%bcond_without tests
%global debug_package %{nil}

%global pypi_name snakemake

%global _description %{expand:
The Snakemake workflow management system is a tool to create reproducible and
scalable data analyses. Workflows are described via a human readable, Python
based language. They can be seamlessly scaled to server, cluster, grid and
cloud environments, without the need to modify the workflow definition.
Finally, Snakemake workflows can entail a description of required software,
which will be automatically deployed to any execution environment.}

Name:           %{pypi_name}
Version:        6.4.1
Release:        1%{?dist}
Summary:        Workflow management system to create reproducible and scalable data analyses

License:        MIT
URL:            https://snakemake.readthedocs.io/en/stable/index.html
Source0:        https://github.com/%{pypi_name}/%{pypi_name}/archive/v%{version}/%{pypi_name}-%{version}.tar.gz

BuildArch:      noarch

BuildRequires:  python3-devel
BuildRequires:  %{py3_dist setuptools}
BuildRequires:  make

Requires:       %{py3_dist smart_open}

%if %{with tests}
BuildRequires:  %{py3_dist pytest}
BuildRequires:  %{py3_dist pytest-cov}
BuildRequires:  %{py3_dist requests-mock}
BuildRequires:  %{py3_dist filelock}
BuildRequires:  %{py3_dist datrie}
BuildRequires:  %{py3_dist ratelimiter}
BuildRequires:  %{py3_dist pyyaml}
BuildRequires:  %{py3_dist numpy}
BuildRequires:  %{py3_dist pandas}
BuildRequires:  %{py3_dist jsonschema}
BuildRequires:  %{py3_dist networkx}
BuildRequires:  %{py3_dist graphviz}
BuildRequires:  %{py3_dist GitPython}
BuildRequires:  %{py3_dist configargparse}
BuildRequires:  %{py3_dist appdirs}
BuildRequires:  %{py3_dist docutils}
BuildRequires:  %{py3_dist boto3}
BuildRequires:  %{py3_dist smart_open}
%endif

%py_provides %{pypi_name}

%description %_description

%package -n snakemake-doc

Summary:        %{summary}

BuildArch:      noarch

BuildRequires:  %{py3_dist sphinx}
BuildRequires:  %{py3_dist sphinx-argparse}
BuildRequires:  %{py3_dist sphinx_rtd_theme}
BuildRequires:  %{py3_dist recommonmark}
BuildRequires:  %{py3_dist docutils}
BuildRequires:  %{py3_dist configargparse}
BuildRequires:  %{py3_dist appdirs}

%description -n snakemake-doc %_description

%prep
%autosetup -n %{pypi_name}-%{version}

rm -rf %{pypi_name}.egg-info
find %{pypi_name}/ -name "*.cpp" -print -delete
find . -type f -name "*.py" -exec sed -i '/^#![  ]*\/usr\/bin\/env.*$/ d' {} 2>/dev/null ';'

# Remove shebang from non-executable script
sed -i '1d' snakemake/executors/jobscript.sh

# Rename subprocess call 'python' to 'python3'
sed -i 's/python/python3/g' tests/test_linting.py

# Remove napoleon template as it is not used.
sed -i '39d' docs/conf.py
cat docs/conf.py

%build
%py3_build

pushd docs/
mkdir -p _build/doctrees
mkdir -p _build/html
make %{?_smp_mflags} html
popd

%install
%py3_install

%check
%if %{with tests}
export PYTHONPATH=%{buildroot}%{python3_sitelib}

# tests/test_tibanna needs a network connection, therefore disabled.
# tests/test_google_lifesciences.py requires the Google Cloud library for python
# tests/test_tes.py requires py-tes. Currently not packaged for Fedora
pytest-%{python3_version}\
	--ignore tests/test_google_lifesciences.py\
	--deselect tests/test_tibanna.py\
	--deselect tests/test_tes.py
%endif

%files
%doc README.md
%license LICENSE.md
%{_bindir}/%{pypi_name}
%{_bindir}/%{pypi_name}-bash-completion
%{python3_sitelib}/%{pypi_name}/
%{python3_sitelib}/%{pypi_name}-%{version}-py%{python3_version}.egg-info/

%files -n snakemake-doc
%license LICENSE.md
%doc docs/_build/html docs/_build/doctrees

%changelog
* Thu Jun 17 2021 Aniket Pradhan <major AT fedoraproject DOT org> - 6.4.1-1
- Initial build