%global srcname sbmlutils

Name:           python-%{srcname}
Version:        0.17.0
Release:        2%{?dist}
Summary:        Python utilities for creating, reading, annotating and reporting SBML models

License:        MIT
URL:            https://github.com/matthiaskoenig/sbmlutils
Source:         %{pypi_source %{srcname}}
# Snapshot of the identifiers.org registry (resolutionApi/getResolverDataset,
# 865 namespaces, fetched 2026-09-25 through pymetadata), CC BY 4.0 per
# https://docs.identifiers.org/pages/terms_of_use.html. Test data only: it is
# not installed. See %%check.
Source1:        identifiers_registry-2026-09-25.json

BuildArch:      noarch
BuildRequires:  python3-devel
BuildRequires:  pyproject-rpm-macros
# No python3dist() tag in Fedora for the PyPI name python-libsbml (see %%prep).
BuildRequires:  python3-libsbml
# %%check: conftest.py imports matplotlib to force the Agg backend, and the
# example and roundtrip tests simulate with roadrunner. Both are upstream
# "examples" extras rather than runtime dependencies of the library.
BuildRequires:  python3-pytest
BuildRequires:  python3-matplotlib
BuildRequires:  python3-roadrunner

%global _description %{expand:
sbmlutils is Matthias Konig's toolbox for SBML: a factory that builds models
from plain Python objects and writes valid SBML, a validator that reports
libsbml's findings readably, HTML model reports, annotation of models from
spreadsheets, and converters to and from Antimony, XPP and ODE code. It
covers the L3 packages -- comp, fbc, distrib, layout -- rather than the core
alone.

It is the model-authoring counterpart to the simulation stack: build and
annotate here, simulate with roadrunner or COPASI.}

%description %_description

%package -n     python3-%{srcname}
Summary:        %{summary}
# Runtime dependency rpm cannot generate: Fedora's python3-libsbml carries no
# python3dist() tag for the PyPI name python-libsbml. It belongs here and not
# in the preamble -- this spec never builds a python-sbmlutils package, so a
# preamble Requires ships on nothing.
Requires:       python3-libsbml

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

%prep
%autosetup -p1 -n %{srcname}-%{version}
# python-libsbml has no dist tag in Fedora; declared by hand above. Upstream
# floors it at 5.21.2, which is what Fedora rawhide carries; 43 to 45 are on
# 5.20.5. %%check is what decides whether that matters on a given branch: the
# suite either passes against the libsbml the chroot has or the build fails
# there, which is the intended signal.
grep -qP '^\t"python-libsbml>=5\.21\.2",$' pyproject.toml || { echo "python-libsbml dependency not found" >&2; exit 1; }
sed -i '/^\t"python-libsbml>=5\.21\.2",$/d' pyproject.toml
# Three more floors are the versions current on upstream's release day rather
# than an API requirement. Fedora 44 carries pint 0.25.2 and xmltodict 0.14.2,
# and certifi 2026.01.04. What sbmlutils uses of each: UnitRegistry and
# UndefinedUnitError from pint; xmltodict.parse; and of certifi nothing at all,
# it is requests' CA bundle, floored for GHSA-6q48-6c7w-9gw2 (the emSign roots),
# and Fedora's python3-certifi serves the system bundle that ca-certificates
# keeps current. All of the API predates these floors by years.
for d in 'pint>=0.25.3:pint>=0.25' 'xmltodict>=1.0.2:xmltodict>=0.14' \
         'certifi>=2026.10.19:certifi>=2025'; do
  old=${d%%:*}; new=${d#*:}
  grep -qP "^\t\"$old\",\$" pyproject.toml || { echo "runtime floor '$old' not found" >&2; exit 1; }
  sed -i "s/^\t\"$old\",\$/\t\"$new\",/" pyproject.toml
done

%generate_buildrequires
%pyproject_buildrequires

%build
%pyproject_wheel

%install
%pyproject_install
%pyproject_save_files -l %{srcname}

%check
# Fedora's libsbml is built with the seven stable L3 packages -- LAYOUT, QUAL,
# COMP, FBC, RENDER, GROUPS, MULTI -- and not DISTRIB, although libsbml's own
# CMakeLists lists distrib among its stable packages (see the %%cmake line in
# Fedora's libsbml.spec). sbmlutils reads
# libsbml.DISTRIB_UNCERTTYPE_* at class-definition time in factory.py, so
# without DISTRIB the module cannot even be imported. Diagnose that here rather
# than leaving 19 files erroring at collection with an AttributeError.
%{python3} -c 'import libsbml, sys; sys.exit(0 if hasattr(libsbml, "DISTRIB_UNCERTTYPE_COEFFIENTOFVARIATION") else 1)' || { \
    echo "This libsbml has no distrib package; sbmlutils cannot be imported." >&2; \
    echo "Fedora's libsbml needs -DENABLE_DISTRIB=ON. See the changelog." >&2; \
    exit 1; }

# Upstream's suite, minus two things it cannot read from a release artifact.
# tests/test_roundtrip.py reads the vendored SBML Test Suite 3.4.0 models and
# test_sbml_testsuite.py sweeps them; upstream's own [tool.hatch.build] exclude
# keeps those 56 MB out of both the sdist and the wheel, so they exist only in
# a git checkout. Against a distrib-enabled libsbml 5.21.2 the rest is green:
# 0.17.0 gives 1456 passed, 75 skipped, offline with loopback up.
# Two more cases read docs/ (interpolation.md, api/factory.md), which the sdist
# also leaves out.
# pymetadata downloads the identifiers.org registry at first use and caches it
# in ~/.cache/pymetadata; Copr and Koji builds are offline, so 119 tests and 10
# fixtures failed on f43 and f44 without it. pymetadata falls back to an
# outdated cached copy when the download fails, so seed one in a scratch HOME.
export HOME=$PWD/test-home
mkdir -p $HOME/.cache/pymetadata
cp %{SOURCE1} $HOME/.cache/pymetadata/identifiers_registry.json

# Deselected, on 0.17.0 against Fedora's libsbml:
# - tests/examples/test_example_scripts.py runs the examples in a subprocess
#   with PYTHONPATH replaced by the source tree, which hides the installed
#   package; the same examples run in-process in test_examples.py.
# - test_read_sbml_reads_a_file_without_an_xml_declaration expects libsbml to
#   report BadXMLDecl; Fedora's libsbml does not (cause not diagnosed).
# - test_demo_annotation uses Model.parameters, which Fedora's libsbml bindings
#   lack (AttributeError); the PyPI wheel passed it in the earlier venv run.
%pytest -q -m 'not sbml_testsuite' --ignore=tests/test_roundtrip.py \
    --ignore=tests/examples/test_example_scripts.py \
    --deselect 'tests/io/test_sbml.py::test_read_sbml_reads_a_file_without_an_xml_declaration' \
    --deselect tests/metadata/test_annotator.py::test_demo_annotation \
    --deselect tests/interpolation/test_interpolation_docs.py::test_guide_code_blocks_run \
    --deselect tests/test_factory_facade.py::test_api_reference_lists_the_classes_and_functions

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

%changelog
* Mon Oct 26 2026 Morgan Hough <morgan.hough@gmail.com> - 0.17.0-2
- %%check seeds pymetadata's identifiers.org registry cache from a bundled
  snapshot (CC BY 4.0, test data only): the offline builders failed 119 tests
  and 10 fixtures on f43/f44 without it. Deselect four environment-dependent
  tests (see %%check). The f45 segfaults were not sbmlutils: the f45 libsbml
  here was 5.21.2 against Fedora's 5.20.5, which antimony was built for.

* Fri Oct 23 2026 Morgan Hough <morgan.hough@gmail.com> - 0.17.0-1
- Update to 0.17.0. New runtime dependency sbmlode >= 0.2.0 (python-sbmlode,
  added to this repo) for the ODE export; pymetadata >= 0.8.0 and antimony
  >= 3.1.3 are met by python-pymetadata 0.8.2 and python3-antimony 3.2.0.
- Runtime floors: pydantic is no longer a dependency, so that relaxation goes.
  pint, xmltodict and certifi are relaxed (pint 0.25.2, xmltodict 0.14.2 and
  certifi 2026.01.04 are what Fedora 44 has); the rest are met as they stand.
- Still not buildable on any Fedora branch: libsbml has no distrib package.
  Verified against PyPI's python-libsbml 5.21.2 and libroadrunner 2.11.0 in a
  venv: 1456 passed, 75 skipped, 0 failed, offline with loopback up.
  %%check skips two cases that read docs/, which the sdist omits (the same
  reason the full docs tree is absent), plus the roundtrip file as before.

* Fri Sep 25 2026 Morgan Hough <morgan.hough@gmail.com> - 0.12.2-1
- Initial package: sbmlutils 0.12.2. Net-new to Fedora.
- NOT YET BUILDABLE ON ANY FEDORA BRANCH, and not for a version reason.
  Fedora's libsbml enables LAYOUT, QUAL, COMP, FBC, RENDER, GROUPS and MULTI
  and not DISTRIB, on 44 and on rawhide alike (checked in the shipped
  libsbml.py of both python3-libsbml-5.20.5-12.fc44 and
  python3-libsbml-5.21.2-1.fc46). sbmlutils names libsbml's DISTRIB_UNCERTTYPE
  constants while defining a class in factory.py, so the module is unimportable
  without them and 19 test files error at collection. The fix is one flag in
  Fedora's libsbml spec, -DENABLE_DISTRIB=ON; the source tarball already
  carries src/sbml/packages/distrib. %%check diagnoses the condition rather
  than letting it surface as an AttributeError.
- Verified that DISTRIB is the only blocker: with PyPI's python-libsbml 5.21.2,
  which does enable it, the suite gives 899 passed, 76 skipped, 57 failed, and
  every one of the 57 is tests/test_roundtrip.py reading an SBML Test Suite
  model that upstream's hatch config excludes from the sdist and the wheel.
  That file and the sbml_testsuite sweep are the only things %%check skips.
- Seven runtime floors relaxed or dropped: python-libsbml has no dist tag in
  Fedora and is declared by hand, and six others (pydantic, pint, rich,
  markdown-it-py, xmltodict, requests) track upstream's release date rather
  than any API sbmlutils uses.