# These are problematic, sometimes they randomly fail or hang

%bcond_with xvfb_tests

%global desc \

The fslpy project is a FSL programming library written in Python. It is used by \

FSLeyes.

%global forgeurl https://github.com/pauldmccarthy/fslpy

Name:           python-fslpy

Version:        3.16.1

Release:        %autorelease

Summary:        The FSL Python Library

%global tag %{version}

%forgemeta

License:        Apache-2.0

URL:            %forgeurl

Source0:        %forgesource

BuildArch:      noarch

# fsleyes dropped it already, so this is a leaf package

# F40+

ExcludeArch:    %{ix86}

BuildRequires:  python3-devel

BuildRequires:  help2man

BuildRequires:  dcm2niix

BuildRequires:  %{py3_dist pytest}

%if %{with xvfb_tests}

BuildRequires:  xorg-x11-server-Xvfb

%endif

%description

%{desc}

%package -n python3-fslpy

Summary:        %{summary}

%description -n python3-fslpy

%{desc}

%pyproject_extras_subpkg -n python3-fslpy extra

%prep

%forgesetup

# remove pytest coverage etc bits

sed -i -e '/"coverage"/ d' \

    -e '/"pytest-cov"/ d' \

    -e '/addopts/ d' \

    pyproject.toml

# remove unneeded shebangs

find . -type f -name "*.py" -exec sed -i '/^#![  ]*\/usr\/bin\/env python$/ d' {} 2>/dev/null ';'

sed -i '/^#![  ]*\/usr\/bin\/env python3$/ d' fsl/wrappers/tbss.py

# some scripts have the shebang, so we correct these

find . -type f -name "*.py" -exec sed -i 's/#![  ]*\/usr\/bin\/env python$/#!\/usr\/bin\/python3/' {} 2>/dev/null ';'

%generate_buildrequires

%pyproject_buildrequires -x extra -x test

%build

%pyproject_wheel

%install

%pyproject_install

%pyproject_save_files fsl

# Remove test packages that are installed in site packages

rm -rvf %{buildroot}%{python3_sitelib}/fsl/tests

sed -r -i '/\bfsl\/tests\b/d' %{pyproject_files}

# generate man pages

# imglob does not have a --help

for binary in "atlasq" "atlasquery" "fsl_apply_x5" "fsl_ents" "fsl_convert_x5" "imcp" "immv" "resample_image" "Text2Vest" "Vest2Text" "fsl_abspath" "imln" "imtest" "remove_ext"

do

    echo "Generating man page for ${binary// /-/}"

    PYTHONPATH="$PYTHONPATH:%{buildroot}/%{python3_sitelib}/" PATH="$PATH:%{buildroot}/%{_bindir}/" help2man --no-info --no-discard-stderr --name="${binary}" --version-string="${binary} %{version}" --output="${binary// /-}.1" "${binary}"

    cat "${binary// /-}.1"

    install -t '%{buildroot}%{_mandir}/man1' -p -m 0644 -D "${binary// /-}.1"

done

# do not have a --help

for binary in "imglob" "imrm"

do

    echo "Generating man page for ${binary// /-/}"

    PYTHONPATH="$PYTHONPATH:%{buildroot}/%{python3_sitelib}/" PATH="$PATH:%{buildroot}/%{_bindir}/" help2man --help-option=" " --no-info --no-discard-stderr --name="${binary}" --version-string="${binary} %{version}" --output="${binary// /-}.1" "${binary}"

    cat "${binary// /-}.1"

    install -t '%{buildroot}%{_mandir}/man1' -p -m 0644 -D "${binary// /-}.1"

done

%check

%if %{with xvfb_tests}

# From https://git.fmrib.ox.ac.uk/fsl/fslpy/blob/master/.ci/test_template.sh

xvfb-run pytest-3 tests/test_idle.py

sleep 10

# Sometimes fails, sometimes passes

xvfb-run pytest-3 tests/test_platform.py || exit 0

%endif

# https://github.com/pauldmccarthy/fslpy/issues/17

# Ignore tests that have already been done

# Ignore immv_imcp because it requires a "nobody" user

# Ignore tests that require downloading data.

# Ignore tests requiring trimesh

# Ignore test using dcm2niix

# Ignore intermittently failing test: https://github.com/pauldmccarthy/fslpy/issues/10

# Ignore submit tests

k="not longtest and not test_submit"

k="${k} and not test_FEATFSFDesign_firstLevelVoxelwiseEV"

k="${k} and not test_compressed_voxelwise_ev"

k="${k} and not test_image_readonly_compressed"

k="${k} and not test_runfunc"

k="${k} and not test_fslmaths_load"

k="${k} and not test_fileOrImage"

k="${k} and not test_fileOrThing_outprefix"

k="${k} and not test_fileOrThing_outprefix_pathlib"

k="${k} and not test_fileOrThing_outprefix_differentTypes"

k="${k} and not test_fileOrThing_outprefix_directory"

k="${k} and not test_chained_fileOrImageAndArray"

k="${k} and not test_fileOrThing_submit_cmdonly"

k="${k} and not test_fileOrImage_all_tempfiles_cleared"

k="${k} and not test_atlas"

k="${k} and not test_read_nifti"

k="${k} and not test_VoxelwiseEVs"

k="${k} and not test_imcp_shouldPass"

k="${k} and not test_immv_shouldPass"

k="${k} and not test_fileOrThing_chained_outprefix"

# requires an FSL installation

k="${k} and not test_cluster"

# unable to find tests module

k="${k} and not test_func_to_cmd"

%{pytest} fsl/tests  -k "${k}" \

  --ignore=fsl/tests/test_idle.py --ignore=fsl/tests/test_platform.py \

  --ignore=fsl/tests/test_atlases.py \

  --ignore=fsl/tests/test_atlases_query.py \

  --ignore=fsl/tests/test_scripts/test_atlasq_list_summary.py \

  --ignore=fsl/tests/test_scripts/test_atlasq_ohi.py \

  --ignore=fsl/tests/test_scripts/test_atlasq_query.py \

  --ignore=fsl/tests/test_dicom.py \

  --ignore=fsl/tests/test_scripts/test_fsl_apply_x5.py \

  --ignore=fsl/tests/test_scripts/test_fsl_convert_x5.py \

  --ignore=fsl/tests/test_scripts/test_immv_imcp.py

%files -n python3-fslpy -f %{pyproject_files}

%doc README.rst

%{_bindir}/atlasq

%{_bindir}/atlasquery

%{_bindir}/fsl_apply_x5

%{_bindir}/fsl_ents

%{_bindir}/fsl_convert_x5

%{_bindir}/imcp

%{_bindir}/imglob

%{_bindir}/immv

%{_bindir}/resample_image

%{_bindir}/Text2Vest

%{_bindir}/Vest2Text

%{_bindir}/fsl_abspath

%{_bindir}/imln

%{_bindir}/imrm

%{_bindir}/imtest

%{_bindir}/remove_ext

%{_mandir}/man1/*.*

%changelog

%autochangelog