sci-libs/nipype: PEP517 fixes and revbump

Signed-off-by: Horea Christian <chr@chymera.eu>

3 files changed, 147 insertions, 0 deletions

diff --git a/sci-libs/nipype/files/nipype-1.8.4-no_etelemetry.patch b/sci-libs/nipype/files/nipype-1.8.4-no_etelemetry.patch
new file mode 100644
index 000000000..b5c223422
--- /dev/null
+++ b/sci-libs/nipype/files/nipype-1.8.4-no_etelemetry.patch
@@ -0,0 +1,50 @@
+diff --git a/nipype/__init__.py b/nipype/__init__.py
+index 06084e823..2e42dcbce 100644
+--- a/nipype/__init__.py
++++ b/nipype/__init__.py
+@@ -73,23 +73,6 @@ from .interfaces import (
+ )
+ 
+ 
+-def check_latest_version(raise_exception=False):
+-    """
+-    Check for the latest version of the library.
+-
+-    Parameters
+-    ----------
+-    raise_exception: bool
+-        Raise a RuntimeError if a bad version is being used
+-    """
+-    import etelemetry
+-
+-    logger = logging.getLogger("nipype.utils")
+-    return etelemetry.check_available_version(
+-        "nipy/nipype", __version__, logger, raise_exception
+-    )
+-
+-
+ # Run telemetry on import for interactive sessions, such as IPython, Jupyter notebooks, Python REPL
+ if config.getboolean("execution", "check_version"):
+     import __main__
+@@ -98,4 +81,4 @@ if config.getboolean("execution", "check_version"):
+         from .interfaces.base import BaseInterface
+ 
+         if BaseInterface._etelemetry_version_data is None:
+-            BaseInterface._etelemetry_version_data = check_latest_version() or "n/a"
++            BaseInterface._etelemetry_version_data = "n/a"
+diff --git a/nipype/interfaces/base/core.py b/nipype/interfaces/base/core.py
+index c8099be63..f7770dbfc 100644
+--- a/nipype/interfaces/base/core.py
++++ b/nipype/interfaces/base/core.py
+@@ -183,10 +183,9 @@ class BaseInterface(Interface):
+             config.getboolean("execution", "check_version")
+             and "NIPYPE_NO_ET" not in os.environ
+         ):
+-            from ... import check_latest_version
+ 
+             if BaseInterface._etelemetry_version_data is None:
+-                BaseInterface._etelemetry_version_data = check_latest_version() or "n/a"
++                BaseInterface._etelemetry_version_data = "n/a"
+ 
+         if not self.input_spec:
+             raise Exception("No input_spec in class: %s" % self.__class__.__name__)
diff --git a/sci-libs/nipype/nipype-1.8.4-r1.ebuild b/sci-libs/nipype/nipype-1.8.4-r1.ebuild
index 8214ccff4..7c2e801ff 100644
--- a/sci-libs/nipype/nipype-1.8.4-r1.ebuild
+++ b/sci-libs/nipype/nipype-1.8.4-r1.ebuild
@@ -3,6 +3,7 @@
 
 EAPI=8
 
+DISTUTILS_USE_PEP517=setuptools
 PYTHON_COMPAT=( python3_{10..11} )
 PYTHON_REQ_USE="threads(+),sqlite"
 
diff --git a/sci-libs/nipype/nipype-1.8.4-r2.ebuild b/sci-libs/nipype/nipype-1.8.4-r2.ebuild
new file mode 100644
index 000000000..4c3da70b3
--- /dev/null
+++ b/sci-libs/nipype/nipype-1.8.4-r2.ebuild
@@ -0,0 +1,96 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_REQ_USE="threads(+),sqlite"
+
+inherit distutils-r1
+
+DESCRIPTION="Neuroimaging in Python: Pipelines and Interfaces"
+HOMEPAGE="https://nipype.readthedocs.io/"
+SRC_URI="https://github.com/nipy/nipype/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+RESTRICT="!test? ( test )"
+
+DEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/prov[${PYTHON_USEDEP}]
+	sci-libs/nibabel[${PYTHON_USEDEP}]
+	test? (
+		dev-python/mock[${PYTHON_USEDEP}]
+		dev-python/pytest[${PYTHON_USEDEP}]
+		${RDEPEND}
+		)
+"
+
+RDEPEND="
+	dev-python/click[${PYTHON_USEDEP}]
+	dev-python/filelock[${PYTHON_USEDEP}]
+	dev-python/looseversion[${PYTHON_USEDEP}]
+	dev-python/networkx[${PYTHON_USEDEP}]
+	dev-python/packaging[${PYTHON_USEDEP}]
+	dev-python/pydot[${PYTHON_USEDEP}]
+	dev-python/python-dateutil[${PYTHON_USEDEP}]
+	dev-python/rdflib[${PYTHON_USEDEP}]
+	dev-python/scipy[${PYTHON_USEDEP}]
+	dev-python/simplejson[${PYTHON_USEDEP}]
+	<dev-python/traits-6.4.0[${PYTHON_USEDEP}]
+"
+
+PATCHES=(
+	"${FILESDIR}/${PN}-1.8.4-dependency_compatibility.patch"
+	"${FILESDIR}/${PN}-1.8.4-no_etelemetry.patch"
+)
+
+src_prepare() {
+	# Remove etelemetry
+	# Doing this separately since the file is affected by another patch.
+	sed -i '/"etelemetry/d' nipype/info.py requirements.txt || die
+
+	# Mark failing tests
+	sed -i \
+		-e "/def test_no_et(tmp_path):/i@pytest.mark.skip('Known to fail by upstream: https://github.com/nipy/nipype/issues/3196#issuecomment-606003186')" \
+		nipype/tests/test_nipype.py || die
+	sed -i \
+		-e "/def test_fslversion():/i@pytest.mark.skip('Known to fail by upstream: https://github.com/nipy/nipype/issues/3196#issuecomment-605997462')" \
+		nipype/interfaces/fsl/tests/test_base.py || die
+	default
+}
+
+python_install_all() {
+	distutils-r1_python_install_all
+	doenvd "${FILESDIR}/98nipype"
+}
+
+# Reported upstream:
+# https://github.com/nipy/nipype/issues/3540
+EPYTEST_DESELECT=(
+	nipype/interfaces/tests/test_io.py::test_s3datagrabber_communication
+)
+
+python_test() {
+	# Setting environment variable to disable etelemetry version check:
+	# https://github.com/nipy/nipype/issues/3196#issuecomment-605980044
+	NIPYPE_NO_ET=1 epytest
+	# Upstream test configuration fails
+		#-c nipype/pytest.ini\
+		#--doctest-modules nipype\
+		#--cov nipype\
+		#--cov-config .coveragerc\
+		#--cov-report xml:cov.xml\
+}
+
+pkg_postinst() {
+	echo
+	einfo "Please run the following commands if you"
+	einfo "intend to use nipype from an existing shell:"
+	einfo "source /etc/profile"
+	echo
+}