname, meta_fname, streamlines_fname):

meta_df = pd.read_csv(meta_fname)

# check subjcts consistent
# check subjects consistent
if "subjectID" not in meta_df.columns:
validation_errors.append(
ValueError("Metadata file missing required column: subjectID")
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6 changes: 2 additions & 4 deletions docs/index.rst
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Expand Up @@ -20,12 +20,10 @@ data.

.. _AFQ: http://github.com/yeatmanlab/AFQ

AFQ-Browser paper
~~~~~~~~~~~~~~~~~
More details and motivation behind this project, are available in the `paper <https://www.nature.com/articles/s41467-018-03297-7>`_:

If you are interested in technical details and motivation behind this project, please read our `paper <https://www.nature.com/articles/s41467-018-03297-7>`_.
`Yeatman, J. D., Richie-Halford, A., Smith, J. K., Keshavan, A., & Rokem, A. (2018). A browser-based tool for visualization and analysis of diffusion MRI data. Nature Communications, 9(1), 940.`

A slide presentation about the project is available `here <https://arokem.github.io/2019-OHBM-AFQ-Browser/>`_.

Acknowledgements
~~~~~~~~~~~~~~~~~~~
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