diff --git a/sci-visualization/gwyddion/Manifest b/sci-visualization/gwyddion/Manifest
index ad1a5fdc2572a..1accbe6e79fe1 100644
--- a/sci-visualization/gwyddion/Manifest
+++ b/sci-visualization/gwyddion/Manifest
@@ -1,2 +1 @@
-DIST gwyddion-2.55.tar.xz 4607560 BLAKE2B 30489d980d3feb6986be4041b59c847673ee589674d5913b4508f28f072eb2f570b98f0b1be01dcf6e1d45e86607582967fd83fe3c859172fcdef3c7bffae741 SHA512 680c33b1f7d36de31274869e7f0af9c06030e04779d6b59f06860ae3f47db4ad45bbf3ee2219bb7b6c01807a807aeafa4f5d0aefe20601e0dda1011acf59fc8e
DIST gwyddion-2.56.tar.xz 4645620 BLAKE2B f4f2ce2bf119a24c3e1919b14db409a81ad286ef2242918f356d2b4c56b498f41cbafa03a136eac5d87b4905529e06982694f19bdf30933454e94d34526962c3 SHA512 cf4a40367ea5b0a671c5df70123ef93f6aecc25322af7eb05e4f32d40e54d9b0d48ddd1df9f2589c468eb511ada3f3ef409603c1513de33ba2482078a9415eae
diff --git a/sci-visualization/gwyddion/files/gwyddion-2.55-automagic.patch b/sci-visualization/gwyddion/files/gwyddion-2.55-automagic.patch
deleted file mode 100644
index 405a2552f08b4..0000000000000
--- a/sci-visualization/gwyddion/files/gwyddion-2.55-automagic.patch
+++ /dev/null
@@ -1,33 +0,0 @@
-diff -ruN gwyddion-2.55.orig/configure.ac gwyddion-2.55/configure.ac
---- gwyddion-2.55.orig/configure.ac 2019-11-04 10:25:16.000000000 +0100
-+++ gwyddion-2.55/configure.ac 2020-01-24 05:22:15.264763441 +0100
-@@ -634,21 +634,25 @@
- #############################################################################
- # OpenEXR
- # Optional. Used for HDR greyscale OpenEXR pixmap import/export.
--enable_exr=$have_cxx
--PKG_CHECK_MODULES(EXR, [OpenEXR],
-+GWY_WITH([exr],,[build with OpenEXR support])
-+if test "x$enable_exr" != "xno" && "x$have_cxx" != "xno"; then
-+ PKG_CHECK_MODULES(EXR, [OpenEXR],
- [AC_DEFINE(HAVE_EXR,1,
- [Define if we have the OpenEXR package.])],
- [enable_exr=no])
-+fi
- AM_CONDITIONAL([HAVE_EXR],[test "x$enable_exr" != xno])
-
- #############################################################################
- # CFITSIO
- # Optional. Used for FITS image import.
--enable_cfitsio=yes
--PKG_CHECK_MODULES(CFITSIO, [cfitsio],
-+GWY_WITH([cfitsio],,[build with cfitsio support])
-+if test "x$enable_cfitsio" != "xno"; then
-+ PKG_CHECK_MODULES(CFITSIO, [cfitsio],
- [AC_DEFINE(HAVE_CFITSIO,1,
- [Define if we have the cfitsio package.])],
- [enable_cfitsio=no])
-+fi
- AM_CONDITIONAL([HAVE_CFITSIO],[test "x$enable_cfitsio" != xno])
-
- #############################################################################
diff --git a/sci-visualization/gwyddion/files/gwyddion-2.55-mime.patch b/sci-visualization/gwyddion/files/gwyddion-2.55-mime.patch
deleted file mode 100644
index 536790c1ac464..0000000000000
--- a/sci-visualization/gwyddion/files/gwyddion-2.55-mime.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-Index: gwyddion/modules/file/ambprofile.c
-===================================================================
---- gwyddion/modules/file/ambprofile.c (revision 22650)
-+++ gwyddion/modules/file/ambprofile.c (revision 22651)
-@@ -32,8 +32,8 @@
- * Ambios XML profile data
- *
- *
-- *
-- *
-+ *
-+ *
- *
- *
- *
diff --git a/sci-visualization/gwyddion/files/gwyddion-2.55-xml.patch b/sci-visualization/gwyddion/files/gwyddion-2.55-xml.patch
deleted file mode 100644
index 3cebcc684b50a..0000000000000
--- a/sci-visualization/gwyddion/files/gwyddion-2.55-xml.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-diff --git a/data/gwyddion.xml b/data/gwyddion.xml
-index d26089f..acb7b90 100644
---- a/data/gwyddion.xml
-+++ b/data/gwyddion.xml
-@@ -55,8 +55,8 @@
- Ambios XML profile data
-
-
--
--
-+
-+
-
-
-
diff --git a/sci-visualization/gwyddion/gwyddion-2.55-r4.ebuild b/sci-visualization/gwyddion/gwyddion-2.55-r4.ebuild
deleted file mode 100644
index 335e80a5c600b..0000000000000
--- a/sci-visualization/gwyddion/gwyddion-2.55-r4.ebuild
+++ /dev/null
@@ -1,76 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit autotools gnome2-utils xdg
-
-DESCRIPTION="Framework for Scanning Mode Microscopy data analysis"
-HOMEPAGE="http://gwyddion.net/"
-SRC_URI="http://gwyddion.net/download/${PV}/${P}.tar.xz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
-IUSE="doc fits gnome nls openexr perl ruby sourceview xml X"
-
-RDEPEND="
- >=dev-libs/glib-2.32
- dev-libs/libzip
- media-libs/libpng:0=
- >=sci-libs/fftw-3.1:3.0=
- x11-libs/cairo
- >=x11-libs/gtk+-2.18:2
- x11-libs/libXmu
- x11-libs/pango
- fits? ( sci-libs/cfitsio )
- gnome? ( gnome-base/gconf:2 )
- openexr? ( media-libs/openexr:= )
- perl? ( dev-lang/perl:= )
- ruby? ( dev-ruby/narray )
- sourceview? ( x11-libs/gtksourceview:2.0 )
- xml? ( dev-libs/libxml2:2 )"
-
-DEPEND="${RDEPEND}
- virtual/pkgconfig
- doc? ( dev-util/gtk-doc )
-"
-
-PATCHES=(
- "${FILESDIR}/${PN}-2.55-automagic.patch"
- "${FILESDIR}/${PN}-2.55-mime.patch"
- "${FILESDIR}/${PN}-2.55-xml.patch"
-)
-
-src_prepare() {
- default
- eautoreconf
-}
-
-src_configure() {
- econf \
- --disable-rpath \
- --without-kde4-thumbnailer \
- $(use_enable doc gtk-doc) \
- $(use_enable nls) \
- --disable-pygwy \
- $(use_with fits cfitsio) \
- $(use_with perl) \
- --without-python \
- $(use_with ruby) \
- --without-gl \
- $(use_with openexr exr) \
- $(use_with sourceview gtksourceview) \
- $(use_with xml libxml2) \
- $(use_with X x) \
- --with-zip=libzip
-}
-
-pkg_postinst() {
- use gnome && gnome2_gconf_install
- xdg_pkg_postinst
-}
-
-pkg_prerm() {
- use gnome && gnome2_gconf_uninstall
-}