From 4cf3eeb9921665aa01f70208126d8ff5ae86d071 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Wed, 23 Oct 2024 10:42:41 -0400
Subject: [PATCH 01/28] CI: Test on Python 3.13t across OSs

---
 .github/workflows/test.yml | 28 +++++++++++++++-------------
 1 file changed, 15 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 3ca5769fe..44ab04e9c 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -113,7 +113,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ['ubuntu-latest', 'windows-latest', 'macos-13', 'macos-latest']
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13t"]
         architecture: ['x64', 'x86', 'arm64']
         dependencies: ['full', 'pre']
         include:
@@ -125,10 +125,6 @@ jobs:
           - os: ubuntu-latest
             python-version: 3.9
             dependencies: 'min'
-          # NoGIL
-          - os: ubuntu-latest
-            python-version: '3.13-dev'
-            dependencies: 'dev'
         exclude:
           # x86 for Windows + Python<3.12
           - os: ubuntu-latest
@@ -139,6 +135,8 @@ jobs:
             architecture: x86
           - python-version: '3.12'
             architecture: x86
+          - python-version: '3.13t'
+            architecture: x86
           # arm64 is available for macos-14+
           - os: ubuntu-latest
             architecture: arm64
@@ -167,25 +165,29 @@ jobs:
         with:
           submodules: recursive
           fetch-depth: 0
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v3
       - name: Set up Python ${{ matrix.python-version }}
-        if: "!endsWith(matrix.python-version, '-dev')"
+        if: "!endsWith(matrix.python-version, 't')"
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
           architecture: ${{ matrix.architecture }}
           allow-prereleases: true
       - name: Set up Python ${{ matrix.python-version }}
-        if: endsWith(matrix.python-version, '-dev')
-        uses: deadsnakes/action@v3.2.0
-        with:
-          python-version: ${{ matrix.python-version }}
-          nogil: true
+        if: endsWith(matrix.python-version, 't')
+        run: |
+          uv python install ${{ matrix.python-version }}
+          uv venv --python ${{ matrix.python-version }} ../.venv
+          . .venv/bin/activate
+          echo "PATH=$PATH" >> $GITHUB_ENV
+          echo "VIRTUAL_ENV=$VIRTUAL_ENV" >> $GITHUB_ENV
+          uv pip install pip
       - name: Display Python version
         run: python -c "import sys; print(sys.version)"
       - name: Install tox
         run: |
-          python -m pip install --upgrade pip
-          python -m pip install tox tox-gh-actions
+          uv tool install tox --with=tox-gh-actions --with=tox-uv
       - name: Show tox config
         run: tox c
       - name: Run tox

From 7b4165ec89430b3c5304cd90d1c07a50eade0815 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Wed, 23 Oct 2024 10:50:17 -0400
Subject: [PATCH 02/28] Add 3.13 without free-threading, reduce non-Linux build
 matrix

---
 .github/workflows/test.yml | 34 ++++++++++++++++++++++++++++++----
 1 file changed, 30 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 44ab04e9c..b14078bfe 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -113,20 +113,42 @@ jobs:
       fail-fast: false
       matrix:
         os: ['ubuntu-latest', 'windows-latest', 'macos-13', 'macos-latest']
-        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13t"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13", "3.13t"]
         architecture: ['x64', 'x86', 'arm64']
         dependencies: ['full', 'pre']
         include:
           # Basic dependencies only
           - os: ubuntu-latest
-            python-version: 3.9
+            python-version: "3.9"
             dependencies: 'none'
           # Absolute minimum dependencies
           - os: ubuntu-latest
-            python-version: 3.9
+            python-version: "3.9"
             dependencies: 'min'
         exclude:
-          # x86 for Windows + Python<3.12
+          # Use ubuntu-latest to cover the whole range of Python. For Windows
+          # and OSX, checking oldest and newest should be sufficient.
+          - os: windows-latest
+            python-version: "3.10"
+          - os: windows-latest
+            python-version: "3.11"
+          - os: windows-latest
+            python-version: "3.12"
+          - os: macos-13
+            python-version: "3.10"
+          - os: macos-13
+            python-version: "3.11"
+          - os: macos-13
+            python-version: "3.12"
+          - os: macos-latest
+            python-version: "3.10"
+          - os: macos-latest
+            python-version: "3.11"
+          - os: macos-latest
+            python-version: "3.12"
+
+          # Unavailable architectures
+          # x86 is only available for Windows + Python<3.12
           - os: ubuntu-latest
             architecture: x86
           - os: macos-13
@@ -135,6 +157,8 @@ jobs:
             architecture: x86
           - python-version: '3.12'
             architecture: x86
+          - python-version: '3.13'
+            architecture: x86
           - python-version: '3.13t'
             architecture: x86
           # arm64 is available for macos-14+
@@ -147,6 +171,8 @@ jobs:
           # x64 is not available for macos-14+
           - os: macos-latest
             architecture: x64
+
+          # Reduced support
           # Drop pre tests for macos-13
           - os: macos-13
             dependencies: pre

From 2c223596757051e5720bf620fcad5be0895debda Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Wed, 23 Oct 2024 10:55:49 -0400
Subject: [PATCH 03/28] Do not update VIRTUAL_ENV

---
 .github/workflows/test.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index b14078bfe..d45ea4f1d 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -207,7 +207,6 @@ jobs:
           uv venv --python ${{ matrix.python-version }} ../.venv
           . .venv/bin/activate
           echo "PATH=$PATH" >> $GITHUB_ENV
-          echo "VIRTUAL_ENV=$VIRTUAL_ENV" >> $GITHUB_ENV
           uv pip install pip
       - name: Display Python version
         run: python -c "import sys; print(sys.version)"

From afe41170d291876e8ebf515c3ab7b0b8b8ab5552 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Wed, 23 Oct 2024 11:03:35 -0400
Subject: [PATCH 04/28] Install pip into tox environment

---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index d45ea4f1d..15ff066a5 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -212,7 +212,7 @@ jobs:
         run: python -c "import sys; print(sys.version)"
       - name: Install tox
         run: |
-          uv tool install tox --with=tox-gh-actions --with=tox-uv
+          uv tool install tox --with=tox-gh-actions --with=tox-uv --with=pip
       - name: Show tox config
         run: tox c
       - name: Run tox

From 3fbc2ef8811c20f00ed17c3181c9c487d8c352f5 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Wed, 23 Oct 2024 11:34:30 -0400
Subject: [PATCH 05/28] Use tomllib over tomli when available

---
 tools/update_requirements.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/tools/update_requirements.py b/tools/update_requirements.py
index eb0343bd7..2259d3188 100755
--- a/tools/update_requirements.py
+++ b/tools/update_requirements.py
@@ -2,7 +2,10 @@
 import sys
 from pathlib import Path
 
-import tomli
+try:
+    import tomllib
+except ImportError:
+    import tomli as tomllib
 
 if sys.version_info < (3, 6):
     print('This script requires Python 3.6 to work correctly')
@@ -15,7 +18,7 @@
 doc_reqs = repo_root / 'doc-requirements.txt'
 
 with open(pyproject_toml, 'rb') as fobj:
-    config = tomli.load(fobj)
+    config = tomllib.load(fobj)
 requirements = config['project']['dependencies']
 doc_requirements = config['project']['optional-dependencies']['doc']
 

From 2e4a124b42a02aefc9328a5ff5c3c6906a0a7132 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Wed, 23 Oct 2024 11:34:48 -0400
Subject: [PATCH 06/28] Sync requirements.txt files

---
 doc-requirements.txt | 2 +-
 min-requirements.txt | 7 ++++---
 requirements.txt     | 7 ++++---
 3 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/doc-requirements.txt b/doc-requirements.txt
index 42400ea57..4136b0f81 100644
--- a/doc-requirements.txt
+++ b/doc-requirements.txt
@@ -1,7 +1,7 @@
 # Auto-generated by tools/update_requirements.py
 -r requirements.txt
 sphinx
-matplotlib>=1.5.3
+matplotlib>=3.5
 numpydoc
 texext
 tomli; python_version < '3.11'
diff --git a/min-requirements.txt b/min-requirements.txt
index 1cdd78bb7..09dee2082 100644
--- a/min-requirements.txt
+++ b/min-requirements.txt
@@ -1,4 +1,5 @@
 # Auto-generated by tools/update_requirements.py
-numpy ==1.20
-packaging ==17
-importlib_resources ==1.3; python_version < '3.9'
+numpy ==1.22
+packaging ==20
+importlib_resources ==5.12; python_version < '3.12'
+typing_extensions ==4.6; python_version < '3.13'
diff --git a/requirements.txt b/requirements.txt
index f74ccc085..c65baf5cb 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,4 +1,5 @@
 # Auto-generated by tools/update_requirements.py
-numpy >=1.20
-packaging >=17
-importlib_resources >=1.3; python_version < '3.9'
+numpy >=1.22
+packaging >=20
+importlib_resources >=5.12; python_version < '3.12'
+typing_extensions >=4.6; python_version < '3.13'

From 30f324b3dcd5a3899db494ddd42a3a48c0bf2e7b Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Wed, 23 Oct 2024 11:45:34 -0400
Subject: [PATCH 07/28] Compile min-requirements.txt

---
 min-requirements.txt | 21 ++++++++++++++++-----
 1 file changed, 16 insertions(+), 5 deletions(-)

diff --git a/min-requirements.txt b/min-requirements.txt
index 09dee2082..455c6c8c6 100644
--- a/min-requirements.txt
+++ b/min-requirements.txt
@@ -1,5 +1,16 @@
-# Auto-generated by tools/update_requirements.py
-numpy ==1.22
-packaging ==20
-importlib_resources ==5.12; python_version < '3.12'
-typing_extensions ==4.6; python_version < '3.13'
+# This file was autogenerated by uv via the following command:
+#    uv pip compile --resolution lowest-direct --python 3.9 -o min-requirements.txt pyproject.toml
+importlib-resources==5.12.0
+    # via nibabel (pyproject.toml)
+numpy==1.22.0
+    # via nibabel (pyproject.toml)
+packaging==20.0
+    # via nibabel (pyproject.toml)
+pyparsing==3.2.0
+    # via packaging
+six==1.16.0
+    # via packaging
+typing-extensions==4.6.0
+    # via nibabel (pyproject.toml)
+zipp==3.20.2
+    # via importlib-resources

From 2894a3ef84ad5afd5878bd4c79737c0f9bd2e313 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Thu, 31 Oct 2024 12:16:16 -0400
Subject: [PATCH 08/28] TOX: Control pip via environment variables

---
 tox.ini | 10 +++-------
 1 file changed, 3 insertions(+), 7 deletions(-)

diff --git a/tox.ini b/tox.ini
index 82c13debc..6dbd57443 100644
--- a/tox.ini
+++ b/tox.ini
@@ -48,12 +48,6 @@ ARCH =
 [testenv]
 description = Pytest with coverage
 labels = test
-install_command =
-  python -I -m pip install -v \
-  dev: --only-binary numpy,scipy,h5py \
-  !dev: --only-binary numpy,scipy,h5py,pillow,matplotlib \
-  pre,dev: --extra-index-url https://pypi.anaconda.org/scientific-python-nightly-wheels/simple \
-    {opts} {packages}
 pip_pre =
   pre,dev: true
 pass_env =
@@ -72,6 +66,9 @@ pass_env =
   CLICOLOR_FORCE
 set_env =
   py313: PYTHON_GIL=0
+  dev: PIP_ONLY_BINARY=numpy,scipy,h5py
+  !dev: PIP_ONLY_BINARY=numpy,scipy,h5py,pillow,matplotlib
+  pre,dev: PIP_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
 extras = test
 deps =
   # General minimum dependencies: pin based on API usage
@@ -118,7 +115,6 @@ description = Install and verify import succeeds
 labels = test
 deps =
 extras =
-install_command = python -I -m pip install {opts} {packages}
 commands =
   python -c "import nibabel; print(nibabel.__version__)"
 

From 62012efa6f344eaee24cc270102aa3531f2596f1 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Thu, 31 Oct 2024 12:29:18 -0400
Subject: [PATCH 09/28] Handle 3.13 better

---
 tox.ini | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/tox.ini b/tox.ini
index 6dbd57443..bd83a79db 100644
--- a/tox.ini
+++ b/tox.ini
@@ -7,7 +7,7 @@ requires =
   tox>=4
 envlist =
   # No preinstallations
-  py3{9,10,11,12,13}-none
+  py3{9,10,11,12,13,13t}-none
   # Minimum Python
   py39-{min,full}
   # x86 support range
@@ -31,6 +31,7 @@ python =
   3.11: py311
   3.12: py312
   3.13: py313
+  3.13t: py313t
 
 [gh-actions:env]
 DEPENDS =
@@ -58,6 +59,8 @@ pass_env =
   USERNAME
   # Environment variables we check for
   NIPY_EXTRA_TESTS
+  # Python variables
+  PYTHON_GIL
   # Pass user color preferences through
   PY_COLORS
   FORCE_COLOR
@@ -65,7 +68,6 @@ pass_env =
   CLICOLOR
   CLICOLOR_FORCE
 set_env =
-  py313: PYTHON_GIL=0
   dev: PIP_ONLY_BINARY=numpy,scipy,h5py
   !dev: PIP_ONLY_BINARY=numpy,scipy,h5py,pillow,matplotlib
   pre,dev: PIP_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple

From cf4ef0634a928524403441192d671716a5fa9aec Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Thu, 31 Oct 2024 12:29:57 -0400
Subject: [PATCH 10/28] Configure uv installation

---
 .github/workflows/test.yml | 2 +-
 pyproject.toml             | 3 +++
 tox.ini                    | 1 +
 3 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 15ff066a5..d45ea4f1d 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -212,7 +212,7 @@ jobs:
         run: python -c "import sys; print(sys.version)"
       - name: Install tox
         run: |
-          uv tool install tox --with=tox-gh-actions --with=tox-uv --with=pip
+          uv tool install tox --with=tox-gh-actions --with=tox-uv
       - name: Show tox config
         run: tox c
       - name: Run tox
diff --git a/pyproject.toml b/pyproject.toml
index b62c0048a..f307d1d8c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -200,3 +200,6 @@ enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool"]
 [tool.codespell]
 skip = "*/data/*,./nibabel-data"
 ignore-words-list = "ans,te,ue,ist,nin,nd,ccompiler,ser"
+
+[tool.uv.pip]
+only-binary = ["numpy", "scipy", "h5py"]
diff --git a/tox.ini b/tox.ini
index bd83a79db..236186f72 100644
--- a/tox.ini
+++ b/tox.ini
@@ -71,6 +71,7 @@ set_env =
   dev: PIP_ONLY_BINARY=numpy,scipy,h5py
   !dev: PIP_ONLY_BINARY=numpy,scipy,h5py,pillow,matplotlib
   pre,dev: PIP_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
+  pre,dev: UV_INDEX=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
 extras = test
 deps =
   # General minimum dependencies: pin based on API usage

From 04c4d30fb45d5aee02b9d566dea3c9f154fc647d Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Thu, 31 Oct 2024 12:40:02 -0400
Subject: [PATCH 11/28] fix virtual environment

---
 .github/workflows/test.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index d45ea4f1d..ac1e9ae4b 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -204,8 +204,8 @@ jobs:
         if: endsWith(matrix.python-version, 't')
         run: |
           uv python install ${{ matrix.python-version }}
-          uv venv --python ${{ matrix.python-version }} ../.venv
-          . .venv/bin/activate
+          uv venv --python ${{ matrix.python-version }} ../venv
+          . ../venv/bin/activate
           echo "PATH=$PATH" >> $GITHUB_ENV
           uv pip install pip
       - name: Display Python version

From 1ad263e1b97f2a35bdddcdb7fe441f5138b38809 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Sat, 7 Dec 2024 09:03:57 -0500
Subject: [PATCH 12/28] chore(ci): Try another way to find the right Python

---
 .github/workflows/test.yml | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index ac1e9ae4b..a79b6d3ba 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -204,15 +204,13 @@ jobs:
         if: endsWith(matrix.python-version, 't')
         run: |
           uv python install ${{ matrix.python-version }}
-          uv venv --python ${{ matrix.python-version }} ../venv
-          . ../venv/bin/activate
-          echo "PATH=$PATH" >> $GITHUB_ENV
-          uv pip install pip
       - name: Display Python version
         run: python -c "import sys; print(sys.version)"
       - name: Install tox
         run: |
           uv tool install tox --with=tox-gh-actions --with=tox-uv
+        env:
+          UV_PYTHON: ${{ matrix.python-version }}
       - name: Show tox config
         run: tox c
       - name: Run tox

From b99ad93142887bbcfe6fc2e6086ce888594909b1 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Sat, 7 Dec 2024 10:23:04 -0500
Subject: [PATCH 13/28] chore(deps): Add missing and set min versions for
 optional deps

---
 pyproject.toml | 24 +++++++++++++-----------
 1 file changed, 13 insertions(+), 11 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index f307d1d8c..3b2dfc99b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -51,13 +51,15 @@ nib-roi = "nibabel.cmdline.roi:main"
 parrec2nii = "nibabel.cmdline.parrec2nii:main"
 
 [project.optional-dependencies]
-all = ["nibabel[dicomfs,minc2,spm,zstd]"]
+all = ["nibabel[dicomfs,indexed_gzip,minc2,spm,zstd]"]
 # Features
+indexed_gzip = ["indexed_gzip >=1.6"]
 dicom = ["pydicom >=2.3"]
-dicomfs = ["nibabel[dicom]", "pillow"]
-minc2 = ["h5py"]
-spm = ["scipy"]
-zstd = ["pyzstd >= 0.14.3"]
+dicomfs = ["nibabel[dicom]", "pillow >=8.4"]
+minc2 = ["h5py >=3.5"]
+spm = ["scipy >=1.8"]
+viewers = ["matplotlib >=3.5"]
+zstd = ["pyzstd >=0.15.2"]
 # For doc and test, make easy to use outside of tox
 # tox should use these with extras instead of duplicating
 doc = [
@@ -68,12 +70,12 @@ doc = [
   "tomli; python_version < '3.11'",
 ]
 test = [
-  "pytest",
-  "pytest-doctestplus",
-  "pytest-cov",
-  "pytest-httpserver",
-  "pytest-xdist",
-  "coverage>=7.2",
+  "pytest >=6",
+  "pytest-doctestplus >=1",
+  "pytest-cov >=2.11",
+  "pytest-httpserver >=1.0.7",
+  "pytest-xdist >=3.5",
+  "coverage[toml]>=7.2",
 ]
 # Remaining: Simpler to centralize in tox
 dev = ["tox"]

From ee091355f6a60d809e0eec19116bbfc8b3e79a63 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Sat, 7 Dec 2024 10:23:41 -0500
Subject: [PATCH 14/28] chore(tox): Use uv_resolution to run minimum tests

---
 tox.ini | 58 ++++++++++++++++++++++++++++-----------------------------
 1 file changed, 29 insertions(+), 29 deletions(-)

diff --git a/tox.ini b/tox.ini
index 236186f72..0b06e7206 100644
--- a/tox.ini
+++ b/tox.ini
@@ -5,6 +5,7 @@
 [tox]
 requires =
   tox>=4
+  tox-uv
 envlist =
   # No preinstallations
   py3{9,10,11,12,13,13t}-none
@@ -71,41 +72,40 @@ set_env =
   dev: PIP_ONLY_BINARY=numpy,scipy,h5py
   !dev: PIP_ONLY_BINARY=numpy,scipy,h5py,pillow,matplotlib
   pre,dev: PIP_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
-  pre,dev: UV_INDEX=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
-extras = test
+  pre,dev: UV_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
+  py313t: PYTHONGIL=0
+extras =
+  test
+
+  # Simple, thanks pillow
+  !none: dicomfs
+  !none: indexed_gzip
+
+  # Matplotlib has wheels for everything except win32 (x86)
+  {min,full,pre,dev}-{x,arm}64: viewers
+
+  # Nightly, but not released cp313t wheels for: scipy
+  # When released, remove the py3* line and add min/full to the pre,dev line
+  py3{9,10,11,12,13}-{min,full}-{x,arm}64: spm
+  {pre,dev}-{x,arm}64: spm
+
+  # No cp313t wheels for: h5py, pyzstd
+  py3{9,10,11,12,13}-{min,full,pre-dev}-{x,arm}64: minc2
+  py3{9,10,11,12,13}-{min,full,pre-dev}-{x,arm}64: zstd
+
+  # No win32 wheels for scipy/matplotlib after py39
+  py39-full-x86: spm
+  py39-full-x86: viewers
+
 deps =
-  # General minimum dependencies: pin based on API usage
-  # matplotlib 3.5 requires packaging 20
-  min: packaging ==20
-  min: importlib_resources ==5.12; python_version < '3.12'
-  min: typing_extensions ==4.6; python_version < '3.13'
-  # NEP29/SPEC0 + 1yr: Test on minor release series within the last 3 years
-  # We're extending this to all optional dependencies
-  # This only affects the range that we test on; numpy is the only non-optional
-  # dependency, and will be the only one to affect pip environment resolution.
-  min: numpy ==1.22
-  min: h5py ==3.5
-  min: indexed_gzip ==1.6
-  min: matplotlib ==3.5
-  min: pillow ==8.4
-  min: pydicom ==2.3
-  min: pyzstd ==0.15.2
-  min: scipy ==1.8
   # Numpy 2.0 is a major breaking release; we cannot put much effort into
   # supporting until it's at least RC stable
   dev: numpy >=2.1.dev0
-  # Scipy stopped producing win32 wheels at py310
-  py39-full-x86,x64,arm64: scipy >=1.8
-  # Matplotlib depends on scipy, so cannot be built for py310 on x86
-  py39-full-x86,x64,arm64: matplotlib >=3.5
-  # h5py stopped producing win32 wheels at py39
-  {full,pre}-{x64,arm64}: h5py >=3.5
-  full,pre,dev: pillow >=8.4
-  full,pre: indexed_gzip >=1.6
-  full,pre,dev: pyzstd >=0.15.2
-  full,pre: pydicom >=2.3
   dev: pydicom @ git+https://github.com/pydicom/pydicom.git@main
 
+uv_resolution =
+  min: lowest-direct
+
 commands =
   pytest --doctest-modules --doctest-plus \
     --cov nibabel --cov-report xml:cov.xml \

From 1acb1fb441b65477194563dade0d4e437dc3862e Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Sat, 7 Dec 2024 14:01:58 -0500
Subject: [PATCH 15/28] Define environment for py313t-full/pre

---
 tox.ini | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tox.ini b/tox.ini
index 0b06e7206..e0e972cfc 100644
--- a/tox.ini
+++ b/tox.ini
@@ -15,7 +15,7 @@ envlist =
   py3{9,10,11}-{full,pre}-{x86,x64}
   py3{9,10,11}-pre-{x86,x64}
   # x64-only range
-  py3{12,13}-{full,pre}-x64
+  py3{12,13,13t}-{full,pre}-x64
   # Special environment for numpy 2.0-dev testing
   py313-dev-x64
   install

From 6023c351061e91e065f38bfb10863fabd6b7bc86 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Sat, 7 Dec 2024 20:04:19 -0500
Subject: [PATCH 16/28] Use tox-gh-actions branch

---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index a79b6d3ba..ddd13e177 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -208,7 +208,7 @@ jobs:
         run: python -c "import sys; print(sys.version)"
       - name: Install tox
         run: |
-          uv tool install tox --with=tox-gh-actions --with=tox-uv
+          uv tool install tox --with=git+https://github.com/effigies/tox-gh-actions@abiflags --with=tox-uv
         env:
           UV_PYTHON: ${{ matrix.python-version }}
       - name: Show tox config

From bcb9f2dc3b174e22c07aeb11aa523c69ffe3a96c Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Sun, 8 Dec 2024 11:25:45 -0500
Subject: [PATCH 17/28] chore(ci): Test win32 with no extras for 3.9 and 3.13

---
 .github/workflows/test.yml | 33 ++++++++++++---------------------
 1 file changed, 12 insertions(+), 21 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index ddd13e177..46a5e1cdc 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -114,17 +114,28 @@ jobs:
       matrix:
         os: ['ubuntu-latest', 'windows-latest', 'macos-13', 'macos-latest']
         python-version: ["3.9", "3.10", "3.11", "3.12", "3.13", "3.13t"]
-        architecture: ['x64', 'x86', 'arm64']
+        architecture: ['x64', 'arm64']
         dependencies: ['full', 'pre']
         include:
           # Basic dependencies only
           - os: ubuntu-latest
             python-version: "3.9"
+            architecture: 'x64'
             dependencies: 'none'
           # Absolute minimum dependencies
           - os: ubuntu-latest
             python-version: "3.9"
+            architecture: 'x64'
             dependencies: 'min'
+          # Only numpy of the scipy stack still supports win32
+          - os: windows-latest
+            python-version: "3.9"
+            architecture: 'x86'
+            dependencies: 'none'
+          - os: windows-latest
+            python-version: "3.13"
+            architecture: 'x86'
+            dependencies: 'none'
         exclude:
           # Use ubuntu-latest to cover the whole range of Python. For Windows
           # and OSX, checking oldest and newest should be sufficient.
@@ -148,26 +159,6 @@ jobs:
             python-version: "3.12"
 
           # Unavailable architectures
-          # x86 is only available for Windows + Python<3.12
-          - os: ubuntu-latest
-            architecture: x86
-          - os: macos-13
-            architecture: x86
-          - os: macos-latest
-            architecture: x86
-          - python-version: '3.12'
-            architecture: x86
-          - python-version: '3.13'
-            architecture: x86
-          - python-version: '3.13t'
-            architecture: x86
-          # arm64 is available for macos-14+
-          - os: ubuntu-latest
-            architecture: arm64
-          - os: windows-latest
-            architecture: arm64
-          - os: macos-13
-            architecture: arm64
           # x64 is not available for macos-14+
           - os: macos-latest
             architecture: x64

From 78a8878ec9eefbe409e1edf6668e7f374b713f7f Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Sun, 8 Dec 2024 11:26:06 -0500
Subject: [PATCH 18/28] chore(tox): Remove unused env vars

---
 tox.ini | 2 --
 1 file changed, 2 deletions(-)

diff --git a/tox.ini b/tox.ini
index e0e972cfc..ec34f7b82 100644
--- a/tox.ini
+++ b/tox.ini
@@ -69,8 +69,6 @@ pass_env =
   CLICOLOR
   CLICOLOR_FORCE
 set_env =
-  dev: PIP_ONLY_BINARY=numpy,scipy,h5py
-  !dev: PIP_ONLY_BINARY=numpy,scipy,h5py,pillow,matplotlib
   pre,dev: PIP_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
   pre,dev: UV_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
   py313t: PYTHONGIL=0

From 91d2e422671a2c019f65e7331661c1d8b7f3968b Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Sun, 8 Dec 2024 11:26:20 -0500
Subject: [PATCH 19/28] chore(tox): Set PYTHONGIL from environment if found

---
 tox.ini | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/tox.ini b/tox.ini
index ec34f7b82..d7081549b 100644
--- a/tox.ini
+++ b/tox.ini
@@ -60,8 +60,6 @@ pass_env =
   USERNAME
   # Environment variables we check for
   NIPY_EXTRA_TESTS
-  # Python variables
-  PYTHON_GIL
   # Pass user color preferences through
   PY_COLORS
   FORCE_COLOR
@@ -71,7 +69,7 @@ pass_env =
 set_env =
   pre,dev: PIP_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
   pre,dev: UV_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
-  py313t: PYTHONGIL=0
+  py313t: PYTHONGIL={env:PYTHONGIL:0}
 extras =
   test
 

From 265257eee31b875335bde9bf9364a13241a552b0 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Sun, 8 Dec 2024 11:29:25 -0500
Subject: [PATCH 20/28] chore(ci): Update setup-uv version

---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 46a5e1cdc..abcf1ed38 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -183,7 +183,7 @@ jobs:
           submodules: recursive
           fetch-depth: 0
       - name: Install the latest version of uv
-        uses: astral-sh/setup-uv@v3
+        uses: astral-sh/setup-uv@v4
       - name: Set up Python ${{ matrix.python-version }}
         if: "!endsWith(matrix.python-version, 't')"
         uses: actions/setup-python@v5

From 6cb49a3c98c17653274facdde0c6a4e85977d32e Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Sun, 8 Dec 2024 11:42:26 -0500
Subject: [PATCH 21/28] chore(ci): Re-add arm64 exclusions

---
 .github/workflows/test.yml | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index abcf1ed38..3599bc2c2 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -158,12 +158,19 @@ jobs:
           - os: macos-latest
             python-version: "3.12"
 
-          # Unavailable architectures
+          ## Unavailable architectures
+          # arm64 is available for macos-14+
+          - os: ubuntu-latest
+            architecture: arm64
+          - os: windows-latest
+            architecture: arm64
+          - os: macos-13
+            architecture: arm64
           # x64 is not available for macos-14+
           - os: macos-latest
             architecture: x64
 
-          # Reduced support
+          ## Reduced support
           # Drop pre tests for macos-13
           - os: macos-13
             dependencies: pre

From 81e2e9fb362df433d2d16defabf3c1288c11794d Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Sun, 8 Dec 2024 11:50:16 -0500
Subject: [PATCH 22/28] chore: Disable writing min-requirements from
 update_requirements.py

---
 tools/update_requirements.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/tools/update_requirements.py b/tools/update_requirements.py
index 2259d3188..13709b22e 100755
--- a/tools/update_requirements.py
+++ b/tools/update_requirements.py
@@ -30,9 +30,10 @@
 lines[1:-1] = requirements
 reqs.write_text('\n'.join(lines))
 
-# Write minimum requirements
-lines[1:-1] = [req.replace('>=', '==').replace('~=', '==') for req in requirements]
-min_reqs.write_text('\n'.join(lines))
+# # Write minimum requirements
+# lines[1:-1] = [req.replace('>=', '==').replace('~=', '==') for req in requirements]
+# min_reqs.write_text('\n'.join(lines))
+print(f"To update {min_reqs.name}, use `uv pip compile` (see comment at top of file).")
 
 # Write documentation requirements
 lines[1:-1] = ['-r requirements.txt'] + doc_requirements

From 6f77556f5b57070979ba4a8b8665caafae06b523 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Sun, 8 Dec 2024 12:06:24 -0500
Subject: [PATCH 23/28] chore(ci): Restore x86 for Windows, will just drop mpl
 in tox

---
 .github/workflows/test.yml | 18 ++++++++----------
 1 file changed, 8 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 3599bc2c2..c99b4367b 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -114,7 +114,7 @@ jobs:
       matrix:
         os: ['ubuntu-latest', 'windows-latest', 'macos-13', 'macos-latest']
         python-version: ["3.9", "3.10", "3.11", "3.12", "3.13", "3.13t"]
-        architecture: ['x64', 'arm64']
+        architecture: ['x86', 'x64', 'arm64']
         dependencies: ['full', 'pre']
         include:
           # Basic dependencies only
@@ -127,15 +127,6 @@ jobs:
             python-version: "3.9"
             architecture: 'x64'
             dependencies: 'min'
-          # Only numpy of the scipy stack still supports win32
-          - os: windows-latest
-            python-version: "3.9"
-            architecture: 'x86'
-            dependencies: 'none'
-          - os: windows-latest
-            python-version: "3.13"
-            architecture: 'x86'
-            dependencies: 'none'
         exclude:
           # Use ubuntu-latest to cover the whole range of Python. For Windows
           # and OSX, checking oldest and newest should be sufficient.
@@ -159,6 +150,13 @@ jobs:
             python-version: "3.12"
 
           ## Unavailable architectures
+          # x86 is available for Windows
+          - os: ubuntu-latest
+            architecture: x86
+          - os: macos-latest
+            architecture: x86
+          - os: macos-13
+            architecture: x86
           # arm64 is available for macos-14+
           - os: ubuntu-latest
             architecture: arm64

From 85a6cfece89b8a551ff8ddd6ce07ce0c5dca80c0 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Sun, 8 Dec 2024 12:07:25 -0500
Subject: [PATCH 24/28] chore(tox): Drop mpl from x86, old numpy constraint

---
 tox.ini | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/tox.ini b/tox.ini
index d7081549b..824993716 100644
--- a/tox.ini
+++ b/tox.ini
@@ -73,7 +73,7 @@ set_env =
 extras =
   test
 
-  # Simple, thanks pillow
+  # Simple, thanks Hugo and Paul
   !none: dicomfs
   !none: indexed_gzip
 
@@ -89,14 +89,10 @@ extras =
   py3{9,10,11,12,13}-{min,full,pre-dev}-{x,arm}64: minc2
   py3{9,10,11,12,13}-{min,full,pre-dev}-{x,arm}64: zstd
 
-  # No win32 wheels for scipy/matplotlib after py39
+  # No win32 wheels for scipy after py39
   py39-full-x86: spm
-  py39-full-x86: viewers
 
 deps =
-  # Numpy 2.0 is a major breaking release; we cannot put much effort into
-  # supporting until it's at least RC stable
-  dev: numpy >=2.1.dev0
   dev: pydicom @ git+https://github.com/pydicom/pydicom.git@main
 
 uv_resolution =

From 5e4c4aeb8f76771a3bcdb37f58886f2f1f9fe283 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Sun, 8 Dec 2024 12:10:04 -0500
Subject: [PATCH 25/28] chore(tox): Drop dev, pre is good enough

---
 tox.ini | 21 +++++++++------------
 1 file changed, 9 insertions(+), 12 deletions(-)

diff --git a/tox.ini b/tox.ini
index 824993716..a0b84ee69 100644
--- a/tox.ini
+++ b/tox.ini
@@ -16,8 +16,6 @@ envlist =
   py3{9,10,11}-pre-{x86,x64}
   # x64-only range
   py3{12,13,13t}-{full,pre}-x64
-  # Special environment for numpy 2.0-dev testing
-  py313-dev-x64
   install
   doctest
   style
@@ -38,7 +36,6 @@ python =
 DEPENDS =
   none: none, install
   pre: pre
-  dev: dev
   full: full, install
   min: min
 
@@ -51,7 +48,7 @@ ARCH =
 description = Pytest with coverage
 labels = test
 pip_pre =
-  pre,dev: true
+  pre: true
 pass_env =
   # getpass.getuser() sources for Windows:
   LOGNAME
@@ -67,8 +64,8 @@ pass_env =
   CLICOLOR
   CLICOLOR_FORCE
 set_env =
-  pre,dev: PIP_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
-  pre,dev: UV_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
+  pre: PIP_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
+  pre: UV_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
   py313t: PYTHONGIL={env:PYTHONGIL:0}
 extras =
   test
@@ -78,22 +75,22 @@ extras =
   !none: indexed_gzip
 
   # Matplotlib has wheels for everything except win32 (x86)
-  {min,full,pre,dev}-{x,arm}64: viewers
+  {min,full,pre}-{x,arm}64: viewers
 
   # Nightly, but not released cp313t wheels for: scipy
-  # When released, remove the py3* line and add min/full to the pre,dev line
+  # When released, remove the py3* line and add min/full to the pre line
   py3{9,10,11,12,13}-{min,full}-{x,arm}64: spm
-  {pre,dev}-{x,arm}64: spm
+  pre-{x,arm}64: spm
 
   # No cp313t wheels for: h5py, pyzstd
-  py3{9,10,11,12,13}-{min,full,pre-dev}-{x,arm}64: minc2
-  py3{9,10,11,12,13}-{min,full,pre-dev}-{x,arm}64: zstd
+  py3{9,10,11,12,13}-{min,full,pre}-{x,arm}64: minc2
+  py3{9,10,11,12,13}-{min,full,pre}-{x,arm}64: zstd
 
   # No win32 wheels for scipy after py39
   py39-full-x86: spm
 
 deps =
-  dev: pydicom @ git+https://github.com/pydicom/pydicom.git@main
+  pre: pydicom @ git+https://github.com/pydicom/pydicom.git@main
 
 uv_resolution =
   min: lowest-direct

From 76b809c9ebe694d1d6a7a080311e029d775ce8b6 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Sun, 8 Dec 2024 13:10:47 -0500
Subject: [PATCH 26/28] chore(tox): Rework default environments, extras

---
 tox.ini | 31 +++++++++++++++++--------------
 1 file changed, 17 insertions(+), 14 deletions(-)

diff --git a/tox.ini b/tox.ini
index a0b84ee69..cba8b17d6 100644
--- a/tox.ini
+++ b/tox.ini
@@ -9,13 +9,10 @@ requires =
 envlist =
   # No preinstallations
   py3{9,10,11,12,13,13t}-none
-  # Minimum Python
-  py39-{min,full}
-  # x86 support range
-  py3{9,10,11}-{full,pre}-{x86,x64}
-  py3{9,10,11}-pre-{x86,x64}
-  # x64-only range
-  py3{12,13,13t}-{full,pre}-x64
+  # Minimum Python with minimum deps
+  py39-min
+  # Run full and pre dependencies against all archs
+  py3{9,10,11,12,13,13t}-{full,pre}-{x86,x64,arm64}
   install
   doctest
   style
@@ -34,7 +31,7 @@ python =
 
 [gh-actions:env]
 DEPENDS =
-  none: none, install
+  none: none
   pre: pre
   full: full, install
   min: min
@@ -74,19 +71,25 @@ extras =
   !none: dicomfs
   !none: indexed_gzip
 
+  # Minimum dependencies
+  min: minc2
+  min: spm
+  min: viewers
+  min: zstd
+
   # Matplotlib has wheels for everything except win32 (x86)
-  {min,full,pre}-{x,arm}64: viewers
+  {full,pre}-{x,arm}64: viewers
 
   # Nightly, but not released cp313t wheels for: scipy
-  # When released, remove the py3* line and add min/full to the pre line
-  py3{9,10,11,12,13}-{min,full}-{x,arm}64: spm
+  # When released, remove the py3* line and add full to the pre line
+  py3{9,10,11,12,13}-full-{x,arm}64: spm
   pre-{x,arm}64: spm
 
   # No cp313t wheels for: h5py, pyzstd
-  py3{9,10,11,12,13}-{min,full,pre}-{x,arm}64: minc2
-  py3{9,10,11,12,13}-{min,full,pre}-{x,arm}64: zstd
+  py3{9,10,11,12,13}-{full,pre}-{x,arm}64: minc2
+  py3{9,10,11,12,13}-{full,pre}-{x,arm}64: zstd
 
-  # No win32 wheels for scipy after py39
+  # win32 (x86) wheels still exist for scipy+py39
   py39-full-x86: spm
 
 deps =

From 821f34bb24c579f5202e120bca2bbefcefe96539 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Sun, 8 Dec 2024 18:25:43 -0500
Subject: [PATCH 27/28] chore(ci): Improve version specification for uv

---
 .github/workflows/test.yml | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index c99b4367b..1effca4d7 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -199,7 +199,18 @@ jobs:
       - name: Set up Python ${{ matrix.python-version }}
         if: endsWith(matrix.python-version, 't')
         run: |
-          uv python install ${{ matrix.python-version }}
+          uv python install ${IMPL}-${VERSION}-${OS%-*}-${ARCH}-${LIBC}
+        env:
+          IMPL: cpython
+          VERSION: ${{ matrix.python-version }}
+          # uv expects linux|macos|windows, we can drop the -* but need to rename ubuntu
+          OS: ${{ matrix.os == 'ubuntu-latest' && 'linux' || matrix.os }}
+          # uv expects x86, x86_64, aarch64 (among others)
+          ARCH: ${{ matrix.architecture == 'x64' && 'x86_64' ||
+                    matrix.architecture == 'arm64' && 'aarch64' ||
+                    matrix.architecture }}
+          # windows and macos have no options, gnu is the only option for the archs
+          LIBC: ${{ matrix.os == 'ubuntu-latest' && 'gnu' || 'none' }}
       - name: Display Python version
         run: python -c "import sys; print(sys.version)"
       - name: Install tox

From 1e8043d4f92b2272094e19aca86f4fb8f4c1a539 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Sun, 12 Jan 2025 09:41:42 -0500
Subject: [PATCH 28/28] chore: Nudge uv a bit harder

---
 .github/workflows/test.yml | 8 ++++----
 tox.ini                    | 2 ++
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 1effca4d7..06143e635 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -199,7 +199,9 @@ jobs:
       - name: Set up Python ${{ matrix.python-version }}
         if: endsWith(matrix.python-version, 't')
         run: |
-          uv python install ${IMPL}-${VERSION}-${OS%-*}-${ARCH}-${LIBC}
+          echo "UV_PYTHON=${IMPL}-${VERSION}-${OS%-*}-${ARCH}-${LIBC}" >> $GITHUB_ENV
+          source $GITHUB_ENV
+          uv python install $UV_PYTHON
         env:
           IMPL: cpython
           VERSION: ${{ matrix.python-version }}
@@ -215,9 +217,7 @@ jobs:
         run: python -c "import sys; print(sys.version)"
       - name: Install tox
         run: |
-          uv tool install tox --with=git+https://github.com/effigies/tox-gh-actions@abiflags --with=tox-uv
-        env:
-          UV_PYTHON: ${{ matrix.python-version }}
+          uv tool install -v tox --with=git+https://github.com/effigies/tox-gh-actions@abiflags --with=tox-uv
       - name: Show tox config
         run: tox c
       - name: Run tox
diff --git a/tox.ini b/tox.ini
index cba8b17d6..05d977951 100644
--- a/tox.ini
+++ b/tox.ini
@@ -60,6 +60,8 @@ pass_env =
   NO_COLOR
   CLICOLOR
   CLICOLOR_FORCE
+  # uv needs help in this case
+  py313t-x86: UV_PYTHON
 set_env =
   pre: PIP_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
   pre: UV_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple