diff --git a/science/py-scipy/Makefile b/science/py-scipy/Makefile
index 50c782729017..f21a66209735 100644
--- a/science/py-scipy/Makefile
+++ b/science/py-scipy/Makefile
@@ -1,48 +1,48 @@
 PORTNAME=	scipy
-DISTVERSION=	1.8.1
+DISTVERSION=	1.9.0
 CATEGORIES=	science python
-MASTER_SITES=	https://docs.scipy.org/doc/scipy-${PORTVERSION}/:doc \
+MASTER_SITES=	https://docs.scipy.org/doc/scipy-1.8.1/:doc \
 		CHEESESHOP:source \
 		SF:source
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 DISTFILES=	${DISTNAME}${EXTRACT_SUFX}:source \
-		scipy-ref-${PORTVERSION}.pdf:doc
+		scipy-ref-1.8.1.pdf:doc
 EXTRACT_ONLY=	${DISTNAME}${EXTRACT_SUFX}
 
 MAINTAINER=	python@FreeBSD.org
 COMMENT=	Scientific tools for Python
 
 LICENSE=	BSD3CLAUSE
 LICENSE_FILE=	${WRKSRC}/LICENSE.txt
 
 BUILD_DEPENDS=	${PYNUMPY} \
 		${PYTHON_PKGNAMEPREFIX}pip>0:devel/py-pip@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}pybind11>0:devel/py-pybind11@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}pythran>=0:devel/py-pythran@${PY_FLAVOR}
 LIB_DEPENDS=	libblas.so:math/blas \
 		libopenblas.so:math/openblas
 RUN_DEPENDS=	${PYNUMPY}
 
 USES=		compiler:c++14-lang cpe fortran python:3.8-3.10 shebangfix
 USE_PYTHON=	autoplist concurrent cython distutils
 
 FFLAGS+=	-std=legacy
 LDFLAGS+=	-shared
 PYDISTUTILS_BUILDARGS=	--fcompiler=gnu95
 PYDISTUTILS_CONFIGUREARGS=	--fcompiler=gnu95
 
-PORTDOCS=	scipy-ref-${PORTVERSION}.pdf
+PORTDOCS=	scipy-ref-1.8.1.pdf
 
 OPTIONS_DEFINE=	DOCS
 
 post-install:
 	${FIND} ${STAGEDIR}${PYTHON_SITELIBDIR}/scipy/ -name '*.so' | ${XARGS} ${STRIP_CMD}
 
 post-install-DOCS-on:
 	@${MKDIR} ${STAGEDIR}${DOCSDIR}
 	${INSTALL_DATA} ${DISTDIR}/${PORTDOCS} ${STAGEDIR}${DOCSDIR}
 
 do-test:
 	@cd ${WRKSRC} && ${PYTHON_CMD} runtests.py
 
 .include <bsd.port.mk>
diff --git a/science/py-scipy/distinfo b/science/py-scipy/distinfo
index ef3ce1066f1a..535c20902c48 100644
--- a/science/py-scipy/distinfo
+++ b/science/py-scipy/distinfo
@@ -1,5 +1,5 @@
-TIMESTAMP = 1653464389
-SHA256 (scipy-1.8.1.tar.gz) = 9e3fb1b0e896f14a85aa9a28d5f755daaeeb54c897b746df7a55ccb02b340f33
-SIZE (scipy-1.8.1.tar.gz) = 38196215
+TIMESTAMP = 1659931615
+SHA256 (scipy-1.9.0.tar.gz) = c0dfd7d2429452e7e94904c6a3af63cbaa3cf51b348bd9d35b42db7e9ad42791
+SIZE (scipy-1.9.0.tar.gz) = 42016757
 SHA256 (scipy-ref-1.8.1.pdf) = b7cb6a203a7bafc97bd643122ad7d23d7b7f9df9d9634ba2156d0c7256d81c88
 SIZE (scipy-ref-1.8.1.pdf) = 35035765
diff --git a/science/py-scipy/files/patch-scipy___lib_boost_boost_math_tools_config.hpp b/science/py-scipy/files/patch-scipy___lib_boost_boost_math_tools_config.hpp
deleted file mode 100644
index bd4ded6a7460..000000000000
--- a/science/py-scipy/files/patch-scipy___lib_boost_boost_math_tools_config.hpp
+++ /dev/null
@@ -1,11 +0,0 @@
---- scipy/_lib/boost/boost/math/tools/config.hpp.orig	2021-11-01 02:28:55 UTC
-+++ scipy/_lib/boost/boost/math/tools/config.hpp
-@@ -28,7 +28,7 @@
- 
- #include <boost/math/tools/user.hpp>
- 
--#if (defined(__CYGWIN__) || defined(__FreeBSD__) || defined(__NetBSD__) || defined(__EMSCRIPTEN__)\
-+#if (defined(__CYGWIN__) || defined(__NetBSD__) || defined(__EMSCRIPTEN__)\
-    || (defined(__hppa) && !defined(__OpenBSD__)) || (defined(__NO_LONG_DOUBLE_MATH) && (DBL_MANT_DIG != LDBL_MANT_DIG))) \
-    && !defined(BOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS)
- #  define BOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS
diff --git a/science/py-scipy/files/patch-scipy_linalg_setup.py b/science/py-scipy/files/patch-scipy_linalg_setup.py
new file mode 100644
index 000000000000..c885d4d4a25f
--- /dev/null
+++ b/science/py-scipy/files/patch-scipy_linalg_setup.py
@@ -0,0 +1,11 @@
+--- scipy/linalg/setup.py.orig	2022-08-08 07:24:08 UTC
++++ scipy/linalg/setup.py
+@@ -160,7 +160,7 @@ def configuration(parent_package='', top_path=None):
+ 
+     # Add any license files
+     config.add_data_files('src/id_dist/doc/doc.tex')
+-    config.add_data_files('src/lapack_deprecations/LICENSE')
++    #config.add_data_files('src/lapack_deprecations/LICENSE')
+ 
+     # Type stubs
+     config.add_data_files('*.pyi')
diff --git a/science/py-scipy/files/patch-scipy_sparse_tests_test__base.py b/science/py-scipy/files/patch-scipy_sparse_tests_test__base.py
index a683fb3412a1..eba1ce48a52c 100644
--- a/science/py-scipy/files/patch-scipy_sparse_tests_test__base.py
+++ b/science/py-scipy/files/patch-scipy_sparse_tests_test__base.py
@@ -1,35 +1,35 @@
---- scipy/sparse/tests/test_base.py.orig	2022-03-02 10:42:47 UTC
+--- scipy/sparse/tests/test_base.py.orig	1970-01-01 00:00:00 UTC
 +++ scipy/sparse/tests/test_base.py
-@@ -4758,19 +4758,19 @@ class TestCSCNonCanonical(_NonCanonicalCSMixin, TestCS
+@@ -4774,19 +4774,19 @@ class TestCSCNonCanonical(_NonCanonicalCSMixin, TestCS
      pass
  
  
 -class TestBSRNonCanonical(_NonCanonicalCompressedMixin, TestBSR):
 -    def _insert_explicit_zero(self, M, i, j):
 -        x = M.tocsr()
 -        x[i,j] = 0
 -        return x.tobsr(blocksize=M.blocksize)
 -
 -    @pytest.mark.xfail(run=False, reason='diagonal broken with non-canonical BSR')
 -    def test_diagonal(self):
 -        pass
 -
 -    @pytest.mark.xfail(run=False, reason='expm broken with non-canonical BSR')
 -    def test_expm(self):
 -        pass
 +#class TestBSRNonCanonical(_NonCanonicalCompressedMixin, TestBSR):
 +#    def _insert_explicit_zero(self, M, i, j):
 +#        x = M.tocsr()
 +#        x[i,j] = 0
 +#        return x.tobsr(blocksize=M.blocksize)
 +#
 +#    @pytest.mark.xfail(run=False, reason='diagonal broken with non-canonical BSR')
 +#    def test_diagonal(self):
 +#        pass
 +#
 +#    @pytest.mark.xfail(run=False, reason='expm broken with non-canonical BSR')
 +#    def test_expm(self):
 +#        pass
  
  
  class TestCOONonCanonical(_NonCanonicalMixin, TestCOO):