%global pypi_name pyafq

Name:           python-%{pypi_name}
Version:        3.4
Release:        1%{?dist}
Summary:        Automated Fiber Quantification: tractometry of diffusion MRI

License:        BSD-2-Clause
URL:            https://github.com/tractometry/pyAFQ
Source0:        %{pypi_source %{pypi_name}}
# The citation export uses bibtexparser 2's parse_file/write_file/Library;
# Fedora ships bibtexparser 1.4. Same result through the 1.x load/dump API.
Patch0:         python-pyafq-bibtexparser1.patch

BuildArch:      noarch
BuildRequires:  python3-devel
BuildRequires:  pyproject-rpm-macros
BuildRequires:  python3dist(pytest)

%global _description %{expand:
pyAFQ runs the Automated Fiber Quantification pipeline on diffusion MRI:
tensor, kurtosis, CSD and multi-shell models; whole-brain tractography;
registration to a template; recognition and cleaning of the major white matter
bundles from waypoint ROIs, probability maps and endpoints; and tract profiles
of any scalar along each bundle, with interactive HTML visualisations. It runs
on a single subject (ParticipantAFQ, or the pyAFQ command) or on a BIDS
dataset (GroupAFQ).

Templates, atlases and neural network models are downloaded on first use
(TemplateFlow, figshare and others); "pyAFQ download" fetches them all in
advance. Static PNG export of the plotly figures needs kaleido, which is not
packaged; the HTML figures do not.}

%description %_description

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

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

# Runtime requirements, adjusted for what Fedora and this COPR provide:
# - python_requires "<3.14": no code reason found; Fedora 44 is Python 3.14 and
#   the import and test runs below are the check.
# - ray, toml: never imported.
# - kaleido ==1.4.0: only plotly's write_image (static PNG montages) uses it,
#   and kaleido 1.x drives a Chrome browser; not packaged.
# - plotly ==7.1.0: this COPR has 6.9; pyAFQ uses only long-stable plotly API.
# - imageio[ffmpeg,pyav]: the extras are for MP4 export (viz_backend "plotly");
#   the default "plotly_no_mp4" and GIF output need imageio alone.
# - bibtexparser >=2.0: see Patch0.
sed -i \
    -e 's/^python_requires = >=3.11, <3.14$/python_requires = >=3.11/' \
    -e '/^\tray$/d' \
    -e '/^\ttoml>=0.10.0$/d' \
    -e '/^\tkaleido==1.4.0$/d' \
    -e 's/^\tplotly==7.1.0$/\tplotly/' \
    -e 's/^\timageio\[ffmpeg,pyav\]>=2.0.0$/\timageio>=2.0.0/' \
    -e 's/^\tbibtexparser>=2.0$/\tbibtexparser/' \
    setup.cfg
! grep -E '<3\.14|^\t(ray|toml|kaleido)|plotly==|imageio\[|bibtexparser>=2' setup.cfg

%py3_shebang_fix bin

%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 AFQ

%check
export HOME=$PWD/home MPLBACKEND=Agg NO_ET=1
mkdir -p $HOME
# AFQ.viz.fury_backend needs fury 2 (this COPR has 0.12, the optional "fury"
# viz backend); AFQ.nn needs onnxruntime (optional "nn" extra).
# AFQ.utils.docs is a documentation helper that needs IPython.
%pyproject_check_import -e '*.tests*' -e 'AFQ.utils.docs' -e 'AFQ.viz.fury_backend' -e 'AFQ.nn*'
%{py3_test_envvars} %{buildroot}%{_bindir}/pyAFQ --help | grep -q 'pyAFQ download'
cd %{_builddir}
# Modules that download data at import or in every test (dipy's Stanford
# HARDI, TemplateFlow, figshare, OpenNeuro) are ignored or deselected: all 7
# failures of the full run in a network-less build were name-resolution errors.
%pytest -v -p no:cacheprovider --pyargs AFQ \
    --ignore-glob='*/AFQ/tests/test_registration.py' \
    --ignore-glob='*/AFQ/tests/test_api.py' \
    --ignore-glob='*/AFQ/tests/test_data.py' \
    --ignore-glob='*/AFQ/tests/test_nn.py' \
    --ignore-glob='*/AFQ/recognition/tests/test_recognition.py' \
    --ignore-glob='*/AFQ/recognition/tests/test_utils.py' \
    --ignore-glob='*/AFQ/nn/tests/*' \
    -k 'not (test_AFQ_custom_bundle_dict or test_BundleDict or test_gaussian_weights or test_matlab_tractography or test_matlab_mori_groups or test_density_map or test_transform_roi_real_mapping)'

%files -n python3-%{pypi_name} -f %{pyproject_files}
%license LICENSE
%doc README.md CHANGES.rst CITATION
%{_bindir}/pyAFQ
%{_bindir}/pyAFQ-bids

%changelog
* Fri Oct 16 2026 Morgan Hough <morgan.hough@gmail.com> - 3.4-1
- Initial package.