%global srcname vivarium-core

Name:           python-%{srcname}
Version:        1.6.5
Release:        1%{?dist}
Summary:        Framework for composing and simulating multi-scale models of cells

# LICENSE.txt in the sdist is the full Apache License 2.0 text. PyPI's metadata says
# "License: MIT" and carries an MIT classifier; the file is the grant and the metadata is
# a stale label, so this follows the file.
License:        Apache-2.0
URL:            https://github.com/vivarium-collective/vivarium-core
Source:         %{pypi_source %{srcname}}

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

%global _description %{expand:
Vivarium is a framework for building multi-scale, agent-based and
process-based models of cells and their environments. Models are written as
processes that read and write to a shared hierarchical store; the engine
schedules them, handles their timescales, and emits the results. It is the
composition and simulation framework of the Build-A-Cell toolchain, beside
BioCRNpyler, bioscrape and SubSBML.

Upstream's `emitter` can write to a MongoDB database; the package works without
one, using the in-memory emitter.}

%description %_description

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

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

%prep
%autosetup -p1 -n %{srcname}-%{version}
# Upstream caps python_requires at <3.14, with classifiers stopping at 3.13. That is the
# range it was TESTED on, not a measured break: run with the cap bypassed on Python 3.14.7
# (f44) and 3.15.0rc2 (f45), every import passes and 110 of the 115 upstream tests pass,
# identically on both (the other five are listed in %%check). Left in place the cap makes
# the package uninstallable on every Fedora release this COPR builds for. DELETE WHEN
# upstream lifts the cap.
n=$(grep -c "python_requires='>=3.10, <3.14'," setup.py || true)
[ "$n" = 1 ] || { echo "ERROR: expected exactly one python_requires line, found $n" >&2; exit 1; }
sed -i "s/python_requires='>=3.10, <3.14',/python_requires='>=3.10',/" setup.py
# An `if`, not `grep -q ... && { ...; exit 1; }`: when the cap is gone grep returns 1, and as
# the LAST command of %%prep that 1 becomes the script's exit status and fails the build.
if grep -q "<3.14" setup.py; then echo "ERROR: python_requires cap is still in setup.py" >&2; exit 1; fi

%generate_buildrequires
%pyproject_buildrequires

%build
%pyproject_wheel

%install
%pyproject_install
%pyproject_save_files vivarium

%check
%pyproject_check_import
# Upstream keeps most of its tests INSIDE the module files (test_* functions beside the code),
# which pytest's default collection skips: the default finds 12 of 115. -o python_files='*.py'
# collects them all. Run against the INSTALLED package from a scratch directory, because
# `python -m pytest` puts the current directory first on sys.path and the source tree would
# otherwise shadow the buildroot.
#
# Excluded, and why (counts measured on f44 and f45):
#  * -k ...      the tests that talk to a MongoDB server or its emitter; there is none in a build
#  * test_large_emits, test_query_db   -> pymongo.errors: need that same server
#  * plots/topology.py::test_merge_port_topology -> IndexError raised inside networkx's own
#      draw_networkx_nodes ("boolean index did not match"): vivarium passes node_shape in a form
#      networkx 3.6.1 indexes differently. A plotting incompatibility, not a Python-version one,
#      and the same on 3.14 and 3.15. Report upstream; delete the deselect when it is fixed.
# Result with these exclusions: 110 passed.
cd "$(mktemp -d)"
# Deselected by NAME with -k, not by --deselect node id: against an installed package the node
# ids carry the install path, so an exact-path --deselect can silently match nothing.
%pytest --pyargs vivarium -o python_files='*.py' \
    -k "not mongo and not Mongo and not database and not emitter and not Database and not test_large_emits and not test_query_db and not test_merge_port_topology"

%files -n python3-%{srcname} -f %{pyproject_files}
%license LICENSE.txt
%doc README.md AUTHORS.md

%changelog
* Mon Oct 05 2026 Morgan Hough <morgan.hough@gmail.com> - 1.6.5-1
- Initial package: vivarium-core 1.6.5, one of the four projects on the Build-A-Cell
  tutorial-models page (the other three, biocrnpyler, bioscrape and subsbml, are already
  built here). It was recorded as blocked by python_requires <3.14.
- That cap is metadata, not a measured failure, so %%prep removes it with a guard that
  fails the build if upstream reformats setup.py. Evidence: with the cap bypassed on
  Python 3.14.7 and 3.15.0rc2, all imports pass and 110 of 115 upstream tests pass on both.
- %%check runs the in-module tests (115, not the 12 default collection finds) against the
  installed package, and excludes five: two need a MongoDB server, two more are selected out
  by the same keyword filter, and test_merge_port_topology fails inside networkx 3.6.1's own
  plotting code.
- Licence follows LICENSE.txt (Apache-2.0); PyPI metadata says MIT.