# spec2nii: conversion of in vivo MR spectroscopy data (Siemens, Philips, GE, Bruker, Varian, UIH, jMRUI, ...) to NIfTI-MRS (Will Clarke, Oxford).
# FMRIB's installer ships it for FSL-MRS users; fsl_mrs itself never imports it (it only tells users to run it). Not in Fedora.

%global pypi_name spec2nii

Name:           python-%{pypi_name}
Version:        0.8.15
Release:        1%{?dist}
Summary:        Multi-format in vivo MR spectroscopy conversion to NIfTI

License:        BSD-3-Clause
URL:            https://github.com/wtclarke/spec2nii
Source0:        %{pypi_source %{pypi_name}}

BuildArch:      noarch
BuildRequires:  python3-devel
BuildRequires:  python3-pytest
BuildRequires:  python3-h5py
BuildRequires:  python3-pillow

%global _description %{expand:
spec2nii converts MR spectroscopy (MRS) and spectroscopic imaging data from vendor formats to NIfTI-MRS, the standard container used by FSL-MRS and
other tools: Siemens twix and DICOM, Philips SDAT/SPAR and DICOM, GE P-files, Bruker, Varian, UIH, jMRUI and LCModel formats.}

%description %_description

%package -n python3-%{pypi_name}
Summary:        %{summary}

%description -n python3-%{pypi_name} %_description

%prep
%autosetup -n %{pypi_name}-%{version}
# upstream pins brukerapi >=0.2.5,<0.2.6; Fedora ships 0.2.6. Relax the upper bound only; tests/test_bruker.py decides whether 0.2.6 is good enough.
grep -q '"brukerapi>=0.2.5,<0.2.6"' pyproject.toml
sed -i 's/"brukerapi>=0.2.5,<0.2.6"/"brukerapi>=0.2.5"/' pyproject.toml
# upstream also wants textual >=7.4,<9 (used only by bruker.py, for the interactive --inspect browser); Fedora has textual 4.0. The widgets bruker.py
# imports exist in 4.0, so relax the lower bound; whether --inspect itself works on 4.0 is NOT covered by the test suite.
grep -q '"textual>=7.4.0,<9"' pyproject.toml
sed -i 's/"textual>=7.4.0,<9"/"textual>=4.0"/' pyproject.toml

# upstream's package search excludes only tests*, so its documentation folder notes/ is installed into site-packages as a top-level package "notes"
grep -q 'exclude = \["tests\*"\]' pyproject.toml
sed -i 's/exclude = \["tests\*"\]/exclude = ["tests*", "notes*"]/' pyproject.toml

%generate_buildrequires
export SETUPTOOLS_SCM_PRETEND_VERSION=%{version}
%pyproject_buildrequires

%build
export SETUPTOOLS_SCM_PRETEND_VERSION=%{version}
%pyproject_wheel

%install
%pyproject_install
%pyproject_save_files %{pypi_name}

%check
%pyproject_check_import
# Upstream keeps its test data (1.3 GB packed) in a separate repository (git.fmrib.ox.ac.uk/wclarke/spec2nii_test_data, a submodule the sdist omits),
# and nearly every test reads it, so only these six run here (the others fail with FileNotFoundError on the missing data, not on the converters).
# The data-backed suite was run once locally against the real data; see the changelog.
%pytest -v \
    tests/test_ge_pfile.py::test_mm_mega tests/test_ge_pfile.py::test_mm_press \
    tests/test_other_func.py::test_insert_not_nmrs tests/test_other_func.py::test_remove_zero_higher_dim_indices \
    tests/test_siemens_rda.py::test_csi_ve_against_dicom tests/test_siemens_rda.py::test_svs_ve_against_dicom

%files -n python3-%{pypi_name} -f %{pyproject_files}
%license LICENSE NOTICE
%doc README.md CHANGELOG.md
%{_bindir}/spec2nii

%changelog
* Fri Oct 09 2026 Morgan Hough <morgan.hough@gmail.com> - 0.8.15-1
- Initial package: spec2nii 0.8.15 (free project, BSD-3-Clause). Two dependency pins are relaxed because Fedora is behind: brukerapi <0.2.6 (Fedora has 0.2.6) and
  textual >=7.4 (Fedora has 4.0; used only by the interactive --inspect browser in bruker.py, which the tests do not exercise). The upstream suite, including
  tests/test_bruker.py, runs in %%check against them.
- Validation against upstream's real test data (spec2nii_test_data, 3.4 GB packed, run once locally in a clean chroot with this package installed, not in the build):
  92 of 105 tests pass. 12 fail only because they call `fsleyes render` (the orientation tests; FSLeyes was not installed in that chroot). 1 genuinely fails:
  tests/test_bruker.py::test_rawdata_pv_360_1_1 (ParaVision 360.1.1 raw data) raises brukerapi MissingProperty "numpy_dtype" under brukerapi 0.2.6, the version
  Fedora ships; upstream pins brukerapi <0.2.6 and that is the likely reason. Every other Bruker test passes, so other Bruker data is unaffected. %%check here runs
  only the six tests that need no data.
- Also excludes upstream's stray top-level `notes` package (its docs folder, installed into site-packages by upstream's package search).