%global pypi_name surfa

Name:           python-%{pypi_name}
Version:        0.6.3
Release:        4%{?dist}
Summary:        Utilities for medical image and surface processing

License:        MIT
URL:            https://github.com/freesurfer/surfa
Source0:        %{url}/archive/v%{version}/%{pypi_name}-%{version}.tar.gz
# Upstream's NumPy 2 fixes after 0.6.3 (no release yet), cherry-picked onto v0.6.3:
# 86c33ae 03d539f a94931c ea821ac eb13679 (its setup.py abi3 part left out)
# 5e45fbd 8aa4a5f. Without them every .mgz read fails on numpy 2.4 (np.fromstring
# binary mode removed) and crop_to_bbox fails (scipy find_objects on a bool mask).
Patch0:         python-surfa-numpy2.patch

BuildRequires:  gcc
BuildRequires:  python3-devel
BuildRequires:  python3-setuptools
BuildRequires:  python3-wheel
BuildRequires:  python3-pip
BuildRequires:  python3-Cython >= 3.0
BuildRequires:  python3-numpy
BuildRequires:  python3-scipy
BuildRequires:  python3-nibabel
BuildRequires:  python3-pillow
BuildRequires:  python3-xxhash

%description
Surfa is a collection of Python utilities for medical image analysis and
mesh-based surface processing. It provides tools that operate on 3D image
arrays and triangular meshes with consideration of their representation in
a world (or scanner) coordinate system.

%package -n python3-%{pypi_name}
Summary:        %{summary}
Requires:       python3-numpy
Requires:       python3-scipy
Requires:       python3-nibabel >= 2.1
Requires:       python3-pillow
Requires:       python3-xxhash

%description -n python3-%{pypi_name}
Surfa is a collection of Python utilities for medical image analysis and
mesh-based surface processing.

%prep
%autosetup -p1 -n %{pypi_name}-%{version}

# Remove abi3 wheel tag override — build a normal platform wheel
sed -i '/bdist_wheel_abi3/d' setup.py
sed -i '/from wheel.bdist_wheel import bdist_wheel/d' setup.py
sed -i '/class bdist_wheel_abi3/,/return python, abi, plat/d' setup.py
sed -i 's/"cmdclass": {"bdist_wheel": bdist_wheel_abi3}//' setup.py
sed -i '/Py_LIMITED_API/d' setup.py
sed -i '/py_limited_api/d' setup.py

%build
%pyproject_wheel

%install
%pyproject_install
%pyproject_save_files %{pypi_name}

%check
# Run from / to avoid source tree shadowing the installed package
cd /
PYTHONPATH=%{buildroot}%{python3_sitearch}:%{buildroot}%{python3_sitelib} \
  %{python3} -c "import surfa; print('surfa', surfa.__version__)"
# An .mgz round trip, crop and resample: what FreeSurfer's Python tools do first.
PYTHONPATH=%{buildroot}%{python3_sitearch}:%{buildroot}%{python3_sitelib} \
  %{python3} - << 'PYEOF'
import os, tempfile
import numpy as np
import surfa as sf
d = np.zeros((32, 32, 32), np.float32)
d[8:20, 10:22, 5:25] = 1
v = sf.Volume(d)
p = os.path.join(tempfile.mkdtemp(), 't.mgz')
v.save(p)
w = sf.load_volume(p)
assert np.array_equal(w.data, d)
assert w.crop_to_bbox().baseshape == (12, 12, 20)
v.resample_like(sf.ImageGeometry((16, 16, 16), voxsize=2))
v.reorient('LIA')
print('surfa mgz/crop/resample OK on numpy', np.__version__)
PYEOF

%files -n python3-%{pypi_name} -f %{pyproject_files}
# License is MIT (declared in setup.py) but upstream has no standalone license file

%changelog
* Tue Oct 13 2026 Morgan Hough <morgan.hough@gmail.com> - 0.6.3-4
- Backport upstream's NumPy 2 fixes (seven commits after 0.6.3, unreleased).
  On F44's numpy 2.4.6 / scipy 1.16.2, 0.6.3 failed every .mgz read ("The
  binary mode of fromstring is removed") and crop_to_bbox ("'numpy.bool' object
  cannot be interpreted as an integer"), which broke FreeSurfer 8's Python
  tools. Found by neurospark's HBN recon-all on aarch64; reproduced on x86_64.
- %%check now does an .mgz round trip, crop, resample and reorient.

* Sun Sep 27 2026 Morgan Hough <morgan.hough@gmail.com> - 0.6.3-3
- Rebuild against f45's current numpy. The -2 build's compiled
  surfa.image.interp extension SEGFAULTS on import on f45. Nothing in the rpm
  dependencies can notice: a numpy ABI change moves no soname, so the package
  installs cleanly and dies at load -- the same shape as the VTK frozen-soname
  class this repo already tracks, in a different disguise.
- Found via python3-samseg, which LOOKS like it crashes in PETSc. It does not.
  PETSc installs its own SIGSEGV handler, so when surfa faulted PETSc caught the
  signal and printed "Caught signal number 11 SEGV" with advice about debugging
  PETSc -- naming itself for someone else's fault. faulthandler gave the real
  chain:
      samseg -> surfa.transform.warp:6 -> surfa.image.framed:25
             -> from surfa.image.interp import interpolate -> SIGSEGV
  Isolated one import per process: petsc4py rc=0, petsc4py.PETSc rc=0, numba
  rc=0, surfa rc=-11. On f44 (python 3.14) samseg imports fine and petsc4py is
  not installed at all.
- The %%check here imports surfa and PASSED when -2 was built, which is the
  point rather than an oversight: a build-time import check cannot catch an ABI
  break that happens to the environment AFTER the build.
* Fri Jun 12 2026 Morgan Hough <morgan.hough@gmail.com> - 0.6.3-2
- Rebuild for rawhide's Python 3.15 transition. The -1 build required
  python(abi)=3.14, blocking the rawhide SimNIBS chain (python-samseg
  BuildRequires python3-surfa and could not resolve on rawhide).

* Tue Mar 10 2026 Morgan Hough <morgan.hough@gmail.com> - 0.6.3-1
- Initial package