From 898ec99c54ab1766daba0fac0f3a13951c76ce87 Mon Sep 17 00:00:00 2001 From: Ariel Rokem Date: Tue, 20 Aug 2024 16:27:52 -0700 Subject: [PATCH 1/5] DOC: Update front page with the full citation to our paper. --- docs/index.rst | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/docs/index.rst b/docs/index.rst index 321e30c..17ec847 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -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 `_: -If you are interested in technical details and motivation behind this project, please read our `paper `_. + `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 `_. Acknowledgements ~~~~~~~~~~~~~~~~~~~ From 3aa6dd66c258cba9b1fb2be959a3e5a0b62ecb2a Mon Sep 17 00:00:00 2001 From: Ariel Rokem Date: Wed, 11 Sep 2024 16:01:49 -0700 Subject: [PATCH 2/5] Some linting, use modern python version for pypi upload. --- .github/workflows/publish-to-test-pypi.yml | 4 ++-- afqbrowser/browser.py | 5 +++-- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/.github/workflows/publish-to-test-pypi.yml b/.github/workflows/publish-to-test-pypi.yml index 391fb42..ccc20d7 100644 --- a/.github/workflows/publish-to-test-pypi.yml +++ b/.github/workflows/publish-to-test-pypi.yml @@ -13,10 +13,10 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v4 - - name: Set up Python 3.7 + - name: Set up Python 3.10 uses: actions/setup-python@v1 with: - python-version: 3.7 + python-version: 3.10 - name: Install pep517 run: >- python -m diff --git a/afqbrowser/browser.py b/afqbrowser/browser.py index 58d68d9..1158579 100644 --- a/afqbrowser/browser.py +++ b/afqbrowser/browser.py @@ -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) @@ -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") From 0b6ef5d33eba2ef90dbdc4e3382d270ede23bfa6 Mon Sep 17 00:00:00 2001 From: Ariel Rokem Date: Wed, 11 Sep 2024 16:02:57 -0700 Subject: [PATCH 3/5] Newer version of this action. --- .github/workflows/publish-to-test-pypi.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/publish-to-test-pypi.yml b/.github/workflows/publish-to-test-pypi.yml index ccc20d7..187fc94 100644 --- a/.github/workflows/publish-to-test-pypi.yml +++ b/.github/workflows/publish-to-test-pypi.yml @@ -14,7 +14,7 @@ jobs: steps: - uses: actions/checkout@v4 - name: Set up Python 3.10 - uses: actions/setup-python@v1 + uses: actions/setup-python@v5 with: python-version: 3.10 - name: Install pep517 From 0b44229d37e143e96612e0a3a5e8d12fed72f384 Mon Sep 17 00:00:00 2001 From: Ariel Rokem Date: Wed, 11 Sep 2024 16:07:45 -0700 Subject: [PATCH 4/5] Two-digit minor versions are so special. --- .github/workflows/publish-to-test-pypi.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/publish-to-test-pypi.yml b/.github/workflows/publish-to-test-pypi.yml index 187fc94..f570479 100644 --- a/.github/workflows/publish-to-test-pypi.yml +++ b/.github/workflows/publish-to-test-pypi.yml @@ -16,7 +16,7 @@ jobs: - name: Set up Python 3.10 uses: actions/setup-python@v5 with: - python-version: 3.10 + python-version: "3.10" - name: Install pep517 run: >- python -m From b7f6accfe95646a8a88bf16b3679be4c1bd61916 Mon Sep 17 00:00:00 2001 From: Ariel Rokem Date: Wed, 11 Sep 2024 16:09:34 -0700 Subject: [PATCH 5/5] Upgrade upload artifact action version. --- .github/workflows/docs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index fa200d1..57cccfe 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -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