%global srcname pymetadata

Name:           python-%{srcname}
Version:        0.8.2
Release:        1%{?dist}
Summary:        Metadata, annotations and COMBINE archives for systems-biology models

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

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

%global _description %{expand:
pymetadata is Matthias Konig's metadata layer for the COMBINE standards: it
reads and writes COMBINE archives (OMEX) with their manifest and metadata,
models MIRIAM-qualified annotations as typed objects, resolves identifiers
against the identifiers.org registry, and ships the SBO, KISAO and other
ontology term sets as importable modules.

Web-service lookups (identifiers.org, OLS, ChEBI, UniChem) are cached on
disk, and an unreachable service falls back to the cached answer with a
warning rather than an error, so an offline machine keeps working.

It is the annotation layer sbmlutils builds on.}

%description %_description

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

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

%prep
%autosetup -p1 -n %{srcname}-%{version}
# Upstream's three runtime floors are the versions current on its release day,
# not an API requirement: the whole surface it uses is BaseModel and
# PrivateAttr from pydantic, Console, RichHandler and Theme from rich, and
# requests.get with an adapter. All of it predates these floors by years.
# Fedora 44 carries pydantic 2.12.5, rich 14.3.2 and requests 2.33.1, so the
# floors as written would make the package unbuildable there and on 43.
# %%check is the evidence that the relaxed floors hold: upstream's suite runs
# against whatever the chroot actually has.
# 0.8.2 relaxes three: pydantic is now >=2.12, which Fedora 44's 2.12.5 meets, and
# certifi>=2026.10.19 is new, which excludes the CA store with the
# compromised emSign roots (GHSA-6q48-6c7w-9gw2). pymetadata never imports
# certifi; requests reaches it, and Fedora's python3-certifi hands out the
# system bundle (/etc/pki), which ca-certificates keeps current, so the PyPI
# bundle that floor protects is not what runs here.
for d in 'rich>=15.0.0:rich>=13' 'requests>=2.34.2:requests>=2.31' \
         'certifi>=2026.10.19:certifi>=2025'; do
  old=${d%%:*}; new=${d#*:}
  grep -q "\"$old\"," pyproject.toml || { echo "runtime floor '$old' not found" >&2; exit 1; }
  sed -i "s/\"$old\",/\"$new\",/" pyproject.toml
done

%generate_buildrequires
%pyproject_buildrequires

%build
%pyproject_wheel

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

%check
# Upstream's suite, offline: 0.8.2 gives 197 pass, 140 deselected (0.8.0: 189 and 136). Every deselected case
# belongs to a test function that asks a web service for an answer it does not
# cache in the source tree, and a build root has no network: identifiers.org
# for every resource normalisation, plus ChEBI, OLS, UniChem, and one OMEX
# archive fetched from a GitHub release. Deselection is by function, so a few
# parameter sets that happened to answer from cache go with them.
#
# What is left still covers the offline behaviour that matters here, including
# test_offline.py, which asserts that an unreachable service falls back to
# cached content rather than failing, and the whole OMEX archive layer.
%pytest -q tests \
    --deselect tests/test_chebi.py::test_chebi \
    --deselect tests/test_ols.py::test_ols_query \
    --deselect tests/test_ols.py::test_annotation_data_to_dict \
    --deselect tests/test_registry.py::test_registry \
    --deselect tests/test_unichem.py::test_get_sources \
    --deselect tests/test_unichem.py::test_get_source_exists \
    --deselect tests/test_unichem.py::test_get_source_missing \
    --deselect tests/test_unichem.py::test_query_xref_for_inchikey_cache \
    --deselect tests/test_unichem.py::test_query_xref_for_inchikey_no_cache \
    --deselect tests/test_unichem.py::test_query_xrefs_server_error \
    --deselect tests/test_omex.py::test_omex_from_url \
    --deselect tests/core/test_annotation.py::test_rdf_annotation \
    --deselect tests/core/test_annotation.py::test_check_term_pass \
    --deselect tests/core/test_annotation.py::test_resource_normalized \
    --deselect tests/core/test_annotation.py::test_resource_normalized_keeps_resource \
    --deselect tests/core/test_annotation.py::test_resource_normalized_roundtrip \
    --deselect tests/core/test_annotation.py::test_resource_normalized_registry \
    --deselect tests/core/test_annotation.py::test_annotation_data_carries_the_ols_term \
    --deselect tests/core/test_annotation.py::test_check_miriam_term_full_match \
    --deselect tests/core/test_annotation.py::test_replaced_collection_before_shortening

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

%changelog
* Fri Oct 23 2026 Morgan Hough <morgan.hough@gmail.com> - 0.8.2-1
- Update to 0.8.2 (sbmlutils 0.17.0 requires >= 0.8.0; 0.8.2 is current).
- Runtime floors: pydantic is now >=2.12 (Fedora has 2.12.5), so that relaxation
  goes; rich and requests stay; certifi>=2026.10.19 is new and relaxed to >=2025, a security
  floor on the PyPI CA bundle, which Fedora's python3-certifi does not use.
  urllib3>=2.5.0 and the pydantic floor are met by Fedora 44 as it stands.
- Offline on f44 (no network namespace): 197 pass, 140 deselected, none failing.

* Wed Oct 07 2026 Morgan Hough <morgan.hough@gmail.com> - 0.8.0-1
- Update to 0.8.0 (sbmlutils 0.16.0 requires pymetadata >= 0.8.0). The three
  relaxed runtime floors are unchanged and still match the sdist's pyproject.
- Deselect five more cases that ask registry.api.identifiers.org
  (test_check_miriam_term_full_match, test_replaced_collection_before_shortening,
  test_annotation_data_carries_the_ols_term); a mock build root has no network.
  Offline on f44: 189 pass, 136 deselected, no failures.

* Fri Sep 25 2026 Morgan Hough <morgan.hough@gmail.com> - 0.6.6-1
- Initial package: pymetadata 0.6.6, the COMBINE archive and annotation
  layer. Net-new to Fedora; pure Python, and the prerequisite sbmlutils is
  missing.
- Relax three runtime floors that track upstream's release date rather than
  any API it uses; the upstream suite in %%check is the evidence. On Fedora 44
  (pydantic 2.12.5, rich 14.3.2, requests 2.33.1) every offline case passes.
- Deselect the test functions that query identifiers.org, ChEBI, OLS or
  UniChem, or fetch an archive over HTTP: 106 pass, 99 deselected. Running
  them offline cost 6m45s of DNS timeouts and 93 failures.