brainiak · mihaic · Apr 2, 2026 · Mar 30, 2026 · Mar 30, 2026 · Mar 30, 2026
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -16,61 +16,86 @@ env:
 jobs:
   checks:
     name: Check Python ${{ matrix.python-version }} on ${{ matrix.os }}
-    env:
-      IGNORE_CONDA: true
     runs-on: ${{ matrix.os }}
+    env:
+      UV_PYTHON: ${{ matrix.python-version }}
+    defaults:
+      run:
+        shell: bash
     strategy:
       matrix:
-        os: [ ubuntu-20.04, macos-latest, windows-latest ]
-        python-version: [ "3.9", "3.10", "3.11", "3.12" ]
-      fail-fast: true
+        os: [ ubuntu-22.04, macos-latest, windows-latest ]
+        python-version: [ "3.10", "3.11", "3.12" ]
+      fail-fast: false
     steps:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
-      - uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version }}
+      - uses: astral-sh/setup-uv@v7
+
+      - name: Install Python ${{ matrix.python-version }}
+        run: uv python install ${UV_PYTHON}
 
       # Use msmpi on windows
       - uses: mpi4py/setup-mpi@v1
         if: ${{ contains(matrix.os, 'windows') }}
         with:
           mpi: msmpi
 
-      # Else, use the default for the OS and setup-mpi action
+      # Use mpich on linux (openmpi tends to hang in GitHub Actions runners)
+      - uses: mpi4py/setup-mpi@v1
+        if: ${{ contains(matrix.os, 'ubuntu') }}
+        with:
+          mpi: mpich
+
+      # Use the default for the OS (openmpi) on macOS
       - uses: mpi4py/setup-mpi@v1
-        if: ${{ !contains(matrix.os, 'windows') }}
+        if: ${{ contains(matrix.os, 'macos') }}
 
       # Setup openmp on macOS
       - name: Install openmp if on macos
         if: ${{ contains(matrix.os, 'macos') }}
         run: |
           brew install libomp llvm
 
-      - name: Upgrade pip
+      - name: Synchronize project environment
         run: |
-          python3 -m pip install -U pip
+          if [[ "$RUNNER_OS" == "macOS" ]]; then
+            export CC=$(brew --prefix llvm)/bin/clang
+            export CXX=$(brew --prefix llvm)/bin/clang++
+          fi
+          # Build mpi4py from source on Linux so it links against the
+          # locally-installed MPI runtime; pre-built wheels cause
+          # "libmpi.so.12: cannot open shared object file" on Linux.
+          # On macOS and Windows the pre-built wheels work fine.
+          ARGS=(--locked --extra dev --extra matnormal --extra examples)
+          if [[ "$RUNNER_OS" == "Linux" ]]; then
+            ARGS+=(--no-binary-package mpi4py)
+          fi
+          uv sync "${ARGS[@]}"
 
-      - name: Run tests and other checks
+      - name: Run static analysis and tests
         if: runner.os == 'Linux'
         run: |
-          ./pr-check.sh
+          uv run ./run-checks.sh
+          uv run ./run-tests.sh --sdist-mode
+          uv run bash -lc 'cd docs && make'
 
-      - name: Run tests and other checks
+      - name: Run static analysis and tests
         if: runner.os == 'macOS'
         run: |
           export CLANG_PREFIX=$(brew --prefix llvm)
           export CC=$CLANG_PREFIX/bin/clang
           export CXX=$CLANG_PREFIX/bin/clang++
-          ./pr-check.sh    
+          uv run ./run-checks.sh
+          uv run ./run-tests.sh --sdist-mode
+          uv run bash -lc 'cd docs && make'
 
-      # On window, just install the package and run tests for now, we need to port the pr-check script to windows
+      # On Windows, just install the package and run tests for now, we need to port the pr-check script to windows
       - name: Run tests and other checks
         if: runner.os == 'Windows'
         run: |
-            python -m pip install .[all] -v
-            python -m pytest -v 
+            uv run python -m pytest -v
 
       # - uses: codecov/codecov-action@v1
diff --git a/.gitignore b/.gitignore
@@ -1,6 +1,7 @@
 src/brainiak/_version.py
 
 venv/
+.venv/
 
 *.iml
 *.eggs

diff --git a/pyproject.toml b/pyproject.toml
@@ -12,7 +12,7 @@ build-backend = "scikit_build_core.build"
 [project]
 name = "brainiak"
 description = "Brain Imaging Analysis Kit"
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 readme = "README.rst"
 license = { file = "LICENSE" }
 authors = [
@@ -66,8 +66,8 @@ dependencies = [
     "psutil",
     "nibabel",
     "joblib",
-    "wheel",                 # See https://github.com/astropy/astropy-helpers/issues/501
-    "pydicom",
+    "wheel>=0.46.2",         # See https://github.com/astropy/astropy-helpers/issues/501
+    "pydicom>=3.0.2",
 ]
 
 [project.optional-dependencies]
@@ -99,7 +99,7 @@ examples = [
     "timecorr",
     "seaborn",
     "holoviews",
-    "pyOpenSSL",
+    "pyOpenSSL>=26.0.0",
     "awscli",
     "bcrypt",
     "indexed_gzip",
@@ -111,13 +111,13 @@ examples = [
     "nilearn",
     "nodejs",
     "numpy",
-    "pydicom",
+    "pydicom>=3.0.2",
     "requests",
     "rpyc",
     "scikit-learn",
     "scipy>=1.6.0",
     "toml",
-    "tornado",
+    "tornado>=6.5.5",
     "websocket-client",
     "wsaccel",
     "inotify",

diff --git a/run-tests.sh b/run-tests.sh
@@ -20,13 +20,14 @@ set -e
 # detect editable mode. Use the "--sdist-mode" flag.
 sdist_mode=$1
 
-python3 -m pip freeze | grep -qi /brainiak \
-        || [ ${sdist_mode:-default} = "--sdist-mode" ] \
-        || {
-    echo "You must install brainiak in editable mode"`
-        `" before calling "$(basename "$0")
-    exit 1
-}
+if [ "${sdist_mode:-default}" != "--sdist-mode" ]; then
+    python3 -m pip freeze | grep -qi /brainiak \
+            || {
+        echo "You must install brainiak in editable mode"`
+            `" before calling "$(basename "$0")
+        exit 1
+    }
+fi
 
 coverage run -m pytest
 

diff --git a/src/brainiak/funcalign/fastsrm.py b/src/brainiak/funcalign/fastsrm.py
@@ -36,10 +36,17 @@ def get_shape(path):
     path: str
         path to np array
     """
-    f = open(path, "rb")
-    version = np.lib.format.read_magic(f)
-    shape, fortran_order, dtype = np.lib.format._read_array_header(f, version)
-    f.close()
+    with open(path, "rb") as f:
+        version = np.lib.format.read_magic(f)
+        if version == (1, 0):
+            shape, fortran_order, dtype = (
+                np.lib.format.read_array_header_1_0(f))
+        elif version == (2, 0):
+            shape, fortran_order, dtype = (
+                np.lib.format.read_array_header_2_0(f))
+        else:
+            raise ValueError(
+                "Unknown numpy .npy format version: %s" % str(version))
     return shape
 
 

diff --git a/tests/conftest.py b/tests/conftest.py
@@ -1,4 +1,3 @@
-import multiprocessing
 import sys
 
 from mpi4py import MPI
@@ -50,17 +49,22 @@ def seeded_rng():
 @pytest.fixture(scope="module", autouse=True)
 def pool_size():
     """
-    Set the pool_size to 1 for MPI tests when start_method for multiprocessing
-    is not fork.
+    Set the pool_size to 1 for MPI tests to avoid forking inside MPI
+    processes.
 
     This replaces the old skip_non_fork fixture. We don't need to skip these
     tests completely, but we need to ensure that the pool_size is set to 1 so
     they don't launch any multiprocessing pools within the MPI environment.
+    Forking inside an MPI process can cause hangs or crashes with certain MPI
+    transports (e.g., libfabric EFA on AWS-based CI runners).
     On windows, it seems like intel mpi and msmpi both have issues with fork,
     so we need to set the pool_size to 1 there as well.
     """
-    if (multiprocessing.get_start_method() != "fork" and
-            MPI.COMM_WORLD.Get_attr(MPI.APPNUM) is not None):
+    # When running inside an MPI subprocess (launched by mpiexec), avoid
+    # forking regardless of the multiprocessing start method.  On Linux the
+    # default start method is "fork", but fork()-after-MPI_Init is unsafe with
+    # many MPI transports (libfabric EFA, OpenMPI shared-memory, …).
+    if MPI.COMM_WORLD.Get_attr(MPI.APPNUM) is not None:
         return 1
 
     # OpenMPI has issues with fork, so we need to set the pool_size to 1
-Original file line number
+Diff line change
@@ -1,6 +1,7 @@
     src/brainiak/_version.py
     venv/
+    .venv/
     *.iml
     *.eggs
@@ Expand Down @@