Port upstream Shapely 2.0.1

Files under `generated/` are created by the upstream build process from
templates; we include these files verbatim for the unikraft build.
Any potential patches should be clearly marked to ease future updates.
Files under `importfix/` are correctly namespaced wrapper modules for
any binary modules that we compile and link into unikraft, and must be
copied over to the python rootfs.
Selecting this library will add its files to the python rootfs build.

Signed-off-by: Andrei Tatar <andrei@unikraft.io>

Config.uk

@@ -0,0 +1,6 @@
+config LIBPYTHON_SHAPELY
+    bool "Shapely - Python package for planar geometric objects"
+    default n
+    select LIBPYTHON3
+    select LIBPYTHON_NUMPY
+    select LIBGEOS

Makefile.uk

@@ -0,0 +1,105 @@
+#  Shapely Makefile.uk
+#
+#  Authors: Andrei Tatar <andrei@unikraft.io>
+#
+#  Copyright (c) 2023, Unikraft GmbH and The Unikraft Authors.
+#
+#  Redistribution and use in source and binary forms, with or without
+#  modification, are permitted provided that the following conditions
+#  are met:
+#
+#  1. Redistributions of source code must retain the above copyright
+#     notice, this list of conditions and the following disclaimer.
+#  2. Redistributions in binary form must reproduce the above copyright
+#     notice, this list of conditions and the following disclaimer in the
+#     documentation and/or other materials provided with the distribution.
+#  3. Neither the name of the copyright holder nor the names of its
+#     contributors may be used to endorse or promote products derived from
+#     this software without specific prior written permission.
+#
+#  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+#  AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+#  IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+#  ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+#  LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+#  CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+#  SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+#  INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+#  CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+#  ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+#  POSSIBILITY OF SUCH DAMAGE.
+#
+
+################################################################################
+# Library registration
+##############################################################################
+$(eval $(call addlib_s,libpython_shapely,$(CONFIG_LIBPYTHON_SHAPELY)))
+
+################################################################################
+# Sources
+##############################################################################
+LIBPYTHON_SHAPELY_VERSION=2.0.1
+LIBPYTHON_SHAPELY_URL=https://github.com/shapely/shapely/releases/download/$(LIBPYTHON_SHAPELY_VERSION)/shapely-$(LIBPYTHON_SHAPELY_VERSION).tar.gz
+LIBPYTHON_SHAPELY_DIRNAME=shapely-$(LIBPYTHON_SHAPELY_VERSION)
+LIBPYTHON_SHAPELY_PATCHDIR=$(LIBPYTHON_SHAPELY_BASE)/patches
+$(eval $(call fetch,libpython_shapely,$(LIBPYTHON_SHAPELY_URL)))
+$(eval $(call patch,libpython_shapely,$(LIBPYTHON_SHAPELY_PATCHDIR),$(LIBPYTHON_SHAPELY_DIRNAME)))
+
+################################################################################
+# Helpers
+##############################################################################
+LIBPYTHON_SHAPELY_SRC = $(LIBPYTHON_SHAPELY_ORIGIN)/$(LIBPYTHON_SHAPELY_DIRNAME)
+
+################################################################################
+# Library includes
+##############################################################################
+LIBPYTHON_SHAPELY_CINCLUDES += -I$(LIBPYTHON_SHAPELY_SRC)/src
+
+################################################################################
+# Global flags
+##############################################################################
+LIBPYTHON_SHAPELY_FLAGS-y += -fwrapv
+LIBPYTHON_SHAPELY_FLAGS-y += -Wno-unused-result
+LIBPYTHON_SHAPELY_FLAGS-y += -Wsign-compare
+LIBPYTHON_SHAPELY_FLAGS-$(call have_clang) += -Wno-documentation
+
+LIBPYTHON_SHAPELY_CFLAGS += $(LIBPYTHON_SHAPELY_FLAGS-y)
+
+################################################################################
+# Library sources
+##############################################################################
+# Upstream C sources
+LIBPYTHON_SHAPELY_SRCS-y += $(LIBPYTHON_SHAPELY_SRC)/src/c_api.c
+LIBPYTHON_SHAPELY_SRCS-y += $(LIBPYTHON_SHAPELY_SRC)/src/coords.c
+LIBPYTHON_SHAPELY_SRCS-y += $(LIBPYTHON_SHAPELY_SRC)/src/geos.c
+LIBPYTHON_SHAPELY_SRCS-y += $(LIBPYTHON_SHAPELY_SRC)/src/lib.c
+LIBPYTHON_SHAPELY_SRCS-y += $(LIBPYTHON_SHAPELY_SRC)/src/pygeom.c
+LIBPYTHON_SHAPELY_SRCS-y += $(LIBPYTHON_SHAPELY_SRC)/src/strtree.c
+LIBPYTHON_SHAPELY_SRCS-y += $(LIBPYTHON_SHAPELY_SRC)/src/ufuncs.c
+LIBPYTHON_SHAPELY_SRCS-y += $(LIBPYTHON_SHAPELY_SRC)/src/vector.c
+
+# Cythonized sources
+LIBPYTHON_SHAPELY_SRCS-y += $(LIBPYTHON_SHAPELY_BASE)/generated/shapely/_geometry_helpers.c
+LIBPYTHON_SHAPELY_SRCS-y += $(LIBPYTHON_SHAPELY_BASE)/generated/shapely/_geos.c
+
+################################################################################
+# Root filesystem
+##############################################################################
+
+ifeq ($(CONFIG_LIBPYTHON_SHAPELY),y)
+# Install into main python rootfs & cleanup non-python files
+$(PYTHON_ROOTFS)/.shapely_done: $(PYTHON_ROOTFS)/.keep
+	. $(PYTHON_ROOTFS)/bin/activate && cd $(LIBPYTHON_SHAPELY_SRC) && pip install . --prefix=$(PYTHON_ROOTFS) --no-compile
+	_dir=`find "$(PYTHON_ROOTFS)" -maxdepth 4 -type d -name shapely`; \
+	find "$$_dir" -type f -name '*.so' -delete; \
+	find "$$_dir" -type d -name '__pycache__' | xargs rm -rf; \
+	find "$$_dir" -type f | grep -v '\.py$$' | tr "\n" "\0" | xargs -0 rm; \
+	find "$(LIBPYTHON_SHAPELY_BASE)/importfix/shapely" -mindepth 1 -maxdepth 1 | xargs $(CP) -rp -t "$$_dir"; \
+	test `basename $$(dirname $$_dir) | cut -d. -f1,2` != $(LIBPYTHON3_VERSION) && \
+		mv "$$_dir" "$(PYTHON_ROOTFS)/lib/python$(LIBPYTHON3_VERSION)/shapely"
+	touch $@
+
+# Add shapely rootfs to main python
+python-rootfs: $(PYTHON_ROOTFS)/.shapely_done
+
+endif