sci-chemistry/sparky: remove unused patches

Closes: https://github.com/gentoo/gentoo/pull/3730

diff --git a/sci-chemistry/sparky/files/3.115-fpic.patch b/sci-chemistry/sparky/files/3.115-fpic.patch
deleted file mode 100644 (file)
index 37725aa..0000000
--- a/sci-chemistry/sparky/files/3.115-fpic.patch
+++ /dev/null
@@ -1,42 +0,0 @@
-diff --git a/c++/Makefile b/c++/Makefile
-index 421ff77..7442ed3 100644
---- a/c++/Makefile
-+++ b/c++/Makefile
-@@ -158,7 +158,7 @@ winsystem-$(PLATFORM).o: winsystem-$(PLATFORM).cc
-       $(CXX) $(CXXFLAGS) $(TKFLAGS) -c $(SPARKY_SRC)/winsystem-$(PLATFORM).cc
- 
- python.o: python.cc
--      $(CXX) $(CXXFLAGS) $(PYFLAGS) $(TKFLAGS) -c $(SPARKY_SRC)/python.cc
-+      $(CXX) $(CXXFLAGS) -fPIC $(PYFLAGS) $(TKFLAGS) -c $(SPARKY_SRC)/python.cc
- 
- _tkinter.so: _tkinter.o
-       $(CXX) $(LDSHARED) $(LDFLAGS) -o $@ _tkinter.o $(TKLIBS)
-diff --git a/c++/Makefile b/c++/Makefile
-index 353122d..84b0c24 100644
---- a/c++/Makefile
-+++ b/c++/Makefile
-@@ -168,7 +168,7 @@ _tkinter.o: _tkinter.c
- 
- Makefile.dep: force
-       cd $(SPARKY_SRC) ; \
--      $(CXX) $(DEPEND) $(CXXFLAGS) $(TKFLAGS) $(PYFLAGS) \
-+      $(CXX) $(DEPEND) $(CXXFLAGS) -fPIC $(TKFLAGS) $(PYFLAGS) \
-               $(SPARKY_OBJS:.o=.cc) $(OTHER_OBJS:.o=.cc) > $@
- 
- TAGS: force
-diff --git a/c++/Makefile b/c++/Makefile
-index 84b0c24..933f347 100644
---- a/c++/Makefile
-+++ b/c++/Makefile
-@@ -30,9 +30,9 @@ TCL_LIBNAME  = tcl$(TCLTK_VERSION)
- PLATFORM      = unix
- 
- CXX           = g++
--CXXFLAGS      = 
-+CXXFLAGS      += -fPIC
- CC            = gcc
--CFLAGS                =
-+CFLAGS                += -fPIC
- PYFLAGS               = -I$(PYTHON_INC) -I$(PYTHON_LIB)/config
- TKFLAGS               = -I$(TK_PREFIX)/include
- TKLIBS                = -L$(TK_PREFIX)/lib -l$(TK_LIBNAME) -l$(TCL_LIBNAME) -lX11

diff --git a/sci-chemistry/sparky/files/3.115-wrapper.patch b/sci-chemistry/sparky/files/3.115-wrapper.patch
deleted file mode 100644 (file)
index 9498c0b..0000000
--- a/sci-chemistry/sparky/files/3.115-wrapper.patch
+++ /dev/null
@@ -1,41 +0,0 @@
-diff --git a/bin/sparky b/bin/sparky
-index 8b51212..270723a 100644
---- a/bin/sparky
-+++ b/bin/sparky
-@@ -4,18 +4,6 @@
- #
- 
- # -----------------------------------------------------------------------------
--# Figure out Sparky installation directory from $0.
--#
--set sparky_exe = "$0"
--while (-l "$sparky_exe")
--  set ls_sparky_exe = `ls -l "$sparky_exe"`
--  set sparky_exe = `echo "$ls_sparky_exe" | sed 's/.* -> //'`
--end
--set sparky_bin = `dirname "$sparky_exe"`
--set sparky_bin = `cd "$sparky_bin"; pwd`
--set sparky_inst = `dirname "$sparky_bin"`
--
--# -----------------------------------------------------------------------------
- # Sparky uses the SPARKY_INSTALL environment variable to find its
- # application resource file and print prolog file.
- #
-@@ -25,7 +13,7 @@ setenv SPARKY_INSTALL                "$sparky_inst"
- # If Python is available start Sparky as a Python extension.
- # Otherwise the standalone version of Sparky is started.
- #
--set PYTHON = "$SPARKY_INSTALL/python2.5/bin/python2.5"
-+set PYTHON = "@GENTOO_PORTAGE_EPREFIX@/usr/bin/python"
- if (! -e "$PYTHON") then
-   set PYTHON = python2.5
- endif
-@@ -79,7 +67,7 @@ if ($status == 0) then
-   # ---------------------------------------------------------------------------
-   # Add the Sparky package and Tkinter to the Python path
-   #
--  set SPARKY_PYTHONPATH = "$SPARKY_INSTALL/python:$SPARKY_INSTALL/python/lib-tk"
-+  set SPARKY_PYTHONPATH = "$SPARKY_INSTALL/python:$SPARKY_INSTALL/python/sparky"
-   if ($?PYTHONPATH) then
-     setenv PYTHONPATH "${SPARKY_PYTHONPATH}:$PYTHONPATH"
-   else

diff --git a/sci-chemistry/sparky/files/fix-install.patch b/sci-chemistry/sparky/files/fix-install.patch
deleted file mode 100644 (file)
index 4eefaa8..0000000
--- a/sci-chemistry/sparky/files/fix-install.patch
+++ /dev/null
@@ -1,259 +0,0 @@
-diff -ur -x make-sparky sparky.orig/bin/sparky sparky/bin/sparky
---- sparky.orig/bin/sparky     2004-03-05 11:32:10.000000000 -0800
-+++ sparky/bin/sparky  2005-12-17 17:36:51.000000000 -0800
-@@ -4,22 +4,10 @@
- #
- 
- # -----------------------------------------------------------------------------
--# Figure out Sparky installation directory from $0.
--#
--set sparky_exe = $0
--while (-l $sparky_exe)
--  set ls_sparky_exe = `ls -l "$sparky_exe"`
--  set sparky_exe = `echo "$ls_sparky_exe" | sed 's/.* -> //'`
--end
--set sparky_bin = `dirname "$sparky_exe"`
--set sparky_bin = `cd "$sparky_bin"; pwd`
--set sparky_inst = `dirname "$sparky_bin"`
--
--# -----------------------------------------------------------------------------
- # Sparky uses the SPARKY_INSTALL environment variable to find its
- # application resource file and print prolog file.
- #
--setenv SPARKY_INSTALL         $sparky_inst
-+setenv SPARKY_INSTALL         @GENTOO_PORTAGE_EPREFIX@/usr/lib/sparky
- 
- # -----------------------------------------------------------------------------
- # If Python is available start Sparky as a Python extension.
-diff -ur -x make-sparky sparky.orig/c++/Makefile sparky/c++/Makefile
---- sparky.orig/c++/Makefile   2004-02-03 15:56:24.000000000 -0800
-+++ sparky/c++/Makefile        2005-12-18 10:49:08.000000000 -0800
-@@ -22,6 +22,7 @@
- PYTHON_PREFIX = /usr/local
- PYTHON_LIB    = $(PYTHON_PREFIX)/lib/python$(PYTHON_VERSION)
- PYTHON_INC    = $(PYTHON_PREFIX)/include/python$(PYTHON_VERSION)
-+PYDIR         = $(SPARKY_INSTALL)/lib/python$(PYTHON_VERSION)/site-packages
- TCLTK_VERSION = 8.4
- TCLTK_VER_WIN32       = 84
- TK_PREFIX     = /usr/local
-@@ -113,21 +114,20 @@
- 
- nopython: $(EXECUTABLES)
- 
--install-python: $(SPY_PYMOD) $(TKINTER_PYMOD) $(SPARKY_INSTALL)/python \
--  $(SPARKY_INSTALL)/python/sparky $(SPARKY_INSTALL)/python/lib-tk
--      $(INSTALL) $(SPY_PYMOD) $(SPARKY_INSTALL)/python/sparky
--      chmod 755 $(SPARKY_INSTALL)/python/sparky/$(SPY_PYMOD)
--      $(INSTALL) $(TKINTER_PYMOD) $(SPARKY_INSTALL)/python/lib-tk
--      chmod 755 $(SPARKY_INSTALL)/python/lib-tk/$(TKINTER_PYMOD)
-+install-python: $(SPY_PYMOD) $(TKINTER_PYMOD) $(PYDIR) \
-+      $(PYDIR)/sparky $(PYDIR)/lib-tk
-+      $(INSTALL) $(SPY_PYMOD) $(PYDIR)/sparky
-+      chmod 755 $(PYDIR)/sparky/$(SPY_PYMOD)
-+      $(INSTALL) $(TKINTER_PYMOD) $(PYDIR)/lib-tk
-+      chmod 755 $(PYDIR)/lib-tk/$(TKINTER_PYMOD)
- 
- install-nopython: $(EXECUTABLES) $(SPARKY_INSTALL)/bin
-       $(INSTALL) $(EXECUTABLES) $(SPARKY_INSTALL)/bin
-       cd $(SPARKY_INSTALL)/bin ; \
-       chmod 755 $(EXECUTABLES)
- 
--$(SPARKY_INSTALL)/bin $(SPARKY_INSTALL)/python \
--$(SPARKY_INSTALL)/python/sparky $(SPARKY_INSTALL)/python/lib-tk:
--      mkdir $@
-+$(SPARKY_INSTALL)/bin $(PYDIR) $(PYDIR)/sparky $(PYDIR)/lib-tk:
-+      mkdir -p $@
-       chmod 755 $@
- 
- sparky-no-python$(EXE_SUFFIX): main.o $(SPARKY_OBJS)
-diff -ur -x make-sparky sparky.orig/c++/paths.h sparky/c++/paths.h
---- sparky.orig/c++/paths.h    2002-01-17 19:15:06.000000000 -0800
-+++ sparky/c++/paths.h 2005-12-17 20:57:15.000000000 -0800
-@@ -19,7 +19,7 @@
- // Installation subdirectories and files
- //
- #define SPARKY_MANUAL         "manual"
--#define SPARKY_LIB            "lib"
-+#define SPARKY_LIB            ""
- #define SPARKY_PRINT          "print-prolog.ps"       // under lib directory
- #define SPARKY_RESOURCE               "Sparky"                // under lib directory
- #define SPARKY_SAMPLE_DATA    "example"
-diff -ur -x make-sparky sparky.orig/c++/system-unix.cc sparky/c++/system-unix.cc
---- sparky.orig/c++/system-unix.cc     2004-02-26 10:57:54.000000000 -0800
-+++ sparky/c++/system-unix.cc  2005-12-17 20:56:58.000000000 -0800
-@@ -95,7 +95,7 @@
- //
- Stringy default_sparky_install_path()
- {
--  return file_path(file_path(file_path("", "usr"), "local"), "sparky");
-+  return file_path(file_path(file_path("", "usr"), "lib"), "sparky");
- }
- 
- // ----------------------------------------------------------------------------
-diff -ur -x make-sparky sparky.orig/lib/Makefile sparky/lib/Makefile
---- sparky.orig/lib/Makefile   2004-02-18 10:53:29.000000000 -0800
-+++ sparky/lib/Makefile        2005-12-17 16:03:21.000000000 -0800
-@@ -18,9 +18,9 @@
- TCL_SHLIB     = lib$(TCL_VERSION)$(TCLTK_SHLIB_SUFFIX)
- TK_SHLIB      = lib$(TK_VERSION)$(TCLTK_SHLIB_SUFFIX)
- 
--install: $(SPARKY_INSTALL)/lib install-tcl-tk
--      $(INSTALL) Sparky print-prolog.ps $(SPARKY_INSTALL)/lib
--      cd $(SPARKY_INSTALL)/lib ; \
-+install: $(SPARKY_INSTALL)/lib
-+      $(INSTALL) Sparky print-prolog.ps $(SPARKY_INSTALL)/lib/sparky
-+      cd $(SPARKY_INSTALL)/lib/sparky ; \
-       chmod 644 Sparky print-prolog.ps
- 
- install-tcl-tk: $(SPARKY_INSTALL)/lib
-diff -ur -x make-sparky sparky.orig/Makefile sparky/Makefile
---- sparky.orig/Makefile       2004-02-18 10:40:04.000000000 -0800
-+++ sparky/Makefile    2005-12-17 19:40:48.000000000 -0800
-@@ -40,18 +40,22 @@
- 
- PYTHON_VERSION        = 2.3
- PYTHON_DIR    = 
-+PYDIR         = $(SPARKY_INSTALL)/lib/python$(PYTHON_VERSION)/site-packages
- 
- PYMOD_SUFFIX  = .so
- SPY_PYMOD     = spy$(PYMOD_SUFFIX)
- TKINTER_PYMOD = _tkinter$(PYMOD_SUFFIX)
- 
-+PYDIR       = $(SPARKY_INSTALL)/lib/sparky/python
-+DOCDIR                = $(SPARKY_INSTALL)/share/doc/sparky
-+
- all nopython $(SPY_PYMOD) $(TKINTER_PYMOD) $(EXECUTABLES) debug-sparky clean: force
-       cd $(SPARKY_OBJ) && $(MAKE) -f $(SPARKY_SRC)/Makefile -e $@
- 
- Makefile.dep TAGS: force
-       cd $(SPARKY_SRC) && $(MAKE) -f Makefile -e $@
- 
--install: install-nopython $(SPARKY_INSTALL) install-python
-+install: install-nopython $(SPARKY_INSTALL)
-       cd $(SPARKY_OBJ) && \
-       $(MAKE) -f $(SPARKY_SRC)/Makefile -e install-python
-       cd $(SPARKY)/python && $(MAKE) -f Makefile -e install
-@@ -67,7 +71,8 @@
-       chmod 755 sparky$(SCRIPT_SUFFIX)
- 
- install-example: $(SPARKY_INSTALL)
--      cd $(SPARKY) ; $(INSTALLDIR) example $(SPARKY_INSTALL)
-+      mkdir -p $(DOCDIR)/example
-+      cd $(SPARKY) ; $(INSTALLDIR) example $(DOCDIR)
- 
- install-lib: $(SPARKY_INSTALL)
-       cd $(SPARKY)/lib && $(MAKE) -f Makefile -e install
-@@ -76,21 +81,14 @@
-       cd $(SPARKY)/manual && $(MAKE) -f Makefile -e install
- 
- install-misc: $(SPARKY_INSTALL)
--      cd $(SPARKY) ; $(INSTALL) LICENSE README $(SPARKY_INSTALL)
--      cd $(SPARKY_INSTALL) ; chmod 644 LICENSE README
--
--install-python: $(SPARKY_INSTALL) $(SPARKY_INSTALL)/python$(PYTHON_VERSION)
--ifdef PYTHON_DIR
--      $(INSTALLDIR) $(PYTHON_DIR)/* $(SPARKY_INSTALL)/python$(PYTHON_VERSION)
--else
--      echo "Not packaging Python with Sparky."
--endif
-+      cd $(SPARKY) ; $(INSTALL) LICENSE README $(DOCDIR)
-+      cd $(DOCDIR) ; chmod 644 LICENSE README
- 
- install-mac:
-       cd $(SPARKY)/mac && $(MAKE) -f Makefile -e install
- 
--$(SPARKY_INSTALL) $(SPARKY_INSTALL)/bin $(SPARKY_INSTALL)/python$(PYTHON_VERSION):
--      mkdir $@
-+$(SPARKY_INSTALL) $(SPARKY_INSTALL)/bin $(PYDIR):
-+      mkdir -p $@
-       chmod 755 $@
- 
- force:
-diff -ur -x make-sparky sparky.orig/manual/Makefile sparky/manual/Makefile
---- sparky.orig/manual/Makefile        2004-03-08 15:40:06.000000000 -0800
-+++ sparky/manual/Makefile     2005-12-17 19:37:45.000000000 -0800
-@@ -13,6 +13,8 @@
- 
- SPARKY_INSTALL        = /usr/local/sparky
- MANUAL_WWW    = /usr/local/html/cgl/sparky/manual
-+DOCDIR                = $(SPARKY_INSTALL)/share/doc/sparky
-+MANUAL_LOC = $(DOCDIR)/manual
- 
- MANUAL_SECTIONS = overview.html intro.html views.html peaks.html \
-                 extensions.html autoassign.html misc.html \
-@@ -45,17 +47,17 @@
- 
- all: $(MANUAL_FILES)
- 
--install: $(MANUAL_FILES) $(SPARKY_INSTALL)/manual \
--              $(SPARKY_INSTALL)/manual/images
--      $(INSTALL) $(MANUAL_FILES) $(SPARKY_INSTALL)/manual
--      cd $(SPARKY_INSTALL)/manual ; \
-+install: $(MANUAL_FILES) $(MANUAL_LOC) \
-+              $(MANUAL_LOC)/images
-+      $(INSTALL) $(MANUAL_FILES) $(MANUAL_LOC)
-+      cd $(MANUAL_LOC) ; \
-       chmod 644 $(MANUAL_FILES)
-       cd images ; \
--      $(INSTALL) $(IMAGE_FILES) $(SPARKY_INSTALL)/manual/images
--      cd $(SPARKY_INSTALL)/manual/images ; \
-+      $(INSTALL) $(IMAGE_FILES) $(MANUAL_LOC)/images
-+      cd $(MANUAL_LOC)/images ; \
-       chmod 644 $(IMAGE_FILES)
- 
--$(SPARKY_INSTALL)/manual $(SPARKY_INSTALL)/manual/images:
-+$(MANUAL_LOC) $(MANUAL_LOC)/images:
-       mkdir $@
-       chmod 755 $@
- 
-Only in sparky/manual: manual-postscript.gz
-diff -ur -x make-sparky sparky.orig/python/Makefile sparky/python/Makefile
---- sparky.orig/python/Makefile        2004-02-18 10:51:06.000000000 -0800
-+++ sparky/python/Makefile     2005-12-17 19:43:06.000000000 -0800
-@@ -9,6 +9,8 @@
- PYTHON_VERSION        = 2.3
- PYTHON                = $(PYTHON_PREFIX)/bin/python$(PYTHON_VERSION)
- PYTHON_LIB    = $(PYTHON_PREFIX)/lib/python$(PYTHON_VERSION)
-+PYDIR         = $(SPARKY_INSTALL)/lib/python$(PYTHON_VERSION)/site-packages
-+DOCDIR                = $(SPARKY_INSTALL)/share/doc/sparky
- 
- PYTHON_CODE   = __init__.py align.py assigngraph.py atomnames.py \
-                 atoms.py autoassign.py axes.py \
-@@ -27,18 +29,13 @@
-                 sputil.py start_in_chimera.py strips.py subprocess.py \
-                 tkutil.py volumeerror.py xeasy.py xplor.py
- 
--install: $(SPARKY_INSTALL)/python $(SPARKY_INSTALL)/python/sparky \
--              $(SPARKY_INSTALL)/python/lib-tk
--      $(INSTALL) README $(SPARKY_INSTALL)/python
--      $(INSTALL) $(PYTHON_CODE) $(SPARKY_INSTALL)/python/sparky
--      $(INSTALL) lib-tk/*.py $(SPARKY_INSTALL)/python/lib-tk
--      chmod 644 $(SPARKY_INSTALL)/python/README
--      cd $(SPARKY_INSTALL)/python/sparky ; chmod 644 $(PYTHON_CODE)
--      chmod 644 $(SPARKY_INSTALL)/python/lib-tk/*.py
--      $(PYTHON) $(PYTHON_LIB)/compileall.py $(SPARKY_INSTALL)/python/sparky
--      $(PYTHON) $(PYTHON_LIB)/compileall.py $(SPARKY_INSTALL)/python/lib-tk
-+install: $(PYDIR) $(PYDIR)/sparky $(DOCDIR)/python
-+      $(INSTALL) README $(DOCDIR)/python
-+      $(INSTALL) $(PYTHON_CODE) $(PYDIR)/sparky
-+      chmod 644 $(DOCDIR)/python/README
-+      cd $(PYDIR)/sparky ; chmod 644 $(PYTHON_CODE)
- 
--$(SPARKY_INSTALL)/python $(SPARKY_INSTALL)/python/sparky \
--  $(SPARKY_INSTALL)/python/lib-tk:
-+$(PYDIR) $(PYDIR)/sparky \
-+  $(PYDIR)/lib-tk $(DOCDIR)/python:
-       mkdir $@
-       chmod 755 $@
-diff -ur -x make-sparky sparky.orig/python/spingraph.py sparky/python/spingraph.py
---- sparky.orig/python/spingraph.py    2001-12-17 10:51:10.000000000 -0800
-+++ sparky/python/spingraph.py 2005-12-17 22:09:17.000000000 -0800
-@@ -831,7 +831,7 @@
-                'by creating a file specifying atom positions, colors,\n' +
-                'sizes, and text label positions.  Sparky provides a\n' +
-                'default layout file\n' +
--               '\n\t/usr/local/sparky/python/spinlayout.py\n\n' +
-+               '\n\t/usr/lib/python*/site-packages/sparky/python/spinlayout.py\n\n' +
-                'You override this file by making your own copy\n' +
-                '\n\t~/Sparky/Python/spinlayout.py\n\n' +
-                'You can create the desired template on the screen\n'