Merge branch 'thof/DENISE-import_Seitosh'

contrib/.gitignore

+doc
+bin
+header

contrib/Makefile_var

-# This is a file for environment variables used in Makefiles in aff fourier stfinv
+# this is <Makefile_var>
+# ----------------------------------------------------------------------------
+# 
+# Copyright (c) 2015 by Thomas Forbriger (BFO Schiltach) 
+# 
+# set variables expected by vendor Makefiles
+# 
+# REVISIONS and CHANGES 
+#    02/11/2015   V1.0   Thomas Forbriger
+# 
+# ============================================================================
+#
+# This file is included (via make include statement) by Makefiles in
+# aff, fourier, stfinv, and libcseife
+#
+# Its purpose is to set make variables which are expected by vendor Makefiles.
+#
+# ============================================================================
 
-LOCINCLUDEDIR=../header
+# extract relative path to contrib with respect of including Makefile
+CONTRIBDIR:=$(abspath $(dir $(lastword $(MAKEFILE_LIST))))
 
-LOCLIBDIR=../bin
-LOCBINDIR=../bin
+# ----------------------------------------------------------------------------
+# set values required by vendor Makefiles
+LOCINCLUDEDIR=$(CONTRIBDIR)/header
 
-TF_WWWBASEDIR=$HOME/public_html/txt/cxx
+LOCLIBDIR=$(CONTRIBDIR)/bin
+LOCBINDIR=$(CONTRIBDIR)/bin
+
+TF_WWWBASEDIR=$(CONTRIBDIR)/doc
 
 TF_BROWSER=firefox
 
+# set Fortran compiler if not yet set in environment
+ifeq "$(origin FC)" "default"
 FC=/usr/bin/g77-3.3
+endif
+
+# ----- END OF Makefile_var ----- 

contrib/aff/COPYING

@@ -2,7 +2,7 @@ this is <COPYING>
 ============================================================================
 libaff
 ------
-$Id: COPYING 4964 2013-02-01 13:27:42Z lrehor $
+$Id$
 ============================================================================
 
 Copyright (C) 2002 by Thomas Forbriger and Wolfgang Friederich

contrib/aff/Carray.h

@@ -3,7 +3,7 @@
  * 
  * ----------------------------------------------------------------------------
  * 
- * $Id: Carray.h 3957 2011-05-16 14:46:43Z tforb $
+ * $Id$
  * \author Thomas Forbriger
  * \date 14/05/2011
  * 
@@ -40,7 +40,7 @@
 #define AFF_CARRAY_H_VERSION \
   "AFF_CARRAY_H   V1.0   "
 #define AFF_CARRAY_H_CVSID \
-  "$Id: Carray.h 3957 2011-05-16 14:46:43Z tforb $"
+  "$Id$"
 
 #include<aff/array.h>
 #include<aff/lib/checkedcast.h>

contrib/aff/Makefile

 # this is <Makefile>
 # ----------------------------------------------------------------------------
-# $Id: Makefile 4964 2013-02-01 13:27:42Z lrehor $
+# $Id$
 # 
 # Copyright (c) 2002 by Thomas Forbriger (IMG Frankfurt) 
 # 
@@ -24,18 +24,9 @@
 # Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
 # ----
 #     
-# A note on header files:
-# We extensively comment class declarations within the header files. The
-# reduce compilation time when using the library code, comments will be
-# stripped from the header files that are exportet. These stripped versions
-# are placed in the source code path with name *.h.strip and will be linked to
-# INCINSTALLPATH with name *.h.
-#
-# Although comment stripping could be done by perl with an elaborate regular
-# expression, we prefer the remcmmnt command by Jari Laaksonen. You can find
-# the code at 
-#   http://www.eti.pg.gda.pl/KATEDRY/kecs/lab-cpp/snippets/
-# If it is not available to you, you should set TF_REMCMMNT=cat (see below)
+# Please have a look at the README file coming along with the source code in
+# this directory for further notes regarding provided functionality,
+# prerequisites and installation.
 #
 # REVISIONS and CHANGES 
 #    06/12/2002   V1.0   Thomas Forbriger
@@ -52,26 +43,12 @@
 #    17/01/2011   V1.9   distinguish library creation and installation
 #    27/07/2011   V1.10  give precedence to $LOCINCLUDEDIR over 
 #                        $SERVERINCLUDEDIR 
+#    26/01/2014          eliminate comment stripping 
 # 
 # ============================================================================
-#
-# environment variables
-# ---------------------
-#
-# You will like to set the following environment variables:
-#
-# LOCINCLUDEDIR         Defines the path where header files will be copied for
-#                       usage in your own projects. You will pass this path to
-#                       the precompiler with the -I option.
-# LOCLIBDIR             Defines the path where the binary library will be
-#                       placed.
-# TF_WWWBASEDIR         Defines the path to your personal homepage. That's the
-#                       place where doxygen output will be written too (see
-#                       below).
-#
-# You will find the installed library header files in $(LOCINCLUDEDIR)/aff
 
-include ../Makefile_var
+CONTRIBDIR=..
+include $(CONTRIBDIR)/Makefile_var
 
 
 .PHONY: all
@@ -113,36 +90,19 @@ SRC=lib/error.cc dump.cc lib/strided.cc lib/stridedstepper.cc \
 # test programs are placed in a subdirectory
 TESTS=$(wildcard tests/*.cc)
 # whereever we find a README, we will use it
-README=$(shell find . -name README) README.changelog README.groups
+README=$(shell find . -name README) 
+# the frame of doxygen documentation is palced in text files
+DOXYTXT=$(shell find . -name doxygen\*.txt) 
 
 # place where we will copy header files
 INCINSTALLPATH=$(LOCINCLUDEDIR)/aff
 # place where we will copy the binary library
 LIBINSTALLPATH=$(LOCLIBDIR)
 
-# name of headers with comments stripped off (these are linked to your include
-# directory)
-STRIPHEADER=$(addsuffix .strip,$(notdir $(HEADERS)))
 # name of installed (exported) header files (these are the names in your
 # include directory)
 INSTHEADER=$(addprefix $(INCINSTALLPATH)/,$(filter-out ./tests/%,$(HEADERS)))
 
-#======================================================================
-# comments can be removed from headers
-# ------------------------------------
- 
-# if defined, empty lines are kept in comment-stripped headers
-# to synchronize line numbers (necessary during library debugging)
-EMPTYPRINT=1
-#EMPTYPRINT=0
-
-# define this to be cat in case you do not have remcmmnt available
-ifndef TF_REMCMMNT
-TF_REMCMMNT=cat
-endif
-#REMCMMNT=remcmmnt
-#REMCMMNT=cat
-
 #======================================================================
 # compiler and preprocessor flags
 # -------------------------------
@@ -158,9 +118,8 @@ CPPFLAGS=$(addprefix -I,$(LOCINCLUDEDIR) $(subst :, ,$(SERVERINCLUDEDIR))) \
 # -------
 
 # files which are to be edited
-flist: Makefile tests/Makefile doxydoc.cfg $(README) COPYING \
-       $(HEADERS) $(SRC) $(TESTS) $(wildcard doxy*.cfg) \
-       tests/f77common.inc tests/f77procs.f
+flist: Makefile doxydoc.cfg $(README) COPYING \
+       $(HEADERS) $(SRC) $(TESTS) $(wildcard doxy*.cfg) $(DOXYTXT) 
 	echo $(filter-out lib/% tests/%,$^) | tr ' ' '\n' | sort > $@
 	echo $(filter lib/%,$^) | tr ' ' '\n' | sort >> $@
 	echo $(filter tests/%,$^) | tr ' ' '\n' | sort >> $@
@@ -177,9 +136,7 @@ clean: ;
 	-find . -name \*.bak | xargs --no-run-if-empty /bin/rm -v
 	-find . -name \*.o | xargs --no-run-if-empty /bin/rm -v
 	-find . -name \*.d | xargs --no-run-if-empty /bin/rm -v
-	-find . -name \*.h.strip | xargs --no-run-if-empty /bin/rm -v
-	-/bin/rm -vf flist *.o install-include libcontxx.a *.xxx junk* *.a *.so
-	cd tests; $(MAKE) clean
+	-/bin/rm -vf flist *.o install-include *.xxx junk* *.a *.so
 
 #======================================================================
 # library part
@@ -218,35 +175,12 @@ include $(patsubst %.cc,%.d,$(SRC))
 #======================================================================
 # header files
 # ------------
-#
-# Since we extensively document the class structures within the header files,
-# these should be stripped for the production version (otherwise the compiler
-# has to scan all comments on each compile). Stripping is done by the rule
-# below and is controlled by the variables TF_REMCMMNT and EMPTYPRINT (see
-# above).
-
-# comment stripping
-# -----------------
-$(call CHECKVARS,TF_REMCMMNT EMPTYPRINT)
-
-# awk rule assumes that the first non-comment line starts with '#'
-# and that the first (copyright) comment end with pattern "^ */"
-%.h.strip: %.h
-	awk 'BEGIN {hot=1;} /^ \*\// { if (hot) { hot=2; print; next;} }\
-        /^#/ { hot=0; } \
-        { if (hot==2) { print ""; } else if (hot) { print; } }' $< > $@
-	$(TF_REMCMMNT) $< | awk 'BEGIN {hot=0;} \
-        /^ *$$/ { if ((hot) && ($(EMPTYPRINT))) { print ""; } next; } \
-        /^#/ { hot=1; } { if (hot) print; }' >> $@
-
-#----------------------------------------------------------------------
-.PRECIOUS: %.h.strip
       
 $(call CHECKVAR,INCINSTALLPATH)
-$(INCINSTALLPATH)/%.h: %.h.strip
-	mkdir -vp $(dir $@)
-	-rm -fv $@
-	/bin/cp -vpd $< $@
+$(INCINSTALLPATH)/%.h: %.h
+	@mkdir -vp $(dir $@)
+	-@rm -fv $@
+	@/bin/cp -vpd $< $@
 
 # install header files
 .PHONY: install-include
@@ -292,9 +226,7 @@ DOXYWWWPATH=$(TF_WWWBASEDIR)/libaff
 
 doxyclean: ;/bin/rm -rfv $(TF_WWWBASEDIR)/libaff doxydoc.xxx
 
-DOXYSRC=$(README) $(HEADERS) $(SRC) \
-  tests/f77procs.P tests/f77procs.f \
-  tests/f77common.inc tests/f77common_com.P
+DOXYSRC=$(DOXYTXT) $(HEADERS) $(SRC) 
 
 # create doxygen intermediate configuration
 PWD=$(shell env pwd)
@@ -326,36 +258,6 @@ kdocview: kdoc; $(TF_BROWSER) file:$(KDOCDIR)/index.html &
 showsections: $(README)
 	egrep -n '\\subsection|\\section|\\page' $^
 
-#======================================================================
-# delegate test targets
-# ---------------------
-
-tests/%.P: 
-	cd tests; echo "#############################"; $(MAKE) $(notdir $@)
-
-tests/f2ctest: tests/f77test.cc install-include libaff.a
-	cd tests; echo "#############################"; $(MAKE) $(notdir $@)
-
-tests/%: tests/%.cc install-include libaff.a
-	cd tests; echo "#############################"; $(MAKE) $(notdir $@)
-
-tests/bin%: tests/bin%.cc install-include libaff.a
-	cd tests; echo "#############################"; $(MAKE) $(notdir $@)
-
-tests/%.run: tests/%
-	echo "#############################"
-	$< $(ARG)
-	/bin/rm -fv $< $<.o
-
-# after each modification to the library this target should be used
-compile-tests: \
-  tests/shapetest.run \
-  tests/reprtest.run \
-  tests/arraytest.run \
-  tests/operatortest.run \
-  tests/helpertest.run \
-  tests/f77test.run 
-
 #======================================================================
 # create package
 # --------------

contrib/aff/README

-/*! \file libaff/README
- * \brief C++ containers for numbers (libaff)
- *
- * ----------------------------------------------------------------------------
- *
- * $Id: README 4964 2013-02-01 13:27:42Z lrehor $
- * 
- * Copyright (c) 2002 by Thomas Forbriger (IMG Frankfurt) 
- *
- * ----
- * This program is free software; you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation; either version 2 of the License, or
- * (at your option) any later version. 
- * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
- * ----
- * 
- * C++ containers for numbers (libaff)
- *
- * This file contains:
- *  - documentation of namespace aff
- *  - mainpage text
- *  - documentation for pages:
- *    - \ref page_design
- *    - \ref page_using
- *    - \ref page_notes
- *    - \ref page_naming
- * 
- * REVISIONS and CHANGES 
- *  - 06/12/2002   V1.0   Thomas Forbriger (copied from libcontxx)
- *  - 20/12/2002   V1.1   (thof)
- *                        - complete revision of this file
- *                        - there are major gaps in
- *                          -# \ref sec_design_multidimensional
- *                          -# \ref page_using
- *  - 28/12/2002   V1.2   (thof)
- *                        - new term for containers of const elements
- *                        - added documentation regarding the concept of 
- *                          const correctness
- *                        - added documentation regarding member typedefs
- *  - 29/12/2002   V1.3   (thof)
- *                        - added section about replicated shared heap base
- *                          class (\ref sec_design_replicated)
- *                        - added section about sparse interface
- *                          (\ref sec_design_interface_sparse)
- *                        - added section about accessing internals
- *                          (\ref sec_design_interface_internals)
- *                        - reflect changes to Subarray and Slice
- *                        - tell about class hierarchies and member data vs.
- *                          inheritance
- *  - 04/01/2003   V1.4   (thof)
- *                        - added section about Tcontainer typedef 
- *                          (\ref sec_design_interface_tcontainer)
- *  - 10/02/2004   V1.5   (thof)
- *                        - added section about decision against interface
- *                          base classes
- *                          (\ref sec_design_interface_nobaseclass)
- *  - 10/11/2010   V1.6   (thof)
- *                        - code fragments for precompiled templates are
- *                          removed from the library (\ref sec_design_binary)
- *  - 14/05/2011   V1.7   (thof)
- *                        - add info on raw-major and column-major order
- *  - 15/05/2011   V1.8   (thof)
- *                        - reordered documentation, movde modules to
- *                          README.groups
- * 
- * ============================================================================
- */
-
-/*! \brief Root namespace of library
-  
-  This namespace contains all modules of the library
-  (see \ref sec_main_modules). 
-  Here you should find all components, the user needs to work with this
-  library.
- */
-namespace aff {
-} // namespace aff
-
-/*======================================================================*/
-
-/*! \mainpage
-
-\author Thomas Forbriger
-\author Wolfgang Friederich
-\since December 2002
-\date December 2002
-\version V1.0
-$Id: README 4964 2013-02-01 13:27:42Z lrehor $
-
-  Contents of this page:
-  - \ref sec_main_aims
-  - \ref sec_main_need
-  - \ref sec_main_peculiar
-  - \ref sec_main_modules
-
-  Additional information:
-  - \ref page_changelog
-  - \ref page_project_status
-  - \ref page_using
-  - \ref page_array_layout
-  - \ref page_design
-  - \ref page_naming
-  - \ref page_representation
-  - \ref page_fortran
-
-\section sec_main_aims Aims of the library
-  
-  The AFF (Array of Friederich and Forbriger) is a lightweight class library.
-  It offers a simple and easy to use container for numbers as is necessary in
-  numerical code. The offered array always has a rectangular strided layout,
-  reference semantics (through counted references) and a Fortran layout in
-  memory. The interface is intentionally kept sparse to keep compilation times
-  small. The array itself is meant to be used to pass numbers from one program
-  module to the other. If you want to exploit the power of expression
-  templates, pass the array contents to something like Blitz++.
-
-
-  Contents of this page:
-
-\section sec_main_peculiar Peculiarities of AFF
-
-\par Containers use counted references
-All containers (e.g. aff::Array, aff::Series) use counted references to access
-global memory. Assigning one container object to another just assigns the
-reference. Both will use the same data in memory afterwards. 
-\sa \ref page_representation.
-
-\par Const-correctness for array elements
-In this library we follow provide functionality to write const-correct code
-with regard to the array container and with regard to its element values.
-\sa \ref sec_design_const.
-
-\par Multidimensional arrays
-Every aff::Array of this class has aff::Strided::Mmax_dimen dimensions.
-Construction and access for lower dimensionality is provided. In the case of
-using less dimensions, the size of the unused dimensions is 1 by default and
-its index is inherently set to the first index.
-\sa \ref sec_design_multidimensional.
-
-\section sec_main_need Why do we need this array library
-  
-  One major reason for replacing Fortran77 by C++ in numerical code is the
-  convenience in expressing logistics. Data of different type and size may be
-  packed into classes and encapsulated from the outside world. Most numerical
-  results are to be stored in arrays, multi-dimensional arrays in particular.
-  This library provides the basic functionality for storing many data of the
-  same type in memory, passing them around between subroutines in an efficient
-  way and accessing them through convenient interfaces. The main purpose of
-  this library is not calculation but managing (passing between program
-  modules, selection of subsets of the data) large amounts of numbers. In the
-  future it might provide interfaces to libraries like blitz++ for finite
-  difference calculations, MTL for linear algebra calculations, and POOMA for
-  parallel computations.
-
-  \sa http://www.sophya.org/, http://www.boost.org
-
-\section sec_main_modules Modules of the library
-
-  The main module is the array class aff::Array. It provides basic
-  functionality through its interface. See the explanation there.
-  It is presented in aff/array.h
-  The object code is placed in libaff.a.
-
-  \sa \ref group_array, \ref group_array_extensions
-*/
-
-/*======================================================================*/
-
-/*! \page page_design Design decisions
-
-  Contents of this page:
-  - \ref sec_design_interface
-    - \ref sec_design_interface_sparse
-    - \ref sec_design_interface_typedef
-    - \ref sec_design_interface_tcontainer
-    - \ref sec_design_interface_internals
-    - \ref sec_design_interface_nobaseclass
-  - \ref sec_design_threeclasses
-  - \ref sec_design_hierarchy
-  - \ref sec_design_replicated
-    - \ref sec_design_replicated_fact
-    - \ref sec_design_replicated_problem
-    - \ref sec_design_replicated_solution
-  - \ref sec_design_copy
-  - \ref sec_design_namespaces
-  - \ref sec_design_binary
-  - \ref sec_design_multidimensional
-  - \ref sec_design_const
-    - \ref sec_design_const_problem
-    - \ref sec_design_const_approach
-    - \ref sec_design_const_alternatives
-    - \ref sec_design_const_general
-
-\section sec_design_interface Common interface concepts
-
-\subsection sec_design_interface_sparse Sparse interfaces
-
-  The class library is intended to be a  light-weight library. This means it
-  should offer basic functionality in terms of multidimensional containers
-  with counted references (and not more in first place). We do not like to
-  include a tremendous amount of code for specialized concepts (like subranges
-  or expression templates in Blitz++) each time we just need a small array.
-  Thus the header files providing array declarations (aff/array.h and the
-  files included therein) should be as sparse as possible. All extra
-  functionality like iterators (aff::Iterator presented in aff/iterator.h) or
-  slices (aff::Slice presented in aff/slice.h) should be external to the
-  aff::Array class. This allows us to load their definitions only where
-  needed. However, this approach requires that the internals of aff::Array are
-  exposed to the outside through appropriate functions (see 
-  \ref sec_design_interface_internals).
-
-\subsection sec_design_interface_typedef Member typedefs
-
-  Class templates like aff::Iterator may be used with any container class,
-  that provides an appropriate interface. This interface convention concerns
-  the access to the type of related objects. I will explain by example:
-
-  We use an iterator \c i which was declared
-  \code aff::Iterator<Cont> i \endcode
-  for a container of type \c Cont, it expects to find a corresponding
-  container class that promises constness of the elements through 
-  \code Cont::Tcontainer_of_const \endcode
-  or short
-  \code Cont::Tcoc \endcode
-
-  For aff::ConstArray the type aff::ConstArray::Tcoc is just the class itself.
-  However aff::Array::Tcoc gives an aff::ConstArray.
-
-  \sa aff::SharedHeap::Tcontainer_of_const
-  \sa aff::ConstSharedHeap::Tcontainer_of_const
-  \sa aff::Array::Tcontainer_of_const
-  \sa aff::ConstArray::Tcontainer_of_const
-  \sa aff::Series::Tcontainer_of_const
-  \sa aff::ConstSeries::Tcontainer_of_const
-
-  In the same way we may access the appropriate element type through
-  \code Cont::Tvalue \endcode
-  which is \c T for aff::Array<T> and \c const \T for aff::ConstArray<T>.
-  However a 
-  \code Cont::Tconst_value \endcode
-  will always provide a type with const qualifier.
-
-  \sa aff::Array::Tvalue
-  \sa aff::Array::Tconst_value
-  \sa aff::ConstArray::Tvalue
-  \sa aff::ConstArray::Tconst_value
-  \sa aff::Series::Tvalue
-  \sa aff::Series::Tconst_value
-  \sa aff::ConstSeries::Tvalue
-  \sa aff::ConstSeries::Tconst_value
-
+this is <README>
+============================================================================
+AFF --- A container for numbers
+-------------------------------
+$Id$
+============================================================================
+
+For compilation instructions see README.1st in the root directory of the tar-ball or
+http://gpitrsvn.gpi.uni-karlsruhe.de:8000/TFSoftware/wiki/docs/installation 
+
+The AFF (Array of Friederich and Forbriger) is a lightweight class library. It
+offers a simple and easy to use container for numbers as is necessary in
+numerical code. The offered array always has a rectangular strided layout,
+reference semantics (through counted references) and a Fortran layout in
+memory. The interface is intentionally kept sparse to keep compilation times
+small. The array itself is meant to be used to pass numbers from one program
+module to the other. If you want to exploit the power of expression templates,
+pass the array contents to something like Blitz++.
+
+Installation
+------------
+ environment variables:
+  LOCINCLUDEDIR   Defines the path where header files will be copied for
+                  usage in your own projects. You will pass this path to
+                  the precompiler with the -I option.
+  LOCLIBDIR       Defines the path where the binary library will be
+                  placed.
+  TF_WWWBASEDIR   Defines the path to your personal homepage. That's the
+                  place where doxygen output will be written too (see
+                  in the Makefile).
+
+ make all             installs headers, binary libraries and documentation
+
+You will find the installed library header files in $(LOCINCLUDEDIR)/aff
+
+Dependencies
+------------
+  external dependencies: -
+  internal dependencies: -
+ 
+
+Detailed documentation is provided through doxygen source code. See target
+doxydoc in the Makefile.
+
+----- END OF README -----