%global srcname fbc_curation

Name:           python-fbc-curation
Version:        0.3.2
Release:        1%{?dist}
Summary:        FROG reports for curating SBML flux balance constraints models

License:        MIT
URL:            https://github.com/matthiaskoenig/fbc_curation
Source:         %{pypi_source %{srcname}}

BuildArch:      noarch
BuildRequires:  python3-devel
BuildRequires:  pyproject-rpm-macros
# %%check
BuildRequires:  python3-pytest

%global _description %{expand:
fbc_curation creates and compares FROG reports (FBC ROG: flux balance,
reaction deletion, objective function and gene deletion results) for SBML
models that use the Flux Balance Constraints package. The report is a set of
files in a COMBINE archive that another tool can reproduce and compare,
which is how a model's expected behaviour is recorded for curation. The
reference implementation runs on COBRApy.

It installs two commands, `runfrog` to create a report for a model or archive
and `runfrog_examples` to rebuild the bundled examples.}

%description %_description

%package -n     python3-fbc-curation
Summary:        %{summary}

%description -n python3-fbc-curation %_description

%prep
%autosetup -p1 -n %{srcname}-%{version}
# fbc_curation 0.3.2 calls pymetadata.log.get_logger(), which pymetadata removed
# in 0.6.0 (0.5.12 has it; 0.6.0 to 0.8.2 do not), while its own requirement
# is the open-ended "pymetadata>=0.5.4". Against any pymetadata Fedora can carry
# nothing in the package imports. Use the standard library's logger, which is
# what pymetadata's own log.py now recommends for libraries.
for f in $(grep -rl 'log\.get_logger(__name__)' src); do
  grep -q '^from pymetadata import log$' $f || { echo "$f: expected import not found" >&2; exit 1; }
  sed -i -e 's/^from pymetadata import log$/import logging/' \
         -e 's/log\.get_logger(__name__)/logging.getLogger(__name__)/' $f
done
! grep -rq 'get_logger' src

%generate_buildrequires
%pyproject_buildrequires

%build
%pyproject_wheel

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

%check
# Upstream's suite: the FROG creation, the report, the worker, the CLI and the
# bundled examples. One case skips itself (cameo, an optional second curator).
%pytest -q tests

%files -n python3-fbc-curation -f %{pyproject_files}
%doc README.md
%{_bindir}/runfrog
%{_bindir}/runfrog_examples

%changelog
* Fri Oct 23 2026 Morgan Hough <morgan.hough@gmail.com> - 0.3.2-1
- Initial package: fbc_curation 0.3.2 (MIT, LICENSE). Net-new to Fedora; pure
  Python on COBRApy, pymetadata, optlang, sympy, pandas, pydantic and orjson,
  all of which are in Fedora or this repo at versions above its floors.
- Upstream defect handled in %%prep: the package imports
  pymetadata.log.get_logger, removed in pymetadata 0.6.0, so it cannot even be
  imported against the 0.8 series. Its pyproject leaves pymetadata open-ended
  (>=0.5.4). The five modules now use logging.getLogger(__name__); the only
  visible difference is that the old helper attached a rich handler, so
  runfrog logs only what the application configures. Worth an upstream issue.
- Upstream suite on f44 (loopback up) with pymetadata 0.8.2 and COBRApy 0.32.1:
  12 passed, 1 skipped, 0 failed.