%global srcname pypesto
%global ghname  pyPESTO

Name:           python-%{srcname}
Version:        0.7.0
Release:        1%{?dist}
Summary:        Python-based parameter estimation toolbox

License:        BSD-3-Clause
URL:            https://github.com/ICB-DCM/pyPESTO
# Not the sdist: PyPI's omits test/.
Source:         %{url}/archive/v%{version}/%{ghname}-%{version}.tar.gz

BuildArch:      noarch
BuildRequires:  python3-devel
BuildRequires:  pyproject-rpm-macros
# %%check. The suite imports autograd in its helpers; emcee, cma and NLopt are
# the optional optimisers and samplers that have tests which can run here.
BuildRequires:  python3-pytest
BuildRequires:  python3-sympy
BuildRequires:  python3-pytest-rerunfailures
BuildRequires:  python3-autograd
BuildRequires:  python3-emcee
BuildRequires:  python3-cma
BuildRequires:  python3-NLopt

%global _description %{expand:
pyPESTO is a toolbox for parameter estimation: define an objective, a prior
and bounds as a problem; optimise it from many start points with SciPy,
Ipopt, dlib, NLopt, CMA-ES or particle swarms; profile the result for
identifiability and confidence intervals; and sample the posterior with
adaptive Metropolis, parallel tempering, emcee or nested sampling. Objectives
can be hand-written Python functions, PEtab problems, or ODE models simulated
by AMICI.

Fedora's package covers the core toolbox. The PEtab import needs
python3-petab, which is pulled in as a weak dependency. AMICI, JAX, fides,
PyMC, dynesty and petab-select are not packaged, so objectives built on them
are not available.}

%description %_description

%package -n     python3-%{srcname}
Summary:        %{summary}
Recommends:     python3-petab
Recommends:     python3-emcee
Recommends:     python3-cma
Recommends:     python3-NLopt
Recommends:     python3-dlib

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

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

%generate_buildrequires
%pyproject_buildrequires

%build
%pyproject_wheel

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

%check
# Upstream's suite is mostly written against optional dependencies Fedora does
# not carry (AMICI, JAX, fides, PyMC, dynesty, petab-select, benchmark models),
# and 19 of its 37 test files do not even import without them. The run below is
# the part that needs only what is packaged: priors, problems, objectives,
# histories, workflows, profiles, the optimiser interface and the samplers.
# Deselected inside those files:
#   test_jax                        - JAX
#   ResModeHistoryTest, test_hdf5_amici_history, test_laplace_approximation_log_evidence - AMICI
#   test_fides_optimizer_support    - fides
#   Pymc and Dynesty/dynesty cases  - PyMC, dynesty
export MPLBACKEND=Agg
%pytest -q -o addopts= --import-mode=importlib \
    test/base/test_logging.py test/base/test_prior.py test/base/test_problem.py \
    test/base/test_workflow.py test/base/test_x_fixed.py test/base/test_objective.py \
    test/base/test_history.py test/profile \
    test/optimize/test_optimizer_common_interface.py test/sample/test_sample.py \
    --deselect test/base/test_objective.py::test_jax \
    --deselect test/base/test_history.py::ResModeHistoryTest \
    --deselect test/base/test_history.py::test_hdf5_amici_history \
    --deselect test/optimize/test_optimizer_common_interface.py::TestOptimizerMaxiterInterface::test_fides_optimizer_support \
    --deselect test/optimize/test_optimizer_common_interface.py::TestOptimizerMaxtimeInterface::test_fides_optimizer_support \
    --deselect test/sample/test_sample.py::test_laplace_approximation_log_evidence \
    -k 'not Pymc and not Dynesty and not dynesty'

%files -n python3-%{srcname} -f %{pyproject_files}
%doc README.md CHANGELOG.rst

%changelog
* Fri Oct 23 2026 Morgan Hough <morgan.hough@gmail.com> - 0.7.0-1
- Initial package: pyPESTO 0.7.0 (BSD-3-Clause, LICENSE). Net-new to Fedora;
  pure Python. All required dependencies are already in Fedora at versions
  above upstream's floors (numpy, scipy, pandas, cloudpickle, matplotlib,
  more-itertools, seaborn, h5py 3.15.1 clear of the !=3.15.0 exclusion, tqdm,
  tabulate), so no floor is relaxed.
- Source is the GitHub tag, not the sdist, which has no tests.
- Offline on f44 (loopback up): 237 pass, 39 deselected, 0 failed, with
  python3-autograd (new, 1.9.1), emcee, cma and NLopt present. The whole
  suite does not run: AMICI, JAX, fides, PyMC, dynesty, petab-select and
  benchmark_models_petab are not in Fedora and 19 test files need them.
- BuildRequires python3-sympy: %%check failed to import it on every chroot.