gentoo resync : 03.11.2019

15 files changed, 355 insertions, 903 deletions

diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index 8e321f13b21e..c70eca4a8dc0 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/azara/Manifest b/sci-chemistry/azara/Manifest
deleted file mode 100644
index 9c43a3f99bac..000000000000
--- a/sci-chemistry/azara/Manifest
+++ /dev/null
@@ -1,7 +0,0 @@
-AUX 2.8-64bit.patch 2919 BLAKE2B 14fff0e7192284e612e336954f7770749170f1dce276e2b892f2b8cd4372c4d16306ce79cb6efdd5f6589648d08201875f1b01c6592e3da7057ee7bd9835e69c SHA512 f2c42875f7c4aaa2110376fae252e53feb19e82c003ce44f9ba4df0c6bff1e0bcf0d55c91faf3480831c7a8c0b868ea29cb59b209aa4d747513b8d20db2a3b7f
-AUX 2.8-impl-dec.patch 5172 BLAKE2B afd61fb773afc2817ec645ca7adba1c46c9c13e564cf517395a79dbe53baa1c2b045d4e57ebf8ed26a6ad880d23076a16a664bcfb0b6902103cc6757738ecb44 SHA512 31dd75bb75427a37691cdacd2caee10ec5ee540daef52131eaf7102ec13f06101649a6bfbe6ee47503ef02986816a3c957b19cdb1308ea7c90ce1c22a02b6d05
-AUX 2.8-prll.patch 8764 BLAKE2B 86a805b5ea0cb0ca475d5aa53d3dee23a6b0705d49ce112f41b123b32ace9e3bcc913a7fd1c741e72591134b3c4102e388494484873d1711a0ff3dd3e7303b82 SHA512 4868cae8d7fe425136728ca751d59a0d8bb2a7906946a004cee1d017ab60f27075199953122bc81873ca4ba4cf462fcef1dfc0b93d748da966548a3d9f61cd7d
-AUX 2.8-python.patch 962 BLAKE2B 76da538b940073ffd97f461411952b58dd95d5e24e4cc4d13016f585aa5c72d02d7fb099409e7f78d4597c8e23c482c2fec3d1eedaa7bcf6d787a1322799c3e9 SHA512 d3c1aa38a1b783dba82ec571fd8d9bb7d4981f2957e728b91ca42562c453075e351a5805862f11e3d13e2036297c14f58c8f0bc97f128055870b2d47ce89a631
-DIST azara-2.8-src.tgz 638120 BLAKE2B 9b5046f1b51a6d7699fa72723355ba1588a2db863daff222473272e465c7c8999d17ed4846aac8b64c36137ef90f372ea3e24156d7492cc2f9c6f92ba7f2af88 SHA512 61a913b041f8ed7dade9d452ca0d99804ffcea0c678f23ad8357c1e7188996eecde9402201399306fcb32a504b17c3d61997f50ce57794f876c9f8d492ca500c
-EBUILD azara-2.8-r5.ebuild 2131 BLAKE2B 007170db674358091608be300a51d955a05a0c792b8f80bfe05fc099cb6f59243003d0d1b40a031db74293cffaf6049bcaf5b17387d74e0279e8a6d4f33aa936 SHA512 f291a469b961f451c2384969b37ef8fa3241084d89a35a6198c500cab37bc1faa3ce4a143bd9423b830754d5b25d95370ac1e29d4781d0a621f60a2f88b5a198
-MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92
diff --git a/sci-chemistry/azara/azara-2.8-r5.ebuild b/sci-chemistry/azara/azara-2.8-r5.ebuild
deleted file mode 100644
index 22a7542cc9d4..000000000000
--- a/sci-chemistry/azara/azara-2.8-r5.ebuild
+++ /dev/null
@@ -1,101 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils python-r1 toolchain-funcs
-
-DESCRIPTION="A suite of programmes to process and view NMR data"
-HOMEPAGE="http://www.bio.cam.ac.uk/azara/"
-SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${PN}/${P}-src.tgz"
-
-LICENSE="AZARA"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux"
-IUSE="xpm X"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-RESTRICT="bindist mirror"
-
-RDEPEND="
-	x11-libs/libX11
-	x11-libs/motif:0
-	${PYTHON_DEPS}
-	xpm? ( x11-libs/libXpm )"
-DEPEND="${RDEPEND}"
-
-src_prepare() {
-	cat > ENVIRONMENT <<- EOF
-	CC=$(tc-getCC)
-	CFLAGS = ${CFLAGS}
-	LFLAGS = ${LDFLAGS}
-	MATH_LIB = -lm
-	X11_INCLUDE_DIR = -I"${EPREFIX}/usr/X11R6/include"
-	MOTIF_INCLUDE_DIR = -I"${EPREFIX}/usr/include" -I../global
-	X11_LIB_DIR = -L"${EPREFIX}/usr/$(get_libdir)"
-	MOTIF_LIB_DIR = -L"${EPREFIX}/usr/$(get_libdir)"
-	X11_LIB = -lX11
-	MOTIF_LIB = -lXm -lXt
-	SHARED_FLAGS = -shared
-	ENDIAN_FLAG = -DBIG_ENDIAN_DATA -DWRITE_ENDIAN_PAR
-	PIC = -fPIC
-	EOF
-
-	use xpm && echo "XPMUSE=\"XPM_FLAG=-DUSE_XPM XPM_LIB=-lXpm\"" >> ENVIRONMENT
-
-	epatch \
-		"${FILESDIR}"/${PV}-prll.patch \
-		"${FILESDIR}"/${PV}-impl-dec.patch \
-		"${FILESDIR}"/${PV}-python.patch \
-		"${FILESDIR}"/${PV}-64bit.patch
-}
-
-src_compile() {
-	local mymake
-	local makeflags
-
-	mymake="${mymake} help nongui"
-	use X && mymake="${mymake} gui"
-
-	emake ${mymake}
-
-	compilation() {
-		python_export PYTHON_CFLAGS PYTHON_LIBS
-		cd "${BUILD_DIR}" || die
-		emake DataRows_clean
-		emake \
-			PYTHON_INCLUDE_DIR="${PYTHON_CFLAGS}" \
-			PYTHON_LIB="${PYTHON_LIBS}" \
-			DataRows
-	}
-	python_copy_sources
-	python_foreach_impl compilation
-}
-
-src_install() {
-	rm bin/pythonAzara || die
-	if ! use X; then
-		rm bin/plot* || die
-	fi
-
-	dodoc CHANGES* README*
-	dohtml -r html/*
-
-	cd bin || die
-	dobin ${PN}
-	rm ${PN} || die
-	for bin in *; do
-		newbin ${bin} ${bin}-${PN}
-	done
-
-	installation() {
-		cd "${BUILD_DIR}" || die
-		python_domodule lib/DataRows.so
-	}
-	python_foreach_impl installation
-}
-
-pkg_postinst() {
-	einfo "Due to collision we moved all binary to *-${PN}"
-}
diff --git a/sci-chemistry/azara/files/2.8-64bit.patch b/sci-chemistry/azara/files/2.8-64bit.patch
deleted file mode 100644
index c65e075c1d30..000000000000
--- a/sci-chemistry/azara/files/2.8-64bit.patch
+++ /dev/null
@@ -1,85 +0,0 @@
-diff --git a/global/par.c b/global/par.c
-index ac87c88..fecfe35 100644
---- a/global/par.c
-+++ b/global/par.c
-@@ -562,9 +562,9 @@ static Status get_varian_header(FILE *fp, String error_msg)
-     return  OK;
- }
- 
--static long get_varian_long(int offset)
-+static int get_varian_int(int offset)
- {
--    long x;
-+    int x;
- 
-     if (swapped)
-     {
-@@ -572,7 +572,7 @@ static long get_varian_long(int offset)
- 	SWAP(varian_header[offset+1], varian_header[offset+2], char);
-     }
- 
--    x = *((long *) (varian_header + offset));
-+    x = *((int *) (varian_header + offset));
- 
-     return  x;
- }
-@@ -591,7 +591,7 @@ static short get_varian_short(int offset)
- 
- static Status check_varian_header(String error_msg)
- {
--    long nblocks, ntraces, np, ebytes, tbytes, /*bbytes,*/ d;
-+    int nblocks, ntraces, np, ebytes, tbytes, /*bbytes,*/ d;
-     short status;
-     FILE *fp;
- 
-@@ -605,17 +605,19 @@ static Status check_varian_header(String error_msg)
-     FCLOSE(fp);
- 
-     /* numbers in parentheses are offsets into header */
--    nblocks = get_varian_long(0);   /* number of blocks in file */
--    ntraces = get_varian_long(4);   /* number of traces per block */
--    np = get_varian_long(8);	    /* number of elements per trace */
--    ebytes = get_varian_long(12);   /* number of bytes per element */
--    tbytes = get_varian_long(16);   /* number of bytes per trace */
--    /*bbytes = get_varian_long(20);*/   /* number of bytes per block */
-+    nblocks = get_varian_int(0);   /* number of blocks in file */
-+    printf("nblocks = %d\n", nblocks);
-+    ntraces = get_varian_int(4);   /* number of traces per block */
-+    printf("ntraces = %d\n", ntraces);
-+    np = get_varian_int(8);	    /* number of elements per trace */
-+    ebytes = get_varian_int(12);   /* number of bytes per element */
-+    tbytes = get_varian_int(16);   /* number of bytes per trace */
-+    /*bbytes = get_varian_int(20);*/   /* number of bytes per block */
- 	    /* short starting at 24 is software version */
-     status = get_varian_short(26);  /* status of whole file */
- 	    /* long starting at 28 is number of block headers */
- 
--    if (ntraces != 1L)
-+    if (ntraces != 1)
- 	RETURN_ERROR_MSG("can only process Varian data with #traces = 1");
- 
-     if (np != npoints[0])
-@@ -646,12 +648,12 @@ static Status check_varian_header(String error_msg)
- 
-     if (integer)
-     {
--	if (ebytes == 2L)
-+	if (ebytes == 2)
- 	{
- 	    if (status & (1<<2))
- 		RETURN_ERROR_MSG("Varian header has inconsistent byte information");
- 	}
--	else if (ebytes == 4L)
-+	else if (ebytes == 4)
- 	{
- 	    if (!(status & (1<<2)))
- 		RETURN_ERROR_MSG("Varian header has inconsistent byte information");
-@@ -666,7 +668,7 @@ static Status check_varian_header(String error_msg)
-     }
-     else /* !integer, i.e. floating point */
-     {
--	if (ebytes != 4L)
-+	if (ebytes != 4)
- 	    RETURN_ERROR_MSG("Varian header has inconsistent byte information");
-     }
- 
diff --git a/sci-chemistry/azara/files/2.8-impl-dec.patch b/sci-chemistry/azara/files/2.8-impl-dec.patch
deleted file mode 100644
index 62e8c7d6873b..000000000000
--- a/sci-chemistry/azara/files/2.8-impl-dec.patch
+++ /dev/null
@@ -1,226 +0,0 @@
-diff --git a/DataRows/data_rows.c b/DataRows/data_rows.c
-index 054fa1f..a07eedc 100644
---- a/DataRows/data_rows.c
-+++ b/DataRows/data_rows.c
-@@ -1,4 +1,5 @@
- #include "data_rows.h"
-+#include "utility.h"
- 
- #include "par.h"
- 
-diff --git a/DataRows/py_data_rows.c b/DataRows/py_data_rows.c
-index fc8b3c8..985e6c3 100644
---- a/DataRows/py_data_rows.c
-+++ b/DataRows/py_data_rows.c
-@@ -1,4 +1,6 @@
- #include "Python.h"             /* Python header files */
-+#include "modsupport.h"
-+#include "intobject.h"
- 
- #include "data_rows.h"
- 
-diff --git a/connect/crosspeak.c b/connect/crosspeak.c
-index 0de57bf..7b016e1 100644
---- a/connect/crosspeak.c
-+++ b/connect/crosspeak.c
-@@ -1,4 +1,5 @@
- #include "crosspeak.h"
-+#include "utility.h"
- 
- #include "atom.h"
- #include "table.h"
-diff --git a/connect/shift.c b/connect/shift.c
-index f54ba9f..a880001 100644
---- a/connect/shift.c
-+++ b/connect/shift.c
-@@ -1,4 +1,5 @@
- #include "shift.h"
-+#include "utility.h"
- 
- #include "atom.h"
- #include "table.h"
-diff --git a/global/macros.h b/global/macros.h
-index 43fc43e..bb1d267 100644
---- a/global/macros.h
-+++ b/global/macros.h
-@@ -8,6 +8,7 @@
- #include <math.h>
- #include <string.h>
- #include <stdlib.h>
-+#include <ctype.h>
- 
- #ifdef WIN32
- #include <ctype.h>
-diff --git a/global/parser.c b/global/parser.c
-index 007d926..0f19575 100644
---- a/global/parser.c
-+++ b/global/parser.c
-@@ -1,4 +1,5 @@
- #include "parser.h"
-+#include "utility.h"
- 
- #define  MAX_NARGS		20
- 
-diff --git a/peak/fitter.c b/peak/fitter.c
-index ba6b175..b58f573 100644
---- a/peak/fitter.c
-+++ b/peak/fitter.c
-@@ -1,4 +1,5 @@
- #include "fitter.h"
-+#include "data.h"
- 
- #include "nonlinear_model.h"
- 
-diff --git a/peak/peak_fit.c b/peak/peak_fit.c
-index 92c69a8..5b9791f 100644
---- a/peak/peak_fit.c
-+++ b/peak/peak_fit.c
-@@ -6,6 +6,7 @@
- #include "output.h"
- #include "ref.h"
- #include "script_fit.h"
-+#include "fitter.h"
- 
- #define  MEGAWORD		(1024 * 1024)
- #define  DEFAULT_STORE		(2 * MEGAWORD)
-diff --git a/plot1/draw.c b/plot1/draw.c
-index 4fdce96..a2a2e8a 100644
---- a/plot1/draw.c
-+++ b/plot1/draw.c
-@@ -1,4 +1,5 @@
- #include "draw.h"
-+#include "ticks.h"
- 
- #include "color.h"
- #include "data.h"
-diff --git a/plot1/object.c b/plot1/object.c
-index 973897c..e043a53 100644
---- a/plot1/object.c
-+++ b/plot1/object.c
-@@ -1,4 +1,5 @@
- #include "object.h"
-+#include "script.h"
- 
- #include "color.h"
- #include "parser.h"
-diff --git a/plot1/output_popup.c b/plot1/output_popup.c
-index 0794584..e73976e 100644
---- a/plot1/output_popup.c
-+++ b/plot1/output_popup.c
-@@ -1,4 +1,5 @@
- #include "output_popup.h"
-+#include "script.h"
- 
- #include "output.hlp"
- 
-diff --git a/plot1/plots.c b/plot1/plots.c
-index 3790f5b..7ac58df 100644
---- a/plot1/plots.c
-+++ b/plot1/plots.c
-@@ -1,4 +1,5 @@
- #include "plots.h"
-+#include "script.h"
- 
- #include "data.h"
- #include "input.h"
-diff --git a/plot1/region_popup.c b/plot1/region_popup.c
-index 68b3930..f049d29 100644
---- a/plot1/region_popup.c
-+++ b/plot1/region_popup.c
-@@ -1,4 +1,5 @@
- #include "region_popup.h"
-+#include "data.h"
- 
- #include "region.hlp"
- 
-diff --git a/plot2/data_popup.c b/plot2/data_popup.c
-index 851b1d4..1c9026e 100644
---- a/plot2/data_popup.c
-+++ b/plot2/data_popup.c
-@@ -1,4 +1,5 @@
- #include "data_popup.h"
-+#include "rowcol_popup.h"
- 
- #include "data.hlp"
- 
-diff --git a/plot2/extract_popup.c b/plot2/extract_popup.c
-index 416aab0..a7fcbf3 100644
---- a/plot2/extract_popup.c
-+++ b/plot2/extract_popup.c
-@@ -1,4 +1,5 @@
- #include "extract_popup.h"
-+#include "script.h"
- 
- #include "extract.hlp"
- 
-diff --git a/plot2/levels_popup.c b/plot2/levels_popup.c
-index 197cf2c..e1ac22c 100644
---- a/plot2/levels_popup.c
-+++ b/plot2/levels_popup.c
-@@ -1,4 +1,5 @@
- #include "levels_popup.h"
-+#include "levels_func.h"
- 
- #include "levels.hlp"
- 
-diff --git a/plot2/plot2.c b/plot2/plot2.c
-index 9ca91c3..0c10d5a 100644
---- a/plot2/plot2.c
-+++ b/plot2/plot2.c
-@@ -1,4 +1,6 @@
- #include "plot2.h"
-+#include "object_popup.h"
-+#include "prop_popup.h"
- 
- #include "baseline_popup.h"
- #include "callback.h"
-diff --git a/plot2/rowcol_popup.c b/plot2/rowcol_popup.c
-index e9f4843..6c50426 100644
---- a/plot2/rowcol_popup.c
-+++ b/plot2/rowcol_popup.c
-@@ -1,4 +1,5 @@
- #include "rowcol_popup.h"
-+#include "ref_popup.h"
- 
- #include "rowcol.hlp"
- 
-diff --git a/plot2/script.c b/plot2/script.c
-index 2f55182..d7d886f 100644
---- a/plot2/script.c
-+++ b/plot2/script.c
-@@ -1,4 +1,5 @@
- #include "script.h"
-+#include "macros.h"
- 
- #include "param.h"
- #include "stack.h"
-diff --git a/plot2/slice_popup.c b/plot2/slice_popup.c
-index b601834..1b1e686 100644
---- a/plot2/slice_popup.c
-+++ b/plot2/slice_popup.c
-@@ -1,4 +1,5 @@
- #include "slice_popup.h"
-+#include "rowcol_func.h"
- 
- #include "baseline.h"
- #include "baseline_popup.h"
-diff --git a/process/files.c b/process/files.c
-index e09127e..d95d681 100644
---- a/process/files.c
-+++ b/process/files.c
-@@ -1,4 +1,5 @@
- #include "files.h"
-+#include "macros.h"
- 
- #include <sys/types.h>
- #include <sys/stat.h>
-diff --git a/project/project.c b/project/project.c
-index 92b70e3..a3e6d94 100644
---- a/project/project.c
-+++ b/project/project.c
-@@ -1,4 +1,5 @@
- #include "project.h"
-+#include "utility.h"
- 
- #include "block.h"
- #include "par.h"
diff --git a/sci-chemistry/azara/files/2.8-prll.patch b/sci-chemistry/azara/files/2.8-prll.patch
deleted file mode 100644
index 4720bb659445..000000000000
--- a/sci-chemistry/azara/files/2.8-prll.patch
+++ /dev/null
@@ -1,387 +0,0 @@
-diff --git a/DataRows/makefile b/DataRows/makefile
-index 587e710..4e0a312 100644
---- a/DataRows/makefile
-+++ b/DataRows/makefile
-@@ -28,7 +28,7 @@ GLOBAL_OBJS = \
- 	$(GLOBAL_DIR)/ref.o \
- 	$(GLOBAL_DIR)/utility.o
- 
--DataRows.so: locals globals
-+DataRows.so: $(LOCAL_OBJS) $(GLOBAL_OBJS)
- 	$(CC) $(SHARED_FLAGS) -o $@ $(CFLAGS) $(LFLAGS) \
- 		$(LOCAL_OBJS) \
- 		$(GLOBAL_OBJS)
-diff --git a/azara/makefile b/azara/makefile
-index 3ba0cd9..f7b4ce5 100644
---- a/azara/makefile
-+++ b/azara/makefile
-@@ -12,7 +12,7 @@ LOCAL_OBJS = \
- GLOBAL_OBJS = \
- 	$(GLOBAL_DIR)/help.o
- 
--azara: locals globals
-+azara: $(LOCAL_OBJS) $(GLOBAL_OBJS)
- 	$(CC) -o $@ $(LFLAGS) \
- 		$(LOCAL_OBJS) \
- 		$(GLOBAL_OBJS) \
-diff --git a/combine/makefile b/combine/makefile
-index a855236..7a83d8f 100644
---- a/combine/makefile
-+++ b/combine/makefile
-@@ -20,7 +20,7 @@ GLOBAL_OBJS = \
- 	$(GLOBAL_DIR)/ref.o \
- 	$(GLOBAL_DIR)/utility.o
- 
--combine: locals globals
-+combine: $(LOCAL_OBJS) $(GLOBAL_OBJS)
- 	$(CC) -o $@ $(LFLAGS) \
- 		$(LOCAL_OBJS) \
- 		$(GLOBAL_OBJS) \
-diff --git a/connect/makefile b/connect/makefile
-index d75e7da..d238507 100644
---- a/connect/makefile
-+++ b/connect/makefile
-@@ -23,7 +23,7 @@ GLOBAL_OBJS = \
- 	$(GLOBAL_DIR)/ref.o \
- 	$(GLOBAL_DIR)/utility.o
- 
--connect: locals globals
-+connect: $(LOCAL_OBJS) $(GLOBAL_OBJS)
- 	$(CC) -o $@ $(LFLAGS) \
- 		$(LOCAL_OBJS) \
- 		$(GLOBAL_OBJS) \
-diff --git a/contours/makefile b/contours/makefile
-index 5b832b8..49175dd 100644
---- a/contours/makefile
-+++ b/contours/makefile
-@@ -19,7 +19,7 @@ GLOBAL_OBJS = \
- 	$(GLOBAL_DIR)/ref.o \
- 	$(GLOBAL_DIR)/utility.o
- 
--contours: locals globals
-+contours: $(LOCAL_OBJS) $(GLOBAL_OBJS)
- 	$(CC) -o $@ $(LFLAGS) \
- 		$(LOCAL_OBJS) \
- 		$(GLOBAL_OBJS) \
-diff --git a/deflate/makefile b/deflate/makefile
-index 4c4e02e..42d5c30 100644
---- a/deflate/makefile
-+++ b/deflate/makefile
-@@ -18,7 +18,7 @@ GLOBAL_OBJS = \
- 	$(GLOBAL_DIR)/ref.o \
- 	$(GLOBAL_DIR)/utility.o
- 
--deflate: locals globals
-+deflate: $(LOCAL_OBJS) $(GLOBAL_OBJS)
- 	$(CC) -o $@ $(LFLAGS) \
- 		$(LOCAL_OBJS) \
- 		$(GLOBAL_OBJS) \
-diff --git a/extract/makefile b/extract/makefile
-index 3212cb9..fed874b 100644
---- a/extract/makefile
-+++ b/extract/makefile
-@@ -18,7 +18,7 @@ GLOBAL_OBJS = \
- 	$(GLOBAL_DIR)/ref.o \
- 	$(GLOBAL_DIR)/utility.o
- 
--extract: locals globals
-+extract: $(LOCAL_OBJS) $(GLOBAL_OBJS)
- 	$(CC) -o $@ $(LFLAGS) \
- 		$(LOCAL_OBJS) \
- 		$(GLOBAL_OBJS) \
-diff --git a/global/makefile b/global/makefile
-index 364fa41..5272a31 100644
---- a/global/makefile
-+++ b/global/makefile
-@@ -42,6 +42,31 @@ LINPACK_OBJS = \
- AZARA_OBJS = \
- 	help.o
- 
-+all: \
-+	azara_objects \
-+	decay_objects \
-+	simulate_objects \
-+	viewer_objects \
-+	components_objects \
-+	shuffle_objects \
-+	connect_objects \
-+	slides_objects \
-+	peak_find_objects \
-+	peak_fit_objects \
-+	plot1_objects \
-+	reflate_objects \
-+	deflate_objects \
-+	combine_objects \
-+	unblock_objects \
-+	extract_objects \
-+	project_objects \
-+	contours_objects \
-+	plot2_nog_objects \
-+	plot2_objects \
-+	process_objects \
-+	python_objects \
-+	integrate_objects
-+
- azara_objects: $(AZARA_OBJS)
- 
- DECAY_OBJS = \
-diff --git a/help/makefile b/help/makefile
-index 9e99a7c..59a86a3 100644
---- a/help/makefile
-+++ b/help/makefile
-@@ -39,7 +39,7 @@ globals:
- 
- .c.o:;  $(CC) -c $(CFLAGS) $<
- 
--hlp:
-+hlp: txt2hlp
- 	$(TXT2HLP) azara
- 	$(TXT2HLP) combine
- 	$(TXT2HLP) connect
-@@ -78,7 +78,7 @@ hlp:
- 	$(TXT2HLP) plot1/text
- 	$(TXT2HLP) DataRows
- 
--html:
-+html: txt2html
- 	$(TXT2HTML) azara
- 	$(TXT2HTML) combine
- 	$(TXT2HTML) connect
-diff --git a/makefile b/makefile
-index 9965b07..f4383af 100644
---- a/makefile
-+++ b/makefile
-@@ -14,7 +14,7 @@ all: help nongui DataRows gui
- help: \
- 	help_program
- 
--nongui: \
-+nongui: help \
- 	process_program \
- 	plot2_nog_program \
- 	peak_program \
-@@ -29,63 +29,66 @@ nongui: \
- 	connect_program \
- 	azara_program
- 
--gui: \
-+gui: help \
- 	plot2_program \
- 	plot1_program
- 
--DataRows: \
-+DataRows: help \
- 	DataRows
- 
--process_program:
--	cd process; $(MAKE)
-+global:
-+	$(MAKE) -C global
- 
--plot2_program:
--	cd plot2; $(MAKE) plot2
-+process_program: global
-+	$(MAKE) -C process
- 
--plot2_nog_program:
--	cd plot2; $(MAKE) plot2_nog
-+plot2_program: global
-+	$(MAKE) -C plot2
- 
--plot1_program:
--	cd plot1; $(MAKE)
-+plot2_nog_program: global
-+	$(MAKE) -C plot2 plot2_nog
- 
--peak_program:
--	cd peak; $(MAKE)
-+plot1_program: global
-+	$(MAKE) -C plot1
- 
--extract_program:
--	cd extract; $(MAKE)
-+peak_program:  global process_program
-+	$(MAKE) -C peak
- 
--project_program:
--	cd project; $(MAKE)
-+extract_program: global
-+	$(MAKE) -C extract
- 
--unblock_program:
--	cd unblock; $(MAKE)
-+project_program: global
-+	$(MAKE) -C project
- 
--contours_program:
--	cd contours; $(MAKE)
-+unblock_program: global
-+	$(MAKE) -C unblock
- 
--combine_program:
--	cd combine; $(MAKE)
-+contours_program: global
-+	$(MAKE) -C contours
- 
--deflate_program:
--	cd deflate; $(MAKE)
-+combine_program: global
-+	$(MAKE) -C combine
- 
--reflate_program:
--	cd reflate; $(MAKE)
-+deflate_program: global
-+	$(MAKE) -C deflate
- 
--utility_program:
--	cd utility; $(MAKE)
-+reflate_program: global
-+	$(MAKE) -C reflate
- 
--connect_program:
--	cd connect; $(MAKE)
-+utility_program: global
-+	$(MAKE) -C utility
- 
--help_program:
--	cd help; $(MAKE)
-+connect_program: global
-+	$(MAKE) -C connect
- 
--azara_program:
--	cd azara; $(MAKE)
-+help_program: global
-+	$(MAKE) -C help
- 
--DataRows:
--	cd DataRows; $(MAKE)
-+azara_program: global
-+	$(MAKE) -C azara
-+
-+DataRows: global
-+	$(MAKE) -C DataRows
- 
- clean: \
- 	global_clean \
-@@ -227,3 +230,5 @@ azara_realclean:
- DataRows_realclean:
- 	cd DataRows; $(MAKE) realclean
- 
-+
-+.PHONY: global process_program
-diff --git a/peak/makefile b/peak/makefile
-index f3c13b7..4211221 100644
---- a/peak/makefile
-+++ b/peak/makefile
-@@ -97,13 +97,13 @@ COMMAND_OBJS = \
- 
- all: peak_find peak_fit
- 
--peak_find: local_find global_find
-+peak_find: $(LOCAL_FIND_OBJS) $(GLOBAL_FIND_OBJS)
- 	$(CC) -o $@ $(LFLAGS) \
- 		$(LOCAL_FIND_OBJS) \
- 		$(GLOBAL_FIND_OBJS) \
- 		$(LIB) $(MATH_LIB)
- 
--peak_fit: local_fit global_fit commands
-+peak_fit: $(LOCAL_FIT_OBJS) $(GLOBAL_FIT_OBJS) $(COMMAND_OBJS)
- 	$(CC) -o $@ $(LFLAGS) \
- 		$(LOCAL_FIT_OBJS) \
- 		$(GLOBAL_FIT_OBJS) \
-diff --git a/plot1/makefile b/plot1/makefile
-index d1dce2d..e729443 100644
---- a/plot1/makefile
-+++ b/plot1/makefile
-@@ -95,7 +95,7 @@ GLOBAL_OBJS = \
- 	$(GLOBAL_DIR)/utility.o \
- 	$(GLOBAL_DIR)/window.o
- 
--plot1: locals globals
-+plot1: $(LOCAL_OBJS) $(GLOBAL_OBJS)
- 	$(CC) -o $@ $(LFLAGS) \
- 		$(LOCAL_OBJS) \
- 		$(GLOBAL_OBJS) \
-@@ -110,7 +110,7 @@ locals:
- globals:
- 	cd $(GLOBAL_DIR); $(MAKE) plot1_objects
- 
--.c.o:;	$(CC) $(X11_INCLUDE_DIR) $(MOTIF_INCLUDE_DIR) -c $(CFLAGS) $<
-+.c.o:;	$(CC) $(X11_INCLUDE_DIR) $(MOTIF_INCLUDE_DIR) -c $(CFLAGS) -I../plot2 $<
- 
- clean:
- 	rm -f *.o
-diff --git a/plot2/makefile b/plot2/makefile
-index a6b7b4a..98e286e 100644
---- a/plot2/makefile
-+++ b/plot2/makefile
-@@ -129,7 +129,7 @@ GLOBAL_PLOT2_NOG_OBJS = \
- 
- all: plot2 plot2_nog
- 
--plot2: local_plot2 global_plot2
-+plot2: $(LOCAL_PLOT2_OBJS) $(GLOBAL_PLOT2_OBJS) 
- 	$(CC) -o $@ $(CFLAGS) $(LFLAGS) \
- 		$(LOCAL_PLOT2_OBJS) \
- 		$(GLOBAL_PLOT2_OBJS) \
-@@ -137,7 +137,7 @@ plot2: local_plot2 global_plot2
- 		$(LIB) $(MATH_LIB) \
- 		$(MOTIF_LIB) $(X11_LIB) $(XPM_LIB)
- 
--plot2_nog: local_plot2_nog global_plot2_nog
-+plot2_nog: $(LOCAL_PLOT2_NOG_OBJS) $(GLOBAL_PLOT2_NOG_OBJS)
- 	$(CC) -o $@ $(CFLAGS) $(LFLAGS) \
- 		$(LOCAL_PLOT2_NOG_OBJS) \
- 		$(GLOBAL_PLOT2_NOG_OBJS) \
-diff --git a/process/makefile b/process/makefile
-index 22ceeed..72d587b 100644
---- a/process/makefile
-+++ b/process/makefile
-@@ -72,7 +72,7 @@ GLOBAL_OBJS = \
- 	$(GLOBAL_DIR)/utility.o \
- 	$(LINPACK_OBJS)
- 
--process: locals globals
-+process: $(LOCAL_OBJS) $(GLOBAL_OBJS)
- 	$(CC) -o $@ $(LFLAGS) \
- 		$(LOCAL_OBJS) \
- 		$(GLOBAL_OBJS) \
-diff --git a/project/makefile b/project/makefile
-index 78143fc..ed0f296 100644
---- a/project/makefile
-+++ b/project/makefile
-@@ -18,7 +18,7 @@ GLOBAL_OBJS = \
- 	$(GLOBAL_DIR)/ref.o \
- 	$(GLOBAL_DIR)/utility.o
- 
--project: locals globals
-+project: $(LOCAL_OBJS) $(GLOBAL_OBJS)
- 	$(CC) -o $@ $(LFLAGS) \
- 		$(LOCAL_OBJS) \
- 		$(GLOBAL_OBJS) \
-diff --git a/reflate/makefile b/reflate/makefile
-index 079a3fc..01ec311 100644
---- a/reflate/makefile
-+++ b/reflate/makefile
-@@ -18,7 +18,7 @@ GLOBAL_OBJS = \
- 	$(GLOBAL_DIR)/ref.o \
- 	$(GLOBAL_DIR)/utility.o
- 
--reflate: locals globals
-+reflate: $(LOCAL_OBJS) $(GLOBAL_OBJS)
- 	$(CC) -o $@ $(LFLAGS) \
- 		$(LOCAL_OBJS) \
- 		$(GLOBAL_OBJS) \
-diff --git a/unblock/makefile b/unblock/makefile
-index 510dc9e..d9a0f2b 100644
---- a/unblock/makefile
-+++ b/unblock/makefile
-@@ -18,7 +18,7 @@ GLOBAL_OBJS = \
- 	$(GLOBAL_DIR)/ref.o \
- 	$(GLOBAL_DIR)/utility.o
- 
--unblock: locals globals
-+unblock: $(LOCAL_OBJS) $(GLOBAL_OBJS)
- 	$(CC) -o $@ $(LFLAGS) \
- 		$(LOCAL_OBJS) \
- 		$(GLOBAL_OBJS) \
diff --git a/sci-chemistry/azara/files/2.8-python.patch b/sci-chemistry/azara/files/2.8-python.patch
deleted file mode 100644
index 9834c77a77dc..000000000000
--- a/sci-chemistry/azara/files/2.8-python.patch
+++ /dev/null
@@ -1,44 +0,0 @@
-diff --git a/DataRows/makefile b/DataRows/makefile
-index 4e0a312..ce261ab 100644
---- a/DataRows/makefile
-+++ b/DataRows/makefile
-@@ -22,16 +22,17 @@ LOCAL_OBJS = \
- 	data_rows.o
- 
- GLOBAL_OBJS = \
--	$(GLOBAL_DIR)/block_io.o \
--	$(GLOBAL_DIR)/par.o \
--	$(GLOBAL_DIR)/parse.o \
--	$(GLOBAL_DIR)/ref.o \
--	$(GLOBAL_DIR)/utility.o
-+	block_io.o \
-+	par.o \
-+	parse.o \
-+	ref.o \
-+	utility.o
- 
- DataRows.so: $(LOCAL_OBJS) $(GLOBAL_OBJS)
- 	$(CC) $(SHARED_FLAGS) -o $@ $(CFLAGS) $(LFLAGS) \
- 		$(LOCAL_OBJS) \
--		$(GLOBAL_OBJS)
-+		$(GLOBAL_OBJS) \
-+		$(PYTHON_LIB)
- 
- local_objects: $(LOCAL_OBJS)
- 
-@@ -42,9 +43,13 @@ globals:
- 	cd $(GLOBAL_DIR); $(MAKE) python_objects
- 
- py_data_rows.o: py_data_rows.c
--	$(CC) -c $(CFLAGS) $(PYTHON_INCLUDE_DIR) $<
-+	$(CC) -c $(CFLAGS) $(PIC) $(PYTHON_INCLUDE_DIR) $<
- 
--.c.o:;	$(CC) -c $(CFLAGS) $<
-+data_rows.o: data_rows.c
-+	$(CC) -c $(CFLAGS) $(PIC) $<
-+
-+%.o: $(GLOBAL_DIR)/%.c
-+	$(CC) -c $(CFLAGS) $(PIC) $<
- 
- clean:
- 	rm -f *.o
diff --git a/sci-chemistry/azara/metadata.xml b/sci-chemistry/azara/metadata.xml
deleted file mode 100644
index 8937bad0b175..000000000000
--- a/sci-chemistry/azara/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-chemistry@gentoo.org</email>
-    <name>Gentoo Chemistry Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 5207714ec30c..203a5b921471 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -1,13 +1,16 @@
+AUX gromacs-2020_beta1-pytest.patch 630 BLAKE2B 1036e06589c24459006f0b579ee89c9d9c4623c7ca32fae90b21646db13280549a23cad717ef7481b03cbf9f2629b6804c0727d4b8c7f3274d0463d2735f976a SHA512 b5880d3a21635892d52b2ac09cbf456194a3db0fa0676bbdd2c2500964da89fbb7f4ebed7ac7843304159bf11f44e279eb505b2af8833127d2e21f10cb254c1e
 DIST gromacs-2018.7.tar.gz 29912662 BLAKE2B 0714b28ec2443f3201275fc2fa6db1202a059161362134d4de03a900a3a67fe9d31ba8c058d5ee971198fecd69379fcd389f03d25c61f50b8460c43ba5c564d5 SHA512 fbc3b847b70b1396f412b8f4a1b977268651f8d53a222dcf6349fe563ff6319e096484209a24351e382bc9162a949b3900591f5b469c32dd9effeb894f03c172
 DIST gromacs-2018.8.tar.gz 29913703 BLAKE2B 8780032305928067fbfe1559efe9eedc4d47e27ab2f6ab54d6dba39edfcbeefbee4673d8910009048a850620b5a08ba8feb622db652c439cfa50a149ec5f0015 SHA512 6717895942f2ab7b54019511ed2aebadadde8e96d3c4b7414bb9168ffe418432d2dee330192e199f7b9d2f665c71f5d4f1ef0911aa7243d525a2ca182ef5b122
 DIST gromacs-2019.2.tar.gz 33437869 BLAKE2B bebe4942688dace148856d4491b687b8e0fd2c86d7fbd9eecdb46824d316a0fc3854464ecafa79d8db92327ee8467be204b050c11f1e71132184efd812c3bf09 SHA512 da7ff24e8485774e22d1c2464fbe64675c3305ef0e21a3d17e363201031952e5d4a9b81f572d5284fb6f2596ed99daf62fe78d653387d9d714274f46bc750183
 DIST gromacs-2019.3.tar.gz 33441419 BLAKE2B 79319dd23982c65c7c4d8e5f633cef0c7fd99a38a4e0cc9030a3ffb0fdfc07a4fbfbcfa942896f23a143b747e044fae645498a3e6992497d1f1a7d966f80b2b0 SHA512 de9f54d095b45ea7efd1043f83a40f6c778a6e3e2067a01f48d1ce843d68d226061933ca28a3edb635b795a8ddd5ef9deb8ed1114aa3235bc8039db8ff7d0218
 DIST gromacs-2019.4.tar.gz 33444527 BLAKE2B 5a01ed0e38faade037de701b72e8d52fd5a947a23228f0b5170a170dc963b00068a6b6880dd9a3f6f2a73140a3787952741dcbcc862bc357a8be8bf5640faa16 SHA512 adc6dea187b7f3a3c13fcd39445ae45248d46d56b0102fda47b1850b83ff1fb77a3fec99d4a4124b01ed04646dab6ab67749eae1bec36d1ba6f2205855cd29f8
+DIST gromacs-2020-beta1.tar.gz 29019829 BLAKE2B 1884e0984aa6cd8a6bf7d9c692c5f465247ed3c396a0b12fa67c1fc763d84dbeaee23905c95e902e9befe1af8617fc9dc46d7280140ce09ba1915bef58a86d0a SHA512 8992dbdd560fa5227d19f59d9a360cd9e5f0c3a1df435f43293bb044ca6414f177e04a4933b8c0f19d5121a44244a4c9c95d026f6c817fd4ba5b0e4f7b3a01a0
 DIST regressiontests-2018.7.tar.gz 67856738 BLAKE2B 955ae8b5e74f90fec704cf41fbd00bd8c09d754f950551fe0adfcd407db6fdb4491a3815149ea37d36c747316c79d462e823b9f6b26f2376bf90d87aad95731b SHA512 c2ff390750bd99faebcd8d5dd8ad6dbf2b00113ed888bddddf985dbf95d7f347093adb67f3c396547b3e2990de330fddb7efe83ded91a72cf97c82a1dac7e826
 DIST regressiontests-2018.8.tar.gz 67855469 BLAKE2B 34c9b339f6229f483afbb5192ee6ba8b8f72d5c26907a853af9c53dfece0d88739e48f6b44b78d1c010f988f9385d077285300522164f533a5861e9dda879275 SHA512 3642389d27bd1942cd0f091c940ae97b197b94856a387fe581dc516b0d4169480f16551d4ba357f9282b3337d605c286d51dd38112ac87c826dda634904836bb
 DIST regressiontests-2019.2.tar.gz 67643003 BLAKE2B 4178de5d62f194a81f97e442c10f123dc59c5e63f2078f7f07135709f3f6e530e0d237bf40264b285c084519d5ace75dfcbcddc16dc740c4f17233dc33542e45 SHA512 c1f25bc770d3f0a873c887d5563c1cd88179e81211b70ce6f5015696e6fa0b6931a8da7a449f2b223f3105b9e2e7eca67248e96fbfc2a7fd5fb360ba616f22ff
 DIST regressiontests-2019.3.tar.gz 67640462 BLAKE2B ed6c176a144e0407be66585be5d6090c31c047498bc5f48f59685108de91f2f9ddb2d22b291a15e6ffa1db848aae19b94a79c8c3d34b1067680f759a179953dd SHA512 822e905fb488ce308eb9324d93f78106da5252c773c7941d49c6162e73bdff109aeca1f0d57216c6dd6536a4c41d80013fa1cee2f5206b0c4160a3e5b4a31315
 DIST regressiontests-2019.4.tar.gz 67639728 BLAKE2B aba912863669a4a6a6a74e385f9b0974d0c0aa30d3aea7834d77c8bb3f4f59effcbe10a480e74e7aa31fe32d64ba6628d67703ca1894839ce7ddfc8da93902dc SHA512 45de03d368da4e6e5c647f3fea61d64defe6d1cbc1c4219eeac2db27559e3cea7f15f9acb3e56ab934b44ca3ae4ce199b4e4969f704776bb9f0b23f1a34ff56d
+DIST regressiontests-2020-beta1.tar.gz 48263088 BLAKE2B 2c5cacb0ff7d5b31e639388bebc755355837242643ad6dc48b7722918328214c8271f894d956960743641eb9cd4ec9df0013ad8490b73f2006b75fc8ebefcb51 SHA512 fba198e5560c01e6239bcddaa8d574c79062684b3f94f71b06436d83da9b9efd865998cea3a1b9369938e8fec69383d3fd6278c22c7a1a72eb50cc282f4b42c2
 EBUILD gromacs-2018.7.ebuild 7852 BLAKE2B 3c9625b06e391e1a28e804ccc9eb196cfd6adc14144867947f7a98052709cc1c400887383d164bfb1d558cf77447ca28924598e2d9b3222d00ca9930d80a2a3e SHA512 63e58f86c5ba37f5e7b52db46f7c665e77686a7f4722807658f7552fbd1f2b5f4555b2a273f9a1a74ef27966462d89a9357ab57821d3e049ff8d4dc565c9f8c8
 EBUILD gromacs-2018.8.ebuild 8787 BLAKE2B 9edbb2ae0bd3f76af41cee9971b70fdc957f22bb61ec131abd3cf44a2da56c208b0b103f72754e17cccfa054d79c1e95a9477228b0c14f4476e58bd7656b641a SHA512 c4548c8436dadf1daaf7f4f41e3c957029a10f5eb7fd11c5c8f42046d2ba38c6baf9f47e69fb8e8eeef550e0463d76bf738d6f708ffce6b4cf556e29d725ed5a
 EBUILD gromacs-2018.9999.ebuild 8787 BLAKE2B 9edbb2ae0bd3f76af41cee9971b70fdc957f22bb61ec131abd3cf44a2da56c208b0b103f72754e17cccfa054d79c1e95a9477228b0c14f4476e58bd7656b641a SHA512 c4548c8436dadf1daaf7f4f41e3c957029a10f5eb7fd11c5c8f42046d2ba38c6baf9f47e69fb8e8eeef550e0463d76bf738d6f708ffce6b4cf556e29d725ed5a
@@ -15,5 +18,6 @@ EBUILD gromacs-2019.2.ebuild 9200 BLAKE2B d4c6bbca2dfc3d376d3c98893a273d405735a2
 EBUILD gromacs-2019.3.ebuild 9229 BLAKE2B 6c7f24dd45eb3d576d069b153f2af1b69eee620e7cbee9157daec43d52b32bdfc9944f9177126b8660df94191bba4191f21181862390751f955b7ba84784b26a SHA512 a32bebd21d3492b5ef30d9440e269b07c2e08010c0ae7eb83f03ebc8316efcd00c7a7b652a107fa1374673d715d3fd930848686396f128425eeeac78f19e2c22
 EBUILD gromacs-2019.4.ebuild 9234 BLAKE2B 076a2a9ff537342156ca94f138c738fbff5a0b8167b7cd34ebab388357acc2f08249675428d19b13abe4d8489aaf94afb69fb32bba1cf7658550a984319dcb30 SHA512 da0007f5e8162efd53b061a564908167f8388c4cf4288d56167e0ab313140d92641d51f1c7384d52a55998de8baf23eaf56a04d633cd20525fbc0e2c46ba4256
 EBUILD gromacs-2019.9999.ebuild 9234 BLAKE2B 076a2a9ff537342156ca94f138c738fbff5a0b8167b7cd34ebab388357acc2f08249675428d19b13abe4d8489aaf94afb69fb32bba1cf7658550a984319dcb30 SHA512 da0007f5e8162efd53b061a564908167f8388c4cf4288d56167e0ab313140d92641d51f1c7384d52a55998de8baf23eaf56a04d633cd20525fbc0e2c46ba4256
+EBUILD gromacs-2020_beta1.ebuild 9703 BLAKE2B 686a81e3267b0a17b43e19ff884221ee4692bfecc21fa3fdc295d6b2ad6156f51688aa5cbe0312e940fea1171ece11794623114ea364ad6dc8d92ff25cf43bd7 SHA512 e29cf02cb175b12d26bd099511b2b2f5692a931772b75a2685333fad16b1ad39422cca28295e3b003f289860c102d4b86df9996d808b396a22a1ac980311a6b3
 EBUILD gromacs-9999.ebuild 8122 BLAKE2B 657e68df7563277a327984be5e23597d80b99cb3eac54c1f07037063ca1b2b7838cb07e00d4c4d41ef65f9bee622c7bba4527dea3d2792bb20b3969b8f5ea546 SHA512 97f5850567b25ca0bd11fc57331770a8d93383299d50b216e2089cd89d23b6618aad8a532d81da9f0d5cf19fc4a315c9f648e5c1dbbc5351fecb1255a02922f6
-MISC metadata.xml 1123 BLAKE2B 5e945fdf580821b62aaf40c5b4b3252b366284f2df16f02e7c3cf913e5ad498a6a8548bc2e4275d8b80373f88d9879ab59d401e619595014262dcebfe8660f9f SHA512 bac0c94aee957487d8af8a1e06323cb286c8773cef2070d91aff9fdad63eb1bd55f2678dd58dca21b33d8d3e7110d2526e280abd538e3653aee638f6de72090d
+MISC metadata.xml 1192 BLAKE2B 560c1c792102747fc16c22d475114480b9897263405da05946721dae5b781c599a02e1401adfa4d929bfb41b4d52791376438aa37d33de18beabc9edbeb779fa SHA512 136c49bfaca76e714e811077c7f7d214a5984c7b6c891c79ad4a754c304752e17450c9aee100dafce04d7bf3893a53224ef9b54504a278654d59fae9acdd0f77
diff --git a/sci-chemistry/gromacs/files/gromacs-2020_beta1-pytest.patch b/sci-chemistry/gromacs/files/gromacs-2020_beta1-pytest.patch
new file mode 100644
index 000000000000..452987f38b96
--- /dev/null
+++ b/sci-chemistry/gromacs/files/gromacs-2020_beta1-pytest.patch
@@ -0,0 +1,12 @@
+diff -urN gromacs-2020-beta1/python_packaging/src/CMakeLists.txt gromacs-2020-beta1-py/python_packaging/src/CMakeLists.txt
+--- gromacs-2020-beta1/python_packaging/src/CMakeLists.txt	2019-09-12 05:48:57.000000000 +0300
++++ gromacs-2020-beta1-py/python_packaging/src/CMakeLists.txt	2019-10-09 17:01:30.845304765 +0300
+@@ -201,5 +201,7 @@
+ # to the `check` target. Normal usage is to first install the Python package,
+ # then run `pytest` on the `tests` directory. Refer to gmxapi package documentation.
+ if(NOT GMXAPI_MASTER_PROJECT)
+-    add_subdirectory(test)
++	if (GMX_BUILD_TESTING)
++		add_subdirectory(test)
++	endif()
+ endif()
diff --git a/sci-chemistry/gromacs/gromacs-2020_beta1.ebuild b/sci-chemistry/gromacs/gromacs-2020_beta1.ebuild
new file mode 100644
index 000000000000..a47062613711
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-2020_beta1.ebuild
@@ -0,0 +1,337 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+CMAKE_MAKEFILE_GENERATOR="ninja"
+
+PYTHON_COMPAT=( python3_{5,6,7} )
+
+inherit bash-completion-r1 cmake-utils cuda distutils-r1 eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
+
+if [[ $PV = *9999* ]]; then
+	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
+		https://gerrit.gromacs.org/gromacs.git
+		https://github.com/gromacs/gromacs.git
+		https://repo.or.cz/r/gromacs.git"
+	[[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}"
+	inherit git-r3
+else
+	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
+		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"
+	KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+fi
+
+ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
+
+DESCRIPTION="The ultimate molecular dynamics simulation package"
+HOMEPAGE="http://www.gromacs.org/"
+
+# see COPYING for details
+# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
+#        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
+LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
+SLOT="0/${PV}"
+IUSE="X blas cuda +doc -double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
+
+CDEPEND="
+	X? (
+		x11-libs/libX11
+		x11-libs/libSM
+		x11-libs/libICE
+		)
+	blas? ( virtual/blas )
+	cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 )
+	opencl? ( virtual/opencl )
+	fftw? ( sci-libs/fftw:3.0 )
+	hwloc? ( sys-apps/hwloc )
+	lapack? ( virtual/lapack )
+	lmfit? ( sci-libs/lmfit )
+	mkl? ( sci-libs/mkl )
+	mpi? ( virtual/mpi )
+	${PYTHON_DEPS}
+	"
+BDEPEND="${CDEPEND}
+	virtual/pkgconfig
+	doc? (
+		app-doc/doxygen
+		dev-python/sphinx[${PYTHON_USEDEP}]
+		media-gfx/mscgen
+		media-gfx/graphviz
+		dev-texlive/texlive-latex
+		dev-texlive/texlive-latexextra
+		media-gfx/imagemagick
+	)"
+RDEPEND="${CDEPEND}"
+
+REQUIRED_USE="
+	|| ( single-precision double-precision )
+	cuda? ( single-precision )
+	cuda? ( !opencl )
+	mkl? ( !blas !fftw !lapack )
+	${PYTHON_REQUIRED_USE}"
+
+DOCS=( AUTHORS README )
+
+RESTRICT="!test? ( test )"
+
+if [[ ${PV} != *9999 ]]; then
+	S="${WORKDIR}/${PN}-${PV/_/-}"
+fi
+
+PATCHES=( "${FILESDIR}/${P}-pytest.patch" )
+
+pkg_pretend() {
+	[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
+	use openmp && ! tc-has-openmp && \
+		die "Please switch to an openmp compatible compiler"
+}
+
+src_unpack() {
+	if [[ ${PV} != *9999 ]]; then
+		default
+	else
+		git-r3_src_unpack
+		if use test; then
+			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
+			EGIT_BRANCH="${EGIT_BRANCH}" \
+			EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
+				git-r3_src_unpack
+		fi
+	fi
+}
+
+src_prepare() {
+	#notes/todos
+	# -on apple: there is framework support
+
+	xdg_environment_reset #591952
+
+	cmake-utils_src_prepare
+
+	use cuda && cuda_src_prepare
+
+	GMX_DIRS=""
+	use single-precision && GMX_DIRS+=" float"
+	use double-precision && GMX_DIRS+=" double"
+
+	if use test; then
+		for x in ${GMX_DIRS}; do
+			mkdir -p "${WORKDIR}/${P}_${x}" || die
+			cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
+		done
+	fi
+
+	DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
+
+	# try to create policy for imagemagik
+	mkdir -p ${HOME}/.config/ImageMagick
+	cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF
+	<?xml version="1.0" encoding="UTF-8"?>
+	<!DOCTYPE policymap [
+	<!ELEMENT policymap (policy)+>
+	!ATTLIST policymap xmlns CDATA #FIXED ''>
+	<!ELEMENT policy EMPTY>
+	<!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED
+			name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED
+			stealth NMTOKEN #IMPLIED value CDATA #IMPLIED>
+	]>
+	<policymap>
+		<policy domain="coder" rights="read | write" pattern="PS" />
+		<policy domain="coder" rights="read | write" pattern="PS2" />
+		<policy domain="coder" rights="read | write" pattern="PS3" />
+		<policy domain="coder" rights="read | write" pattern="EPS" />
+		<policy domain="coder" rights="read | write" pattern="PDF" />
+		<policy domain="coder" rights="read | write" pattern="XPS" />
+	</policymap>
+	EOF
+}
+
+src_configure() {
+	local mycmakeargs_pre=( ) extra fft_opts=( )
+
+	#go from slowest to fastest acceleration
+	local acce="None"
+	use cpu_flags_x86_sse2 && acce="SSE2"
+	use cpu_flags_x86_sse4_1 && acce="SSE4.1"
+	use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
+	use cpu_flags_x86_avx && acce="AVX_256"
+	use cpu_flags_x86_avx2 && acce="AVX2_256"
+
+	#to create man pages, build tree binaries are executed (bug #398437)
+	[[ ${CHOST} = *-darwin* ]] && \
+		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
+
+	if use fftw; then
+		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
+	elif use mkl && has_version "=sci-libs/mkl-10*"; then
+		fft_opts=( -DGMX_FFT_LIBRARY=mkl
+			-DMKL_INCLUDE_DIR="${MKLROOT}/include"
+			-DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
+		)
+	elif use mkl; then
+		local bits=$(get_libdir)
+		fft_opts=( -DGMX_FFT_LIBRARY=mkl
+			-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
+			-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
+		)
+	else
+		fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
+	fi
+
+	if use lmfit; then
+		local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL )
+	else
+		local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL )
+	fi
+
+	mycmakeargs_pre+=(
+		"${fft_opts[@]}"
+		"${lmfit_opts[@]}"
+		-DGMX_X11=$(usex X)
+		-DGMX_EXTERNAL_BLAS=$(usex blas)
+		-DGMX_EXTERNAL_LAPACK=$(usex lapack)
+		-DGMX_OPENMP=$(usex openmp)
+		-DGMX_COOL_QUOTES=$(usex offensive)
+		-DGMX_USE_TNG=$(usex tng)
+		-DGMX_BUILD_MANUAL=$(usex doc)
+		-DGMX_HWLOC=$(usex hwloc)
+		-DGMX_DEFAULT_SUFFIX=off
+		-DGMX_SIMD="$acce"
+		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
+		-DBUILD_TESTING=$(usex test)
+		-DGMX_BUILD_UNITTESTS=$(usex test)
+		-DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}"
+		${extra}
+	)
+
+	for x in ${GMX_DIRS}; do
+		einfo "Configuring for ${x} precision"
+		local suffix=""
+		#if we build single and double - double is suffixed
+		use double-precision && use single-precision && \
+			[[ ${x} = "double" ]] && suffix="_d"
+		local p
+		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
+		local cuda=( "-DGMX_GPU=OFF" )
+		[[ ${x} = "float" ]] && use cuda && \
+			cuda=( "-DGMX_GPU=ON" )
+		local opencl=( "-DGMX_USE_OPENCL=OFF" )
+		use opencl && opencl=( "-DGMX_USE_OPENCL=ON" ) cuda=( "-DGMX_GPU=ON" )
+		mycmakeargs=(
+			${mycmakeargs_pre[@]} ${p}
+			-DGMX_MPI=OFF
+			-DGMX_THREAD_MPI=$(usex threads)
+			-DGMXAPI=$(usex gmxapi)
+			-DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy)
+			"${opencl[@]}"
+			"${cuda[@]}"
+			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
+			-DGMX_BINARY_SUFFIX="${suffix}"
+			-DGMX_LIBS_SUFFIX="${suffix}"
+			)
+		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
+		[[ ${CHOST} != *-darwin* ]] || \
+		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
+		use mpi || continue
+		einfo "Configuring for ${x} precision with mpi"
+		mycmakeargs=(
+			${mycmakeargs_pre[@]} ${p}
+			-DGMX_THREAD_MPI=OFF
+			-DGMX_MPI=ON
+			-DGMX_OPENMM=OFF
+			-DGMXAPI=OFF
+			"${opencl[@]}"
+			"${cuda[@]}"
+			-DGMX_BUILD_MDRUN_ONLY=ON
+			-DBUILD_SHARED_LIBS=OFF
+			-DGMX_BUILD_MANUAL=OFF
+			-DGMX_BINARY_SUFFIX="_mpi${suffix}"
+			-DGMX_LIBS_SUFFIX="_mpi${suffix}"
+			)
+		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
+		[[ ${CHOST} != *-darwin* ]] || \
+		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
+	done
+	if use python; then
+		cd python_packaging
+		distutils-r1_src_configure
+		cd ..
+	fi
+}
+
+src_compile() {
+	for x in ${GMX_DIRS}; do
+		einfo "Compiling for ${x} precision"
+		BUILD_DIR="${WORKDIR}/${P}_${x}"\
+			cmake-utils_src_compile
+		# not 100% necessary for rel ebuilds as available from website
+		if use doc; then
+			BUILD_DIR="${WORKDIR}/${P}_${x}"\
+				cmake-utils_src_compile manual
+		fi
+		use mpi || continue
+		einfo "Compiling for ${x} precision with mpi"
+		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
+			cmake-utils_src_compile
+	done
+	if use python; then
+		cd python_packaging
+		distutils-r1_src_compile
+		cd ..
+	fi
+}
+
+src_test() {
+	for x in ${GMX_DIRS}; do
+		BUILD_DIR="${WORKDIR}/${P}_${x}"\
+			cmake-utils_src_make check
+	done
+	if use python; then
+		cd python_packaging
+		distutils-r1_src_test
+		cd ..
+	fi
+}
+
+src_install() {
+	for x in ${GMX_DIRS}; do
+		BUILD_DIR="${WORKDIR}/${P}_${x}" \
+			cmake-utils_src_install ${GMX_PYTHON_INSTALL}
+		if use doc; then
+			newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
+		fi
+		use mpi || continue
+		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
+			cmake-utils_src_install
+	done
+
+	if use tng; then
+		insinto /usr/include/tng
+		doins src/external/tng_io/include/tng/*h
+	fi
+	if use python; then
+		cd python_packaging
+		distutils-r1_src_install
+		cd ..
+	fi
+	# drop unneeded stuff
+	rm "${ED}"/usr/bin/GMXRC* || die
+	for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do
+		local n=${x##*/gmx-completion-}
+		n="${n%.bash}"
+		cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die
+		newbashcomp "${T}"/"${n}" "${n}"
+	done
+	rm "${ED}"/usr/bin/gmx-completion*.bash || die
+	readme.gentoo_create_doc
+}
+
+pkg_postinst() {
+	einfo
+	einfo  "Please read and cite:"
+	einfo  "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
+	einfo  "https://dx.doi.org/10.1021/ct700301q"
+	einfo
+	readme.gentoo_print_elog
+}
diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index 7c756657ae42..c31594084c8f 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -13,6 +13,7 @@
 		<flag name="cuda">Enable cuda non-bonded kernels</flag>
 		<flag name="double-precision">More precise calculations at the expense of speed</flag>
 		<flag name="gmxapi">Add support for gmxapi library</flag>
+		<flag name="gmxapi-legacy">Enable installing lagacy headers</flag>
 		<flag name="hwloc">Enable HWLoc lib support</flag>
 		<flag name="lmfit">Use external <pkg>sci-libs/lmfit</pkg></flag>
 		<flag name="opencl">Enable opencl non-bonded kernels</flag>
diff --git a/sci-chemistry/xdsstat-bin/Manifest b/sci-chemistry/xdsstat-bin/Manifest
deleted file mode 100644
index 9c3447b89a16..000000000000
--- a/sci-chemistry/xdsstat-bin/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-DIST xdsstat-linux32.bz2 505522 BLAKE2B 5956483b3b73513398e7dcef4b7b0f358477453132e5ab55cd119c757e54ab5883f03273ac199e87c2c5b75e0623c00ddc0127d3a892d9d8935d9dfaa2111925 SHA512 2488ea0bb136d46f70648eca20012ba2f687ac2a81dad44a7f97a00762aac19ffbcdfe78ac42d4b3d2ab4ced9b9627b73b185f17126ef2311e1939788f4561be
-DIST xdsstat-linux64.bz2 172909 BLAKE2B 0cccf4ca4ea7c69daa6051d068d4387fbe361f2831d4fb3e811ca11b5c2506467ca902a35f9441679de0ae78f850a5ae53b03d0b659a44bbfeca43051280ed56 SHA512 5a649cbe2937f13696e6a85cda46eef3b9e3e0ec38717b5ddf2bfacb69919e5e4476070413a7ac80d454390c58006f5b17adc52373f17182bc2bcb8bcac2a235
-EBUILD xdsstat-bin-171217.ebuild 700 BLAKE2B 898930d813b1b6810884b11f592d9daab9e8c480c1963571f8a1a1871a5e3709bd2cc26faa18de2a7a53f3fd3d6dbe87fbcc359d72449aab30c3569851863f28 SHA512 78469ce2a1c09bd165a688a0260d8bdc500dcdaabaa2785bdb620646b88d272b438dbf2d4db68b4230d603d52900c4db64f30619afa4be03dcf56a208fa78b48
-MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92
diff --git a/sci-chemistry/xdsstat-bin/metadata.xml b/sci-chemistry/xdsstat-bin/metadata.xml
deleted file mode 100644
index 8937bad0b175..000000000000
--- a/sci-chemistry/xdsstat-bin/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-chemistry@gentoo.org</email>
-    <name>Gentoo Chemistry Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/xdsstat-bin/xdsstat-bin-171217.ebuild b/sci-chemistry/xdsstat-bin/xdsstat-bin-171217.ebuild
deleted file mode 100644
index 0c144d9b28e2..000000000000
--- a/sci-chemistry/xdsstat-bin/xdsstat-bin-171217.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-MY_PN="${PN/-bin}"
-
-DESCRIPTION="Prints various statistics (that are not available from XDS itself)"
-HOMEPAGE="https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XDSSTAT"
-SRC_URI="
-	amd64? ( ftp://turn5.biologie.uni-konstanz.de/pub/${MY_PN}-linux64.bz2 )
-	x86? ( ftp://turn5.biologie.uni-konstanz.de/pub/${MY_PN}-linux32.bz2 )
-"
-
-LICENSE="all-rights-reserved"
-SLOT="0"
-KEYWORDS="~amd64 ~amd64-linux"
-IUSE=""
-
-RDEPEND="sci-chemistry/xds-bin"
-DEPEND=""
-
-RESTRICT="mirror"
-
-QA_PREBUILT="opt/bin/*"
-
-S="${WORKDIR}"
-
-src_install() {
-	exeinto /opt/bin
-	newexe ${MY_PN}* ${MY_PN}
-}