From f9cd1a51604ad19ff182703c83a1d0899695654c Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Thu, 8 Jan 2026 13:51:25 -0500
Subject: [PATCH 01/20] ENH: Test wheels [wheels]

---
 .github/workflows/cibuildwheel.yml | 80 +++++++++++++++++++++++++++---
 pyproject.toml                     |  7 ++-
 2 files changed, 78 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/cibuildwheel.yml b/.github/workflows/cibuildwheel.yml
index 89d664b..edaa192 100644
--- a/.github/workflows/cibuildwheel.yml
+++ b/.github/workflows/cibuildwheel.yml
@@ -1,8 +1,6 @@
 # Build wheels, sdist, and upload to PyPI
 
 # code adapted from antio and openmeeg
-# TODO: once numpy 1 support is dropped, enable these jobs; set to only run on
-# tagged releases, and only if the test.yml workflow is successful 
 
 name: Build
 concurrency:
@@ -10,17 +8,54 @@ concurrency:
   cancel-in-progress: true
 on:  # yamllint disable-line rule:truthy
   workflow_dispatch:
-  release:
-    types: [published]
+  push:
+    tags:
+      - 'v*.*.*'
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
 
 jobs:
+  # Adapted from dipy (BSD)
+  check-commit:
+    name: Check [wheels] in commit message
+    runs-on: ubuntu-latest
+    outputs:
+      proceed: ${{ steps.commit-message.outputs.PROCEED }}
+    defaults:
+      run:
+        shell: bash -el {0}
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 2
+      - name: Check commit message for [wheels]
+        id: commit-message
+        run: |
+          if [[ "${{ github.event_name }}" == "pull_request" ]]; then
+            MSG=$(git show -s --format=%s ${{ github.event.pull_request.head.sha }})
+            echo "Got commit message: $MSG"
+            if echo "$MSG" | grep -iq '\[wheels\]'; then
+              PROCEED=true
+            else
+              PROCEED=false
+            fi
+          else
+            PROCEED=true
+          fi
+          echo "PROCEED=$PROCEED" | tee -a $GITHUB_OUTPUT
+
   build_wheels:
-    if: false # disabeling until we can drop support for numpy 1
     name: Wheels ${{ matrix.os }} ${{ matrix.arch }}
+    needs: [check-commit]
+    if: needs.check-commit.outputs.proceed == 'true'
     runs-on: ${{ matrix.os }}
+    timeout-minutes: 20
     strategy:
       matrix:
-        os: [ubuntu-22.04, ubuntu-24.04, macos-14, macos-15, macos-15-intel]  # windows-11 windows-11-arm
+        os: [ubuntu-latest, ubuntu-24.04-arm, macos-15, macos-15-intel, windows-latest]  # windows-11-arm
         arch: [native]
         # TODO: Someday this can be enabled, but need to add emulation and it's slow,
         # can use docker/setup-qemu-action
@@ -38,9 +73,38 @@ jobs:
           CIBW_ARCHS: ${{ matrix.arch }}
       - uses: actions/upload-artifact@v4
         with:
-          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
+          name: cibw-wheels-${{ runner.os }}-${{ strategy.job-index }}
           path: ./wheelhouse/*.whl
 
+  test_wheels:
+    needs: [build_wheels]
+    name: Test wheels
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 5
+    defaults:
+      run:
+        shell: bash -el {0}
+    strategy:
+      matrix:
+        os: [ubuntu-22.04, macos-14, macos-14-intel, windows-11]
+        python: [3.8, 3.14]  # old, newest (including pip-prelease)
+        arch: [native]
+    steps:
+      - uses: actions/download-artifact@v5
+        with:
+          pattern: cibw-wheels-*
+          merge-multiple: true
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python }}
+      # Choose versions from 2022 (somewhat arbitrarily)
+      - run: python -m pip install numpy==1.23 scipy=1.8 nibabel pillow xxhash --only-binary="numpy,scipy,nibabel,pillow,xxhash"
+        if: matrix.python == '3.8'
+      - run: python -m pip install --pre --upgrade numpy scipy nibabel pillow xxhash --only-binary="numpy,scipy,nibabel,pillow,xxhash" --extra-index-url=https://pypi.anaconda.org/scipy-wheels-nightly/simple
+        if: matrix.python == '3.14'
+      - run: pip install --no-index --find-links=file://${PWD}/dist surfa
+      - run: python -c "import surfa; print(surfa.__version__)"
+
   sdist:
     timeout-minutes: 10
     name: Create sdist
@@ -74,7 +138,7 @@ jobs:
       - run: twine check --strict dist/*
 
   publish:
-    if: ${{ github.repository == 'freesurfer/surfa' && github.event_name == 'release' }}
+    if: ${{ github.repository == 'freesurfer/surfa' && github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v') }}
     needs: [check]
     name: publish PyPI
     runs-on: ubuntu-latest
diff --git a/pyproject.toml b/pyproject.toml
index 962f9f8..0f44255 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,8 +1,13 @@
 [build-system]
-requires = ['setuptools', 'wheel', 'Cython>=3.0', 'numpy']
+# Cython 3.1+ needed for proper abi3 support
+# Should change to `numpy >=2,<3` when NumPy 1.x support is dropped
+requires = ['setuptools', 'wheel', 'Cython>=3.1', 'numpy']
 
 [tool.cibuildwheel]
 build = ["cp3{8,9,10,11}-*"]
+skip = [
+  "cp38-*musl*",  # no SciPy wheels, no need to make them for us
+]
 archs = "native"
 before-build = "pip install abi3audit"
 test-command = "python -c \"import surfa; print(surfa.__version__)\""

From fc541f0c1ce261cacc7cad1818dc722cf9ff5e3a Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Thu, 8 Jan 2026 14:01:38 -0500
Subject: [PATCH 02/20] FIX: Name [wheels]

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

diff --git a/.github/workflows/cibuildwheel.yml b/.github/workflows/cibuildwheel.yml
index edaa192..f17558c 100644
--- a/.github/workflows/cibuildwheel.yml
+++ b/.github/workflows/cibuildwheel.yml
@@ -12,10 +12,10 @@ on:  # yamllint disable-line rule:truthy
     tags:
       - 'v*.*.*'
     branches:
-      - main
+      - master
   pull_request:
     branches:
-      - main
+      - master
 
 jobs:
   # Adapted from dipy (BSD)

From c2dd989fdde3f660a268992cd2938644069c0283 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Thu, 8 Jan 2026 14:11:10 -0500
Subject: [PATCH 03/20] FIX: Faster [wheels]

---
 .github/workflows/cibuildwheel.yml | 33 +++++++++++++++---------------
 pyproject.toml                     |  7 +++++--
 2 files changed, 21 insertions(+), 19 deletions(-)

diff --git a/.github/workflows/cibuildwheel.yml b/.github/workflows/cibuildwheel.yml
index f17558c..2d963b5 100644
--- a/.github/workflows/cibuildwheel.yml
+++ b/.github/workflows/cibuildwheel.yml
@@ -13,6 +13,8 @@ on:  # yamllint disable-line rule:truthy
       - 'v*.*.*'
     branches:
       - master
+  # In a PR, needs "[wheels]" in the message to run
+  # In a PR, needs "[musl]" in the message to build musl wheels
   pull_request:
     branches:
       - master
@@ -20,10 +22,11 @@ on:  # yamllint disable-line rule:truthy
 jobs:
   # Adapted from dipy (BSD)
   check-commit:
-    name: Check [wheels] in commit message
+    name: Check [wheels] and [musl] in commit message
     runs-on: ubuntu-latest
     outputs:
       proceed: ${{ steps.commit-message.outputs.PROCEED }}
+      cibw_skip: ${{ steps.commit-message.outputs.CIBW_SKIP }}
     defaults:
       run:
         shell: bash -el {0}
@@ -34,6 +37,8 @@ jobs:
       - name: Check commit message for [wheels]
         id: commit-message
         run: |
+          PROCEED=true
+          CIBW_SKIP="cp38-*musllinux* cp39-musllinux_aarch64"
           if [[ "${{ github.event_name }}" == "pull_request" ]]; then
             MSG=$(git show -s --format=%s ${{ github.event.pull_request.head.sha }})
             echo "Got commit message: $MSG"
@@ -42,13 +47,15 @@ jobs:
             else
               PROCEED=false
             fi
-          else
-            PROCEED=true
+            if ! echo "$MSG" | grep -iq '\[musl\]'; then
+              CIBW_SKIP="*musllinux*"
+            fi
           fi
           echo "PROCEED=$PROCEED" | tee -a $GITHUB_OUTPUT
+          echo "CIBW_SKIP=$CIBW_SKIP" | tee -a $GITHUB_OUTPUT
 
   build_wheels:
-    name: Wheels ${{ matrix.os }} ${{ matrix.arch }}
+    name: Wheels ${{ matrix.os }}
     needs: [check-commit]
     if: needs.check-commit.outputs.proceed == 'true'
     runs-on: ${{ matrix.os }}
@@ -56,24 +63,15 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, ubuntu-24.04-arm, macos-15, macos-15-intel, windows-latest]  # windows-11-arm
-        arch: [native]
-        # TODO: Someday this can be enabled, but need to add emulation and it's slow,
-        # can use docker/setup-qemu-action
-        # include:
-        #   - os: ubuntu-latest
-        #     arch: aarch64
       fail-fast: false
-
     steps:
       - uses: actions/checkout@v5
       - uses: pypa/cibuildwheel@v3.2.0
-        with:
-          output-dir: wheelhouse
         env:
-          CIBW_ARCHS: ${{ matrix.arch }}
+          CIBW_SKIP: ${{ needs.check-commit.outputs.cibw_skip }}
       - uses: actions/upload-artifact@v4
         with:
-          name: cibw-wheels-${{ runner.os }}-${{ strategy.job-index }}
+          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
           path: ./wheelhouse/*.whl
 
   test_wheels:
@@ -87,8 +85,9 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-22.04, macos-14, macos-14-intel, windows-11]
-        python: [3.8, 3.14]  # old, newest (including pip-prelease)
-        arch: [native]
+        # oldest using oldest deps, newest using prerelease deps
+        python: ['3.8', '3.14']
+      fail-fast: false
     steps:
       - uses: actions/download-artifact@v5
         with:
diff --git a/pyproject.toml b/pyproject.toml
index 0f44255..91dec38 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -6,10 +6,13 @@ requires = ['setuptools', 'wheel', 'Cython>=3.1', 'numpy']
 [tool.cibuildwheel]
 build = ["cp3{8,9,10,11}-*"]
 skip = [
-  "cp38-*musl*",  # no SciPy wheels, no need to make them for us
+  # no SciPy wheels, no need to make them for us
+  "cp38-*musllinux*",
+  "cp39-musllinux_aarch64"
 ]
 archs = "native"
-before-build = "pip install abi3audit"
+# Fail early if no binary wheels for the given platform
+before-build = "pip install abi3audit numpy scipy --only-binary=\"numpy,scipy\""
 test-command = "python -c \"import surfa; print(surfa.__version__)\""
 
 [tool.cibuildwheel.linux]

From 3f6793ebc0a70202ce0bd623e1e0ea6f26ea5aef Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Thu, 8 Jan 2026 14:23:24 -0500
Subject: [PATCH 04/20] FIX: Unify [wheels] [musl]

---
 .github/workflows/cibuildwheel.yml | 19 ++++++++++++-------
 pyproject.toml                     |  2 +-
 2 files changed, 13 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/cibuildwheel.yml b/.github/workflows/cibuildwheel.yml
index 2d963b5..38a6259 100644
--- a/.github/workflows/cibuildwheel.yml
+++ b/.github/workflows/cibuildwheel.yml
@@ -84,9 +84,9 @@ jobs:
         shell: bash -el {0}
     strategy:
       matrix:
-        os: [ubuntu-22.04, macos-14, macos-14-intel, windows-11]
-        # oldest using oldest deps, newest using prerelease deps
-        python: ['3.8', '3.14']
+        os: [ubuntu-22.04, macos-14, windows-2022]
+        # oldest using oldest deps, one with newest using prerelease deps
+        python: ['3.8', '3.11', '3.14']
       fail-fast: false
     steps:
       - uses: actions/download-artifact@v5
@@ -97,10 +97,15 @@ jobs:
         with:
           python-version: ${{ matrix.python }}
       # Choose versions from 2022 (somewhat arbitrarily)
-      - run: python -m pip install numpy==1.23 scipy=1.8 nibabel pillow xxhash --only-binary="numpy,scipy,nibabel,pillow,xxhash"
-        if: matrix.python == '3.8'
-      - run: python -m pip install --pre --upgrade numpy scipy nibabel pillow xxhash --only-binary="numpy,scipy,nibabel,pillow,xxhash" --extra-index-url=https://pypi.anaconda.org/scipy-wheels-nightly/simple
-        if: matrix.python == '3.14'
+      - run: |
+          NUMPY_SCIPY="numpy scipy"
+          if [[ "${{ matrix.python }}" == "3.8" ]]; then
+            NUMPY_SCIPY="numpy==1.23 scipy==1.8"
+          elif [[ "${{ matrix.python }}" == "3.14" ]]; then
+            NUMPY_SCIPY="numpy scipy --pre --extra-index-url=https://pypi.anaconda.org/scipy-wheels-nightly/simple"
+          fi
+          set -x
+          python -m pip install $NUMPY_SCIPY nibabel pillow xxhash --only-binary=":all:"
       - run: pip install --no-index --find-links=file://${PWD}/dist surfa
       - run: python -c "import surfa; print(surfa.__version__)"
 
diff --git a/pyproject.toml b/pyproject.toml
index 91dec38..73153a5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -29,7 +29,7 @@ repair-wheel-command = [
 ]
 
 [tool.cibuildwheel.windows]
-before-build = "pip install delvewheel abi3audit"
+before-build = "pip install delvewheel abi3audit numpy scipy --only-binary=:all:\"numpy,scipy\""
 repair-wheel-command = [
   "delvewheel repair -w {dest_dir} {wheel}",
   "bash tools/audit_wheel.sh {wheel}",

From bfe5f9a60db7026e3cb27c92a860f9231ab51caf Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Thu, 8 Jan 2026 14:24:13 -0500
Subject: [PATCH 05/20] FIX: No explosion [wheels] [musl]

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

diff --git a/.github/workflows/cibuildwheel.yml b/.github/workflows/cibuildwheel.yml
index 38a6259..6b63b6b 100644
--- a/.github/workflows/cibuildwheel.yml
+++ b/.github/workflows/cibuildwheel.yml
@@ -86,7 +86,7 @@ jobs:
       matrix:
         os: [ubuntu-22.04, macos-14, windows-2022]
         # oldest using oldest deps, one with newest using prerelease deps
-        python: ['3.8', '3.11', '3.14']
+        python: ['3.8', '3.14']
       fail-fast: false
     steps:
       - uses: actions/download-artifact@v5

From cec03471d59d566ee3818b4b9f3ec3aabcebdf61 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Thu, 8 Jan 2026 14:25:47 -0500
Subject: [PATCH 06/20] FIX: Name

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

diff --git a/.github/workflows/cibuildwheel.yml b/.github/workflows/cibuildwheel.yml
index 6b63b6b..6b32068 100644
--- a/.github/workflows/cibuildwheel.yml
+++ b/.github/workflows/cibuildwheel.yml
@@ -125,7 +125,7 @@ jobs:
   check:
     needs: [build_wheels, sdist]
     timeout-minutes: 10
-    name: run twine check
+    name: Twine check
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v5

From 60c9285ff58db9a5ccf84d7f4757e1dc1fb415ab Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Thu, 8 Jan 2026 14:37:22 -0500
Subject: [PATCH 07/20] FIX: More [wheels]

---
 .github/workflows/cibuildwheel.yml | 17 +++++++++++++----
 1 file changed, 13 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/cibuildwheel.yml b/.github/workflows/cibuildwheel.yml
index 6b32068..755d210 100644
--- a/.github/workflows/cibuildwheel.yml
+++ b/.github/workflows/cibuildwheel.yml
@@ -93,20 +93,29 @@ jobs:
         with:
           pattern: cibw-wheels-*
           merge-multiple: true
+          path: dist
+      - run: ls -alt dist/
       - uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python }}
       # Choose versions from 2022 (somewhat arbitrarily)
-      - run: |
+      - name: Triage env vars
+        run: |
           NUMPY_SCIPY="numpy scipy"
           if [[ "${{ matrix.python }}" == "3.8" ]]; then
             NUMPY_SCIPY="numpy==1.23 scipy==1.8"
           elif [[ "${{ matrix.python }}" == "3.14" ]]; then
             NUMPY_SCIPY="numpy scipy --pre --extra-index-url=https://pypi.anaconda.org/scipy-wheels-nightly/simple"
           fi
-          set -x
-          python -m pip install $NUMPY_SCIPY nibabel pillow xxhash --only-binary=":all:"
-      - run: pip install --no-index --find-links=file://${PWD}/dist surfa
+          echo "NUMPY_SCIPY=$NUMPY_SCIPY" | tee -a $GITHUB_ENV
+          if [[ "${{ runner.os }}" == "Windows"* ]]; then
+            FIND_LINKS="file://$(cygpath -w ${PWD})\dist"
+          else
+            FIND_LINKS="file://${PWD}/dist"
+          fi
+          echo "FIND_LINKS=$FIND_LINKS" | tee -a $GITHUB_ENV
+      - run: pip install $NUMPY_SCIPY nibabel pillow xxhash --only-binary=":all:"
+      - run: pip install --no-index $FIND_LINKS surfa
       - run: python -c "import surfa; print(surfa.__version__)"
 
   sdist:

From 3a22428a3be136f9abd0ec2accef19f9adb77251 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Thu, 8 Jan 2026 14:42:59 -0500
Subject: [PATCH 08/20] FIX: Try [wheels thin]

---
 .github/workflows/cibuildwheel.yml | 30 ++++++++++++++++--------------
 1 file changed, 16 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/cibuildwheel.yml b/.github/workflows/cibuildwheel.yml
index 755d210..6f7be15 100644
--- a/.github/workflows/cibuildwheel.yml
+++ b/.github/workflows/cibuildwheel.yml
@@ -13,8 +13,10 @@ on:  # yamllint disable-line rule:truthy
       - 'v*.*.*'
     branches:
       - master
-  # In a PR, needs "[wheels]" in the message to run
-  # In a PR, needs "[musl]" in the message to build musl wheels
+  # A PR's commit message:
+  # - Containing "[wheels]" will build all wheels
+  # - Containing "[wheels thin]" will build just the wheels required for testing
+  # Non-PR triggers build all wheels.
   pull_request:
     branches:
       - master
@@ -44,12 +46,12 @@ jobs:
             echo "Got commit message: $MSG"
             if echo "$MSG" | grep -iq '\[wheels\]'; then
               PROCEED=true
+            elif echo "$MSG" | grep -iq '\[wheels thin\]'; then
+              PROCEED=true
+              CIBW_SKIP="*musllinux* cp39-* cp310-*"
             else
               PROCEED=false
             fi
-            if ! echo "$MSG" | grep -iq '\[musl\]'; then
-              CIBW_SKIP="*musllinux*"
-            fi
           fi
           echo "PROCEED=$PROCEED" | tee -a $GITHUB_OUTPUT
           echo "CIBW_SKIP=$CIBW_SKIP" | tee -a $GITHUB_OUTPUT
@@ -65,11 +67,11 @@ jobs:
         os: [ubuntu-latest, ubuntu-24.04-arm, macos-15, macos-15-intel, windows-latest]  # windows-11-arm
       fail-fast: false
     steps:
-      - uses: actions/checkout@v5
-      - uses: pypa/cibuildwheel@v3.2.0
+      - uses: actions/checkout@v6
+      - uses: pypa/cibuildwheel@v3.3.1
         env:
           CIBW_SKIP: ${{ needs.check-commit.outputs.cibw_skip }}
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@v6
         with:
           name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
           path: ./wheelhouse/*.whl
@@ -89,7 +91,7 @@ jobs:
         python: ['3.8', '3.14']
       fail-fast: false
     steps:
-      - uses: actions/download-artifact@v5
+      - uses: actions/download-artifact@v6
         with:
           pattern: cibw-wheels-*
           merge-multiple: true
@@ -123,10 +125,10 @@ jobs:
     name: Create sdist
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - uses: astral-sh/setup-uv@v6
       - run: uv build --sdist
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@v6
         with:
           name: cibw-wheels-sdist
           path: ./dist/*.tar.gz
@@ -137,8 +139,8 @@ jobs:
     name: Twine check
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v5
-      - uses: actions/download-artifact@v5
+      - uses: actions/checkout@v6
+      - uses: actions/download-artifact@v6
         with:
           pattern: cibw-wheels-*
           merge-multiple: true
@@ -162,7 +164,7 @@ jobs:
       url: https://pypi.org/p/surfa
     timeout-minutes: 10
     steps:
-      - uses: actions/download-artifact@v5
+      - uses: actions/download-artifact@v6
         with:
           pattern: cibw-wheels-*
           merge-multiple: true

From 84dd9d3ca308a0883000a60f09b3a953f3733807 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Thu, 8 Jan 2026 14:49:55 -0500
Subject: [PATCH 09/20] FIX: Faster [wheels thin]

---
 .github/workflows/cibuildwheel.yml | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/cibuildwheel.yml b/.github/workflows/cibuildwheel.yml
index 6f7be15..1701424 100644
--- a/.github/workflows/cibuildwheel.yml
+++ b/.github/workflows/cibuildwheel.yml
@@ -7,6 +7,7 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
   cancel-in-progress: true
 on:  # yamllint disable-line rule:truthy
+  # Non-PR triggers build all wheels.
   workflow_dispatch:
   push:
     tags:
@@ -15,8 +16,7 @@ on:  # yamllint disable-line rule:truthy
       - master
   # A PR's commit message:
   # - Containing "[wheels]" will build all wheels
-  # - Containing "[wheels thin]" will build just the wheels required for testing
-  # Non-PR triggers build all wheels.
+  # - Containing "[wheels thin]" will build just the wheels required for testing (3.8, 3.11-abi3)
   pull_request:
     branches:
       - master
@@ -24,7 +24,7 @@ on:  # yamllint disable-line rule:truthy
 jobs:
   # Adapted from dipy (BSD)
   check-commit:
-    name: Check [wheels] and [musl] in commit message
+    name: Triage wheel build
     runs-on: ubuntu-latest
     outputs:
       proceed: ${{ steps.commit-message.outputs.PROCEED }}
@@ -48,7 +48,8 @@ jobs:
               PROCEED=true
             elif echo "$MSG" | grep -iq '\[wheels thin\]'; then
               PROCEED=true
-              CIBW_SKIP="*musllinux* cp39-* cp310-*"
+              # We don't need the Intel macOS or Ubuntu aarch64 builds at all
+              CIBW_SKIP="*musllinux* cp39-* cp310-* cp*-macosx_*_x86_64" cp*-*linux*aarch64"
             else
               PROCEED=false
             fi
@@ -71,6 +72,7 @@ jobs:
       - uses: pypa/cibuildwheel@v3.3.1
         env:
           CIBW_SKIP: ${{ needs.check-commit.outputs.cibw_skip }}
+          CIBW_ALLOW_EMPTY: "True"
       - uses: actions/upload-artifact@v6
         with:
           name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}

From 5e11dcbdb17ab40d3d112a2fc23418c4028f3b22 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Thu, 8 Jan 2026 14:52:36 -0500
Subject: [PATCH 10/20] FIX: More [wheels thin]

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

diff --git a/.github/workflows/cibuildwheel.yml b/.github/workflows/cibuildwheel.yml
index 1701424..35ef41b 100644
--- a/.github/workflows/cibuildwheel.yml
+++ b/.github/workflows/cibuildwheel.yml
@@ -49,7 +49,7 @@ jobs:
             elif echo "$MSG" | grep -iq '\[wheels thin\]'; then
               PROCEED=true
               # We don't need the Intel macOS or Ubuntu aarch64 builds at all
-              CIBW_SKIP="*musllinux* cp39-* cp310-* cp*-macosx_*_x86_64" cp*-*linux*aarch64"
+              CIBW_SKIP="*musllinux* cp39-* cp310-* *-macosx_*_x86_64 *-*linux*aarch64"
             else
               PROCEED=false
             fi

From 29e0098f37208c5837875146e2dd0aa75f355750 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Thu, 8 Jan 2026 14:54:26 -0500
Subject: [PATCH 11/20] FIX: Sel [wheels thin]

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

diff --git a/.github/workflows/cibuildwheel.yml b/.github/workflows/cibuildwheel.yml
index 35ef41b..fc40f8c 100644
--- a/.github/workflows/cibuildwheel.yml
+++ b/.github/workflows/cibuildwheel.yml
@@ -49,7 +49,7 @@ jobs:
             elif echo "$MSG" | grep -iq '\[wheels thin\]'; then
               PROCEED=true
               # We don't need the Intel macOS or Ubuntu aarch64 builds at all
-              CIBW_SKIP="*musllinux* cp39-* cp310-* *-macosx_*_x86_64 *-*linux*aarch64"
+              CIBW_SKIP="*musllinux* cp39-* cp310-* *-macosx*x86_64 *-*linux*aarch64"
             else
               PROCEED=false
             fi

From b4058a3a87fc392766a2e5ee91b40bce2315c840 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Thu, 8 Jan 2026 15:01:03 -0500
Subject: [PATCH 12/20] FIX: Better [wheels thin]

---
 .github/workflows/cibuildwheel.yml | 8 ++++----
 .github/workflows/test.yml         | 6 +++++-
 2 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/cibuildwheel.yml b/.github/workflows/cibuildwheel.yml
index fc40f8c..d2a81a6 100644
--- a/.github/workflows/cibuildwheel.yml
+++ b/.github/workflows/cibuildwheel.yml
@@ -14,9 +14,9 @@ on:  # yamllint disable-line rule:truthy
       - 'v*.*.*'
     branches:
       - master
-  # A PR's commit message:
-  # - Containing "[wheels]" will build all wheels
-  # - Containing "[wheels thin]" will build just the wheels required for testing (3.8, 3.11-abi3)
+  # A PR's commit message containing the following text will build:
+  # - "[wheels]" : all wheels
+  # - "[wheels thin]" : just the wheels required for the test_wheels jobs (3.8, 3.11-abi3)
   pull_request:
     branches:
       - master
@@ -119,7 +119,7 @@ jobs:
           fi
           echo "FIND_LINKS=$FIND_LINKS" | tee -a $GITHUB_ENV
       - run: pip install $NUMPY_SCIPY nibabel pillow xxhash --only-binary=":all:"
-      - run: pip install --no-index $FIND_LINKS surfa
+      - run: pip install --no-index --find-links=$FIND_LINKS surfa
       - run: python -c "import surfa; print(surfa.__version__)"
 
   sdist:
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index d39e0aa..68e6a87 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -4,6 +4,10 @@ on:
   push:
   pull_request:
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
+  cancel-in-progress: true
+
 jobs:
   test:
     runs-on: ${{ matrix.os }}
@@ -21,7 +25,7 @@ jobs:
       uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
-    
+
     - name: Display python and system info
       run: |
         python -c "import sys; print(f'python {sys.version}')"

From d938308af665c37dce7e94ff7aafde62edb6007e Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Thu, 8 Jan 2026 15:01:39 -0500
Subject: [PATCH 13/20] FIX: Better [wheels thin]

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

diff --git a/.github/workflows/cibuildwheel.yml b/.github/workflows/cibuildwheel.yml
index d2a81a6..74e15d2 100644
--- a/.github/workflows/cibuildwheel.yml
+++ b/.github/workflows/cibuildwheel.yml
@@ -119,7 +119,7 @@ jobs:
           fi
           echo "FIND_LINKS=$FIND_LINKS" | tee -a $GITHUB_ENV
       - run: pip install $NUMPY_SCIPY nibabel pillow xxhash --only-binary=":all:"
-      - run: pip install --no-index --find-links=$FIND_LINKS surfa
+      - run: pip install --no-index --find-links="$FIND_LINKS" surfa
       - run: python -c "import surfa; print(surfa.__version__)"
 
   sdist:

From a040ffeb00e9c0e0d5971fd0a6626871db9e8b7d Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Thu, 8 Jan 2026 15:04:18 -0500
Subject: [PATCH 14/20] FIX: URL [wheels thin]

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

diff --git a/.github/workflows/cibuildwheel.yml b/.github/workflows/cibuildwheel.yml
index 74e15d2..4b51068 100644
--- a/.github/workflows/cibuildwheel.yml
+++ b/.github/workflows/cibuildwheel.yml
@@ -109,7 +109,7 @@ jobs:
           if [[ "${{ matrix.python }}" == "3.8" ]]; then
             NUMPY_SCIPY="numpy==1.23 scipy==1.8"
           elif [[ "${{ matrix.python }}" == "3.14" ]]; then
-            NUMPY_SCIPY="numpy scipy --pre --extra-index-url=https://pypi.anaconda.org/scipy-wheels-nightly/simple"
+            NUMPY_SCIPY="numpy scipy --pre --extra-index-url="https://pypi.anaconda.org/scientific-python-nightly-wheels/simple"
           fi
           echo "NUMPY_SCIPY=$NUMPY_SCIPY" | tee -a $GITHUB_ENV
           if [[ "${{ runner.os }}" == "Windows"* ]]; then

From 3335cb77675e98c053f43d8a1ec2f72230816a73 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Thu, 8 Jan 2026 15:15:27 -0500
Subject: [PATCH 15/20] FIX: URL [wheels thin]

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

diff --git a/.github/workflows/cibuildwheel.yml b/.github/workflows/cibuildwheel.yml
index 4b51068..6a7ca1b 100644
--- a/.github/workflows/cibuildwheel.yml
+++ b/.github/workflows/cibuildwheel.yml
@@ -109,7 +109,7 @@ jobs:
           if [[ "${{ matrix.python }}" == "3.8" ]]; then
             NUMPY_SCIPY="numpy==1.23 scipy==1.8"
           elif [[ "${{ matrix.python }}" == "3.14" ]]; then
-            NUMPY_SCIPY="numpy scipy --pre --extra-index-url="https://pypi.anaconda.org/scientific-python-nightly-wheels/simple"
+            NUMPY_SCIPY="numpy scipy --pre --extra-index-url=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple"
           fi
           echo "NUMPY_SCIPY=$NUMPY_SCIPY" | tee -a $GITHUB_ENV
           if [[ "${{ runner.os }}" == "Windows"* ]]; then

From 54fedc421ac155b4f5ec552d3f2d2e2035a67f2d Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Thu, 8 Jan 2026 15:34:49 -0500
Subject: [PATCH 16/20] FIX: Where [wheels thin]

---
 .github/workflows/cibuildwheel.yml | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/.github/workflows/cibuildwheel.yml b/.github/workflows/cibuildwheel.yml
index 6a7ca1b..b88883b 100644
--- a/.github/workflows/cibuildwheel.yml
+++ b/.github/workflows/cibuildwheel.yml
@@ -112,14 +112,8 @@ jobs:
             NUMPY_SCIPY="numpy scipy --pre --extra-index-url=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple"
           fi
           echo "NUMPY_SCIPY=$NUMPY_SCIPY" | tee -a $GITHUB_ENV
-          if [[ "${{ runner.os }}" == "Windows"* ]]; then
-            FIND_LINKS="file://$(cygpath -w ${PWD})\dist"
-          else
-            FIND_LINKS="file://${PWD}/dist"
-          fi
-          echo "FIND_LINKS=$FIND_LINKS" | tee -a $GITHUB_ENV
       - run: pip install $NUMPY_SCIPY nibabel pillow xxhash --only-binary=":all:"
-      - run: pip install --no-index --find-links="$FIND_LINKS" surfa
+      - run: pip install --no-index --find-links=dist/ surfa
       - run: python -c "import surfa; print(surfa.__version__)"
 
   sdist:

From 89ff3b4c649a0e20499a0a9c3c62e5907b81d592 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Thu, 8 Jan 2026 15:37:01 -0500
Subject: [PATCH 17/20] FIX: Where [wheels thin]

---
 .github/workflows/cibuildwheel.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/cibuildwheel.yml b/.github/workflows/cibuildwheel.yml
index b88883b..6f64afa 100644
--- a/.github/workflows/cibuildwheel.yml
+++ b/.github/workflows/cibuildwheel.yml
@@ -93,15 +93,15 @@ jobs:
         python: ['3.8', '3.14']
       fail-fast: false
     steps:
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python }}
       - uses: actions/download-artifact@v6
         with:
           pattern: cibw-wheels-*
           merge-multiple: true
           path: dist
       - run: ls -alt dist/
-      - uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python }}
       # Choose versions from 2022 (somewhat arbitrarily)
       - name: Triage env vars
         run: |

From 06117bd171cbd3cd3d09e127cf755d58c72f6ddf Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Fri, 9 Jan 2026 09:26:59 -0500
Subject: [PATCH 18/20] FIX: Comment [wheels]

---
 .github/workflows/cibuildwheel.yml | 3 ++-
 pyproject.toml                     | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/cibuildwheel.yml b/.github/workflows/cibuildwheel.yml
index 6f64afa..4e25015 100644
--- a/.github/workflows/cibuildwheel.yml
+++ b/.github/workflows/cibuildwheel.yml
@@ -14,7 +14,8 @@ on:  # yamllint disable-line rule:truthy
       - 'v*.*.*'
     branches:
       - master
-  # A PR's commit message containing the following text will build:
+  # By default, PRs do not build wheels (for speed/efficiency). However,
+  # a PR's commit message containing the following text will build:
   # - "[wheels]" : all wheels
   # - "[wheels thin]" : just the wheels required for the test_wheels jobs (3.8, 3.11-abi3)
   pull_request:
diff --git a/pyproject.toml b/pyproject.toml
index 73153a5..bae83f7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -29,7 +29,7 @@ repair-wheel-command = [
 ]
 
 [tool.cibuildwheel.windows]
-before-build = "pip install delvewheel abi3audit numpy scipy --only-binary=:all:\"numpy,scipy\""
+before-build = "pip install delvewheel abi3audit numpy scipy --only-binary=\"numpy,scipy\""
 repair-wheel-command = [
   "delvewheel repair -w {dest_dir} {wheel}",
   "bash tools/audit_wheel.sh {wheel}",

From 7d9587b7001fce684df0bef7fbf57599f4bde44f Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Fri, 9 Jan 2026 09:28:42 -0500
Subject: [PATCH 19/20] FIX: Better [wheels]

---
 .github/workflows/cibuildwheel.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/cibuildwheel.yml b/.github/workflows/cibuildwheel.yml
index 4e25015..995e543 100644
--- a/.github/workflows/cibuildwheel.yml
+++ b/.github/workflows/cibuildwheel.yml
@@ -150,7 +150,9 @@ jobs:
       - run: twine check --strict dist/*
 
   publish:
-    if: ${{ github.repository == 'freesurfer/surfa' && github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v') }}
+    # once ready to cut wheels to PyPI (e.g., numpy 1 support is dropped), remove the
+    # "false &&" below
+    if: false && github.repository == 'freesurfer/surfa' && github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
     needs: [check]
     name: publish PyPI
     runs-on: ubuntu-latest

From e4c2234978c116acb01fe7fb0308869ef10d0bd6 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Fri, 9 Jan 2026 09:29:29 -0500
Subject: [PATCH 20/20] FIX: Better [wheels]

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

diff --git a/.github/workflows/cibuildwheel.yml b/.github/workflows/cibuildwheel.yml
index 995e543..86ee386 100644
--- a/.github/workflows/cibuildwheel.yml
+++ b/.github/workflows/cibuildwheel.yml
@@ -66,7 +66,7 @@ jobs:
     timeout-minutes: 20
     strategy:
       matrix:
-        os: [ubuntu-latest, ubuntu-24.04-arm, macos-15, macos-15-intel, windows-latest]  # windows-11-arm
+        os: [ubuntu-latest, ubuntu-24.04-arm, macos-latest, macos-15-intel, windows-latest]  # windows-11-arm
       fail-fast: false
     steps:
       - uses: actions/checkout@v6