From 25ac46b96f4c4c7d4e13861c93f6fe1f3e02e111 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fran=C3=A7ois=20Bissey?= Date: Fri, 15 Nov 2019 00:02:07 +1300 Subject: [PATCH 01/54] sci-biology/fsl: use generic blas/lapack revert stuff. Package-Manager: Portage-2.3.76, Repoman-2.3.16 --- sci-biology/fsl/ChangeLog | 3 +++ sci-biology/fsl/fsl-6.0.2.ebuild | 12 ++++++------ 2 files changed, 9 insertions(+), 6 deletions(-) diff --git a/sci-biology/fsl/ChangeLog b/sci-biology/fsl/ChangeLog index 1d1d42a..80eea53 100644 --- a/sci-biology/fsl/ChangeLog +++ b/sci-biology/fsl/ChangeLog @@ -1,3 +1,6 @@ + 14 Nov 2019; François Bissey fsl-6.0.2.ebuild: + sci-biology/fsl: use generic blas/lapack revert stuff. + 08 Nov 2019; François Bissey fsl-6.0.2.ebuild: sci-biology/fsl: final touches. Skip mist-clean. diff --git a/sci-biology/fsl/fsl-6.0.2.ebuild b/sci-biology/fsl/fsl-6.0.2.ebuild index 6b5ff00..fbc7476 100644 --- a/sci-biology/fsl/fsl-6.0.2.ebuild +++ b/sci-biology/fsl/fsl-6.0.2.ebuild @@ -25,8 +25,8 @@ DEPEND=" sys-libs/zlib dev-lang/tcl:0= dev-lang/tk:0= - virtual/lapack - virtual/blas + >=virtual/lapack-3.8 + >=virtual/blas-3.8 " RDEPEND="${DEPEND}" @@ -78,10 +78,6 @@ src_prepare(){ $(grep -rl "\${FSLDIR}/bin" etc/matlab/*)\ $(grep -rl "\$FSLDIR/bin" etc/matlab/*) || die - # Not caught by the previous sed. Usually append - sed -e "s:\${FSLDIR}/bin::g" \ - -i $(grep -rl "\${FSLDIR}/bin" src/*) || die - sed -e "s:\$FSLDIR/data:${EPREFIX}/usr/share/fsl/data:g" \ -e "s:\${FSLDIR}/data:${EPREFIX}/usr/share/fsl/data:g" \ -i $(grep -rl "\$FSLDIR/data" src/*) \ @@ -100,6 +96,10 @@ src_prepare(){ -i $(grep -rlI "\$FSLDIR/etc" *) \ -i $(grep -rlI "\${FSLDIR}/etc" *) || die + # Use generic blas/lapack rather than openblas + sed -e "s:-lopenblas:-llapack -lblas:g" \ + -i $(grep -rlI lopenblas *) || die + # script wanting to have access to flsversion at buildtime sed -e "s:/etc/fslversion:${S}/etc/fslversion:g" \ -i ${makefilelist} || die From 402bc1bf30e89eb6d4e8f329210b411e34fe86f2 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Wed, 20 Nov 2019 10:55:32 +0100 Subject: [PATCH 02/54] Added zenodo reposited archive URI --- sci-biology/opfvta_bidsdata/opfvta_bidsdata-1.1.ebuild | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/sci-biology/opfvta_bidsdata/opfvta_bidsdata-1.1.ebuild b/sci-biology/opfvta_bidsdata/opfvta_bidsdata-1.1.ebuild index e8ac9ff..f1c0f59 100644 --- a/sci-biology/opfvta_bidsdata/opfvta_bidsdata-1.1.ebuild +++ b/sci-biology/opfvta_bidsdata/opfvta_bidsdata-1.1.ebuild @@ -8,8 +8,8 @@ inherit check-reqs DESCRIPTION="BIDS data files released with the OPFVTA publication" HOMEPAGE="http://www.aic-fmi.ethz.ch/" SRC_URI=" - https://zenodo.org/record/3236930/files/${P}.tar.xz http://chymera.eu/distfiles/${P}.tar.xz + https://zenodo.org/record/3546177/files/${P}.tar.xz " LICENSE="CC-BY-SA-4.0" @@ -20,7 +20,7 @@ RDEPEND="" DEPEND="" pkg_pretend() { - CHECKREQS_DISK_BUILD="11G" + CHECKREQS_DISK_BUILD="33G" check-reqs_pkg_pretend } From 40de0dd4739098b360eb4e41ee43c09a577a0e05 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Fri, 22 Nov 2019 17:30:48 +0100 Subject: [PATCH 03/54] Migrated to Gentoo Science https://gitweb.gentoo.org/proj/sci.git/commit/?id=ff1850d2ef581a3cb4564cccf1a4ef451aefb4ef --- sci-biology/opfvta_bidsdata/ChangeLog | 4 --- sci-biology/opfvta_bidsdata/Manifest | 1 - sci-biology/opfvta_bidsdata/metadata.xml | 20 ----------- .../opfvta_bidsdata-1.1.ebuild | 33 ------------------- 4 files changed, 58 deletions(-) delete mode 100644 sci-biology/opfvta_bidsdata/ChangeLog delete mode 100644 sci-biology/opfvta_bidsdata/Manifest delete mode 100644 sci-biology/opfvta_bidsdata/metadata.xml delete mode 100644 sci-biology/opfvta_bidsdata/opfvta_bidsdata-1.1.ebuild diff --git a/sci-biology/opfvta_bidsdata/ChangeLog b/sci-biology/opfvta_bidsdata/ChangeLog deleted file mode 100644 index 19350f5..0000000 --- a/sci-biology/opfvta_bidsdata/ChangeLog +++ /dev/null @@ -1,4 +0,0 @@ -*opfvta_bidsdata-1.1 (06 Nov 2019) - - 06 Nov 2019; +metadata.xml, +opfvta_bidsdata-1.1.ebuild: - sci-biology/opfvta_bidsdata: version bump 1.1 ahead of Gentoo Science diff --git a/sci-biology/opfvta_bidsdata/Manifest b/sci-biology/opfvta_bidsdata/Manifest deleted file mode 100644 index 1304ca6..0000000 --- a/sci-biology/opfvta_bidsdata/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST opfvta_bidsdata-1.1.tar.xz 12029390364 SHA256 73410f67899da24e79138082062ca11394ec5089626c635a491897c47f0d70ad SHA512 80d213b5539a254605f3ce3162a5b5f4f0e7b0b1dbaff6862dbe0fa7fd173020fd38978c97d335939ca667df677feef954ad122e970295f0c28a8bc827e13aec WHIRLPOOL 0d35dea47d5752a24ef4eda933e50b199ea7cf5e571081debf0416d4632cb3f979744c39cd3b665139a95372a9f0484d0539989ff8f80511c5620c9ee34a129e diff --git a/sci-biology/opfvta_bidsdata/metadata.xml b/sci-biology/opfvta_bidsdata/metadata.xml deleted file mode 100644 index 729ebaa..0000000 --- a/sci-biology/opfvta_bidsdata/metadata.xml +++ /dev/null @@ -1,20 +0,0 @@ - - - - - chr@chymera.eu - Horea Christian - - - sci@gentoo.org - Gentoo Science Project - - - BIDS-formatted MRI data recorded at the ETH/UZH Animal Imaging Center - and first associated with the OPFVTA publication. The data represents - f/MRI mouse brain scans with both BOLD and CBV contrasts, using block - and phasic stimulation protocols delivered via a laser to the VTA, - which is rendered sensitive by channelrhodopsin expression under - the dopamine transporter promoter. - - diff --git a/sci-biology/opfvta_bidsdata/opfvta_bidsdata-1.1.ebuild b/sci-biology/opfvta_bidsdata/opfvta_bidsdata-1.1.ebuild deleted file mode 100644 index f1c0f59..0000000 --- a/sci-biology/opfvta_bidsdata/opfvta_bidsdata-1.1.ebuild +++ /dev/null @@ -1,33 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit check-reqs - -DESCRIPTION="BIDS data files released with the OPFVTA publication" -HOMEPAGE="http://www.aic-fmi.ethz.ch/" -SRC_URI=" - http://chymera.eu/distfiles/${P}.tar.xz - https://zenodo.org/record/3546177/files/${P}.tar.xz - " - -LICENSE="CC-BY-SA-4.0" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" - -RDEPEND="" -DEPEND="" - -pkg_pretend() { - CHECKREQS_DISK_BUILD="33G" - check-reqs_pkg_pretend -} - -# We disable this phase to not check requirements twice. -pkg_setup() { :; } - -src_install() { - insinto "/usr/share/${PN}" - doins -r * -} From a91802ccabb07efbd66833455c05ca513b49dd2a Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Sat, 23 Nov 2019 17:06:53 +0100 Subject: [PATCH 04/54] dev-lang/lazarus: fixed Python USE flag ahead of Gentoo Main Package-Manager: Portage-2.3.79, Repoman-2.3.18 Signed-off-by: Horea Christian --- dev-lang/lazarus/ChangeLog | 5 + dev-lang/lazarus/Manifest | 2 + .../lazarus/files/lazarus-0.9.26-fpcsrc.patch | 13 +++ dev-lang/lazarus/lazarus-2.0.2-r1.ebuild | 106 ++++++++++++++++++ dev-lang/lazarus/metadata.xml | 17 +++ 5 files changed, 143 insertions(+) create mode 100644 dev-lang/lazarus/ChangeLog create mode 100644 dev-lang/lazarus/Manifest create mode 100644 dev-lang/lazarus/files/lazarus-0.9.26-fpcsrc.patch create mode 100644 dev-lang/lazarus/lazarus-2.0.2-r1.ebuild create mode 100644 dev-lang/lazarus/metadata.xml diff --git a/dev-lang/lazarus/ChangeLog b/dev-lang/lazarus/ChangeLog new file mode 100644 index 0000000..f9dc236 --- /dev/null +++ b/dev-lang/lazarus/ChangeLog @@ -0,0 +1,5 @@ +*lazarus-2.0.2-r1 (23 Nov 2019) + + 23 Nov 2019; +files/lazarus-0.9.26-fpcsrc.patch, + +lazarus-2.0.2-r1.ebuild, +metadata.xml: + dev-lang/lazarus: fixed Python USE flag ahead of Gentoo Main diff --git a/dev-lang/lazarus/Manifest b/dev-lang/lazarus/Manifest new file mode 100644 index 0000000..e9fac8d --- /dev/null +++ b/dev-lang/lazarus/Manifest @@ -0,0 +1,2 @@ +DIST lazarus-2.0.2.tar.gz 67092332 SHA256 e9d07f176e63c6ff7cf693a135ee66135c147ba398f67b8c6fe892c726f6a476 SHA512 0d2bf26afa3128104181fbe57b1adeaba3bb589b0a3b72598507825a3f08201d4480c6cff510a6f866dca4d49417fac3a2f68ca7e58fabe4f4e3bad97323c071 WHIRLPOOL 81bbaf476e121d335a493ed5021fc7b8aadd53dcc22f42e426d3278fa7675ea798c8d9fc30140808bb382c44b824442c6f7863ac83862604cf38a0a4deb11d84 +DIST lazarus-python-f362a0ea44a1981558539833a0354c1cf4b10eca.tar.gz 1254207 SHA256 3483e38fd84488e2321575e8549cc20041a7c3f89bb10319dfe6a135b967388c SHA512 3b93ac44838e09bdd61bde50f93d116d113779679f6dff1288a0b16003bbfcea0fca2edcc77cfc013ef605e3e7fca5dc71322f4cf9b5b6f78d25c18e7a74ce8f WHIRLPOOL e863641020ddf80365065f2e27145095fe5e5fc303d15ac867f371a4129a3a39f85960c63a19902386d3dfc8ab652496a8e12b7bd41ce66f081e6e5f5e6620e6 diff --git a/dev-lang/lazarus/files/lazarus-0.9.26-fpcsrc.patch b/dev-lang/lazarus/files/lazarus-0.9.26-fpcsrc.patch new file mode 100644 index 0000000..8f9aee3 --- /dev/null +++ b/dev-lang/lazarus/files/lazarus-0.9.26-fpcsrc.patch @@ -0,0 +1,13 @@ +--- lazarus/ide/include/unix/lazbaseconf.inc ++++ lazarus/ide/include/unix/lazbaseconf.inc +@@ -24,8 +24,9 @@ + } + + const +- DefaultFPCSrcDirs: array[1..15] of string = ( ++ DefaultFPCSrcDirs: array[1..16] of string = ( + // search first for sources with right version ++ '/usr/lib/fpc/$(FPCVer)/source', + '/usr/share/fpcsrc/$(FPCVer)', + // then search for global paths + '/usr/share/fpcsrc', diff --git a/dev-lang/lazarus/lazarus-2.0.2-r1.ebuild b/dev-lang/lazarus/lazarus-2.0.2-r1.ebuild new file mode 100644 index 0000000..14dcb03 --- /dev/null +++ b/dev-lang/lazarus/lazarus-2.0.2-r1.ebuild @@ -0,0 +1,106 @@ +# Copyright 1999-2019 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +inherit desktop + +FPCVER="3.0.4" +PYTHON_HASH="f362a0ea44a1981558539833a0354c1cf4b10eca" + +DESCRIPTION="Lazarus IDE is a feature rich visual programming environment emulating Delphi" +HOMEPAGE="https://www.lazarus-ide.org/" +SRC_URI=" + python? ( https://github.com/Alexey-T/Python-for-Lazarus/archive/${PYTHON_HASH}.tar.gz ->\ + ${PN}-python-${PYTHON_HASH}.tar.gz ) + https://sourceforge.net/projects/${PN}/files/Lazarus%20Zip%20_%20GZip/Lazarus%20${PV}/${P}.tar.gz" + +LICENSE="GPL-2 LGPL-2.1-with-linking-exception" +SLOT="0" # Note: Slotting Lazarus needs slotting fpc, see DEPEND. +KEYWORDS="~amd64 ~x86" +IUSE="minimal python" + +DEPEND=">=dev-lang/fpc-${FPCVER}[source] + net-misc/rsync + x11-libs/gtk+:2 + >=sys-devel/binutils-2.19.1-r1:=" +RDEPEND="${DEPEND}" + +RESTRICT="strip" #269221 + +S="${WORKDIR}/${PN}" + +PATCHES=( "${FILESDIR}"/${PN}-0.9.26-fpcsrc.patch ) + +src_prepare() { + default + # Use default configuration (minus stripping) unless specifically requested otherwise + if ! test ${PPC_CONFIG_PATH+set} ; then + local FPCVER=$(fpc -iV) + export PPC_CONFIG_PATH="${WORKDIR}" + sed -e 's/^FPBIN=/#&/' /usr/lib/fpc/${FPCVER}/samplecfg | + sh -s /usr/lib/fpc/${FPCVER} "${PPC_CONFIG_PATH}" || die + fi + sed -i \ + -e "s;SecondaryConfigPath:='/etc/lazarus';SecondaryConfigPath:=ExpandFileNameUTF8('~/.lazarus');g" \ + -e "s;PrimaryConfigPath:=ExpandFileNameUTF8('~/.lazarus');PrimaryConfigPath:='/etc/lazarus';g" \ + ide/include/unix/lazbaseconf.inc \ + || die +} + +src_compile() { + LCL_PLATFORM=gtk2 emake \ + $(usex minimal "" "bigide") \ + -j1 + if use python; then + addpredict ide/exttools.pas + ./lazbuild -B --lazarusdir="." --pcp="../lazarus-package-config" --build-ide= \ + --add-package ../Python-for-Lazarus-${PYTHON_HASH}/python4lazarus/python4lazarus_package.lpk \ + || die + sed -i -e "s:${WORKDIR}/Python-for-Lazarus-${PYTHON_HASH}:/etc/lazarus:g" \ + ../lazarus-package-config/packagefiles.xml \ + ../lazarus-package-config/idemake.cfg \ + ../Python-for-Lazarus-${PYTHON_HASH}/python4lazarus/lib/x86_64-linux/python4lazarus_package.compiled \ + || die + sed -i -e "s:${WORKDIR}/lazarus-package-config:/etc/lazarus:g" \ + ../lazarus-package-config/idemake.cfg \ + || die + fi +} + +src_install() { + diropts -m0755 + dodir /usr/share + # Using rsync to avoid unnecessary copies and cleaning... + # Note: *.o and *.ppu are needed + rsync -a \ + --exclude="CVS" --exclude=".cvsignore" \ + --exclude="*.ppw" --exclude="*.ppl" \ + --exclude="*.ow" --exclude="*.a"\ + --exclude="*.rst" --exclude=".#*" \ + --exclude="*.~*" --exclude="*.bak" \ + --exclude="*.orig" --exclude="*.rej" \ + --exclude=".xvpics" --exclude="*.compiled" \ + --exclude="killme*" --exclude=".gdb_hist*" \ + --exclude="debian" --exclude="COPYING*" \ + --exclude="*.app" \ + "${S}" "${ED%/}"/usr/share \ + || die "Unable to copy files!" + + dosym ../share/lazarus/startlazarus /usr/bin/startlazarus + dosym ../share/lazarus/startlazarus /usr/bin/lazarus + dosym ../share/lazarus/lazbuild /usr/bin/lazbuild + use minimal || dosym ../share/lazarus/components/chmhelp/lhelp/lhelp /usr/bin/lhelp + dosym ../lazarus/images/ide_icon48x48.png /usr/share/pixmaps/lazarus.png + + if use python; then + diropts -m0755 + dodir /etc/lazarus + cp -rf ../lazarus-package-config/* \ + "${ED%/}"/etc/lazarus || die + cp -rf ../Python-for-Lazarus-${PYTHON_HASH}/python4lazarus \ + "${ED%/}"/etc/lazarus || die + fi + + make_desktop_entry startlazarus "Lazarus IDE" "lazarus" +} diff --git a/dev-lang/lazarus/metadata.xml b/dev-lang/lazarus/metadata.xml new file mode 100644 index 0000000..82e27ea --- /dev/null +++ b/dev-lang/lazarus/metadata.xml @@ -0,0 +1,17 @@ + + + + + amynka@gentoo.org + + + A Borland Delphi lookalike for linux. + Uses the free pascal compiler. + + + Don't build extra packages from the bigide component + + + downloads + + From 6bef212520cd2a3c325ec085e3e728f1da303d1d Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Mon, 25 Nov 2019 17:52:04 +0100 Subject: [PATCH 05/54] sci-biology/afni: afni version bump ahead of Gentoo Science Package-Manager: Portage-2.3.79, Repoman-2.3.18 Signed-off-by: Horea Christian --- sci-biology/afni/ChangeLog | 6 +++ sci-biology/afni/Manifest | 1 + sci-biology/afni/afni-19.3.12.ebuild | 72 ++++++++++++++++++++++++++++ sci-biology/afni/afni-9999.ebuild | 70 +++++++++++++++++++++++++++ sci-biology/afni/metadata.xml | 16 +++++++ 5 files changed, 165 insertions(+) create mode 100644 sci-biology/afni/ChangeLog create mode 100644 sci-biology/afni/Manifest create mode 100644 sci-biology/afni/afni-19.3.12.ebuild create mode 100644 sci-biology/afni/afni-9999.ebuild create mode 100644 sci-biology/afni/metadata.xml diff --git a/sci-biology/afni/ChangeLog b/sci-biology/afni/ChangeLog new file mode 100644 index 0000000..2314672 --- /dev/null +++ b/sci-biology/afni/ChangeLog @@ -0,0 +1,6 @@ +*afni-19.3.12 (25 Nov 2019) +*afni-9999 (25 Nov 2019) + + 25 Nov 2019; +afni-19.3.12.ebuild, +afni-9999.ebuild, + +metadata.xml: + sci-biology/afni: afni version bump ahead of Gentoo Science diff --git a/sci-biology/afni/Manifest b/sci-biology/afni/Manifest new file mode 100644 index 0000000..a8eee7e --- /dev/null +++ b/sci-biology/afni/Manifest @@ -0,0 +1 @@ +DIST afni-19.3.12.tar.gz 42337320 SHA256 c2181e365f319f62f292f85562fdffde47cea39028941bd66d5cac0675744c27 SHA512 c4f9303312a89a6e87285646f58223df40b07329cf155bf251a48e8e63302988f103a97363d0666ddd8e9f62f762cf0c219bfc995265b4fe1f1ff5f782025371 WHIRLPOOL cda9340a465051653f0bb6f82d1a0da282dba24ddd159c87b1b54b198dd9208486c11fd8c67367c9e94d8b4042f0298556b222fb1a54074eae1cf054cf5fc9eb diff --git a/sci-biology/afni/afni-19.3.12.ebuild b/sci-biology/afni/afni-19.3.12.ebuild new file mode 100644 index 0000000..c60a871 --- /dev/null +++ b/sci-biology/afni/afni-19.3.12.ebuild @@ -0,0 +1,72 @@ +# Copyright 1999-2019 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +inherit eutils multilib pax-utils toolchain-funcs + +DESCRIPTION="An open-source environment for processing and displaying functional MRI data" +HOMEPAGE="http://afni.nimh.nih.gov/" +SRC_URI="https://github.com/afni/afni/archive/AFNI_${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +RDEPEND="dev-libs/expat + media-libs/glu + media-libs/netpbm + media-libs/qhull + media-video/mpeg-tools + sci-libs/gsl + sys-devel/llvm:* + virtual/jpeg:0 + x11-libs/libGLw + x11-libs/libXft + x11-libs/libXi + x11-libs/libXpm + x11-libs/motif[-static-libs]" + +# x11-libs/motif[static-libs] breaks the build. +# See upstream discussion +# http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348 + +DEPEND="${RDEPEND} + app-shells/tcsh" + +S="${WORKDIR}/${PN}-AFNI_${PV}/src" +BUILD="linux_fedora_19_64" +BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode) + +src_prepare() { + find -type f -exec sed -i -e "s/-lXp //g" {} + + cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile" + # Unbundle imcat + sed -e "s/ imcat / /g" \ + -i Makefile.INCLUDE || die "Could not edit includes files." + sed -e "s~CC = /usr/bin/gcc -O2 -m64~CC = $(tc-getCC) \$(CFLAGS)~" \ + -e "s~CCMIN = /usr/bin/gcc -m64~CCMIN = $(tc-getCC) \$(CFLAGS)~" \ + -e "s~LD = /usr/bin/gcc~LD = $(tc-getCC)~" \ + -e "s~AR = /usr/bin/ar~AR = $(tc-getAR)~" \ + -e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \ + -i Makefile || die "Could not edit Makefile" + # they provide somewhat problematic makefiles :( + sed -e "s~ifeq ($(CC),gcc)~ifeq (1,1)~"\ + -i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile" + # upstream checks if $CC is EXACTLY gcc, else sets variables for Mac + find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EROOT}/usr/~g;" -i + eapply_user +} + +src_compile() { + emake -j1 all plugins suma_exec +} + +src_install() { + emake INSTALLDIR="${ED}/usr/bin" -j1 install install_plugins + emake INSTALLDIR="${ED}/usr/$(get_libdir)" -j1 install_lib + for CONFLICT in ${BIN_CONFLICTS[@]}; do + rm "${ED}/usr/bin/${CONFLICT}" + done +} diff --git a/sci-biology/afni/afni-9999.ebuild b/sci-biology/afni/afni-9999.ebuild new file mode 100644 index 0000000..e30be55 --- /dev/null +++ b/sci-biology/afni/afni-9999.ebuild @@ -0,0 +1,70 @@ +# Copyright 1999-2019 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +inherit eutils multilib pax-utils git-r3 toolchain-funcs + +DESCRIPTION="An open-source environment for processing and displaying functional MRI data" +HOMEPAGE="http://afni.nimh.nih.gov/" +SRC_URI="" +EGIT_REPO_URI="https://github.com/AFNI/AFNI" + +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="" +IUSE="" + +RDEPEND="dev-libs/expat + media-libs/glu + media-libs/netpbm + media-libs/qhull + media-video/mpeg-tools + sci-libs/gsl + sys-devel/llvm:* + virtual/jpeg:0 + x11-libs/libGLw + x11-libs/libXft + x11-libs/libXi + x11-libs/libXpm + x11-libs/motif[-static-libs]" + +# x11-libs/motif[static-libs] breaks the build. +# See upstream discussion +# http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348 + +DEPEND="${RDEPEND} + app-shells/tcsh" + +S="${WORKDIR}/${P}/src" +BUILD="linux_fedora_19_64" +BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode) + +src_prepare() { + find -type f -exec sed -i -e "s/-lXp //g" {} + + cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile" + sed -e "s~CC = /usr/bin/gcc -O2 -m64~CC = $(tc-getCC) \$(CFLAGS)~" \ + -e "s~CCMIN = /usr/bin/gcc -m64~CCMIN = $(tc-getCC) \$(CFLAGS)~" \ + -e "s~LD = /usr/bin/gcc~LD = $(tc-getCC)~" \ + -e "s~AR = /usr/bin/ar~AR = $(tc-getAR)~" \ + -e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \ + -i Makefile || die "Could not edit Makefile" + # they provide somewhat problematic makefiles :( + sed -e "s~ifeq ($(CC),gcc)~ifeq (1,1)~"\ + -i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile" + # upstream checks if $CC is EXACTLY gcc, else sets variables for Mac + find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EROOT}/usr/~g;" -i + eapply_user +} + +src_compile() { + emake -j1 all plugins suma_exec +} + +src_install() { + emake INSTALLDIR="${ED}/usr/bin" -j1 install install_plugins + emake INSTALLDIR="${ED}/usr/$(get_libdir)" -j1 install_lib + for CONFLICT in ${BIN_CONFLICTS[@]}; do + rm "${ED}/usr/bin/${CONFLICT}" + done +} diff --git a/sci-biology/afni/metadata.xml b/sci-biology/afni/metadata.xml new file mode 100644 index 0000000..0f549f3 --- /dev/null +++ b/sci-biology/afni/metadata.xml @@ -0,0 +1,16 @@ + + + + + chr@chymera.eu + Horea Christian + + + sci@gentoo.org + Gentoo Science Project + + + Analysis of Functional NeuroImages (AFNI) is an open-source environment for processing and displaying + functional MRI data—a technique for mapping human brain activity. + + From d3539004e7750ffbd0350909d1d5da61eca973eb Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Mon, 25 Nov 2019 18:59:14 +0100 Subject: [PATCH 06/54] sci-biology/ants: migrated version bump to Gentoo Scinece https://gitweb.gentoo.org/proj/sci.git/commit/?id=402183f38c721910fe038ed4ce04e0a98a37c584 Package-Manager: Portage-2.3.79, Repoman-2.3.18 Signed-off-by: Horea Christian --- sci-biology/ants/ChangeLog | 4 ++ sci-biology/ants/ants-2.3.1_p20191013.ebuild | 72 -------------------- 2 files changed, 4 insertions(+), 72 deletions(-) delete mode 100644 sci-biology/ants/ants-2.3.1_p20191013.ebuild diff --git a/sci-biology/ants/ChangeLog b/sci-biology/ants/ChangeLog index a2f159a..a6e2e47 100644 --- a/sci-biology/ants/ChangeLog +++ b/sci-biology/ants/ChangeLog @@ -1,3 +1,7 @@ + 25 Nov 2019; -ants-2.3.1_p20191013.ebuild: + sci-biology/ants: migrated version bump to Gentoo Scinece https://gitweb.gent + oo.org/proj/sci.git/commit/?id=402183f38c721910fe038ed4ce04e0a98a37c584 + 17 Oct 2019; ants-9999.ebuild: sci-biology/ants: patch merged by ANTs upstream diff --git a/sci-biology/ants/ants-2.3.1_p20191013.ebuild b/sci-biology/ants/ants-2.3.1_p20191013.ebuild deleted file mode 100644 index 5dd2c81..0000000 --- a/sci-biology/ants/ants-2.3.1_p20191013.ebuild +++ /dev/null @@ -1,72 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -CMAKE_MAKEFILE_GENERATOR="emake" - -inherit cmake-utils git-r3 multilib - -DESCRIPTION="Advanced Normalitazion Tools for neuroimaging" -HOMEPAGE="http://stnava.github.io/ANTs/" -SRC_URI=" - test? ( - http://chymera.eu/distfiles/ants_testdata-${PV}.tar.xz - ) -" -EGIT_REPO_URI="https://github.com/stnava/ANTs.git" -EGIT_COMMIT="f78b2d4a382d3090230641b5ade5da28962dad04" - -SLOT="0" -LICENSE="BSD" -KEYWORDS="~amd64 ~x86" -IUSE="test vtk" - -DEPEND=" - vtk? ( - ~sci-libs/itk-5.0.1[vtkglue] - sci-libs/vtk - ) - !vtk? ( ~sci-libs/itk-5.0.1 ) -" -RDEPEND="${DEPEND}" - -PATCHES=( - "${FILESDIR}/${P}-logic.patch" - "${FILESDIR}/${P}-paths.patch" -) - -src_unpack() { - git-r3_src_unpack - if use test; then - mkdir -p "${S}/.ExternalData/MD5" || die "Could not create test data directory." - tar xvf "${DISTDIR}/ants_testdata-${PV}.tar.xz" -C "${S}/.ExternalData/MD5/" > /dev/null || die "Could not unpack test data." - fi -} - -src_configure() { - local mycmakeargs=( - -DUSE_SYSTEM_ITK=ON - -DITK_DIR="/usr/include/ITK-5.0/" - -DBUILD_TESTING="$(usex test ON OFF)" - -DUSE_VTK=$(usex vtk ON OFF) - -DUSE_SYSTEM_VTK=$(usex vtk ON OFF) - ) - use vtk && mycmakeargs+=( - -DVTK_DIR="/usr/include/vtk-8.1/" - ) - use test && mycmakeargs+=( - -DExternalData_OBJECT_STORES="${S}/.ExternalData/MD5" - ) - cmake-utils_src_configure -} - -src_install() { - BUILD_DIR="${WORKDIR}/${P}_build/ANTS-build" - cmake-utils_src_install - cd "${WORKDIR}/${P}/Scripts" || die "scripts dir not found" - dobin *.sh - dodir /usr/$(get_libdir)/ants - install -t "${D}"/usr/$(get_libdir)/ants * || die - doenvd "${FILESDIR}"/99ants -} From 68d184ab67c4c3035c2ebf3323c45ede5fa137bf Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Mon, 25 Nov 2019 19:27:10 +0100 Subject: [PATCH 07/54] sci-biology/samri_bidsdata: migrated to Gentoo Science https://gitweb.gentoo.org/proj/sci.git/commit/?id=3ff7f7144a335cd5ab1bdf1bb477dca36461d9a1 --- sci-biology/samri_bidsdata/ChangeLog | 4 ---- sci-biology/samri_bidsdata/Manifest | 1 - sci-biology/samri_bidsdata/metadata.xml | 15 ------------ .../samri_bidsdata/samri_bidsdata-0.3.ebuild | 23 ------------------- 4 files changed, 43 deletions(-) delete mode 100644 sci-biology/samri_bidsdata/ChangeLog delete mode 100644 sci-biology/samri_bidsdata/Manifest delete mode 100644 sci-biology/samri_bidsdata/metadata.xml delete mode 100644 sci-biology/samri_bidsdata/samri_bidsdata-0.3.ebuild diff --git a/sci-biology/samri_bidsdata/ChangeLog b/sci-biology/samri_bidsdata/ChangeLog deleted file mode 100644 index 0239043..0000000 --- a/sci-biology/samri_bidsdata/ChangeLog +++ /dev/null @@ -1,4 +0,0 @@ -*samri_bidsdata-0.3 (25 Oct 2019) - - 25 Oct 2019; +metadata.xml, +samri_bidsdata-0.3.ebuild: - sci-biology/samri_bidsdata: version bump 0.3 diff --git a/sci-biology/samri_bidsdata/Manifest b/sci-biology/samri_bidsdata/Manifest deleted file mode 100644 index 10959c3..0000000 --- a/sci-biology/samri_bidsdata/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST samri_bidsdata-0.3.tar.xz 11498387144 SHA256 6d8d01f100793bb930d531630c8c1badcef66e90878421bf75a2910195271836 SHA512 bed72df1e5288c0597168f3100b4e839cee869173217df0f3cbdc47ea5b5167d4fcd7f1e8efa681a723bd47d017e6a502a2acf4ce2b225487fff7b8911aa0ff1 WHIRLPOOL b6b53c78ececd4bb2ca3f0cbfd1ed35f4bd592f25b140651c5ced5df407466e47e294344972a48eae09ce529970b34dc04d118bf284bb7f97c66d6acdfce0fa1 diff --git a/sci-biology/samri_bidsdata/metadata.xml b/sci-biology/samri_bidsdata/metadata.xml deleted file mode 100644 index 5d9ef7d..0000000 --- a/sci-biology/samri_bidsdata/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ - - - - - horea.christ@gmail.com - Horea Christian - - - sci@gentoo.org - Gentoo Science Project - - - Larger BIDS example data package for sci-biology/samri. - - diff --git a/sci-biology/samri_bidsdata/samri_bidsdata-0.3.ebuild b/sci-biology/samri_bidsdata/samri_bidsdata-0.3.ebuild deleted file mode 100644 index 0a94ae3..0000000 --- a/sci-biology/samri_bidsdata/samri_bidsdata-0.3.ebuild +++ /dev/null @@ -1,23 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="BIDS-formatted example mouse brain data for SAMRI" -HOMEPAGE="https://github.com/IBT-FMI/SAMRI" -SRC_URI=" - http://chymera.eu/distfiles/${P}.tar.xz - " - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="" - -RDEPEND="" -DEPEND="" - -src_install() { - insinto "/usr/share/${PN}" - doins -r * -} From 73774dee9a5c733dd4e8e7a6649552920fed3beb Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Mon, 25 Nov 2019 19:27:51 +0100 Subject: [PATCH 08/54] sci-biology/samri_bindata: migrated to Gentoo Science https://gitweb.gentoo.org/proj/sci.git/commit/?id=f9cdefeab78ff36690d786f49fac541b56484038 --- sci-biology/samri_bindata/ChangeLog | 4 ---- sci-biology/samri_bindata/Manifest | 1 - sci-biology/samri_bindata/metadata.xml | 15 ------------ .../samri_bindata/samri_bindata-0.3.ebuild | 23 ------------------- 4 files changed, 43 deletions(-) delete mode 100644 sci-biology/samri_bindata/ChangeLog delete mode 100644 sci-biology/samri_bindata/Manifest delete mode 100644 sci-biology/samri_bindata/metadata.xml delete mode 100644 sci-biology/samri_bindata/samri_bindata-0.3.ebuild diff --git a/sci-biology/samri_bindata/ChangeLog b/sci-biology/samri_bindata/ChangeLog deleted file mode 100644 index ffc4111..0000000 --- a/sci-biology/samri_bindata/ChangeLog +++ /dev/null @@ -1,4 +0,0 @@ -*samri_bindata-0.3 (17 Oct 2019) - - 17 Oct 2019; +metadata.xml, +samri_bindata-0.3.ebuild: - sci-biology/samri_bindata: version bump ahead of Gentoo Science diff --git a/sci-biology/samri_bindata/Manifest b/sci-biology/samri_bindata/Manifest deleted file mode 100644 index 6135e2e..0000000 --- a/sci-biology/samri_bindata/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST samri_bindata-0.3.tar.xz 1878468940 SHA256 1ebbaad697d3fdf59978ea2bab55c66759642886c3c4b4ad4c7dfc76cdad4157 SHA512 069c0d84ea651156c38062eea409109aaf00c0b2ef52e2e77e205935ecda5d84b047f8b7f36eaf26526f9d720df514ffe3fa494a0742447db9212916c1347ce2 WHIRLPOOL 65ca37ea6ef67e2e1eb5242267b15643bfa3c43c9ec667633cdaa90e9cbf7a054d233d593ffeafc0ad719ccdebced4703ca47213083047f058d1e90ad1fe1eac diff --git a/sci-biology/samri_bindata/metadata.xml b/sci-biology/samri_bindata/metadata.xml deleted file mode 100644 index 32dc63d..0000000 --- a/sci-biology/samri_bindata/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ - - - - - horea.christ@gmail.com - Horea Christian - - - sci@gentoo.org - Gentoo Science Project - - - Larger binary testing data package for sci-biology/samri. - - diff --git a/sci-biology/samri_bindata/samri_bindata-0.3.ebuild b/sci-biology/samri_bindata/samri_bindata-0.3.ebuild deleted file mode 100644 index 798e01c..0000000 --- a/sci-biology/samri_bindata/samri_bindata-0.3.ebuild +++ /dev/null @@ -1,23 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="ParaVision Mouse, Rat, and Lemur Testing Data for SAMRI" -HOMEPAGE="https://github.com/IBT-FMI/SAMRI" -SRC_URI=" - http://chymera.eu/distfiles/${P}.tar.xz - " - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="" - -RDEPEND="" -DEPEND="" - -src_install() { - insinto "/usr/share/${PN}" - doins -r * -} From c04c12d96ffe63c1e8391efe11eea8a4cd3198d7 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Mon, 25 Nov 2019 19:36:17 +0100 Subject: [PATCH 09/54] sci-biology/afni: migrated to Gentoo Science https://gitweb.gentoo.org/proj/sci.git/commit/?id=b3db3a9c0d4b6e6a7c24003a12eef93e4a79c73d --- sci-biology/afni/ChangeLog | 6 --- sci-biology/afni/Manifest | 1 - sci-biology/afni/afni-19.3.12.ebuild | 72 ---------------------------- sci-biology/afni/afni-9999.ebuild | 70 --------------------------- sci-biology/afni/metadata.xml | 16 ------- 5 files changed, 165 deletions(-) delete mode 100644 sci-biology/afni/ChangeLog delete mode 100644 sci-biology/afni/Manifest delete mode 100644 sci-biology/afni/afni-19.3.12.ebuild delete mode 100644 sci-biology/afni/afni-9999.ebuild delete mode 100644 sci-biology/afni/metadata.xml diff --git a/sci-biology/afni/ChangeLog b/sci-biology/afni/ChangeLog deleted file mode 100644 index 2314672..0000000 --- a/sci-biology/afni/ChangeLog +++ /dev/null @@ -1,6 +0,0 @@ -*afni-19.3.12 (25 Nov 2019) -*afni-9999 (25 Nov 2019) - - 25 Nov 2019; +afni-19.3.12.ebuild, +afni-9999.ebuild, - +metadata.xml: - sci-biology/afni: afni version bump ahead of Gentoo Science diff --git a/sci-biology/afni/Manifest b/sci-biology/afni/Manifest deleted file mode 100644 index a8eee7e..0000000 --- a/sci-biology/afni/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST afni-19.3.12.tar.gz 42337320 SHA256 c2181e365f319f62f292f85562fdffde47cea39028941bd66d5cac0675744c27 SHA512 c4f9303312a89a6e87285646f58223df40b07329cf155bf251a48e8e63302988f103a97363d0666ddd8e9f62f762cf0c219bfc995265b4fe1f1ff5f782025371 WHIRLPOOL cda9340a465051653f0bb6f82d1a0da282dba24ddd159c87b1b54b198dd9208486c11fd8c67367c9e94d8b4042f0298556b222fb1a54074eae1cf054cf5fc9eb diff --git a/sci-biology/afni/afni-19.3.12.ebuild b/sci-biology/afni/afni-19.3.12.ebuild deleted file mode 100644 index c60a871..0000000 --- a/sci-biology/afni/afni-19.3.12.ebuild +++ /dev/null @@ -1,72 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit eutils multilib pax-utils toolchain-funcs - -DESCRIPTION="An open-source environment for processing and displaying functional MRI data" -HOMEPAGE="http://afni.nimh.nih.gov/" -SRC_URI="https://github.com/afni/afni/archive/AFNI_${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3+" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -RDEPEND="dev-libs/expat - media-libs/glu - media-libs/netpbm - media-libs/qhull - media-video/mpeg-tools - sci-libs/gsl - sys-devel/llvm:* - virtual/jpeg:0 - x11-libs/libGLw - x11-libs/libXft - x11-libs/libXi - x11-libs/libXpm - x11-libs/motif[-static-libs]" - -# x11-libs/motif[static-libs] breaks the build. -# See upstream discussion -# http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348 - -DEPEND="${RDEPEND} - app-shells/tcsh" - -S="${WORKDIR}/${PN}-AFNI_${PV}/src" -BUILD="linux_fedora_19_64" -BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode) - -src_prepare() { - find -type f -exec sed -i -e "s/-lXp //g" {} + - cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile" - # Unbundle imcat - sed -e "s/ imcat / /g" \ - -i Makefile.INCLUDE || die "Could not edit includes files." - sed -e "s~CC = /usr/bin/gcc -O2 -m64~CC = $(tc-getCC) \$(CFLAGS)~" \ - -e "s~CCMIN = /usr/bin/gcc -m64~CCMIN = $(tc-getCC) \$(CFLAGS)~" \ - -e "s~LD = /usr/bin/gcc~LD = $(tc-getCC)~" \ - -e "s~AR = /usr/bin/ar~AR = $(tc-getAR)~" \ - -e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \ - -i Makefile || die "Could not edit Makefile" - # they provide somewhat problematic makefiles :( - sed -e "s~ifeq ($(CC),gcc)~ifeq (1,1)~"\ - -i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile" - # upstream checks if $CC is EXACTLY gcc, else sets variables for Mac - find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EROOT}/usr/~g;" -i - eapply_user -} - -src_compile() { - emake -j1 all plugins suma_exec -} - -src_install() { - emake INSTALLDIR="${ED}/usr/bin" -j1 install install_plugins - emake INSTALLDIR="${ED}/usr/$(get_libdir)" -j1 install_lib - for CONFLICT in ${BIN_CONFLICTS[@]}; do - rm "${ED}/usr/bin/${CONFLICT}" - done -} diff --git a/sci-biology/afni/afni-9999.ebuild b/sci-biology/afni/afni-9999.ebuild deleted file mode 100644 index e30be55..0000000 --- a/sci-biology/afni/afni-9999.ebuild +++ /dev/null @@ -1,70 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit eutils multilib pax-utils git-r3 toolchain-funcs - -DESCRIPTION="An open-source environment for processing and displaying functional MRI data" -HOMEPAGE="http://afni.nimh.nih.gov/" -SRC_URI="" -EGIT_REPO_URI="https://github.com/AFNI/AFNI" - -LICENSE="GPL-3+" -SLOT="0" -KEYWORDS="" -IUSE="" - -RDEPEND="dev-libs/expat - media-libs/glu - media-libs/netpbm - media-libs/qhull - media-video/mpeg-tools - sci-libs/gsl - sys-devel/llvm:* - virtual/jpeg:0 - x11-libs/libGLw - x11-libs/libXft - x11-libs/libXi - x11-libs/libXpm - x11-libs/motif[-static-libs]" - -# x11-libs/motif[static-libs] breaks the build. -# See upstream discussion -# http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348 - -DEPEND="${RDEPEND} - app-shells/tcsh" - -S="${WORKDIR}/${P}/src" -BUILD="linux_fedora_19_64" -BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode) - -src_prepare() { - find -type f -exec sed -i -e "s/-lXp //g" {} + - cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile" - sed -e "s~CC = /usr/bin/gcc -O2 -m64~CC = $(tc-getCC) \$(CFLAGS)~" \ - -e "s~CCMIN = /usr/bin/gcc -m64~CCMIN = $(tc-getCC) \$(CFLAGS)~" \ - -e "s~LD = /usr/bin/gcc~LD = $(tc-getCC)~" \ - -e "s~AR = /usr/bin/ar~AR = $(tc-getAR)~" \ - -e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \ - -i Makefile || die "Could not edit Makefile" - # they provide somewhat problematic makefiles :( - sed -e "s~ifeq ($(CC),gcc)~ifeq (1,1)~"\ - -i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile" - # upstream checks if $CC is EXACTLY gcc, else sets variables for Mac - find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EROOT}/usr/~g;" -i - eapply_user -} - -src_compile() { - emake -j1 all plugins suma_exec -} - -src_install() { - emake INSTALLDIR="${ED}/usr/bin" -j1 install install_plugins - emake INSTALLDIR="${ED}/usr/$(get_libdir)" -j1 install_lib - for CONFLICT in ${BIN_CONFLICTS[@]}; do - rm "${ED}/usr/bin/${CONFLICT}" - done -} diff --git a/sci-biology/afni/metadata.xml b/sci-biology/afni/metadata.xml deleted file mode 100644 index 0f549f3..0000000 --- a/sci-biology/afni/metadata.xml +++ /dev/null @@ -1,16 +0,0 @@ - - - - - chr@chymera.eu - Horea Christian - - - sci@gentoo.org - Gentoo Science Project - - - Analysis of Functional NeuroImages (AFNI) is an open-source environment for processing and displaying - functional MRI data—a technique for mapping human brain activity. - - From 7dd8956de0729eb1785d6ff700e3c1ce76e77fd1 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Wed, 27 Nov 2019 00:20:26 +0100 Subject: [PATCH 10/54] sci-biology/nvcz_data: new ebuild ahead of Gentoo Science Package-Manager: Portage-2.3.78, Repoman-2.3.17 Signed-off-by: Horea Christian --- sci-biology/nvcz_data/ChangeLog | 4 ++++ sci-biology/nvcz_data/Manifest | 1 + sci-biology/nvcz_data/metadata.xml | 16 +++++++++++++++ sci-biology/nvcz_data/nvcz_data-0.1.ebuild | 23 ++++++++++++++++++++++ 4 files changed, 44 insertions(+) create mode 100644 sci-biology/nvcz_data/ChangeLog create mode 100644 sci-biology/nvcz_data/Manifest create mode 100644 sci-biology/nvcz_data/metadata.xml create mode 100644 sci-biology/nvcz_data/nvcz_data-0.1.ebuild diff --git a/sci-biology/nvcz_data/ChangeLog b/sci-biology/nvcz_data/ChangeLog new file mode 100644 index 0000000..ffc4111 --- /dev/null +++ b/sci-biology/nvcz_data/ChangeLog @@ -0,0 +1,4 @@ +*samri_bindata-0.3 (17 Oct 2019) + + 17 Oct 2019; +metadata.xml, +samri_bindata-0.3.ebuild: + sci-biology/samri_bindata: version bump ahead of Gentoo Science diff --git a/sci-biology/nvcz_data/Manifest b/sci-biology/nvcz_data/Manifest new file mode 100644 index 0000000..c450f5b --- /dev/null +++ b/sci-biology/nvcz_data/Manifest @@ -0,0 +1 @@ +DIST nvcz_data-0.1.tar.xz 1634626696 SHA256 995a5cdffbcdc975ca95baea3e637a306ac6839a687e040ef7dd020c5a082674 SHA512 e16cc16c718237a97c0c7f05acea2e0b0a511cb3826cac50af2cd67ea59ebfd0a8646961ebe3cbceafea3607cc1c65ae89c32b49c5647f58007033f42d0eb37c WHIRLPOOL 846b7c05417f10c658c7de9be3afa88fcf666227ad96ff2e7f3f3510aa097bf3435ef6633aa4fb0003e72b6fb3cf8c77a3b90a61f0e5c089ea22091a15e0e0e1 diff --git a/sci-biology/nvcz_data/metadata.xml b/sci-biology/nvcz_data/metadata.xml new file mode 100644 index 0000000..f8c17ce --- /dev/null +++ b/sci-biology/nvcz_data/metadata.xml @@ -0,0 +1,16 @@ + + + + + chr@chymera.eu + Horea Christian + + + sci@gentoo.org + Gentoo Science Project + + + Bruker raw data and BIDS data (recomputed from AFNI HEAD/BRIK files) + from mouse fMRI and optical recordings during hindpaw stimulation. + + diff --git a/sci-biology/nvcz_data/nvcz_data-0.1.ebuild b/sci-biology/nvcz_data/nvcz_data-0.1.ebuild new file mode 100644 index 0000000..30c9000 --- /dev/null +++ b/sci-biology/nvcz_data/nvcz_data-0.1.ebuild @@ -0,0 +1,23 @@ +# Copyright 1999-2019 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +DESCRIPTION="Bruker and BIDS data from neurovascular coupling experiments" +HOMEPAGE="https://gitlab.com/Chymera/nvcz" +SRC_URI=" + http://chymera.eu/distfiles/${P}.tar.xz + " + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND="" +DEPEND="" + +src_install() { + insinto "/usr/share/${PN}" + doins -r * +} From ab6429cc86c3201b571af647a5cf26b28b654460 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Wed, 27 Nov 2019 20:47:41 +0100 Subject: [PATCH 11/54] sci-biology/nvcz_data: version bump 0.2 removed optical pipeline files Package-Manager: Portage-2.3.79, Repoman-2.3.18 Signed-off-by: Horea Christian --- sci-biology/nvcz_data/ChangeLog | 5 +++++ sci-biology/nvcz_data/Manifest | 1 + sci-biology/nvcz_data/nvcz_data-0.2.ebuild | 23 ++++++++++++++++++++++ 3 files changed, 29 insertions(+) create mode 100644 sci-biology/nvcz_data/nvcz_data-0.2.ebuild diff --git a/sci-biology/nvcz_data/ChangeLog b/sci-biology/nvcz_data/ChangeLog index ffc4111..d8aa48e 100644 --- a/sci-biology/nvcz_data/ChangeLog +++ b/sci-biology/nvcz_data/ChangeLog @@ -1,3 +1,8 @@ +*nvcz_data-0.2 (27 Nov 2019) + + 27 Nov 2019; +nvcz_data-0.2.ebuild: + sci-biology/nvcz_data: version bump 0.2 removed optical pipeline files + *samri_bindata-0.3 (17 Oct 2019) 17 Oct 2019; +metadata.xml, +samri_bindata-0.3.ebuild: diff --git a/sci-biology/nvcz_data/Manifest b/sci-biology/nvcz_data/Manifest index c450f5b..767bec0 100644 --- a/sci-biology/nvcz_data/Manifest +++ b/sci-biology/nvcz_data/Manifest @@ -1 +1,2 @@ DIST nvcz_data-0.1.tar.xz 1634626696 SHA256 995a5cdffbcdc975ca95baea3e637a306ac6839a687e040ef7dd020c5a082674 SHA512 e16cc16c718237a97c0c7f05acea2e0b0a511cb3826cac50af2cd67ea59ebfd0a8646961ebe3cbceafea3607cc1c65ae89c32b49c5647f58007033f42d0eb37c WHIRLPOOL 846b7c05417f10c658c7de9be3afa88fcf666227ad96ff2e7f3f3510aa097bf3435ef6633aa4fb0003e72b6fb3cf8c77a3b90a61f0e5c089ea22091a15e0e0e1 +DIST nvcz_data-0.2.tar.xz 1588276256 SHA256 bf88ae8a29d2d658b24a3e749fe9566017690aa4a926acc56948fbc7563610ba SHA512 6193354451be5fa04d473c06396c1cd1eda2cc14484c20a2aff626aaa02d6ebfbaf49ea12fdaf0d14c02f02e4a77ac383e1b396c006ee90c2e5d34b9f0c34889 WHIRLPOOL 9f2897ea955c563f0c3d67070f149470c4d94b68c76e84936e1390f938e9d927b36e724bd8e7582e8dd493d8e112cd544e66cc99c15884499c0428ff20852285 diff --git a/sci-biology/nvcz_data/nvcz_data-0.2.ebuild b/sci-biology/nvcz_data/nvcz_data-0.2.ebuild new file mode 100644 index 0000000..30c9000 --- /dev/null +++ b/sci-biology/nvcz_data/nvcz_data-0.2.ebuild @@ -0,0 +1,23 @@ +# Copyright 1999-2019 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +DESCRIPTION="Bruker and BIDS data from neurovascular coupling experiments" +HOMEPAGE="https://gitlab.com/Chymera/nvcz" +SRC_URI=" + http://chymera.eu/distfiles/${P}.tar.xz + " + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND="" +DEPEND="" + +src_install() { + insinto "/usr/share/${PN}" + doins -r * +} From cb2d6aa04c35614ef48bfed724a5e2df8c54d6a6 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Sat, 30 Nov 2019 19:18:19 +0100 Subject: [PATCH 12/54] Updated description --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index b1eba4f..1eed300 100644 --- a/README.md +++ b/README.md @@ -15,8 +15,8 @@ mkdir /etc/portage/repos.conf wget https://raw.githubusercontent.com/TheChymera/overlay/master/metadata/chymeric.conf -O /etc/portage/repos.conf/chymeric ``` -Afterwards, simply run `emerge --sync`, and Portage should seamlessly make all our ebuilds availabl. -Many of our packages are available as live (`*-9999`) ebuilds, and also need manual unmasking in `/etc/portage/package.accept_keywords` before they can be emerged. +Afterwards, simply run `emerge --sync`, and Portage should seamlessly make all our ebuilds available. +Some of our packages are available as live (`*-9999`) ebuilds, and if you wish to use this feature (only advisable if you are well-informed on the day-to-day development of these packages) these versions can be manually unmasked in a case-by-case basis under `/etc/portage/package.accept_keywords`. --- From 161e89d9fbb1672ece5045242241b092ff305bfe Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Sat, 30 Nov 2019 19:19:16 +0100 Subject: [PATCH 13/54] live package description --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 1eed300..78f3648 100644 --- a/README.md +++ b/README.md @@ -16,7 +16,7 @@ wget https://raw.githubusercontent.com/TheChymera/overlay/master/metadata/chymer ``` Afterwards, simply run `emerge --sync`, and Portage should seamlessly make all our ebuilds available. -Some of our packages are available as live (`*-9999`) ebuilds, and if you wish to use this feature (only advisable if you are well-informed on the day-to-day development of these packages) these versions can be manually unmasked in a case-by-case basis under `/etc/portage/package.accept_keywords`. +Some of our packages are available as live (`*-9999`) ebuilds, and if you wish to use this feature (only advisable if you are well-informed on the day-to-day development of a package) these versions can be manually unmasked in a case-by-case basis under `/etc/portage/package.accept_keywords`. --- From 6b0196ac7332d0205659c1254220afb570320a64 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Sat, 30 Nov 2019 19:20:35 +0100 Subject: [PATCH 14/54] Better description of relationship with Gentoo Science --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 78f3648..1a436a5 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,7 @@ An overlay for Gentoo, with various packages used and/or maintained by [TheChymera](https://github.com/TheChymera). A number of the ebuilds available from this overlay are regularly copied from external sources (see respective commit mesages), and thus have a different maintainer. -If you are looking for the neuroscience software packages maintained by [TheChymera](https://github.com/TheChymera), use the [Gentoo Science](https://github.com/gentoo/sci) instead. +If you are looking for the neuroscience software packages maintained by [TheChymera](https://github.com/TheChymera), and are not interested in the absolutely newest versions, use the [Gentoo Science](https://github.com/gentoo/sci) overlay instead. ## Install From a15e2a42c48b616e335d489bb511604ca7af546d Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Wed, 4 Dec 2019 05:22:51 +0100 Subject: [PATCH 15/54] dev-python/pyparsing: version bump 2.4.5 ahead of Gentoo Main Package-Manager: Portage-2.3.78, Repoman-2.3.17 Signed-off-by: Horea Christian --- dev-python/pyparsing/ChangeLog | 4 +++ dev-python/pyparsing/Manifest | 1 + dev-python/pyparsing/metadata.xml | 19 +++++++++++ dev-python/pyparsing/pyparsing-2.4.5.ebuild | 38 +++++++++++++++++++++ 4 files changed, 62 insertions(+) create mode 100644 dev-python/pyparsing/ChangeLog create mode 100644 dev-python/pyparsing/Manifest create mode 100644 dev-python/pyparsing/metadata.xml create mode 100644 dev-python/pyparsing/pyparsing-2.4.5.ebuild diff --git a/dev-python/pyparsing/ChangeLog b/dev-python/pyparsing/ChangeLog new file mode 100644 index 0000000..1ec5dc6 --- /dev/null +++ b/dev-python/pyparsing/ChangeLog @@ -0,0 +1,4 @@ +*pyparsing-2.4.5 (04 Dec 2019) + + 04 Dec 2019; +metadata.xml, +pyparsing-2.4.5.ebuild: + dev-python/pyparsing: version bump 2.4.5 ahead of Gentoo Main diff --git a/dev-python/pyparsing/Manifest b/dev-python/pyparsing/Manifest new file mode 100644 index 0000000..97018b5 --- /dev/null +++ b/dev-python/pyparsing/Manifest @@ -0,0 +1 @@ +DIST pyparsing_2.4.5.tar.gz 645229 SHA256 8c74536281303ef5e1a5be06874d979171cc72b1eee0129f05bebd453383e5ee SHA512 156cfdd28b4eadd5a29abfec8818fe4d038b220cf27aaa9d499f68ec87867c9048dfa79fd6efd85e940d47a7e7fcb21b93d527be05d27a5b58e2900fffb6b132 WHIRLPOOL 3c4b7a33f3029999dcd8a9a378c20c8e07c6d95a59be1e4dbec3adad732726dfe82608a258e5a29e1b71d0a7e402969ac8217b08a672d273aec496fe88980e6d diff --git a/dev-python/pyparsing/metadata.xml b/dev-python/pyparsing/metadata.xml new file mode 100644 index 0000000..9a57fea --- /dev/null +++ b/dev-python/pyparsing/metadata.xml @@ -0,0 +1,19 @@ + + + + + python@gentoo.org + Python + + + The pyparsing module is an alternative approach to creating and + executing simple grammars, vs. the traditional lex/yacc approach, or the + use of regular expressions. The pyparsing module provides a library of + classes that client code uses to construct the grammar directly in + Python code. + + + pyparsing + pyparsing + + diff --git a/dev-python/pyparsing/pyparsing-2.4.5.ebuild b/dev-python/pyparsing/pyparsing-2.4.5.ebuild new file mode 100644 index 0000000..d5e6f6a --- /dev/null +++ b/dev-python/pyparsing/pyparsing-2.4.5.ebuild @@ -0,0 +1,38 @@ +# Copyright 2004-2019 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 +PYTHON_COMPAT=( python2_7 python3_{5,6,7} pypy pypy3 ) + +inherit distutils-r1 + +MY_P=${P/-/_} +DESCRIPTION="Easy-to-use Python module for text parsing" +HOMEPAGE="https://github.com/pyparsing/pyparsing https://pypi.org/project/pyparsing/" +SRC_URI="https://github.com/${PN}/${PN}/archive/${MY_P}.tar.gz" +# pypi releases and generated github tarballs lack tests +#SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~hppa ~ia64 ~mips ~ppc ~ppc64 ~s390 ~sh ~sparc ~x86 ~x64-cygwin ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos ~sparc-solaris ~sparc64-solaris ~x64-solaris ~x86-solaris" +IUSE="examples" + +# setuptools currently vendors its own copy of pyparsing to avoid bootstrapping +# issues so depend on it here for consistency +DEPEND="dev-python/setuptools[${PYTHON_USEDEP}]" +RDEPEND="" + +S=${WORKDIR}/${PN}-${MY_P} + +python_test() { + esetup.py test +} + +python_install_all() { + if use examples; then + docompress -x /usr/share/doc/${PF}/examples + dodoc -r examples + fi + distutils-r1_python_install_all +} From 6951486013348a8b0f1f56efe7805e8bccaefa96 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Wed, 4 Dec 2019 06:01:25 +0100 Subject: [PATCH 16/54] app-misc/python-dice: new package ahead of Gentoo Main Package-Manager: Portage-2.3.78, Repoman-2.3.17 Signed-off-by: Horea Christian --- app-misc/python-dice/ChangeLog | 7 +++ app-misc/python-dice/Manifest | 1 + app-misc/python-dice/metadata.xml | 11 +++++ app-misc/python-dice/python-dice-2.4.2.ebuild | 45 +++++++++++++++++++ 4 files changed, 64 insertions(+) create mode 100644 app-misc/python-dice/ChangeLog create mode 100644 app-misc/python-dice/Manifest create mode 100644 app-misc/python-dice/metadata.xml create mode 100644 app-misc/python-dice/python-dice-2.4.2.ebuild diff --git a/app-misc/python-dice/ChangeLog b/app-misc/python-dice/ChangeLog new file mode 100644 index 0000000..4854aee --- /dev/null +++ b/app-misc/python-dice/ChangeLog @@ -0,0 +1,7 @@ + 04 Nov 2019; typing-3.7.4.1.ebuild: + dev-python/typing: KEYWORDS + +*typing-3.7.4.1 (09 Oct 2019) + + 09 Oct 2019; +metadata.xml, +typing-3.7.4.1.ebuild: + dev-python/typing: version bump 3.7.4.1 and PYTHON_COMPAT to 3 series diff --git a/app-misc/python-dice/Manifest b/app-misc/python-dice/Manifest new file mode 100644 index 0000000..abdd813 --- /dev/null +++ b/app-misc/python-dice/Manifest @@ -0,0 +1 @@ +DIST python-dice-2.4.2.tar.gz 18922 SHA256 f7738436cfc8976bc5e61809bfb5c6a910d892601d46042a91c314a3b6a98f29 SHA512 821171d762deecf1b5a9cd9be20207c923a0ff37f35b3de339127e69ef588c9a63ad5d4680f286c3415ad130f4e156cd1c31135285fd00153f6ee6ba55ea01da WHIRLPOOL 5295b60214d439f2215880c54eade25ac907bd240986d25907e4439578bf3aadcb0dff02ea1cb1a2ff1b2d6d3a4610d87625bb2212db6ce7ccb8042b8742d3af diff --git a/app-misc/python-dice/metadata.xml b/app-misc/python-dice/metadata.xml new file mode 100644 index 0000000..631cb58 --- /dev/null +++ b/app-misc/python-dice/metadata.xml @@ -0,0 +1,11 @@ + + + + + chr@chymera.eu + Horea Christian + + + borntyping/python-dice + + diff --git a/app-misc/python-dice/python-dice-2.4.2.ebuild b/app-misc/python-dice/python-dice-2.4.2.ebuild new file mode 100644 index 0000000..c68142a --- /dev/null +++ b/app-misc/python-dice/python-dice-2.4.2.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2019 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +PYTHON_COMPAT=( python3_6 ) + +inherit distutils-r1 + +DESCRIPTION="Dice parsing and evaluation library" +HOMEPAGE="https://github.com/borntyping/python-dice" +SRC_URI="https://github.com/borntyping/python-dice/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" +IUSE="test" +RESTRICT="test" +# Tests do not run, which may be an upstream issue: +# https://github.com/borntyping/python-dice/issues/25 + +DEPEND="test? ( dev-python/tox[${PYTHON_USEDEP}] )" +RDEPEND=" + dev-python/coverage[${PYTHON_USEDEP}] + dev-python/docopt[${PYTHON_USEDEP}] + dev-python/pyparsing[${PYTHON_USEDEP}] + dev-python/termcolor[${PYTHON_USEDEP}] + dev-python/pyflakes[${PYTHON_USEDEP}] + dev-python/pytest[${PYTHON_USEDEP}] + dev-python/pytest-cov[${PYTHON_USEDEP}] + dev-python/pytest-flakes[${PYTHON_USEDEP}] + dev-python/pytest-pep8[${PYTHON_USEDEP}] +" + +src_prepare() { + if use test; then + sed -i -e "s/pytest<3.7.0/pytest/g" tox.ini + fi + default +} + +python_test() { + #pytest -vv || die + tox || die "tests failed under ${EPYTHON}" +} From 9a12b874e2d13ef3363f313ed85a0150c31edab3 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Wed, 4 Dec 2019 17:01:03 +0100 Subject: [PATCH 17/54] app-misc/python-dice: updated dependency lists Package-Manager: Portage-2.3.79, Repoman-2.3.18 Signed-off-by: Horea Christian --- app-misc/python-dice/ChangeLog | 3 +++ app-misc/python-dice/python-dice-2.4.2.ebuild | 13 ++++++++----- 2 files changed, 11 insertions(+), 5 deletions(-) diff --git a/app-misc/python-dice/ChangeLog b/app-misc/python-dice/ChangeLog index 4854aee..dbf25f4 100644 --- a/app-misc/python-dice/ChangeLog +++ b/app-misc/python-dice/ChangeLog @@ -1,3 +1,6 @@ + 04 Dec 2019; python-dice-2.4.2.ebuild: + app-misc/python-dice: updated dependency lists + 04 Nov 2019; typing-3.7.4.1.ebuild: dev-python/typing: KEYWORDS diff --git a/app-misc/python-dice/python-dice-2.4.2.ebuild b/app-misc/python-dice/python-dice-2.4.2.ebuild index c68142a..8ee05dd 100644 --- a/app-misc/python-dice/python-dice-2.4.2.ebuild +++ b/app-misc/python-dice/python-dice-2.4.2.ebuild @@ -19,17 +19,20 @@ RESTRICT="test" # Tests do not run, which may be an upstream issue: # https://github.com/borntyping/python-dice/issues/25 -DEPEND="test? ( dev-python/tox[${PYTHON_USEDEP}] )" -RDEPEND=" +DEPEND="test? ( dev-python/coverage[${PYTHON_USEDEP}] - dev-python/docopt[${PYTHON_USEDEP}] - dev-python/pyparsing[${PYTHON_USEDEP}] - dev-python/termcolor[${PYTHON_USEDEP}] dev-python/pyflakes[${PYTHON_USEDEP}] dev-python/pytest[${PYTHON_USEDEP}] dev-python/pytest-cov[${PYTHON_USEDEP}] dev-python/pytest-flakes[${PYTHON_USEDEP}] dev-python/pytest-pep8[${PYTHON_USEDEP}] + dev-python/termcolor[${PYTHON_USEDEP}] + dev-python/tox[${PYTHON_USEDEP}] + ) +" +RDEPEND=" + dev-python/docopt[${PYTHON_USEDEP}] + >=dev-python/pyparsing-2.4.1[${PYTHON_USEDEP}] " src_prepare() { From 741a627d97c1dfa683b998509d59a1e9f59cd6ad Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Thu, 5 Dec 2019 06:46:43 +0100 Subject: [PATCH 18/54] sci-biology/samri_bindata: version bump 0.4 ahead of Gentoo Science Package-Manager: Portage-2.3.78, Repoman-2.3.17 Signed-off-by: Horea Christian --- sci-biology/samri_bindata/ChangeLog | 4 ++++ sci-biology/samri_bindata/Manifest | 1 + sci-biology/samri_bindata/metadata.xml | 15 ++++++++++++ .../samri_bindata/samri_bindata-0.4.ebuild | 23 +++++++++++++++++++ 4 files changed, 43 insertions(+) create mode 100644 sci-biology/samri_bindata/ChangeLog create mode 100644 sci-biology/samri_bindata/Manifest create mode 100644 sci-biology/samri_bindata/metadata.xml create mode 100644 sci-biology/samri_bindata/samri_bindata-0.4.ebuild diff --git a/sci-biology/samri_bindata/ChangeLog b/sci-biology/samri_bindata/ChangeLog new file mode 100644 index 0000000..11b0d0b --- /dev/null +++ b/sci-biology/samri_bindata/ChangeLog @@ -0,0 +1,4 @@ +*samri_bindata-0.4 (05 Dec 2019) + + 05 Dec 2019; +metadata.xml, +samri_bindata-0.4.ebuild: + sci-biology/samri_bindata: version bump 0.4 ahead of Gentoo Science diff --git a/sci-biology/samri_bindata/Manifest b/sci-biology/samri_bindata/Manifest new file mode 100644 index 0000000..eadd00f --- /dev/null +++ b/sci-biology/samri_bindata/Manifest @@ -0,0 +1 @@ +DIST samri_bindata-0.4.tar.xz 2349556936 SHA256 e63b51a53b0114e71aac5ef1d56c286118a62afe400645ebed9ba18bc45d4ce8 SHA512 18a16e9e3bd75497f50923f2e304364dff78fa66308290350ca72717e01217e24b2fdeedfda56a5ba07a436d3643ceebc104bc802025ddd776b07986f45d53e0 WHIRLPOOL 36bbe8496460cd5cee65a004eabb09f1746b601cbbe0d5067dbb8cfc1fe204112863797034b79486db8c3175b9174489c4bf795075709ddf070c869720078a92 diff --git a/sci-biology/samri_bindata/metadata.xml b/sci-biology/samri_bindata/metadata.xml new file mode 100644 index 0000000..32dc63d --- /dev/null +++ b/sci-biology/samri_bindata/metadata.xml @@ -0,0 +1,15 @@ + + + + + horea.christ@gmail.com + Horea Christian + + + sci@gentoo.org + Gentoo Science Project + + + Larger binary testing data package for sci-biology/samri. + + diff --git a/sci-biology/samri_bindata/samri_bindata-0.4.ebuild b/sci-biology/samri_bindata/samri_bindata-0.4.ebuild new file mode 100644 index 0000000..798e01c --- /dev/null +++ b/sci-biology/samri_bindata/samri_bindata-0.4.ebuild @@ -0,0 +1,23 @@ +# Copyright 1999-2019 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +DESCRIPTION="ParaVision Mouse, Rat, and Lemur Testing Data for SAMRI" +HOMEPAGE="https://github.com/IBT-FMI/SAMRI" +SRC_URI=" + http://chymera.eu/distfiles/${P}.tar.xz + " + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND="" +DEPEND="" + +src_install() { + insinto "/usr/share/${PN}" + doins -r * +} From 26e22747397239a2c2101497d2aca198d5d24941 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Fri, 6 Dec 2019 18:32:10 +0100 Subject: [PATCH 19/54] sci-libs/nibabel: migrated to Gentoo Science --- sci-libs/nibabel/ChangeLog | 4 --- sci-libs/nibabel/Manifest | 1 - sci-libs/nibabel/metadata.xml | 25 ---------------- sci-libs/nibabel/nibabel-2.5.1.ebuild | 43 --------------------------- 4 files changed, 73 deletions(-) delete mode 100644 sci-libs/nibabel/ChangeLog delete mode 100644 sci-libs/nibabel/Manifest delete mode 100644 sci-libs/nibabel/metadata.xml delete mode 100644 sci-libs/nibabel/nibabel-2.5.1.ebuild diff --git a/sci-libs/nibabel/ChangeLog b/sci-libs/nibabel/ChangeLog deleted file mode 100644 index 8a72651..0000000 --- a/sci-libs/nibabel/ChangeLog +++ /dev/null @@ -1,4 +0,0 @@ -*nibabel-2.5.1 (04 Nov 2019) - - 04 Nov 2019; +metadata.xml, +nibabel-2.5.1.ebuild: - sci-libs/nibabel: version bump 2.5.1 ahead of Gentoo Science diff --git a/sci-libs/nibabel/Manifest b/sci-libs/nibabel/Manifest deleted file mode 100644 index 0271242..0000000 --- a/sci-libs/nibabel/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST nibabel-2.5.1.tar.gz 4281663 SHA256 47b445abee203a9ab4068d826588f926352ea55f20a894178ad5b56215a22fd8 SHA512 49de1a42113e64a56336e02f3143588b574c7b063b10b892ee125048451be701955e505bd1d51183327e2ee221f8364005fdd9fa7d256343113ab6ca1994820d WHIRLPOOL cb0337a753c7f3827da8954c354a65ce09ecb96fba3ffd637028f4634ff3aa29eeb3975ad012bced12fbad13adf94fd5d7e1313983f6598467330ac001615500 diff --git a/sci-libs/nibabel/metadata.xml b/sci-libs/nibabel/metadata.xml deleted file mode 100644 index 59e566e..0000000 --- a/sci-libs/nibabel/metadata.xml +++ /dev/null @@ -1,25 +0,0 @@ - - - - - horea.christ@gmail.com - Horea Christian - - - sci@gentoo.org - Gentoo Science Project - - -The package provides read and write access to some common medical and -neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2), GIFTI, -NIfTI1, MINC, MGH and ECAT as well as PAR/REC. It can read and write Freesurfer -geometry, and read Freesurfer morphometry and annotation files. There is some -very limited support for DICOM. NiBabel is the successor of PyNIfTI. - - - Adds limited read support for the DICOM imaging format. - - - nipy/nibabel - - diff --git a/sci-libs/nibabel/nibabel-2.5.1.ebuild b/sci-libs/nibabel/nibabel-2.5.1.ebuild deleted file mode 100644 index e7570f1..0000000 --- a/sci-libs/nibabel/nibabel-2.5.1.ebuild +++ /dev/null @@ -1,43 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6,3_7} ) - -inherit distutils-r1 - -DESCRIPTION="Access a cacophony of neuro-imaging file formats" -HOMEPAGE="http://nipy.org/nibabel/" -SRC_URI="https://github.com/nipy/nibabel/archive/${PV}.tar.gz -> ${P}.tar.gz" - -KEYWORDS="~amd64 ~x86" - -LICENSE="MIT" -SLOT="0" -IUSE="dicom doc test" - -RDEPEND=" - dev-python/numpy[${PYTHON_USEDEP}] - sci-libs/scipy[${PYTHON_USEDEP}] - dev-python/mock[${PYTHON_USEDEP}] - dicom? ( - sci-libs/pydicom[${PYTHON_USEDEP}] - dev-python/pillow[${PYTHON_USEDEP}] - ) - " - -DEPEND=" - dev-python/setuptools[${PYTHON_USEDEP}] - test? ( - ${RDEPEND} - dev-python/nose[${PYTHON_USEDEP}] - ) - doc? ( dev-python/sphinx[${PYTHON_USEDEP}] ) - " - -python_test() { - cd "${BUILD_DIR}" || die - echo "backend: Agg" > matplotlibrc - MPLCONFIGDIR=. nosetests || die -} From b3a73cae6a7c6b009ec6f7e610fcf90d2e962224 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Fri, 6 Dec 2019 23:31:23 +0100 Subject: [PATCH 20/54] sci-biology/opfvta_bidsdata: version bump 1.2 ahead of Gentoo Science Package-Manager: Portage-2.3.79, Repoman-2.3.18 Signed-off-by: Horea Christian --- sci-biology/opfvta_bidsdata/ChangeLog | 4 +++ sci-biology/opfvta_bidsdata/Manifest | 1 + sci-biology/opfvta_bidsdata/metadata.xml | 20 +++++++++++ .../opfvta_bidsdata-1.2.ebuild | 33 +++++++++++++++++++ 4 files changed, 58 insertions(+) create mode 100644 sci-biology/opfvta_bidsdata/ChangeLog create mode 100644 sci-biology/opfvta_bidsdata/Manifest create mode 100644 sci-biology/opfvta_bidsdata/metadata.xml create mode 100644 sci-biology/opfvta_bidsdata/opfvta_bidsdata-1.2.ebuild diff --git a/sci-biology/opfvta_bidsdata/ChangeLog b/sci-biology/opfvta_bidsdata/ChangeLog new file mode 100644 index 0000000..09af341 --- /dev/null +++ b/sci-biology/opfvta_bidsdata/ChangeLog @@ -0,0 +1,4 @@ +*opfvta_bidsdata-1.2 (06 Dec 2019) + + 06 Dec 2019; +metadata.xml, +opfvta_bidsdata-1.2.ebuild: + sci-biology/opfvta_bidsdata: version bump 1.2 ahead of Gentoo Science diff --git a/sci-biology/opfvta_bidsdata/Manifest b/sci-biology/opfvta_bidsdata/Manifest new file mode 100644 index 0000000..b015f61 --- /dev/null +++ b/sci-biology/opfvta_bidsdata/Manifest @@ -0,0 +1 @@ +DIST opfvta_bidsdata-1.2.tar.xz 12101699696 SHA256 5c48b4214abc8d7cc8c0b8820bba52950427cd44ee397031bfe674503762693f SHA512 213100ccf561b2d805199a876e85f0793545df5d2fed5ac0039e008d0fe9706f9836ca94a351e9651032d2f96b0b91182e1c2d4b129dbf3ec824d852c77880aa WHIRLPOOL 0f0d0fc4a1fcb9324547841517f0584431baef3346c94fcf1e56ff81b5bb62848b72587a0c2d8ca8b53d74a3ac76c2f8c641c38e01290c8637a464db1190f8c1 diff --git a/sci-biology/opfvta_bidsdata/metadata.xml b/sci-biology/opfvta_bidsdata/metadata.xml new file mode 100644 index 0000000..729ebaa --- /dev/null +++ b/sci-biology/opfvta_bidsdata/metadata.xml @@ -0,0 +1,20 @@ + + + + + chr@chymera.eu + Horea Christian + + + sci@gentoo.org + Gentoo Science Project + + + BIDS-formatted MRI data recorded at the ETH/UZH Animal Imaging Center + and first associated with the OPFVTA publication. The data represents + f/MRI mouse brain scans with both BOLD and CBV contrasts, using block + and phasic stimulation protocols delivered via a laser to the VTA, + which is rendered sensitive by channelrhodopsin expression under + the dopamine transporter promoter. + + diff --git a/sci-biology/opfvta_bidsdata/opfvta_bidsdata-1.2.ebuild b/sci-biology/opfvta_bidsdata/opfvta_bidsdata-1.2.ebuild new file mode 100644 index 0000000..3c1317f --- /dev/null +++ b/sci-biology/opfvta_bidsdata/opfvta_bidsdata-1.2.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2019 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +inherit check-reqs + +DESCRIPTION="BIDS data files released with the OPFVTA publication" +HOMEPAGE="http://www.aic-fmi.ethz.ch/" +SRC_URI=" + http://chymera.eu/distfiles/${P}.tar.xz + https://zenodo.org/record/3565897/files/${P}.tar.xz + " + +LICENSE="CC-BY-SA-4.0" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + +RDEPEND="" +DEPEND="" + +pkg_pretend() { + CHECKREQS_DISK_BUILD="33G" + check-reqs_pkg_pretend +} + +# We disable this phase to not check requirements twice. +pkg_setup() { :; } + +src_install() { + insinto "/usr/share/${PN}" + doins -r * +} From 78457340df699de88045837353cfc1b0d36f391e Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Fri, 6 Dec 2019 23:33:20 +0100 Subject: [PATCH 21/54] app-misc/python-dice: version bump 3.0.0 Package-Manager: Portage-2.3.79, Repoman-2.3.18 Signed-off-by: Horea Christian --- app-misc/python-dice/ChangeLog | 5 +++ app-misc/python-dice/Manifest | 1 + app-misc/python-dice/python-dice-3.0.0.ebuild | 41 +++++++++++++++++++ 3 files changed, 47 insertions(+) create mode 100644 app-misc/python-dice/python-dice-3.0.0.ebuild diff --git a/app-misc/python-dice/ChangeLog b/app-misc/python-dice/ChangeLog index dbf25f4..d34e18c 100644 --- a/app-misc/python-dice/ChangeLog +++ b/app-misc/python-dice/ChangeLog @@ -1,3 +1,8 @@ +*python-dice-3.0.0 (06 Dec 2019) + + 06 Dec 2019; +python-dice-3.0.0.ebuild: + app-misc/python-dice: version bump 3.0.0 + 04 Dec 2019; python-dice-2.4.2.ebuild: app-misc/python-dice: updated dependency lists diff --git a/app-misc/python-dice/Manifest b/app-misc/python-dice/Manifest index abdd813..4144b9e 100644 --- a/app-misc/python-dice/Manifest +++ b/app-misc/python-dice/Manifest @@ -1 +1,2 @@ DIST python-dice-2.4.2.tar.gz 18922 SHA256 f7738436cfc8976bc5e61809bfb5c6a910d892601d46042a91c314a3b6a98f29 SHA512 821171d762deecf1b5a9cd9be20207c923a0ff37f35b3de339127e69ef588c9a63ad5d4680f286c3415ad130f4e156cd1c31135285fd00153f6ee6ba55ea01da WHIRLPOOL 5295b60214d439f2215880c54eade25ac907bd240986d25907e4439578bf3aadcb0dff02ea1cb1a2ff1b2d6d3a4610d87625bb2212db6ce7ccb8042b8742d3af +DIST python-dice-3.0.0.tar.gz 23514 SHA256 eacd7d0c044d1b0f88ec6d33625952e594c900b7ebea6329058461cdad64bcf6 SHA512 181a0fc9057052e252bac817f7e076a9367cf74537de7182d5842804498f43c0e7a69b65975bbee03c9de340fd05d712fabb5207df5c7dae1faf4717912741dd WHIRLPOOL 1b86068d02807672c1d79c4f8274f723d5ba98c40170e27140abde80802b393ba447d3fc08a9c268ed2fd6deaa45a6c9d18902abda2ba74eb869cf79b9c4d0b4 diff --git a/app-misc/python-dice/python-dice-3.0.0.ebuild b/app-misc/python-dice/python-dice-3.0.0.ebuild new file mode 100644 index 0000000..e12d606 --- /dev/null +++ b/app-misc/python-dice/python-dice-3.0.0.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2019 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +PYTHON_COMPAT=( python3_6 ) + +inherit distutils-r1 + +DESCRIPTION="Dice parsing and evaluation library" +HOMEPAGE="https://github.com/borntyping/python-dice" +SRC_URI="https://github.com/borntyping/python-dice/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" +IUSE="test" + +DEPEND="test? ( + dev-python/coverage[${PYTHON_USEDEP}] + dev-python/pytest[${PYTHON_USEDEP}] + dev-python/pytest-cov[${PYTHON_USEDEP}] + ) +" +#dev-python/tox[${PYTHON_USEDEP}] +RDEPEND=" + dev-python/docopt[${PYTHON_USEDEP}] + >=dev-python/pyparsing-2.4.1[${PYTHON_USEDEP}] +" + +src_prepare() { + if use test; then + sed -i -e "s/pytest<3.7.0/pytest/g" tox.ini + fi + default +} + +python_test() { + pytest -vv || die + #tox || die "tests failed under ${EPYTHON}" +} From 0baf8e8cfcaacb4af128a1c0de3d3c9cfd3ab77f Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Sun, 8 Dec 2019 01:18:53 +0100 Subject: [PATCH 22/54] sci-libs/dcmtk: version bump to 3.6.5 and prefix fix Package-Manager: Portage-2.3.78, Repoman-2.3.17 Signed-off-by: Horea Christian --- sci-libs/dcmtk/ChangeLog | 9 + sci-libs/dcmtk/Manifest | 1 + sci-libs/dcmtk/dcmtk-3.6.5.ebuild | 87 +++++++++ .../dcmtk/files/dcmtk-3.6.3-dcmqrdb-cfg.patch | 87 +++++++++ .../dcmtk/files/dcmtk-3.6.3-fix-gcc9.patch | 29 +++ .../dcmtk/files/dcmtk-3.6.3-nostrip.patch | 171 ++++++++++++++++++ sci-libs/dcmtk/metadata.xml | 8 + 7 files changed, 392 insertions(+) create mode 100644 sci-libs/dcmtk/ChangeLog create mode 100644 sci-libs/dcmtk/Manifest create mode 100644 sci-libs/dcmtk/dcmtk-3.6.5.ebuild create mode 100644 sci-libs/dcmtk/files/dcmtk-3.6.3-dcmqrdb-cfg.patch create mode 100644 sci-libs/dcmtk/files/dcmtk-3.6.3-fix-gcc9.patch create mode 100644 sci-libs/dcmtk/files/dcmtk-3.6.3-nostrip.patch create mode 100644 sci-libs/dcmtk/metadata.xml diff --git a/sci-libs/dcmtk/ChangeLog b/sci-libs/dcmtk/ChangeLog new file mode 100644 index 0000000..c236f09 --- /dev/null +++ b/sci-libs/dcmtk/ChangeLog @@ -0,0 +1,9 @@ + 08 Dec 2019; dcmtk-3.6.5.ebuild: + sci-libs/dcmtk: f + +*dcmtk-3.6.5 (08 Dec 2019) + + 08 Dec 2019; +dcmtk-3.6.5.ebuild, + +files/dcmtk-3.6.3-dcmqrdb-cfg.patch, +files/dcmtk-3.6.3-fix-gcc9.patch, + +files/dcmtk-3.6.3-nostrip.patch, +metadata.xml: + sci-libs/dcmtk: version bump to 3.6.5 and prefix fix diff --git a/sci-libs/dcmtk/Manifest b/sci-libs/dcmtk/Manifest new file mode 100644 index 0000000..f51c939 --- /dev/null +++ b/sci-libs/dcmtk/Manifest @@ -0,0 +1 @@ +DIST dcmtk-3.6.5.tar.gz 6483626 SHA256 a05178665f21896dbb0974106dba1ad144975414abd760b4cf8f5cc979f9beb9 SHA512 c0cf61b0095c5708709406bfef5e8bb82dd01dbf77df7f2af2118004920bda68218eb1e4174bf92941cdae0acdb275c886570dafd29476eee2eb815e9a82830a WHIRLPOOL 14c0be8f35d0e513bb9cb03e5f30adf9b6bb1a5464a5cfee16e8261f9f304a73bd06e79c8d441d9ab8085f414a46112d58a1ccc5286dda11df6169df70dc4691 diff --git a/sci-libs/dcmtk/dcmtk-3.6.5.ebuild b/sci-libs/dcmtk/dcmtk-3.6.5.ebuild new file mode 100644 index 0000000..c7441d1 --- /dev/null +++ b/sci-libs/dcmtk/dcmtk-3.6.5.ebuild @@ -0,0 +1,87 @@ +# Copyright 1999-2019 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +inherit cmake-utils + +DESCRIPTION="The DICOM Toolkit" +HOMEPAGE="https://dicom.offis.de/dcmtk.php.en" +SRC_URI="http://dicom.offis.de/download/dcmtk/release/${P}.tar.gz" + +LICENSE="OFFIS" +KEYWORDS="~amd64 ~arm ~x86" +SLOT="0" +IUSE="doc png ssl tcpd tiff +threads xml zlib" + +RDEPEND=" + dev-libs/icu:= + virtual/jpeg:0 + png? ( media-libs/libpng:* ) + ssl? ( dev-libs/openssl:0= ) + tcpd? ( sys-apps/tcp-wrappers ) + tiff? ( media-libs/tiff:0 ) + xml? ( dev-libs/libxml2:2 ) + zlib? ( sys-libs/zlib )" +DEPEND="${RDEPEND} + media-gfx/graphviz + doc? ( app-doc/doxygen )" + +src_prepare() { + cmake-utils_src_prepare + + sed -e "s:share/doc/dcmtk:&-${PV}:" \ + -e "s:DIR \"/:DIR \"/usr/:" \ + -e "s:usr/etc:etc:" \ + -e "s:/lib\":/$(get_libdir)\":" \ + -e "s:COPYRIGHT::" \ + -i CMakeLists.txt || die + sed -e 's:${CMAKE_INSTALL_PREFIX}/::' \ + -i dcmwlm/data/CMakeLists.txt doxygen/CMakeLists.txt || die + # Temporary workaround: docs are not built with CMake + sed -i -e '/include/d' doxygen/Makefile.in || die + + # fix -D deprecation warnings + sed -i -e "s|_BSD_SOURCE|_DEFAULT_SOURCE|g" \ + "${S}"/config/configure.in \ + "${S}"/CMakeLists.txt || die +} + +src_configure() { + local mycmakeargs=( + -DBUILD_SHARED_LIBS=ON + -DCMAKE_INSTALL_SYSCONFDIR=${EROOT%/}/etc + -DDCMTK_WITH_ICU=ON + -DDCMTK_WITH_TIFF=$(usex tiff) + -DDCMTK_WITH_PNG=$(usex png) + -DDCMTK_WITH_XML=$(usex xml) + -DDCMTK_WITH_ZLIB=$(usex zlib) + -DDCMTK_WITH_OPENSSL=$(usex ssl) + -DDCMTK_WITH_DOXYGEN=$(usex doc) + -DDCMTK_WITH_THREADS=$(usex threads) + ) + + cmake-utils_src_configure + + if use doc; then + cd "${S}"/doxygen || die + econf + fi +} + +src_compile() { + cmake-utils_src_compile + + if use doc; then + emake -C "${S}"/doxygen + fi +} + +src_install() { + doman doxygen/manpages/man1/* + + if use doc; then + local HTML_DOCS=( "${S}"/doxygen/htmldocs/. ) + fi + cmake-utils_src_install +} diff --git a/sci-libs/dcmtk/files/dcmtk-3.6.3-dcmqrdb-cfg.patch b/sci-libs/dcmtk/files/dcmtk-3.6.3-dcmqrdb-cfg.patch new file mode 100644 index 0000000..4ccb58d --- /dev/null +++ b/sci-libs/dcmtk/files/dcmtk-3.6.3-dcmqrdb-cfg.patch @@ -0,0 +1,87 @@ +Author: Jürgen Salk +Description: The original maintainer Jürgen Salk applied + a set of patches to the original code. This file contains + changes to C++ code + +Index: dcmtk-3.6.0/dcmqrdb/etc/dcmqrscp.cfg +=================================================================== +--- a/dcmqrdb/etc/dcmqrscp.cfg 2010-09-09 19:20:25.000000000 +0200 ++++ b/dcmqrdb/etc/dcmqrscp.cfg 2011-01-28 09:49:02.000000000 +0100 +@@ -10,7 +10,9 @@ + NetworkTCPPort = 104 + MaxPDUSize = 16384 + MaxAssociations = 16 ++UserName = "dcmtk" ++GroupName = "dcmtk" + + # + # Default settings for specific character set behavior: + # SpecificCharacterSet = fallback +@@ -28,12 +30,13 @@ + # NOTE: in the current implementation you cannot substitute an IP address + # for a hostname. + # +-acme1 = (ACME1, acmehost1, 5678) +-acme2 = (ACME2, acmehost2, 5678) +-acmeCTcompany = acme1, acme2 +-united1 = (UNITED1, unitedhost1, 104) +-united2 = (UNITED2, unitedhost2, 104) +-unitedMRcompany = united1, united2 ++# Example: ++#acme1 = (ACME1, acmehost1, 5678) ++#acme2 = (ACME2, acmehost2, 5678) ++#acmeCTcompany = acme1, acme2 ++#united1 = (UNITED1, unitedhost1, 104) ++#united2 = (UNITED2, unitedhost2, 104) ++#unitedMRcompany = united1, united2 + # + HostTable END + +@@ -51,8 +54,9 @@ + # VendorName = SymbolicName + # The symbolic name should be defined in the HostTable. + # +-"Acme CT Company" = acmeCTcompany +-"United MR Company" = unitedMRcompany ++# Example: ++#"Acme CT Company" = acmeCTcompany ++#"United MR Company" = unitedMRcompany + # + VendorTable END + +@@ -70,8 +74,13 @@ + # Entry in HostTable | + # ANY + # +-COMMON /home/dicom/db/COMMON R (200, 1024mb) ANY +-ACME_STORE /home/dicom/db/ACME_STORE RW (9, 1024mb) acmeCTcompany +-UNITED_STORE /home/dicom/db/UNITED_STORE RW (9, 1024mb) unitedMRcompany ++# Example: ++# ++#ACME_STORE /var/lib/dcmtk/db/ACME_STORE RW (9, 1024mb) acmeCTcompany ++#UNITED_STORE /var/lib/dcmtk/db/UNITED_STORE RW (9, 1024mb) unitedMRcompany ++# ++# Uncomment and adjust the following lines for a common r/rw storage area: ++#READWRITE /var/lib/dcmtk/db/READWRITE RW (10, 1024mb) ANY ++#READ /var/lib/dcmtk/db/READ R (200, 1024mb) ANY + # + AETable END +Index: dcmtk-3.6.0/dcmqrdb/docs/dcmqrcnf.txt +--- a/dcmqrdb/docs/dcmqrcnf.txt 2010-09-09 19:20:12.000000000 +0200 ++++ b/dcmqrdb/docs/dcmqrcnf.txt 2011-01-28 09:46:02.000000000 +0100 +@@ -44,8 +44,8 @@ + MaxPDUSize = 8192 + MaxAssociations = 20 + SpecificCharacterSet = fallback +-UserName = (do not change user) +-GroupName = (do not change group) ++UserName = "dcmtk" ++GroupName = "dcmtk" + + Available options for specific character sets are: + +Index: dcmtk-3.6.0/dcmwlm/wlistdb/OFFIS/lockfile +--- /dev/null 1970-01-01 00:00:00.000000000 +0000 ++++ dcmtk-3.6.0/dcmwlm/wlistdb/OFFIS/lockfile 2011-01-28 09:46:02.000000000 +0100 +@@ -0,0 +1 @@ ++ diff --git a/sci-libs/dcmtk/files/dcmtk-3.6.3-fix-gcc9.patch b/sci-libs/dcmtk/files/dcmtk-3.6.3-fix-gcc9.patch new file mode 100644 index 0000000..596a1ae --- /dev/null +++ b/sci-libs/dcmtk/files/dcmtk-3.6.3-fix-gcc9.patch @@ -0,0 +1,29 @@ +https://bugs.gentoo.org/686592 + +In file included from /var/tmp/portage/sci-libs/dcmtk-3.6.3/work/dcmtk-3.6.3/ofstd/include/dcmtk/ofstd/variadic/variant.h:19, + from /var/tmp/portage/sci-libs/dcmtk-3.6.3/work/dcmtk-3.6.3/ofstd/include/dcmtk/ofstd/ofvriant.h:379, + from /var/tmp/portage/sci-libs/dcmtk-3.6.3/work/dcmtk-3.6.3/ofstd/tests/tvariant.cc:26: +/var/tmp/portage/sci-libs/dcmtk-3.6.3/work/dcmtk-3.6.3/ofstd/include/dcmtk/ofstd/variadic/helpers.h:57:32: error: narrowing conversion of ‘-1’ from ‘int’ to ‘long unsigned int’ [-Wnarrowing] + 57 | : OFintegral_constant {}; + | + +--- a/ofstd/include/dcmtk/ofstd/variadic/helpers.h ++++ b/ofstd/include/dcmtk/ofstd/variadic/helpers.h +@@ -14,6 +14,8 @@ + #ifndef VARIADIC_HELPERS_H + #define VARIADIC_HELPERS_H + ++#include ++ + #include "dcmtk/config/osconfig.h" /* make sure OS specific configuration is included first */ + + #include "dcmtk/ofstd/oftraits.h" +@@ -54,7 +56,7 @@ + + template + struct OFvariadic_find_type_t +-: OFintegral_constant {}; ++: OFintegral_constant::max()> {}; + + template + struct OFvariadic_find_type diff --git a/sci-libs/dcmtk/files/dcmtk-3.6.3-nostrip.patch b/sci-libs/dcmtk/files/dcmtk-3.6.3-nostrip.patch new file mode 100644 index 0000000..83bd3a6 --- /dev/null +++ b/sci-libs/dcmtk/files/dcmtk-3.6.3-nostrip.patch @@ -0,0 +1,171 @@ +Remove all hardcoded calls to `strip` command + +Index: dcmtk-3.6.0/config/templates/Makefile.src +=================================================================== +--- a/config/templates/Makefile.src 2009-01-30 10:27:58.000000000 +0100 ++++ b/config/templates/Makefile.src 2011-01-28 09:53:28.000000000 +0100 +@@ -31,7 +31,7 @@ + install-bin: all + $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) + for prog in $(progs); do \ +- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && $(STRIP) $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ ++ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ + done + + +Index: dcmtk-3.6.0/dcmdata/apps/Makefile.in +=================================================================== +--- a/dcmdata/apps/Makefile.in 2009-11-04 10:58:05.000000000 +0100 ++++ b/dcmdata/apps/Makefile.in 2011-01-28 09:53:45.000000000 +0100 +@@ -76,7 +76,7 @@ + install-bin: all + $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) + for prog in $(progs); do \ +- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && $(STRIP) $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ ++ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ + done + + +Index: dcmtk-3.6.0/dcmimage/apps/Makefile.in +=================================================================== +--- a/dcmimage/apps/Makefile.in 2009-10-13 16:08:33.000000000 +0200 ++++ b/dcmimage/apps/Makefile.in 2011-01-28 09:53:59.000000000 +0100 +@@ -42,7 +42,7 @@ + install: all + $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) + for prog in $(progs); do \ +- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && $(STRIP) $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ ++ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ + done + + +Index: dcmtk-3.6.0/dcmimgle/apps/Makefile.in +=================================================================== +--- a/dcmimgle/apps/Makefile.in 2009-10-28 10:53:39.000000000 +0100 ++++ b/dcmimgle/apps/Makefile.in 2011-01-28 09:54:11.000000000 +0100 +@@ -39,7 +39,7 @@ + install: all + $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) + for prog in $(progs); do \ +- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && $(STRIP) $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ ++ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ + done + + +Index: dcmtk-3.6.0/dcmjpeg/apps/Makefile.in +=================================================================== +--- a/dcmjpeg/apps/Makefile.in 2009-10-07 14:44:33.000000000 +0200 ++++ b/dcmjpeg/apps/Makefile.in 2011-01-28 09:54:28.000000000 +0100 +@@ -72,7 +72,7 @@ + install: all + $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) + for prog in $(progs); do \ +- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && $(STRIP) $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ ++ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ + done + + clean: +Index: dcmtk-3.6.0/dcmnet/apps/Makefile.in +=================================================================== +--- a/dcmnet/apps/Makefile.in 2009-11-04 11:24:29.000000000 +0100 ++++ b/dcmnet/apps/Makefile.in 2011-01-28 09:54:50.000000000 +0100 +@@ -52,7 +52,7 @@ + install: all + $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) + for prog in $(progs); do \ +- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && $(STRIP) $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ ++ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ + done + + +Index: dcmtk-3.6.0/dcmpstat/apps/Makefile.in +=================================================================== +--- a/dcmpstat/apps/Makefile.in 2009-10-13 16:57:49.000000000 +0200 ++++ b/dcmpstat/apps/Makefile.in 2011-01-28 09:55:10.000000000 +0100 +@@ -113,7 +113,7 @@ + install: all + $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) + for prog in $(progs); do \ +- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && $(STRIP) $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ ++ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ + done + + +Index: dcmtk-3.6.0/dcmqrdb/apps/Makefile.in +=================================================================== +--- a/dcmqrdb/apps/Makefile.in 2009-11-04 11:24:30.000000000 +0100 ++++ b/dcmqrdb/apps/Makefile.in 2011-01-28 09:55:24.000000000 +0100 +@@ -57,7 +57,7 @@ + install: all + $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) + for prog in $(progs); do \ +- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && $(STRIP) $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ ++ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ + done + + +Index: dcmtk-3.6.0/dcmsign/apps/Makefile.in +=================================================================== +--- a/dcmsign/apps/Makefile.in 2009-09-04 17:42:31.000000000 +0200 ++++ b/dcmsign/apps/Makefile.in 2011-01-28 09:55:35.000000000 +0100 +@@ -33,7 +33,7 @@ + install: all + $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) + for prog in $(progs); do \ +- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && $(STRIP) $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ ++ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ + done + + +Index: dcmtk-3.6.0/dcmsr/apps/Makefile.in +=================================================================== +--- a/dcmsr/apps/Makefile.in 2009-10-13 16:57:49.000000000 +0200 ++++ b/dcmsr/apps/Makefile.in 2011-01-28 09:55:48.000000000 +0100 +@@ -44,7 +44,7 @@ + install-bin: all + $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) + for prog in $(progs); do \ +- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && $(STRIP) $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ ++ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ + done + + +Index: dcmtk-3.6.0/dcmwlm/apps/Makefile.in +=================================================================== +--- a/dcmwlm/apps/Makefile.in 2009-11-04 11:24:30.000000000 +0100 ++++ b/dcmwlm/apps/Makefile.in 2011-01-28 09:55:58.000000000 +0100 +@@ -49,7 +49,7 @@ + install: all + $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) + for prog in $(progs); do \ +- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && $(STRIP) $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ ++ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ + done + + +Index: dcmtk-3.6.0/dcmwlm/wwwapps/Makefile.in +=================================================================== +--- a/dcmrt/apps/Makefile.in 2009-11-04 11:24:30.000000000 +0100 ++++ b/dcmrt/apps/Makefile.in 2011-01-28 09:56:33.000000000 +0100 +@@ -55,7 +55,7 @@ + install-bin: all + $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) + for prog in $(progs); do \ +- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && $(STRIP) $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ ++ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ + done + + +Index: dcmtk-3.6.0/dcmjpls/apps/Makefile.in +=================================================================== +--- a/dcmjpls/apps/Makefile.in 2011-01-28 09:56:54.000000000 +0100 ++++ b/dcmjpls/apps/Makefile.in 2011-01-28 09:57:00.000000000 +0100 +@@ -71,7 +71,7 @@ + install: all + $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) + for prog in $(progs); do \ +- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && $(STRIP) $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ ++ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ + done + + diff --git a/sci-libs/dcmtk/metadata.xml b/sci-libs/dcmtk/metadata.xml new file mode 100644 index 0000000..ed91732 --- /dev/null +++ b/sci-libs/dcmtk/metadata.xml @@ -0,0 +1,8 @@ + + + + + sci-biology@gentoo.org + + DICOM ToolKit core medical imaging library and tools + From 16a7aa9502667da069bc1c70c2793d26c0c0e0fa Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Sun, 8 Dec 2019 15:41:27 +0100 Subject: [PATCH 23/54] sci-biology/samri: version bump 0.4.1 ahead of Gentoo Science Package-Manager: Portage-2.3.78, Repoman-2.3.17 Signed-off-by: Horea Christian --- sci-biology/samri/ChangeLog | 5 +++++ sci-biology/samri/Manifest | 2 +- sci-biology/samri/{samri-0.4.ebuild => samri-0.4.1.ebuild} | 4 ++-- 3 files changed, 8 insertions(+), 3 deletions(-) rename sci-biology/samri/{samri-0.4.ebuild => samri-0.4.1.ebuild} (96%) diff --git a/sci-biology/samri/ChangeLog b/sci-biology/samri/ChangeLog index a6b3459..7802d8f 100644 --- a/sci-biology/samri/ChangeLog +++ b/sci-biology/samri/ChangeLog @@ -1,3 +1,8 @@ +*samri-0.4.1 (08 Dec 2019) + + 08 Dec 2019; +samri-0.4.1.ebuild, -samri-0.4.ebuild: + sci-biology/samri: version bump 0.4.1 ahead of Gentoo Science + *samri-9999 (12 Nov 2019) 12 Nov 2019; +samri-9999.ebuild: diff --git a/sci-biology/samri/Manifest b/sci-biology/samri/Manifest index 87400a3..1c1d72c 100644 --- a/sci-biology/samri/Manifest +++ b/sci-biology/samri/Manifest @@ -1 +1 @@ -DIST samri-0.4.tar.gz 4110506 SHA256 1344d27f7af8088d3796b27e32395511fc9ea1d27baed36432963da72ccd0c5b SHA512 5d3f148707df7484be4ba17d3abe9e964510bf830f66919f9b0b9d85f739c37ebff84439a69fc0eb074f4dfb48eec74eef79c6764fcac9895d37f1f4c292c8ab WHIRLPOOL f629a06e79ca6f67a08c087a34ee7bf766dd0bb809ad5ad464b77b49e74aedcc173a01c25be825c24005b6af1caddaf6e6b21348a8e51560eab8726e8092d1ac +DIST samri-0.4.1.tar.gz 4115417 SHA256 aacf7f02d7d7adb46b31aeb85bf85abbe3c28d9f4aa92d2149114fb0416fdd04 SHA512 c2eef33e725d0d5b87f30ce8da51d9c46ce735a8d82e41f93eba8d225b58eead4777441db4be9078e7f29b3f92d12525d729dddea888fd7e9a66ba5e607d8caf WHIRLPOOL 6ca655dd4b28dc1f194bf40fc830645c179cad67d3f85deffd6251a0cc9054e936372566caae1daa608025eec6fc0e892fc8e1d2b62c3491ea71c1581d21a1e9 diff --git a/sci-biology/samri/samri-0.4.ebuild b/sci-biology/samri/samri-0.4.1.ebuild similarity index 96% rename from sci-biology/samri/samri-0.4.ebuild rename to sci-biology/samri/samri-0.4.1.ebuild index bfd4390..547b8e9 100644 --- a/sci-biology/samri/samri-0.4.ebuild +++ b/sci-biology/samri/samri-0.4.1.ebuild @@ -3,7 +3,7 @@ EAPI=7 -PYTHON_COMPAT=( python3_{5,6} ) +PYTHON_COMPAT=( python3_6 ) inherit distutils-r1 @@ -14,7 +14,7 @@ SRC_URI="https://github.com/IBT-FMI/SAMRI/archive/${PV}.tar.gz -> ${P}.tar.gz" LICENSE="GPL-3" SLOT="0" IUSE="labbookdb test" -KEYWORDS="~amd64 ~x86" +KEYWORDS="~amd64" DEPEND=" test? ( From 39b0c7077592d1aecbe662cb7ef715e286ecebf5 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Sun, 8 Dec 2019 15:56:13 +0100 Subject: [PATCH 24/54] sci-biology/samri: migrated version to Gentoo Science https://gitweb.gentoo.org/proj/sci.git/commit/?id=e68c1eb1aea94ee2860d3b9feb079932114904ea Package-Manager: Portage-2.3.78, Repoman-2.3.17 Signed-off-by: Horea Christian --- sci-biology/samri/ChangeLog | 4 ++ sci-biology/samri/Manifest | 1 - sci-biology/samri/samri-0.4.1.ebuild | 57 ---------------------------- 3 files changed, 4 insertions(+), 58 deletions(-) delete mode 100644 sci-biology/samri/Manifest delete mode 100644 sci-biology/samri/samri-0.4.1.ebuild diff --git a/sci-biology/samri/ChangeLog b/sci-biology/samri/ChangeLog index 7802d8f..f318c6b 100644 --- a/sci-biology/samri/ChangeLog +++ b/sci-biology/samri/ChangeLog @@ -1,3 +1,7 @@ + 08 Dec 2019; -Manifest, -samri-0.4.1.ebuild: + sci-biology/samri: migrated version to Gentoo Science https://gitweb.gentoo.o + rg/proj/sci.git/commit/?id=e68c1eb1aea94ee2860d3b9feb079932114904ea + *samri-0.4.1 (08 Dec 2019) 08 Dec 2019; +samri-0.4.1.ebuild, -samri-0.4.ebuild: diff --git a/sci-biology/samri/Manifest b/sci-biology/samri/Manifest deleted file mode 100644 index 1c1d72c..0000000 --- a/sci-biology/samri/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST samri-0.4.1.tar.gz 4115417 SHA256 aacf7f02d7d7adb46b31aeb85bf85abbe3c28d9f4aa92d2149114fb0416fdd04 SHA512 c2eef33e725d0d5b87f30ce8da51d9c46ce735a8d82e41f93eba8d225b58eead4777441db4be9078e7f29b3f92d12525d729dddea888fd7e9a66ba5e607d8caf WHIRLPOOL 6ca655dd4b28dc1f194bf40fc830645c179cad67d3f85deffd6251a0cc9054e936372566caae1daa608025eec6fc0e892fc8e1d2b62c3491ea71c1581d21a1e9 diff --git a/sci-biology/samri/samri-0.4.1.ebuild b/sci-biology/samri/samri-0.4.1.ebuild deleted file mode 100644 index 547b8e9..0000000 --- a/sci-biology/samri/samri-0.4.1.ebuild +++ /dev/null @@ -1,57 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_6 ) - -inherit distutils-r1 - -DESCRIPTION="Small Animal Magnetic Resonance Imaging" -HOMEPAGE="https://github.com/IBT-FMI/SAMRI" -SRC_URI="https://github.com/IBT-FMI/SAMRI/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -IUSE="labbookdb test" -KEYWORDS="~amd64" - -DEPEND=" - test? ( - dev-python/pytest[${PYTHON_USEDEP}] - sci-biology/samri_bidsdata - sci-biology/samri_bindata - ) -" -RDEPEND=" - dev-python/argh[${PYTHON_USEDEP}] - dev-python/joblib[${PYTHON_USEDEP}] - >=dev-python/matplotlib-2.0.2[${PYTHON_USEDEP}] - >=dev-python/numpy-1.13.3[${PYTHON_USEDEP}] - dev-python/pandas[${PYTHON_USEDEP}] - dev-python/seaborn[${PYTHON_USEDEP}] - dev-python/statsmodels[${PYTHON_USEDEP}] - media-gfx/blender - >=sci-biology/fsl-5.0.9 - sci-biology/bru2nii - sci-biology/mouse-brain-atlases - labbookdb? ( sci-libs/labbookdb[${PYTHON_USEDEP}] ) - sci-libs/nibabel[${PYTHON_USEDEP}] - >=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}] - >=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}] - <=sci-libs/pybids-0.6.5[${PYTHON_USEDEP}] - sci-libs/scikits_image[${PYTHON_USEDEP}] - sci-libs/scipy[${PYTHON_USEDEP}] - sci-biology/ants - sci-biology/afni - sci-biology/nilearn[${PYTHON_USEDEP}] -" - -S="${WORKDIR}/SAMRI-${PV}" - -src_prepare() { - distutils-r1_src_prepare - sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI \'/usr/ samri` - sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI /usr/ test_scripts.sh` - eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX samri/* test_scripts.sh) -} From 7c4012b4c4a44aee5808373f933a7475190872c3 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Mon, 9 Dec 2019 09:25:10 +0100 Subject: [PATCH 25/54] sci-biology/opfvta_bidsdata: version bump 2.0 ahead of Gentoo Science Package-Manager: Portage-2.3.78, Repoman-2.3.17 Signed-off-by: Horea Christian --- sci-biology/opfvta_bidsdata/ChangeLog | 5 +++ sci-biology/opfvta_bidsdata/Manifest | 1 + .../opfvta_bidsdata-2.0.ebuild | 33 +++++++++++++++++++ 3 files changed, 39 insertions(+) create mode 100644 sci-biology/opfvta_bidsdata/opfvta_bidsdata-2.0.ebuild diff --git a/sci-biology/opfvta_bidsdata/ChangeLog b/sci-biology/opfvta_bidsdata/ChangeLog index 09af341..9b0bb35 100644 --- a/sci-biology/opfvta_bidsdata/ChangeLog +++ b/sci-biology/opfvta_bidsdata/ChangeLog @@ -1,3 +1,8 @@ +*opfvta_bidsdata-2.0 (09 Dec 2019) + + 09 Dec 2019; +opfvta_bidsdata-2.0.ebuild: + sci-biology/opfvta_bidsdata: version bump 2.0 ahead of Gentoo Science + *opfvta_bidsdata-1.2 (06 Dec 2019) 06 Dec 2019; +metadata.xml, +opfvta_bidsdata-1.2.ebuild: diff --git a/sci-biology/opfvta_bidsdata/Manifest b/sci-biology/opfvta_bidsdata/Manifest index b015f61..1076871 100644 --- a/sci-biology/opfvta_bidsdata/Manifest +++ b/sci-biology/opfvta_bidsdata/Manifest @@ -1 +1,2 @@ DIST opfvta_bidsdata-1.2.tar.xz 12101699696 SHA256 5c48b4214abc8d7cc8c0b8820bba52950427cd44ee397031bfe674503762693f SHA512 213100ccf561b2d805199a876e85f0793545df5d2fed5ac0039e008d0fe9706f9836ca94a351e9651032d2f96b0b91182e1c2d4b129dbf3ec824d852c77880aa WHIRLPOOL 0f0d0fc4a1fcb9324547841517f0584431baef3346c94fcf1e56ff81b5bb62848b72587a0c2d8ca8b53d74a3ac76c2f8c641c38e01290c8637a464db1190f8c1 +DIST opfvta_bidsdata-2.0.tar.xz 12372152444 SHA256 10453e5d9d8e5f747a19d7c8a571cafb8bb2f93128c6ddd97c267520ab8ed781 SHA512 4e8769e358a8f0e2c25b46db094d0cbf375bf4aa83365834be5ee6a1db012d6be6174f0416f0158354a17e9616863a459f9d89ea3df8694bf23d4ecd75b289fc WHIRLPOOL 1738d8257ce18473f7522e175bf893d9b0087b17a8eaff900108fe04e9bc9d8a8ee27cb3d109df1be0b1aa9126a5b6d4a2929dc7014c27b6c0dbc51fec38f7c8 diff --git a/sci-biology/opfvta_bidsdata/opfvta_bidsdata-2.0.ebuild b/sci-biology/opfvta_bidsdata/opfvta_bidsdata-2.0.ebuild new file mode 100644 index 0000000..3c1317f --- /dev/null +++ b/sci-biology/opfvta_bidsdata/opfvta_bidsdata-2.0.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2019 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +inherit check-reqs + +DESCRIPTION="BIDS data files released with the OPFVTA publication" +HOMEPAGE="http://www.aic-fmi.ethz.ch/" +SRC_URI=" + http://chymera.eu/distfiles/${P}.tar.xz + https://zenodo.org/record/3565897/files/${P}.tar.xz + " + +LICENSE="CC-BY-SA-4.0" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + +RDEPEND="" +DEPEND="" + +pkg_pretend() { + CHECKREQS_DISK_BUILD="33G" + check-reqs_pkg_pretend +} + +# We disable this phase to not check requirements twice. +pkg_setup() { :; } + +src_install() { + insinto "/usr/share/${PN}" + doins -r * +} From 95d7a3a3b786a0083614be09b96666a439f8da65 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Tue, 10 Dec 2019 09:09:45 +0100 Subject: [PATCH 26/54] sci-biology/drlfom_bidsdata: version bump 1.1 ahead of Gentoo Science Package-Manager: Portage-2.3.78, Repoman-2.3.17 Signed-off-by: Horea Christian --- sci-biology/drlfom_bidsdata/ChangeLog | 7 ++++ sci-biology/drlfom_bidsdata/Manifest | 1 + .../drlfom_bidsdata-1.1.ebuild | 33 +++++++++++++++++++ sci-biology/drlfom_bidsdata/metadata.xml | 18 ++++++++++ 4 files changed, 59 insertions(+) create mode 100644 sci-biology/drlfom_bidsdata/ChangeLog create mode 100644 sci-biology/drlfom_bidsdata/Manifest create mode 100644 sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild create mode 100644 sci-biology/drlfom_bidsdata/metadata.xml diff --git a/sci-biology/drlfom_bidsdata/ChangeLog b/sci-biology/drlfom_bidsdata/ChangeLog new file mode 100644 index 0000000..3914151 --- /dev/null +++ b/sci-biology/drlfom_bidsdata/ChangeLog @@ -0,0 +1,7 @@ + 28 Jun 2019; drlfom_bidsdata-1.0.ebuild: + sci-biology/drlfom_bidsdata: alternative download link + +*drlfom_bidsdata-1.0 (28 Jun 2019) + + 28 Jun 2019; +drlfom_bidsdata-1.0.ebuild, +metadata.xml: + sci-biology/drlfom_bidsdata: new package ahead of Gentoo Science diff --git a/sci-biology/drlfom_bidsdata/Manifest b/sci-biology/drlfom_bidsdata/Manifest new file mode 100644 index 0000000..8c937cb --- /dev/null +++ b/sci-biology/drlfom_bidsdata/Manifest @@ -0,0 +1 @@ +DIST drlfom_bidsdata-1.1.tar.xz 22144796704 SHA256 4b33cb51be1c560ff12f37de027a697631979ef2fe8fe20fec25484feae0015b SHA512 84e574cb6714060292d07cacb6ae84aed051100f966713db6b6ac0dd08d3c01e84da8afde66980eb9b0625e8de2f100444ab84d933d7a280af5a39b4b6eab531 WHIRLPOOL 0b74171b9b356397c1b12f7247d602bd1da77ff409fa522c126febf9cde387f9931d61cef3360b11388d4094a53ff0c5990cc0257418c3bafae203c224264e68 diff --git a/sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild b/sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild new file mode 100644 index 0000000..d997dd1 --- /dev/null +++ b/sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2019 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +inherit check-reqs + +DESCRIPTION="BIDS data files released with the DRLFOM publication" +HOMEPAGE="http://www.aic-fmi.ethz.ch/" +SRC_URI=" + https://zenodo.org/record/3260745/files/${P}.tar.xz + http://chymera.eu/distfiles/${P}.tar.xz + " + +LICENSE="CC-BY-SA-4.0" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + +RDEPEND="" +DEPEND="" + +pkg_pretend() { + CHECKREQS_DISK_BUILD="21G" + check-reqs_pkg_pretend +} + +# We disable this phase to not check requirements twice. +pkg_setup() { :; } + +src_install() { + insinto "/usr/share/${PN}" + doins -r * +} diff --git a/sci-biology/drlfom_bidsdata/metadata.xml b/sci-biology/drlfom_bidsdata/metadata.xml new file mode 100644 index 0000000..0df40cb --- /dev/null +++ b/sci-biology/drlfom_bidsdata/metadata.xml @@ -0,0 +1,18 @@ + + + + + chr@chymera.eu + Horea Christian + + + sci@gentoo.org + Gentoo Science Project + + + BIDS-formatted MRI data recorded at the ETH/UZH Animal Imaging Center + and first associated with the DRLFOM publication. The data represents + optp-fMRI mouse brain scans with CBV contrast, tracking serotonergic + stimulation over the course of a fluoxetine drinking water treatment. + + From 87853a77b413504adc5695eb4ffbbfaedba2d454 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Tue, 10 Dec 2019 09:14:15 +0100 Subject: [PATCH 27/54] sci-biology/irsabi_bidsdata: version bump 1.4 ahead of Gentoo Science Package-Manager: Portage-2.3.78, Repoman-2.3.17 Signed-off-by: Horea Christian --- sci-biology/irsabi_bidsdata/ChangeLog | 6 ++++++ sci-biology/irsabi_bidsdata/Manifest | 2 +- ...abi_bidsdata-1.3.1.ebuild => irsabi_bidsdata-1.4.ebuild} | 0 3 files changed, 7 insertions(+), 1 deletion(-) rename sci-biology/irsabi_bidsdata/{irsabi_bidsdata-1.3.1.ebuild => irsabi_bidsdata-1.4.ebuild} (100%) diff --git a/sci-biology/irsabi_bidsdata/ChangeLog b/sci-biology/irsabi_bidsdata/ChangeLog index a7529d5..f1c8949 100644 --- a/sci-biology/irsabi_bidsdata/ChangeLog +++ b/sci-biology/irsabi_bidsdata/ChangeLog @@ -1,3 +1,9 @@ +*irsabi_bidsdata-1.4 (10 Dec 2019) + + 10 Dec 2019; +irsabi_bidsdata-1.4.ebuild, + -irsabi_bidsdata-1.3.1.ebuild: + sci-biology/irsabi_bidsdata: version bump 1.4 ahead of Gentoo Science + *irsabi_bidsdata-1.3.1 (08 Nov 2019) 08 Nov 2019; +irsabi_bidsdata-1.3.1.ebuild, diff --git a/sci-biology/irsabi_bidsdata/Manifest b/sci-biology/irsabi_bidsdata/Manifest index af39e5a..ab2e388 100644 --- a/sci-biology/irsabi_bidsdata/Manifest +++ b/sci-biology/irsabi_bidsdata/Manifest @@ -1 +1 @@ -DIST irsabi_bidsdata-1.3.1.tar.xz 4503360924 SHA256 e8ef649c16cd414d39c3d687850a2bfa6e08eefded50f1f1b4cc0c1c84541ea7 SHA512 c4516bce690b6d7e576ef491895b0bb6d9e21cb16da1ab892e8822f7bc358ba4ca7011bdab0e4e7bf9f774ac53404bee341531e8f834ee47e68ab7bb3be67e40 WHIRLPOOL 1cdbe4cdbf71c5ec657827db6d72ff34a2a17a0041c9d21a9ab9dbc30a5b20ca29e3024839626623d7e6d7dc09dbeb706dc0a77363a3aacdcdf7542c86ece389 +DIST irsabi_bidsdata-1.4.tar.xz 4503367352 SHA256 d837835ddf43d1e8322ba2444a1d9ef51b59f8312252207c5f7a2a302eca0149 SHA512 20a6e486d74ca57b3a8cced87db7fc110ae7ad2e466bd76cfd3ad46ec317c30597a4569005696c509dc2f9fc40dd1d0dbee0c0bf174e5ae8cab53058ce980b10 WHIRLPOOL 7a5600766ba35a5808ac6520abcce35eabebc168b4f3930e264caa8377bdd274bbf68aa625e8857feeb3cfc45689e7687b132f2af8c8a2a109b1b7c9a67c2acf diff --git a/sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.3.1.ebuild b/sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild similarity index 100% rename from sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.3.1.ebuild rename to sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild From 217dac5169da4ec73a5ec0a6263aaa7cef27012a Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Sat, 14 Dec 2019 11:28:21 +0100 Subject: [PATCH 28/54] sci-biology/ants: prefix fix ahead of Gentoo Science Package-Manager: Portage-2.3.78, Repoman-2.3.17 Signed-off-by: Horea Christian --- sci-biology/ants/ChangeLog | 6 ++++++ ...s-9999.ebuild => ants-2.3.1_p20191013.ebuild} | 16 +++++++++------- sci-biology/ants/metadata.xml | 2 +- 3 files changed, 16 insertions(+), 8 deletions(-) rename sci-biology/ants/{ants-9999.ebuild => ants-2.3.1_p20191013.ebuild} (71%) diff --git a/sci-biology/ants/ChangeLog b/sci-biology/ants/ChangeLog index a6e2e47..7a89409 100644 --- a/sci-biology/ants/ChangeLog +++ b/sci-biology/ants/ChangeLog @@ -1,3 +1,9 @@ +*ants-2.3.1_p20191013 (14 Dec 2019) + + 14 Dec 2019; +ants-2.3.1_p20191013.ebuild, + -ants-9999.ebuild, metadata.xml: + sci-biology/ants: prefix fix ahead of Gentoo Science + 25 Nov 2019; -ants-2.3.1_p20191013.ebuild: sci-biology/ants: migrated version bump to Gentoo Scinece https://gitweb.gent oo.org/proj/sci.git/commit/?id=402183f38c721910fe038ed4ce04e0a98a37c584 diff --git a/sci-biology/ants/ants-9999.ebuild b/sci-biology/ants/ants-2.3.1_p20191013.ebuild similarity index 71% rename from sci-biology/ants/ants-9999.ebuild rename to sci-biology/ants/ants-2.3.1_p20191013.ebuild index b759acb..060a38c 100644 --- a/sci-biology/ants/ants-9999.ebuild +++ b/sci-biology/ants/ants-2.3.1_p20191013.ebuild @@ -11,14 +11,15 @@ DESCRIPTION="Advanced Normalitazion Tools for neuroimaging" HOMEPAGE="http://stnava.github.io/ANTs/" SRC_URI=" test? ( - http://chymera.eu/distfiles/ants_testdata-2.3.1_p20191013.tar.xz + http://chymera.eu/distfiles/ants_testdata-${PV}.tar.xz ) " EGIT_REPO_URI="https://github.com/stnava/ANTs.git" +EGIT_COMMIT="f78b2d4a382d3090230641b5ade5da28962dad04" SLOT="0" LICENSE="BSD" -KEYWORDS="" +KEYWORDS="~amd64 ~x86" IUSE="test vtk" DEPEND=" @@ -31,27 +32,28 @@ DEPEND=" RDEPEND="${DEPEND}" PATCHES=( - "${FILESDIR}/${PN}-2.3.1_p20191013-paths.patch" + "${FILESDIR}/${P}-logic.patch" + "${FILESDIR}/${P}-paths.patch" ) src_unpack() { git-r3_src_unpack if use test; then mkdir -p "${S}/.ExternalData/MD5" || die "Could not create test data directory." - tar xvf "${DISTDIR}/ants_testdata-2.3.1_p20191013.tar.xz" -C "${S}/.ExternalData/MD5/" > /dev/null || die "Could not unpack test data." + tar xvf "${DISTDIR}/ants_testdata-${PV}.tar.xz" -C "${S}/.ExternalData/MD5/" > /dev/null || die "Could not unpack test data." fi } src_configure() { local mycmakeargs=( -DUSE_SYSTEM_ITK=ON - -DITK_DIR="/usr/include/ITK-5.0/" + -DITK_DIR="${EROOT}/usr/include/ITK-5.0/" -DBUILD_TESTING="$(usex test ON OFF)" -DUSE_VTK=$(usex vtk ON OFF) -DUSE_SYSTEM_VTK=$(usex vtk ON OFF) ) use vtk && mycmakeargs+=( - -DVTK_DIR="/usr/include/vtk-8.1/" + -DVTK_DIR="${EROOT}/usr/include/vtk-8.1/" ) use test && mycmakeargs+=( -DExternalData_OBJECT_STORES="${S}/.ExternalData/MD5" @@ -65,6 +67,6 @@ src_install() { cd "${WORKDIR}/${P}/Scripts" || die "scripts dir not found" dobin *.sh dodir /usr/$(get_libdir)/ants - install -t "${D}"/usr/$(get_libdir)/ants * || die + install -t "${D}"/"${EROOT%/}"/usr/$(get_libdir)/ants * || die doenvd "${FILESDIR}"/99ants } diff --git a/sci-biology/ants/metadata.xml b/sci-biology/ants/metadata.xml index efbe326..87d2feb 100644 --- a/sci-biology/ants/metadata.xml +++ b/sci-biology/ants/metadata.xml @@ -2,7 +2,7 @@ - horea.christ@gmail.com + chr@chymera.eu Horea Christian From b0d778a6d1321baffe1f4eba9e977e19b92242c6 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Tue, 17 Dec 2019 16:39:43 +0100 Subject: [PATCH 29/54] app-misc/python-dice: new package ahead of gentoo main Package-Manager: Portage-2.3.81, Repoman-2.3.20 Signed-off-by: Horea Christian --- app-misc/python-dice/ChangeLog | 6 +++ app-misc/python-dice/Manifest | 3 +- app-misc/python-dice/python-dice-2.4.2.ebuild | 48 ------------------- ...-3.0.0.ebuild => python-dice-3.1.0.ebuild} | 5 +- 4 files changed, 8 insertions(+), 54 deletions(-) delete mode 100644 app-misc/python-dice/python-dice-2.4.2.ebuild rename app-misc/python-dice/{python-dice-3.0.0.ebuild => python-dice-3.1.0.ebuild} (80%) diff --git a/app-misc/python-dice/ChangeLog b/app-misc/python-dice/ChangeLog index d34e18c..ecd59c5 100644 --- a/app-misc/python-dice/ChangeLog +++ b/app-misc/python-dice/ChangeLog @@ -1,3 +1,9 @@ +*python-dice-3.1.0 (17 Dec 2019) + + 17 Dec 2019; +python-dice-3.1.0.ebuild, + -python-dice-2.4.2.ebuild, -python-dice-3.0.0.ebuild: + app-misc/python-dice: new package ahead of gentoo main + *python-dice-3.0.0 (06 Dec 2019) 06 Dec 2019; +python-dice-3.0.0.ebuild: diff --git a/app-misc/python-dice/Manifest b/app-misc/python-dice/Manifest index 4144b9e..4026f43 100644 --- a/app-misc/python-dice/Manifest +++ b/app-misc/python-dice/Manifest @@ -1,2 +1 @@ -DIST python-dice-2.4.2.tar.gz 18922 SHA256 f7738436cfc8976bc5e61809bfb5c6a910d892601d46042a91c314a3b6a98f29 SHA512 821171d762deecf1b5a9cd9be20207c923a0ff37f35b3de339127e69ef588c9a63ad5d4680f286c3415ad130f4e156cd1c31135285fd00153f6ee6ba55ea01da WHIRLPOOL 5295b60214d439f2215880c54eade25ac907bd240986d25907e4439578bf3aadcb0dff02ea1cb1a2ff1b2d6d3a4610d87625bb2212db6ce7ccb8042b8742d3af -DIST python-dice-3.0.0.tar.gz 23514 SHA256 eacd7d0c044d1b0f88ec6d33625952e594c900b7ebea6329058461cdad64bcf6 SHA512 181a0fc9057052e252bac817f7e076a9367cf74537de7182d5842804498f43c0e7a69b65975bbee03c9de340fd05d712fabb5207df5c7dae1faf4717912741dd WHIRLPOOL 1b86068d02807672c1d79c4f8274f723d5ba98c40170e27140abde80802b393ba447d3fc08a9c268ed2fd6deaa45a6c9d18902abda2ba74eb869cf79b9c4d0b4 +DIST python-dice-3.1.0.tar.gz 23510 SHA256 f28a497fd59ffb44cb3c957445feff9677ba4768e8d784cf080986f20fa0d56d SHA512 121ab7d09b2b7b799f0894ee0ab2ee45b7ebc3c8f721849cdefe5c8f7bb6bb07560dd9af009d03a0ac8a40da7dd106f593bd884fc20f4e899da67ce08e46b705 WHIRLPOOL 047ce6cb95afa800324144ed970bcab407c3486fbecaab5881430bea968df18b84ed22767cd5a756796b61084c6dc4c1a304abc587101258297cecf25103d3a1 diff --git a/app-misc/python-dice/python-dice-2.4.2.ebuild b/app-misc/python-dice/python-dice-2.4.2.ebuild deleted file mode 100644 index 8ee05dd..0000000 --- a/app-misc/python-dice/python-dice-2.4.2.ebuild +++ /dev/null @@ -1,48 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_6 ) - -inherit distutils-r1 - -DESCRIPTION="Dice parsing and evaluation library" -HOMEPAGE="https://github.com/borntyping/python-dice" -SRC_URI="https://github.com/borntyping/python-dice/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64" -IUSE="test" -RESTRICT="test" -# Tests do not run, which may be an upstream issue: -# https://github.com/borntyping/python-dice/issues/25 - -DEPEND="test? ( - dev-python/coverage[${PYTHON_USEDEP}] - dev-python/pyflakes[${PYTHON_USEDEP}] - dev-python/pytest[${PYTHON_USEDEP}] - dev-python/pytest-cov[${PYTHON_USEDEP}] - dev-python/pytest-flakes[${PYTHON_USEDEP}] - dev-python/pytest-pep8[${PYTHON_USEDEP}] - dev-python/termcolor[${PYTHON_USEDEP}] - dev-python/tox[${PYTHON_USEDEP}] - ) -" -RDEPEND=" - dev-python/docopt[${PYTHON_USEDEP}] - >=dev-python/pyparsing-2.4.1[${PYTHON_USEDEP}] -" - -src_prepare() { - if use test; then - sed -i -e "s/pytest<3.7.0/pytest/g" tox.ini - fi - default -} - -python_test() { - #pytest -vv || die - tox || die "tests failed under ${EPYTHON}" -} diff --git a/app-misc/python-dice/python-dice-3.0.0.ebuild b/app-misc/python-dice/python-dice-3.1.0.ebuild similarity index 80% rename from app-misc/python-dice/python-dice-3.0.0.ebuild rename to app-misc/python-dice/python-dice-3.1.0.ebuild index e12d606..358b38f 100644 --- a/app-misc/python-dice/python-dice-3.0.0.ebuild +++ b/app-misc/python-dice/python-dice-3.1.0.ebuild @@ -19,10 +19,8 @@ IUSE="test" DEPEND="test? ( dev-python/coverage[${PYTHON_USEDEP}] dev-python/pytest[${PYTHON_USEDEP}] - dev-python/pytest-cov[${PYTHON_USEDEP}] ) " -#dev-python/tox[${PYTHON_USEDEP}] RDEPEND=" dev-python/docopt[${PYTHON_USEDEP}] >=dev-python/pyparsing-2.4.1[${PYTHON_USEDEP}] @@ -30,12 +28,11 @@ RDEPEND=" src_prepare() { if use test; then - sed -i -e "s/pytest<3.7.0/pytest/g" tox.ini + sed -i -e "s/--cov=dice //g" tox.ini || die "Could not remove pytest-cov usage for tests." fi default } python_test() { pytest -vv || die - #tox || die "tests failed under ${EPYTHON}" } From b0e571533e3650d48b1b2e71776b25dc670a77e3 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Sat, 21 Dec 2019 16:26:53 +0100 Subject: [PATCH 30/54] dev-python/pyvote: new package ahead of Gentoo Main Package-Manager: Portage-2.3.78, Repoman-2.3.17 Signed-off-by: Horea Christian --- dev-python/pyvote/ChangeLog | 4 ++++ dev-python/pyvote/Manifest | 1 + dev-python/pyvote/metadata.xml | 19 +++++++++++++++++++ dev-python/pyvote/pyvote-0.1.ebuild | 24 ++++++++++++++++++++++++ dev-python/pyvote/pyvote-9999.ebuild | 24 ++++++++++++++++++++++++ 5 files changed, 72 insertions(+) create mode 100644 dev-python/pyvote/ChangeLog create mode 100644 dev-python/pyvote/Manifest create mode 100644 dev-python/pyvote/metadata.xml create mode 100644 dev-python/pyvote/pyvote-0.1.ebuild create mode 100644 dev-python/pyvote/pyvote-9999.ebuild diff --git a/dev-python/pyvote/ChangeLog b/dev-python/pyvote/ChangeLog new file mode 100644 index 0000000..7218508 --- /dev/null +++ b/dev-python/pyvote/ChangeLog @@ -0,0 +1,4 @@ +*trimesh-3.3.5 (04 Nov 2019) + + 04 Nov 2019; +metadata.xml, +trimesh-3.3.5.ebuild: + dev-python/trimesh: version bump ahead of Genoo Science diff --git a/dev-python/pyvote/Manifest b/dev-python/pyvote/Manifest new file mode 100644 index 0000000..1878349 --- /dev/null +++ b/dev-python/pyvote/Manifest @@ -0,0 +1 @@ +DIST pyvote-0.1.tar.gz 17689 SHA256 5c8f104866e2bfe47047524cbb2b6b773c0aeaee11f13800257112b93220028c SHA512 be6a0b5aa71ef4e151a5d95411c8614d956217d71ab53d3b0ff3f1a209c7980efa87545ab234465b6411daa1d9b63722670500323aff55e27240cc1d5ce8aa88 WHIRLPOOL 3c3be95e37b69a7df5a4a25dbb50ab7f4f91127af097e5f8435514495b22dad4db678a60c6ca3ffa2ede99b2de3d3c78979ae95382a65dd09e071201683d2d4c diff --git a/dev-python/pyvote/metadata.xml b/dev-python/pyvote/metadata.xml new file mode 100644 index 0000000..7e56746 --- /dev/null +++ b/dev-python/pyvote/metadata.xml @@ -0,0 +1,19 @@ + + + + + horea.christ@gmail.com + Horea Christian + + + sci@gentoo.org + Gentoo Science Project + + + This package provides a Python module and a Bash interface which can + compute the probability of a 2-choice popular election being decided by + one vote. Predictions are based on either a series of forecasts, a beta + (or normal) probability density function for outcomes, or a fixed + outcome probability. + + diff --git a/dev-python/pyvote/pyvote-0.1.ebuild b/dev-python/pyvote/pyvote-0.1.ebuild new file mode 100644 index 0000000..2dc1ebe --- /dev/null +++ b/dev-python/pyvote/pyvote-0.1.ebuild @@ -0,0 +1,24 @@ +# Copyright 1999-2019 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +PYTHON_COMPAT=( python2_7 python3_{5,6} ) + +inherit distutils-r1 + +DESCRIPTION="Estimate the probability of votes changing election outcomes" +HOMEPAGE="https://github.com/TheChymera/pyvote.git" +SRC_URI="https://github.com/TheChymera/pyvote/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test" + +DEPEND="" +RDEPEND=" + dev-python/argh[${PYTHON_USEDEP}] + dev-python/mpmath[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] +" diff --git a/dev-python/pyvote/pyvote-9999.ebuild b/dev-python/pyvote/pyvote-9999.ebuild new file mode 100644 index 0000000..6eb5b82 --- /dev/null +++ b/dev-python/pyvote/pyvote-9999.ebuild @@ -0,0 +1,24 @@ +# Copyright 1999-2019 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +PYTHON_COMPAT=( python2_7 python3_{5,6} ) + +inherit distutils-r1 git-r3 + +DESCRIPTION="Estimate the probability of votes changing election outcomes" +HOMEPAGE="https://github.com/TheChymera/pyvote.git" +EGIT_REPO_URI="https://github.com/TheChymera/pyvote.git" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="" +IUSE="test" + +DEPEND="" +RDEPEND=" + dev-python/argh[${PYTHON_USEDEP}] + dev-python/mpmath[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] +" From cf348cd8dcd36000e69754b2d770c7f99be3f624 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Mon, 23 Dec 2019 15:08:00 +0100 Subject: [PATCH 31/54] dev-python/statsmodels: version bump ahead of Gentoo Main Package-Manager: Portage-2.3.82, Repoman-2.3.20 Signed-off-by: Horea Christian --- dev-python/statsmodels/ChangeLog | 6 ++ dev-python/statsmodels/Manifest | 1 + .../files/statsmodels-0.6.1-numpy-1.10.patch | 20 +++++ .../statsmodels-0.6.1-pandas-0.17.0.patch | 30 ++++++++ dev-python/statsmodels/metadata.xml | 34 +++++++++ .../statsmodels/statsmodels-0.10.1.ebuild | 73 +++++++++++++++++++ 6 files changed, 164 insertions(+) create mode 100644 dev-python/statsmodels/ChangeLog create mode 100644 dev-python/statsmodels/Manifest create mode 100644 dev-python/statsmodels/files/statsmodels-0.6.1-numpy-1.10.patch create mode 100644 dev-python/statsmodels/files/statsmodels-0.6.1-pandas-0.17.0.patch create mode 100644 dev-python/statsmodels/metadata.xml create mode 100644 dev-python/statsmodels/statsmodels-0.10.1.ebuild diff --git a/dev-python/statsmodels/ChangeLog b/dev-python/statsmodels/ChangeLog new file mode 100644 index 0000000..077f945 --- /dev/null +++ b/dev-python/statsmodels/ChangeLog @@ -0,0 +1,6 @@ +*statsmodels-0.10.1 (23 Dec 2019) + + 23 Dec 2019; +files/statsmodels-0.6.1-numpy-1.10.patch, + +files/statsmodels-0.6.1-pandas-0.17.0.patch, +metadata.xml, + +statsmodels-0.10.1.ebuild: + dev-python/statsmodels: version bump ahead of Gentoo Main diff --git a/dev-python/statsmodels/Manifest b/dev-python/statsmodels/Manifest new file mode 100644 index 0000000..ad2fe3e --- /dev/null +++ b/dev-python/statsmodels/Manifest @@ -0,0 +1 @@ +DIST statsmodels-0.10.1.tar.gz 14056607 SHA256 320659a80f916c2edf9dfbe83512d9004bb562b72eedb7d9374562038697fa10 SHA512 eebbdd02af841f66c93e3ea8998c2a74dcf785e12d95c33e0ff791e4abee932b2b76750cd9734a23e260d99f952be5392204607c42a99122e06340f61c96ae6f WHIRLPOOL 730547f525f9eac48bb057ae0dd7f5863ea688828ec71c99c9ea5eaf813efb534d979b45f8c3db8bfffd25bc3a6cb1e9f8fd9925de46572c838b310e194e55cd diff --git a/dev-python/statsmodels/files/statsmodels-0.6.1-numpy-1.10.patch b/dev-python/statsmodels/files/statsmodels-0.6.1-numpy-1.10.patch new file mode 100644 index 0000000..2d9720c --- /dev/null +++ b/dev-python/statsmodels/files/statsmodels-0.6.1-numpy-1.10.patch @@ -0,0 +1,20 @@ + statsmodels/tsa/ar_model.py | 6 ++---- + 1 file changed, 2 insertions(+), 4 deletions(-) + +diff --git a/statsmodels/tsa/ar_model.py b/statsmodels/tsa/ar_model.py +index f0af7ee..fe05634 100644 +--- a/statsmodels/tsa/ar_model.py ++++ b/statsmodels/tsa/ar_model.py +@@ -256,10 +256,8 @@ class AR(tsbase.TimeSeriesModel): + + Vpinv = np.zeros((p, p), dtype=params.dtype) + for i in range(1, p1): +- Vpinv[i-1, i-1:] = np.correlate(params0, params0[:i], +- old_behavior=False)[:-1] +- Vpinv[i-1, i-1:] -= np.correlate(params0[-i:], params0, +- old_behavior=False)[:-1] ++ Vpinv[i-1, i-1:] = np.correlate(params0, params0[:i])[:-1] ++ Vpinv[i-1, i-1:] -= np.correlate(params0[-i:], params0)[:-1] + + Vpinv = Vpinv + Vpinv.T - np.diag(Vpinv.diagonal()) + return Vpinv diff --git a/dev-python/statsmodels/files/statsmodels-0.6.1-pandas-0.17.0.patch b/dev-python/statsmodels/files/statsmodels-0.6.1-pandas-0.17.0.patch new file mode 100644 index 0000000..540135c --- /dev/null +++ b/dev-python/statsmodels/files/statsmodels-0.6.1-pandas-0.17.0.patch @@ -0,0 +1,30 @@ + setup.py | 2 +- + statsmodels/tools/testing.py | 2 +- + 2 files changed, 2 insertions(+), 2 deletions(-) + +diff --git a/setup.py b/setup.py +index 1a7da9a..a6d1b33 100644 +--- a/setup.py ++++ b/setup.py +@@ -134,7 +134,7 @@ def check_dependency_versions(min_versions): + (spversion, min_versions['scipy'])) + + try: +- from pandas.version import short_version as pversion ++ from pandas import __version__ as pversion + except ImportError: + install_requires.append('pandas') + else: +diff --git a/statsmodels/tools/testing.py b/statsmodels/tools/testing.py +index 1fde1de..92e77fc 100644 +--- a/statsmodels/tools/testing.py ++++ b/statsmodels/tools/testing.py +@@ -17,7 +17,7 @@ def strip_rc(version): + def is_pandas_min_version(min_version): + '''check whether pandas is at least min_version + ''' +- from pandas.version import short_version as pversion ++ from pandas import __version__ as pversion + return StrictVersion(strip_rc(pversion)) >= min_version + + diff --git a/dev-python/statsmodels/metadata.xml b/dev-python/statsmodels/metadata.xml new file mode 100644 index 0000000..0a394be --- /dev/null +++ b/dev-python/statsmodels/metadata.xml @@ -0,0 +1,34 @@ + + + + + python@gentoo.org + Python + + + sci-mathematics@gentoo.org + Gentoo Mathematics Project + + + horea.christ@gmail.com + Horea Christian + + + proxy-maint@gentoo.org + Proxy Maintainers + + + statsmodels is a Python module that allows users to explore data, + estimate statistical models, and perform statistical tests. An + extensive list of descriptive statistics, statistical tests, + plotting functions, and result statistics are available for + different types of data and each estimator. Researchers across + fields may find that statsmodels fully meets their needs for + statistical computing and data analysis in Python. + + + statsmodels + statsmodels + statsmodels + + diff --git a/dev-python/statsmodels/statsmodels-0.10.1.ebuild b/dev-python/statsmodels/statsmodels-0.10.1.ebuild new file mode 100644 index 0000000..087d3f0 --- /dev/null +++ b/dev-python/statsmodels/statsmodels-0.10.1.ebuild @@ -0,0 +1,73 @@ +# Copyright 1999-2019 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 +PYTHON_COMPAT=( python2_7 python3_{5,6,7} ) + +inherit distutils-r1 eutils + +DESCRIPTION="Statistical computations and models for use with SciPy" +HOMEPAGE="https://www.statsmodels.org/stable/index.html" +SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples test" + +COMMON_DEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + >=dev-python/pandas-0.23.0[${PYTHON_USEDEP}] + dev-python/patsy[${PYTHON_USEDEP}] + sci-libs/scipy[${PYTHON_USEDEP}] +" +RDEPEND="${COMMON_DEPEND}" +DEPEND="${COMMON_DEPEND} + dev-python/cython[${PYTHON_USEDEP}] + dev-python/setuptools[${PYTHON_USEDEP}] + doc? ( + dev-python/ipykernel[${PYTHON_USEDEP}] + dev-python/jupyter_client[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/nbconvert[${PYTHON_USEDEP}] + dev-python/nbformat[${PYTHON_USEDEP}] + dev-python/numpydoc[${PYTHON_USEDEP}] + dev-python/sphinx[${PYTHON_USEDEP}] + ) + test? ( + dev-python/pytest[${PYTHON_USEDEP}] + dev-python/nose[${PYTHON_USEDEP}] + ) +" + +python_prepare_all() { + # Prevent un-needed d'loading + sed -e "/sphinx.ext.intersphinx/d" -i docs/source/conf.py || die + export VARTEXFONTS="${T}"/fonts + export MPLCONFIGDIR="${T}" + echo "backend : Agg" > "${MPLCONFIGDIR}"/matplotlibrc || die + distutils-r1_python_prepare_all +} + +python_compile_all() { + use doc && esetup.py build_sphinx -b html --build-dir=docs/build +} + +python_test() { + cd "${BUILD_DIR}" || die + python -c 'import statsmodels; statsmodels.test()' || die +} + +python_install_all() { + find . -name \*LICENSE.txt -delete || die + use doc && HTML_DOCS=( docs/build/html/. ) + if use examples; then + docompress -x /usr/share/doc/${PF}/examples + dodoc -r examples + fi + distutils-r1_python_install_all +} + +pkg_postinst() { + optfeature "Plotting functionality" "dev-python/matplotlib" +} From 5f092224a50484700dde4a2b4c0748d876c23809 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Mon, 23 Dec 2019 16:01:37 +0100 Subject: [PATCH 32/54] app-misc/gebuilder: new versioned ebuild Package-Manager: Portage-2.3.82, Repoman-2.3.20 Signed-off-by: Horea Christian --- app-misc/gebuilder/ChangeLog | 6 ++++++ app-misc/gebuilder/Manifest | 1 + .../{gebuilder-9999.ebuild => gebuilder-0.1.ebuild} | 7 ++----- 3 files changed, 9 insertions(+), 5 deletions(-) create mode 100644 app-misc/gebuilder/Manifest rename app-misc/gebuilder/{gebuilder-9999.ebuild => gebuilder-0.1.ebuild} (92%) diff --git a/app-misc/gebuilder/ChangeLog b/app-misc/gebuilder/ChangeLog index f48b6d3..9aa55b3 100644 --- a/app-misc/gebuilder/ChangeLog +++ b/app-misc/gebuilder/ChangeLog @@ -1,3 +1,9 @@ +*gebuilder-0.1 (23 Dec 2019) + + 23 Dec 2019; +gebuilder-0.1.ebuild, + -gebuilder-9999.ebuild: + app-misc/gebuilder: new versioned ebuild + 26 Oct 2019; gebuilder-9999.ebuild: app-misc/gebuilder: improved USE flag specification diff --git a/app-misc/gebuilder/Manifest b/app-misc/gebuilder/Manifest new file mode 100644 index 0000000..858d80d --- /dev/null +++ b/app-misc/gebuilder/Manifest @@ -0,0 +1 @@ +DIST gebuilder-0.1.tar.gz 69313 SHA256 a872200abdde4d4bb70fc3c783ec7fa15472ab2448034ef336e9aae0496a8b70 SHA512 53c736698cc6fb4ffbda38835b09b536e1b5bf0bcdb52ae25a0a1aefd42c65da137c08a3206939e36cb12d7ccc4daba683f2fcb0d6ec58f717b21ea15acad9ed WHIRLPOOL 3415d7fa242a08b6f5aae0be8968420ceb6d319aeeeb5da233c8ae28b07e1a3774cbc06ded09ad169e11f6333971c9eeba1221cabe3d4d6ae0733094f4e89bdc diff --git a/app-misc/gebuilder/gebuilder-9999.ebuild b/app-misc/gebuilder/gebuilder-0.1.ebuild similarity index 92% rename from app-misc/gebuilder/gebuilder-9999.ebuild rename to app-misc/gebuilder/gebuilder-0.1.ebuild index fd3458b..0e1d88c 100644 --- a/app-misc/gebuilder/gebuilder-9999.ebuild +++ b/app-misc/gebuilder/gebuilder-0.1.ebuild @@ -3,16 +3,13 @@ EAPI=7 -inherit git-r3 - DESCRIPTION="Gentoo System and Image Builder" HOMEPAGE="https://github.com/IBT-FMI/gebuilder" -SRC_URI="" -EGIT_REPO_URI="https://github.com/IBT-FMI/gebuilder.git" +SRC_URI="https://github.com/IBT-FMI/gebuilder/archive/${PV}.tar.gz -> ${P}.tar.gz" LICENSE="GPL-3" SLOT="0" -KEYWORDS="" +KEYWORDS="~amd64" IUSE="autoupdate btrfs docker openstack test" COMMON_DEPEND=" From 884755b2b37744049b12b7f2f07c16e3bbf3faef Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Mon, 6 Jan 2020 05:27:21 +0100 Subject: [PATCH 33/54] sys-fs/tmsu: version bump ahead of Gentoo main https://github.com/gentoo/gentoo/pull/10626#issuecomment-570885146 Package-Manager: Portage-2.3.83, Repoman-2.3.20 Signed-off-by: Horea Christian --- sys-fs/tmsu/ChangeLog | 5 ++++ sys-fs/tmsu/Manifest | 2 ++ sys-fs/tmsu/metadata.xml | 21 ++++++++++++++ sys-fs/tmsu/tmsu-0.7.5.ebuild | 54 +++++++++++++++++++++++++++++++++++ 4 files changed, 82 insertions(+) create mode 100644 sys-fs/tmsu/ChangeLog create mode 100644 sys-fs/tmsu/Manifest create mode 100644 sys-fs/tmsu/metadata.xml create mode 100644 sys-fs/tmsu/tmsu-0.7.5.ebuild diff --git a/sys-fs/tmsu/ChangeLog b/sys-fs/tmsu/ChangeLog new file mode 100644 index 0000000..fc0014e --- /dev/null +++ b/sys-fs/tmsu/ChangeLog @@ -0,0 +1,5 @@ +*tmsu-0.7.5 (06 Jan 2020) + + 06 Jan 2020; +metadata.xml, +tmsu-0.7.5.ebuild: + sys-fs/tmsu: version bump ahead of Gentoo main + https://github.com/gentoo/gentoo/pull/10626#issuecomment-570885146 diff --git a/sys-fs/tmsu/Manifest b/sys-fs/tmsu/Manifest new file mode 100644 index 0000000..0f39625 --- /dev/null +++ b/sys-fs/tmsu/Manifest @@ -0,0 +1,2 @@ +DIST github.com-mattn-go-sqlite3-v1.12.0.tar.gz 2282527 SHA256 f74a75ba86ecb52e1deef5102cdf3702e6c6bb524f399b7dfcd7d6d99e35fb30 SHA512 7e8656ecf70b2ffc40f6351b661f5eb75caa63c3e9784a805821bf0ca1f087203f1afe80f58af0e5520ff04baff728c93d670fd7ecb6662bb0fed1dd798ada96 WHIRLPOOL f0791e23d54fa87dd9f8852bddf3cfc078579844c37b3b68b577d1b8efd27c09c49fb054b8f20a319170074f6f5728879809e65f1126c4942b18c0d998d11846 +DIST tmsu-0.7.5.tar.gz 98766 SHA256 0ac7f09336aaedf73623c4f486c05137c024a726c16dd32525463aee9d70b46a SHA512 6f89eb156d2be86650ab84847ca0ddea985cdddf35db5f5843632b6a54f88681584b6864e4a14bc36cf1949713e098067e6f8dda0242f27b6061720165f71be1 WHIRLPOOL 6981f11f5313f3c222b0adaeb8bb75e7d439f328a92c5c6771a68f169df0ee774daf713d4f646456647ce74782c2e97a73e02c03a9b6f146f1455ded4cbf875c diff --git a/sys-fs/tmsu/metadata.xml b/sys-fs/tmsu/metadata.xml new file mode 100644 index 0000000..06bdd80 --- /dev/null +++ b/sys-fs/tmsu/metadata.xml @@ -0,0 +1,21 @@ + + + + + horea.christ@gmail.com + Horea Christian + + + proxy-maint@gentoo.org + Proxy Maintainers + + + TMSU is a tool for tagging your files. It provides a simple + command-line utility for applying tags and a virtual + filesystem to give you a tag-based view of your files from + any other program. + + + oniony/TMSU + + diff --git a/sys-fs/tmsu/tmsu-0.7.5.ebuild b/sys-fs/tmsu/tmsu-0.7.5.ebuild new file mode 100644 index 0000000..59bbfc3 --- /dev/null +++ b/sys-fs/tmsu/tmsu-0.7.5.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +EGO_PN="github.com/oniony/TMSU/" +EGO_VENDOR=( "github.com/mattn/go-sqlite3 v1.12.0" ) + +inherit golang-build golang-vcs-snapshot + +DESCRIPTION="Files tagger and virtual tag-based filesystem" +HOMEPAGE="https://github.com/oniony/TMSU/wiki" +SRC_URI=" + https://${EGO_PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz + ${EGO_VENDOR_URI} +" + +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="~amd64" +IUSE="test" +RESTRICT="!test? ( test )" + +RDEPEND="sys-fs/fuse:0" +DEPEND=" + dev-lang/go + dev-libs/go-fuse + test? ( ${RDEPEND} ) +" + +src_prepare() { + default + mkdir "${WORKDIR}/${P}/src/${EGO_PN}vendor/src" + mv "${WORKDIR}/${P}/src/${EGO_PN}vendor/github.com" "${WORKDIR}/${P}/src/${EGO_PN}vendor/src/" +} + +src_compile() { + pushd "${WORKDIR}/${P}/src/${EGO_PN}" + GOPATH="${WORKDIR}/${P}/src/${EGO_PN}vendor/" emake + popd || die +} + +src_install() { + dobin "${WORKDIR}/${P}/src/${EGO_PN}bin/tmsu" + dobin "${WORKDIR}/${P}/src/${EGO_PN}misc/bin/"* + doman "${WORKDIR}/${P}/src/${EGO_PN}misc/man/tmsu."* + insinto /usr/share/zsh/site-functions + doins "${WORKDIR}/${P}/src/${EGO_PN}misc/zsh/_tmsu" +} + +src_test() { + cd "${WORKDIR}/${P}/tests" || die + ./runall || die +} From e46bc241e5f97d7c41881436c4836b6dac200bc7 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Mon, 6 Jan 2020 05:28:24 +0100 Subject: [PATCH 34/54] sys-fs/tmsu: license update Package-Manager: Portage-2.3.83, Repoman-2.3.20 Signed-off-by: Horea Christian --- sys-fs/tmsu/ChangeLog | 3 +++ sys-fs/tmsu/tmsu-0.7.5.ebuild | 2 +- 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/sys-fs/tmsu/ChangeLog b/sys-fs/tmsu/ChangeLog index fc0014e..a27b563 100644 --- a/sys-fs/tmsu/ChangeLog +++ b/sys-fs/tmsu/ChangeLog @@ -1,3 +1,6 @@ + 06 Jan 2020; tmsu-0.7.5.ebuild: + sys-fs/tmsu: license update + *tmsu-0.7.5 (06 Jan 2020) 06 Jan 2020; +metadata.xml, +tmsu-0.7.5.ebuild: diff --git a/sys-fs/tmsu/tmsu-0.7.5.ebuild b/sys-fs/tmsu/tmsu-0.7.5.ebuild index 59bbfc3..5b89a90 100644 --- a/sys-fs/tmsu/tmsu-0.7.5.ebuild +++ b/sys-fs/tmsu/tmsu-0.7.5.ebuild @@ -15,7 +15,7 @@ SRC_URI=" ${EGO_VENDOR_URI} " -LICENSE="GPL-3+" +LICENSE="AGPL-3 AGPL-3+ BSD-4 GPL-3+ MIT" SLOT="0" KEYWORDS="~amd64" IUSE="test" From 9243aabab8aa3e94d2154a8fe9a3d562b007390f Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Mon, 6 Jan 2020 06:37:34 +0100 Subject: [PATCH 35/54] moved to Gentoo main: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e3dcd32cbcaa230535eccb1f4f4fb30b902c556c --- dev-python/statsmodels/ChangeLog | 6 -- dev-python/statsmodels/Manifest | 1 - .../files/statsmodels-0.6.1-numpy-1.10.patch | 20 ----- .../statsmodels-0.6.1-pandas-0.17.0.patch | 30 -------- dev-python/statsmodels/metadata.xml | 34 --------- .../statsmodels/statsmodels-0.10.1.ebuild | 73 ------------------- 6 files changed, 164 deletions(-) delete mode 100644 dev-python/statsmodels/ChangeLog delete mode 100644 dev-python/statsmodels/Manifest delete mode 100644 dev-python/statsmodels/files/statsmodels-0.6.1-numpy-1.10.patch delete mode 100644 dev-python/statsmodels/files/statsmodels-0.6.1-pandas-0.17.0.patch delete mode 100644 dev-python/statsmodels/metadata.xml delete mode 100644 dev-python/statsmodels/statsmodels-0.10.1.ebuild diff --git a/dev-python/statsmodels/ChangeLog b/dev-python/statsmodels/ChangeLog deleted file mode 100644 index 077f945..0000000 --- a/dev-python/statsmodels/ChangeLog +++ /dev/null @@ -1,6 +0,0 @@ -*statsmodels-0.10.1 (23 Dec 2019) - - 23 Dec 2019; +files/statsmodels-0.6.1-numpy-1.10.patch, - +files/statsmodels-0.6.1-pandas-0.17.0.patch, +metadata.xml, - +statsmodels-0.10.1.ebuild: - dev-python/statsmodels: version bump ahead of Gentoo Main diff --git a/dev-python/statsmodels/Manifest b/dev-python/statsmodels/Manifest deleted file mode 100644 index ad2fe3e..0000000 --- a/dev-python/statsmodels/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST statsmodels-0.10.1.tar.gz 14056607 SHA256 320659a80f916c2edf9dfbe83512d9004bb562b72eedb7d9374562038697fa10 SHA512 eebbdd02af841f66c93e3ea8998c2a74dcf785e12d95c33e0ff791e4abee932b2b76750cd9734a23e260d99f952be5392204607c42a99122e06340f61c96ae6f WHIRLPOOL 730547f525f9eac48bb057ae0dd7f5863ea688828ec71c99c9ea5eaf813efb534d979b45f8c3db8bfffd25bc3a6cb1e9f8fd9925de46572c838b310e194e55cd diff --git a/dev-python/statsmodels/files/statsmodels-0.6.1-numpy-1.10.patch b/dev-python/statsmodels/files/statsmodels-0.6.1-numpy-1.10.patch deleted file mode 100644 index 2d9720c..0000000 --- a/dev-python/statsmodels/files/statsmodels-0.6.1-numpy-1.10.patch +++ /dev/null @@ -1,20 +0,0 @@ - statsmodels/tsa/ar_model.py | 6 ++---- - 1 file changed, 2 insertions(+), 4 deletions(-) - -diff --git a/statsmodels/tsa/ar_model.py b/statsmodels/tsa/ar_model.py -index f0af7ee..fe05634 100644 ---- a/statsmodels/tsa/ar_model.py -+++ b/statsmodels/tsa/ar_model.py -@@ -256,10 +256,8 @@ class AR(tsbase.TimeSeriesModel): - - Vpinv = np.zeros((p, p), dtype=params.dtype) - for i in range(1, p1): -- Vpinv[i-1, i-1:] = np.correlate(params0, params0[:i], -- old_behavior=False)[:-1] -- Vpinv[i-1, i-1:] -= np.correlate(params0[-i:], params0, -- old_behavior=False)[:-1] -+ Vpinv[i-1, i-1:] = np.correlate(params0, params0[:i])[:-1] -+ Vpinv[i-1, i-1:] -= np.correlate(params0[-i:], params0)[:-1] - - Vpinv = Vpinv + Vpinv.T - np.diag(Vpinv.diagonal()) - return Vpinv diff --git a/dev-python/statsmodels/files/statsmodels-0.6.1-pandas-0.17.0.patch b/dev-python/statsmodels/files/statsmodels-0.6.1-pandas-0.17.0.patch deleted file mode 100644 index 540135c..0000000 --- a/dev-python/statsmodels/files/statsmodels-0.6.1-pandas-0.17.0.patch +++ /dev/null @@ -1,30 +0,0 @@ - setup.py | 2 +- - statsmodels/tools/testing.py | 2 +- - 2 files changed, 2 insertions(+), 2 deletions(-) - -diff --git a/setup.py b/setup.py -index 1a7da9a..a6d1b33 100644 ---- a/setup.py -+++ b/setup.py -@@ -134,7 +134,7 @@ def check_dependency_versions(min_versions): - (spversion, min_versions['scipy'])) - - try: -- from pandas.version import short_version as pversion -+ from pandas import __version__ as pversion - except ImportError: - install_requires.append('pandas') - else: -diff --git a/statsmodels/tools/testing.py b/statsmodels/tools/testing.py -index 1fde1de..92e77fc 100644 ---- a/statsmodels/tools/testing.py -+++ b/statsmodels/tools/testing.py -@@ -17,7 +17,7 @@ def strip_rc(version): - def is_pandas_min_version(min_version): - '''check whether pandas is at least min_version - ''' -- from pandas.version import short_version as pversion -+ from pandas import __version__ as pversion - return StrictVersion(strip_rc(pversion)) >= min_version - - diff --git a/dev-python/statsmodels/metadata.xml b/dev-python/statsmodels/metadata.xml deleted file mode 100644 index 0a394be..0000000 --- a/dev-python/statsmodels/metadata.xml +++ /dev/null @@ -1,34 +0,0 @@ - - - - - python@gentoo.org - Python - - - sci-mathematics@gentoo.org - Gentoo Mathematics Project - - - horea.christ@gmail.com - Horea Christian - - - proxy-maint@gentoo.org - Proxy Maintainers - - - statsmodels is a Python module that allows users to explore data, - estimate statistical models, and perform statistical tests. An - extensive list of descriptive statistics, statistical tests, - plotting functions, and result statistics are available for - different types of data and each estimator. Researchers across - fields may find that statsmodels fully meets their needs for - statistical computing and data analysis in Python. - - - statsmodels - statsmodels - statsmodels - - diff --git a/dev-python/statsmodels/statsmodels-0.10.1.ebuild b/dev-python/statsmodels/statsmodels-0.10.1.ebuild deleted file mode 100644 index 087d3f0..0000000 --- a/dev-python/statsmodels/statsmodels-0.10.1.ebuild +++ /dev/null @@ -1,73 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 -PYTHON_COMPAT=( python2_7 python3_{5,6,7} ) - -inherit distutils-r1 eutils - -DESCRIPTION="Statistical computations and models for use with SciPy" -HOMEPAGE="https://www.statsmodels.org/stable/index.html" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="doc examples test" - -COMMON_DEPEND=" - dev-python/numpy[${PYTHON_USEDEP}] - >=dev-python/pandas-0.23.0[${PYTHON_USEDEP}] - dev-python/patsy[${PYTHON_USEDEP}] - sci-libs/scipy[${PYTHON_USEDEP}] -" -RDEPEND="${COMMON_DEPEND}" -DEPEND="${COMMON_DEPEND} - dev-python/cython[${PYTHON_USEDEP}] - dev-python/setuptools[${PYTHON_USEDEP}] - doc? ( - dev-python/ipykernel[${PYTHON_USEDEP}] - dev-python/jupyter_client[${PYTHON_USEDEP}] - dev-python/matplotlib[${PYTHON_USEDEP}] - dev-python/nbconvert[${PYTHON_USEDEP}] - dev-python/nbformat[${PYTHON_USEDEP}] - dev-python/numpydoc[${PYTHON_USEDEP}] - dev-python/sphinx[${PYTHON_USEDEP}] - ) - test? ( - dev-python/pytest[${PYTHON_USEDEP}] - dev-python/nose[${PYTHON_USEDEP}] - ) -" - -python_prepare_all() { - # Prevent un-needed d'loading - sed -e "/sphinx.ext.intersphinx/d" -i docs/source/conf.py || die - export VARTEXFONTS="${T}"/fonts - export MPLCONFIGDIR="${T}" - echo "backend : Agg" > "${MPLCONFIGDIR}"/matplotlibrc || die - distutils-r1_python_prepare_all -} - -python_compile_all() { - use doc && esetup.py build_sphinx -b html --build-dir=docs/build -} - -python_test() { - cd "${BUILD_DIR}" || die - python -c 'import statsmodels; statsmodels.test()' || die -} - -python_install_all() { - find . -name \*LICENSE.txt -delete || die - use doc && HTML_DOCS=( docs/build/html/. ) - if use examples; then - docompress -x /usr/share/doc/${PF}/examples - dodoc -r examples - fi - distutils-r1_python_install_all -} - -pkg_postinst() { - optfeature "Plotting functionality" "dev-python/matplotlib" -} From 2e575ddf9b4481b491d0234462cd791ce27061a8 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Mon, 6 Jan 2020 06:45:01 +0100 Subject: [PATCH 36/54] Moved to Gentoo main https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=2663d018168059a7843fe516405f77a52742b200 --- sci-libs/dcmtk/ChangeLog | 9 - sci-libs/dcmtk/Manifest | 1 - sci-libs/dcmtk/dcmtk-3.6.5.ebuild | 87 --------- .../dcmtk/files/dcmtk-3.6.3-dcmqrdb-cfg.patch | 87 --------- .../dcmtk/files/dcmtk-3.6.3-fix-gcc9.patch | 29 --- .../dcmtk/files/dcmtk-3.6.3-nostrip.patch | 171 ------------------ sci-libs/dcmtk/metadata.xml | 8 - 7 files changed, 392 deletions(-) delete mode 100644 sci-libs/dcmtk/ChangeLog delete mode 100644 sci-libs/dcmtk/Manifest delete mode 100644 sci-libs/dcmtk/dcmtk-3.6.5.ebuild delete mode 100644 sci-libs/dcmtk/files/dcmtk-3.6.3-dcmqrdb-cfg.patch delete mode 100644 sci-libs/dcmtk/files/dcmtk-3.6.3-fix-gcc9.patch delete mode 100644 sci-libs/dcmtk/files/dcmtk-3.6.3-nostrip.patch delete mode 100644 sci-libs/dcmtk/metadata.xml diff --git a/sci-libs/dcmtk/ChangeLog b/sci-libs/dcmtk/ChangeLog deleted file mode 100644 index c236f09..0000000 --- a/sci-libs/dcmtk/ChangeLog +++ /dev/null @@ -1,9 +0,0 @@ - 08 Dec 2019; dcmtk-3.6.5.ebuild: - sci-libs/dcmtk: f - -*dcmtk-3.6.5 (08 Dec 2019) - - 08 Dec 2019; +dcmtk-3.6.5.ebuild, - +files/dcmtk-3.6.3-dcmqrdb-cfg.patch, +files/dcmtk-3.6.3-fix-gcc9.patch, - +files/dcmtk-3.6.3-nostrip.patch, +metadata.xml: - sci-libs/dcmtk: version bump to 3.6.5 and prefix fix diff --git a/sci-libs/dcmtk/Manifest b/sci-libs/dcmtk/Manifest deleted file mode 100644 index f51c939..0000000 --- a/sci-libs/dcmtk/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST dcmtk-3.6.5.tar.gz 6483626 SHA256 a05178665f21896dbb0974106dba1ad144975414abd760b4cf8f5cc979f9beb9 SHA512 c0cf61b0095c5708709406bfef5e8bb82dd01dbf77df7f2af2118004920bda68218eb1e4174bf92941cdae0acdb275c886570dafd29476eee2eb815e9a82830a WHIRLPOOL 14c0be8f35d0e513bb9cb03e5f30adf9b6bb1a5464a5cfee16e8261f9f304a73bd06e79c8d441d9ab8085f414a46112d58a1ccc5286dda11df6169df70dc4691 diff --git a/sci-libs/dcmtk/dcmtk-3.6.5.ebuild b/sci-libs/dcmtk/dcmtk-3.6.5.ebuild deleted file mode 100644 index c7441d1..0000000 --- a/sci-libs/dcmtk/dcmtk-3.6.5.ebuild +++ /dev/null @@ -1,87 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit cmake-utils - -DESCRIPTION="The DICOM Toolkit" -HOMEPAGE="https://dicom.offis.de/dcmtk.php.en" -SRC_URI="http://dicom.offis.de/download/dcmtk/release/${P}.tar.gz" - -LICENSE="OFFIS" -KEYWORDS="~amd64 ~arm ~x86" -SLOT="0" -IUSE="doc png ssl tcpd tiff +threads xml zlib" - -RDEPEND=" - dev-libs/icu:= - virtual/jpeg:0 - png? ( media-libs/libpng:* ) - ssl? ( dev-libs/openssl:0= ) - tcpd? ( sys-apps/tcp-wrappers ) - tiff? ( media-libs/tiff:0 ) - xml? ( dev-libs/libxml2:2 ) - zlib? ( sys-libs/zlib )" -DEPEND="${RDEPEND} - media-gfx/graphviz - doc? ( app-doc/doxygen )" - -src_prepare() { - cmake-utils_src_prepare - - sed -e "s:share/doc/dcmtk:&-${PV}:" \ - -e "s:DIR \"/:DIR \"/usr/:" \ - -e "s:usr/etc:etc:" \ - -e "s:/lib\":/$(get_libdir)\":" \ - -e "s:COPYRIGHT::" \ - -i CMakeLists.txt || die - sed -e 's:${CMAKE_INSTALL_PREFIX}/::' \ - -i dcmwlm/data/CMakeLists.txt doxygen/CMakeLists.txt || die - # Temporary workaround: docs are not built with CMake - sed -i -e '/include/d' doxygen/Makefile.in || die - - # fix -D deprecation warnings - sed -i -e "s|_BSD_SOURCE|_DEFAULT_SOURCE|g" \ - "${S}"/config/configure.in \ - "${S}"/CMakeLists.txt || die -} - -src_configure() { - local mycmakeargs=( - -DBUILD_SHARED_LIBS=ON - -DCMAKE_INSTALL_SYSCONFDIR=${EROOT%/}/etc - -DDCMTK_WITH_ICU=ON - -DDCMTK_WITH_TIFF=$(usex tiff) - -DDCMTK_WITH_PNG=$(usex png) - -DDCMTK_WITH_XML=$(usex xml) - -DDCMTK_WITH_ZLIB=$(usex zlib) - -DDCMTK_WITH_OPENSSL=$(usex ssl) - -DDCMTK_WITH_DOXYGEN=$(usex doc) - -DDCMTK_WITH_THREADS=$(usex threads) - ) - - cmake-utils_src_configure - - if use doc; then - cd "${S}"/doxygen || die - econf - fi -} - -src_compile() { - cmake-utils_src_compile - - if use doc; then - emake -C "${S}"/doxygen - fi -} - -src_install() { - doman doxygen/manpages/man1/* - - if use doc; then - local HTML_DOCS=( "${S}"/doxygen/htmldocs/. ) - fi - cmake-utils_src_install -} diff --git a/sci-libs/dcmtk/files/dcmtk-3.6.3-dcmqrdb-cfg.patch b/sci-libs/dcmtk/files/dcmtk-3.6.3-dcmqrdb-cfg.patch deleted file mode 100644 index 4ccb58d..0000000 --- a/sci-libs/dcmtk/files/dcmtk-3.6.3-dcmqrdb-cfg.patch +++ /dev/null @@ -1,87 +0,0 @@ -Author: Jürgen Salk -Description: The original maintainer Jürgen Salk applied - a set of patches to the original code. This file contains - changes to C++ code - -Index: dcmtk-3.6.0/dcmqrdb/etc/dcmqrscp.cfg -=================================================================== ---- a/dcmqrdb/etc/dcmqrscp.cfg 2010-09-09 19:20:25.000000000 +0200 -+++ b/dcmqrdb/etc/dcmqrscp.cfg 2011-01-28 09:49:02.000000000 +0100 -@@ -10,7 +10,9 @@ - NetworkTCPPort = 104 - MaxPDUSize = 16384 - MaxAssociations = 16 -+UserName = "dcmtk" -+GroupName = "dcmtk" - - # - # Default settings for specific character set behavior: - # SpecificCharacterSet = fallback -@@ -28,12 +30,13 @@ - # NOTE: in the current implementation you cannot substitute an IP address - # for a hostname. - # --acme1 = (ACME1, acmehost1, 5678) --acme2 = (ACME2, acmehost2, 5678) --acmeCTcompany = acme1, acme2 --united1 = (UNITED1, unitedhost1, 104) --united2 = (UNITED2, unitedhost2, 104) --unitedMRcompany = united1, united2 -+# Example: -+#acme1 = (ACME1, acmehost1, 5678) -+#acme2 = (ACME2, acmehost2, 5678) -+#acmeCTcompany = acme1, acme2 -+#united1 = (UNITED1, unitedhost1, 104) -+#united2 = (UNITED2, unitedhost2, 104) -+#unitedMRcompany = united1, united2 - # - HostTable END - -@@ -51,8 +54,9 @@ - # VendorName = SymbolicName - # The symbolic name should be defined in the HostTable. - # --"Acme CT Company" = acmeCTcompany --"United MR Company" = unitedMRcompany -+# Example: -+#"Acme CT Company" = acmeCTcompany -+#"United MR Company" = unitedMRcompany - # - VendorTable END - -@@ -70,8 +74,13 @@ - # Entry in HostTable | - # ANY - # --COMMON /home/dicom/db/COMMON R (200, 1024mb) ANY --ACME_STORE /home/dicom/db/ACME_STORE RW (9, 1024mb) acmeCTcompany --UNITED_STORE /home/dicom/db/UNITED_STORE RW (9, 1024mb) unitedMRcompany -+# Example: -+# -+#ACME_STORE /var/lib/dcmtk/db/ACME_STORE RW (9, 1024mb) acmeCTcompany -+#UNITED_STORE /var/lib/dcmtk/db/UNITED_STORE RW (9, 1024mb) unitedMRcompany -+# -+# Uncomment and adjust the following lines for a common r/rw storage area: -+#READWRITE /var/lib/dcmtk/db/READWRITE RW (10, 1024mb) ANY -+#READ /var/lib/dcmtk/db/READ R (200, 1024mb) ANY - # - AETable END -Index: dcmtk-3.6.0/dcmqrdb/docs/dcmqrcnf.txt ---- a/dcmqrdb/docs/dcmqrcnf.txt 2010-09-09 19:20:12.000000000 +0200 -+++ b/dcmqrdb/docs/dcmqrcnf.txt 2011-01-28 09:46:02.000000000 +0100 -@@ -44,8 +44,8 @@ - MaxPDUSize = 8192 - MaxAssociations = 20 - SpecificCharacterSet = fallback --UserName = (do not change user) --GroupName = (do not change group) -+UserName = "dcmtk" -+GroupName = "dcmtk" - - Available options for specific character sets are: - -Index: dcmtk-3.6.0/dcmwlm/wlistdb/OFFIS/lockfile ---- /dev/null 1970-01-01 00:00:00.000000000 +0000 -+++ dcmtk-3.6.0/dcmwlm/wlistdb/OFFIS/lockfile 2011-01-28 09:46:02.000000000 +0100 -@@ -0,0 +1 @@ -+ diff --git a/sci-libs/dcmtk/files/dcmtk-3.6.3-fix-gcc9.patch b/sci-libs/dcmtk/files/dcmtk-3.6.3-fix-gcc9.patch deleted file mode 100644 index 596a1ae..0000000 --- a/sci-libs/dcmtk/files/dcmtk-3.6.3-fix-gcc9.patch +++ /dev/null @@ -1,29 +0,0 @@ -https://bugs.gentoo.org/686592 - -In file included from /var/tmp/portage/sci-libs/dcmtk-3.6.3/work/dcmtk-3.6.3/ofstd/include/dcmtk/ofstd/variadic/variant.h:19, - from /var/tmp/portage/sci-libs/dcmtk-3.6.3/work/dcmtk-3.6.3/ofstd/include/dcmtk/ofstd/ofvriant.h:379, - from /var/tmp/portage/sci-libs/dcmtk-3.6.3/work/dcmtk-3.6.3/ofstd/tests/tvariant.cc:26: -/var/tmp/portage/sci-libs/dcmtk-3.6.3/work/dcmtk-3.6.3/ofstd/include/dcmtk/ofstd/variadic/helpers.h:57:32: error: narrowing conversion of ‘-1’ from ‘int’ to ‘long unsigned int’ [-Wnarrowing] - 57 | : OFintegral_constant {}; - | - ---- a/ofstd/include/dcmtk/ofstd/variadic/helpers.h -+++ b/ofstd/include/dcmtk/ofstd/variadic/helpers.h -@@ -14,6 +14,8 @@ - #ifndef VARIADIC_HELPERS_H - #define VARIADIC_HELPERS_H - -+#include -+ - #include "dcmtk/config/osconfig.h" /* make sure OS specific configuration is included first */ - - #include "dcmtk/ofstd/oftraits.h" -@@ -54,7 +56,7 @@ - - template - struct OFvariadic_find_type_t --: OFintegral_constant {}; -+: OFintegral_constant::max()> {}; - - template - struct OFvariadic_find_type diff --git a/sci-libs/dcmtk/files/dcmtk-3.6.3-nostrip.patch b/sci-libs/dcmtk/files/dcmtk-3.6.3-nostrip.patch deleted file mode 100644 index 83bd3a6..0000000 --- a/sci-libs/dcmtk/files/dcmtk-3.6.3-nostrip.patch +++ /dev/null @@ -1,171 +0,0 @@ -Remove all hardcoded calls to `strip` command - -Index: dcmtk-3.6.0/config/templates/Makefile.src -=================================================================== ---- a/config/templates/Makefile.src 2009-01-30 10:27:58.000000000 +0100 -+++ b/config/templates/Makefile.src 2011-01-28 09:53:28.000000000 +0100 -@@ -31,7 +31,7 @@ - install-bin: all - $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) - for prog in $(progs); do \ -- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && $(STRIP) $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ -+ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ - done - - -Index: dcmtk-3.6.0/dcmdata/apps/Makefile.in -=================================================================== ---- a/dcmdata/apps/Makefile.in 2009-11-04 10:58:05.000000000 +0100 -+++ b/dcmdata/apps/Makefile.in 2011-01-28 09:53:45.000000000 +0100 -@@ -76,7 +76,7 @@ - install-bin: all - $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) - for prog in $(progs); do \ -- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && $(STRIP) $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ -+ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ - done - - -Index: dcmtk-3.6.0/dcmimage/apps/Makefile.in -=================================================================== ---- a/dcmimage/apps/Makefile.in 2009-10-13 16:08:33.000000000 +0200 -+++ b/dcmimage/apps/Makefile.in 2011-01-28 09:53:59.000000000 +0100 -@@ -42,7 +42,7 @@ - install: all - $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) - for prog in $(progs); do \ -- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && $(STRIP) $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ -+ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ - done - - -Index: dcmtk-3.6.0/dcmimgle/apps/Makefile.in -=================================================================== ---- a/dcmimgle/apps/Makefile.in 2009-10-28 10:53:39.000000000 +0100 -+++ b/dcmimgle/apps/Makefile.in 2011-01-28 09:54:11.000000000 +0100 -@@ -39,7 +39,7 @@ - install: all - $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) - for prog in $(progs); do \ -- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && $(STRIP) $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ -+ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ - done - - -Index: dcmtk-3.6.0/dcmjpeg/apps/Makefile.in -=================================================================== ---- a/dcmjpeg/apps/Makefile.in 2009-10-07 14:44:33.000000000 +0200 -+++ b/dcmjpeg/apps/Makefile.in 2011-01-28 09:54:28.000000000 +0100 -@@ -72,7 +72,7 @@ - install: all - $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) - for prog in $(progs); do \ -- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && $(STRIP) $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ -+ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ - done - - clean: -Index: dcmtk-3.6.0/dcmnet/apps/Makefile.in -=================================================================== ---- a/dcmnet/apps/Makefile.in 2009-11-04 11:24:29.000000000 +0100 -+++ b/dcmnet/apps/Makefile.in 2011-01-28 09:54:50.000000000 +0100 -@@ -52,7 +52,7 @@ - install: all - $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) - for prog in $(progs); do \ -- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && $(STRIP) $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ -+ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ - done - - -Index: dcmtk-3.6.0/dcmpstat/apps/Makefile.in -=================================================================== ---- a/dcmpstat/apps/Makefile.in 2009-10-13 16:57:49.000000000 +0200 -+++ b/dcmpstat/apps/Makefile.in 2011-01-28 09:55:10.000000000 +0100 -@@ -113,7 +113,7 @@ - install: all - $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) - for prog in $(progs); do \ -- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && $(STRIP) $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ -+ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ - done - - -Index: dcmtk-3.6.0/dcmqrdb/apps/Makefile.in -=================================================================== ---- a/dcmqrdb/apps/Makefile.in 2009-11-04 11:24:30.000000000 +0100 -+++ b/dcmqrdb/apps/Makefile.in 2011-01-28 09:55:24.000000000 +0100 -@@ -57,7 +57,7 @@ - install: all - $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) - for prog in $(progs); do \ -- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && $(STRIP) $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ -+ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ - done - - -Index: dcmtk-3.6.0/dcmsign/apps/Makefile.in -=================================================================== ---- a/dcmsign/apps/Makefile.in 2009-09-04 17:42:31.000000000 +0200 -+++ b/dcmsign/apps/Makefile.in 2011-01-28 09:55:35.000000000 +0100 -@@ -33,7 +33,7 @@ - install: all - $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) - for prog in $(progs); do \ -- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && $(STRIP) $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ -+ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ - done - - -Index: dcmtk-3.6.0/dcmsr/apps/Makefile.in -=================================================================== ---- a/dcmsr/apps/Makefile.in 2009-10-13 16:57:49.000000000 +0200 -+++ b/dcmsr/apps/Makefile.in 2011-01-28 09:55:48.000000000 +0100 -@@ -44,7 +44,7 @@ - install-bin: all - $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) - for prog in $(progs); do \ -- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && $(STRIP) $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ -+ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ - done - - -Index: dcmtk-3.6.0/dcmwlm/apps/Makefile.in -=================================================================== ---- a/dcmwlm/apps/Makefile.in 2009-11-04 11:24:30.000000000 +0100 -+++ b/dcmwlm/apps/Makefile.in 2011-01-28 09:55:58.000000000 +0100 -@@ -49,7 +49,7 @@ - install: all - $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) - for prog in $(progs); do \ -- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && $(STRIP) $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ -+ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ - done - - -Index: dcmtk-3.6.0/dcmwlm/wwwapps/Makefile.in -=================================================================== ---- a/dcmrt/apps/Makefile.in 2009-11-04 11:24:30.000000000 +0100 -+++ b/dcmrt/apps/Makefile.in 2011-01-28 09:56:33.000000000 +0100 -@@ -55,7 +55,7 @@ - install-bin: all - $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) - for prog in $(progs); do \ -- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && $(STRIP) $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ -+ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ - done - - -Index: dcmtk-3.6.0/dcmjpls/apps/Makefile.in -=================================================================== ---- a/dcmjpls/apps/Makefile.in 2011-01-28 09:56:54.000000000 +0100 -+++ b/dcmjpls/apps/Makefile.in 2011-01-28 09:57:00.000000000 +0100 -@@ -71,7 +71,7 @@ - install: all - $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) - for prog in $(progs); do \ -- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && $(STRIP) $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ -+ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ - done - - diff --git a/sci-libs/dcmtk/metadata.xml b/sci-libs/dcmtk/metadata.xml deleted file mode 100644 index ed91732..0000000 --- a/sci-libs/dcmtk/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ - - - - - sci-biology@gentoo.org - - DICOM ToolKit core medical imaging library and tools - From 38eb7ca80b682b3e19fa8adb9a7916dc54784e3c Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Mon, 6 Jan 2020 13:03:41 +0100 Subject: [PATCH 37/54] updated in Gentoo main --- dev-python/typing/ChangeLog | 7 ------ dev-python/typing/Manifest | 1 - dev-python/typing/metadata.xml | 11 --------- dev-python/typing/typing-3.7.4.1.ebuild | 30 ------------------------- 4 files changed, 49 deletions(-) delete mode 100644 dev-python/typing/ChangeLog delete mode 100644 dev-python/typing/Manifest delete mode 100644 dev-python/typing/metadata.xml delete mode 100644 dev-python/typing/typing-3.7.4.1.ebuild diff --git a/dev-python/typing/ChangeLog b/dev-python/typing/ChangeLog deleted file mode 100644 index 4854aee..0000000 --- a/dev-python/typing/ChangeLog +++ /dev/null @@ -1,7 +0,0 @@ - 04 Nov 2019; typing-3.7.4.1.ebuild: - dev-python/typing: KEYWORDS - -*typing-3.7.4.1 (09 Oct 2019) - - 09 Oct 2019; +metadata.xml, +typing-3.7.4.1.ebuild: - dev-python/typing: version bump 3.7.4.1 and PYTHON_COMPAT to 3 series diff --git a/dev-python/typing/Manifest b/dev-python/typing/Manifest deleted file mode 100644 index 6391b2f..0000000 --- a/dev-python/typing/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST typing-3.7.4.1.tar.gz 77982 SHA256 91dfe6f3f706ee8cc32d38edbbf304e9b7583fb37108fef38229617f8b3eba23 SHA512 5f5080bf66b1de094b7984ed3d1de22651de8ca018ffde927dfa67fe65b13f91602a877faa24e73d44558638b609be276b924b894d63999bb93b0657a2d5ec6e WHIRLPOOL 37b349c5be66a21b7cc433d8daa5f5648614f71cd50ec657c5fb1261ee73918c3c14aba7f4b5c3be2f2c571a2f6ef40fa0daaeb0c93581a748a732e582c36e4a diff --git a/dev-python/typing/metadata.xml b/dev-python/typing/metadata.xml deleted file mode 100644 index 8fac39f..0000000 --- a/dev-python/typing/metadata.xml +++ /dev/null @@ -1,11 +0,0 @@ - - - - - python@gentoo.org - Python - - - typing - - diff --git a/dev-python/typing/typing-3.7.4.1.ebuild b/dev-python/typing/typing-3.7.4.1.ebuild deleted file mode 100644 index bf906a3..0000000 --- a/dev-python/typing/typing-3.7.4.1.ebuild +++ /dev/null @@ -1,30 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 python3_6 pypy ) - -inherit distutils-r1 - -DESCRIPTION="Type Hints for Python" -HOMEPAGE="https://docs.python.org/3/library/typing.html https://pypi.org/project/typing/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="PSF-2" -SLOT="0" -KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~hppa ~ia64 ~mips ~ppc ~ppc64 ~s390 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-solaris" -IUSE="" - -DEPEND="dev-python/setuptools[${PYTHON_USEDEP}]" -RDEPEND="" - -python_test() { - if [[ ${EPYTHON} == python2* || ${EPYTHON} == pypy ]]; then - cd "${S}"/python2 || die - else - cd "${S}"/src || die - fi - - "${PYTHON}" test_typing.py || die "tests failed under ${EPYTHON}" -} From 441317ecf510698b624d5d0d6167c01796c8b5a0 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Mon, 6 Jan 2020 16:02:22 +0100 Subject: [PATCH 38/54] sci-biology/opfvta_bidsdata: updated mirror Package-Manager: Portage-2.3.82, Repoman-2.3.20 Signed-off-by: Horea Christian --- sci-biology/opfvta_bidsdata/ChangeLog | 3 +++ sci-biology/opfvta_bidsdata/opfvta_bidsdata-2.0.ebuild | 4 ++-- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/sci-biology/opfvta_bidsdata/ChangeLog b/sci-biology/opfvta_bidsdata/ChangeLog index 9b0bb35..3a5bd0b 100644 --- a/sci-biology/opfvta_bidsdata/ChangeLog +++ b/sci-biology/opfvta_bidsdata/ChangeLog @@ -1,3 +1,6 @@ + 06 Jan 2020; opfvta_bidsdata-2.0.ebuild: + sci-biology/opfvta_bidsdata: + *opfvta_bidsdata-2.0 (09 Dec 2019) 09 Dec 2019; +opfvta_bidsdata-2.0.ebuild: diff --git a/sci-biology/opfvta_bidsdata/opfvta_bidsdata-2.0.ebuild b/sci-biology/opfvta_bidsdata/opfvta_bidsdata-2.0.ebuild index 3c1317f..44c761c 100644 --- a/sci-biology/opfvta_bidsdata/opfvta_bidsdata-2.0.ebuild +++ b/sci-biology/opfvta_bidsdata/opfvta_bidsdata-2.0.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 2019-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 @@ -9,7 +9,7 @@ DESCRIPTION="BIDS data files released with the OPFVTA publication" HOMEPAGE="http://www.aic-fmi.ethz.ch/" SRC_URI=" http://chymera.eu/distfiles/${P}.tar.xz - https://zenodo.org/record/3565897/files/${P}.tar.xz + https://zenodo.org/record/3575149/files/${P}.tar.xz " LICENSE="CC-BY-SA-4.0" From 9356048bf57c1ad7a54a2cb3e86311b2ecbcfd93 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Tue, 7 Jan 2020 22:37:16 +0100 Subject: [PATCH 39/54] sci-libs/scikits_image: version bump and Python 2.7 drop Package-Manager: Portage-2.3.84, Repoman-2.3.20 Signed-off-by: Horea Christian --- sci-libs/scikits_image/ChangeLog | 6 ++ sci-libs/scikits_image/Manifest | 1 + .../scikits_image/scikits_image-0.14.2.ebuild | 4 +- .../scikits_image/scikits_image-0.14.3.ebuild | 73 +++++++++++++++++++ 4 files changed, 82 insertions(+), 2 deletions(-) create mode 100644 sci-libs/scikits_image/scikits_image-0.14.3.ebuild diff --git a/sci-libs/scikits_image/ChangeLog b/sci-libs/scikits_image/ChangeLog index fb35df5..a4079ee 100644 --- a/sci-libs/scikits_image/ChangeLog +++ b/sci-libs/scikits_image/ChangeLog @@ -1,3 +1,9 @@ +*scikits_image-0.14.3 (07 Jan 2020) + + 07 Jan 2020; +scikits_image-0.14.3.ebuild, + scikits_image-0.14.2.ebuild: + sci-libs/scikits_image: version bump and Python 2.7 drop + *scikits_image-0.14.2 (26 Mar 2019) 26 Mar 2019; +metadata.xml, diff --git a/sci-libs/scikits_image/Manifest b/sci-libs/scikits_image/Manifest index eba9f26..cdfc86e 100644 --- a/sci-libs/scikits_image/Manifest +++ b/sci-libs/scikits_image/Manifest @@ -1 +1,2 @@ DIST scikit-image-0.14.2.tar.gz 27785514 SHA256 1afd0b84eefd77afd1071c5c1c402553d67be2d7db8950b32d6f773f25850c1f SHA512 ab31fdb5b1d16b794ccc4d673f6c8bce0a8a54b81c0e43c9a4cdd5eb0465ef69ac184a06e395a1d27da51c2e0911db9afa2be4e740f44bceab952428eb7f599a WHIRLPOOL 9be56b58bff3b6d4706a907fedb5c5545e31630e49f9f5a8d0adf9afbabf63076694313b79904065331e552311278f64e3a49ff47540af1b2b3867e2c65d417f +DIST scikit-image-0.14.3.tar.gz 27312311 SHA256 f05eab2df885fb6fde3df0e4d24c9c620d6474ea0eb949fd45f6f634925dd514 SHA512 7c3a09004eeb0f075532c38d14f8b402491c39a4ca56bc68aea17804756f5907f01cba4d1b8b45e1c20d1b233b84564015cf9f4124b1f5a19e103120c2466a2f WHIRLPOOL de0f2520e28b2e44db109b1a09229b8330584eb9162f5000c3c96098f523aa30ba381162cc67c1851ca1a67aafa002878e5271fc9d3173268451763dd56643bc diff --git a/sci-libs/scikits_image/scikits_image-0.14.2.ebuild b/sci-libs/scikits_image/scikits_image-0.14.2.ebuild index 4535ca7..e98dba1 100644 --- a/sci-libs/scikits_image/scikits_image-0.14.2.ebuild +++ b/sci-libs/scikits_image/scikits_image-0.14.2.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 -PYTHON_COMPAT=( python2_7 python3_{4,5,6} ) +PYTHON_COMPAT=( python3_{4,5,6} ) inherit distutils-r1 eutils virtualx diff --git a/sci-libs/scikits_image/scikits_image-0.14.3.ebuild b/sci-libs/scikits_image/scikits_image-0.14.3.ebuild new file mode 100644 index 0000000..e98dba1 --- /dev/null +++ b/sci-libs/scikits_image/scikits_image-0.14.3.ebuild @@ -0,0 +1,73 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +PYTHON_COMPAT=( python3_{4,5,6} ) + +inherit distutils-r1 eutils virtualx + +MYPN="${PN/scikits_/scikit-}" +MYP="${MYPN}-${PV}" + +DESCRIPTION="Image processing routines for SciPy" +HOMEPAGE="https://scikit-image.org/" +SRC_URI="mirror://pypi/${PN:0:1}/${MYPN}/${MYP}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc freeimage pyamg test" + +RDEPEND=" + dev-python/cloudpickle[${PYTHON_USEDEP}] + dev-python/dask[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/networkx[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pillow[${PYTHON_USEDEP}] + dev-python/pywavelets[${PYTHON_USEDEP}] + dev-python/six[${PYTHON_USEDEP}] + sci-libs/scipy[sparse,${PYTHON_USEDEP}] + freeimage? ( media-libs/freeimage ) + pyamg? ( dev-python/pyamg[${PYTHON_USEDEP}] )" +DEPEND="${RDEPEND} + >=dev-python/cython-0.23[${PYTHON_USEDEP}] + dev-python/setuptools[${PYTHON_USEDEP}] + test? ( dev-python/nose[${PYTHON_USEDEP}] )" + +S="${WORKDIR}/${MYP}" + +DOCS=( CONTRIBUTORS.txt RELEASE.txt TODO.txt ) + +# Fails on Gentoo +#RESTRICT="test" + +python_prepare_all() { + # Remove pip dependency + sed -i '1iimport os.path as osp'\ + skimage/__init__.py\ + skimage/data/__init__.py\ + || die + distutils-r1_python_prepare_all +} + +python_test() { + distutils_install_for_testing + #cd "${TEST_DIR}" || die "no ${TEST_DIR} available" + echo "backend : Agg" > matplotlibrc || die + #echo "backend.qt4 : PyQt4" >> matplotlibrc || die + #echo "backend.qt4 : PySide" >> matplotlibrc || die + mkdir "${WORKDIR}/empty_test_dir" || die + cd "${WORKDIR}/empty_test_dir" || die + pytest --pyargs skimage || die + #pytest -vv || die +} + +pkg_postinst() { + optfeature "FITS io capability" dev-python/astropy + optfeature "GTK" dev-python/pygtk + # not in portage yet + #optfeature "io plugin providing a wide variety of formats, including specialized formats using in medical imaging." dev-python/simpleitk + #optfeature "io plugin providing most standard formats" dev-python/imread +} From dbd6cc62673a8ceb6316c7a80038afa9bec04425 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Wed, 8 Jan 2020 19:24:39 +0100 Subject: [PATCH 40/54] Moved to Gentoo Science https://gitweb.gentoo.org/proj/sci.git/commit/?id=f18c18c90ca94192ca170f656b62586ee44f068c --- sci-biology/drlfom_bidsdata/ChangeLog | 7 ---- sci-biology/drlfom_bidsdata/Manifest | 1 - .../drlfom_bidsdata-1.1.ebuild | 33 ------------------- sci-biology/drlfom_bidsdata/metadata.xml | 18 ---------- 4 files changed, 59 deletions(-) delete mode 100644 sci-biology/drlfom_bidsdata/ChangeLog delete mode 100644 sci-biology/drlfom_bidsdata/Manifest delete mode 100644 sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild delete mode 100644 sci-biology/drlfom_bidsdata/metadata.xml diff --git a/sci-biology/drlfom_bidsdata/ChangeLog b/sci-biology/drlfom_bidsdata/ChangeLog deleted file mode 100644 index 3914151..0000000 --- a/sci-biology/drlfom_bidsdata/ChangeLog +++ /dev/null @@ -1,7 +0,0 @@ - 28 Jun 2019; drlfom_bidsdata-1.0.ebuild: - sci-biology/drlfom_bidsdata: alternative download link - -*drlfom_bidsdata-1.0 (28 Jun 2019) - - 28 Jun 2019; +drlfom_bidsdata-1.0.ebuild, +metadata.xml: - sci-biology/drlfom_bidsdata: new package ahead of Gentoo Science diff --git a/sci-biology/drlfom_bidsdata/Manifest b/sci-biology/drlfom_bidsdata/Manifest deleted file mode 100644 index 8c937cb..0000000 --- a/sci-biology/drlfom_bidsdata/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST drlfom_bidsdata-1.1.tar.xz 22144796704 SHA256 4b33cb51be1c560ff12f37de027a697631979ef2fe8fe20fec25484feae0015b SHA512 84e574cb6714060292d07cacb6ae84aed051100f966713db6b6ac0dd08d3c01e84da8afde66980eb9b0625e8de2f100444ab84d933d7a280af5a39b4b6eab531 WHIRLPOOL 0b74171b9b356397c1b12f7247d602bd1da77ff409fa522c126febf9cde387f9931d61cef3360b11388d4094a53ff0c5990cc0257418c3bafae203c224264e68 diff --git a/sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild b/sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild deleted file mode 100644 index d997dd1..0000000 --- a/sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild +++ /dev/null @@ -1,33 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit check-reqs - -DESCRIPTION="BIDS data files released with the DRLFOM publication" -HOMEPAGE="http://www.aic-fmi.ethz.ch/" -SRC_URI=" - https://zenodo.org/record/3260745/files/${P}.tar.xz - http://chymera.eu/distfiles/${P}.tar.xz - " - -LICENSE="CC-BY-SA-4.0" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" - -RDEPEND="" -DEPEND="" - -pkg_pretend() { - CHECKREQS_DISK_BUILD="21G" - check-reqs_pkg_pretend -} - -# We disable this phase to not check requirements twice. -pkg_setup() { :; } - -src_install() { - insinto "/usr/share/${PN}" - doins -r * -} diff --git a/sci-biology/drlfom_bidsdata/metadata.xml b/sci-biology/drlfom_bidsdata/metadata.xml deleted file mode 100644 index 0df40cb..0000000 --- a/sci-biology/drlfom_bidsdata/metadata.xml +++ /dev/null @@ -1,18 +0,0 @@ - - - - - chr@chymera.eu - Horea Christian - - - sci@gentoo.org - Gentoo Science Project - - - BIDS-formatted MRI data recorded at the ETH/UZH Animal Imaging Center - and first associated with the DRLFOM publication. The data represents - optp-fMRI mouse brain scans with CBV contrast, tracking serotonergic - stimulation over the course of a fluoxetine drinking water treatment. - - From d2ab14211a60edee5c00ed6b6a20ec3f8a90d064 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Wed, 8 Jan 2020 21:46:01 +0100 Subject: [PATCH 41/54] Moved to Gentoo Science https://gitweb.gentoo.org/proj/sci.git/commit/?id=94b4bbd913306a325d619686593e96870770d0d1 --- sci-biology/irsabi_bidsdata/ChangeLog | 16 ---------- sci-biology/irsabi_bidsdata/Manifest | 1 - .../irsabi_bidsdata-1.4.ebuild | 32 ------------------- sci-biology/irsabi_bidsdata/metadata.xml | 19 ----------- 4 files changed, 68 deletions(-) delete mode 100644 sci-biology/irsabi_bidsdata/ChangeLog delete mode 100644 sci-biology/irsabi_bidsdata/Manifest delete mode 100644 sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild delete mode 100644 sci-biology/irsabi_bidsdata/metadata.xml diff --git a/sci-biology/irsabi_bidsdata/ChangeLog b/sci-biology/irsabi_bidsdata/ChangeLog deleted file mode 100644 index f1c8949..0000000 --- a/sci-biology/irsabi_bidsdata/ChangeLog +++ /dev/null @@ -1,16 +0,0 @@ -*irsabi_bidsdata-1.4 (10 Dec 2019) - - 10 Dec 2019; +irsabi_bidsdata-1.4.ebuild, - -irsabi_bidsdata-1.3.1.ebuild: - sci-biology/irsabi_bidsdata: version bump 1.4 ahead of Gentoo Science - -*irsabi_bidsdata-1.3.1 (08 Nov 2019) - - 08 Nov 2019; +irsabi_bidsdata-1.3.1.ebuild, - -irsabi_bidsdata-1.3.ebuild: - sci-biology/irsabi_bidsdata: version bump 1.3.1 ahead of Gentoo Science - -*irsabi_bidsdata-1.3 (19 Sep 2019) - - 19 Sep 2019; +irsabi_bidsdata-1.3.ebuild, +metadata.xml: - sci-biology/irsabi_bidsdata: version bump 1.3 diff --git a/sci-biology/irsabi_bidsdata/Manifest b/sci-biology/irsabi_bidsdata/Manifest deleted file mode 100644 index ab2e388..0000000 --- a/sci-biology/irsabi_bidsdata/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST irsabi_bidsdata-1.4.tar.xz 4503367352 SHA256 d837835ddf43d1e8322ba2444a1d9ef51b59f8312252207c5f7a2a302eca0149 SHA512 20a6e486d74ca57b3a8cced87db7fc110ae7ad2e466bd76cfd3ad46ec317c30597a4569005696c509dc2f9fc40dd1d0dbee0c0bf174e5ae8cab53058ce980b10 WHIRLPOOL 7a5600766ba35a5808ac6520abcce35eabebc168b4f3930e264caa8377bdd274bbf68aa625e8857feeb3cfc45689e7687b132f2af8c8a2a109b1b7c9a67c2acf diff --git a/sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild b/sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild deleted file mode 100644 index 599a826..0000000 --- a/sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild +++ /dev/null @@ -1,32 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit check-reqs - -DESCRIPTION="BIDS data files released with the IRSABI publication" -HOMEPAGE="http://www.aic-fmi.ethz.ch/" -SRC_URI=" - http://chymera.eu/distfiles/${P}.tar.xz - " - -LICENSE="CC-BY-SA-4.0" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" - -RDEPEND="" -DEPEND="" - -pkg_pretend() { - CHECKREQS_DISK_BUILD="10G" - check-reqs_pkg_pretend -} - -# We disable this phase to not check requirements twice. -pkg_setup() { :; } - -src_install() { - insinto "/usr/share/${PN}" - doins -r * -} diff --git a/sci-biology/irsabi_bidsdata/metadata.xml b/sci-biology/irsabi_bidsdata/metadata.xml deleted file mode 100644 index 9c6323c..0000000 --- a/sci-biology/irsabi_bidsdata/metadata.xml +++ /dev/null @@ -1,19 +0,0 @@ - - - - - horea.christ@gmail.com - Horea Christian - - - sci@gentoo.org - Gentoo Science Project - - - BIDS-formatted MRI data recorded at the ETH/UZH Animal Imaging Center - and first associated with the IRSABI publication. The data represents - f/MRI mouse brain scans with both BOLD and CBV contrasts, and acquired - during optogenetic stimulation over multiple sessions including acute - (i.v.) and chronic (s.c.) fluoxetine administration sessions. - - From 8a65dfb6f4f9c3056bbb68e7fa31ace6275aa2d0 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Wed, 8 Jan 2020 22:24:03 +0100 Subject: [PATCH 42/54] Moved to Gentoo Science https://gitweb.gentoo.org/proj/sci.git/commit/?id=41f2ece91276dd5de9b90161c290507932cc9d6f --- sci-biology/opfvta_bidsdata/ChangeLog | 12 ------- sci-biology/opfvta_bidsdata/Manifest | 2 -- sci-biology/opfvta_bidsdata/metadata.xml | 20 ----------- .../opfvta_bidsdata-1.2.ebuild | 33 ------------------- .../opfvta_bidsdata-2.0.ebuild | 33 ------------------- 5 files changed, 100 deletions(-) delete mode 100644 sci-biology/opfvta_bidsdata/ChangeLog delete mode 100644 sci-biology/opfvta_bidsdata/Manifest delete mode 100644 sci-biology/opfvta_bidsdata/metadata.xml delete mode 100644 sci-biology/opfvta_bidsdata/opfvta_bidsdata-1.2.ebuild delete mode 100644 sci-biology/opfvta_bidsdata/opfvta_bidsdata-2.0.ebuild diff --git a/sci-biology/opfvta_bidsdata/ChangeLog b/sci-biology/opfvta_bidsdata/ChangeLog deleted file mode 100644 index 3a5bd0b..0000000 --- a/sci-biology/opfvta_bidsdata/ChangeLog +++ /dev/null @@ -1,12 +0,0 @@ - 06 Jan 2020; opfvta_bidsdata-2.0.ebuild: - sci-biology/opfvta_bidsdata: - -*opfvta_bidsdata-2.0 (09 Dec 2019) - - 09 Dec 2019; +opfvta_bidsdata-2.0.ebuild: - sci-biology/opfvta_bidsdata: version bump 2.0 ahead of Gentoo Science - -*opfvta_bidsdata-1.2 (06 Dec 2019) - - 06 Dec 2019; +metadata.xml, +opfvta_bidsdata-1.2.ebuild: - sci-biology/opfvta_bidsdata: version bump 1.2 ahead of Gentoo Science diff --git a/sci-biology/opfvta_bidsdata/Manifest b/sci-biology/opfvta_bidsdata/Manifest deleted file mode 100644 index 1076871..0000000 --- a/sci-biology/opfvta_bidsdata/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST opfvta_bidsdata-1.2.tar.xz 12101699696 SHA256 5c48b4214abc8d7cc8c0b8820bba52950427cd44ee397031bfe674503762693f SHA512 213100ccf561b2d805199a876e85f0793545df5d2fed5ac0039e008d0fe9706f9836ca94a351e9651032d2f96b0b91182e1c2d4b129dbf3ec824d852c77880aa WHIRLPOOL 0f0d0fc4a1fcb9324547841517f0584431baef3346c94fcf1e56ff81b5bb62848b72587a0c2d8ca8b53d74a3ac76c2f8c641c38e01290c8637a464db1190f8c1 -DIST opfvta_bidsdata-2.0.tar.xz 12372152444 SHA256 10453e5d9d8e5f747a19d7c8a571cafb8bb2f93128c6ddd97c267520ab8ed781 SHA512 4e8769e358a8f0e2c25b46db094d0cbf375bf4aa83365834be5ee6a1db012d6be6174f0416f0158354a17e9616863a459f9d89ea3df8694bf23d4ecd75b289fc WHIRLPOOL 1738d8257ce18473f7522e175bf893d9b0087b17a8eaff900108fe04e9bc9d8a8ee27cb3d109df1be0b1aa9126a5b6d4a2929dc7014c27b6c0dbc51fec38f7c8 diff --git a/sci-biology/opfvta_bidsdata/metadata.xml b/sci-biology/opfvta_bidsdata/metadata.xml deleted file mode 100644 index 729ebaa..0000000 --- a/sci-biology/opfvta_bidsdata/metadata.xml +++ /dev/null @@ -1,20 +0,0 @@ - - - - - chr@chymera.eu - Horea Christian - - - sci@gentoo.org - Gentoo Science Project - - - BIDS-formatted MRI data recorded at the ETH/UZH Animal Imaging Center - and first associated with the OPFVTA publication. The data represents - f/MRI mouse brain scans with both BOLD and CBV contrasts, using block - and phasic stimulation protocols delivered via a laser to the VTA, - which is rendered sensitive by channelrhodopsin expression under - the dopamine transporter promoter. - - diff --git a/sci-biology/opfvta_bidsdata/opfvta_bidsdata-1.2.ebuild b/sci-biology/opfvta_bidsdata/opfvta_bidsdata-1.2.ebuild deleted file mode 100644 index 3c1317f..0000000 --- a/sci-biology/opfvta_bidsdata/opfvta_bidsdata-1.2.ebuild +++ /dev/null @@ -1,33 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit check-reqs - -DESCRIPTION="BIDS data files released with the OPFVTA publication" -HOMEPAGE="http://www.aic-fmi.ethz.ch/" -SRC_URI=" - http://chymera.eu/distfiles/${P}.tar.xz - https://zenodo.org/record/3565897/files/${P}.tar.xz - " - -LICENSE="CC-BY-SA-4.0" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" - -RDEPEND="" -DEPEND="" - -pkg_pretend() { - CHECKREQS_DISK_BUILD="33G" - check-reqs_pkg_pretend -} - -# We disable this phase to not check requirements twice. -pkg_setup() { :; } - -src_install() { - insinto "/usr/share/${PN}" - doins -r * -} diff --git a/sci-biology/opfvta_bidsdata/opfvta_bidsdata-2.0.ebuild b/sci-biology/opfvta_bidsdata/opfvta_bidsdata-2.0.ebuild deleted file mode 100644 index 44c761c..0000000 --- a/sci-biology/opfvta_bidsdata/opfvta_bidsdata-2.0.ebuild +++ /dev/null @@ -1,33 +0,0 @@ -# Copyright 2019-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit check-reqs - -DESCRIPTION="BIDS data files released with the OPFVTA publication" -HOMEPAGE="http://www.aic-fmi.ethz.ch/" -SRC_URI=" - http://chymera.eu/distfiles/${P}.tar.xz - https://zenodo.org/record/3575149/files/${P}.tar.xz - " - -LICENSE="CC-BY-SA-4.0" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" - -RDEPEND="" -DEPEND="" - -pkg_pretend() { - CHECKREQS_DISK_BUILD="33G" - check-reqs_pkg_pretend -} - -# We disable this phase to not check requirements twice. -pkg_setup() { :; } - -src_install() { - insinto "/usr/share/${PN}" - doins -r * -} From f9b979d7d960061641be1333f7c99c9888a5f3d2 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Fri, 10 Jan 2020 14:29:46 +0100 Subject: [PATCH 43/54] moved to Gentoo Science https://gitweb.gentoo.org/proj/sci.git/commit/?id=c939a6bdec9371a7e75811188895ea2ed70a4d54 --- sci-libs/pybids/Manifest | 1 - sci-libs/pybids/metadata.xml | 20 -------------- sci-libs/pybids/pybids-0.6.5.ebuild | 42 ----------------------------- 3 files changed, 63 deletions(-) delete mode 100644 sci-libs/pybids/Manifest delete mode 100644 sci-libs/pybids/metadata.xml delete mode 100644 sci-libs/pybids/pybids-0.6.5.ebuild diff --git a/sci-libs/pybids/Manifest b/sci-libs/pybids/Manifest deleted file mode 100644 index e598d71..0000000 --- a/sci-libs/pybids/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST pybids-0.6.5.tar.gz 2915557 SHA256 06fab79c0f2db87a6a9527a3b0043cbd3cf6961e95f9307a763593d89fad36c1 SHA512 9eef42f00440dddf0147d91f90e07db81f9f95a650f0e47c04304771173ca8691cdb366bd0df1d752c0444f102a4aa010c2343ba75df96528cceb9a98f9d8a0e WHIRLPOOL 8a0cecd8fcdfc1c03038f1d1c9b753ff7dc80ea05c695b0b3f579716ec95b402a42b0628eeb2a9dc430a4b5ee41508b212f054a64d521ea0455bfe30f64fff9c diff --git a/sci-libs/pybids/metadata.xml b/sci-libs/pybids/metadata.xml deleted file mode 100644 index 143b3ea..0000000 --- a/sci-libs/pybids/metadata.xml +++ /dev/null @@ -1,20 +0,0 @@ - - - - - horea.christ@gmail.com - Horea Christian - - - sci@gentoo.org - Gentoo Science Project - - - PyBIDS is a Python library to centralize interactions with datasets - conforming BIDS (Brain Imaging Data Structure) format. For more - information about BIDS visit http://bids.neuroimaging.io. - - - INCF/pybids - - diff --git a/sci-libs/pybids/pybids-0.6.5.ebuild b/sci-libs/pybids/pybids-0.6.5.ebuild deleted file mode 100644 index e98eb2d..0000000 --- a/sci-libs/pybids/pybids-0.6.5.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 1999-2019 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} ) - -inherit distutils-r1 - -DESCRIPTION="Python package to access BIDS datasets" -HOMEPAGE="https://github.com/INCF/pybids" -SRC_URI="https://github.com/INCF/pybids/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64" -IUSE="" - -DEPEND=" - dev-python/setuptools[${PYTHON_USEDEP}] - " -RDEPEND=" - dev-python/grabbit[${PYTHON_USEDEP}] - dev-python/num2words[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/pandas[${PYTHON_USEDEP}] - dev-python/patsy[${PYTHON_USEDEP}] - dev-python/six[${PYTHON_USEDEP}] - sci-libs/nibabel[${PYTHON_USEDEP}] - sci-libs/scipy[${PYTHON_USEDEP}] - " - -RESTRICT="test" -# Fails because fixtures are called directly -# https://github.com/bids-standard/pybids/issues/289#issuecomment-476853673 - -python_test() { - rm bids/tests/test_config.py || die - distutils_install_for_testing - pytest -vv || die - die -} From 5fecd139085ffae7aa186d4c597a9f6bc8729b2f Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Fri, 10 Jan 2020 19:39:51 +0100 Subject: [PATCH 44/54] Deprecated old packages --- net-im/utox/Manifest | 2 - net-im/utox/metadata.xml | 23 ------- net-im/utox/utox-0.16.0.ebuild | 52 --------------- net-im/utox/utox-0.16.1.ebuild | 52 --------------- net-im/utox/utox-9999.ebuild | 51 --------------- net-libs/tox/ChangeLog | 10 --- net-libs/tox/Manifest | 3 - net-libs/tox/files/confd | 2 - net-libs/tox/files/initd | 30 --------- net-libs/tox/files/tox-bootstrapd.conf | 65 ------------------- net-libs/tox/files/tox-bootstrapd.service | 15 ----- net-libs/tox/metadata.xml | 19 ------ net-libs/tox/tox-0.1.6.ebuild | 77 ----------------------- net-libs/tox/tox-0.2.3.ebuild | 77 ----------------------- net-libs/tox/tox-0_pre20160904.ebuild | 75 ---------------------- net-libs/tox/tox-9999.ebuild | 75 ---------------------- 16 files changed, 628 deletions(-) delete mode 100755 net-im/utox/Manifest delete mode 100755 net-im/utox/metadata.xml delete mode 100755 net-im/utox/utox-0.16.0.ebuild delete mode 100755 net-im/utox/utox-0.16.1.ebuild delete mode 100644 net-im/utox/utox-9999.ebuild delete mode 100644 net-libs/tox/ChangeLog delete mode 100644 net-libs/tox/Manifest delete mode 100644 net-libs/tox/files/confd delete mode 100644 net-libs/tox/files/initd delete mode 100644 net-libs/tox/files/tox-bootstrapd.conf delete mode 100644 net-libs/tox/files/tox-bootstrapd.service delete mode 100644 net-libs/tox/metadata.xml delete mode 100644 net-libs/tox/tox-0.1.6.ebuild delete mode 100644 net-libs/tox/tox-0.2.3.ebuild delete mode 100644 net-libs/tox/tox-0_pre20160904.ebuild delete mode 100644 net-libs/tox/tox-9999.ebuild diff --git a/net-im/utox/Manifest b/net-im/utox/Manifest deleted file mode 100755 index b3d2f8c..0000000 --- a/net-im/utox/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST utox-0.16.0.tar.gz 2412270 SHA256 f2a09b6e9daae0152a08ae4085cfb2294ddcce8514a866134fee40dc0684dbe6 SHA512 d0ae6f20bdb99651a355d0d03b376497a6573cd62b379f010b8dc6192967bf43fb16066d2129f8368c62760361f659031133ed15e3908f81d5fc32f14a52b245 WHIRLPOOL c9b45fce564ac2562b0770a8cabfef63b3e23ab7d87b5c5c885b083f71953ed397523bf6d6e488707a4b359288b9c6893c6fd3869558f9c37ff3fec9a0696885 -DIST utox-0.16.1.tar.gz 2412331 SHA256 d8fcee0dbf25596e67c4323fc153069552eeeb4d99cdcdc09ca2074ebc38b493 SHA512 60350bf28b8ac067287550ce42bfb9b10502fbe94298ea9d4f00fb257bfc76c6cd9a7ef843719732e8d3e84789a391a95f3f1be732427b99ab8af472844e62a4 WHIRLPOOL b4e6be767d15ecd93010f95d4b58e3473d9fcff4b8929bbab62a09272694bdb780b8e2df8a348d49c4484a2b809c7e39e209840d990eef68c752599adec9aa67 diff --git a/net-im/utox/metadata.xml b/net-im/utox/metadata.xml deleted file mode 100755 index 463b38c..0000000 --- a/net-im/utox/metadata.xml +++ /dev/null @@ -1,23 +0,0 @@ - - - - - horea.christ@gmail.com - Horea Christian - - - proxy-maint@gentoo.org - Proxy Maintainers - - - A secure and lightning-fast messaging platform for the TOX protocol. - - - uTox/uTox - - - Adds dbus support for desktop notifications - Adds support for filtering audio input - - - diff --git a/net-im/utox/utox-0.16.0.ebuild b/net-im/utox/utox-0.16.0.ebuild deleted file mode 100755 index 3bf351a..0000000 --- a/net-im/utox/utox-0.16.0.ebuild +++ /dev/null @@ -1,52 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit xdg-utils gnome2-utils cmake-utils - -DESCRIPTION="Lightweight Tox client" -HOMEPAGE="https://utox.io" -SRC_URI="https://github.com/uTox/uTox/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -IUSE="+dbus filter_audio test" -KEYWORDS="~amd64" - -RDEPEND="net-libs/tox[av] - media-libs/freetype - filter_audio? ( media-libs/libfilteraudio ) - media-libs/libv4l - media-libs/opus - media-libs/libvpx - x11-libs/libXrender - media-libs/fontconfig - media-libs/openal - x11-libs/libX11 - x11-libs/libXext - dbus? ( sys-apps/dbus )" -DEPEND="${RDEPEND} - test? ( dev-libs/check ) - virtual/pkgconfig" - -S=${WORKDIR}/uTox-${PV} - -src_configure() { - local mycmakeargs=( - -DENABLE_FILTERAUDIO=$(usex filter_audio ON OFF) - -DENABLE_DBUS=$(usex dbus ON OFF) - -DENABLE_TESTS=$(usex test ON OFF) - ) - cmake-utils_src_configure -} - -pkg_postinst() { - xdg_desktop_database_update - gnome2_icon_cache_update -} - -pkg_postrm() { - xdg_desktop_database_update - gnome2_icon_cache_update -} diff --git a/net-im/utox/utox-0.16.1.ebuild b/net-im/utox/utox-0.16.1.ebuild deleted file mode 100755 index 3bf351a..0000000 --- a/net-im/utox/utox-0.16.1.ebuild +++ /dev/null @@ -1,52 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit xdg-utils gnome2-utils cmake-utils - -DESCRIPTION="Lightweight Tox client" -HOMEPAGE="https://utox.io" -SRC_URI="https://github.com/uTox/uTox/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -IUSE="+dbus filter_audio test" -KEYWORDS="~amd64" - -RDEPEND="net-libs/tox[av] - media-libs/freetype - filter_audio? ( media-libs/libfilteraudio ) - media-libs/libv4l - media-libs/opus - media-libs/libvpx - x11-libs/libXrender - media-libs/fontconfig - media-libs/openal - x11-libs/libX11 - x11-libs/libXext - dbus? ( sys-apps/dbus )" -DEPEND="${RDEPEND} - test? ( dev-libs/check ) - virtual/pkgconfig" - -S=${WORKDIR}/uTox-${PV} - -src_configure() { - local mycmakeargs=( - -DENABLE_FILTERAUDIO=$(usex filter_audio ON OFF) - -DENABLE_DBUS=$(usex dbus ON OFF) - -DENABLE_TESTS=$(usex test ON OFF) - ) - cmake-utils_src_configure -} - -pkg_postinst() { - xdg_desktop_database_update - gnome2_icon_cache_update -} - -pkg_postrm() { - xdg_desktop_database_update - gnome2_icon_cache_update -} diff --git a/net-im/utox/utox-9999.ebuild b/net-im/utox/utox-9999.ebuild deleted file mode 100644 index 597896f..0000000 --- a/net-im/utox/utox-9999.ebuild +++ /dev/null @@ -1,51 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit git-r3 xdg-utils gnome2-utils cmake-utils - -DESCRIPTION="Lightweight Tox client" -HOMEPAGE="https://utox.io" -SRC_URI="" -EGIT_REPO_URI="https://github.com/uTox/uTox.git" - -LICENSE="GPL-3" -SLOT="0" -IUSE="+dbus filter_audio test" -KEYWORDS="" - -RDEPEND="net-libs/tox[av] - media-libs/freetype - filter_audio? ( media-libs/libfilteraudio ) - media-libs/libv4l - media-libs/opus - media-libs/libvpx - x11-libs/libXrender - media-libs/fontconfig - media-libs/openal - x11-libs/libX11 - x11-libs/libXext - dbus? ( sys-apps/dbus )" -DEPEND="${RDEPEND} - test? ( dev-libs/check ) - virtual/pkgconfig" - -src_configure() { - local mycmakeargs=( - -DENABLE_FILTERAUDIO=$(usex filter_audio ON OFF) - -DENABLE_DBUS=$(usex dbus ON OFF) - -DENABLE_TESTS=$(usex test ON OFF) - ) - cmake-utils_src_configure -} - -pkg_postinst() { - xdg_desktop_database_update - gnome2_icon_cache_update -} - -pkg_postrm() { - xdg_desktop_database_update - gnome2_icon_cache_update -} diff --git a/net-libs/tox/ChangeLog b/net-libs/tox/ChangeLog deleted file mode 100644 index 7065458..0000000 --- a/net-libs/tox/ChangeLog +++ /dev/null @@ -1,10 +0,0 @@ -*tox-0.1.6 (20 Jul 2018) -*tox-0.2.3 (20 Jul 2018) -*tox-0_pre20160904 (20 Jul 2018) -*tox-9999 (20 Jul 2018) - - 20 Jul 2018; Horea Christian +files/confd, +files/initd, - +files/tox-bootstrapd.conf, +files/tox-bootstrapd.service, +metadata.xml, - +tox-0.1.6.ebuild, +tox-0.2.3.ebuild, +tox-0_pre20160904.ebuild, - +tox-9999.ebuild: - net-libs/tox: new package with attempted version bump diff --git a/net-libs/tox/Manifest b/net-libs/tox/Manifest deleted file mode 100644 index ec6739e..0000000 --- a/net-libs/tox/Manifest +++ /dev/null @@ -1,3 +0,0 @@ -DIST tox-0.1.6.tar.lz 314837 SHA256 c51dfaf30cddbfb9a6080c8202d68113452224570109cd9a6f1b7d9709eae6af SHA512 57ed7cee2c621c57e24f5ab36d68d99414d9820cdb3e8b7c4390818222f9d885f352f9cf76c8eb522c238bebc7d420bcf3cdd5f6ab65b9801aadbd225765166c WHIRLPOOL f75b27ade0f87f3793affbd291aba4b9e2387a29cd89deaf1351ed0797f634737938ff68d95a9fa1866891a68fa7a3b7f1c7ff0b68e3865eb7835fb9c4e5ff8b -DIST tox-0.2.3.tar.gz 471336 SHA256 22c52f286c46d3f802edb6978bcf2a53f8301363e2b745784613427a33ba3a34 SHA512 25433cbbc0aa7e32174c8517a93c6351a23bd04cef34945876290bbd01e6074a5d7df2f5dcd39e67e3e18a6817346f98c45d55d789d462055643271ce44e49ee WHIRLPOOL 2a33e3d8e98d13b81a84248c7e289a321ab7e17ae438a17019d16b814f32f1545b86862cffc51c63353f7b9b9a2b2ba8e8394f4e9bfc7576a473ab59a3f240cd -DIST tox-0_pre20160904.tar.gz 395495 SHA256 2d4a0d096bdb81b12b10551765fb9f87270e170f10f387f700b3def68cb6c35c SHA512 c0da52ac908141e97e96510a05431cbfb4b9aae81faf4c136c95e21b90a23e3bbe6db88303e48c0f4f3c74ca954229787564b7aa41bfb462afb0d8f8430cdaa1 WHIRLPOOL abd3f61784fac93d983e453515d1e8bc87f7d76651a53ce6f566a277d7ec7c1e03294d95781364ce9ab30f2698c6f5cd552bfa4888f8d5d0d315daf038980c63 diff --git a/net-libs/tox/files/confd b/net-libs/tox/files/confd deleted file mode 100644 index 33f850b..0000000 --- a/net-libs/tox/files/confd +++ /dev/null @@ -1,2 +0,0 @@ -TOX_GROUP=tox -TOX_USER=tox diff --git a/net-libs/tox/files/initd b/net-libs/tox/files/initd deleted file mode 100644 index 101d329..0000000 --- a/net-libs/tox/files/initd +++ /dev/null @@ -1,30 +0,0 @@ -#!/sbin/openrc-run - -PIDDIR=/run/tox-bootstrapd -PIDFILE="${PIDDIR}"/tox-bootstrap.pid - -depend() { - need net -} - -start() { - ebegin "Starting tox-dht-bootstrap daemon" - - checkpath -d -q -o "${TOX_USER}":"${TOX_GROUP}" "${PIDDIR}" - - start-stop-daemon --start \ - --pidfile "${PIDFILE}" \ - --user="${TOX_USER}" --group="${TOX_GROUP}" \ - --exec /usr/bin/tox-bootstrapd -- --config /etc/tox-bootstrapd.conf - - eend $? -} - -stop() { - ebegin "Stopping tox-dht-bootstrap daemon" - - start-stop-daemon --stop \ - --pidfile "${PIDFILE}" - - eend $? -} diff --git a/net-libs/tox/files/tox-bootstrapd.conf b/net-libs/tox/files/tox-bootstrapd.conf deleted file mode 100644 index 3413f59..0000000 --- a/net-libs/tox/files/tox-bootstrapd.conf +++ /dev/null @@ -1,65 +0,0 @@ -// Tox DHT bootstrap daemon configuration file. - -// Listening port (UDP). -port = 33445 - -// A key file is like a password, so keep it where no one can read it. -// If there is no key file, a new one will be generated. -// The daemon should have permission to read/write it. -keys_file_path = "/var/lib/tox-bootstrapd/keys" - -// The PID file written to by the daemon. -// Make sure that the user that daemon runs as has permissions to write to the -// PID file. -pid_file_path = "/var/run/tox-bootstrapd/tox-bootstrapd.pid" - -// Enable IPv6. -enable_ipv6 = true - -// Fallback to IPv4 in case IPv6 fails. -enable_ipv4_fallback = true - -// Automatically bootstrap with nodes on local area network. -enable_lan_discovery = true - -enable_tcp_relay = true - -// While Tox uses 33445 port by default, 443 (https) and 3389 (rdp) ports are very -// common among nodes, so it's encouraged to keep them in place. -tcp_relay_ports = [443, 3389, 33445] - -// Reply to MOTD (Message Of The Day) requests. -enable_motd = true - -// Just a message that is sent when someone requests MOTD. -// Put anything you want, but note that it will be trimmed to fit into 255 bytes. -motd = "tox-bootstrapd" - -// Any number of nodes the daemon will bootstrap itself off. -// -// Remember to replace the provided example with your own node list. -// There is a maintained list of bootstrap nodes on Tox's wiki, if you need it -// (https://wiki.tox.chat/users/nodes). -// -// You may leave the list empty or remove "bootstrap_nodes" completely, -// in both cases this will be interpreted as if you don't want to bootstrap -// from anyone. -// -// address = any IPv4 or IPv6 address and also any US-ASCII domain name. -bootstrap_nodes = ( - { // Example Node 1 (IPv4) - address = "127.0.0.1" - port = 33445 - public_key = "728925473812C7AAC482BE7250BCCAD0B8CB9F737BF3D42ABD34459C1768F854" - }, - { // Example Node 2 (IPv6) - address = "::1/128" - port = 33445 - public_key = "3E78BACF0F84235B30054B54898F56793E1DEF8BD46B1038B9D822E8460FAB67" - }, - { // Example Node 3 (US-ASCII domain name) - address = "example.org" - port = 33445 - public_key = "8CD5A9BF0A6CE358BA36F7A653F99FA6B258FF756E490F52C1F98CC420F78858" - } -) diff --git a/net-libs/tox/files/tox-bootstrapd.service b/net-libs/tox/files/tox-bootstrapd.service deleted file mode 100644 index ae2f238..0000000 --- a/net-libs/tox/files/tox-bootstrapd.service +++ /dev/null @@ -1,15 +0,0 @@ -[Unit] -Description=Tox DHT Bootstrap Daemon -After=network.target - -[Service] -User=tox -Group=tox -RuntimeDirectory=tox-bootstrapd -PIDFile=/run/tox-bootstrapd/tox-bootstrapd.pid -WorkingDirectory=/var/lib/tox-bootstrapd -ExecStart=/usr/bin/tox-bootstrapd --config /etc/tox-bootstrapd.conf -#CapabilityBoundingSet=CAP_NET_BIND_SERVICE - -[Install] -WantedBy=multi-user.target diff --git a/net-libs/tox/metadata.xml b/net-libs/tox/metadata.xml deleted file mode 100644 index 0dc9808..0000000 --- a/net-libs/tox/metadata.xml +++ /dev/null @@ -1,19 +0,0 @@ - - - - - - Adds support for audio and video. - Log level: 0 (no debug info logged) - Log level: 1 - Log level: 2 - Log level: 3 - Log level: 4 - Log level: 5 - Enable the testing nTox client. - Enable the DHT Bootstrap Daemon. - - - TokTok/c-toxcore - - diff --git a/net-libs/tox/tox-0.1.6.ebuild b/net-libs/tox/tox-0.1.6.ebuild deleted file mode 100644 index 62dd43f..0000000 --- a/net-libs/tox/tox-0.1.6.ebuild +++ /dev/null @@ -1,77 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit autotools systemd unpacker user - -DESCRIPTION="Encrypted P2P, messaging, and audio/video calling platform" -HOMEPAGE="https://tox.chat" -SRC_URI="https://github.com/TokTok/c-toxcore/releases/download/v${PV}/c-toxcore-v${PV}.tar.lz -> ${P}.tar.lz" - -LICENSE="GPL-3+" -SLOT="0/0.1" -KEYWORDS="~amd64 ~arm ~x86" -IUSE="+av daemon log-debug log-error log-info log-trace log-warn +no-log ntox static-libs test" - -REQUIRED_USE="^^ ( no-log log-trace log-debug log-info log-warn log-error )" - -RDEPEND=" - av? ( media-libs/libvpx:= - media-libs/opus ) - daemon? ( dev-libs/libconfig ) - ntox? ( sys-libs/ncurses:0= ) - >=dev-libs/libsodium-0.6.1:=[asm,urandom]" -DEPEND="${RDEPEND} - $(unpacker_src_uri_depends) - test? ( dev-libs/check ) - virtual/pkgconfig" - -S=${WORKDIR} - -src_prepare() { - default - eautoreconf -} - -src_configure() { - econf \ - $(usex log-trace "--enable-logging --with-log-level=TRACE" "") \ - $(usex log-debug "--enable-logging --with-log-level=DEBUG" "") \ - $(usex log-info "--enable-logging --with-log-level=INFO" "") \ - $(usex log-warn "--enable-logging --with-log-level=WARNING" "") \ - $(usex log-error "--enable-logging --with-log-level=ERROR" "") \ - $(use_enable av) \ - $(use_enable test tests) \ - $(use_enable ntox) \ - $(use_enable daemon) \ - $(use_enable static-libs static) -} - -src_install() { - default - if use daemon; then - newinitd "${FILESDIR}"/initd tox-dht-daemon - newconfd "${FILESDIR}"/confd tox-dht-daemon - insinto /etc - doins "${FILESDIR}"/tox-bootstrapd.conf - systemd_dounit "${FILESDIR}"/tox-bootstrapd.service - fi - - find "${D}" -name '*.la' -delete || die -} - -pkg_postinst() { - if use daemon; then - enewgroup ${PN} - enewuser ${PN} -1 -1 -1 ${PN} - if [[ -f ${EROOT%/}/var/lib/tox-dht-bootstrap/key ]]; then - ewarn "Backwards compatability with the bootstrap daemon might have been" - ewarn "broken a while ago. To resolve this issue, REMOVE the following files:" - ewarn " ${EROOT%/}/var/lib/tox-dht-bootstrap/key" - ewarn " ${EROOT%/}/etc/tox-bootstrapd.conf" - ewarn " ${EROOT%/}/run/tox-dht-bootstrap/tox-dht-bootstrap.pid" - ewarn "Then just re-emerge net-libs/tox" - fi - fi -} diff --git a/net-libs/tox/tox-0.2.3.ebuild b/net-libs/tox/tox-0.2.3.ebuild deleted file mode 100644 index 02aa63d..0000000 --- a/net-libs/tox/tox-0.2.3.ebuild +++ /dev/null @@ -1,77 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit autotools systemd unpacker user - -DESCRIPTION="Encrypted P2P, messaging, and audio/video calling platform" -HOMEPAGE="https://tox.chat" -SRC_URI="https://github.com/TokTok/c-toxcore/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3+" -SLOT="0/0.1" -KEYWORDS="~amd64 ~arm ~x86" -IUSE="+av daemon log-debug log-error log-info log-trace log-warn +no-log ntox static-libs test" - -REQUIRED_USE="^^ ( no-log log-trace log-debug log-info log-warn log-error )" - -RDEPEND=" - av? ( media-libs/libvpx:= - media-libs/opus ) - daemon? ( dev-libs/libconfig ) - ntox? ( sys-libs/ncurses:0= ) - >=dev-libs/libsodium-0.6.1:=[asm,urandom]" -DEPEND="${RDEPEND} - $(unpacker_src_uri_depends) - test? ( dev-libs/check ) - virtual/pkgconfig" - -S=${WORKDIR} - -src_prepare() { - default - eautoreconf -} - -src_configure() { - econf \ - $(usex log-trace "--enable-logging --with-log-level=TRACE" "") \ - $(usex log-debug "--enable-logging --with-log-level=DEBUG" "") \ - $(usex log-info "--enable-logging --with-log-level=INFO" "") \ - $(usex log-warn "--enable-logging --with-log-level=WARNING" "") \ - $(usex log-error "--enable-logging --with-log-level=ERROR" "") \ - $(use_enable av) \ - $(use_enable test tests) \ - $(use_enable ntox) \ - $(use_enable daemon) \ - $(use_enable static-libs static) -} - -src_install() { - default - if use daemon; then - newinitd "${FILESDIR}"/initd tox-dht-daemon - newconfd "${FILESDIR}"/confd tox-dht-daemon - insinto /etc - doins "${FILESDIR}"/tox-bootstrapd.conf - systemd_dounit "${FILESDIR}"/tox-bootstrapd.service - fi - - find "${D}" -name '*.la' -delete || die -} - -pkg_postinst() { - if use daemon; then - enewgroup ${PN} - enewuser ${PN} -1 -1 -1 ${PN} - if [[ -f ${EROOT%/}/var/lib/tox-dht-bootstrap/key ]]; then - ewarn "Backwards compatability with the bootstrap daemon might have been" - ewarn "broken a while ago. To resolve this issue, REMOVE the following files:" - ewarn " ${EROOT%/}/var/lib/tox-dht-bootstrap/key" - ewarn " ${EROOT%/}/etc/tox-bootstrapd.conf" - ewarn " ${EROOT%/}/run/tox-dht-bootstrap/tox-dht-bootstrap.pid" - ewarn "Then just re-emerge net-libs/tox" - fi - fi -} diff --git a/net-libs/tox/tox-0_pre20160904.ebuild b/net-libs/tox/tox-0_pre20160904.ebuild deleted file mode 100644 index 0d148a0..0000000 --- a/net-libs/tox/tox-0_pre20160904.ebuild +++ /dev/null @@ -1,75 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit autotools systemd user vcs-snapshot - -DESCRIPTION="Encrypted P2P, messaging, and audio/video calling platform" -HOMEPAGE="https://tox.chat" -EGIT_COMMIT="755f084e8720b349026c85afbad58954cb7ff1d4" -SRC_URI="https://github.com/irungentoo/toxcore/archive/${EGIT_COMMIT}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3+" -SLOT="0/0.0" -KEYWORDS="~amd64 ~arm ~x86" -IUSE="+av daemon log-debug log-error log-info log-trace log-warn +no-log ntox static-libs test" - -REQUIRED_USE="^^ ( no-log log-trace log-debug log-info log-warn log-error )" - -RDEPEND=" - av? ( media-libs/libvpx:= - media-libs/opus ) - daemon? ( dev-libs/libconfig ) - ntox? ( sys-libs/ncurses:0= ) - >=dev-libs/libsodium-0.6.1:=[asm,urandom]" -DEPEND="${RDEPEND} - test? ( dev-libs/check ) - virtual/pkgconfig" - -src_prepare() { - default - eautoreconf -} - -src_configure() { - econf \ - $(usex log-trace "--enable-logging --with-log-level=TRACE" "") \ - $(usex log-debug "--enable-logging --with-log-level=DEBUG" "") \ - $(usex log-info "--enable-logging --with-log-level=INFO" "") \ - $(usex log-warn "--enable-logging --with-log-level=WARNING" "") \ - $(usex log-error "--enable-logging --with-log-level=ERROR" "") \ - $(use_enable av) \ - $(use_enable test tests) \ - $(use_enable ntox) \ - $(use_enable daemon) \ - $(use_enable static-libs static) -} - -src_install() { - default - if use daemon; then - newinitd "${FILESDIR}"/initd tox-dht-daemon - newconfd "${FILESDIR}"/confd tox-dht-daemon - insinto /etc - doins "${FILESDIR}"/tox-bootstrapd.conf - systemd_dounit "${FILESDIR}"/tox-bootstrapd.service - fi - - find "${D}" -name '*.la' -delete || die -} - -pkg_postinst() { - if use daemon; then - enewgroup ${PN} - enewuser ${PN} -1 -1 -1 ${PN} - if [[ -f ${EROOT}var/lib/tox-dht-bootstrap/key ]]; then - ewarn "Backwards compatability with the bootstrap daemon might have been" - ewarn "broken a while ago. To resolve this issue, REMOVE the following files:" - ewarn " ${EROOT}var/lib/tox-dht-bootstrap/key" - ewarn " ${EROOT}etc/tox-bootstrapd.conf" - ewarn " ${EROOT}run/tox-dht-bootstrap/tox-dht-bootstrap.pid" - ewarn "Then just re-emerge net-libs/tox" - fi - fi -} diff --git a/net-libs/tox/tox-9999.ebuild b/net-libs/tox/tox-9999.ebuild deleted file mode 100644 index c3bf186..0000000 --- a/net-libs/tox/tox-9999.ebuild +++ /dev/null @@ -1,75 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit autotools git-r3 user systemd - -DESCRIPTION="Encrypted P2P, messaging, and audio/video calling platform" -HOMEPAGE="https://tox.chat" -SRC_URI="" -EGIT_REPO_URI="https://github.com/TokTok/c-toxcore.git" - -LICENSE="GPL-3+" -SLOT="0/0.1" -KEYWORDS="" -IUSE="+av daemon log-debug log-error log-info log-trace log-warn +no-log ntox static-libs test" - -REQUIRED_USE="^^ ( no-log log-trace log-debug log-info log-warn log-error )" - -RDEPEND=" - av? ( media-libs/libvpx:= - media-libs/opus ) - daemon? ( dev-libs/libconfig ) - ntox? ( sys-libs/ncurses:0= ) - >=dev-libs/libsodium-0.6.1:=[asm,urandom]" -DEPEND="${RDEPEND} - test? ( dev-libs/check ) - virtual/pkgconfig" - -src_prepare() { - default - eautoreconf -} - -src_configure() { - econf \ - $(usex log-trace "--enable-logging --with-log-level=TRACE" "") \ - $(usex log-debug "--enable-logging --with-log-level=DEBUG" "") \ - $(usex log-info "--enable-logging --with-log-level=INFO" "") \ - $(usex log-warn "--enable-logging --with-log-level=WARNING" "") \ - $(usex log-error "--enable-logging --with-log-level=ERROR" "") \ - $(use_enable av) \ - $(use_enable test tests) \ - $(use_enable ntox) \ - $(use_enable daemon) \ - $(use_enable static-libs static) -} - -src_install() { - default - if use daemon; then - newinitd "${FILESDIR}"/initd tox-dht-daemon - newconfd "${FILESDIR}"/confd tox-dht-daemon - insinto /etc - doins "${FILESDIR}"/tox-bootstrapd.conf - systemd_dounit "${FILESDIR}"/tox-bootstrapd.service - fi - - find "${D}" -name '*.la' -delete || die -} - -pkg_postinst() { - if use daemon; then - enewgroup ${PN} - enewuser ${PN} -1 -1 -1 ${PN} - if [[ -f ${EROOT%/}/var/lib/tox-dht-bootstrap/key ]]; then - ewarn "Backwards compatability with the bootstrap daemon might have been" - ewarn "broken a while ago. To resolve this issue, REMOVE the following files:" - ewarn " ${EROOT%/}/var/lib/tox-dht-bootstrap/key" - ewarn " ${EROOT%/}/etc/tox-bootstrapd.conf" - ewarn " ${EROOT%/}/run/tox-dht-bootstrap/tox-dht-bootstrap.pid" - ewarn "Then just re-emerge net-libs/tox" - fi - fi -} From ee2eaede0b5cc9d254be3a569b6b730b95cd6d26 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Fri, 10 Jan 2020 19:40:45 +0100 Subject: [PATCH 45/54] Deprecated old package --- .../chr-helpers/chr-helpers-9999.ebuild | 29 ------------------- 1 file changed, 29 deletions(-) delete mode 100644 dev-python/chr-helpers/chr-helpers-9999.ebuild diff --git a/dev-python/chr-helpers/chr-helpers-9999.ebuild b/dev-python/chr-helpers/chr-helpers-9999.ebuild deleted file mode 100644 index c034ba6..0000000 --- a/dev-python/chr-helpers/chr-helpers-9999.ebuild +++ /dev/null @@ -1,29 +0,0 @@ -# Distributed under the terms of the GNU General Public License v3 - -EAPI=5 - -PYTHON_COMPAT=( python{2_7,3_2,3_3} ) - -inherit python-single-r1 git-2 - -DESCRIPTION="Helper Functions for TheChymera's python scripts" -HOMEPAGE="https://github.com/TheChymera/chr-helpers" -EGIT_REPO_URI="https://github.com/TheChymera/chr-helpers.git" -SRC_URI="" - - -SLOT="0" -LICENSE="LPPL-1.3 BSD" -KEYWORDS="~amd64" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -DEPEND="" -RDEPEND="dev-python/pandas" - -src_install() { - python_optimize . - python_domodule "${S}"/chr_helpers.py - python_domodule "${S}"/chr_matplotlib.py -} - - From 96c965c4291eac1ae650b6bb11aef45a3ae3cce3 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Fri, 10 Jan 2020 19:41:30 +0100 Subject: [PATCH 46/54] sci-biology/samri: version bump 0.4.2 ahead of Gentoo Science Package-Manager: Portage-2.3.84, Repoman-2.3.20 Signed-off-by: Horea Christian --- sci-biology/samri/ChangeLog | 5 +++ sci-biology/samri/Manifest | 1 + sci-biology/samri/samri-0.4.2.ebuild | 56 ++++++++++++++++++++++++++++ 3 files changed, 62 insertions(+) create mode 100644 sci-biology/samri/Manifest create mode 100644 sci-biology/samri/samri-0.4.2.ebuild diff --git a/sci-biology/samri/ChangeLog b/sci-biology/samri/ChangeLog index f318c6b..34f57e2 100644 --- a/sci-biology/samri/ChangeLog +++ b/sci-biology/samri/ChangeLog @@ -1,3 +1,8 @@ +*samri-0.4.2 (10 Jan 2020) + + 10 Jan 2020; +samri-0.4.2.ebuild: + sci-biology/samri: version bump 0.4.2 ahead of Gentoo Science + 08 Dec 2019; -Manifest, -samri-0.4.1.ebuild: sci-biology/samri: migrated version to Gentoo Science https://gitweb.gentoo.o rg/proj/sci.git/commit/?id=e68c1eb1aea94ee2860d3b9feb079932114904ea diff --git a/sci-biology/samri/Manifest b/sci-biology/samri/Manifest new file mode 100644 index 0000000..69cc282 --- /dev/null +++ b/sci-biology/samri/Manifest @@ -0,0 +1 @@ +DIST samri-0.4.2.tar.gz 4115783 SHA256 bf2d14a57e153d1dbfdb6471434412a1ab00c92dd8cd4a858fa9c9b7703dfae6 SHA512 cb5853ea0d47a3cfd61a0064a1ab776f34dc5178fbe53d515452c03b5b3b24e39d1fe22f6f75e3918c86aaac7517aac05bc911ea8ffdb5a4c3ef07b5cff63880 WHIRLPOOL dd9f42ec3b5d3280968560f5d81bb8db252f9256ad42f888af1b8ceaed57946febe69d3e6dc11824a9713fa5ae51d62f38e7ee1b333d6f2c7279c76af9b18e32 diff --git a/sci-biology/samri/samri-0.4.2.ebuild b/sci-biology/samri/samri-0.4.2.ebuild new file mode 100644 index 0000000..e729f5a --- /dev/null +++ b/sci-biology/samri/samri-0.4.2.ebuild @@ -0,0 +1,56 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +PYTHON_COMPAT=( python3_6 ) + +inherit distutils-r1 + +DESCRIPTION="Small Animal Magnetic Resonance Imaging" +HOMEPAGE="https://github.com/IBT-FMI/SAMRI" +SRC_URI="https://github.com/IBT-FMI/SAMRI/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +IUSE="labbookdb test" +KEYWORDS="~amd64" + +DEPEND=" + test? ( + dev-python/pytest[${PYTHON_USEDEP}] + sci-biology/samri_bidsdata + sci-biology/samri_bindata + ) +" +RDEPEND=" + dev-python/argh[${PYTHON_USEDEP}] + dev-python/joblib[${PYTHON_USEDEP}] + >=dev-python/matplotlib-2.0.2[${PYTHON_USEDEP}] + >=dev-python/numpy-1.13.3[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/seaborn[${PYTHON_USEDEP}] + dev-python/statsmodels[${PYTHON_USEDEP}] + media-gfx/blender + >=sci-biology/fsl-5.0.9 + sci-biology/bru2nii + sci-biology/mouse-brain-atlases + labbookdb? ( sci-libs/labbookdb[${PYTHON_USEDEP}] ) + sci-libs/nibabel[${PYTHON_USEDEP}] + >=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}] + >=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}] + <=sci-libs/pybids-0.6.5[${PYTHON_USEDEP}] + sci-libs/scikits_image[${PYTHON_USEDEP}] + sci-libs/scipy[${PYTHON_USEDEP}] + sci-biology/ants + sci-biology/afni + sci-biology/nilearn[${PYTHON_USEDEP}] +" + +S="${WORKDIR}/SAMRI-${PV}" + +src_prepare() { + sed -i -e "s:/usr:${EPREFIX}/usr:g" `grep -rlI \'/usr/ samri` || die + sed -i -e "s:/usr:${EPREFIX}/usr:g" `grep -rlI /usr/ test_scripts.sh` || die + distutils-r1_src_prepare +} From 0e927920241b2e75fd44f408f89bd8ec85f80678 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Sat, 11 Jan 2020 23:40:19 +0100 Subject: [PATCH 47/54] sci-biology/irsabi_brudata: new package ahead of Gentoo Science Package-Manager: Portage-2.3.83, Repoman-2.3.20 Signed-off-by: Horea Christian --- sci-biology/irsabi_brudata/ChangeLog | 4 +++ sci-biology/irsabi_brudata/Manifest | 1 + .../irsabi_brudata/irsabi_brudata-1.4.ebuild | 30 +++++++++++++++++++ sci-biology/irsabi_brudata/metadata.xml | 20 +++++++++++++ 4 files changed, 55 insertions(+) create mode 100644 sci-biology/irsabi_brudata/ChangeLog create mode 100644 sci-biology/irsabi_brudata/Manifest create mode 100644 sci-biology/irsabi_brudata/irsabi_brudata-1.4.ebuild create mode 100644 sci-biology/irsabi_brudata/metadata.xml diff --git a/sci-biology/irsabi_brudata/ChangeLog b/sci-biology/irsabi_brudata/ChangeLog new file mode 100644 index 0000000..21260bb --- /dev/null +++ b/sci-biology/irsabi_brudata/ChangeLog @@ -0,0 +1,4 @@ +*irsabi_brudata-1.4 (11 Jan 2020) + + 11 Jan 2020; +irsabi_brudata-1.4.ebuild, +metadata.xml: + sci-biology/irsabi_brudata: new package ahead of Gentoo Science diff --git a/sci-biology/irsabi_brudata/Manifest b/sci-biology/irsabi_brudata/Manifest new file mode 100644 index 0000000..04070b1 --- /dev/null +++ b/sci-biology/irsabi_brudata/Manifest @@ -0,0 +1 @@ +DIST irsabi_brudata-1.4.tar.xz 11214820256 SHA256 9291df5142d5ad6ae8ac0cfd22943d54a6ab20c76502bf45c6283270631985d9 SHA512 0caebefeb2bd7b708d59d0ca83fa11bcc6e5d4e74eaec087eedaf8f2627b15e9a6ba5baa2cb5edb6724570ad7dcaf05a40758ab4c9c997e5770eb84180fc63f1 WHIRLPOOL b7815a1acc8076efd0c1b849f299ad3d16e53367f62103ee35a229dba194d6fe544021e460a919473a155fc9784c36baca42df65e29647aba7113127bb3a7054 diff --git a/sci-biology/irsabi_brudata/irsabi_brudata-1.4.ebuild b/sci-biology/irsabi_brudata/irsabi_brudata-1.4.ebuild new file mode 100644 index 0000000..9ad0a8e --- /dev/null +++ b/sci-biology/irsabi_brudata/irsabi_brudata-1.4.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +inherit check-reqs + +DESCRIPTION="Raw data files released with the IRSABI publication" +HOMEPAGE="http://www.aic-fmi.ethz.ch/" +SRC_URI="http://chymera.eu/distfiles/${P}.tar.xz" + +LICENSE="CC-BY-SA-4.0" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + +RDEPEND="" +DEPEND="" + +pkg_pretend() { + CHECKREQS_DISK_BUILD="12G" + check-reqs_pkg_pretend +} + +# We disable this phase to not check requirements twice. +pkg_setup() { :; } + +src_install() { + insinto "/usr/share/${PN}" + doins -r * +} diff --git a/sci-biology/irsabi_brudata/metadata.xml b/sci-biology/irsabi_brudata/metadata.xml new file mode 100644 index 0000000..d39662e --- /dev/null +++ b/sci-biology/irsabi_brudata/metadata.xml @@ -0,0 +1,20 @@ + + + + + horea.christ@gmail.com + Horea Christian + + + sci@gentoo.org + Gentoo Science Project + + + Bruker ParaVision raw data recorded at the ETH/UZH Animal Imaging + Center and first associated with the IRSABI publication. The data + represents f/MRI mouse brain scans with both BOLD and CBV contrasts, + and acquired during optogenetic stimulation over multiple sessions + including acute (i.v.) and chronic (s.c.) fluoxetine administration + sessions. + + From e663dc5256bfeb259db8078c99e0aa7fe141bae5 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Sun, 12 Jan 2020 14:36:01 +0100 Subject: [PATCH 48/54] Deprecated package in favour of irsabi_brudata --- sci-biology/irsabi_data/ChangeLog | 5 ---- sci-biology/irsabi_data/Manifest | 1 - .../irsabi_data/irsabi_data-1.0.ebuild | 30 ------------------- sci-biology/irsabi_data/metadata.xml | 20 ------------- 4 files changed, 56 deletions(-) delete mode 100644 sci-biology/irsabi_data/ChangeLog delete mode 100644 sci-biology/irsabi_data/Manifest delete mode 100644 sci-biology/irsabi_data/irsabi_data-1.0.ebuild delete mode 100644 sci-biology/irsabi_data/metadata.xml diff --git a/sci-biology/irsabi_data/ChangeLog b/sci-biology/irsabi_data/ChangeLog deleted file mode 100644 index 182b821..0000000 --- a/sci-biology/irsabi_data/ChangeLog +++ /dev/null @@ -1,5 +0,0 @@ -*irsabi_data-1.0 (06 Jan 2019) - - 06 Jan 2019; Horea Christian +irsabi_data-1.0.ebuild, - +metadata.xml: - sci-biology/irsabi_data: new package ahead of Gentoo Science diff --git a/sci-biology/irsabi_data/Manifest b/sci-biology/irsabi_data/Manifest deleted file mode 100644 index a2e44e1..0000000 --- a/sci-biology/irsabi_data/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST irsabi_data-1.0.tar.xz 11245040468 SHA256 ba07c493d10766ac1ff30bf94556453d48a33225c945bc5f709f4787c5daf551 SHA512 615f5ee77a67f10ab2e895f4387908f8becf37477e26d7e1acacfa91d96dbcd72d85690147b379688373a08155347e637a658bc5de89f0432588362d7b642179 WHIRLPOOL 90c6fcf754e58c563f44d07cf95a4deca42049af6fc44c8c6984583bea885a33a55f70b38bb0052efc2c8d2203f8004fd8d333ed198c09f1ff1ce158597ae48a diff --git a/sci-biology/irsabi_data/irsabi_data-1.0.ebuild b/sci-biology/irsabi_data/irsabi_data-1.0.ebuild deleted file mode 100644 index 3bc8b48..0000000 --- a/sci-biology/irsabi_data/irsabi_data-1.0.ebuild +++ /dev/null @@ -1,30 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit check-reqs - -DESCRIPTION="Raw data files released with the IRSABI publication" -HOMEPAGE="http://www.aic-fmi.ethz.ch/" -SRC_URI="http://chymera.eu/distfiles/${P}.tar.xz" - -LICENSE="CC-BY-SA-4.0" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" - -RDEPEND="" -DEPEND="" - -pkg_pretend() { - CHECKREQS_DISK_BUILD="10G" - check-reqs_pkg_pretend -} - -# We disable this phase to not check requirements twice. -pkg_setup() { :; } - -src_install() { - insinto "/usr/share/${PN}" - doins -r * -} diff --git a/sci-biology/irsabi_data/metadata.xml b/sci-biology/irsabi_data/metadata.xml deleted file mode 100644 index d39662e..0000000 --- a/sci-biology/irsabi_data/metadata.xml +++ /dev/null @@ -1,20 +0,0 @@ - - - - - horea.christ@gmail.com - Horea Christian - - - sci@gentoo.org - Gentoo Science Project - - - Bruker ParaVision raw data recorded at the ETH/UZH Animal Imaging - Center and first associated with the IRSABI publication. The data - represents f/MRI mouse brain scans with both BOLD and CBV contrasts, - and acquired during optogenetic stimulation over multiple sessions - including acute (i.v.) and chronic (s.c.) fluoxetine administration - sessions. - - From 2aabbbca1f108038e1d1361ac72086d35a33eee8 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Tue, 14 Jan 2020 04:02:55 +0100 Subject: [PATCH 49/54] Improved instructions --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 1a436a5..4c2ceee 100644 --- a/README.md +++ b/README.md @@ -16,7 +16,7 @@ wget https://raw.githubusercontent.com/TheChymera/overlay/master/metadata/chymer ``` Afterwards, simply run `emerge --sync`, and Portage should seamlessly make all our ebuilds available. -Some of our packages are available as live (`*-9999`) ebuilds, and if you wish to use this feature (only advisable if you are well-informed on the day-to-day development of a package) these versions can be manually unmasked in a case-by-case basis under `/etc/portage/package.accept_keywords`. +Some of our packages are available as live (`*-9999`) ebuilds, and if you wish to use this feature (only advisable if you are well-informed on the day-to-day development of the specific package) these versions can be manually unmasked on a case-by-case basis under `/etc/portage/package.accept_keywords`. --- From 03dffcf6b046aa0d2005b8ad49d30bff2eb05da4 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Wed, 15 Jan 2020 04:47:37 +0100 Subject: [PATCH 50/54] sci-biology/fsl: added dependency and bumped EAPI Package-Manager: Portage-2.3.83, Repoman-2.3.20 Signed-off-by: Horea Christian --- sci-biology/fsl/ChangeLog | 3 +++ sci-biology/fsl/fsl-6.0.2.ebuild | 5 +++-- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/sci-biology/fsl/ChangeLog b/sci-biology/fsl/ChangeLog index 80eea53..9345c9c 100644 --- a/sci-biology/fsl/ChangeLog +++ b/sci-biology/fsl/ChangeLog @@ -1,3 +1,6 @@ + 15 Jan 2020; fsl-6.0.2.ebuild: + sci-biology/fsl: added dependency and bumped EAPI + 14 Nov 2019; François Bissey fsl-6.0.2.ebuild: sci-biology/fsl: use generic blas/lapack revert stuff. diff --git a/sci-biology/fsl/fsl-6.0.2.ebuild b/sci-biology/fsl/fsl-6.0.2.ebuild index fbc7476..492cbdd 100644 --- a/sci-biology/fsl/fsl-6.0.2.ebuild +++ b/sci-biology/fsl/fsl-6.0.2.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 inherit flag-o-matic toolchain-funcs prefix @@ -16,6 +16,7 @@ IUSE="" DEPEND=" dev-libs/boost + dev-python/fslpy media-gfx/graphviz media-libs/gd media-libs/glu From 463348b272aec2b6730b7e40e55b43452f39fb68 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Thu, 16 Jan 2020 04:46:38 +0100 Subject: [PATCH 51/54] sci-biology/fsl: dropped commented matlab USE flag Package-Manager: Portage-2.3.83, Repoman-2.3.20 Signed-off-by: Horea Christian --- sci-biology/fsl/ChangeLog | 3 +++ sci-biology/fsl/fsl-6.0.2.ebuild | 3 --- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/sci-biology/fsl/ChangeLog b/sci-biology/fsl/ChangeLog index 9345c9c..26bbff1 100644 --- a/sci-biology/fsl/ChangeLog +++ b/sci-biology/fsl/ChangeLog @@ -1,3 +1,6 @@ + 16 Jan 2020; fsl-6.0.2.ebuild: + sci-biology/fsl: dropped commented matlab USE flag + 15 Jan 2020; fsl-6.0.2.ebuild: sci-biology/fsl: added dependency and bumped EAPI diff --git a/sci-biology/fsl/fsl-6.0.2.ebuild b/sci-biology/fsl/fsl-6.0.2.ebuild index 492cbdd..cde4794 100644 --- a/sci-biology/fsl/fsl-6.0.2.ebuild +++ b/sci-biology/fsl/fsl-6.0.2.ebuild @@ -143,9 +143,6 @@ src_install() { insinto /etc doins etc/fslversion doins -r etc/default_flobs.flobs etc/flirtsch etc/js etc/luts - #if use matlab; then - # doins etc/matlab - #fi #the following is needed for FSL and depending programs to be able #to find its files, since FSL uses an uncommon installation path: From 12ab12b63c6fd00aaf4a32303640e5a8e537ccc5 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Thu, 16 Jan 2020 13:09:30 +0100 Subject: [PATCH 52/54] sci-biology/irsabi_brudata: version bump 1.4.1 Package-Manager: Portage-2.3.83, Repoman-2.3.20 Signed-off-by: Horea Christian --- sci-biology/irsabi_brudata/ChangeLog | 6 ++++++ sci-biology/irsabi_brudata/Manifest | 2 +- ...rsabi_brudata-1.4.ebuild => irsabi_brudata-1.4.1.ebuild} | 0 3 files changed, 7 insertions(+), 1 deletion(-) rename sci-biology/irsabi_brudata/{irsabi_brudata-1.4.ebuild => irsabi_brudata-1.4.1.ebuild} (100%) diff --git a/sci-biology/irsabi_brudata/ChangeLog b/sci-biology/irsabi_brudata/ChangeLog index 21260bb..1fc14f4 100644 --- a/sci-biology/irsabi_brudata/ChangeLog +++ b/sci-biology/irsabi_brudata/ChangeLog @@ -1,3 +1,9 @@ +*irsabi_brudata-1.4.1 (16 Jan 2020) + + 16 Jan 2020; +irsabi_brudata-1.4.1.ebuild, + -irsabi_brudata-1.4.ebuild: + sci-biology/irsabi_brudata: version bump 1.4.1 + *irsabi_brudata-1.4 (11 Jan 2020) 11 Jan 2020; +irsabi_brudata-1.4.ebuild, +metadata.xml: diff --git a/sci-biology/irsabi_brudata/Manifest b/sci-biology/irsabi_brudata/Manifest index 04070b1..acdb9c9 100644 --- a/sci-biology/irsabi_brudata/Manifest +++ b/sci-biology/irsabi_brudata/Manifest @@ -1 +1 @@ -DIST irsabi_brudata-1.4.tar.xz 11214820256 SHA256 9291df5142d5ad6ae8ac0cfd22943d54a6ab20c76502bf45c6283270631985d9 SHA512 0caebefeb2bd7b708d59d0ca83fa11bcc6e5d4e74eaec087eedaf8f2627b15e9a6ba5baa2cb5edb6724570ad7dcaf05a40758ab4c9c997e5770eb84180fc63f1 WHIRLPOOL b7815a1acc8076efd0c1b849f299ad3d16e53367f62103ee35a229dba194d6fe544021e460a919473a155fc9784c36baca42df65e29647aba7113127bb3a7054 +DIST irsabi_brudata-1.4.1.tar.xz 11245088748 SHA256 312c9b4c5e2380806c39d164d101e1e8b2cbdbebf839224bbafb43a7f24c35cf SHA512 1cdd0653ad652ee52a03377d97c4e7fff71a30e90af91a1c5b8678a100abd3b6bf40c9d78765ed113d280a7ae24c6c83cce22b9dd50907289c21935c572dda10 WHIRLPOOL ff8b64e88300e940786e4a67e757f2b91fb507752396315d8f2ad44ee883f8903750f59fa38fe0ee73d71f099f59325baa75f050be9865c4826a7398677a2d52 diff --git a/sci-biology/irsabi_brudata/irsabi_brudata-1.4.ebuild b/sci-biology/irsabi_brudata/irsabi_brudata-1.4.1.ebuild similarity index 100% rename from sci-biology/irsabi_brudata/irsabi_brudata-1.4.ebuild rename to sci-biology/irsabi_brudata/irsabi_brudata-1.4.1.ebuild From af200298e928799db81cfb51ec7ff37d660d887c Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Thu, 16 Jan 2020 20:18:50 +0100 Subject: [PATCH 53/54] sci-visualization/fsleyes-widgets: version bump 0.8.4 ahead of Gentoo Science Package-Manager: Portage-2.3.84, Repoman-2.3.20 Signed-off-by: Horea Christian --- sci-visualization/fsleyes-widgets/ChangeLog | 7 ++ sci-visualization/fsleyes-widgets/Manifest | 2 +- .../fsleyes-widgets-0.8.4-coverage.patch | 10 +++ .../files/fsleyes-widgets-0.8.4-tests.patch | 69 +++++++++++++++++++ ....5.ebuild => fsleyes-widgets-0.8.4.ebuild} | 16 +++-- .../{manifest.xml => metadata.xml} | 0 6 files changed, 98 insertions(+), 6 deletions(-) create mode 100644 sci-visualization/fsleyes-widgets/ChangeLog create mode 100644 sci-visualization/fsleyes-widgets/files/fsleyes-widgets-0.8.4-coverage.patch create mode 100644 sci-visualization/fsleyes-widgets/files/fsleyes-widgets-0.8.4-tests.patch rename sci-visualization/fsleyes-widgets/{fsleyes-widgets-0.6.5.ebuild => fsleyes-widgets-0.8.4.ebuild} (69%) rename sci-visualization/fsleyes-widgets/{manifest.xml => metadata.xml} (100%) diff --git a/sci-visualization/fsleyes-widgets/ChangeLog b/sci-visualization/fsleyes-widgets/ChangeLog new file mode 100644 index 0000000..14d9553 --- /dev/null +++ b/sci-visualization/fsleyes-widgets/ChangeLog @@ -0,0 +1,7 @@ +*fsleyes-widgets-0.8.4 (16 Jan 2020) + + 16 Jan 2020; + +files/fsleyes-widgets-0.8.4-coverage.patch, + +files/fsleyes-widgets-0.8.4-tests.patch, +fsleyes-widgets-0.8.4.ebuild, + +metadata.xml, -fsleyes-widgets-0.6.5.ebuild, -manifest.xml: + sci-visualization/fsleyes-widgets: version bump 0.8.4 ahead of Gentoo Science diff --git a/sci-visualization/fsleyes-widgets/Manifest b/sci-visualization/fsleyes-widgets/Manifest index 4244bde..f89c24b 100644 --- a/sci-visualization/fsleyes-widgets/Manifest +++ b/sci-visualization/fsleyes-widgets/Manifest @@ -1 +1 @@ -DIST fsleyes-widgets-0.6.5.tar.gz 1035501 SHA256 498af133b6ee811f3e77657975fb198eee52880ff5b10bd55becc4e59a56dd16 SHA512 686f248276eaead7de26547f27d03c089cef06e3bbadb745527a22fad4c89ca14569bcf267a108ecb6bde64055256f24ca66f2940e1fe896787660ce6b2b672b WHIRLPOOL 768eba8d56e41c53c24c65c63b0ff27a78dc3e6af183bbf5e6ef55d86d4d915a3d0910f3fdc6d032bda434a253713e02bb58dfb135afc6097ff6da7e3db85515 +DIST fsleyes-widgets-0.8.4.tar.gz 1063873 SHA256 c9de830fe097c9f5a38b31c5acadfeffd26b52f00ed68d9c4906a0010875f444 SHA512 b3b3a5f1a963022f82456c2d6978e02e6f0eb459a76d3aa9f924dbb484ad8359fe9344e9d914c859bd213406707b1b3456de8543b1400728b84fb503ae1fddc8 WHIRLPOOL a306e0209888c4b0b85cf3b77b34889fb205a29a838a8fc26f51011e69e5aaff8e802fa95182fbcd3bf5e00dfd376bb6743f613373dd1ae24ec4d8bf6ca50e62 diff --git a/sci-visualization/fsleyes-widgets/files/fsleyes-widgets-0.8.4-coverage.patch b/sci-visualization/fsleyes-widgets/files/fsleyes-widgets-0.8.4-coverage.patch new file mode 100644 index 0000000..6db8c01 --- /dev/null +++ b/sci-visualization/fsleyes-widgets/files/fsleyes-widgets-0.8.4-coverage.patch @@ -0,0 +1,10 @@ +diff --git a/setup.cfg b/setup.cfg +index c3ebd936..d678d2df 100644 +--- a/setup.cfg ++++ b/setup.cfg +@@ -9,4 +9,4 @@ ignore = E127,E201,E203,E221,E222,E241,E271,E272,E301,E302,E303,E701 + + [tool:pytest] + testpaths = tests +-addopts = -v --cov=fsleyes_widgets ++addopts = -v diff --git a/sci-visualization/fsleyes-widgets/files/fsleyes-widgets-0.8.4-tests.patch b/sci-visualization/fsleyes-widgets/files/fsleyes-widgets-0.8.4-tests.patch new file mode 100644 index 0000000..20ef1a9 --- /dev/null +++ b/sci-visualization/fsleyes-widgets/files/fsleyes-widgets-0.8.4-tests.patch @@ -0,0 +1,69 @@ +diff --git a/tests/test_floatslider.py b/tests/test_floatslider.py +index 87a2477..6bbedb7 100644 +--- a/tests/test_floatslider.py ++++ b/tests/test_floatslider.py +@@ -140,8 +140,14 @@ def _test_FloatSlider_changeRange(): + _test_widget_changeRange(slider) + + ++@pytest.mark.skip(reason="Known to fail on Gentoo:" ++ "https://github.com/pauldmccarthy/fsleyes-widgets/issues/1" ++ ) + def test_FloatSlider_mouse_non_gtk(): + run_with_wx(_test_FloatSlider_mouse) ++@pytest.mark.skip(reason="Known to fail on Gentoo:" ++ "https://github.com/pauldmccarthy/fsleyes-widgets/issues/1" ++ ) + def test_FloatSlider_mouse_gtk(): + with mock.patch('fsleyes_widgets.floatslider.wx.Platform', '__WXGTK__'): + run_with_wx(_test_FloatSlider_mouse) +@@ -322,7 +328,9 @@ def _test_SliderSpinPanel_show_edit_limits(): + if shouldEv: assert result[0] == expected + else: assert result[0] is None + +- ++@pytest.mark.skip(reason="Known to fail on Gentoo:" ++ "https://github.com/pauldmccarthy/fsleyes-widgets/issues/1" ++ ) + def test_SliderSpinPanel_events(): + run_with_wx(_test_SliderSpinPanel_events) + def _test_SliderSpinPanel_events(): +diff --git a/tests/test_notebook.py b/tests/test_notebook.py +index a02226c..74e8f63 100644 +--- a/tests/test_notebook.py ++++ b/tests/test_notebook.py +@@ -190,6 +190,9 @@ def _test_enable_disable_show_hide(side, ornt): + assert notebook.GetSelection() == 1 + + ++@pytest.mark.skip(reason="Known to fail on Gentoo:" ++ "https://github.com/pauldmccarthy/fsleyes-widgets/issues/1" ++ ) + def test_event(): + nb_run_with_wx(_test_event) + def _test_event(side, ornt): +diff --git a/tests/test_rangeslider.py b/tests/test_rangeslider.py +index 7ddbed6..51267b3 100644 +--- a/tests/test_rangeslider.py ++++ b/tests/test_rangeslider.py +@@ -103,6 +103,9 @@ def _test_RangePanel_logic_spin(): + _test_RangePanel_logic(panel) + + ++@pytest.mark.skip(reason="Known to fail on Gentoo:" ++ "https://github.com/pauldmccarthy/fsleyes-widgets/issues/1" ++ ) + def test_RangePanel_events_slider(): + run_with_wx(_test_RangePanel_events_slider) + def _test_RangePanel_events_slider(): +@@ -236,6 +239,9 @@ def _test_RangeSliderSpinPanel_logic(): + _test_RangePanel_logic(panel) + + ++@pytest.mark.skip(reason="Known to fail on Gentoo:" ++ "https://github.com/pauldmccarthy/fsleyes-widgets/issues/1" ++ ) + def test_RangeSliderSpinPanel_onchange(): + run_with_wx(_test_RangeSliderSpinPanel_onchange) + def _test_RangeSliderSpinPanel_onchange(): + diff --git a/sci-visualization/fsleyes-widgets/fsleyes-widgets-0.6.5.ebuild b/sci-visualization/fsleyes-widgets/fsleyes-widgets-0.8.4.ebuild similarity index 69% rename from sci-visualization/fsleyes-widgets/fsleyes-widgets-0.6.5.ebuild rename to sci-visualization/fsleyes-widgets/fsleyes-widgets-0.8.4.ebuild index 456f63c..cac0c60 100644 --- a/sci-visualization/fsleyes-widgets/fsleyes-widgets-0.6.5.ebuild +++ b/sci-visualization/fsleyes-widgets/fsleyes-widgets-0.8.4.ebuild @@ -1,15 +1,15 @@ -# Copyright 1999-2018 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 -PYTHON_COMPAT=( python2_7 python3_{5,6} ) +PYTHON_COMPAT=( python3_{6,7} ) inherit distutils-r1 virtualx MY_P="widgets-${PV}" -DESCRIPTION="The new FSL image viewer, released with FSL 5.0.10" +DESCRIPTION="The new FSL image viewer, first released with FSL 5.0.10" HOMEPAGE="https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/tree/master" SRC_URI="https://git.fmrib.ox.ac.uk/fsl/fsleyes/widgets/-/archive/${PV}/${MY_P}.tar.gz -> ${P}.tar.gz" @@ -19,7 +19,9 @@ KEYWORDS="~amd64 ~x86" IUSE="test" DEPEND=" - test? ( dev-python/pytest[${PYTHON_USEDEP}] ) + test? ( + dev-python/pytest[${PYTHON_USEDEP}] + ) dev-python/setuptools[${PYTHON_USEDEP}] " RDEPEND=" @@ -32,7 +34,11 @@ RDEPEND=" S="${WORKDIR}/${MY_P}" +PATCHES=( + "${FILESDIR}/fsleyes-widgets-0.8.4-coverage.patch" + "${FILESDIR}/fsleyes-widgets-0.8.4-tests.patch" +) + python_test() { virtx pytest --verbose || die } - diff --git a/sci-visualization/fsleyes-widgets/manifest.xml b/sci-visualization/fsleyes-widgets/metadata.xml similarity index 100% rename from sci-visualization/fsleyes-widgets/manifest.xml rename to sci-visualization/fsleyes-widgets/metadata.xml From 2dd43a1dc2597f76af71f8072f1eea6d7880afa5 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Mon, 20 Jan 2020 21:12:31 +0100 Subject: [PATCH 54/54] sci-libs/scikits_video: new package Package-Manager: Portage-2.3.84, Repoman-2.3.20 Signed-off-by: Horea Christian --- sci-libs/scikits_video/ChangeLog | 5 +++ sci-libs/scikits_video/Manifest | 1 + sci-libs/scikits_video/metadata.xml | 22 +++++++++++ .../scikits_video-1.1.11_p20200114.ebuild | 39 +++++++++++++++++++ 4 files changed, 67 insertions(+) create mode 100644 sci-libs/scikits_video/ChangeLog create mode 100644 sci-libs/scikits_video/Manifest create mode 100644 sci-libs/scikits_video/metadata.xml create mode 100644 sci-libs/scikits_video/scikits_video-1.1.11_p20200114.ebuild diff --git a/sci-libs/scikits_video/ChangeLog b/sci-libs/scikits_video/ChangeLog new file mode 100644 index 0000000..596bd05 --- /dev/null +++ b/sci-libs/scikits_video/ChangeLog @@ -0,0 +1,5 @@ +*scikits_video-1.1.11_p20200114 (20 Jan 2020) + + 20 Jan 2020; +metadata.xml, + +scikits_video-1.1.11_p20200114.ebuild: + sci-libs/scikits_video: new package diff --git a/sci-libs/scikits_video/Manifest b/sci-libs/scikits_video/Manifest new file mode 100644 index 0000000..c1c0266 --- /dev/null +++ b/sci-libs/scikits_video/Manifest @@ -0,0 +1 @@ +DIST scikits_video-1.1.11_p20200114.tar.gz 32059826 SHA256 1a81440c8be749defdd8a2d07a1a11e0a62839a986bfd9dd5976aeb3d60ca71d SHA512 4e0b337c54ffc2394be30de84113c4ec3f8f0217c5059712a40668b03ba7516a721f99786a6f7bea58a9eeb25324702f5ff90ecbb8976b059ce71331d526b0c8 WHIRLPOOL 5d802e459eab4462c65c6509439cfc591ea9568425b46cac4d2070cf8adc5152fecaa43324680c85ea4aee38105e6ab50d07250d47b7e637f0325c52edeccf58 diff --git a/sci-libs/scikits_video/metadata.xml b/sci-libs/scikits_video/metadata.xml new file mode 100644 index 0000000..8e05ce3 --- /dev/null +++ b/sci-libs/scikits_video/metadata.xml @@ -0,0 +1,22 @@ + + + + + sci@gentoo.org + Gentoo Science Project + + + This SciKit (toolkit for SciPy) includes useful image processing + algorithms for use with Python and NumPy. While SciPy’s ndimage + provides low-level manipulation, scikits.image centres around + algorithms and applications. + + + Enable support for image i/o via + media-libs/freeimage + Enable support for algebraic solvers via dev-python/pyamg + + + scikit-image + + diff --git a/sci-libs/scikits_video/scikits_video-1.1.11_p20200114.ebuild b/sci-libs/scikits_video/scikits_video-1.1.11_p20200114.ebuild new file mode 100644 index 0000000..a2651da --- /dev/null +++ b/sci-libs/scikits_video/scikits_video-1.1.11_p20200114.ebuild @@ -0,0 +1,39 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +PYTHON_COMPAT=( python3_{6,7} ) + +inherit distutils-r1 eutils virtualx + +MY_PN="scikit-video" +MY_HASH="66919e0828410938a4d52f37987b07f7f5de96af" + +DESCRIPTION="Video processing in Python" +HOMEPAGE="https://scikit-image.org/" +SRC_URI="https://github.com/scikit-video/scikit-video/archive/${MY_HASH}.tar.gz -> ${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc freeimage pyamg test" +RESTRICT="!test? ( test )" + +RDEPEND=" + || ( media-video/ffmpeg media-video/libav ) + dev-python/numpy[${PYTHON_USEDEP}] + sci-libs/scipy[${PYTHON_USEDEP}] + dev-python/pillow[${PYTHON_USEDEP}] + sci-libs/scikits_learn[${PYTHON_USEDEP}] + media-video/mediainfo +" +DEPEND="${RDEPEND} + test? ( dev-python/pytest[${PYTHON_USEDEP}] ) +" + +S="${WORKDIR}/${MY_PN}-${MY_HASH}" + +python_test() { + nosetests -v || die +}