%global srcname petab
%global ghname  libpetab-python

Name:           python-%{srcname}
Version:        0.9.0
Release:        1%{?dist}
Summary:        Parameter estimation tabular data (PEtab) format library

License:        MIT
URL:            https://github.com/PEtab-dev/libpetab-python
# Not the sdist: PyPI's omits tests/ (and the lexer .interp/.tokens files).
Source:         %{url}/archive/v%{version}/%{ghname}-%{version}.tar.gz

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. Upstream's "tests" extra also names pysb, petab_sciml and the
# petabtests suite from git; none is in Fedora and the files that need them are
# ignored below. python3-libCombine is the optional COMBINE-archive reader.
BuildRequires:  python3-pytest
BuildRequires:  python3-libCombine
BuildRequires:  python3-antimony
BuildRequires:  python3-scipy
BuildRequires:  python3-matplotlib
BuildRequires:  python3-seaborn

%global _description %{expand:
PEtab is a data format for specifying parameter estimation problems in
systems biology: an SBML model, a table of measurements, of observables, of
experimental conditions and of the parameters to estimate, tied together by a
YAML file. libpetab-python reads, writes, lints and manipulates PEtab problems
(versions 1 and 2), converts between them, simulates them with an SBML model
plus a simulator, and plots measurements and simulations.

It ships `petablint`, which validates a problem, and `petab_visualize`.}

%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-petab package.
Requires:       python3-libsbml
# Optional readers and plotting, imported lazily.
Recommends:     python3-matplotlib
Recommends:     python3-seaborn
Recommends:     python3-scipy
Recommends:     python3-libCombine

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

%prep
%autosetup -p1 -n %{ghname}-%{version}
# python-libsbml has no dist tag in Fedora; declared by hand above.
grep -q '^    "python-libsbml>=5.17.0",$' pyproject.toml || { echo "python-libsbml dependency not found" >&2; exit 1; }
sed -i '/^    "python-libsbml>=5.17.0",$/d' pyproject.toml
# Upstream pins the ANTLR runtime to exactly 4.13.1 because its generated
# lexer and parser (petab/v1/math/_generated) were produced by that ANTLR.
# Fedora has the 4.13.2 runtime. Same minor series, and the grammar tests in
# %%check pass against it, so the pin is relaxed to the series.
grep -q '"antlr4-python3-runtime==4.13.1",' pyproject.toml || { echo "antlr4 pin not found" >&2; exit 1; }
sed -i 's/"antlr4-python3-runtime==4.13.1",/"antlr4-python3-runtime>=4.13.1,<4.14",/' pyproject.toml

%generate_buildrequires
%pyproject_buildrequires

%build
%pyproject_wheel

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

%check
%{py3_test_envvars} %{python3} -c 'import petab.v1, petab.v2'
# Upstream's suite, offline. Files not collected because they import modules
# that are not in Fedora: test_math (petabtests, a git-only suite), test_priors
# (benchmark_models_petab), test_model_pysb and v2/test_lint (pysb), v2/test_sciml
# (petab_sciml). Deselected because a build root has no network: five *_remote
# and auto_upgrade cases fetch from GitHub; test_simulate_experiment_to_events
# needs COPASI's Python module, which is not in the build root.
%pytest -q -o addopts= --import-mode=importlib tests \
    --ignore=tests/v1/math/test_math.py \
    --ignore=tests/v1/test_model_pysb.py \
    --ignore=tests/v1/test_priors.py \
    --ignore=tests/v2/test_lint.py \
    --ignore=tests/v2/test_sciml.py \
    --deselect tests/v1/test_petab.py::test_load_remote \
    --deselect tests/v1/test_yaml.py::test_validate_remote \
    --deselect tests/v2/test_conversion.py::test_petab1to2_remote \
    --deselect tests/v2/test_core.py::test_load_remote \
    --deselect tests/v2/test_core.py::test_auto_upgrade \
    --deselect tests/v2/test_converters.py::test_simulate_experiment_to_events
# The console scripts, as installed.
PATH=%{buildroot}%{_bindir}:$PATH PYTHONPATH=%{buildroot}%{python3_sitelib} petablint --help >/dev/null

%files -n python3-%{srcname} -f %{pyproject_files}
%doc README.md CHANGELOG.md
%{_bindir}/petablint
%{_bindir}/petab_visualize

%changelog
* Fri Oct 23 2026 Morgan Hough <morgan.hough@gmail.com> - 0.9.0-1
- Initial package: libpetab-python 0.9.0 (MIT). Net-new to Fedora; pure Python.
  Prerequisite of pyPESTO's PEtab interface and of COPASI's petab importer.
- Source is the GitHub tag, not the sdist, which has no tests.
- Two dependency edits: python-libsbml has no dist tag in Fedora and is declared
  by hand; the exact pin antlr4-python3-runtime==4.13.1 becomes >=4.13.1,<4.14
  (Fedora has 4.13.2; the generated math lexer and parser pass the suite on it).
- Offline on f44 (loopback up): 199 pass, 3 skip, 6 deselected (five need the
  network, one needs COPASI's Python module); five test files not collected
  because pysb, petab_sciml, petabtests and benchmark_models_petab are not in
  Fedora.