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Work in progress! Reorganizing codebase to conform to GNU library

standards.  Enables proper library versioning, avoidance of namespace
collisions, etc.  Using autotools now.
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koadman committed Jun 13, 2009
1 parent 4b87042 commit 79c81c834fef53094e6e9316e11bc2fe819cb842
Showing with 522 additions and 61 deletions.
  1. +1 −0 AUTHORS
  2. 0 ChangeLog
  3. 0 NEWS
  4. +186 −0 aminclude.am
  5. +2 −0 autogen.sh
  6. +19 −19 beagle.dox
  7. +172 −0 configure.ac
  8. +80 −0 cudalt.py
  9. +5 −1 {include → libbeagle-lib}/BeagleImpl.h
  10. +10 −7 {src → libbeagle-lib}/CPU/BeagleCPUImpl.cpp
  11. +8 −1 {src → libbeagle-lib}/CPU/BeagleCPUImpl.h
  12. +9 −7 {src → libbeagle-lib}/CUDA/BeagleCUDAImpl.cpp
  13. +2 −2 {src → libbeagle-lib}/CUDA/BeagleCUDAImpl.h
  14. 0 {src → libbeagle-lib}/CUDA/CUDASharedFunctions.c
  15. 0 {src → libbeagle-lib}/CUDA/CUDASharedFunctions.cu
  16. 0 {src → libbeagle-lib}/CUDA/CUDASharedFunctions.h
  17. +2 −2 {src → libbeagle-lib}/CUDA/PeelingFunctions.cu
  18. 0 {src → libbeagle-lib}/CUDA/PeelingKernels.cu
  19. 0 {src → libbeagle-lib}/CUDA/TransitionFunctions.cu
  20. 0 {src → libbeagle-lib}/CUDA/TransitionKernels.cu
  21. 0 {java → libbeagle-lib}/JNI/beagle_BeagleJNIWrapper.c
  22. 0 {java → libbeagle-lib}/JNI/beagle_BeagleJNIWrapper.cpp
  23. 0 {java → libbeagle-lib}/JNI/beagle_BeagleJNIWrapper.h
  24. +26 −22 {src → libbeagle-lib}/beagle.cpp
  25. 0 {include → libbeagle-lib}/beagle.h
  26. 0 { → libbeagle-lib}/java/beagle/Beagle.java
  27. 0 { → libbeagle-lib}/java/beagle/BeagleFactory.java
  28. 0 { → libbeagle-lib}/java/beagle/BeagleInfo.java
  29. 0 { → libbeagle-lib}/java/beagle/BeagleJNIWrapper.java
  30. 0 { → libbeagle-lib}/java/beagle/DependencyAwareBeagleImpl.java
  31. 0 { → libbeagle-lib}/java/beagle/FourStateBeagleImpl.java
  32. 0 { → libbeagle-lib}/java/beagle/GeneralBeagleImpl.java
@@ -0,0 +1 @@
The BEAGLE Developer group (http://beagle-lib.googlecode.com)
No changes.
0 NEWS
No changes.
@@ -0,0 +1,186 @@
# Copyright (C) 2004 Oren Ben-Kiki
# This file is distributed under the same terms as the Automake macro files.

# Generate automatic documentation using Doxygen. Goals and variables values
# are controlled by the various DX_COND_??? conditionals set by autoconf.
#
# The provided goals are:
# doxygen-doc: Generate all doxygen documentation.
# doxygen-run: Run doxygen, which will generate some of the documentation
# (HTML, CHM, CHI, MAN, RTF, XML) but will not do the post
# processing required for the rest of it (PS, PDF, and some MAN).
# doxygen-man: Rename some doxygen generated man pages.
# doxygen-ps: Generate doxygen PostScript documentation.
# doxygen-pdf: Generate doxygen PDF documentation.
#
# Note that by default these are not integrated into the automake goals. If
# doxygen is used to generate man pages, you can achieve this integration by
# setting man3_MANS to the list of man pages generated and then adding the
# dependency:
#
# $(man3_MANS): doxygen-doc
#
# This will cause make to run doxygen and generate all the documentation.
#
# The following variable is intended for use in Makefile.am:
#
# DX_CLEANFILES = everything to clean.
#
# This is usually added to MOSTLYCLEANFILES.

## --------------------------------- ##
## Format-independent Doxygen rules. ##
## --------------------------------- ##

if DX_COND_doc

## ------------------------------- ##
## Rules specific for HTML output. ##
## ------------------------------- ##

if DX_COND_html

DX_CLEAN_HTML = @DX_DOCDIR@/html

endif DX_COND_html

## ------------------------------ ##
## Rules specific for CHM output. ##
## ------------------------------ ##

if DX_COND_chm

DX_CLEAN_CHM = @DX_DOCDIR@/chm

if DX_COND_chi

DX_CLEAN_CHI = @DX_DOCDIR@/@PACKAGE@.chi

endif DX_COND_chi

endif DX_COND_chm

## ------------------------------ ##
## Rules specific for MAN output. ##
## ------------------------------ ##

if DX_COND_man

DX_CLEAN_MAN = @DX_DOCDIR@/man

endif DX_COND_man

## ------------------------------ ##
## Rules specific for RTF output. ##
## ------------------------------ ##

if DX_COND_rtf

DX_CLEAN_RTF = @DX_DOCDIR@/rtf

endif DX_COND_rtf

## ------------------------------ ##
## Rules specific for XML output. ##
## ------------------------------ ##

if DX_COND_xml

DX_CLEAN_XML = @DX_DOCDIR@/xml

endif DX_COND_xml

## ----------------------------- ##
## Rules specific for PS output. ##
## ----------------------------- ##

if DX_COND_ps

DX_CLEAN_PS = @DX_DOCDIR@/@PACKAGE@.ps

DX_PS_GOAL = doxygen-ps

doxygen-ps: @DX_DOCDIR@/@PACKAGE@.ps

@DX_DOCDIR@/@PACKAGE@.ps: @DX_DOCDIR@/@PACKAGE@.tag
cd @DX_DOCDIR@/latex; \
rm -f *.aux *.toc *.idx *.ind *.ilg *.log *.out; \
$(DX_LATEX) refman.tex; \
$(MAKEINDEX_PATH) refman.idx; \
$(DX_LATEX) refman.tex; \
countdown=5; \
while $(DX_EGREP) 'Rerun (LaTeX|to get cross-references right)' \
refman.log > /dev/null 2>&1 \
&& test $$countdown -gt 0; do \
$(DX_LATEX) refman.tex; \
countdown=`expr $$countdown - 1`; \
done; \
$(DX_DVIPS) -o ../@PACKAGE@.ps refman.dvi

endif DX_COND_ps

## ------------------------------ ##
## Rules specific for PDF output. ##
## ------------------------------ ##

if DX_COND_pdf

DX_CLEAN_PDF = @DX_DOCDIR@/@PACKAGE@.pdf

DX_PDF_GOAL = doxygen-pdf

doxygen-pdf: @DX_DOCDIR@/@PACKAGE@.pdf

@DX_DOCDIR@/@PACKAGE@.pdf: @DX_DOCDIR@/@PACKAGE@.tag
cd @DX_DOCDIR@/latex; \
rm -f *.aux *.toc *.idx *.ind *.ilg *.log *.out; \
$(DX_PDFLATEX) refman.tex; \
$(DX_MAKEINDEX) refman.idx; \
$(DX_PDFLATEX) refman.tex; \
countdown=5; \
while $(DX_EGREP) 'Rerun (LaTeX|to get cross-references right)' \
refman.log > /dev/null 2>&1 \
&& test $$countdown -gt 0; do \
$(DX_PDFLATEX) refman.tex; \
countdown=`expr $$countdown - 1`; \
done; \
mv refman.pdf ../@PACKAGE@.pdf

endif DX_COND_pdf

## ------------------------------------------------- ##
## Rules specific for LaTeX (shared for PS and PDF). ##
## ------------------------------------------------- ##

if DX_COND_latex

DX_CLEAN_LATEX = @DX_DOCDIR@/latex

endif DX_COND_latex

.PHONY: doxygen-run doxygen-doc $(DX_PS_GOAL) $(DX_PDF_GOAL)

.INTERMEDIATE: doxygen-run $(DX_PS_GOAL) $(DX_PDF_GOAL)

doxygen-run: @DX_DOCDIR@/@PACKAGE@.tag

doxygen-doc: doxygen-run $(DX_PS_GOAL) $(DX_PDF_GOAL)

@DX_DOCDIR@/@PACKAGE@.tag: $(DX_CONFIG) $(pkginclude_HEADERS)
rm -rf @DX_DOCDIR@
$(DX_ENV) $(DX_DOXYGEN) $(srcdir)/$(DX_CONFIG)

DX_CLEANFILES = \
@DX_DOCDIR@/@PACKAGE@.tag \
-r \
$(DX_CLEAN_HTML) \
$(DX_CLEAN_CHM) \
$(DX_CLEAN_CHI) \
$(DX_CLEAN_MAN) \
$(DX_CLEAN_RTF) \
$(DX_CLEAN_XML) \
$(DX_CLEAN_PS) \
$(DX_CLEAN_PDF) \
$(DX_CLEAN_LATEX)

endif DX_COND_doc
@@ -0,0 +1,2 @@
#!/bin/sh
autoreconf --force --install -I config -I m4
@@ -31,14 +31,14 @@ PROJECT_NAME = BEAGLE
# This could be handy for archiving the generated documentation or
# if some version control system is used.

PROJECT_NUMBER = 0.1
PROJECT_NUMBER = $(VERSION)

# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
# base path where the generated documentation will be put.
# If a relative path is entered, it will be relative to the location
# where doxygen was started. If left blank the current directory will be used.

OUTPUT_DIRECTORY = ./docs
OUTPUT_DIRECTORY = $(DOCDIR)

# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create
# 4096 sub-directories (in 2 levels) under the output directory of each output
@@ -114,7 +114,7 @@ FULL_PATH_NAMES = YES
# If left blank the directory from which doxygen is run is used as the
# path to strip.

STRIP_FROM_PATH =
STRIP_FROM_PATH = $(SRCDIR)

# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of
# the path mentioned in the documentation of a class, which tells
@@ -123,7 +123,7 @@ STRIP_FROM_PATH =
# definition is used. Otherwise one should specify the include paths that
# are normally passed to the compiler using the -I flag.

STRIP_FROM_INC_PATH =
STRIP_FROM_INC_PATH = $(SRCDIR)

# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter
# (but less readable) file names. This can be useful is your file systems
@@ -534,7 +534,7 @@ WARN_LOGFILE =
# directories like "/usr/src/myproject". Separate the files or directories
# with spaces.

INPUT = ./include
INPUT = $(SRCDIR)

# This tag can be used to specify the character encoding of the source files
# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is
@@ -723,7 +723,7 @@ IGNORE_PREFIX =
# If the GENERATE_HTML tag is set to YES (the default) Doxygen will
# generate HTML output.

GENERATE_HTML = YES
GENERATE_HTML = $(GENERATE_HTML)

# The HTML_OUTPUT tag is used to specify where the HTML docs will be put.
# If a relative path is entered the value of OUTPUT_DIRECTORY will be
@@ -769,7 +769,7 @@ HTML_ALIGN_MEMBERS = YES
# Microsoft HTML help workshop to generate a compiled HTML help file (.chm)
# of the generated HTML documentation.

GENERATE_HTMLHELP = NO
GENERATE_HTMLHELP = $(GENERATE_CHM)

# If the GENERATE_DOCSET tag is set to YES, additional index files
# will be generated that can be used as input for Apple's Xcode 3
@@ -809,20 +809,20 @@ HTML_DYNAMIC_SECTIONS = NO
# can add a path in front of the file if the result should not be
# written to the html output directory.

CHM_FILE =
CHM_FILE = ../$(PROJECT).chm

# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can
# be used to specify the location (absolute path including file name) of
# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run
# the HTML help compiler on the generated index.hhp.

HHC_LOCATION =
HHC_LOCATION = $(HHC_PATH)

# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag
# controls if a separate .chi index file is generated (YES) or that
# it should be included in the master .chm file (NO).

GENERATE_CHI = NO
GENERATE_CHI = $(GENERATE_CHI)

# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING
# is used to encode HtmlHelp index (hhk), content (hhc) and project file
@@ -890,7 +890,7 @@ FORMULA_FONTSIZE = 10
# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will
# generate Latex output.

GENERATE_LATEX = YES
GENERATE_LATEX = $(GENERATE_LATEX)

# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put.
# If a relative path is entered the value of OUTPUT_DIRECTORY will be
@@ -919,7 +919,7 @@ COMPACT_LATEX = NO
# by the printer. Possible values are: a4, a4wide, letter, legal and
# executive. If left blank a4wide will be used.

PAPER_TYPE = a4wide
PAPER_TYPE = $(PAPER_SIZE)

# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX
# packages that should be included in the LaTeX output.
@@ -967,7 +967,7 @@ LATEX_HIDE_INDICES = NO
# The RTF output is optimized for Word 97 and may not look very pretty with
# other RTF readers or editors.

GENERATE_RTF = NO
GENERATE_RTF = $(GENERATE_RTF)

# The RTF_OUTPUT tag is used to specify where the RTF docs will be put.
# If a relative path is entered the value of OUTPUT_DIRECTORY will be
@@ -1008,7 +1008,7 @@ RTF_EXTENSIONS_FILE =
# If the GENERATE_MAN tag is set to YES (the default) Doxygen will
# generate man pages

GENERATE_MAN = NO
GENERATE_MAN = $(GENERATE_MAN)

# The MAN_OUTPUT tag is used to specify where the man pages will be put.
# If a relative path is entered the value of OUTPUT_DIRECTORY will be
@@ -1037,7 +1037,7 @@ MAN_LINKS = NO
# generate an XML file that captures the structure of
# the code including all documentation.

GENERATE_XML = NO
GENERATE_XML = $(GENERATE_XML)

# The XML_OUTPUT tag is used to specify where the XML pages will be put.
# If a relative path is entered the value of OUTPUT_DIRECTORY will be
@@ -1199,7 +1199,7 @@ TAGFILES =
# When a file name is specified after GENERATE_TAGFILE, doxygen will create
# a tag file that is based on the input files it reads.

GENERATE_TAGFILE =
GENERATE_TAGFILE = $(DOCDIR)/$(PROJECT).tag

# If the ALLEXTERNALS tag is set to YES all external classes will be listed
# in the class index. If set to NO only the inherited external classes
@@ -1216,7 +1216,7 @@ EXTERNAL_GROUPS = YES
# The PERL_PATH should be the absolute path and name of the perl script
# interpreter (i.e. the result of `which perl').

PERL_PATH = /usr/bin/perl
PERL_PATH = $(PERL_PATH)

#---------------------------------------------------------------------------
# Configuration options related to the dot tool
@@ -1251,7 +1251,7 @@ HIDE_UNDOC_RELATIONS = YES
# toolkit from AT&T and Lucent Bell Labs. The other options in this section
# have no effect if this option is set to NO (the default)

HAVE_DOT = NO
HAVE_DOT = $(HAVE_DOT)

# By default doxygen will write a font called FreeSans.ttf to the output
# directory and reference it in all dot files that doxygen generates. This
@@ -1352,7 +1352,7 @@ DOT_IMAGE_FORMAT = png
# The tag DOT_PATH can be used to specify the path where the dot tool can be
# found. If left blank, it is assumed the dot tool can be found in the path.

DOT_PATH =
DOT_PATH = $(DOT_PATH)

# The DOTFILE_DIRS tag can be used to specify one or more directories that
# contain dot files that are included in the documentation (see the

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