gentoo resync : 17.02.2020

9 files changed, 212 insertions, 323 deletions

diff --git a/sci-geosciences/gmt/Manifest b/sci-geosciences/gmt/Manifest
index 30abe842436f..33e01f8b4906 100644
--- a/sci-geosciences/gmt/Manifest
+++ b/sci-geosciences/gmt/Manifest
@@ -1,7 +1,5 @@
 AUX gmt-4.5.0-no-strip.patch 1963 BLAKE2B b261058d5e6eefa2b6b4286158d971991f351c0a66da36b45a53b9f4c6298cb3d378cd79155c8791aea848ddb455cf2c539358cab02df821b0e8c962c508d2a4 SHA512 8ef2ca6acf17b092989ce7b8c91a3f42b82b074d606d2635c7b5a03355fcd3f83b3d08ef83747e51f5eb6e6ed9cb9a683208797d49da7b8f0714ed0c8f2e6155
 AUX gmt-4.5.6-respect-ldflags.patch 2396 BLAKE2B 66d15afd6a6cbc7f4fbd16d34bfc8b3e02df56c1c3a72b55732bf2694b9699cb6059522d3648f8651af331a92a87d158ecdb43ff758cf3208d04531b0dd0e89d SHA512 c2cc4986a1211a75856391cd0c731f37d9cf8e2ad28fdf29f532ed03308f2ef7f309a0bc525bb08c976c4535e8cbe77789546eb8585ddcedf016af32769e5420
-AUX gmt-4.5.8-bfr-overflow.patch 1576 BLAKE2B 01ec91d3bf94dbc1497f4f233bc1df86ce7dc9f0de9c7bf8e4fd433699db154c6b74854129c67cc89f8bb9a850417bcdaf55dbfce6a404d10290c43dc80c76f1 SHA512 fd2c137047333ef4494bba28339c1f8a34e83acc2646db514e0d2289e60acca5f6ac360d1dab27d84a088ce4a1c8c3af5f5cd4ae57485bb14eb08a668ea8ecc9
-AUX gmt-4.5.8-impl-dec.patch 291 BLAKE2B c6d393a8985a66dd5398fc30fd268ee4291298181eefb01c04a0e29a7e3807f4add43dd0889828cbe2cfa3010806e28d72eeef8447607dc26142305108dc2ee2 SHA512 ed977bd1a19024a60682d6e422c202cb3c29ed5da1450d85558544d6aa300ac967595811c90143a4858213a6b60b8fffee453de8351666c55676371e00b144ad
 AUX gmt-4.5.9-no-strip.patch 1246 BLAKE2B f834f1b514a2ce59a56f52290b54ef80ec1580d88facfb77f2af6aa4472609638d627ff5a10a2b692a8b3357adb12cfde0f9587f0529e5c257c9c56037be946d SHA512 271be4c32607bd4776cace933ed0a81a76fb5ea8ccc0c92f0f11cdf17f6b4f8740e2345323236af94dd4eb52323625cc82e5c661e22a008dcdc85f4d1d452b23
 AUX gmt-4.5.9-unistd.h.patch 358 BLAKE2B 48a577c87e521fe89ff815a88e0f40a6031ce4dfb388116081125f2847115786f8ae20f6797aa477edb36a602907b20fe9ca1725f89aae0b9b9e9ea00bd0a449 SHA512 877e73b161d9fbb1fe17d5f575852be67cfd9eec31ff8b74ffeb7b00569e3061d5a85c55e6633c06f12147bf7e3ab2838ab2738c5fe4adf93065ce55e7884df6
 DIST gmt-4.5.18-non-gpl-src.tar.bz2 103378 BLAKE2B 3a52b547940f3e79a6dd8076b8279310e90b3f7a01a5b9e68186fc3d1711af4f5730fa20a8a04bdc57a8e06f9a656c8db71c5bc2b8d42292cb7434ad07880732 SHA512 57281e78cd40b168cfd49818a25523c1d1b44a8c4cab59aa5683052f14df25016b70485f79327bac37f5dd8b7c77d01a2264fe08045b7c13c3e1bd216323e50e
@@ -11,17 +9,11 @@ DIST gmt-4.5.6-share.tar.bz2 43704 BLAKE2B 56c4c2e29a97824245c8b8cc9afbf5e865886
 DIST gmt-4.5.6-src.tar.bz2 1134118 BLAKE2B 6519002bfcafd91c420d56fb356d70cb6a814a62c8b7d9d30d77015f8401ea71ffb87b9ea4ea5b2af7917b0bce3794d66566150ce2ae82c7a5d9bb52bf5414ef SHA512 0cb06f6be7cf6a3f586f7d9b4579d5520fb15f6ef14eec216c60aa4b3fa9a3ca3308bf4683c8cc0bcf71f3c02ba74a0f9bf296fec4c1980d10adc4ba4a12024e
 DIST gmt-4.5.6-suppl.tar.bz2 4137369 BLAKE2B 9150e54385c4ee3df6dee6f8598cb2e91b4b23a3e4531fad7fee7e4eef80cbe6f06efd4a5a06882aff90782a5f07824cb6ed744da5c10e73402bdb1930984b9d SHA512 7e1cd35da0a7f75800074cac4dd7f82ce17721953251c951c4f585f0cf159af6c2450fba20d9c02fad69ec7a689483de55cc652fcc600535255cf17ab528a027
 DIST gmt-4.5.6-triangle.tar.bz2 103426 BLAKE2B cb6372a0980a660a7e70725d43681c0a251698ff89329f92c37965c70d180cfb63ee2741702c8f9cbfef0f41c95cf6676dabcef3aefb18801367efc32e833f44 SHA512 3daabba610a50e72c2e9e5dd7fb22ff02547c598ff22f40f145f3f794447cde995ddbdcd2560954478806fc5edc2af4fb59615e405622daa4292e6dc2f0e4f5e
-DIST gmt-4.5.8-non-gpl.tar.bz2 109125 BLAKE2B 7b6eef77a7c15f6d5acfc9ca4cc4d2a8db8ef00362b2f1fc7c50edd76ffb14810da0eb1837a31f8a4b31391308f45f4c7289303d3bc4885f5c152d62b49151b5 SHA512 04b3eefd1490b194d7797af86fc726dd84960d65dd955e5ddefaf6ea4ec5a98f6f00085acc0cc846aa70e986facf65221256dd6a625f918c6abe6ba0b6b06f64
-DIST gmt-4.5.8.tar.bz2 39350328 BLAKE2B 8d1e0c588ef4ecef1d64a4071101d9a0c14ba9780a213ce1b121840c0acd676f43931f4a4f03a539b40bfba57935f8a9e9bae3cb3630410f15cccb3bd57eb87b SHA512 5bc3be1f7963df6a3035195e2123645d8a8b7a8a9aa17c89a6dd50560485706c628e0e0aca779930c4a28f2305fcc184981db728085d3373b2cad89e59d5c6fd
-DIST gmt-4.5.9-non-gpl.tar.bz2 103494 BLAKE2B a056845917a7eb2c6e66a8797a2d47a2fe4c9a659b98242ff6953f9194d86d56a85c3e1e973f562d060a3d3396845847de683e06b6b929effb84ca0c625afe8e SHA512 a41cd94acbd014bed780797be1ac1b492388c7c8e0fcfc5e773e894e803a024bdc60b897589ad4db9af973f20606a87ac9cff606f0391641236bca95c0b7a4c5
-DIST gmt-4.5.9.tar.bz2 39325492 BLAKE2B 012afa7555d7262a4b8ae9af90309653f6f374fdb34bffbc1f0052e2cbee93b17d1f6e70934e3de555f83774a34c278bc81f5a6cc7521840a35bc70001d9ee6f SHA512 1edda71787fa2e1434a6891618d4523c39d04c2db285dadc66c1d52b425cfff6866c492926cae41d78d2a4e5118e8d003ef3d71d164e0c0695d71aaddb598242
-DIST gshhg-gmt-2.3.7.tar.gz 57052180 BLAKE2B 5b618c874cca97da819263c3c436db1235d3293712a72c21ac4ca3ae78e95b5d36915312de3df361f978b14c697884ca278bebc41ac4c1d054adda6c417eb5b9 SHA512 27e97efe9d146a58d1c6674c5b6cde6b7545be60c1f7d3d93faca1034986d1648e73b589de571897fc53cd0d050a5875dcc9923e3f861f8473ca568a8142d727
+DIST gmt-5.4.4-src.tar.xz 105073748 BLAKE2B bd083eeb1a71c5a2e554edadb7d8b9160f9b6d8e7510358b55d31b5f147d6719dbe8ce75510ffd844e74b787b7a6a6498fe5dfdd40755c7e6a28c018c024139b SHA512 cd22f65e7efc1704b06a5e94523af6a3b949dfe9339875abf805f1d00db6533d963ea61afc69d443e21b8070608e2043d712ffad74d1228c758f549f1ac46c22
 DIST gshhs-2.1.1-coast.tar.bz2 4322743 BLAKE2B e171b6a41ceee6c15a9a7679c6a9145c1ffcede7be61bc26b351371a7bde7f4ddd68bbd5104638da56a66af3e930fc11d9dc6c215d3c3b528f0d56b855e3b496 SHA512 6009139cc4760925817e789e0c9980ec6bde1310f521e6f43e5643b9eba1e859bb9a23bdc4bb661e66d32f4886ad3ad93f5af76ca93ac847307f9acd37eeb332
 DIST gshhs-2.1.1-full.tar.bz2 29916230 BLAKE2B 80ae867a46fc5f9cab60c3e4cedb0db7d683cb58294865a228b8853b458647179382d8fc7fefcbfff7f33ee0e12b527e402376b78f1be0ff8388a81ba682d52d SHA512 f4759d21514a63b1cf3a65c75aeab951740091235e3f19d832ad2c09416d2ab8d516a8f5bf0f6068c81f6c18f76734c4bf3772c37406c1df5abd4ae445f3d375
 DIST gshhs-2.1.1-high.tar.bz2 9712697 BLAKE2B fa81ee855916566e135eb0522b414da9cf28f1cc29847fbccf80a485f337e6b8a1e051df95d38454679e0405cfa6777cc7f0139772425c082d46b6bd65c17c98 SHA512 a9c22d7ce285320d4ae22a1a446e7d7d446d1b0641abeb39d50e358d65011fd3e39761a61a41820a373df4d4ef950160f5aab71d2df899a8425caf7d162e6e0e
-DIST gshhs-2.2.0.tar.bz2 47021761 BLAKE2B 89ffbca48d782a64ec1ecf7945915a64ab70385c1db3fef65bf1d41db46f3c047554d51c13de20706fe84d1568593679fb822b23d8ab580c100159475edd9cf1 SHA512 a9c1550f24feeefbc7ae633cce41e737f8153bb7df974e942fb5b9f0c931a49707c737f34bf6316ac89aa9bf487a091ada08ca8d798e2a5385e75f3dc05fdf83
-EBUILD gmt-4.5.18.ebuild 1880 BLAKE2B 64ea1e4b79139bfbbd24e500edea6dd6d38edf211863b7cd70aa44527a4dff4349ce163c8a4666a6cedc54b146909c46c47079336c4fe97dcce9dc4db4f93eb8 SHA512 c6504708e8549b010bb0190458b12d42e5bbc796c8498caf1f22d1568ee88579f4e8d64a0442c8e8e01f76f1c680f2b2cb612445976917e8b29a42edaf264019
+EBUILD gmt-4.5.18-r1.ebuild 1969 BLAKE2B add5f0c069904260201ba9fd77efef09b42f27c81843401410931284516a39dc7356c516e8086d5e44d31fbfdc7aad815d41deaf911886138afaa2da9c452f6e SHA512 d6cb51bf827a5fa4f4655928fdf4f4c43120542ed134f789fb0e01b62666dbbeea750aaed1c0ba84382e7e1c043ddaeda9d546f5e7e68a89191ed61fc745264c
 EBUILD gmt-4.5.6.ebuild 2311 BLAKE2B 019492348e921aec08fd1d25d84b653c43e4c69837c1114cecc739137ad1ecfa1f157a3e5937816caa32da6a2c4656c159f010c91e850e35b9660aaed0673f07 SHA512 c3ce34dbd2e000416eae85e98b582e4729de4ee4b1e09107e8930c9802970207b35a56c76e918bf89bbff4f582f8310b6dc8bc3d89a346b25cd4ac20e021cf8c
-EBUILD gmt-4.5.8.ebuild 1972 BLAKE2B 9cbeaecc962ef48d36c1f356f62d72ff95a1c3a44f79daa46e934b0296625bd85c7a0cdfe12fbb3f13a2b789f886a717a53c4d10ec9dd56985a6aceaba7122e7 SHA512 c8f810de340e6205c5b97a6e9c2accccda2f589941c435b2f09670761960858c43ab6fb42b20fdf62895052c96f6e59969036c71df3ee2f551e51f7dd110bee1
-EBUILD gmt-4.5.9.ebuild 1954 BLAKE2B 52acf9053715f5582e7fcf89e855551574e4841de2320db4b7000aea8cedd83d42089cfd0b52adbab51e686681520709299e44bc68906cc8258e6352113acd1d SHA512 31974c6a7e26f02cf457aa4b178e32a5c556b1fce8226162b7178211e73569a2eb9df0f0e14d45c878a7c561a26e04a8e8d7e917aab9f7379c9dfba7dc1ab996
-MISC metadata.xml 810 BLAKE2B 1f18691a86313c7132834b43a5c03091d2d3e7df9369defa7ded979f6b900374762c3bef7bc79046a9a68a940b155135adc3a2b9a935f2df19a0f1eaf3f0446a SHA512 647d1a082313d0894a6203cde5afbe729d084e3ed923a9f22850022acb632b0af1fe2dd14aaba6801b5656d1277be39559fa5f76a03e621a88eb6634fa2ec645
+EBUILD gmt-5.4.4.ebuild 2942 BLAKE2B b36f87c108b351561f768d0ba927c3e9966f7c4f19002f0ccbc84ba822d037211e8ed543ecbd723582975720b957ecc51e91c82c0f74b11cbb789a9e10db0acc SHA512 eae39ad69124ce00d7400b24555e249fc5397e1bf3c4f849c4bd7e92c9e9f2cf9499fdbcf1507e202410653c713cafbff76240d1fba41f4d77da61d1ed77ad79
+MISC metadata.xml 1058 BLAKE2B 2ec919d568907a8abd029b0a5f05a1ab39b0b50bfa288a29029294052f0005bb224f086274e5230970549727995bbf10c8e98c7e5855e694201b736578eef7f0 SHA512 bfdbbd4ec022edb67091957d8215d88ab25b5cf545b3912eec118aae0fd3783f4a352b3195c5a7dc916827593702d677fae9e1a2a80dd8d678f4c5556442d55e
diff --git a/sci-geosciences/gmt/files/gmt-4.5.8-bfr-overflow.patch b/sci-geosciences/gmt/files/gmt-4.5.8-bfr-overflow.patch
deleted file mode 100644
index 216149d93f78..000000000000
--- a/sci-geosciences/gmt/files/gmt-4.5.8-bfr-overflow.patch
+++ /dev/null
@@ -1,27 +0,0 @@
-diff --git a/src/mgd77/mgd77.c b/src/mgd77/mgd77.c
-index b27b1d9..6a25576 100644
---- a/src/mgd77/mgd77.c
-+++ b/src/mgd77/mgd77.c
-@@ -854,7 +854,7 @@ int MGD77_Decode_Header_m77t (struct MGD77_HEADER_PARAMS *P, char *record)
- 			case  3:	strcpy (P->Parameters_Surveyed_Code, word);			break;
- 			case  4:	strncpy (P->File_Creation_Year, word, 4);
- 					strncpy (P->File_Creation_Month, &word[4], 2);
--					strncpy (P->File_Creation_Day, &word[6], 4);			break;
-+					strncpy (P->File_Creation_Day, &word[6], 2);			break;
- 			case  5:	strcpy (P->Source_Institution, word);				break;
- 			case  6:	strcpy (P->Country, word);					break;
- 			case  7:	strcpy (P->Platform_Name, word);				break;
-@@ -865,11 +865,11 @@ int MGD77_Decode_Header_m77t (struct MGD77_HEADER_PARAMS *P, char *record)
- 			case 12:	strcpy (P->Funding, word);					break;
- 			case 13:	strncpy (P->Survey_Departure_Year, word, 4);
- 					strncpy (P->Survey_Departure_Month, &word[4], 2);
--					strncpy (P->Survey_Departure_Day, &word[6], 4);			break;
-+					strncpy (P->Survey_Departure_Day, &word[6], 2);			break;
- 			case 14:	strcpy (P->Port_of_Departure, word);				break;
- 			case 15:	strncpy (P->Survey_Arrival_Year, word, 4);
- 					strncpy (P->Survey_Arrival_Month, &word[4], 2);
--					strncpy (P->Survey_Arrival_Day, &word[6], 4);			break;
-+					strncpy (P->Survey_Arrival_Day, &word[6], 2);			break;
- 			case 16:	strcpy (P->Port_of_Arrival, word);				break;
- 			case 17:	strcpy (P->Navigation_Instrumentation, word);			break;
- 			case 18:	strcpy (P->Geodetic_Datum_Position_Determination_Method, word);	break;
diff --git a/sci-geosciences/gmt/files/gmt-4.5.8-impl-dec.patch b/sci-geosciences/gmt/files/gmt-4.5.8-impl-dec.patch
deleted file mode 100644
index 5c63bb209578..000000000000
--- a/sci-geosciences/gmt/files/gmt-4.5.8-impl-dec.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-diff --git a/src/gmt.h b/src/gmt.h
-index d4c9c20..ea6ddc5 100644
---- a/src/gmt.h
-+++ b/src/gmt.h
-@@ -34,9 +34,11 @@ extern "C" {
- 
- /*  GMT is POSIX.1 COMPLIANT  */
- 
-+/*
- #ifndef _POSIX_SOURCE
- #define _POSIX_SOURCE 1
- #endif
-+*/
- 
- /* Declaration modifiers for DLL support (MSC et al) */
- 
\ No newline at end of file
diff --git a/sci-geosciences/gmt/gmt-4.5.18-r1.ebuild b/sci-geosciences/gmt/gmt-4.5.18-r1.ebuild
new file mode 100644
index 000000000000..ac668505bc6b
--- /dev/null
+++ b/sci-geosciences/gmt/gmt-4.5.18-r1.ebuild
@@ -0,0 +1,93 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit autotools
+
+DESCRIPTION="Powerful map generator"
+HOMEPAGE="https://gmt.soest.hawaii.edu/"
+SRC_URI="mirror://gmt/${P}-src.tar.bz2
+	gmttria? ( mirror://gmt/${P}-non-gpl-src.tar.bz2 )"
+
+LICENSE="GPL-2+ gmttria? ( Artistic )"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc examples debug +gdal gmttria +gshhg htmldoc +metric mex +netcdf octave postscript tutorial"
+
+# mex can use matlab too which i can't test
+REQUIRED_USE="mex? ( octave )"
+
+DEPEND="
+	gdal? ( sci-libs/gdal:= )
+	gshhg? ( sci-geosciences/gshhg-gmt )
+	netcdf? ( sci-libs/netcdf:= )
+	octave? ( sci-mathematics/octave:= )
+"
+RDEPEND="${DEPEND}
+	!sci-biology/probcons
+"
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-4.5.9-no-strip.patch
+	"${FILESDIR}"/${PN}-4.5.6-respect-ldflags.patch
+)
+
+src_prepare() {
+	default
+	eautoreconf
+}
+
+src_configure() {
+	local myconf=(
+		--datadir=/usr/share/${P}
+		--includedir=/usr/include/${P}
+		--disable-update
+		--disable-matlab
+		--disable-xgrid
+		--disable-debug
+		$(use_enable gdal)
+		$(use_enable netcdf)
+		$(use_enable octave)
+		$(use_enable debug devdebug)
+		$(use_enable !metric US)
+		$(use_enable postscript eps)
+		$(use_enable mex)
+		$(use_enable gmttria triangle)
+		$(use_with gshhg gshhg-dir /usr/share/gshhg)
+	)
+	econf "${myconf[@]}"
+}
+
+src_compile() {
+	emake -j1
+}
+
+src_install() {
+	emake DESTDIR="${D}" -j1 install-all
+	einstalldocs
+
+	# Remove various documentation
+	if ! use doc; then
+		rm -rf "${ED}/usr/share/doc/${PF}/pdf" || die
+	fi
+
+	if use examples; then
+		docompress -x /usr/share/doc/${PF}/examples
+	else
+		rm -r "${ED}/usr/share/doc/${PF}/examples" || die
+	fi
+
+	if ! use htmldoc; then
+		rm -r "${ED}/usr/share/doc/${PF}/html" || die
+	fi
+
+	if use tutorial; then
+		docompress -x /usr/share/doc/${PF}/tutorial
+	else
+		rm -r "${ED}/usr/share/doc/${PF}/tutorial" || die
+	fi
+
+	# remove static libs
+	find "${ED}/usr/$(get_libdir)" -name '*.a' -delete || die
+}
diff --git a/sci-geosciences/gmt/gmt-4.5.18.ebuild b/sci-geosciences/gmt/gmt-4.5.18.ebuild
deleted file mode 100644
index 9730b119d3cb..000000000000
--- a/sci-geosciences/gmt/gmt-4.5.18.ebuild
+++ /dev/null
@@ -1,85 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit autotools
-
-GSHHG="gshhg-gmt-2.3.7"
-
-DESCRIPTION="Powerful map generator"
-HOMEPAGE="https://gmt.soest.hawaii.edu/"
-SRC_URI="
-	mirror://gmt/${P}-src.tar.bz2
-	mirror://gmt/${GSHHG}.tar.gz
-	gmttria? ( mirror://gmt/${P}-non-gpl-src.tar.bz2 )"
-
-LICENSE="GPL-2 gmttria? ( Artistic )"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="debug +gdal gmttria +metric mex +netcdf octave postscript"
-
-RDEPEND="
-	!sci-biology/probcons
-	gdal? ( sci-libs/gdal )
-	netcdf? ( >=sci-libs/netcdf-4.1 )
-	octave? ( sci-mathematics/octave )"
-DEPEND="${RDEPEND}"
-
-# mex can use matlab too which i can't test
-REQUIRED_USE="
-	mex? ( octave )
-"
-
-# hand written make files that are not parallel safe
-MAKEOPTS+=" -j1"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-4.5.9-no-strip.patch
-	"${FILESDIR}"/${PN}-4.5.6-respect-ldflags.patch
-	)
-
-AUTOTOOLS_IN_SOURCE_BUILD=1
-
-src_prepare() {
-	default
-
-	mkdir "${S}/share/coast" || die
-	mv -f "${WORKDIR}/${GSHHG}/"*.nc "${S}/share/coast/" || die
-}
-
-src_configure() {
-	econf \
-		--libdir=/usr/$(get_libdir)/${P} \
-		--includedir=/usr/include/${P} \
-		--datadir=/usr/share/${P} \
-		--docdir=/usr/share/doc/${PF} \
-		--disable-update \
-		--disable-matlab \
-		--disable-xgrid \
-		--disable-debug \
-		$(use_enable gdal) \
-		$(use_enable netcdf) \
-		$(use_enable octave) \
-		$(use_enable debug devdebug) \
-		$(use_enable !metric US) \
-		$(use_enable postscript eps) \
-		$(use_enable mex) \
-		$(use_enable gmttria triangle)
-}
-
-src_install() {
-	emake DESTDIR="${D}" install-all
-	einstalldocs
-
-	docompress -x /usr/share/doc/${PF}/{examples,tutorial}
-
-	# remove static libs
-	find "${ED}/usr/$(get_libdir)" -name '*.a' -exec rm -f {} + || die
-
-	cat <<- _EOF_ > "${T}/99gmt"
-	GMTHOME="${EPREFIX}/usr/share/${P}"
-	GMT_SHAREDIR="${EPREFIX}/usr/share/${P}"
-	_EOF_
-	doenvd "${T}/99gmt"
-}
diff --git a/sci-geosciences/gmt/gmt-4.5.8.ebuild b/sci-geosciences/gmt/gmt-4.5.8.ebuild
deleted file mode 100644
index 69ac9baca347..000000000000
--- a/sci-geosciences/gmt/gmt-4.5.8.ebuild
+++ /dev/null
@@ -1,91 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=yes
-
-inherit autotools-utils multilib
-
-GSHHS="gshhs-2.2.0"
-
-DESCRIPTION="Powerful map generator"
-HOMEPAGE="http://gmt.soest.hawaii.edu/"
-SRC_URI="
-	mirror://gmt/legacy/${P}.tar.bz2
-	mirror://gmt/legacy/${GSHHS}.tar.bz2
-	gmttria? ( mirror://gmt/legacy/${P}-non-gpl.tar.bz2 )"
-
-LICENSE="GPL-2 gmttria? ( Artistic )"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="debug +gdal gmttria +metric mex +netcdf octave postscript"
-
-RDEPEND="
-	!sci-biology/probcons
-	gdal? ( sci-libs/gdal )
-	netcdf? ( >=sci-libs/netcdf-4.1 )
-	octave? ( sci-mathematics/octave )"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/GMT${PV}"
-
-# mex can use matlab too which i can't test
-REQUIRED_USE="
-	mex? ( octave )
-"
-
-# hand written make files that are not parallel safe
-MAKEOPTS+=" -j1"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-4.5.0-no-strip.patch
-	"${FILESDIR}"/${PN}-4.5.6-respect-ldflags.patch
-	"${FILESDIR}"/${P}-bfr-overflow.patch
-	"${FILESDIR}"/${P}-impl-dec.patch
-	)
-
-AUTOTOOLS_IN_SOURCE_BUILD=1
-
-src_prepare() {
-	mv -f "${WORKDIR}/share/"* "${S}/share/" || die
-
-	tc-export AR RANLIB
-
-	autotools-utils_src_prepare
-}
-
-src_configure() {
-	local myeconfargs=(
-		--libdir=/usr/$(get_libdir)/${P}
-		--includedir=/usr/include/${P}
-		--datadir=/usr/share/${P}
-		--docdir=/usr/share/doc/${PF}
-		--disable-update
-		--disable-matlab
-		--disable-xgrid
-		--disable-debug
-		$(use_enable gdal)
-		$(use_enable netcdf)
-		$(use_enable octave)
-		$(use_enable debug devdebug)
-		$(use_enable !metric US)
-		$(use_enable postscript eps)
-		$(use_enable mex)
-		$(use_enable gmttria triangle)
-		)
-	autotools-utils_src_configure
-}
-
-src_install() {
-	autotools-utils_src_install install-all
-
-	# remove static libs
-	find "${ED}/usr/$(get_libdir)" -name '*.a' -exec rm -f {} +
-
-	cat <<- _EOF_ > "${T}/99gmt"
-	GMTHOME="${EPREFIX}/usr/share/${P}"
-	GMT_SHAREDIR="${EPREFIX}/usr/share/${P}"
-	_EOF_
-	doenvd "${T}/99gmt"
-}
diff --git a/sci-geosciences/gmt/gmt-4.5.9.ebuild b/sci-geosciences/gmt/gmt-4.5.9.ebuild
deleted file mode 100644
index 7aefd90eb08c..000000000000
--- a/sci-geosciences/gmt/gmt-4.5.9.ebuild
+++ /dev/null
@@ -1,92 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=yes
-
-inherit autotools-utils multilib
-
-GSHHS="gshhs-2.2.0"
-
-DESCRIPTION="Powerful map generator"
-HOMEPAGE="http://gmt.soest.hawaii.edu/"
-SRC_URI="
-	mirror://gmt/legacy/${P}.tar.bz2
-	mirror://gmt/legacy/${GSHHS}.tar.bz2
-	gmttria? ( mirror://gmt/legacy/${P}-non-gpl.tar.bz2 )"
-
-LICENSE="GPL-2 gmttria? ( Artistic )"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="debug +gdal gmttria +metric mex +netcdf octave postscript"
-
-RDEPEND="
-	!sci-biology/probcons
-	gdal? ( sci-libs/gdal )
-	netcdf? ( >=sci-libs/netcdf-4.1 )
-	octave? ( sci-mathematics/octave )"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/GMT${PV}"
-
-# mex can use matlab too which i can't test
-REQUIRED_USE="
-	mex? ( octave )
-"
-
-# hand written make files that are not parallel safe
-MAKEOPTS+=" -j1"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-4.5.9-no-strip.patch
-	"${FILESDIR}"/${PN}-4.5.6-respect-ldflags.patch
-	"${FILESDIR}"/${PN}-4.5.9-unistd.h.patch
-	)
-
-AUTOTOOLS_IN_SOURCE_BUILD=1
-
-src_prepare() {
-	mv -f "${WORKDIR}/share/"* "${S}/share/" || die
-
-	tc-export AR RANLIB
-
-	autotools-utils_src_prepare
-
-	eautoreconf
-}
-
-src_configure() {
-	local myeconfargs=(
-		--libdir=/usr/$(get_libdir)/${P}
-		--includedir=/usr/include/${P}
-		--datadir=/usr/share/${P}
-		--docdir=/usr/share/doc/${PF}
-		--disable-update
-		--disable-matlab
-		--disable-xgrid
-		--disable-debug
-		$(use_enable gdal)
-		$(use_enable netcdf)
-		$(use_enable octave)
-		$(use_enable debug devdebug)
-		$(use_enable !metric US)
-		$(use_enable postscript eps)
-		$(use_enable mex)
-		$(use_enable gmttria triangle)
-		)
-	autotools-utils_src_configure
-}
-
-src_install() {
-	autotools-utils_src_install install-all
-
-	# remove static libs
-	find "${ED}/usr/$(get_libdir)" -name '*.a' -exec rm -f {} +
-
-	cat <<- _EOF_ > "${T}/99gmt"
-	GMTHOME="${EPREFIX}/usr/share/${P}"
-	GMT_SHAREDIR="${EPREFIX}/usr/share/${P}"
-	_EOF_
-	doenvd "${T}/99gmt"
-}
diff --git a/sci-geosciences/gmt/gmt-5.4.4.ebuild b/sci-geosciences/gmt/gmt-5.4.4.ebuild
new file mode 100644
index 000000000000..c2e3c983f507
--- /dev/null
+++ b/sci-geosciences/gmt/gmt-5.4.4.ebuild
@@ -0,0 +1,111 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit bash-completion-r1 cmake
+
+DESCRIPTION="Powerful map generator"
+HOMEPAGE="https://gmt.soest.hawaii.edu/"
+SRC_URI="mirror://gmt/${P}-src.tar.xz"
+
+LICENSE="GPL-3+ gmttria? ( Artistic )"
+SLOT="5"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc examples +fftw +gdal gmttria htmldoc lapack openmp pcre pcre2 threads tutorial"
+
+REQUIRED_USE="?? ( pcre pcre2 )"
+
+DEPEND="
+	app-text/ghostscript-gpl
+	net-misc/curl
+	>=sci-libs/netcdf-4.1:=[hdf5]
+	sys-libs/zlib
+	fftw? ( sci-libs/fftw:3.0= )
+	gdal? ( sci-libs/gdal:= )
+	lapack? ( virtual/lapack )
+	pcre? ( dev-libs/libpcre )
+	pcre2? ( dev-libs/libpcre2 )
+"
+RDEPEND="${DEPEND}
+	!sci-biology/probcons
+	sci-geosciences/dcw-gmt
+	sci-geosciences/gshhg-gmt
+"
+
+src_prepare() {
+	cmake_src_prepare
+	# Rename man pages to avoid a name conflict with gmt4
+	pushd man_release || die
+	local m c suffix newc
+		for m in *.gz; do
+			c=${m%%.*}
+			suffix=${m#*.}
+			newc=gmt_${c}
+			# This man pages does'nt conflict
+			case ${c} in
+				gmt|gmt.conf|postscriptlight)
+					continue ;;
+				gmt_shell_functions)
+					newc=gmt5_shell_functions ;;
+				gmtcolors)
+					newc=gmt5colors ;;
+			esac
+			mv "${c}.${suffix}" "${newc}.${suffix}" || die
+		done
+	popd || die
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DGMT_DATADIR="share/${P}"
+		-DGMT_DOCDIR="share/doc/${PF}"
+		-DGMT_MANDIR="share/man"
+		-DLICENSE_RESTRICTED=$(usex gmttria no yes)
+		-DGMT_OPENMP=$(usex openmp)
+		-DGMT_USE_THREADS=$(usex threads)
+		-DGMT_INSTALL_TRADITIONAL_FOLDERNAMES=OFF # Install bash completions properly
+		-DGMT_INSTALL_MODULE_LINKS=OFF # Don't install symlinks on gmt binary, they are conflicted with gmt4
+		-DBASH_COMPLETION_DIR="$(get_bashcompdir)"
+		$(cmake_use_find_package gdal GDAL)
+		$(cmake_use_find_package fftw FFTW3)
+		$(cmake_use_find_package lapack LAPACK)
+		$(cmake_use_find_package pcre PCRE)
+	)
+	use pcre || mycmakeargs+=( $(cmake_use_find_package pcre2 PCRE2) )
+
+	cmake_src_configure
+}
+
+src_install() {
+	cmake_src_install
+	# Remove various documentation
+	if ! use doc; then
+		rm -rf "${ED}/usr/share/doc/${PF}/pdf" || die
+	fi
+
+	if use examples; then
+		docompress -x /usr/share/doc/${PF}/examples
+	else
+		rm -rf "${ED}/usr/share/doc/${PF}/examples" || die
+	fi
+
+	if ! use htmldoc; then
+		rm -rf "${ED}/usr/share/doc/${PF}/html" || die
+	fi
+
+	if use tutorial; then
+		docompress -x /usr/share/doc/${PF}/tutorial
+	else
+		rm -rf "${ED}/usr/share/doc/${PF}/tutorial" || die
+	fi
+
+	# Decompress manuals
+	find "${ED}/usr/share/man" -name "*.gz" -exec gunzip {} + || die
+	# Rename some files to avoid a name conflict with gmt4
+	mv "${ED}/usr/bin/gmt_shell_functions.sh" "${ED}/usr/bin/gmt5_shell_functions.sh" || die
+	mv "${ED}/usr/bin/isogmt" "${ED}/usr/bin/isogmt5" || die
+	rm "${ED}/usr/bin/gmtswitch" || die
+	# Rename bash completion file
+	mv "${D}$(get_bashcompdir)/gmt_completion.bash" "${D}$(get_bashcompdir)/gmt" || die
+}
diff --git a/sci-geosciences/gmt/metadata.xml b/sci-geosciences/gmt/metadata.xml
index c31969b5f364..d0db455197ca 100644
--- a/sci-geosciences/gmt/metadata.xml
+++ b/sci-geosciences/gmt/metadata.xml
@@ -10,8 +10,12 @@
     <flag name="gmtfull">Full resolution bathymetry database</flag>
     <flag name="gmthigh">Add high resolution bathymetry database</flag>
     <flag name="gmttria">Non GNU triangulation method, more efficient</flag>
+    <flag name="gshhg">Install coastline database</flag>
+    <flag name="htmldoc">Install html documentation</flag>
     <flag name="metric">Use SI (cm) units instead of US (inches) ones</flag>
     <flag name="mex">Enable compilation of mex supplement which requires Octave/Matlab</flag>
     <flag name="octave">Enable octave support</flag>
+    <flag name="pcre2">Use libpcre2 for regular expressions</flag>
+    <flag name="tutorial">Install data files for tutorial</flag>
   </use>
 </pkgmetadata>