reinit the tree, so we can have metadata

7 files changed, 859 insertions, 0 deletions

diff --git a/sci-chemistry/azara/Manifest b/sci-chemistry/azara/Manifest
new file mode 100644
index 000000000000..d356c0818ea0
--- /dev/null
+++ b/sci-chemistry/azara/Manifest
@@ -0,0 +1,9 @@
+AUX 2.8-64bit.patch 2919 SHA256 857d4200ab3f59c535e620a577788995dec5aa889cdf73582d6bee374a9df50d SHA512 f2c42875f7c4aaa2110376fae252e53feb19e82c003ce44f9ba4df0c6bff1e0bcf0d55c91faf3480831c7a8c0b868ea29cb59b209aa4d747513b8d20db2a3b7f WHIRLPOOL 50c819365068948d2699bc0cc42e4f46d68a14b8fa977caaee90574fb61079cc82fbeeec3075db0bd17fe83d5697310e6a121b7781c3a45fe191ad6d79d6a6b3
+AUX 2.8-impl-dec.patch 5172 SHA256 a99cd51a1cdbc010760bb35ffc5f74c0f70ce10c874e4392f0e1dffc5559b410 SHA512 31dd75bb75427a37691cdacd2caee10ec5ee540daef52131eaf7102ec13f06101649a6bfbe6ee47503ef02986816a3c957b19cdb1308ea7c90ce1c22a02b6d05 WHIRLPOOL 8bec275ab95472d84dcbb91ebcb4972dc32bce633639c2e679a44c3ce04b03d007472b9a4dea2f419695b0e0b623c9a60ba39e614bce148a152830f8b291a32a
+AUX 2.8-prll.patch 8764 SHA256 79a8efb86f1a8162c943a02dae2ba49688648dac07525aec3516fe619e4937ba SHA512 4868cae8d7fe425136728ca751d59a0d8bb2a7906946a004cee1d017ab60f27075199953122bc81873ca4ba4cf462fcef1dfc0b93d748da966548a3d9f61cd7d WHIRLPOOL 7d43e3ddc42283bca89678a15c1d92ba7860e6ce7e2e53dde8cfd7c446e49cfcb52703ec095f27056656f8298663665ba8eceee319d77b6ca986e912fd828491
+AUX 2.8-python.patch 962 SHA256 74c04c60763f3dc0286fea59f8fe96aa5d83258fab6f9447f91b8ebf4eaac16e SHA512 d3c1aa38a1b783dba82ec571fd8d9bb7d4981f2957e728b91ca42562c453075e351a5805862f11e3d13e2036297c14f58c8f0bc97f128055870b2d47ce89a631 WHIRLPOOL 068ea87c512b6f4f20ac7a121a1041a1b590d288b983cbc5052d5ee45e09fb069d1dfac77f586333b17c305fb8ffcbe4a33812b7e8f6e55f5b0da69d8063d192
+DIST azara-2.8-src.tgz 638120 SHA256 1f9b86d368ca3b4818c88490c40b2055c7a6d1732e746e4c117e045a73269a98 SHA512 61a913b041f8ed7dade9d452ca0d99804ffcea0c678f23ad8357c1e7188996eecde9402201399306fcb32a504b17c3d61997f50ce57794f876c9f8d492ca500c WHIRLPOOL b7512fe29ad97830d2f96811e71c2ab74e9e71c62354f65a499484a1a57fbe8b74a8ecd27a0b72c48cf0ec5bb48c78148433e32f4f2a880c6317d516f3aa644a
+EBUILD azara-2.8-r5.ebuild 2108 SHA256 7e24fa7bc15524e7bbdec6aebcafe7271ec1f80138ee35cdb638704590b4f1f9 SHA512 a21a0dda6ce17bf0ee3bf1aee2397ce5a27d65a57b4e5044f13686eec4f1ad49e2758997605717b6e19a88f130f4dbb669819661a7de4491704739dc73b6e394 WHIRLPOOL 170fd4d77c9cd0177054660d047693caf5157d63d75dae3b283bd6107eebac1a1354f5fa4249594bee4aabb4c6ae91da60ee248883772c376ec8448536164f8c
+MISC ChangeLog 2719 SHA256 e9269136b67afae7de81f0118f5b89082907db373ccd5bff567c7a27d4baeac3 SHA512 feb77309c136bc0fa444c2a619b9829268175e30dac87c09b2e877bbdad26967813a10e254f886600a8d3cd428370cee6ac7ab60d161b5a0a0569bf3ae641197 WHIRLPOOL efcede0d019666f11808d3cc8171b4ab04c012ec9b44902f6f192b53b187b40b922f3eea29bc25ef5a3e8032117d888f572be6db0bd3bb77b51127f6b7b38e19
+MISC ChangeLog-2015 2827 SHA256 51f112fe10250db9ae0b72aa949a06fda8b3f69caa3d23eb851da28cd117bf73 SHA512 e837eb936918a9e611af6c09448082f12628377b008a73f5842c96fab14eeb2829d322f5f88edc88ff1f68aa7c620a761f2031e717c1964830862c2af8751675 WHIRLPOOL f853a7c94e410a4241e58c52d3a0505fad4ebb544fdaf648c23422443ce77cd8121b2324159c4bf1ae1abd96df11b80d5cff9e924cab10d9a66e0bda1730cfcd
+MISC metadata.xml 271 SHA256 70036ea85140f86ed670bc2791c9de861c4b6164755ee36a2560d1c812ec13f6 SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 WHIRLPOOL 1ccb964819c99258af550a41c6712ba8ebdecbec1c821106de2f22c37b1c981cd4f324856a8014b08bd186bcd2a7fa45a7e772cc15705d1a39016b5229e77269
diff --git a/sci-chemistry/azara/azara-2.8-r5.ebuild b/sci-chemistry/azara/azara-2.8-r5.ebuild
new file mode 100644
index 000000000000..4403482cf77e
--- /dev/null
+++ b/sci-chemistry/azara/azara-2.8-r5.ebuild
@@ -0,0 +1,100 @@
+# Copyright 1999-2017 Gentoo Foundation
+# 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}"
+
+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
new file mode 100644
index 000000000000..c65e075c1d30
--- /dev/null
+++ b/sci-chemistry/azara/files/2.8-64bit.patch
@@ -0,0 +1,85 @@
+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
new file mode 100644
index 000000000000..62e8c7d6873b
--- /dev/null
+++ b/sci-chemistry/azara/files/2.8-impl-dec.patch
@@ -0,0 +1,226 @@
+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
new file mode 100644
index 000000000000..4720bb659445
--- /dev/null
+++ b/sci-chemistry/azara/files/2.8-prll.patch
@@ -0,0 +1,387 @@
+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
new file mode 100644
index 000000000000..9834c77a77dc
--- /dev/null
+++ b/sci-chemistry/azara/files/2.8-python.patch
@@ -0,0 +1,44 @@
+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
new file mode 100644
index 000000000000..8937bad0b175
--- /dev/null
+++ b/sci-chemistry/azara/metadata.xml
@@ -0,0 +1,8 @@
+<?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>