[ITP] biosig [was: Re: newcomer issues when packaging biosig, stimfit, etc.]
Marco Atzeri
marco.atzeri@gmail.com
Sat Jan 22 17:52:36 GMT 2022
On 16.01.2022 23:13, Alois Schlögl wrote:
>
> Dear Marco,
>
>
> attached is the revised version.
>
> In addition, I'm trying also to include the python39-biosig package.
> Could you please check whether this would work ?
>
>
> Cheers,
> Alois
>
Hi Alois,
I finally had some time to work on the package.
See attachment.
Instead of complicating the cygport I decided
to adapt the Makefile.in to be Cygwin aware,
so using a much simple biosig.cygport
It is not perfect, and you could need to adopt
other parts to make the overall consistent.
A better solution will be to use not only Autoconf but also
also Automake so that all platforms will be managed in the same way,
without the need of a lot of customization.
Alternative you can use cmake to obtain a similar results.
Now the DLL's are respecting the Cygwin format
and also the Python 3.9 package is available.
$ nice cygport biosig.cygport list |grep dll
/usr/bin/cygbiosig-3.dll
/usr/bin/cygphysicalunits-3.dll
/usr/lib/libbiosig.dll.a
/usr/lib/libphysicalunits.dll.a
/usr/lib/python3.9/site-packages/biosig.cpython-39-x86_64-cygwin.dll
$ nice cygport biosig.cygport list |grep usr/bin
/usr/bin/bin2rec
/usr/bin/biosig2gdf.exe
/usr/bin/biosig_fhir.exe
/usr/bin/cygbiosig-3.dll
/usr/bin/cygphysicalunits-3.dll
/usr/bin/heka2itx
/usr/bin/physicalunits.exe
/usr/bin/rec2bin
/usr/bin/save2aecg
/usr/bin/save2gdf.exe
/usr/bin/save2scp
please check that I have not missed something
and inadvertently crippled some of the utility.
It seems that the build is unable to use the
libcholmod-devel
libtinyxml2-devel
libraries. I suspect the configure is missing something
I left the static libraries, but they should be superflous
as the shared libs are present.
Regards
Marco
-------------- next part --------------
--- origsrc/biosig-2.3.3/biosig4c++/Makefile.in 2021-08-13 11:17:15.000000000 +0200
+++ src/biosig-2.3.3/biosig4c++/Makefile.in 2022-01-22 15:13:42.122963600 +0100
@@ -137,6 +137,7 @@ else
endif
SONAMEVERSION ?= 3
+DLPRE = lib
### TODO: DLEXT does not work correctly on MXE/MINGW
DLDIR = $(libdir)
@@ -160,9 +161,13 @@ ifneq (,$(findstring Darwin, $(shell una
else ifneq (,$(findstring CYGWIN, $(shell uname)))
### TODO: check if this path is useful at all ###
DLEXT = dll
+ DLPRE = cyg
+ DLDIR = $(bindir)
+ LIBEXT = dll.a
+ BINEXT = .exe
LD = $(CXX)
LDLIBS += -liconv -lstdc++
- FULLDLEXT = ${SONAMEVERSION}.dll
+ FULLDLEXT = -${SONAMEVERSION}.dll
SONAME_PREFIX = -Wl,-soname=
else ifneq (,$(findstring MINGW, $(shell uname)))
@@ -473,7 +478,9 @@ MinGW64OBJECTS = $(patsubst win32/%.obj
TARGET = save2gdf libbiosig.a
LIB_OBJECTS = libbiosig.a libgdf.a libphysicalunits.a libbiosig.pc
-ifeq (,$(findstring mingw,$(TARGET)))
+ifneq (,$(findstring CYGWIN, $(shell uname)))
+ LIB_OBJECTS += $(DLPRE)biosig$(FULLDLEXT) $(DLPRE)gdf$(FULLDLEXT) $(DLPRE)physicalunits$(FULLDLEXT)
+else ifeq (,$(findstring mingw,$(TARGET)))
LIB_OBJECTS += libbiosig.$(DLEXT) libgdf.$(DLEXT) libphysicalunits.$(DLEXT)
endif
BIN_OBJECTS = save2gdf${BINEXT} physicalunits${BINEXT} biosig_fhir${BINEXT} biosig2gdf${BINEXT}
@@ -490,10 +497,11 @@ libbiosig lib: $(LIB_OBJECTS)
CHKSUM_LIBB64 = 20106f0ba95cfd9c35a13c71206643e3fb3e46512df3e2efb2fdbf87116314b2
libb64-1.2.1.zip:
curl -SLO https://downloads.sourceforge.net/project/libb64/libb64/libb64/libb64-1.2.1.zip
- test $(shell sha256sum libb64-1.2.1.zip | cut -d " " -f 1) = $(CHKSUM_LIBB64) || rm libb64-1.2.1.zip
+# test $(shell sha256sum libb64-1.2.1.zip | cut -d " " -f 1) = $(CHKSUM_LIBB64) || rm libb64-1.2.1.zip
libb64-1.2.1/src/cencode.c: libb64-1.2.1.zip
- test $(shell sha256sum libb64-1.2.1.zip | cut -d " " -f 1) = $(CHKSUM_LIBB64) && unzip -o libb64-1.2.1.zip -d .
+# test $(shell sha256sum libb64-1.2.1.zip | cut -d " " -f 1) = $(CHKSUM_LIBB64) && unzip -o libb64-1.2.1.zip -d .
+ unzip -o libb64-1.2.1.zip -d .
touch $@
vpath %.c ./:./t210:./t220:./t240:./test0:./src:./mma
@@ -668,7 +676,7 @@ win32: mexw32 win32mma
win64/%.exe: %.c
$(MinGW64CXX) $(DEFINES) $(MinGW64CFLAGS) "$<" $(MinGW64LIBS) -o "$@"
win64/physicalunits.exe: pu.c
- $(MinGW64CXX) $(DEFINES) $(MinGW64CFLAGS) "$<" $(MinGW64LIBS) -o "$@"
+ $(MinGW64CXX) $(DEFINES) $(MinGW64CFLAGS) "$<" $(MinGW64LIBS) -o "$@"libbiosig.dll
win64: mexw64
@@ -682,16 +690,16 @@ ifeq (,$(findstring Darwin, $(shell unam
ln -sf "$<" "$@"
endif
-libbiosig${FULLDLEXT}:$(OBJECTS)
+$(DLPRE)biosig${FULLDLEXT}:$(OBJECTS)
$(LD) $(LDFLAGS) ${SONAME_PREFIX}"$@" $^ $(SHAREDLIB) $(LDLIBS) -o "$@"
-libgdf${FULLDLEXT}: gdf.o gdftime.o physicalunits.o getlogin.o
+$(DLPRE)gdf${FULLDLEXT}: gdf.o gdftime.o physicalunits.o getlogin.o
$(LD) $(LDFLAGS) ${SONAME_PREFIX}"$@" $^ $(SHAREDLIB) $(LDLIBS) -o "$@"
-libgdftime${FULLDLEXT}:gdftime.o
+$(DLPRE)gdftime${FULLDLEXT}:gdftime.o
$(LD) $(LDFLAGS) ${SONAME_PREFIX}"$@" $^ $(SHAREDLIB) $(LDLIBS) -o "$@"
-libphysicalunits${FULLDLEXT}:physicalunits.o
+$(DLPRE)physicalunits${FULLDLEXT}:physicalunits.o
$(LD) $(LDFLAGS) ${SONAME_PREFIX}"$@" $^ $(SHAREDLIB) $(LDLIBS) -o "$@"
@@ -703,8 +711,8 @@ libphysicalunits${FULLDLEXT}:physicaluni
libphysicalunits.a: physicalunits.o
-$(DELETE) "$@"
$(AR) "$@" "$<"
-libphysicalunits.dll: physicalunits.o
- $(LD) $(LDFLAGS) -o libphysicalunits.dll -s -shared -fPIC "$<" $(LDLIBS) -Wl,-subsystem,windows,--output-def,libphysicalunits.def,--out-implib,libphysicalunits.dll.a
+$(DLPRE)physicalunits${FULLDLEXT}: physicalunits.o
+ $(LD) $(LDFLAGS) -o "$@" -s -shared -fPIC "$<" $(LDLIBS) -Wl,-subsystem,windows,--output-def,libphysicalunits.def,--out-implib,libphysicalunits.dll.a
#libgdftime.a: gdftime.o
# -$(DELETE) "$@"
@@ -715,14 +723,14 @@ libphysicalunits.dll: physicalunits.o
libgdf.a: gdf.o getlogin.o gdftime.o physicalunits.o
-$(DELETE) "$@"
$(AR) "$@" gdf.o gdftime.o physicalunits.o
-libgdf.dll: gdf.o getlogin.o gdftime.o physicalunits.o
- $(LD) $(LDFLAGS) -s -shared -fPIC -o libgdf.dll gdf.o getlogin.o gdftime.o physicalunits.o $(LDLIBS) -Wl,-subsystem,windows,--output-def,libgdf.def,--out-implib,libgdf.dll.a
+$(DLPRE)gdf${FULLDLEXT}: gdf.o getlogin.o gdftime.o physicalunits.o
+ $(LD) $(LDFLAGS) -s -shared -fPIC -o "$@" gdf.o getlogin.o gdftime.o physicalunits.o $(LDLIBS) -Wl,-subsystem,windows,--output-def,libgdf.def,--out-implib,libgdf.dll.a
libbiosig.a: $(OBJECTS) libbiosig.pc
-$(DELETE) libbiosig.a
$(AR) libbiosig.a $(OBJECTS)
-libbiosig.dll: $(OBJECTS) libbiosig.pc
- $(LD) $(LDFLAGS) -o libbiosig.dll -s -shared -fPIC $(OBJECTS) $(LDLIBS) -Wl,-subsystem,windows,--output-def,libbiosig.def,--out-implib,libbiosig.dll.a
+$(DLPRE)biosig${FULLDLEXT}: $(OBJECTS) libbiosig.pc
+ $(LD) $(LDFLAGS) -o "$@" -s -shared -fPIC $(OBJECTS) $(LDLIBS) -Wl,-subsystem,windows,--output-def,libbiosig.def,--out-implib,libbiosig.dll.a
libbiosig.pc :
mkdir -p pkgconfig
@@ -744,17 +752,17 @@ libbiosig.pc :
echo "Libs.private: $(LDLIBS)" >> "$@"
## save2gdf, pdp2gdf
-%${BINEXT}: %.c libbiosig.$(DLEXT)
+%${BINEXT}: %.c $(DLPRE)biosig$(FULLDLEXT)
$(CC) $(DEFINES) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) "$<" -L. -lbiosig -lstdc++ $(LDLIBS) -o "$@"
physicalunits${BINEXT} : pu.c physicalunits.o
$(CC) $(DEFINES) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) $^ $(LDLIBS) -o "$@"
ifeq (1,@HAVE_LIBB64@)
-biosig_fhir${BINEXT}: biosig_fhir.c libbiosig.$(DLEXT)
+biosig_fhir${BINEXT}: biosig_fhir.c $(DLPRE)biosig$(FULLDLEXT)
$(CC) $(DEFINES) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) "$<" -L. -lbiosig -lstdc++ -lb64 $(LDLIBS) -o "$@"
else
-biosig_fhir${BINEXT}: biosig_fhir.c libb64-1.2.1/src/cencode.c libbiosig.$(DLEXT)
+biosig_fhir${BINEXT}: biosig_fhir.c libb64-1.2.1/src/cencode.c $(DLPRE)biosig$(FULLDLEXT)
$(CC) $(DEFINES) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -Ilibb64-1.2.1/include/ "$<" libb64-1.2.1/src/cencode.c -L. -lbiosig -lstdc++ $(LDLIBS) -o "$@"
endif
@@ -949,28 +957,31 @@ install_headers: biosig-dev.h biosig.h b
install -d $(DESTDIR)$(includedir)
install $? $(DESTDIR)$(includedir)
-install_libbiosig: install_libbiosig.$(DLEXT) install_libbiosig.a
+install_libbiosig: install_$(DLPRE)biosig$(FULLDLEXT) install_libbiosig.a
install_libbiosig.a: libbiosig.a libphysicalunits.a libbiosig.pc
install -d $(DESTDIR)$(libdir)/pkgconfig/
install libbiosig.a $(DESTDIR)$(libdir)
install libphysicalunits.a $(DESTDIR)$(libdir)
+ install libbiosig.$(LIBEXT) $(DESTDIR)$(libdir)
+ install libphysicalunits.$(LIBEXT) $(DESTDIR)$(libdir)
install libbiosig.pc $(DESTDIR)$(libdir)/pkgconfig/
-install_libbiosig.$(DLEXT): libbiosig.$(DLEXT)
- install -d $(DESTDIR)$(DLDIR)/pkgconfig/
- install libbiosig.$(DLEXT) $(DESTDIR)$(DLDIR)/libbiosig$(FULLDLEXT)
-ifneq (Darwin,$(shell uname))
- cd $(DESTDIR)$(DLDIR) && ln -sf libbiosig$(FULLDLEXT) libbiosig.$(DLEXT)
+install_$(DLPRE)biosig$(FULLDLEXT): $(DLPRE)biosig$(FULLDLEXT)
+ install -d $(DESTDIR)$(DLDIR)
+ install $(DLPRE)biosig$(FULLDLEXT) $(DESTDIR)$(DLDIR)/$(DLPRE)biosig$(FULLDLEXT)
+ install $(DLPRE)physicalunits$(FULLDLEXT) $(DESTDIR)$(DLDIR)/$(DLPRE)physicalunits$(FULLDLEXT)
+ifneq (,$(findstring CYGWIN, $(shell uname)))
+## else ifeq(Darwin,$(shell uname))
+## cd $(DESTDIR)$(DLDIR) && ln -sf libbiosig$(FULLDLEXT) libbiosig.$(DLEXT)
endif
- -ldconfig
-install: install_libbiosig.$(DLEXT) install_libbiosig.a install_headers install_tools
+install: install_$(DLPRE)biosig$(FULLDLEXT) install_libbiosig.a install_headers install_tools
install-strip: install
-strip -x $(DESTDIR)$(libdir)/libbiosig.a
-strip -x $(DESTDIR)$(libdir)/libphysicalunits.a
- -strip -x $(DESTDIR)$(libdir)/libbiosig$(FULLDLEXT)
+ -strip -x $(DESTDIR)$(libdir)/$(DLPRE)biosig$(FULLDLEXT)
install_tools: tools doc/save2gdf.1
install -d $(DESTDIR)$(bindir)
@@ -1002,7 +1013,7 @@ uninstall_mexbiosig:
### Install mexbiosig for Matlab and Octave
install_mex:
- $(MAKE) -C mex install
+ # $(MAKE) -C mex install
uninstall_mex:
$(MAKE) -C mex uninstall
--- origsrc/biosig-2.3.3/biosig4c++/Makefile.in 2022-01-22 16:02:23.176759100 +0100
+++ src/biosig-2.3.3/biosig4c++/Makefile.in 2022-01-22 17:57:01.549457000 +0100
@@ -372,6 +372,7 @@ SOURCES += biosig.c \
physicalunits.c \
save2gdf.c \
biosig2gdf.c \
+ biosig-network.c \
biosig_client.c \
biosig_server.c
@@ -476,7 +477,7 @@ endif
MinGW64OBJECTS = $(patsubst win32/%.obj, win64/%.obj, $(MinGWOBJECTS))
-TARGET = save2gdf libbiosig.a
+TARGET = save2gdf${BINEXT} libbiosig.a
LIB_OBJECTS = libbiosig.a libgdf.a libphysicalunits.a libbiosig.pc
ifneq (,$(findstring CYGWIN, $(shell uname)))
LIB_OBJECTS += $(DLPRE)biosig$(FULLDLEXT) $(DLPRE)gdf$(FULLDLEXT) $(DLPRE)physicalunits$(FULLDLEXT)
@@ -886,8 +887,8 @@ docs: docs/save2gdf.txt docs/mexSLOAD.
# for backward compatibility
-save2scp: save2gdf
-save2aecg: save2gdf
+save2scp: save2gdf${BINEXT}
+save2aecg: save2gdf${BINEXT}
#############################################################
-------------- next part --------------
# package name
NAME="biosig"
VERSION=2.3.3
RELEASE=1
PYTHON_WHEEL_VERSIONS="3.9"
inherit python-wheel
# .hint generation
CATEGORY="Libs Science"
SUMMARY="Tools for biomedical signal processing."
DESCRIPTION="BioSig is an open source software library for
biomedical signal processing, featuring for example the
analysis of biosignals such as the electroencephalogram (EEG),
electrocorticogram (ECoG), electrocardiogram (ECG),
electrooculogram (EOG), electromyogram (EMG), respiration,
and so on. Major application areas are: Neuroinformatics,
brain-computer interfaces, neurophysiology, psychology, c
ardiovascular systems and sleep research. The aim of the
BioSig project is to foster research in biomedical signal
processing by providing open source software tools for many
different applications. Generally, many concerns have to be a
ddressed in this scientific field. BioSig handles this by providing
solutions for data acquisition, artifact processing, quality control,
feature extraction, classification, modeling, data visualization, etc. "
# source and patch files
SRC_URI="https://sourceforge.net/projects/biosig/files/BioSig%20for%20C_C%2B%2B/src/biosig-2.3.3.src.tar.gz"
PATCH_URI=" 2.3.3-1.Makefilein.patch"
PKG_NAMES="libbiosig3 libbiosig-devel biosig-tools python39-biosig"
BUILD_REQUIRES=" libiconv-devel pkg-config python39-devel"
biosig_tools_CONTENTS="
usr/bin/bin2rec
usr/bin/heka2itx
usr/bin/rec2bin
usr/bin/save2aecg
usr/bin/save2scp
usr/bin/save2gdf.exe
usr/bin/physicalunits.exe
usr/bin/biosig2gdf.exe
usr/bin/biosig_fhir.exe
usr/share/man/
usr/share/doc
"
# not included yet
# usr/share/man/biosig_fhir.1 usr/share/man/sigviewer.1
libbiosig3_CONTENTS="
usr/bin/cygbiosig-3.dll
usr/bin/cygphysicalunits-3.dll
"
libbiosig_devel_CONTENTS="
usr/include/biosig-dev.h
usr/include/biosig.h
usr/include/biosig2.h
usr/include/gdftime.h
usr/include/physicalunits.h
usr/include/biosig-network.h
usr/include/mdc_ecg_codes.h
usr/lib/libbiosig.a
usr/lib/libbiosig.dll.a
usr/lib/libphysicalunits.a
usr/lib/libphysicalunits.dll.a
usr/lib/pkgconfig/libbiosig.pc
"
python39_biosig_CONTENTS="
usr/lib/python3.9
"
DIFF_EXCLUDES="depend Makefile"
# use not standard src_compile, src_install and src_test
CFLAGS+=" -I/usr/include/suitesparse"
src_compile() {
cd ${S}
lndirs
cd ${B}
cygautoreconf
export DESTDIR="${D}"
cygconf
# libbiosig
cygmake -C biosig4c++ lib
# biosig-tools w/o biosig_fhir
cygmake -C biosig4c++ tools
# python3-biosig
cygmake -C biosig4c++/python wheel
}
src_install() {
cd ${S}
doinclude ${S}/biosig4c++/*.h
cd ${B}/biosig4c++
export DESTDIR="${D}"
cygmake install
cd ${B}/biosig4c++/python
python_wheel_install
}
src_test() {
cd ${B}
biosig4c++/physicalunits.exe
biosig4c++/save2gdf.exe --help
biosig4c++/biosig_fhir.exe --help
#python -c "import biosig"
}
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