Test against numpy 2.0

.github/CONTRIBUTING.md

@@ -94,19 +94,19 @@ is difficult to be described as one unit of work, please consider splitting it i
 
 The current list of issue labels are [here][link_labels] and include:
 
-* [![Good first issue](https://img.shields.io/github/labels/yeatmanlab/pyAFQ/good%20first%20issue)][link_firstissue] *These issues contain a task that is amenable to new contributors because it doesn't entail a steep learning curve.*
+* [![Good first issue](https://img.shields.io/github/labels/tractometry/pyAFQ/good%20first%20issue)][link_firstissue] *These issues contain a task that is amenable to new contributors because it doesn't entail a steep learning curve.*
 
     If you feel that you can contribute to one of these issues,
     we especially encourage you to do so!
 
-* [![Bug](https://img.shields.io/github/labels/yeatmanlab/pyAFQ/bug)][link_bugs] *These issues point to problems in the project.*
+* [![Bug](https://img.shields.io/github/labels/tractometry/pyAFQ/bug)][link_bugs] *These issues point to problems in the project.*
 
     If you find new a bug, please give as much detail as possible in your issue,
     including steps to recreate the error.
     If you experience the same bug as one already listed,
     please add any additional information that you have as a comment.
 
-* [![Enhancement](https://img.shields.io/github/labels/yeatmanlab/pyAFQ/enhancement)][link_enhancement] *These issues are asking for new features and improvements to be considered by the project.*
+* [![Enhancement](https://img.shields.io/github/labels/tractometry/pyAFQ/enhancement)][link_enhancement] *These issues are asking for new features and improvements to be considered by the project.*
 
     Please try to make sure that your requested feature is distinct from any others
     that have already been requested or implemented.
@@ -118,16 +118,16 @@ we have two sets of special labels:
 
 | Label                                                                                           | Description                                                                                           |
 |--------------------------------------------------------------------------------------------|-------------------------------------------------------------------------------------------|
-| ![GitHub labels](https://img.shields.io/github/labels/yeatmanlab/pyAFQ/impact%3A%20high) <br> ![GitHub labels](https://img.shields.io/github/labels/yeatmanlab/pyAFQ/impact%3A%20medium) <br> ![GitHub labels](https://img.shields.io/github/labels/yeatmanlab/pyAFQ/impact%3A%20low)    | Estimation of the downstream impact the proposed feature/bugfix will have.                |
-| ![GitHub labels](https://img.shields.io/github/labels/yeatmanlab/pyAFQ/effort%3A%20high) <br> ![GitHub labels](https://img.shields.io/github/labels/yeatmanlab/pyAFQ/effort%3A%20medium) <br> ![GitHub labels](https://img.shields.io/github/labels/yeatmanlab/pyAFQ/effort%3A%20low)    | Estimation of effort required to implement the requested feature or fix the reported bug. |
+| ![GitHub labels](https://img.shields.io/github/labels/tractometry/pyAFQ/impact%3A%20high) <br> ![GitHub labels](https://img.shields.io/github/labels/tractometry/pyAFQ/impact%3A%20medium) <br> ![GitHub labels](https://img.shields.io/github/labels/tractometry/pyAFQ/impact%3A%20low)    | Estimation of the downstream impact the proposed feature/bugfix will have.                |
+| ![GitHub labels](https://img.shields.io/github/labels/tractometry/pyAFQ/effort%3A%20high) <br> ![GitHub labels](https://img.shields.io/github/labels/tractometry/pyAFQ/effort%3A%20medium) <br> ![GitHub labels](https://img.shields.io/github/labels/tractometry/pyAFQ/effort%3A%20low)    | Estimation of effort required to implement the requested feature or fix the reported bug. |
 
 These labels help triage and set priorities to the development tasks.
 For instance, one bug regression that has been reported to affect most of the users after
 a release with an easy fix because it is a known old problem that came back.
-Such an issue will typically be assigned the following labels ![GitHub labels](https://img.shields.io/github/labels/yeatmanlab/pyAFQ/bug) ![GitHub labels](https://img.shields.io/github/labels/yeatmanlab/pyAFQ/impact%3A%20high) ![GitHub labels](https://img.shields.io/github/labels/yeatmanlab/pyAFQ/effort%3A%20low), and its priority will be maximal since addressing low-effort high-impact deliver the maximum turnout without increasing the churn by much.
+Such an issue will typically be assigned the following labels ![GitHub labels](https://img.shields.io/github/labels/tractometry/pyAFQ/bug) ![GitHub labels](https://img.shields.io/github/labels/tractometry/pyAFQ/impact%3A%20high) ![GitHub labels](https://img.shields.io/github/labels/tractometry/pyAFQ/effort%3A%20low), and its priority will be maximal since addressing low-effort high-impact deliver the maximum turnout without increasing the churn by much.
 
-Of course, the implementation of long-term goaled lines may include the scheduling of ![GitHub labels](https://img.shields.io/github/labels/yeatmanlab/pyAFQ/impact%3A%20medium) ![GitHub labels](https://img.shields.io/github/labels/yeatmanlab/pyAFQ/effort%3A%20high).
-Finally, ![GitHub labels](https://img.shields.io/github/labels/yeatmanlab/pyAFQ/impact%3A%20low) ![GitHub labels](https://img.shields.io/github/labels/yeatmanlab/pyAFQ/effort%3A%20high) issues are less likely to be addressed.
+Of course, the implementation of long-term goaled lines may include the scheduling of ![GitHub labels](https://img.shields.io/github/labels/tractometry/pyAFQ/impact%3A%20medium) ![GitHub labels](https://img.shields.io/github/labels/tractometry/pyAFQ/effort%3A%20high).
+Finally, ![GitHub labels](https://img.shields.io/github/labels/tractometry/pyAFQ/impact%3A%20low) ![GitHub labels](https://img.shields.io/github/labels/tractometry/pyAFQ/effort%3A%20high) issues are less likely to be addressed.
 
 ## Making a change
 
@@ -156,7 +156,7 @@ but those accepted fastest will follow a workflow similar to the following:
   add the ["upstream" pyAFQ repository as a remote][link_addremote]
   to your locally cloned repository.
     ```Shell
-    git remote add upstream https://github.com/yeatmanlab/pyAFQ.git
+    git remote add upstream https://github.com/tractometry/pyAFQ.git
     ```
     Make sure to [keep your fork up to date][link_updateupstreamwiki] with the upstream repository.<br />
     For example, to update your master branch on your local cloned repository:
@@ -240,7 +240,7 @@ acknowledge that any contributions will be licensed under the same terms.
     [MetPy project](https://github.com/Unidata/MetPy).
 
 [link_github]: https://github.com/
-[link_pyAFQ]: https://github.com/yeatmanlab/pyAFQ
+[link_pyAFQ]: https://github.com/tractometry/pyAFQ
 [link_signupinstructions]: https://help.github.com/articles/signing-up-for-a-new-github-account
 
 [link_neurostars]: https://neurostars.org/tags/pyAFQ
@@ -254,13 +254,13 @@ acknowledge that any contributions will be licensed under the same terms.
 [rick_roll]: https://www.youtube.com/watch?v=dQw4w9WgXcQ
 
 [autofq]: https://autofq.org/
-[link_issues]: https://github.com/yeatmanlab/pyAFQ/issues
-[link_labels]: https://github.com/yeatmanlab/pyAFQ/labels
+[link_issues]: https://github.com/tractometry/pyAFQ/issues
+[link_labels]: https://github.com/tractometry/pyAFQ/labels
 [link_discussingissues]: https://help.github.com/articles/discussing-projects-in-issues-and-pull-requests
 
-[link_bugs]: https://github.com/yeatmanlab/pyAFQ/labels/bug
-[link_firstissue]: https://github.com/yeatmanlab/pyAFQ/labels/good%20first%20issue
-[link_enhancement]: https://github.com/yeatmanlab/pyAFQ/labels/enhancement
+[link_bugs]: https://github.com/tractometry/pyAFQ/labels/bug
+[link_firstissue]: https://github.com/tractometry/pyAFQ/labels/good%20first%20issue
+[link_enhancement]: https://github.com/tractometry/pyAFQ/labels/enhancement
 
 [link_pullrequest]: https://help.github.com/articles/creating-a-pull-request-from-a-fork
 [link_fork]: https://help.github.com/articles/fork-a-repo/

.github/workflows/docbuild.yml

@@ -2,13 +2,19 @@ name: Documentation build
 
 on: [push, pull_request]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: write
+
 jobs:
   build:
     runs-on: ubuntu-latest
     strategy:
-      max-parallel: 4
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.11"]
 
     steps:
     - name: Checkout repo
@@ -31,14 +37,13 @@ jobs:
         cd docs
         make html
     - name: Upload docs
-      uses: actions/upload-artifact@v1
+      if: matrix.python-version == '3.11'
+      uses: actions/upload-artifact@v4
       with:
         name: docs
         path: docs/build/html
     - name: Publish docs to Github Pages
       if: startsWith(github.event.ref, 'refs/tags')
-      uses: JamesIves/github-pages-deploy-action@releases/v3
+      uses: JamesIves/github-pages-deploy-action@releases/v4
       with:
-        ACCESS_TOKEN: ${{ secrets.ACCESS_TOKEN }}
-        BRANCH: gh-pages # The branch the action should deploy to.
-        FOLDER: docs/build/html # The folder the action should deploy.
+        folder: docs/build/html

.github/workflows/docker_pyafq.yml

@@ -35,7 +35,7 @@ jobs:
         sh ./gpu_docker/docker-build.sh \
           "${GITHUB_REF:10}" "nrdg" "11.4.3-devel-ubuntu20.04" "11"
 
-    - name: Login to GHCR 
+    - name: Login to GHCR
       if: github.ref == 'refs/heads/master' || startsWith(github.event.ref, 'refs/tags')
       uses: docker/login-action@v1
       with:

.github/workflows/docker_pyafq_cuda12.yml

@@ -25,9 +25,9 @@ jobs:
         sh ./gpu_docker/docker-build.sh \
           "${GITHUB_REF:10}" "nrdg" "12.0.1-devel-ubuntu20.04" "12"
 
-    - name: Login to GHCR 
+    - name: Login to GHCR
       if: github.ref == 'refs/heads/master' || startsWith(github.event.ref, 'refs/tags')
-      uses: docker/login-action@v1
+      uses: docker/login-action@v3
       with:
         registry: ghcr.io
         username: nrdg

.github/workflows/nightly_anisotropic_test.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11"]
 
     steps:
     - name: Checkout repo

.github/workflows/nightly_basic_test.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11"]
 
     steps:
     - name: Checkout repo

.github/workflows/nightly_custom_test.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11"]
 
     steps:
     - name: Checkout repo

.github/workflows/nightly_pft_test.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11"]
 
     steps:
     - name: Checkout repo

.github/workflows/nightly_reco80_test.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11"]
 
     steps:
     - name: Checkout repo

.github/workflows/nightly_reco_test.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11"]
 
     steps:
     - name: Checkout repo

.github/workflows/nightly_test.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11"]
 
     steps:
     - name: Checkout repo

.github/workflows/publish-to-test-pypi.yml

@@ -6,34 +6,34 @@ jobs:
     name: Build and publish Python 🐍 distributions 📦 to PyPI and TestPyPI
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@master
-    - name: Set up Python 3.9
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.11
       uses: actions/setup-python@v1
       with:
-        python-version: 3.9
-    - name: Install pypa/build
+        python-version: 3.11
+    - name: Install pep517
       run: >-
         python -m
         pip install
-        build
+        pep517
         --user
     - name: Build a binary wheel and a source tarball
       run: >-
         python -m
-        build
-        --sdist
-        --wheel
-        --outdir dist/
+        pep517.build
+        --source
+        --binary
+        --out-dir dist/
         .
     - name: Publish distribution 📦 to Test PyPI
-      uses: pypa/gh-action-pypi-publish@master
+      uses: pypa/gh-action-pypi-publish@release/v1
       with:
         user: __token__
         password: ${{ secrets.test_pypi_password }}
-        repository_url: https://test.pypi.org/legacy/
+        repository-url: https://test.pypi.org/legacy/
     - name: Publish distribution 📦 to PyPI
       if: startsWith(github.event.ref, 'refs/tags')
-      uses: pypa/gh-action-pypi-publish@master
+      uses: pypa/gh-action-pypi-publish@release/v1
       with:
         user: __token__
-        password: ${{ secrets.pypi_password }}
+        password: ${{ secrets.pypi_password }}

.github/workflows/test.yml

@@ -2,14 +2,18 @@ name: Test suite
 
 on: [push, pull_request]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   build:
 
     runs-on: ubuntu-latest
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11"]
         nibabel-pre: [true, false]
 
     steps:

.zenodo.json

@@ -69,7 +69,7 @@
   "license": "BSD-3-Clause",
   "related_identifiers": [
     {
-      "identifier": "http://yeatmanlab.github.io/pyAFQ",
+      "identifier": "http://tractometry.org/pyAFQ",
       "relation": "isPartOf",
       "scheme": "url"
     }

AFQ/data/fetch.py

@@ -203,7 +203,7 @@ def read_callosum_templates(as_img=True, resample_to=False):
 #
 # - atlas: https://www.nitrc.org/projects/pediatricatlas
 #
-# - pediatric templates: https://github.com/yeatmanlab/AFQ/tree/babyAFQ
+# - pediatric templates: https://github.com/tractometry/AFQ/tree/babyAFQ
 #
 # Templates downloaded from:
 #

AFQ/tasks/viz.py

@@ -404,7 +404,7 @@ def init_viz_backend(viz_backend_spec="plotly_no_gif",
     viz_backend_spec : str, optional
         Which visualization backend to use.
         See Visualization Backends page in documentation for details:
-        https://yeatmanlab.github.io/pyAFQ/usage/viz_backend.html
+        https://tractometry.org/pyAFQ/usage/viz_backend.html
         One of {"fury", "plotly", "plotly_no_gif"}.
         Default: "plotly_no_gif"
     """

README.md

@@ -1,7 +1,7 @@
 # pyAFQ
 Automated Fiber Quantification ... in Python.
 
-For details, see [Documentation](https://yeatmanlab.github.io/pyAFQ)
+For details, see [Documentation](https://tractometry.org/pyAFQ)
 
 For further analysis of results, see [AFQ-Insight](https://github.com/richford/AFQ-Insight)
 

bin/pyAFQ

@@ -23,7 +23,7 @@ usage = \
 Runs full AFQ processing as specified in the configuration file.
 
 For details about configuration, see instructions in:
-https://yeatmanlab.github.io/pyAFQ/usage/config.html
+https://tractometry.org/pyAFQ/usage/config.html
 
 The default configuration file looks like:
 
@@ -104,7 +104,7 @@ def parse_cli(arg_dict):
         logger.info(
             "Your use of pyAFQ is being recorded using Google Analytics. "
             "For more information, please refer to the pyAFQ documentation: "
-            "https://yeatmanlab.github.io/pyAFQ/usage.html#usage-tracking-with-google-analytics. "  # noqa
+            "https://tractometry.org/pyAFQ/usage.html#usage-tracking-with-google-analytics. "  # noqa
             "To turn this off, use the `--notrack` "
             "flag when using the pyAFQ CLI")
         import popylar

docs/Makefile

@@ -20,7 +20,7 @@ help:
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
 upload: html
-		./upload-gh-pages.sh build/html/ pyAFQ yeatmanlab
+		./upload-gh-pages.sh build/html/ pyAFQ tractometry
 
 .PHONY: distclean realclean
 

docs/source/conf.py

@@ -110,7 +110,7 @@
     "icon_links": [
         {
             "name": "GitHub",
-            "url": "https://github.com/yeatmanlab/pyAFQ",
+            "url": "https://github.com/tractometry/pyAFQ",
             "icon": "fab fa-github-square",
         }]
 
@@ -122,7 +122,7 @@
 
 html_context = {
     "github_url": "https://github.com",
-    "github_user": "yeatmanlab",
+    "github_user": "tractometry",
     "github_repo": "pyAFQ",
     "github_version": "master",
     "doc_path": "docs/source",

docs/source/explanations/modeling.rst

@@ -11,7 +11,7 @@ For an interesting perspective on modeling of tissue properties from diffusion
 MRI data, please refer to a recent paper by Novikov and colleagues
 [Novikov2018]_.
 
-`This page <https://yeatmanlab.github.io/pyAFQ/reference/methods.rst>` includes
+`This page <https://tractometry.org/pyAFQ/reference/methods.rst>` includes
 a list of the model parameters that are accessible through the
 :class:`AFQ.api.group.GroupAFQ` and :class:`AFQ.api.participant.ParticipantAFQ`
 objects.

docs/source/howto/contributing.rst

@@ -4,9 +4,9 @@ How to contribute to pyAFQ
 ~~~~~~~~~~~~~~~~~~~~~
 
 pyAFQ is an open-source software project. This means that you are welcome
-to use it (see `LICENSE <https://github.com/yeatmanlab/pyAFQ/blob/master/LICENSE>`_ for details).
+to use it (see `LICENSE <https://github.com/tractometry/pyAFQ/blob/master/LICENSE>`_ for details).
 
 It also means that we welcome contributions from developers outside of our
 research collaboration and we will credit these contributions appropriately.
 
-Detailed guidelines for contribution are available `here <https://github.com/yeatmanlab/pyAFQ/blob/master/.github/CONTRIBUTING.md>`_.
+Detailed guidelines for contribution are available `here <https://github.com/tractometry/pyAFQ/blob/master/.github/CONTRIBUTING.md>`_.