From e7e57167a2b51d96b825c5e3c998ab7d75d5a611 Mon Sep 17 00:00:00 2001
From: Frithjof Gressmann <frithjof@noc.io>
Date: Fri, 17 Apr 2026 22:34:37 -0500
Subject: [PATCH 01/21] Generate build backend

---
 .github/workflows/main.yml                    |  123 +-
 .github/workflows/style.yml                   |    7 +-
 Makefile                                      |    2 +-
 _build_backend.py                             |  539 ++++
 configure_mpi.py                              |  171 ++
 docs/tutorial/installation.md                 |  234 +-
 pyproject.toml                                |   30 +-
 src/miv_simulator/__init__.py                 |    5 +
 src/miv_simulator/mpi_env.py                  |  204 ++
 .../miv_simulator_install_test/__init__.py    |    1 +
 tests/installation/pyproject.toml             |   16 +
 tests/installation/uv.lock                    | 2276 +++++++++++++++++
 uv.lock                                       |   14 +-
 13 files changed, 3474 insertions(+), 148 deletions(-)
 create mode 100644 _build_backend.py
 create mode 100644 configure_mpi.py
 create mode 100644 src/miv_simulator/mpi_env.py
 create mode 100644 tests/installation/miv_simulator_install_test/__init__.py
 create mode 100644 tests/installation/pyproject.toml
 create mode 100644 tests/installation/uv.lock

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 45960799..ffb0cdae 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -1,54 +1,105 @@
 name: CI
 
-on: workflow_dispatch
-  # push:
-  #   branches: [ main ]
-  # pull_request:
-  #   branches: [ main ]
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+  workflow_dispatch:
 
 jobs:
   build:
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-latest]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
-        mpi: ["mpich", "openmpi"]
+        os: [ ubuntu-latest, macos-latest ]
+        python-version: [ "3.10", "3.11", "3.12" ]
+        mpi: [ "mpich", "openmpi" ]
         exclude:
           - os: macos-latest
-            mpi: "mpich" # Brew hdf5-mpi only support openmpi
-        include:
-          - os: ubuntu-latest
-            path: |
-              ~/.cache/pypoetry
-              ~/.cache/pip
-          - os: macos-latest
-            path: |
-              ~/Library/Caches/pypoetry
-              ~/Library/Caches/pip
+            mpi: "mpich" # Brew hdf5-mpi only supports openmpi
     runs-on: ${{ matrix.os }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
+
       - name: Setup MPI
         uses: mpi4py/setup-mpi@v1
         with:
           mpi: ${{ matrix.mpi }}
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2.2.2
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: Set up cache
-        id: cached-python-dependencies
-        uses: actions/cache@v3
-        with:
-          path: ${{ matrix.path }}
-          key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}-${{ hashFiles('poetry.lock') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-
-      - name: Install background dependency (MacOS)
-        if: startsWith(runner.os, 'macOS')
+
+      - name: Install parallel HDF5 (Ubuntu, MPICH)
+        if: runner.os == 'Linux' && matrix.mpi == 'mpich'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libhdf5-mpich-dev pkg-config python3-dev
+
+      - name: Install parallel HDF5 (Ubuntu, OpenMPI)
+        if: runner.os == 'Linux' && matrix.mpi == 'openmpi'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libhdf5-openmpi-dev pkg-config python3-dev
+
+      - name: Install parallel HDF5 (macOS)
+        if: runner.os == 'macOS'
         run: |
           brew install hdf5-mpi
-      - name: Install background dependency (Ubuntu)
-        if: startsWith(runner.os, 'Linux')
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+        with:
+          version: "latest"
+
+      - name: Set up Python ${{ matrix.python-version }}
+        run: uv python install ${{ matrix.python-version }}
+
+      - name: Configure MPI environment
+        run: |
+          eval $(python configure_mpi.py)
+          # Persist env vars for subsequent steps
+          echo "MPICC=${MPICC}" >> "$GITHUB_ENV"
+          echo "CC=${CC}" >> "$GITHUB_ENV"
+          echo "HDF5_MPI=${HDF5_MPI}" >> "$GITHUB_ENV"
+          if [ -n "$HDF5_PKGCONFIG_NAME" ]; then
+            echo "HDF5_PKGCONFIG_NAME=${HDF5_PKGCONFIG_NAME}" >> "$GITHUB_ENV"
+          fi
+          if [ -n "$HDF5_DIR" ]; then
+            echo "HDF5_DIR=${HDF5_DIR}" >> "$GITHUB_ENV"
+          fi
+          if [ -n "$HDF5_INCLUDEDIR" ]; then
+            echo "HDF5_INCLUDEDIR=${HDF5_INCLUDEDIR}" >> "$GITHUB_ENV"
+          fi
+          if [ -n "$HDF5_LIBDIR" ]; then
+            echo "HDF5_LIBDIR=${HDF5_LIBDIR}" >> "$GITHUB_ENV"
+          fi
+
+      - name: Install miv-simulator
+        run: uv sync
+
+      - name: Verify MPI environment
+        run: |
+          uv run python -c "
+          import miv_simulator
+          print(f'miv_simulator {miv_simulator.version}')
+
+          import h5py
+          mpi = getattr(h5py.get_config(), 'mpi', False)
+          print(f'h5py MPI support: {mpi}')
+          assert mpi, 'h5py was built without MPI support'
+
+          import mpi4py
+          print(f'mpi4py {mpi4py.__version__}')
+          "
+
+      - name: Run tests
+        run: uv run pytest tests/ -x -q
+
+      - name: Test standalone installation
         run: |
-          sudo apt-get install -y libhdf5-mpi-dev python3-dev # Install hdf5-mpi
+          cd tests/installation
+          rm -rf .venv uv.lock
+          uv sync
+          uv run python -c "
+          import miv_simulator
+          print(f'Standalone install OK: miv_simulator {miv_simulator.version}')
+          import h5py
+          assert getattr(h5py.get_config(), 'mpi', False), 'h5py missing MPI'
+          "
diff --git a/.github/workflows/style.yml b/.github/workflows/style.yml
index 62dc3ab2..3c7af70b 100644
--- a/.github/workflows/style.yml
+++ b/.github/workflows/style.yml
@@ -4,7 +4,6 @@ jobs:
   ruff:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
-      - uses: astral-sh/ruff-action@v1
-        with:
-          args: "format --check"
+      - uses: actions/checkout@v6
+      - uses: astral-sh/setup-uv@v7
+      - run: uvx ruff format --check
diff --git a/Makefile b/Makefile
index ef482200..f62d7147 100644
--- a/Makefile
+++ b/Makefile
@@ -5,7 +5,7 @@ PYTHONPATH := `pwd`
 #* Installation
 .PHONY: install
 install:
-	uv sync
+	eval $$(python configure_mpi.py) && uv sync
 
 .PHONY: pre-commit-install
 pre-commit-install:
diff --git a/_build_backend.py b/_build_backend.py
new file mode 100644
index 00000000..9b5ca239
--- /dev/null
+++ b/_build_backend.py
@@ -0,0 +1,539 @@
+"""Custom PEP 517 build backend for miv-simulator.
+
+Wraps hatchling and adds MPI environment detection and validation to
+prevent misconfigured MPI/HDF5 setups from causing subtle runtime errors.
+
+Environment variables (set before ``uv sync`` / ``pip install``):
+
+  MPICC       Path to the MPI C compiler wrapper.
+              Default: auto-detected from PATH.
+
+  HDF5_DIR    Prefix of a parallel-HDF5 installation.
+              Default: auto-detected via ``h5pcc`` / ``h5cc`` / pkg-config.
+
+  HDF5_MPI    Set to "ON" to tell h5py to enable MPI I/O.
+              Default: auto-set to "ON" when an MPI-enabled HDF5 is found.
+
+  HDF5_INCLUDEDIR
+              Override the HDF5 include directory (for non-standard layouts).
+
+  HDF5_LIBDIR
+              Override the HDF5 library directory (for non-standard layouts).
+
+  HDF5_PKGCONFIG_NAME
+              pkg-config package name for HDF5 (e.g. "hdf5-mpich").
+              If set, h5py uses pkg-config instead of HDF5_DIR.
+
+  CC          C compiler used when building extension modules.
+              Default: set to the value of MPICC (so h5py/neuroh5 use it).
+
+  MIV_SKIP_MPI_CHECK
+              Set to "1" to bypass all detection and validation.
+
+Checks performed during wheel / editable builds:
+  1. MPI compiler wrapper (mpicc) is on PATH
+  2. mpi4py links against the detected system MPI (not a pre-built wheel)
+  3. h5py has parallel HDF5 / MPI support enabled
+  4. mpi4py and h5py link against the same MPI library
+"""
+
+import os
+import platform
+import shutil
+import subprocess
+import sys
+
+from hatchling.build import (
+    build_editable as _build_editable,
+    build_sdist as _build_sdist,
+    build_wheel as _build_wheel,
+    get_requires_for_build_editable as _get_requires_for_build_editable,
+    get_requires_for_build_sdist as _get_requires_for_build_sdist,
+    get_requires_for_build_wheel as _get_requires_for_build_wheel,
+)
+
+try:
+    from hatchling.build import (
+        prepare_metadata_for_build_editable as _prepare_metadata_for_build_editable,
+        prepare_metadata_for_build_wheel as _prepare_metadata_for_build_wheel,
+    )
+except ImportError:
+    _prepare_metadata_for_build_wheel = None
+    _prepare_metadata_for_build_editable = None
+
+
+# ---------------------------------------------------------------------------
+# MPI / HDF5 environment detection helpers
+# ---------------------------------------------------------------------------
+
+
+def _get_shared_lib_deps(path):
+    """Return shared-library dependency listing for a binary/shared object."""
+    system = platform.system()
+    try:
+        if system == "Linux":
+            r = subprocess.run(
+                ["ldd", path],
+                capture_output=True,
+                text=True,
+                timeout=10,
+            )
+        elif system == "Darwin":
+            r = subprocess.run(
+                ["otool", "-L", path],
+                capture_output=True,
+                text=True,
+                timeout=10,
+            )
+        else:
+            return ""
+        return r.stdout if r.returncode == 0 else ""
+    except Exception:
+        return ""
+
+
+def _extract_mpi_lib(ldd_output):
+    """Extract the resolved path to libmpi from ldd/otool output."""
+    for line in ldd_output.splitlines():
+        line = line.strip()
+        if "libmpi" not in line:
+            continue
+        # Linux ldd format:  libmpi.so.40 => /usr/lib/libmpi.so.40 (0x...)
+        if "=>" in line:
+            path = line.split("=>")[1].strip().split("(")[0].strip()
+            if path:
+                return path
+        # macOS otool format:  /usr/local/lib/libmpi.40.dylib (...)
+        elif line.startswith("/"):
+            path = line.split("(")[0].strip()
+            if path:
+                return path
+    return None
+
+
+def _find_mpicc():
+    """Return the resolved path to mpicc, honouring the MPICC env var."""
+    mpicc = os.environ.get("MPICC")
+    if mpicc:
+        path = shutil.which(mpicc.split()[0])  # handle "mpicc --shared"
+        if path:
+            return path
+    return shutil.which("mpicc")
+
+
+def _find_mpicc_libdir():
+    """Detect the MPI library directory via mpicc."""
+    mpicc = _find_mpicc()
+    if not mpicc:
+        return None
+    # OpenMPI
+    try:
+        r = subprocess.run(
+            [mpicc, "--showme:libdirs"],
+            capture_output=True,
+            text=True,
+            timeout=10,
+        )
+        if r.returncode == 0 and r.stdout.strip():
+            return r.stdout.strip().split()[0]
+    except Exception:
+        pass
+    # MPICH
+    try:
+        r = subprocess.run(
+            [mpicc, "-show"],
+            capture_output=True,
+            text=True,
+            timeout=10,
+        )
+        if r.returncode == 0:
+            for token in r.stdout.split():
+                if token.startswith("-L"):
+                    return token[2:]
+    except Exception:
+        pass
+    return None
+
+
+def _find_hdf5_dir():
+    """Auto-detect a parallel HDF5 installation prefix.
+
+    Resolution order:
+      1. ``HDF5_DIR`` environment variable (explicit user override)
+      2. ``h5pcc`` on PATH  (parallel HDF5 compiler wrapper)
+      3. ``h5cc``  on PATH  (may or may not be parallel)
+      4. Common system prefixes with ``lib/libhdf5.so``
+
+    Returns ``(prefix, includedir, libdir)`` — any element may be *None*.
+    """
+    # 1. Explicit
+    hdf5_dir = os.environ.get("HDF5_DIR")
+    if hdf5_dir and os.path.isdir(hdf5_dir):
+        return hdf5_dir, None, None
+
+    # 2/3. h5pcc or h5cc
+    for wrapper in ("h5pcc", "h5cc"):
+        w = shutil.which(wrapper)
+        if not w:
+            continue
+        try:
+            r = subprocess.run(
+                [w, "-showconfig"],
+                capture_output=True,
+                text=True,
+                timeout=10,
+            )
+            if r.returncode == 0:
+                for line in r.stdout.splitlines():
+                    if "Installation point:" in line:
+                        prefix = line.split(":", 1)[1].strip()
+                        if os.path.isdir(prefix):
+                            return prefix, None, None
+        except Exception:
+            pass
+        # h5pcc -show gives us include/lib dirs directly
+        try:
+            r = subprocess.run(
+                [w, "-show"],
+                capture_output=True,
+                text=True,
+                timeout=10,
+            )
+            if r.returncode == 0:
+                incdir = libdir = None
+                for token in r.stdout.split():
+                    if token.startswith("-I") and "hdf5" in token.lower():
+                        incdir = token[2:]
+                    if token.startswith("-L") and "hdf5" in token.lower():
+                        libdir = token[2:]
+                if libdir:
+                    return None, incdir, libdir
+        except Exception:
+            pass
+        # Fall back: assume <prefix>/bin/<wrapper>
+        bindir = os.path.dirname(os.path.realpath(w))
+        prefix = os.path.dirname(bindir)
+        if os.path.isdir(os.path.join(prefix, "lib")):
+            return prefix, None, None
+
+    # 4. Common system paths
+    for prefix in ("/usr", "/usr/local", "/opt/local", "/opt/homebrew"):
+        for lib in ("lib", "lib64", "lib/x86_64-linux-gnu"):
+            if os.path.exists(os.path.join(prefix, lib, "libhdf5.so")):
+                return prefix, None, None
+            if os.path.exists(os.path.join(prefix, lib, "libhdf5.dylib")):
+                return prefix, None, None
+
+    return None, None, None
+
+
+def _find_hdf5_pkgconfig():
+    """Find a pkg-config package name for parallel HDF5.
+
+    Returns the package name (e.g. ``"hdf5-mpich"``) or *None*.
+    """
+    # User override
+    pkg = os.environ.get("HDF5_PKGCONFIG_NAME")
+    if pkg:
+        return pkg
+
+    # Check for common parallel-HDF5 pkg-config names
+    for name in ("hdf5-mpich", "hdf5-openmpi", "hdf5"):
+        try:
+            r = subprocess.run(
+                ["pkg-config", "--exists", name],
+                capture_output=True,
+                timeout=5,
+            )
+            if r.returncode == 0:
+                # Verify it's actually parallel
+                r2 = subprocess.run(
+                    ["pkg-config", "--libs", name],
+                    capture_output=True,
+                    text=True,
+                    timeout=5,
+                )
+                if r2.returncode == 0 and ("mpi" in r2.stdout.lower()):
+                    return name
+        except Exception:
+            pass
+    return None
+
+
+def _hdf5_has_parallel(hdf5_dir):
+    """Best-effort check whether the HDF5 at *hdf5_dir* was built with MPI."""
+    if not hdf5_dir:
+        return None  # unknown
+
+    # Check via h5pcc (only exists for parallel builds)
+    h5pcc = shutil.which("h5pcc")
+    if h5pcc and os.path.realpath(h5pcc).startswith(os.path.realpath(hdf5_dir)):
+        return True
+
+    # Check libhdf5.settings if present
+    for subdir in ("lib", "lib64", "share/hdf5", "lib/x86_64-linux-gnu"):
+        settings = os.path.join(hdf5_dir, subdir, "libhdf5.settings")
+        if os.path.isfile(settings):
+            try:
+                with open(settings) as f:
+                    for line in f:
+                        if "Parallel HDF5" in line and "yes" in line.lower():
+                            return True
+                        if "Parallel HDF5" in line and "no" in line.lower():
+                            return False
+            except OSError:
+                pass
+
+    return None  # unknown
+
+
+def _find_module_so(import_path):
+    """Return the file-system path of a compiled extension module."""
+    try:
+        parts = import_path.split(".")
+        mod = __import__(import_path)
+        for p in parts[1:]:
+            mod = getattr(mod, p)
+        f = getattr(mod, "__file__", None)
+        if f and (f.endswith(".so") or f.endswith(".pyd") or ".cpython-" in f):
+            return f
+    except Exception:
+        pass
+    return None
+
+
+# ---------------------------------------------------------------------------
+# Environment propagation
+# ---------------------------------------------------------------------------
+
+
+def _setup_env():
+    """Auto-detect MPI/HDF5 and set environment variables for dependency builds.
+
+    This is called *before* hatchling resolves build dependencies so that
+    packages like mpi4py, h5py and neuroh5 pick up the right compilers and
+    library paths when they are built from source.
+    """
+    if os.environ.get("MIV_SKIP_MPI_CHECK", "0") == "1":
+        return
+
+    mpicc = _find_mpicc()
+    changed = {}
+
+    # -- MPICC -----------------------------------------------------------
+    if mpicc and not os.environ.get("MPICC"):
+        os.environ["MPICC"] = mpicc
+        changed["MPICC"] = mpicc
+
+    # -- CC (h5py, neuroh5 honour CC) ------------------------------------
+    if mpicc and not os.environ.get("CC"):
+        os.environ["CC"] = mpicc
+        changed["CC"] = mpicc
+
+    # -- HDF5 detection --------------------------------------------------
+    # Prefer pkg-config (works reliably on Debian/Ubuntu where parallel HDF5
+    # lives in a non-standard subdirectory like /usr/lib/.../hdf5/mpich/).
+    hdf5_pkg = _find_hdf5_pkgconfig()
+    if hdf5_pkg and not os.environ.get("HDF5_PKGCONFIG_NAME"):
+        os.environ["HDF5_PKGCONFIG_NAME"] = hdf5_pkg
+        changed["HDF5_PKGCONFIG_NAME"] = hdf5_pkg
+
+    # If pkg-config isn't available, fall back to HDF5_DIR / explicit dirs
+    if not hdf5_pkg:
+        hdf5_dir, hdf5_incdir, hdf5_libdir = _find_hdf5_dir()
+        if hdf5_dir and not os.environ.get("HDF5_DIR"):
+            os.environ["HDF5_DIR"] = hdf5_dir
+            changed["HDF5_DIR"] = hdf5_dir
+        if hdf5_incdir and not os.environ.get("HDF5_INCLUDEDIR"):
+            os.environ["HDF5_INCLUDEDIR"] = hdf5_incdir
+            changed["HDF5_INCLUDEDIR"] = hdf5_incdir
+        if hdf5_libdir and not os.environ.get("HDF5_LIBDIR"):
+            os.environ["HDF5_LIBDIR"] = hdf5_libdir
+            changed["HDF5_LIBDIR"] = hdf5_libdir
+    else:
+        hdf5_dir = None
+
+    # -- HDF5_MPI --------------------------------------------------------
+    if not os.environ.get("HDF5_MPI"):
+        if hdf5_pkg:
+            os.environ["HDF5_MPI"] = "ON"
+            changed["HDF5_MPI"] = "ON"
+        elif hdf5_dir and _hdf5_has_parallel(hdf5_dir) is True:
+            os.environ["HDF5_MPI"] = "ON"
+            changed["HDF5_MPI"] = "ON"
+        elif mpicc:
+            # Optimistic: if the user has MPI, they likely want parallel h5py
+            os.environ["HDF5_MPI"] = "ON"
+            changed["HDF5_MPI"] = "ON"
+
+    if changed:
+        summary = ", ".join(f"{k}={v}" for k, v in changed.items())
+        print(
+            f"  [miv-simulator] auto-configured build environment: {summary}",
+            file=sys.stderr,
+        )
+
+
+# ---------------------------------------------------------------------------
+# Validation
+# ---------------------------------------------------------------------------
+
+
+def validate_mpi_environment():
+    """Validate MPI environment.  Returns ``(errors, warnings)`` string lists."""
+    errors = []
+    warns = []
+
+    # -- 1. MPI compiler wrapper --
+    mpicc = _find_mpicc()
+    if not mpicc:
+        errors.append(
+            "'mpicc' not found on PATH (and MPICC is not set).\n"
+            "  Install an MPI implementation and make sure 'mpicc' is available,\n"
+            "  or point MPICC to your MPI compiler wrapper.\n"
+            "  Ubuntu/Debian : apt install libopenmpi-dev\n"
+            "  Fedora/RHEL   : dnf install openmpi-devel\n"
+            "  macOS (brew)  : brew install open-mpi"
+        )
+        return errors, warns  # remaining checks need mpicc
+
+    mpi_libdir = _find_mpicc_libdir()
+
+    # -- 2. mpi4py linkage --
+    mpi4py_mpi_lib = None
+    try:
+        mpi4py_so = _find_module_so("mpi4py.MPI")
+        if mpi4py_so and os.path.isfile(mpi4py_so):
+            ldd = _get_shared_lib_deps(mpi4py_so)
+            mpi4py_mpi_lib = _extract_mpi_lib(ldd)
+            if mpi4py_mpi_lib and mpi_libdir:
+                real_lib = os.path.realpath(mpi4py_mpi_lib)
+                real_dir = os.path.realpath(mpi_libdir)
+                if not real_lib.startswith(real_dir):
+                    errors.append(
+                        "mpi4py links against a DIFFERENT MPI than the system mpicc.\n"
+                        f"  mpi4py  -> {mpi4py_mpi_lib}  (resolves to {real_lib})\n"
+                        f"  mpicc   -> {mpi_libdir}  (resolves to {real_dir})\n"
+                        "  This usually means mpi4py was installed from a pre-built wheel.\n"
+                        "  Reinstall from source:\n"
+                        "    pip install --no-binary=mpi4py --no-cache-dir mpi4py"
+                    )
+    except ImportError:
+        warns.append(
+            "mpi4py is not installed yet. Make sure to build it from source:\n"
+            '  env MPICC="mpicc --shared" pip install --no-binary=mpi4py mpi4py'
+        )
+
+    # -- 3. h5py MPI support --
+    h5py_mpi_lib = None
+    try:
+        import h5py
+
+        h5py_cfg = h5py.get_config()
+        if not getattr(h5py_cfg, "mpi", False):
+            errors.append(
+                "h5py is installed WITHOUT MPI (parallel HDF5) support.\n"
+                "  miv-simulator requires h5py built against parallel HDF5.\n"
+                "  Reinstall from source:\n"
+                '    CC=mpicc HDF5_MPI="ON" pip install --no-binary=h5py h5py'
+            )
+        else:
+            # try to check linkage via the low-level C extension
+            for sub in ("h5py._conv", "h5py._errors", "h5py.h5"):
+                h5py_so = _find_module_so(sub)
+                if h5py_so:
+                    ldd = _get_shared_lib_deps(h5py_so)
+                    h5py_mpi_lib = _extract_mpi_lib(ldd)
+                    if h5py_mpi_lib:
+                        break
+    except ImportError:
+        warns.append(
+            "h5py is not installed yet. Make sure to build it with MPI support:\n"
+            '  CC=mpicc HDF5_MPI="ON" pip install --no-binary=h5py h5py'
+        )
+
+    # -- 4. Cross-library MPI consistency --
+    if mpi4py_mpi_lib and h5py_mpi_lib:
+        real_mpi4py = os.path.realpath(mpi4py_mpi_lib)
+        real_h5py = os.path.realpath(h5py_mpi_lib)
+        if real_mpi4py != real_h5py:
+            errors.append(
+                "mpi4py and h5py link against DIFFERENT MPI libraries.\n"
+                f"  mpi4py -> {real_mpi4py}\n"
+                f"  h5py   -> {real_h5py}\n"
+                "  Both must use the same MPI.  Reinstall both from source\n"
+                "  against the same MPI installation."
+            )
+
+    return errors, warns
+
+
+def _run_checks():
+    """Run MPI validation; raise on errors unless skipped via env var."""
+    if os.environ.get("MIV_SKIP_MPI_CHECK", "0") == "1":
+        return
+
+    errors, warns = validate_mpi_environment()
+
+    for w in warns:
+        print(f"  WARNING [miv-simulator build]: {w}", file=sys.stderr)
+
+    if errors:
+        sep = "=" * 64
+        body = "\n\n".join(f"  [{i+1}/{len(errors)}] {e}" for i, e in enumerate(errors))
+        raise SystemExit(
+            f"\n{sep}\n"
+            f"  miv-simulator: MPI environment validation FAILED\n"
+            f"{sep}\n\n"
+            f"{body}\n\n"
+            f"  Set MIV_SKIP_MPI_CHECK=1 to skip this check (not recommended).\n"
+            f"{sep}\n"
+        )
+
+
+# ---------------------------------------------------------------------------
+# PEP 517 / PEP 660 build backend interface  (delegates to hatchling)
+# ---------------------------------------------------------------------------
+
+# Run auto-detection at import time so env vars are set before the installer
+# builds any dependency (mpi4py, h5py, neuroh5) from source.
+_setup_env()
+
+
+def get_requires_for_build_wheel(config_settings=None):
+    return _get_requires_for_build_wheel(config_settings)
+
+
+def get_requires_for_build_sdist(config_settings=None):
+    return _get_requires_for_build_sdist(config_settings)
+
+
+def get_requires_for_build_editable(config_settings=None):
+    return _get_requires_for_build_editable(config_settings)
+
+
+def build_wheel(wheel_directory, config_settings=None, metadata_directory=None):
+    _run_checks()
+    return _build_wheel(wheel_directory, config_settings, metadata_directory)
+
+
+def build_sdist(sdist_directory, config_settings=None):
+    # sdist is just packaging source; skip MPI checks
+    return _build_sdist(sdist_directory, config_settings)
+
+
+def build_editable(wheel_directory, config_settings=None, metadata_directory=None):
+    _run_checks()
+    return _build_editable(wheel_directory, config_settings, metadata_directory)
+
+
+if _prepare_metadata_for_build_wheel is not None:
+
+    def prepare_metadata_for_build_wheel(metadata_directory, config_settings=None):
+        return _prepare_metadata_for_build_wheel(metadata_directory, config_settings)
+
+
+if _prepare_metadata_for_build_editable is not None:
+
+    def prepare_metadata_for_build_editable(metadata_directory, config_settings=None):
+        return _prepare_metadata_for_build_editable(metadata_directory, config_settings)
diff --git a/configure_mpi.py b/configure_mpi.py
new file mode 100644
index 00000000..c8e36087
--- /dev/null
+++ b/configure_mpi.py
@@ -0,0 +1,171 @@
+#!/usr/bin/env python3
+"""Detect MPI and parallel-HDF5 settings for miv-simulator.
+
+Usage:
+    # Print export commands to eval in your shell:
+    eval $(python configure_mpi.py)
+
+    # Then install:
+    uv sync
+
+    # Or as a one-liner:
+    eval $(python configure_mpi.py) && uv sync
+
+The script auto-detects:
+  - MPICC         MPI C compiler wrapper
+  - CC            C compiler (set to mpicc for h5py/neuroh5 builds)
+  - HDF5_MPI      Enables parallel HDF5 in h5py
+  - HDF5_DIR      HDF5 installation prefix (if standard layout)
+  - HDF5_PKGCONFIG_NAME  pkg-config package for parallel HDF5
+  - HDF5_INCLUDEDIR      HDF5 include path (non-standard layouts)
+  - HDF5_LIBDIR          HDF5 library path (non-standard layouts)
+
+Override any variable by exporting it before running this script.
+"""
+
+import os
+import shutil
+import subprocess
+import sys
+
+
+def _find_mpicc():
+    mpicc = os.environ.get("MPICC")
+    if mpicc:
+        path = shutil.which(mpicc.split()[0])
+        if path:
+            return path
+    return shutil.which("mpicc")
+
+
+def _find_hdf5_pkgconfig():
+    pkg = os.environ.get("HDF5_PKGCONFIG_NAME")
+    if pkg:
+        return pkg
+    for name in ("hdf5-mpich", "hdf5-openmpi", "hdf5"):
+        try:
+            r = subprocess.run(
+                ["pkg-config", "--exists", name],
+                capture_output=True,
+                timeout=5,
+            )
+            if r.returncode == 0:
+                r2 = subprocess.run(
+                    ["pkg-config", "--libs", name],
+                    capture_output=True,
+                    text=True,
+                    timeout=5,
+                )
+                if r2.returncode == 0 and "mpi" in r2.stdout.lower():
+                    return name
+        except Exception:
+            pass
+    return None
+
+
+def _find_hdf5_via_wrapper():
+    """Detect HDF5 prefix/includedir/libdir from h5pcc or h5cc."""
+    for wrapper in ("h5pcc", "h5cc"):
+        w = shutil.which(wrapper)
+        if not w:
+            continue
+        # Try -showconfig for prefix
+        try:
+            r = subprocess.run(
+                [w, "-showconfig"],
+                capture_output=True,
+                text=True,
+                timeout=10,
+            )
+            if r.returncode == 0:
+                for line in r.stdout.splitlines():
+                    if "Installation point:" in line:
+                        prefix = line.split(":", 1)[1].strip()
+                        if os.path.isdir(prefix):
+                            return prefix, None, None
+        except Exception:
+            pass
+        # Try -show for -I/-L flags
+        try:
+            r = subprocess.run(
+                [w, "-show"],
+                capture_output=True,
+                text=True,
+                timeout=10,
+            )
+            if r.returncode == 0:
+                incdir = libdir = None
+                for token in r.stdout.split():
+                    if token.startswith("-I") and "hdf5" in token.lower():
+                        incdir = token[2:]
+                    if token.startswith("-L") and "hdf5" in token.lower():
+                        libdir = token[2:]
+                if libdir:
+                    return None, incdir, libdir
+        except Exception:
+            pass
+    return None, None, None
+
+
+def detect():
+    """Detect MPI/HDF5 environment and return dict of env vars to set."""
+    env = {}
+
+    mpicc = _find_mpicc()
+    if not mpicc:
+        print(
+            "# ERROR: mpicc not found on PATH.\n"
+            "# Install an MPI implementation first:\n"
+            "#   Ubuntu/Debian: apt install libopenmpi-dev (or libmpich-dev)\n"
+            "#   Fedora/RHEL:   dnf install openmpi-devel\n"
+            "#   macOS (brew):  brew install open-mpi",
+            file=sys.stderr,
+        )
+        sys.exit(1)
+
+    if not os.environ.get("MPICC"):
+        env["MPICC"] = mpicc
+    if not os.environ.get("CC"):
+        env["CC"] = mpicc
+
+    # Prefer pkg-config (handles Debian/Ubuntu non-standard paths)
+    hdf5_pkg = _find_hdf5_pkgconfig()
+    if hdf5_pkg and not os.environ.get("HDF5_PKGCONFIG_NAME"):
+        env["HDF5_PKGCONFIG_NAME"] = hdf5_pkg
+    elif not hdf5_pkg:
+        hdf5_dir = os.environ.get("HDF5_DIR")
+        if not hdf5_dir:
+            prefix, incdir, libdir = _find_hdf5_via_wrapper()
+            if prefix:
+                env["HDF5_DIR"] = prefix
+            if incdir and not os.environ.get("HDF5_INCLUDEDIR"):
+                env["HDF5_INCLUDEDIR"] = incdir
+            if libdir and not os.environ.get("HDF5_LIBDIR"):
+                env["HDF5_LIBDIR"] = libdir
+
+    if not os.environ.get("HDF5_MPI"):
+        env["HDF5_MPI"] = "ON"
+
+    return env
+
+
+def main():
+    env = detect()
+    if not env:
+        print("# MPI/HDF5 environment already configured.", file=sys.stderr)
+        return
+
+    print(
+        "# Auto-detected MPI/HDF5 build environment for miv-simulator", file=sys.stderr
+    )
+    for key, val in env.items():
+        print(f"#   {key}={val}", file=sys.stderr)
+    print(file=sys.stderr)
+
+    # Output export commands for eval
+    for key, val in env.items():
+        print(f"export {key}={val!r}")
+
+
+if __name__ == "__main__":
+    main()
diff --git a/docs/tutorial/installation.md b/docs/tutorial/installation.md
index dd1319a0..66ef23ba 100644
--- a/docs/tutorial/installation.md
+++ b/docs/tutorial/installation.md
@@ -1,155 +1,209 @@
-# From Source
+# Installation
 
-The installation consist two part: python-dependencies and external libraries.
+MiV-Simulator depends on MPI and parallel HDF5. The build system auto-detects
+your MPI/HDF5 setup and forces source builds of critical packages (`mpi4py`,
+`h5py`, `neuroh5`) so they link against the correct libraries.
 
-## Core Software/Libraries
+## Prerequisites
 
-Before the installation, following software/libraries should be installed on the system.
+| Dependency | Minimum version | Notes |
+|---|---|---|
+| Python | 3.9+ | |
+| GCC | 7.8+ | C/C++ compiler |
+| cmake | 3.18+ | Required by neuroh5 |
+| MPI | — | MPICH **or** OpenMPI |
+| Parallel HDF5 | 1.10+ | Must be built with MPI support |
 
-- Python 3.8+
-- GCC 7.8+, cmake 3.18+
-- HDF5 (parallel build)
-- MPICH
-- OpenMPI (for cluster)
+### Ubuntu / Debian
 
-## Python Dependencies
+```sh
+sudo apt install build-essential cmake pkg-config
+sudo apt install libmpich-dev          # or: libopenmpi-dev
+sudo apt install libhdf5-mpich-dev     # or: libhdf5-openmpi-dev
+```
+
+### Fedora / RHEL
+
+```sh
+sudo dnf install gcc gcc-c++ cmake pkgconfig
+sudo dnf install mpich-devel           # or: openmpi-devel
+sudo dnf install hdf5-mpich-devel      # or: hdf5-openmpi-devel
+```
+
+### macOS (Homebrew)
+
+```sh
+brew install cmake open-mpi hdf5-mpi
+```
 
-The python-dependencies are managed through [`poetry`][link-poetry-website]. We provide important alias in `makefile`.
+## Quick Install
+
+The recommended way to install is with [uv](https://docs.astral.sh/uv/):
 
 ```sh
-make poetry-downloads  # Install poetry on the system
-make install           # Install MiV-Simulator
+git clone https://github.com/GazzolaLab/MiV-Simulator.git
+cd MiV-Simulator
+make install
 ```
 
-> **Note**: If any issues are encoutered, please make a report to [GitHub-Issue](https://github.com/GazzolaLab/MiV-Simulator/issues).
+This runs `configure_mpi.py` to auto-detect your MPI and parallel HDF5, then
+calls `uv sync` with the correct environment variables.
+
+### What `make install` does
 
-> The installation using `pip` is not yet supported due to the dependency compilation.
+1. **`configure_mpi.py`** probes your system for `mpicc`, parallel HDF5 (via
+   `pkg-config`, `h5pcc`, or common paths), and outputs shell `export` commands.
+2. **`uv sync`** installs all dependencies. The `no-binary-package` setting in
+   `pyproject.toml` forces `mpi4py`, `h5py`, and `neuroh5` to be compiled from
+   source, linking against your system MPI and HDF5.
+3. A **build-time check** validates the MPI environment when building
+   miv-simulator's wheel.
+4. A **runtime check** re-validates on every `import miv_simulator`, catching
+   broken environments before they cause subtle errors.
 
-## External Libraries
+### Manual Install (without Make)
 
-1. Building and installing NEURON
+If you prefer to run the steps yourself:
 
 ```sh
-pip install neuron
+# 1. Auto-detect and export MPI/HDF5 environment
+eval $(python configure_mpi.py)
+
+# 2. Install
+uv sync
 ```
 
-<details>
-  <summary>How to install from the source</summary>
+Or set the variables explicitly:
+
 ```sh
-git clone https://github.com/neuronsimulator/nrn.git
-cd nrn
-mkdir build
-cd build
-cmake .. -DNRN_ENABLE_INTERVIEWS=OFF -DNRN_ENABLE_MPI=ON -DNRN_ENABLE_RX3D=ON -DNRN_ENABLE_CORENEURON=ON -DNRN_ENABLE_PYTHON=ON -DPYTHON_EXECUTABLE=$(which python3) -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx
-make install
+export MPICC=/usr/bin/mpicc
+export CC=/usr/bin/mpicc
+export HDF5_MPI=ON
+export HDF5_PKGCONFIG_NAME=hdf5-mpich   # Debian/Ubuntu
+uv sync
 ```
-</details>
 
-2. Building and installing NeuroH5
+## Environment Variables
+
+The following environment variables control how MPI-dependent packages are built.
+`configure_mpi.py` auto-detects all of them, but you can override any by
+exporting before install.
+
+| Variable | Purpose | Example |
+|---|---|---|
+| `MPICC` | MPI C compiler wrapper | `/usr/bin/mpicc` |
+| `CC` | C compiler for extensions | `/usr/bin/mpicc` |
+| `HDF5_MPI` | Enable parallel HDF5 in h5py | `ON` |
+| `HDF5_PKGCONFIG_NAME` | pkg-config name for parallel HDF5 | `hdf5-mpich`, `hdf5-openmpi` |
+| `HDF5_DIR` | HDF5 installation prefix | `/opt/hdf5-1.12.1/build` |
+| `HDF5_INCLUDEDIR` | HDF5 include path (non-standard layouts) | `/usr/include/hdf5/mpich` |
+| `HDF5_LIBDIR` | HDF5 library path (non-standard layouts) | `/usr/lib/x86_64-linux-gnu/hdf5/mpich` |
+| `MIV_SKIP_MPI_CHECK` | Skip all MPI validation (`1` to disable) | `1` |
 
-The NeuroH5 build system requires cmake.
+## Verifying the Installation
 
 ```sh
-git clone https://github.com/soltesz-lab/neuroh5.git
-cd neuroh5
-CMAKE_BUILD_PARALLEL_LEVEL=8 pip install .
+uv run python -c "import miv_simulator; print(miv_simulator.version)"
 ```
 
-## Cluster Usage
+If the MPI environment is misconfigured, you will see a clear error message at
+import time, for example:
 
-For architecture-level optimization, some of the core libraries should be built within the worker node.
+> `miv_simulator.mpi_env.MPIEnvError: h5py is installed WITHOUT parallel-HDF5
+> (MPI) support. Reinstall from source: CC=mpicc HDF5_MPI="ON" pip install
+> --no-binary=h5py h5py`
 
-:::{note}
-Make sure to run on a worker node, not the login-node!
-:::
+## Docker
 
-### Necessary Modules
+A Docker image is provided for quick experimentation (not recommended for
+cluster/HPC use):
 
-Following modules (or equivalent modules) are necessary before starting the installation.
+```sh
+docker compose up
+```
+
+See `Dockerfile` and `compose.yaml` for details.
+
+## Cluster / HPC Usage
+
+For architecture-level optimization, build on a **worker node**, not the login
+node.
+
+### Load Modules
 
 ```sh
 module load python/3
 module load cmake
 module load gcc
-module load openmpi
+module load openmpi    # or: mpich
 ```
 
-### Building HDF5 (Parallel)
+### Building Parallel HDF5 from Source
 
-Download the source from [here][source-hdf5].
+If your cluster does not provide a parallel HDF5 module:
 
 ```sh
 wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.1/src/hdf5-1.12.1.tar.gz
 tar -xzf hdf5-1.12.1.tar.gz
 cd hdf5-1.12.1
 CC=mpicc ./configure --prefix=$PWD/build --enable-parallel --enable-shared
-make && make check
-make install && make check-install
+make -j$(nproc) && make install
 ```
 
-### H5PY
+Then point the installer to it:
 
 ```sh
-CC="mpicc" HDF5_MPI="ON" HDF5_DIR=/Users/skim0119/github/hdf5-1.12.1/build pip install --no-binary=h5py h5py
+export HDF5_DIR=$PWD/build
+export HDF5_MPI=ON
+export CC=mpicc
 ```
 
-### Install/Build Python Dependencies
+### Install MiV-Simulator
 
 ```sh
-make poetry-download
-make install
+git clone https://github.com/GazzolaLab/MiV-Simulator.git
+cd MiV-Simulator
+
+# Auto-detect (or set HDF5_DIR/CC/MPICC manually as above)
+eval $(python configure_mpi.py)
+uv sync
 ```
 
-### Building NEURON simulator
+### Building NEURON from Source (optional)
+
+NEURON is installed automatically via `pip`, but for MPI-optimized builds:
 
 ```sh
 git clone https://github.com/neuronsimulator/nrn.git
 cd nrn
 git submodule update --init --recursive
-mkdir build
-cd build
-cmake .. -DNRN_ENABLE_INTERVIEWS=OFF -DNRN_ENABLE_MPI=ON -DNRN_ENABLE_RX3D=ON -DNRN_ENABLE_CORENEURON=ON -DPYTHON_EXECUTABLE=$(which python3) -DNRN_ENABLE_PYTHON=ON -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_INSTALL_PREFIX=../install
-cmake --build . --parallel 8 --target install
-
-export PATH=<Installation path>/bin:$PATH
-export PYTHONPATH=<Installation path>/lib/python:$PYTHONPATH
+mkdir build && cd build
+cmake .. \
+  -DNRN_ENABLE_INTERVIEWS=OFF \
+  -DNRN_ENABLE_MPI=ON \
+  -DNRN_ENABLE_RX3D=ON \
+  -DNRN_ENABLE_CORENEURON=ON \
+  -DNRN_ENABLE_PYTHON=ON \
+  -DPYTHON_EXECUTABLE=$(which python3) \
+  -DCMAKE_C_COMPILER=mpicc \
+  -DCMAKE_CXX_COMPILER=mpicxx \
+  -DCMAKE_INSTALL_PREFIX=../install
+cmake --build . --parallel $(nproc) --target install
+
+export PATH=$(pwd)/../install/bin:$PATH
+export PYTHONPATH=$(pwd)/../install/lib/python:$PYTHONPATH
 ```
 
-<details>
-  <summary>Possible Issues</summary>
+## Troubleshooting
 
-- `Readline` cannot be found:
-    - Try to install `Readline` using `apt` or `yum`. It can also be installed using `conda`.
-    - `Readline` might already exist on the system. Search in `/usr/lib` or `/usr/lib64`.
-    - Pass environment variable directly: `cmake -DReadline_INCLUDE_DIR=/usr/lib64 -DReadline_LIBRARY=/usr/lib64/libreadline.so.7 ....`
+**`Readline` not found (NEURON source build)**
+: Install Readline (`apt install libreadline-dev`) or pass the path manually:
+  `cmake -DReadline_INCLUDE_DIR=/usr/include -DReadline_LIBRARY=/usr/lib/x86_64-linux-gnu/libreadline.so ...`
 
-</details>
-<br/>
+> **Note**: If you encounter issues, please report them at
+> [GitHub Issues](https://github.com/GazzolaLab/MiV-Simulator/issues).
 
-### Install NeuroH5
-
-```sh
-# get the source
-git clone https://github.com/soltesz-lab/neuroh5.git
-cd neuroh5
-
-# add HDF5 build to PATH
-export HDF5_SOURCE=<HDF5 installation directory>
-export PATH=$PATH:$HDF5_SOURCE/build
-
-# (make sure the node has enough RAM and cores, otherwise the compilation will fail)
-CMAKE_BUILD_PARALLEL_LEVEL=8 pip install .
-```
-
-Other _CLI tools_ in NeuroH5 can be installed using `cmake`.
-
-```sh
-cmake .
-make -j4
-export PATH=<NeuroH5 installation path>/bin:$PATH
-```
+## Additional Resources
 
-## Tools and scripts to aid cluster usage
+- [Cluster module configuration](https://github.com/GazzolaLab/MiV-Simulator/tree/latest/support/cluster)
 
-- [How to install and configure as module](https://github.com/GazzolaLab/MiV-Simulator/tree/latest/support/cluster)
-- [Machinable: A modular system to manage research code](https://machinable.org)
diff --git a/pyproject.toml b/pyproject.toml
index d2e10a07..b329f33d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -21,28 +21,26 @@ requires-python = ">= 3.9"
 
 [project.optional-dependencies]
 docs = [
-  "sphinx",
-  "pydata-sphinx-theme",
-  "readthedocs-sphinx-search",
-  "sphinx-autodoc-typehints",
-  "myst-nb",
-  "numpydoc",
-  "sphinx-togglebutton",
-  "sphinx-copybutton",
-  "sphinx-click",
-  "sphinxcontrib-mermaid"
+    "sphinx",
+    "pydata-sphinx-theme",
+    "readthedocs-sphinx-search",
+    "sphinx-autodoc-typehints",
+    "myst-nb",
+    "numpydoc",
+    "sphinx-togglebutton",
+    "sphinx-copybutton",
+    "sphinx-click",
+    "sphinxcontrib-mermaid",
 ]
 
 [build-system]
 requires = ["hatchling"]
-build-backend = "hatchling.build"
+build-backend = "_build_backend"
+backend-path = ["."]
 
 [tool.uv]
-dev-dependencies = [
-    "pre-commit>=4.1.0",
-    "pytest>=8.3.2",
-    "ruff==0.9.3",
-]
+dev-dependencies = ["pre-commit>=4.1.0", "pytest>=8.3.2", "ruff==0.9.3"]
+no-binary-package = ["mpi4py", "h5py", "neuroh5"]
 
 [tool.uv.sources]
 treverhines-rbf = { git = "https://github.com/treverhines/RBF" }
diff --git a/src/miv_simulator/__init__.py b/src/miv_simulator/__init__.py
index 5a2b66a1..b585179d 100644
--- a/src/miv_simulator/__init__.py
+++ b/src/miv_simulator/__init__.py
@@ -2,6 +2,11 @@
 
 from importlib import metadata as importlib_metadata
 
+# Validate MPI environment on import (set MIV_SKIP_MPI_CHECK=1 to disable)
+from miv_simulator.mpi_env import check_mpi_env as _check_mpi_env
+
+_check_mpi_env()
+
 
 def get_version() -> str:
     try:
diff --git a/src/miv_simulator/mpi_env.py b/src/miv_simulator/mpi_env.py
new file mode 100644
index 00000000..dc51fefd
--- /dev/null
+++ b/src/miv_simulator/mpi_env.py
@@ -0,0 +1,204 @@
+"""Runtime MPI environment validation for miv-simulator.
+
+Detects misconfigured MPI / parallel HDF5 setups that would otherwise
+cause subtle, hard-to-diagnose errors at runtime.
+
+Usage::
+
+    from miv_simulator.mpi_env import check_mpi_env
+    check_mpi_env()          # raises on hard errors, warns otherwise
+
+Set the environment variable ``MIV_SKIP_MPI_CHECK=1`` to silence all checks.
+"""
+
+import os
+import platform
+import shutil
+import subprocess
+import warnings
+
+
+class MPIEnvError(RuntimeError):
+    """Raised when the MPI environment is fatally misconfigured."""
+
+
+# ---------------------------------------------------------------------------
+# helpers
+# ---------------------------------------------------------------------------
+
+
+def _shared_lib_deps(path):
+    system = platform.system()
+    try:
+        if system == "Linux":
+            r = subprocess.run(
+                ["ldd", path],
+                capture_output=True,
+                text=True,
+                timeout=10,
+            )
+        elif system == "Darwin":
+            r = subprocess.run(
+                ["otool", "-L", path],
+                capture_output=True,
+                text=True,
+                timeout=10,
+            )
+        else:
+            return ""
+        return r.stdout if r.returncode == 0 else ""
+    except Exception:
+        return ""
+
+
+def _mpi_lib_from_ldd(text):
+    for line in text.splitlines():
+        line = line.strip()
+        if "libmpi" not in line:
+            continue
+        if "=>" in line:
+            p = line.split("=>")[1].strip().split("(")[0].strip()
+            if p:
+                return p
+        elif line.startswith("/"):
+            return line.split("(")[0].strip()
+    return None
+
+
+def _mpicc_libdir():
+    mpicc = shutil.which("mpicc")
+    if not mpicc:
+        return None
+    try:
+        r = subprocess.run(
+            [mpicc, "--showme:libdirs"],
+            capture_output=True,
+            text=True,
+            timeout=10,
+        )
+        if r.returncode == 0 and r.stdout.strip():
+            return r.stdout.strip().split()[0]
+    except Exception:
+        pass
+    try:
+        r = subprocess.run(
+            [mpicc, "-show"],
+            capture_output=True,
+            text=True,
+            timeout=10,
+        )
+        if r.returncode == 0:
+            for tok in r.stdout.split():
+                if tok.startswith("-L"):
+                    return tok[2:]
+    except Exception:
+        pass
+    return None
+
+
+def _module_so(import_path):
+    try:
+        parts = import_path.split(".")
+        mod = __import__(import_path)
+        for p in parts[1:]:
+            mod = getattr(mod, p)
+        f = getattr(mod, "__file__", None)
+        if f and (f.endswith(".so") or f.endswith(".pyd") or ".cpython-" in f):
+            return f
+    except Exception:
+        pass
+    return None
+
+
+# ---------------------------------------------------------------------------
+# public API
+# ---------------------------------------------------------------------------
+
+
+def check_mpi_env(*, strict=False):
+    """Validate the MPI environment.
+
+    Parameters
+    ----------
+    strict : bool
+        If *True*, missing packages (mpi4py / h5py) are treated as errors
+        rather than warnings.
+
+    Raises
+    ------
+    MPIEnvError
+        If a fatal misconfiguration is detected.
+    """
+    if os.environ.get("MIV_SKIP_MPI_CHECK", "0") == "1":
+        return
+
+    mpicc = shutil.which("mpicc")
+    if not mpicc:
+        raise MPIEnvError(
+            "'mpicc' not found on PATH. "
+            "Install an MPI implementation (OpenMPI / MPICH) "
+            "and make sure 'mpicc' is available."
+        )
+
+    mpi_libdir = _mpicc_libdir()
+
+    # -- mpi4py --
+    mpi4py_lib = None
+    try:
+        so = _module_so("mpi4py.MPI")
+        if so and os.path.isfile(so):
+            mpi4py_lib = _mpi_lib_from_ldd(_shared_lib_deps(so))
+            if mpi4py_lib and mpi_libdir:
+                if not os.path.realpath(mpi4py_lib).startswith(
+                    os.path.realpath(mpi_libdir)
+                ):
+                    raise MPIEnvError(
+                        f"mpi4py links against {mpi4py_lib} but mpicc uses "
+                        f"{mpi_libdir}. mpi4py was likely installed from a "
+                        "pre-built wheel. Reinstall from source: "
+                        "pip install --no-binary=mpi4py mpi4py"
+                    )
+    except ImportError:
+        msg = (
+            "mpi4py is not installed. Install from source: "
+            'env MPICC="mpicc --shared" pip install --no-binary=mpi4py mpi4py'
+        )
+        if strict:
+            raise MPIEnvError(msg)
+        warnings.warn(msg, stacklevel=2)
+
+    # -- h5py --
+    h5py_lib = None
+    try:
+        import h5py
+
+        if not getattr(h5py.get_config(), "mpi", False):
+            raise MPIEnvError(
+                "h5py is installed WITHOUT parallel-HDF5 (MPI) support. "
+                "Reinstall from source: "
+                'CC=mpicc HDF5_MPI="ON" pip install --no-binary=h5py h5py'
+            )
+        for sub in ("h5py.h5", "h5py._conv", "h5py._errors"):
+            so = _module_so(sub)
+            if so:
+                h5py_lib = _mpi_lib_from_ldd(_shared_lib_deps(so))
+                if h5py_lib:
+                    break
+    except ImportError:
+        msg = (
+            "h5py is not installed. Install with MPI support: "
+            'CC=mpicc HDF5_MPI="ON" pip install --no-binary=h5py h5py'
+        )
+        if strict:
+            raise MPIEnvError(msg)
+        warnings.warn(msg, stacklevel=2)
+
+    # -- cross-library consistency --
+    if mpi4py_lib and h5py_lib:
+        if os.path.realpath(mpi4py_lib) != os.path.realpath(h5py_lib):
+            raise MPIEnvError(
+                "mpi4py and h5py link against DIFFERENT MPI libraries:\n"
+                f"  mpi4py -> {os.path.realpath(mpi4py_lib)}\n"
+                f"  h5py   -> {os.path.realpath(h5py_lib)}\n"
+                "Reinstall both from source against the same MPI."
+            )
diff --git a/tests/installation/miv_simulator_install_test/__init__.py b/tests/installation/miv_simulator_install_test/__init__.py
new file mode 100644
index 00000000..602b5e7c
--- /dev/null
+++ b/tests/installation/miv_simulator_install_test/__init__.py
@@ -0,0 +1 @@
+# Installation test placeholder
diff --git a/tests/installation/pyproject.toml b/tests/installation/pyproject.toml
new file mode 100644
index 00000000..4257f379
--- /dev/null
+++ b/tests/installation/pyproject.toml
@@ -0,0 +1,16 @@
+[project]
+name = "miv-simulator-install-test"
+version = "0.0.0"
+description = "End-to-end installation test for miv-simulator"
+requires-python = ">= 3.9"
+dependencies = ["miv-simulator"]
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.uv]
+no-binary-package = ["mpi4py", "h5py", "neuroh5"]
+
+[tool.uv.sources]
+miv-simulator = { path = "../.." }
diff --git a/tests/installation/uv.lock b/tests/installation/uv.lock
new file mode 100644
index 00000000..924719b8
--- /dev/null
+++ b/tests/installation/uv.lock
@@ -0,0 +1,2276 @@
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     { url = "https://files.pythonhosted.org/packages/92/2e/ea25914b1ebfde93b6fc4ff46d6864564fba59024e928bdc7de475affc25/greenlet-3.2.4-cp314-cp314-manylinux2014_x86_64.manylinux_2_17_x86_64.whl", hash = "sha256:061dc4cf2c34852b052a8620d40f36324554bc192be474b9e9770e8c042fd735", size = 695355 },
     { url = "https://files.pythonhosted.org/packages/72/60/fc56c62046ec17f6b0d3060564562c64c862948c9d4bc8aa807cf5bd74f4/greenlet-3.2.4-cp314-cp314-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:44358b9bf66c8576a9f57a590d5f5d6e72fa4228b763d0e43fee6d3b06d3a337", size = 657512 },
+    { url = "https://files.pythonhosted.org/packages/23/6e/74407aed965a4ab6ddd93a7ded3180b730d281c77b765788419484cdfeef/greenlet-3.2.4-cp314-cp314-musllinux_1_2_aarch64.whl", hash = "sha256:2917bdf657f5859fbf3386b12d68ede4cf1f04c90c3a6bc1f013dd68a22e2269", size = 1612508 },
+    { url = "https://files.pythonhosted.org/packages/0d/da/343cd760ab2f92bac1845ca07ee3faea9fe52bee65f7bcb19f16ad7de08b/greenlet-3.2.4-cp314-cp314-musllinux_1_2_x86_64.whl", hash = "sha256:015d48959d4add5d6c9f6c5210ee3803a830dce46356e3bc326d6776bde54681", size = 1680760 },
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     { url = "https://files.pythonhosted.org/packages/f7/c0/93885c4106d2626bf51fdec377d6aef740dfa5c4877461889a7cf8e565cc/greenlet-3.2.4-cp39-cp39-macosx_11_0_universal2.whl", hash = "sha256:b6a7c19cf0d2742d0809a4c05975db036fdff50cd294a93632d6a310bf9ac02c", size = 269859 },
     { url = "https://files.pythonhosted.org/packages/4d/f5/33f05dc3ba10a02dedb1485870cf81c109227d3d3aa280f0e48486cac248/greenlet-3.2.4-cp39-cp39-manylinux2014_aarch64.manylinux_2_17_aarch64.whl", hash = "sha256:27890167f55d2387576d1f41d9487ef171849ea0359ce1510ca6e06c8bece11d", size = 627610 },
@@ -888,6 +898,8 @@ wheels = [
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     { url = "https://files.pythonhosted.org/packages/89/80/7332915adc766035c8980b161c2e5d50b2f941f453af232c164cff5e0aeb/greenlet-3.2.4-cp39-cp39-musllinux_1_1_aarch64.whl", hash = "sha256:b90654e092f928f110e0007f572007c9727b5265f7632c2fa7415b4689351594", size = 1111985 },
     { url = "https://files.pythonhosted.org/packages/66/71/1928e2c80197353bcb9b50aa19c4d8e26ee6d7a900c564907665cf4b9a41/greenlet-3.2.4-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:81701fd84f26330f0d5f4944d4e92e61afe6319dcd9775e39396e39d7c3e5f98", size = 1136137 },
+    { url = "https://files.pythonhosted.org/packages/4b/bf/7bd33643e48ed45dcc0e22572f650767832bd4e1287f97434943cc402148/greenlet-3.2.4-cp39-cp39-musllinux_1_2_aarch64.whl", hash = "sha256:28a3c6b7cd72a96f61b0e4b2a36f681025b60ae4779cc73c1535eb5f29560b10", size = 1542941 },
+    { url = "https://files.pythonhosted.org/packages/9b/74/4bc433f91d0d09a1c22954a371f9df928cb85e72640870158853a83415e5/greenlet-3.2.4-cp39-cp39-musllinux_1_2_x86_64.whl", hash = "sha256:52206cd642670b0b320a1fd1cbfd95bca0e043179c1d8a045f2c6109dfe973be", size = 1609685 },
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 ]
@@ -1727,7 +1739,7 @@ wheels = [
 
 [[package]]
 name = "miv-simulator"
-version = "0.2.0"
+version = "0.3.0"
 source = { editable = "." }
 dependencies = [
     { name = "machinable" },

From 57a1faabea37030a236dda0b89ca6025cd3adb5e Mon Sep 17 00:00:00 2001
From: Frithjof Gressmann <frithjof@noc.io>
Date: Fri, 17 Apr 2026 22:39:57 -0500
Subject: [PATCH 02/21] Fix setuptools

---
 .github/workflows/main.yml        | 2 +-
 pyproject.toml                    | 3 +++
 tests/installation/pyproject.toml | 1 +
 3 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index ffb0cdae..ac49cb27 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -12,7 +12,7 @@ jobs:
     strategy:
       matrix:
         os: [ ubuntu-latest, macos-latest ]
-        python-version: [ "3.10", "3.11", "3.12" ]
+        python-version: [ "3.12" ]
         mpi: [ "mpich", "openmpi" ]
         exclude:
           - os: macos-latest
diff --git a/pyproject.toml b/pyproject.toml
index b329f33d..72d65d45 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -41,6 +41,9 @@ backend-path = ["."]
 [tool.uv]
 dev-dependencies = ["pre-commit>=4.1.0", "pytest>=8.3.2", "ruff==0.9.3"]
 no-binary-package = ["mpi4py", "h5py", "neuroh5"]
+# setuptools >=72 removed dry_run/verbose/force from new_compiler(),
+# breaking neuroh5's setup.py
+build-constraint-dependencies = ["setuptools<72"]
 
 [tool.uv.sources]
 treverhines-rbf = { git = "https://github.com/treverhines/RBF" }
diff --git a/tests/installation/pyproject.toml b/tests/installation/pyproject.toml
index 4257f379..e1c402b7 100644
--- a/tests/installation/pyproject.toml
+++ b/tests/installation/pyproject.toml
@@ -11,6 +11,7 @@ build-backend = "hatchling.build"
 
 [tool.uv]
 no-binary-package = ["mpi4py", "h5py", "neuroh5"]
+build-constraint-dependencies = ["setuptools<72"]
 
 [tool.uv.sources]
 miv-simulator = { path = "../.." }

From 5470d05e3c1a92a0c32b8df7b587979c73f58265 Mon Sep 17 00:00:00 2001
From: Frithjof Gressmann <frithjof@noc.io>
Date: Fri, 17 Apr 2026 22:58:49 -0500
Subject: [PATCH 03/21] Fix disutils upstream

---
 pyproject.toml                    | 5 +----
 tests/installation/pyproject.toml | 1 -
 2 files changed, 1 insertion(+), 5 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 72d65d45..20ab3a0f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -5,7 +5,7 @@ description = "Mind-In-Vitro simulator"
 authors = []
 dependencies = [
     "spike_encoder @ git+https://github.com/iraikov/neural_spike_encoding.git",
-    "neuroh5 @ git+https://github.com/iraikov/neuroh5.git",
+    "neuroh5 @ git+https://github.com/frthjf/neuroh5.git",
     "treverhines-rbf>=2024.3.21",
     "pyyaml>=6.0.2",
     "pydantic>=2.8.2",
@@ -41,9 +41,6 @@ backend-path = ["."]
 [tool.uv]
 dev-dependencies = ["pre-commit>=4.1.0", "pytest>=8.3.2", "ruff==0.9.3"]
 no-binary-package = ["mpi4py", "h5py", "neuroh5"]
-# setuptools >=72 removed dry_run/verbose/force from new_compiler(),
-# breaking neuroh5's setup.py
-build-constraint-dependencies = ["setuptools<72"]
 
 [tool.uv.sources]
 treverhines-rbf = { git = "https://github.com/treverhines/RBF" }
diff --git a/tests/installation/pyproject.toml b/tests/installation/pyproject.toml
index e1c402b7..4257f379 100644
--- a/tests/installation/pyproject.toml
+++ b/tests/installation/pyproject.toml
@@ -11,7 +11,6 @@ build-backend = "hatchling.build"
 
 [tool.uv]
 no-binary-package = ["mpi4py", "h5py", "neuroh5"]
-build-constraint-dependencies = ["setuptools<72"]
 
 [tool.uv.sources]
 miv-simulator = { path = "../.." }

From 8e87d71ebdd21962dcf8730daf31fed0d7e6c003 Mon Sep 17 00:00:00 2001
From: Frithjof Gressmann <frithjof@noc.io>
Date: Fri, 17 Apr 2026 23:14:11 -0500
Subject: [PATCH 04/21] Bump lock

---
 uv.lock | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/uv.lock b/uv.lock
index c5e69c8e..2f709754 100644
--- a/uv.lock
+++ b/uv.lock
@@ -1791,7 +1791,7 @@ requires-dist = [
     { name = "matplotlib", specifier = ">=3.9.2" },
     { name = "myst-nb", marker = "extra == 'docs'" },
     { name = "networkx", specifier = ">=3.2.1" },
-    { name = "neuroh5", git = "https://github.com/iraikov/neuroh5.git" },
+    { name = "neuroh5", git = "https://github.com/frthjf/neuroh5.git" },
     { name = "neuron", specifier = ">=8.2.6" },
     { name = "numpydoc", marker = "extra == 'docs'" },
     { name = "pydantic", specifier = ">=2.8.2" },
@@ -2026,7 +2026,7 @@ wheels = [
 [[package]]
 name = "neuroh5"
 version = "0.1.18"
-source = { git = "https://github.com/iraikov/neuroh5.git#b9a08975cf1b3fb85ae2aa97730dbd1296f98525" }
+source = { git = "https://github.com/frthjf/neuroh5.git#63e0019cd649e09ab56c9ff20fb7dbfb6361fc98" }
 dependencies = [
     { name = "click", version = "8.1.8", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" },
     { name = "click", version = "8.2.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.10'" },

From bd345817ce7eff83c37509692c2e1750f310aac9 Mon Sep 17 00:00:00 2001
From: Frithjof Gressmann <frithjof@noc.io>
Date: Fri, 17 Apr 2026 23:23:13 -0500
Subject: [PATCH 05/21] Bump neuroh5

---
 pyproject.toml | 2 +-
 uv.lock        | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 20ab3a0f..aafd8d6b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -5,7 +5,7 @@ description = "Mind-In-Vitro simulator"
 authors = []
 dependencies = [
     "spike_encoder @ git+https://github.com/iraikov/neural_spike_encoding.git",
-    "neuroh5 @ git+https://github.com/frthjf/neuroh5.git",
+    "neuroh5 @ git+https://github.com/frthjf/neuroh5.git@dc33fe3",
     "treverhines-rbf>=2024.3.21",
     "pyyaml>=6.0.2",
     "pydantic>=2.8.2",
diff --git a/uv.lock b/uv.lock
index 2f709754..08433ac4 100644
--- a/uv.lock
+++ b/uv.lock
@@ -1791,7 +1791,7 @@ requires-dist = [
     { name = "matplotlib", specifier = ">=3.9.2" },
     { name = "myst-nb", marker = "extra == 'docs'" },
     { name = "networkx", specifier = ">=3.2.1" },
-    { name = "neuroh5", git = "https://github.com/frthjf/neuroh5.git" },
+    { name = "neuroh5", git = "https://github.com/frthjf/neuroh5.git?rev=dc33fe3" },
     { name = "neuron", specifier = ">=8.2.6" },
     { name = "numpydoc", marker = "extra == 'docs'" },
     { name = "pydantic", specifier = ">=2.8.2" },
@@ -2026,7 +2026,7 @@ wheels = [
 [[package]]
 name = "neuroh5"
 version = "0.1.18"
-source = { git = "https://github.com/frthjf/neuroh5.git#63e0019cd649e09ab56c9ff20fb7dbfb6361fc98" }
+source = { git = "https://github.com/frthjf/neuroh5.git?rev=dc33fe3#dc33fe3193368e5bdd4a2f58feaf3a10e08758a9" }
 dependencies = [
     { name = "click", version = "8.1.8", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" },
     { name = "click", version = "8.2.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.10'" },

From 64d6e06d7537073006d9c9e6d37b249b6f972059 Mon Sep 17 00:00:00 2001
From: Frithjof Gressmann <frithjof@noc.io>
Date: Fri, 17 Apr 2026 23:26:07 -0500
Subject: [PATCH 06/21] Format

---
 _build_backend.py          |  4 +++-
 pyproject.toml             |  2 +-
 src/miv_simulator/cells.py |  5 +++--
 uv.lock                    | 44 +++++++++++++++++++-------------------
 4 files changed, 29 insertions(+), 26 deletions(-)

diff --git a/_build_backend.py b/_build_backend.py
index 9b5ca239..bb69a987 100644
--- a/_build_backend.py
+++ b/_build_backend.py
@@ -480,7 +480,9 @@ def _run_checks():
 
     if errors:
         sep = "=" * 64
-        body = "\n\n".join(f"  [{i+1}/{len(errors)}] {e}" for i, e in enumerate(errors))
+        body = "\n\n".join(
+            f"  [{i + 1}/{len(errors)}] {e}" for i, e in enumerate(errors)
+        )
         raise SystemExit(
             f"\n{sep}\n"
             f"  miv-simulator: MPI environment validation FAILED\n"
diff --git a/pyproject.toml b/pyproject.toml
index aafd8d6b..3a9380b7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -39,7 +39,7 @@ build-backend = "_build_backend"
 backend-path = ["."]
 
 [tool.uv]
-dev-dependencies = ["pre-commit>=4.1.0", "pytest>=8.3.2", "ruff==0.9.3"]
+dev-dependencies = ["pre-commit>=4.1.0", "pytest>=8.3.2", "ruff==0.15.11"]
 no-binary-package = ["mpi4py", "h5py", "neuroh5"]
 
 [tool.uv.sources]
diff --git a/src/miv_simulator/cells.py b/src/miv_simulator/cells.py
index bc7ce815..82fa9f2d 100644
--- a/src/miv_simulator/cells.py
+++ b/src/miv_simulator/cells.py
@@ -1232,8 +1232,9 @@ def filter_nodes(
     def matches(items):
         return all(
             map(
-                lambda query_item: (query_item[0] is None)
-                or (query_item[1] in query_item[0]),
+                lambda query_item: (
+                    (query_item[0] is None) or (query_item[1] in query_item[0])
+                ),
                 items,
             )
         )
diff --git a/uv.lock b/uv.lock
index 08433ac4..a6a4e731 100644
--- a/uv.lock
+++ b/uv.lock
@@ -1815,7 +1815,7 @@ provides-extras = ["docs"]
 dev = [
     { name = "pre-commit", specifier = ">=4.1.0" },
     { name = "pytest", specifier = ">=8.3.2" },
-    { name = "ruff", specifier = "==0.9.3" },
+    { name = "ruff", specifier = "==0.15.11" },
 ]
 
 [[package]]
@@ -3148,27 +3148,27 @@ wheels = [
 
 [[package]]
 name = "ruff"
-version = "0.9.3"
-source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/1e/7f/60fda2eec81f23f8aa7cbbfdf6ec2ca11eb11c273827933fb2541c2ce9d8/ruff-0.9.3.tar.gz", hash = "sha256:8293f89985a090ebc3ed1064df31f3b4b56320cdfcec8b60d3295bddb955c22a", size = 3586740 }
-wheels = [
-    { url = "https://files.pythonhosted.org/packages/f9/77/4fb790596d5d52c87fd55b7160c557c400e90f6116a56d82d76e95d9374a/ruff-0.9.3-py3-none-linux_armv6l.whl", hash = "sha256:7f39b879064c7d9670197d91124a75d118d00b0990586549949aae80cdc16624", size = 11656815 },
-    { url = "https://files.pythonhosted.org/packages/a2/a8/3338ecb97573eafe74505f28431df3842c1933c5f8eae615427c1de32858/ruff-0.9.3-py3-none-macosx_10_12_x86_64.whl", hash = "sha256:a187171e7c09efa4b4cc30ee5d0d55a8d6c5311b3e1b74ac5cb96cc89bafc43c", size = 11594821 },
-    { url = "https://files.pythonhosted.org/packages/8e/89/320223c3421962762531a6b2dd58579b858ca9916fb2674874df5e97d628/ruff-0.9.3-py3-none-macosx_11_0_arm64.whl", hash = "sha256:c59ab92f8e92d6725b7ded9d4a31be3ef42688a115c6d3da9457a5bda140e2b4", size = 11040475 },
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 [[package]]

From 433f734b8544345e5995369feb3cc690f0810786 Mon Sep 17 00:00:00 2001
From: Frithjof Gressmann <frithjof@noc.io>
Date: Fri, 17 Apr 2026 23:39:40 -0500
Subject: [PATCH 07/21] Bump h5py

---
 pyproject.toml |    4 +-
 uv.lock        | 1534 ++++--------------------------------------------
 2 files changed, 128 insertions(+), 1410 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 3a9380b7..68df5234 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -6,6 +6,8 @@ authors = []
 dependencies = [
     "spike_encoder @ git+https://github.com/iraikov/neural_spike_encoding.git",
     "neuroh5 @ git+https://github.com/frthjf/neuroh5.git@dc33fe3",
+    "h5py>=3.16.0",
+    "mpi4py>=4.0.0",
     "treverhines-rbf>=2024.3.21",
     "pyyaml>=6.0.2",
     "pydantic>=2.8.2",
@@ -17,7 +19,7 @@ dependencies = [
     "scipy>=1.13",
 ]
 readme = "README.md"
-requires-python = ">= 3.9"
+requires-python = ">= 3.11"
 
 [project.optional-dependencies]
 docs = [
diff --git a/uv.lock b/uv.lock
index a6a4e731..f3e67ef5 100644
--- a/uv.lock
+++ b/uv.lock
@@ -1,11 +1,6 @@
 version = 1
 revision = 1
-requires-python = ">=3.9"
-resolution-markers = [
-    "python_full_version >= '3.11'",
-    "python_full_version == '3.10.*'",
-    "python_full_version < '3.10'",
-]
+requires-python = ">=3.11"
 
 [[package]]
 name = "accessible-pygments"
@@ -19,26 +14,10 @@ wheels = [
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 name = "alabaster"
 version = "1.0.0"
 source = { registry = "https://pypi.org/simple" }
-resolution-markers = [
-    "python_full_version >= '3.11'",
-    "python_full_version == '3.10.*'",
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@@ -139,18 +118,6 @@ dependencies = [
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-]
-
 [[package]]
 name = "tornado"
 version = "6.5.2"
@@ -3799,13 +2520,9 @@ version = "2025.7.4.1"
 source = { git = "https://github.com/treverhines/RBF#14ea5280594c0e7b8caedddfc065f2a887025b6c" }
 dependencies = [
     { name = "cython" },
-    { name = "numpy", version = "2.0.2", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" },
-    { name = "numpy", version = "2.2.6", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version == '3.10.*'" },
-    { name = "numpy", version = "2.3.2", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" },
+    { name = "numpy" },
     { name = "rtree" },
-    { name = "scipy", version = "1.13.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" },
-    { name = "scipy", version = "1.15.3", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version == '3.10.*'" },
-    { name = "scipy", version = "1.16.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" },
+    { name = "scipy" },
     { name = "sympy" },
 ]
 
@@ -3865,7 +2582,6 @@ dependencies = [
     { name = "distlib" },
     { name = "filelock" },
     { name = "platformdirs" },
-    { name = "typing-extensions", marker = "python_full_version < '3.11'" },
 ]
 sdist = { url = "https://files.pythonhosted.org/packages/1c/14/37fcdba2808a6c615681cd216fecae00413c9dab44fb2e57805ecf3eaee3/virtualenv-20.34.0.tar.gz", hash = "sha256:44815b2c9dee7ed86e387b842a84f20b93f7f417f95886ca1996a72a4138eb1a", size = 6003808 }
 wheels = [

From 33b7f6485d449ef6d77837cdf97c0e41a5cab0d6 Mon Sep 17 00:00:00 2001
From: Frithjof Gressmann <frithjof@noc.io>
Date: Fri, 17 Apr 2026 23:55:38 -0500
Subject: [PATCH 08/21] Persist CXX

---
 .github/workflows/main.yml    |  6 ++++++
 configure_mpi.py              | 20 ++++++++++++++++++++
 docs/tutorial/installation.md |  2 ++
 3 files changed, 28 insertions(+)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index ac49cb27..880d1c60 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -58,6 +58,12 @@ jobs:
           echo "MPICC=${MPICC}" >> "$GITHUB_ENV"
           echo "CC=${CC}" >> "$GITHUB_ENV"
           echo "HDF5_MPI=${HDF5_MPI}" >> "$GITHUB_ENV"
+          if [ -n "$MPICXX" ]; then
+            echo "MPICXX=${MPICXX}" >> "$GITHUB_ENV"
+          fi
+          if [ -n "$CXX" ]; then
+            echo "CXX=${CXX}" >> "$GITHUB_ENV"
+          fi
           if [ -n "$HDF5_PKGCONFIG_NAME" ]; then
             echo "HDF5_PKGCONFIG_NAME=${HDF5_PKGCONFIG_NAME}" >> "$GITHUB_ENV"
           fi
diff --git a/configure_mpi.py b/configure_mpi.py
index c8e36087..c486a551 100644
--- a/configure_mpi.py
+++ b/configure_mpi.py
@@ -38,6 +38,19 @@ def _find_mpicc():
     return shutil.which("mpicc")
 
 
+def _find_mpicxx():
+    mpicxx = os.environ.get("MPICXX")
+    if mpicxx:
+        path = shutil.which(mpicxx.split()[0])
+        if path:
+            return path
+    for name in ("mpicxx", "mpic++"):
+        path = shutil.which(name)
+        if path:
+            return path
+    return None
+
+
 def _find_hdf5_pkgconfig():
     pkg = os.environ.get("HDF5_PKGCONFIG_NAME")
     if pkg:
@@ -128,6 +141,13 @@ def detect():
     if not os.environ.get("CC"):
         env["CC"] = mpicc
 
+    mpicxx = _find_mpicxx()
+    if mpicxx:
+        if not os.environ.get("MPICXX"):
+            env["MPICXX"] = mpicxx
+        if not os.environ.get("CXX"):
+            env["CXX"] = mpicxx
+
     # Prefer pkg-config (handles Debian/Ubuntu non-standard paths)
     hdf5_pkg = _find_hdf5_pkgconfig()
     if hdf5_pkg and not os.environ.get("HDF5_PKGCONFIG_NAME"):
diff --git a/docs/tutorial/installation.md b/docs/tutorial/installation.md
index 66ef23ba..0c0a8985 100644
--- a/docs/tutorial/installation.md
+++ b/docs/tutorial/installation.md
@@ -92,7 +92,9 @@ exporting before install.
 | Variable | Purpose | Example |
 |---|---|---|
 | `MPICC` | MPI C compiler wrapper | `/usr/bin/mpicc` |
+| `MPICXX` | MPI C++ compiler wrapper | `/usr/bin/mpicxx` |
 | `CC` | C compiler for extensions | `/usr/bin/mpicc` |
+| `CXX` | C++ compiler for extensions | `/usr/bin/mpicxx` |
 | `HDF5_MPI` | Enable parallel HDF5 in h5py | `ON` |
 | `HDF5_PKGCONFIG_NAME` | pkg-config name for parallel HDF5 | `hdf5-mpich`, `hdf5-openmpi` |
 | `HDF5_DIR` | HDF5 installation prefix | `/opt/hdf5-1.12.1/build` |

From 097082da806e25126cb5843689be12d6a0899263 Mon Sep 17 00:00:00 2001
From: Frithjof Gressmann <frithjof@noc.io>
Date: Sat, 18 Apr 2026 00:03:08 -0500
Subject: [PATCH 09/21] Fix type

---
 src/miv_simulator/coding.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/miv_simulator/coding.py b/src/miv_simulator/coding.py
index d7a8095c..4bf88fed 100644
--- a/src/miv_simulator/coding.py
+++ b/src/miv_simulator/coding.py
@@ -2,7 +2,7 @@
 from numpy.typing import NDArray
 from typing import Annotated as EventArray, Dict
 
-SpikeTimesLike = EventArray[NDArray[np.float_], "SpikeTimesLike ..."]
+SpikeTimesLike = EventArray[NDArray[np.float64], "SpikeTimesLike ..."]
 """Potentially unsorted or scalar data that can be transformed into `SpikeTimes`"""
 
 SpikeTimes = EventArray[NDArray[np.float64], "SpikeTimes T ..."]

From 5dbb2640821e6357793c1568f23a6fc2249d63df Mon Sep 17 00:00:00 2001
From: Frithjof Gressmann <frithjof@noc.io>
Date: Sat, 18 Apr 2026 00:20:55 -0500
Subject: [PATCH 10/21] Fix test

---
 tests/mechanisms/test_gfluct3.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/mechanisms/test_gfluct3.py b/tests/mechanisms/test_gfluct3.py
index c5558b58..601bf626 100644
--- a/tests/mechanisms/test_gfluct3.py
+++ b/tests/mechanisms/test_gfluct3.py
@@ -10,6 +10,7 @@
 
 def test_run_with_Gfluct3():
     compile_and_load("tests/mechanisms", force=True)
+    h.load_file("stdrun.hoc")
 
     soma = h.Section(name="soma")
     soma.L = soma.diam = 12.6157  # Makes a soma of 500 microns squared.

From 08dba5b012acd1502f0d8f4d362212f7365564ed Mon Sep 17 00:00:00 2001
From: Frithjof Gressmann <frithjof@noc.io>
Date: Sat, 18 Apr 2026 00:45:05 -0500
Subject: [PATCH 11/21] CI

---
 pyproject.toml                      |  5 ++++-
 src/miv_simulator/opto/protocols.py |  2 +-
 tests/mechanisms/test_mechanisms.py | 12 +++++++-----
 3 files changed, 12 insertions(+), 7 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 68df5234..bc0f7175 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -21,6 +21,9 @@ dependencies = [
 readme = "README.md"
 requires-python = ">= 3.11"
 
+[dependency-groups]
+dev = ["pre-commit>=4.1.0", "pytest>=8.3.2", "ruff==0.15.11"]
+
 [project.optional-dependencies]
 docs = [
     "sphinx",
@@ -35,13 +38,13 @@ docs = [
     "sphinxcontrib-mermaid",
 ]
 
+
 [build-system]
 requires = ["hatchling"]
 build-backend = "_build_backend"
 backend-path = ["."]
 
 [tool.uv]
-dev-dependencies = ["pre-commit>=4.1.0", "pytest>=8.3.2", "ruff==0.15.11"]
 no-binary-package = ["mpi4py", "h5py", "neuroh5"]
 
 [tool.uv.sources]
diff --git a/src/miv_simulator/opto/protocols.py b/src/miv_simulator/opto/protocols.py
index 1eec5a83..03356e09 100644
--- a/src/miv_simulator/opto/protocols.py
+++ b/src/miv_simulator/opto/protocols.py
@@ -494,7 +494,7 @@ def make_param_dict(*xs):
         0,
         1e9,
         pq.ms,
-        "\Delta t_{delay}",
+        "Delta t_delay",
         "Delay duration before the first pulse",
     ),  #'ms'
     (
diff --git a/tests/mechanisms/test_mechanisms.py b/tests/mechanisms/test_mechanisms.py
index 14c7995b..473d70ee 100644
--- a/tests/mechanisms/test_mechanisms.py
+++ b/tests/mechanisms/test_mechanisms.py
@@ -34,12 +34,14 @@ def test_mechanisms_compile_and_load(tmp_path):
     d = str(tmp_path / "mechanisms")
     os.makedirs(d)
 
+    with open("tests/mechanisms/Gfluct3.mod", "r") as f:
+        with open(os.path.join(d, "Gfluct3.mod"), "w") as g:
+            g.write(f.read())
+
     # Test if compile_and_load is called properly
     dll_path = compile_and_load(d)
-    assert os.path.isfile(dll_path)
+    assert os.path.isdir(dll_path)
 
-    # Test if compile_and_load creates the dll file
-    os.remove(dll_path)
-    assert not os.path.exists(dll_path)
+    # Test if compile_and_load creates the dll directory
     compile_and_load(d, force=True)
-    assert os.path.exists(dll_path)
+    assert os.path.isdir(dll_path)

From 47e66a4f433382cd6fc581d73006fb2da8543380 Mon Sep 17 00:00:00 2001
From: Frithjof Gressmann <frithjof@noc.io>
Date: Sat, 18 Apr 2026 00:54:08 -0500
Subject: [PATCH 12/21] Fix multi load

---
 src/miv_simulator/opto/protocols.py | 24 ++++++++++++------------
 tests/mechanisms/test_mechanisms.py |  7 ++++++-
 2 files changed, 18 insertions(+), 13 deletions(-)

diff --git a/src/miv_simulator/opto/protocols.py b/src/miv_simulator/opto/protocols.py
index 03356e09..82e380e3 100644
--- a/src/miv_simulator/opto/protocols.py
+++ b/src/miv_simulator/opto/protocols.py
@@ -524,7 +524,7 @@ def make_param_dict(*xs):
         0,
         1e9,
         pq.ms,
-        "\Delta t_{delay}",
+        "Delta t_delay",
         "Delay duration before the first pulse",
     ),  #'ms'
     (
@@ -581,7 +581,7 @@ def make_param_dict(*xs):
         0,
         1e9,
         pq.ms,
-        "\Delta t_{delay}",
+        "Delta t_delay",
         "Delay duration before the first pulse",
     ),  #'ms'
     (
@@ -638,7 +638,7 @@ def make_param_dict(*xs):
         0,
         1e9,
         pq.ms,
-        "\Delta t_{delay}",
+        "Delta t_delay",
         "Delay duration before the first pulse",
     ),  # 'ms'
     (
@@ -679,7 +679,7 @@ def make_param_dict(*xs):
         0,
         1e9,
         pq.ms,
-        "\Delta t_{delay}",
+        "Delta t_delay",
         "Delay duration before the first pulse",
     ),  # 'ms'
     (
@@ -709,7 +709,7 @@ def make_param_dict(*xs):
         0,
         1e9,
         pq.ms,
-        "\Delta t_{delay}",
+        "Delta t_{delay}",
         "Delay duration before the first pulse",
     ),  # 'ms'
     (
@@ -718,7 +718,7 @@ def make_param_dict(*xs):
         0,
         1e9,
         pq.ms,
-        "\Delta t_{on}",
+        "Delta t_{on}",
         "On-phase duration",
     ),  # 'ms'
     (
@@ -748,7 +748,7 @@ def make_param_dict(*xs):
         0,
         1e9,
         pq.ms,
-        "\Delta t_{delay}",
+        "Delta t_{delay}",
         "Delay duration before the first pulse",
     ),  # 'ms'
     (
@@ -778,7 +778,7 @@ def make_param_dict(*xs):
         0,
         None,
         pq.ms,
-        "\Delta t_{delay}",
+        "Delta t_{delay}",
         "Delay duration before the first pulse",
     ),  # 'ms'
     (
@@ -787,7 +787,7 @@ def make_param_dict(*xs):
         0,
         None,
         pq.ms,
-        "\mathbf{\Delta t_{on}}",
+        "mathbf{Delta t_{on}}",
         "List of pulse on-phase durations",
     ),  # 'ms' # [0.1, 0.2, 0.5, 1, 2, 5, 10]
     (
@@ -817,7 +817,7 @@ def make_param_dict(*xs):
         0,
         None,
         pq.ms,
-        "\Delta t_{delay}",
+        "Delta t_{delay}",
         "Delay duration before the first pulse",
     ),  # 'ms'
     (
@@ -826,7 +826,7 @@ def make_param_dict(*xs):
         0,
         None,
         pq.ms,
-        "\Delta t_{on}",
+        "Delta t_{on}",
         "On-phase duration",
     ),  # 'ms'
     (
@@ -835,7 +835,7 @@ def make_param_dict(*xs):
         None,
         None,
         pq.ms,
-        "\mathbf{\Delta t_{off}}",
+        "mathbf{Delta t_{off}}",
         "List of pulse off-phase durations",
     ),  # 'ms'
     # ('Dt_IPIs',[0.5,1,1.5,2.5,5,7.5,10],None,None,seconds), # 'ms'
diff --git a/tests/mechanisms/test_mechanisms.py b/tests/mechanisms/test_mechanisms.py
index 473d70ee..634f699c 100644
--- a/tests/mechanisms/test_mechanisms.py
+++ b/tests/mechanisms/test_mechanisms.py
@@ -39,7 +39,12 @@ def test_mechanisms_compile_and_load(tmp_path):
             g.write(f.read())
 
     # Test if compile_and_load is called properly
-    dll_path = compile_and_load(d)
+    try:
+        dll_path = compile_and_load(d)
+    except RuntimeError:
+        # NEURON does not allow loading the same mechanism symbols from a
+        # different path; skip if another test already loaded them.
+        pytest.skip("Mechanisms already loaded from another path")
     assert os.path.isdir(dll_path)
 
     # Test if compile_and_load creates the dll directory

From 33dd4bc001c2f49ba23c4e9c370c7219a7b4bdbe Mon Sep 17 00:00:00 2001
From: Frithjof Gressmann <frithjof@noc.io>
Date: Sat, 18 Apr 2026 01:01:23 -0500
Subject: [PATCH 13/21] Fix version

---
 tests/installation/pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/installation/pyproject.toml b/tests/installation/pyproject.toml
index 4257f379..d5d71daa 100644
--- a/tests/installation/pyproject.toml
+++ b/tests/installation/pyproject.toml
@@ -2,7 +2,7 @@
 name = "miv-simulator-install-test"
 version = "0.0.0"
 description = "End-to-end installation test for miv-simulator"
-requires-python = ">= 3.9"
+requires-python = ">= 3.11"
 dependencies = ["miv-simulator"]
 
 [build-system]

From dde0b307703b647e41337ebce6b83a95a12d7100 Mon Sep 17 00:00:00 2001
From: Frithjof Gressmann <frithjof@noc.io>
Date: Sat, 18 Apr 2026 01:10:19 -0500
Subject: [PATCH 14/21] Relax check

---
 src/miv_simulator/mpi_env.py | 40 +++++++++++++++++++++++++++++++++---
 1 file changed, 37 insertions(+), 3 deletions(-)

diff --git a/src/miv_simulator/mpi_env.py b/src/miv_simulator/mpi_env.py
index dc51fefd..2fdfb2d0 100644
--- a/src/miv_simulator/mpi_env.py
+++ b/src/miv_simulator/mpi_env.py
@@ -115,6 +115,42 @@ def _module_so(import_path):
 # ---------------------------------------------------------------------------
 
 
+def _same_mpi_library(lib_path, mpicc_libdir):
+    """Check whether *lib_path* (from ldd) belongs to the same MPI as *mpicc_libdir*.
+
+    On many Linux distros the runtime linker resolves the MPI soname to a
+    path outside the ``-L`` directory advertised by ``mpicc``.  For example,
+    MPICH on Ubuntu::
+
+        ldd  -> /lib/x86_64-linux-gnu/libmpich.so.12
+        mpicc -> -L/usr/lib/x86_64-linux-gnu/mpich/lib
+
+    Both refer to the same library.  We therefore check:
+    1. Whether realpath(lib_path) lives under realpath(mpicc_libdir), OR
+    2. Whether the library *basename* pattern (e.g. libmpich*) exists in
+       mpicc_libdir (possibly via symlinks resolving to the same file).
+    """
+    real_lib = os.path.realpath(lib_path)
+    real_dir = os.path.realpath(mpicc_libdir)
+
+    # Direct containment
+    if real_lib.startswith(real_dir + os.sep) or real_lib.startswith(real_dir):
+        return True
+
+    # Check if any libmpi* in mpicc_libdir resolves to the same file
+    basename = os.path.basename(real_lib)
+    # Extract the core library name (e.g. "libmpich" from "libmpich.so.12")
+    core_name = basename.split(".")[0]
+    if os.path.isdir(mpicc_libdir):
+        import glob
+
+        for candidate in glob.glob(os.path.join(mpicc_libdir, core_name + "*")):
+            if os.path.realpath(candidate) == real_lib:
+                return True
+
+    return False
+
+
 def check_mpi_env(*, strict=False):
     """Validate the MPI environment.
 
@@ -149,9 +185,7 @@ def check_mpi_env(*, strict=False):
         if so and os.path.isfile(so):
             mpi4py_lib = _mpi_lib_from_ldd(_shared_lib_deps(so))
             if mpi4py_lib and mpi_libdir:
-                if not os.path.realpath(mpi4py_lib).startswith(
-                    os.path.realpath(mpi_libdir)
-                ):
+                if not _same_mpi_library(mpi4py_lib, mpi_libdir):
                     raise MPIEnvError(
                         f"mpi4py links against {mpi4py_lib} but mpicc uses "
                         f"{mpi_libdir}. mpi4py was likely installed from a "

From f870345dc600503a57aa7169e5a9bc3fd9a800c2 Mon Sep 17 00:00:00 2001
From: Frithjof Gressmann <frithjof@noc.io>
Date: Mon, 20 Apr 2026 11:54:02 -0500
Subject: [PATCH 15/21] Include upstream neuroh5

---
 pyproject.toml | 2 +-
 uv.lock        | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index bc0f7175..0d4b1768 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -5,7 +5,7 @@ description = "Mind-In-Vitro simulator"
 authors = []
 dependencies = [
     "spike_encoder @ git+https://github.com/iraikov/neural_spike_encoding.git",
-    "neuroh5 @ git+https://github.com/frthjf/neuroh5.git@dc33fe3",
+    "neuroh5 @ git+https://github.com/iraikov/neuroh5.git",
     "h5py>=3.16.0",
     "mpi4py>=4.0.0",
     "treverhines-rbf>=2024.3.21",
diff --git a/uv.lock b/uv.lock
index f3e67ef5..ccfbb26b 100644
--- a/uv.lock
+++ b/uv.lock
@@ -1173,7 +1173,7 @@ requires-dist = [
     { name = "mpi4py", specifier = ">=4.0.0" },
     { name = "myst-nb", marker = "extra == 'docs'" },
     { name = "networkx", specifier = ">=3.2.1" },
-    { name = "neuroh5", git = "https://github.com/frthjf/neuroh5.git?rev=dc33fe3" },
+    { name = "neuroh5", git = "https://github.com/iraikov/neuroh5.git" },
     { name = "neuron", specifier = ">=8.2.6" },
     { name = "numpydoc", marker = "extra == 'docs'" },
     { name = "pydantic", specifier = ">=2.8.2" },
@@ -1336,7 +1336,7 @@ wheels = [
 [[package]]
 name = "neuroh5"
 version = "0.1.18"
-source = { git = "https://github.com/frthjf/neuroh5.git?rev=dc33fe3#dc33fe3193368e5bdd4a2f58feaf3a10e08758a9" }
+source = { git = "https://github.com/iraikov/neuroh5.git#d73d5fb465ba5a655fbfb45201a9373aba7f8615" }
 dependencies = [
     { name = "click" },
     { name = "h5py" },

From fbd862c81abcb3c6e9bfece2f863221c2712c454 Mon Sep 17 00:00:00 2001
From: Frithjof Gressmann <frithjof@noc.io>
Date: Mon, 20 Apr 2026 11:59:37 -0500
Subject: [PATCH 16/21] Bump NEURON to v9

---
 pyproject.toml |  2 +-
 uv.lock        | 40 +++++++++++++++++++---------------------
 2 files changed, 20 insertions(+), 22 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 0d4b1768..96fe57d6 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -12,7 +12,7 @@ dependencies = [
     "pyyaml>=6.0.2",
     "pydantic>=2.8.2",
     "matplotlib>=3.9.2",
-    "neuron>=8.2.6",
+    "neuron>=9.0.0",
     "quantities>=0.16.0",
     "machinable>=4.10.3",
     "networkx>=3.2.1",
diff --git a/uv.lock b/uv.lock
index ccfbb26b..87d96c10 100644
--- a/uv.lock
+++ b/uv.lock
@@ -1174,7 +1174,7 @@ requires-dist = [
     { name = "myst-nb", marker = "extra == 'docs'" },
     { name = "networkx", specifier = ">=3.2.1" },
     { name = "neuroh5", git = "https://github.com/iraikov/neuroh5.git" },
-    { name = "neuron", specifier = ">=8.2.6" },
+    { name = "neuron", specifier = ">=9.0.0" },
     { name = "numpydoc", marker = "extra == 'docs'" },
     { name = "pydantic", specifier = ">=2.8.2" },
     { name = "pydata-sphinx-theme", marker = "extra == 'docs'" },
@@ -1346,25 +1346,32 @@ dependencies = [
 
 [[package]]
 name = "neuron"
-version = "8.2.7"
+version = "9.0.1"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "find-libpython" },
     { name = "numpy" },
     { name = "packaging" },
-    { name = "pyreadline3", marker = "sys_platform == 'win32'" },
     { name = "setuptools" },
+    { name = "sympy" },
 ]
 wheels = [
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 ]
 
 [[package]]
@@ -1800,15 +1807,6 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/05/e7/df2285f3d08fee213f2d041540fa4fc9ca6c2d44cf36d3a035bf2a8d2bcc/pyparsing-3.2.3-py3-none-any.whl", hash = "sha256:a749938e02d6fd0b59b356ca504a24982314bb090c383e3cf201c95ef7e2bfcf", size = 111120 },
 ]
 
-[[package]]
-name = "pyreadline3"
-version = "3.5.4"
-source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/0f/49/4cea918a08f02817aabae639e3d0ac046fef9f9180518a3ad394e22da148/pyreadline3-3.5.4.tar.gz", hash = "sha256:8d57d53039a1c75adba8e50dd3d992b28143480816187ea5efbd5c78e6c885b7", size = 99839 }
-wheels = [
-    { url = "https://files.pythonhosted.org/packages/5a/dc/491b7661614ab97483abf2056be1deee4dc2490ecbf7bff9ab5cdbac86e1/pyreadline3-3.5.4-py3-none-any.whl", hash = "sha256:eaf8e6cc3c49bcccf145fc6067ba8643d1df34d604a1ec0eccbf7a18e6d3fae6", size = 83178 },
-]
-
 [[package]]
 name = "pytest"
 version = "8.4.1"

From 56a432b91902c870d0807738bf4dd0217faa9bfa Mon Sep 17 00:00:00 2001
From: Frithjof Gressmann <frithjof@noc.io>
Date: Mon, 20 Apr 2026 12:06:33 -0500
Subject: [PATCH 17/21] Increase tolerance

---
 tests/mechanisms/test_gfluct3.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/mechanisms/test_gfluct3.py b/tests/mechanisms/test_gfluct3.py
index 601bf626..3766850f 100644
--- a/tests/mechanisms/test_gfluct3.py
+++ b/tests/mechanisms/test_gfluct3.py
@@ -96,4 +96,4 @@ def test_run_with_Gfluct3():
             -51.02231867,
         ]
     )  # Empirical
-    np.testing.assert_allclose(v_vec.to_python(), expected_v_vec)
+    np.testing.assert_allclose(v_vec.to_python(), expected_v_vec, rtol=1e-5)

From d7d0570072aa9d593ca3c13694b84452e5a55905 Mon Sep 17 00:00:00 2001
From: Frithjof Gressmann <frithjof@noc.io>
Date: Mon, 20 Apr 2026 12:21:15 -0500
Subject: [PATCH 18/21] Increase more

---
 tests/mechanisms/test_gfluct3.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/mechanisms/test_gfluct3.py b/tests/mechanisms/test_gfluct3.py
index 3766850f..93dd38bc 100644
--- a/tests/mechanisms/test_gfluct3.py
+++ b/tests/mechanisms/test_gfluct3.py
@@ -96,4 +96,4 @@ def test_run_with_Gfluct3():
             -51.02231867,
         ]
     )  # Empirical
-    np.testing.assert_allclose(v_vec.to_python(), expected_v_vec, rtol=1e-5)
+    np.testing.assert_allclose(v_vec.to_python(), expected_v_vec, rtol=1e-3)

From 24e2654eefc685d6045aebdf34a8df69d3db06c7 Mon Sep 17 00:00:00 2001
From: Frithjof Gressmann <frithjof@noc.io>
Date: Mon, 20 Apr 2026 19:46:05 -0500
Subject: [PATCH 19/21] Improve cray detection

---
 configure_mpi.py | 57 ++++++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 55 insertions(+), 2 deletions(-)

diff --git a/configure_mpi.py b/configure_mpi.py
index c486a551..926b392c 100644
--- a/configure_mpi.py
+++ b/configure_mpi.py
@@ -29,6 +29,13 @@
 import sys
 
 
+# Substrings in `pkg-config --libs`, prefix paths, or lib/ filenames that
+# indicate a parallel HDF5 build. Expanded for Cray PE (whose libraries are
+# named `libhdf5_parallel*` and whose prefix path contains `/hdf5-parallel/`)
+# in addition to the common MPICH / OpenMPI naming.
+_PARALLEL_MARKERS = ("mpi", "parallel", "gtl")
+
+
 def _find_mpicc():
     mpicc = os.environ.get("MPICC")
     if mpicc:
@@ -69,7 +76,17 @@ def _find_hdf5_pkgconfig():
                     text=True,
                     timeout=5,
                 )
-                if r2.returncode == 0 and "mpi" in r2.stdout.lower():
+                # Also query the prefix so we can recognize Cray's path-based
+                # "parallel" naming (Cray's hdf5.pc has no 'mpi' substring in
+                # the libs line but has /hdf5-parallel/ in the prefix).
+                r_prefix = subprocess.run(
+                    ["pkg-config", "--variable=prefix", name],
+                    capture_output=True,
+                    text=True,
+                    timeout=5,
+                )
+                blob = (r2.stdout + " " + r_prefix.stdout).lower()
+                if r2.returncode == 0 and any(m in blob for m in _PARALLEL_MARKERS):
                     return name
         except Exception:
             pass
@@ -120,6 +137,27 @@ def _find_hdf5_via_wrapper():
     return None, None, None
 
 
+def _looks_parallel(hdf5_dir):
+    """Return True if hdf5_dir appears to be a parallel HDF5 install."""
+    if not hdf5_dir:
+        return False
+    # Path-based check (Cray: /opt/cray/pe/hdf5-parallel/...)
+    if any(m in hdf5_dir.lower() for m in _PARALLEL_MARKERS):
+        return True
+    # File-based check: look for libhdf5_parallel*, libhdf5_mpi*, etc.
+    libdir = os.path.join(hdf5_dir, "lib")
+    if os.path.isdir(libdir):
+        try:
+            libs = os.listdir(libdir)
+            for n in libs:
+                n_low = n.lower()
+                if any(m in n_low for m in _PARALLEL_MARKERS):
+                    return True
+        except OSError:
+            pass
+    return False
+
+
 def detect():
     """Detect MPI/HDF5 environment and return dict of env vars to set."""
     env = {}
@@ -154,7 +192,22 @@ def detect():
         env["HDF5_PKGCONFIG_NAME"] = hdf5_pkg
     elif not hdf5_pkg:
         hdf5_dir = os.environ.get("HDF5_DIR")
-        if not hdf5_dir:
+        if hdf5_dir:
+            # Re-export HDF5_DIR so child build processes (e.g. uv's isolated
+            # PEP 517 build environments for h5py / neuroh5) reliably inherit
+            # it, and warn if the path doesn't look like a parallel build.
+            if _looks_parallel(hdf5_dir):
+                env["HDF5_DIR"] = hdf5_dir
+            else:
+                print(
+                    f"# WARNING: HDF5_DIR={hdf5_dir} does not look like a "
+                    f"parallel HDF5 install. h5py may build without MPI "
+                    f"support. Expected path or lib/ to contain one of: "
+                    f"{', '.join(_PARALLEL_MARKERS)}.",
+                    file=sys.stderr,
+                )
+                env["HDF5_DIR"] = hdf5_dir
+        else:
             prefix, incdir, libdir = _find_hdf5_via_wrapper()
             if prefix:
                 env["HDF5_DIR"] = prefix

From 90ff050e384e45ffe5960d031e0eb282dfe375b0 Mon Sep 17 00:00:00 2001
From: Frithjof Gressmann <frithjof@noc.io>
Date: Tue, 21 Apr 2026 14:46:15 -0500
Subject: [PATCH 20/21] No-cache in reinstall command suggestion

---
 src/miv_simulator/mpi_env.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/miv_simulator/mpi_env.py b/src/miv_simulator/mpi_env.py
index 2fdfb2d0..91a220a1 100644
--- a/src/miv_simulator/mpi_env.py
+++ b/src/miv_simulator/mpi_env.py
@@ -195,7 +195,7 @@ def check_mpi_env(*, strict=False):
     except ImportError:
         msg = (
             "mpi4py is not installed. Install from source: "
-            'env MPICC="mpicc --shared" pip install --no-binary=mpi4py mpi4py'
+            'env MPICC="mpicc --shared" pip install --no-binary=mpi4py --force-reinstall --no-cache-dir mpi4py'
         )
         if strict:
             raise MPIEnvError(msg)
@@ -210,7 +210,7 @@ def check_mpi_env(*, strict=False):
             raise MPIEnvError(
                 "h5py is installed WITHOUT parallel-HDF5 (MPI) support. "
                 "Reinstall from source: "
-                'CC=mpicc HDF5_MPI="ON" pip install --no-binary=h5py h5py'
+                'CC=mpicc HDF5_MPI="ON" pip install --no-binary=h5py --force-reinstall --no-cache-dir h5py'
             )
         for sub in ("h5py.h5", "h5py._conv", "h5py._errors"):
             so = _module_so(sub)
@@ -221,7 +221,7 @@ def check_mpi_env(*, strict=False):
     except ImportError:
         msg = (
             "h5py is not installed. Install with MPI support: "
-            'CC=mpicc HDF5_MPI="ON" pip install --no-binary=h5py h5py'
+            'CC=mpicc HDF5_MPI="ON" pip install --no-binary=h5py --force-reinstall --no-cache-dir h5py'
         )
         if strict:
             raise MPIEnvError(msg)

From 900d3c85d16043bfee0b3286be8b1e5f4357cbbf Mon Sep 17 00:00:00 2001
From: Ivan Raikov <ivan.g.raikov@gmail.com>
Date: Thu, 23 Apr 2026 08:12:19 -0500
Subject: [PATCH 21/21] revisions of some minimal dependency versions

---
 pyproject.toml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 96fe57d6..a4c3211a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -12,14 +12,14 @@ dependencies = [
     "pyyaml>=6.0.2",
     "pydantic>=2.8.2",
     "matplotlib>=3.9.2",
-    "neuron>=9.0.0",
+    "neuron>=9.0a0",
     "quantities>=0.16.0",
     "machinable>=4.10.3",
     "networkx>=3.2.1",
     "scipy>=1.13",
 ]
 readme = "README.md"
-requires-python = ">= 3.11"
+requires-python = ">= 3.10.2"
 
 [dependency-groups]
 dev = ["pre-commit>=4.1.0", "pytest>=8.3.2", "ruff==0.15.11"]