From f18f8ec9fae3bc6cea2e6ff1dccb156c19ed122c Mon Sep 17 00:00:00 2001 From: maho Date: Sat, 3 May 2003 03:45:31 +0000 Subject: Updated to 0.8.6. Submitted by: M. L. Dodson Pkg-plist by: maho --- biology/pymol/Makefile | 3 +- biology/pymol/distinfo | 2 +- biology/pymol/files/patch-Rules.make | 92 +++ biology/pymol/files/patch-aa | 91 --- biology/pymol/files/patch-ab | 18 - .../pymol/files/patch-setup+pymol+com+linux-rh7x | 18 + biology/pymol/pkg-plist | 629 +++++++++------------ 7 files changed, 387 insertions(+), 466 deletions(-) create mode 100644 biology/pymol/files/patch-Rules.make delete mode 100644 biology/pymol/files/patch-aa delete mode 100644 biology/pymol/files/patch-ab create mode 100644 biology/pymol/files/patch-setup+pymol+com+linux-rh7x (limited to 'biology') diff --git a/biology/pymol/Makefile b/biology/pymol/Makefile index 267c761a5647..6af4fd3c6fab 100644 --- a/biology/pymol/Makefile +++ b/biology/pymol/Makefile @@ -5,8 +5,7 @@ # $FreeBSD$ PORTNAME= pymol -PORTVERSION= 0.82 -PORTREVISION= 3 +PORTVERSION= 0.86 CATEGORIES= biology python MASTER_SITES= ${MASTER_SITE_SOURCEFORGE} MASTER_SITE_SUBDIR= pymol diff --git a/biology/pymol/distinfo b/biology/pymol/distinfo index fd4363004806..eb546ea16d68 100644 --- a/biology/pymol/distinfo +++ b/biology/pymol/distinfo @@ -1 +1 @@ -MD5 (pymol-0_82-src.tgz) = d01bf39dbaa3ada27809a0ba013a162a +MD5 (pymol-0_86-src.tgz) = 7610bb7689230eff2ec945236fdce0b8 diff --git a/biology/pymol/files/patch-Rules.make b/biology/pymol/files/patch-Rules.make new file mode 100644 index 000000000000..ead488b0a7d9 --- /dev/null +++ b/biology/pymol/files/patch-Rules.make @@ -0,0 +1,92 @@ +--- Rules.make.orig Wed Apr 30 11:42:37 2003 ++++ Rules.make Wed Apr 30 11:52:50 2003 +@@ -4,42 +4,42 @@ + # + #- Building ---------------------------------------------------------- + #--- Tell "make" how to get to PyMOL +-PYMOL_PATH = /users/warren/pymol ++PYMOL_PATH = ${PREFIX} + #--------------------------------------------------------------------- + # + #- Dependencies ------------------------------------------------------ + #--- X-windows +-XLIB_DIR = -L/usr/X11R6/lib +-XINC_DIR = -I/usr/X11R6/include ++XLIB_DIR = -L${X11BASE}/lib ++XINC_DIR = -I${X11BASE}/include + #--- Python +-PYTHON_EXE = $(PYMOL_PATH)/ext/bin/python ++PYTHON_EXE = $(PYMOL_PATH)/bin/python + PYTHON_LIB = + PYTHON_LIB_DIR = +-PYTHON_INC_DIR = -I$(PYMOL_PATH)/ext/include/python2.1 \ +- -I$(PYMOL_PATH)/ext/include/python2.1/Numeric ++PYTHON_INC_DIR = -I$(PYMOL_PATH)/include/@PYTHON_VERSION@ \ ++ -I$(PYMOL_PATH)/include/@PYTHON_VERSION@/Numeric + #--- Other external dependencies +-EXT_INC_DIR = -I$(PYMOL_PATH)/ext/include +-EXT_LIB_DIR = -L$(PYMOL_PATH)/ext/lib ++EXT_INC_DIR = -I$(PYMOL_PATH)/include -I. ++EXT_LIB_DIR = -L$(PYMOL_PATH)/lib + #--------------------------------------------------------------------- + # +-#- Build for LINUX as an importable module --------------------------- ++#- Build for FreeBSD as an importable module --------------------------- + #--- System libraries +-LIBS = $(PYTHON_LIB) -lglut -lGL -lGLU -ldl -lpng -lXmu $(ZLIB) -lm ++LIBS = $(PYTHON_LIB) -lglut -lGL -lGLU -lpng -lXmu $(ZLIB) -lm + #--- PyMOL configuration + DEFS = -D_PYMOL_MODULE -D_PYMOL_NUMPY + #--- How we build shared libraries + BUILD = -shared + #--- What are we trying to build? +-DEST = -o modules/pymol/_cmd.so +-#--- Gcc Options for Linux +-CCOPT1 = -march=i486 -D__i686__ -ffast-math -Wall -ansi -Wmissing-prototypes ++DEST = -o modules/_cmd.so ++#--- Gcc Options for FreeBSD ++CCOPT1 = #-march=i486 -D__i686__ -ffast-math -Wall -ansi -Wmissing-prototypes + #--- libraries for PyOpenGL + PYOGL_LIB = -lglut -lGL -lGLU -lXmu -lXi + #--------------------------------------------------------------------- + # + #- Choose One -------------------------------------------------------- + #--- GCC Optimized +-CCOPT2 = -O3 -funroll-loops -fomit-frame-pointer ++CCOPT2 = #-O3 -funroll-loops -fomit-frame-pointer + #--- GCC Profiling + #CCOPT2 = -pg -O3 -funroll-loops + #--- Debugging +@@ -47,7 +47,7 @@ + #--------------------------------------------------------------------- + # + #- Choose One -------------------------------------------------------- +-#--- Workaround for XFree86/DRI linux dll problem for module build ++#--- Workaround for XFree86/DRI FreeBSD dll problem for module build + BUGS = -D_DRI_WORKAROUND + #--- + #BUGS = +@@ -69,18 +69,19 @@ + # No changes normally required below here + #--------------------------------------------------------------------- + +-CC = cc ++override CC := ${CC} + + LIB_DIRS = $(EXT_LIB_DIR) $(PYTHON_LIB_DIR) $(XLIB_DIR) + + # Enable source files to find headers + PYMOL_INC_DIRS = -I../layer0 -I../layer1 -I../layer2 \ +- -I../layer3 -I../layer4 -I../layer5 ++ -I../layer3 -I../layer4 -I../layer5 -I../modules/ + + C_FLAGS = $(CCOPT1) $(CCOPT2) $(EXT_INC_DIR) $(PYTHON_INC_DIR) \ +- $(XINC_DIR) $(PNG) $(DEFS) $(BUGS) ++ $(XINC_DIR) $(PNG) $(DEFS) $(BUGS) $(PYMOL_INC_DIRS) ++ ++override CFLAGS := $(C_FLAGS) ${CFLAGS} + +-CFLAGS = $(C_FLAGS) + + + diff --git a/biology/pymol/files/patch-aa b/biology/pymol/files/patch-aa deleted file mode 100644 index cd49db0abc36..000000000000 --- a/biology/pymol/files/patch-aa +++ /dev/null @@ -1,91 +0,0 @@ ---- Rules.make.orig Thu Jul 11 08:11:51 2002 -+++ Rules.make Thu Jul 11 08:23:03 2002 -@@ -4,42 +4,42 @@ - # - #- Building ---------------------------------------------------------- - #--- Tell "make" how to get to PyMOL --PYMOL_PATH = /users/warren/pymol -+PYMOL_PATH = ${PREFIX} - #--------------------------------------------------------------------- - # - #- Dependencies ------------------------------------------------------ - #--- X-windows --XLIB_DIR = -L/usr/X11R6/lib --XINC_DIR = -I/usr/X11R6/include -+XLIB_DIR = -L${X11BASE}/lib -+XINC_DIR = -I${X11BASE}/include - #--- Python --PYTHON_EXE = $(PYMOL_PATH)/ext/bin/python -+PYTHON_EXE = $(PYMOL_PATH)/bin/python - PYTHON_LIB = - PYTHON_LIB_DIR = --PYTHON_INC_DIR = -I$(PYMOL_PATH)/ext/include/python2.1 \ -- -I$(PYMOL_PATH)/ext/include/python2.1/Numeric -+PYTHON_INC_DIR = -I$(PYMOL_PATH)/include/@PYTHON_VERSION@ \ -+ -I$(PYMOL_PATH)/include/@PYTHON_VERSION@/Numeric - #--- Other external dependencies --EXT_INC_DIR = -I$(PYMOL_PATH)/ext/include --EXT_LIB_DIR = -L$(PYMOL_PATH)/ext/lib -+EXT_INC_DIR = -I$(PYMOL_PATH)/include -I. -+EXT_LIB_DIR = -L$(PYMOL_PATH)/lib - #--------------------------------------------------------------------- - # --#- Build for LINUX as an importable module --------------------------- -+#- Build for FreeBSD as an importable module --------------------------- - #--- System libraries --LIBS = $(PYTHON_LIB) -lglut -lGL -lGLU -ldl -lpng -lXmu $(ZLIB) -lm -+LIBS = $(PYTHON_LIB) -lglut -lGL -lGLU -lpng -lXmu $(ZLIB) -lm - #--- PyMOL configuration - DEFS = -D_PYMOL_MODULE -D_PYMOL_NUMPY - #--- How we build shared libraries - BUILD = -shared - #--- What are we trying to build? - DEST = -o modules/_cmd.so --#--- Gcc Options for Linux --CCOPT1 = -m486 -D__i686__ -ffast-math -Wall -ansi -Wmissing-prototypes -+#--- Gcc Options for FreeBSD -+CCOPT1 = #-m486 -D__i686__ -ffast-math -Wall -ansi -Wmissing-prototypes - #--- libraries for PyOpenGL - PYOGL_LIB = -lglut -lGL -lGLU -lXmu -lXi - #--------------------------------------------------------------------- - # - #- Choose One -------------------------------------------------------- - #--- GCC Optimized --CCOPT2 = -O3 -funroll-loops -fomit-frame-pointer -+CCOPT2 = #-O3 -funroll-loops -fomit-frame-pointer - #--- GCC Profiling - #CCOPT2 = -pg -O3 -funroll-loops - #--- Debugging -@@ -47,7 +47,7 @@ - #--------------------------------------------------------------------- - # - #- Choose One -------------------------------------------------------- --#--- Workaround for XFree86/DRI linux dll problem for module build -+#--- Workaround for XFree86/DRI FreeBSD dll problem for module build - BUGS = -D_DRI_WORKAROUND - #--- - #BUGS = -@@ -69,18 +69,19 @@ - # No changes normally required below here - #--------------------------------------------------------------------- - --CC = cc -+override CC := ${CC} - - LIB_DIRS = $(EXT_LIB_DIR) $(PYTHON_LIB_DIR) $(XLIB_DIR) - - # Enable source files to find headers - PYMOL_INC_DIRS = -I../layer0 -I../layer1 -I../layer2 \ -- -I../layer3 -I../layer4 -I../layer5 -+ -I../layer3 -I../layer4 -I../layer5 -I../modules/ - - C_FLAGS = $(CCOPT1) $(CCOPT2) $(EXT_INC_DIR) $(PYTHON_INC_DIR) \ -- $(XINC_DIR) $(PNG) $(DEFS) $(BUGS) -+ $(XINC_DIR) $(PNG) $(DEFS) $(BUGS) $(PYMOL_INC_DIRS) -+ -+override CFLAGS := $(C_FLAGS) ${CFLAGS} - --CFLAGS = $(C_FLAGS) - - - diff --git a/biology/pymol/files/patch-ab b/biology/pymol/files/patch-ab deleted file mode 100644 index 07ae40a91fc9..000000000000 --- a/biology/pymol/files/patch-ab +++ /dev/null @@ -1,18 +0,0 @@ ---- setup/pymol.com.linux-rh7x.orig Thu Jul 11 08:33:42 2002 -+++ setup/pymol.com.linux-rh7x Thu Jul 11 08:34:37 2002 -@@ -5,7 +5,7 @@ - # ============================================================== - # Set PYMOL_PATH to point at the correct location on your system - # --setenv PYMOL_PATH /usr/local/pymol -+setenv PYMOL_PATH @PREFIX@/share/pymol - # - # ============================================================== - # (no changes usually required below here) -@@ -21,5 +21,5 @@ - # - #dbx /usr/bin/python - #gdb /usr/bin/python --/usr/bin/python $PYMOL_PATH/modules/launch_pymol.py $* -+@PREFIX@/bin/python $PYMOL_PATH/modules/launch_pymol.py $* - diff --git a/biology/pymol/files/patch-setup+pymol+com+linux-rh7x b/biology/pymol/files/patch-setup+pymol+com+linux-rh7x new file mode 100644 index 000000000000..07ae40a91fc9 --- /dev/null +++ b/biology/pymol/files/patch-setup+pymol+com+linux-rh7x @@ -0,0 +1,18 @@ +--- setup/pymol.com.linux-rh7x.orig Thu Jul 11 08:33:42 2002 ++++ setup/pymol.com.linux-rh7x Thu Jul 11 08:34:37 2002 +@@ -5,7 +5,7 @@ + # ============================================================== + # Set PYMOL_PATH to point at the correct location on your system + # +-setenv PYMOL_PATH /usr/local/pymol ++setenv PYMOL_PATH @PREFIX@/share/pymol + # + # ============================================================== + # (no changes usually required below here) +@@ -21,5 +21,5 @@ + # + #dbx /usr/bin/python + #gdb /usr/bin/python +-/usr/bin/python $PYMOL_PATH/modules/launch_pymol.py $* ++@PREFIX@/bin/python $PYMOL_PATH/modules/launch_pymol.py $* + diff --git a/biology/pymol/pkg-plist b/biology/pymol/pkg-plist index 56e793c8072e..843bbcdc555a 100644 --- a/biology/pymol/pkg-plist +++ b/biology/pymol/pkg-plist @@ -14,481 +14,395 @@ bin/pymol %%PORTDOCS%%share/examples/pymol/devel/cgo03.py %%PORTDOCS%%share/examples/pymol/devel/cgo_3Dtext01.py %%PORTDOCS%%share/examples/pymol/devel/cgo_label_hack.py +%%PORTDOCS%%share/examples/pymol/devel/chempy_model01.py +%%PORTDOCS%%share/examples/pymol/devel/chempy_model02.py +%%PORTDOCS%%share/examples/pymol/devel/chempy_model03.py %%PORTDOCS%%share/examples/pymol/devel/gl01.py %%PORTDOCS%%share/examples/pymol/devel/gl02.py %%PORTDOCS%%share/examples/pymol/devel/gl03.py %%PORTDOCS%%share/examples/pymol/devel/povray01.py +%%PORTDOCS%%share/examples/pymol/devel/sele_wiz.py %%PORTDOCS%%share/examples/pymol/devel/start_pymol.py -share/pymol/modules/ExtensionClass.so -share/pymol/modules/_cmd.so -share/pymol/modules/_glu_nummodule.so -share/pymol/modules/_glumodule.so -share/pymol/modules/_glutmodule.so -share/pymol/modules/_opengl_nummodule.so -share/pymol/modules/_openglmodule.so -share/pymol/modules/chempy/__init__.py -share/pymol/modules/chempy/__init__.pyc -share/pymol/modules/chempy/__init__.pyo -share/pymol/modules/chempy/arc.py -share/pymol/modules/chempy/arc.pyc -share/pymol/modules/chempy/arc.pyo +%%PORTDOCS%%share/examples/pymol/devel/xmlrpc01.py share/pymol/modules/chempy/bmin/__init__.py -share/pymol/modules/chempy/bmin/__init__.pyc -share/pymol/modules/chempy/bmin/__init__.pyo share/pymol/modules/chempy/bmin/commands.py -share/pymol/modules/chempy/bmin/commands.pyc -share/pymol/modules/chempy/bmin/commands.pyo share/pymol/modules/chempy/bmin/realtime.py -share/pymol/modules/chempy/bmin/realtime.pyc -share/pymol/modules/chempy/bmin/realtime.pyo share/pymol/modules/chempy/bmin/state.py -share/pymol/modules/chempy/bmin/state.pyc -share/pymol/modules/chempy/bmin/state.pyo share/pymol/modules/chempy/bmin/util.py +share/pymol/modules/chempy/bmin/__init__.pyc +share/pymol/modules/chempy/bmin/commands.pyc +share/pymol/modules/chempy/bmin/realtime.pyc +share/pymol/modules/chempy/bmin/state.pyc share/pymol/modules/chempy/bmin/util.pyc +share/pymol/modules/chempy/bmin/__init__.pyo +share/pymol/modules/chempy/bmin/commands.pyo +share/pymol/modules/chempy/bmin/realtime.pyo +share/pymol/modules/chempy/bmin/state.pyo share/pymol/modules/chempy/bmin/util.pyo +share/pymol/modules/chempy/fast/__init__.py +share/pymol/modules/chempy/fast/__init__.pyc +share/pymol/modules/chempy/fast/__init__.pyo +share/pymol/modules/chempy/__init__.py +share/pymol/modules/chempy/arc.py share/pymol/modules/chempy/bond_amber.py 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+share/pymol/test/ref/L0030isomesh.log +share/pymol/test/ref/L0040isomesh2.log +share/pymol/test/ref/L0100isomisc.log share/pymol/test/ref/U01.log -share/pymol/test/run -share/pymol/test/show -share/pymol/test/trim.py -share/pymol/test/vdiff -share/pymol/test/win.py @dirrm share/pymol/test/ref @dirrm share/pymol/test/inp @dirrm share/pymol/test/dat @@ -555,13 +476,13 @@ share/pymol/test/win.py @dirrm share/pymol/modules/pymol/opengl/glu @dirrm share/pymol/modules/pymol/opengl/gl @dirrm share/pymol/modules/pymol/opengl -@dirrm share/pymol/modules/pymol/matrices +@dirrm share/pymol/modules/pymol/embed/wxpymol +@dirrm share/pymol/modules/pymol/embed @dirrm share/pymol/modules/pymol @dirrm share/pymol/modules/pmg_wx @dirrm share/pymol/modules/pmg_tk/startup @dirrm share/pymol/modules/pmg_tk @dirrm share/pymol/modules/chempy/tinker -@dirrm share/pymol/modules/chempy/sidechains @dirrm share/pymol/modules/chempy/fragments @dirrm share/pymol/modules/chempy/fast @dirrm share/pymol/modules/chempy/champ -- cgit