%global pypi_name abagen

Name:           python-%{pypi_name}
Version:        0.1.3
Release:        2%{?dist}
Summary:        Allen Human Brain Atlas gene expression, mapped to brain parcellations

License:        BSD-3-Clause
URL:            https://github.com/netneurolab/abagen
Source0:        %{pypi_source %{pypi_name} %{version}}
# The vendored versioneer.py calls configparser.SafeConfigParser, removed in Python
# 3.12, so the sdist cannot be built at all on a current Python.
Patch0:         abagen-versioneer-configparser.patch
# Six modules import pkg_resources, which setuptools removed and Fedora 45 no
# longer ships, so abagen was not importable there at all.
Patch1:         abagen-importlib-resources.patch

BuildArch:      noarch
BuildRequires:  python3-devel
BuildRequires:  pyproject-rpm-macros

%description
abagen turns the Allen Human Brain Atlas microarray data into regional gene
expression matrices: it fetches the donor data, applies the probe-selection,
normalisation and sample-assignment choices that the literature disagrees about, and
writes a region-by-gene matrix for whatever parcellation you hand it. The point is
that those choices are explicit and reproducible rather than buried in a script.

This is the freely licensed sibling of neuromaps from the same lab, and the natural
bridge between imaging and transcriptomics.

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

The Allen Atlas donor data is downloaded on first use rather than shipped: it is
roughly four gigabytes and has its own terms of use.

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

%generate_buildrequires
%pyproject_buildrequires

%build
%pyproject_wheel

%install
%pyproject_install
%pyproject_save_files -l abagen

%check
# The test suite downloads donor data from the Allen API, so it cannot run here.
# Import every module instead; that is what catches a missing dependency.
%pyproject_check_import -e 'abagen.tests*'
# The command line interface is the documented entry point, and it parses its
# arguments against the full option set, so this exercises more than an import.
PYTHONPATH=%{buildroot}%{python3_sitelib} %{buildroot}%{_bindir}/abagen --help >/dev/null

%files -n python3-%{pypi_name} -f %{pyproject_files}
%license LICENSE
%doc README.rst
%{_bindir}/abagen

%changelog
* Sun Sep 27 2026 Morgan Hough <morgan.hough@gmail.com> - 0.1.3-2
- Replace pkg_resources with importlib.resources. setuptools removed pkg_resources
  and Fedora 45 no longer provides it, so -1 built on f44 and failed on f45 with
  ModuleNotFoundError before any of abagen's own logic ran -- abagen/__init__.py
  reaches it through abagen.mouse, so nothing was importable.
- Same defect shape as python-nrtest earlier this week, and the same fix:
  importlib.resources has been standard library since 3.9, so no version guard is
  needed. A shim keeps the resource_filename call sites unchanged.

* Sun Sep 27 2026 Morgan Hough <morgan.hough@gmail.com> - 0.1.3-1
- Initial package. BSD-3-Clause, so it goes in the main repository rather than
  alongside neuromaps in nonfree; nibabel, numpy, pandas and scipy are all in Fedora,
  so nothing is bundled and nothing needed packaging first.
- Relevant to the lab's own work: this is the imaging-to-transcriptomics bridge, and
  it pairs with the organoid RNA-seq direction rather than only with surface analysis.