Re: newcomer issues when packaging biosig,stimfit, etc.

Re: newcomer issues when packaging biosig,stimfit, etc.

[Marco Atzeri]

On 08.01.2022 18:34, Alois Schlögl wrote:
> Dear Cygwin community,
> 

Hi Alois,

> I intend to package Stimfit [1] and Biosig [2] (and perhaps 
> libb64,libbiosig,sigviewer) for cygwin. The packages are already 
> available in Debian, but when trying to package them for cygwin, I run 
> into some difficulties.
> I read the documentation [3-5], but I got stuck, and I'd appreciate your 
> help on this. Attached are my current versions of  *.cygports and *.hint 
> files

please subscribe to cygwin-apps.
The discussion about maintainership and packaging are handled there

> 
> When trying to build them with cygport I run into these difficulties:
> 
> $ cygport libb64.cygport all
>  >>> Preparing libb64-1.2.1-1.x86_64
>  >>> Unpacking source libb64-1.2.1.zip
>  >>> Preparing working source directory
>  >>> Compiling libb64-1.2.1-1.x86_64
> *** ERROR: Could not find configure.ac or configure.in
> 
> libb64 does not require running configure, the Makefile is already 
> available and a simple "make" command would do.
> How can I specifiy this in the libb64.cygport file ?
> 
> 
> "cygport biosig.cygport all"
> ....
> config.status: creating biosig4c++/tcl/Makefile
> config.status: creating config.h
> config.status: config.h is unchanged
> make: *** No rule to make target 'Makefile.in', needed by 'Makefile'.  
> Stop.
> *** ERROR: make failed
> 
> Makefile.in is in the sources, why do I see this error when trying to 
> build it with cygport ?
> 
> Attached are also stimfit.cygport and sigviewer.cygport, they require 
> libbiosig, and are most likely incomplete. If you have suggestions to 
> make it work, please let me know.
> 
> 
> Cheers,
>     Alois
> 
> 
> 
> [1] https://github.com/neurodroid/stimfit
> [2] http://biosig.sourceforge.net/
> [3] https://cygwin.com/packages.html
> [4] https://cygwin.com/packaging-contributors-guide.html
> [5] https://cygwin.com/packaging-hint-files.html
> 

regards
Marco

Re: newcomer issues when packaging biosig,stimfit, etc.

[Marco Atzeri]

[-- Attachment #1: Type: text/plain, Size: 1008 bytes --]

following on cygwin-apps

On 08.01.2022 18:41, Marco Atzeri wrote:
> On 08.01.2022 18:34, Alois Schlögl wrote:
>> Dear Cygwin community,
>>
> 
> Hi Alois,
> 
>> I intend to package Stimfit [1] and Biosig [2] (and perhaps 
>> libb64,libbiosig,sigviewer) for cygwin. The packages are already 
>> available in Debian, but when trying to package them for cygwin, I run 
>> into some difficulties.
>> I read the documentation [3-5], but I got stuck, and I'd appreciate 
>> your help on this. Attached are my current versions of  *.cygports and 
>> *.hint files
> 
> please subscribe to cygwin-apps.
> The discussion about maintainership and packaging are handled there
> 

I looked on libb64, as it is not using autoconf/automake
you can not use the default src_* but you need to define them.

As the Makefile is building only static lib and has no install
procedure I modified to build only shared and I used
cygport for the installation.
I also separated the test.

See attached update cygport and patch.





[-- Attachment #2: libb64.cygport --]
[-- Type: text/plain, Size: 1039 bytes --]

# package name
NAME="libb64"
VERSION=1.2.1
RELEASE=1

# .hint generation
CATEGORY="Libs"
SUMMARY="libary for base64-encoding"
DESCRIPTION="A library of ANSI C routines for fast 
encoding/decoding data into and from a base64-encoded format"

SRC_URI="https://sourceforge.net/projects/libb64/files/libb64/libb64/libb64-${PV}.zip"

PKG_NAMES="libb64 libb64-devel libb64-util"

libb64_util_CONTENTS="usr/bin/base64.exe"

libb64_CONTENTS="usr/bin/cygb64.dll"

libb64_devel_CONTENTS="
  usr/share/doc/
  usr/include
  usr/lib
"

DIFF_EXCLUDES="depend"

# use not standard src_compile, src_install and src_test

src_compile() {
	cd ${S}
	lndirs
	cd ${B}
	make 
}

src_install() {
	cd ${D}

	dodir usr/include/b64
	insinto /usr/include/b64
	doins ${S}/include/b64/*
	
	dobin ${B}/base64/base64.exe 
	dobin ${B}/src/cygb64.dll 
	dolib ${B}/src/libb64.dll.a 

	dodir usr/share/b64/examples
	insinto usr/share/b64/examples
	dodoc ${S}/examples/*.c ${S}/examples/*.txt ${S}/examples/README.md
}	

src_test() {
    cd ${B}
    make -C examples test
}


[-- Attachment #3: libb64-1.2.1-1.src.patch --]
[-- Type: text/plain, Size: 1993 bytes --]

--- origsrc/libb64-1.2.1/base64/Makefile	2013-06-18 14:49:36.000000000 +0200
+++ src/libb64-1.2.1/base64/Makefile	2022-01-08 19:42:26.156240800 +0100
@@ -34,10 +34,8 @@ vpath %.a ../src
 
 all: $(TARGETS) #strip
 
-base64: libb64.a
-
-strip:
-	strip $(BINARIES) *.exe
+base64: ../src/cygb64.dll
+	g++ $(CXXFLAGS) $(SOURCES) -L../src -lb64 -o $@
 
 clean: clean_VisualStudioProject
 	rm -f *.exe* *.o $(TARGETS) *.bak *~
--- origsrc/libb64-1.2.1/examples/Makefile	2013-06-18 14:49:36.000000000 +0200
+++ src/libb64-1.2.1/examples/Makefile	2022-01-08 20:12:21.021189700 +0100
@@ -19,9 +19,13 @@ vpath %.a ../src
 
 .PHONY : clean
 
-all: $(TARGETS) test
+all: $(TARGETS) 
 
-c-example1 c-example2: libb64.a
+c-example1: ../src/cygb64.dll
+	gcc $(CXXFLAGS) c-example1.c -L../src -lb64 -o $@
+
+c-example2: ../src/cygb64.dll
+	gcc $(CXXFLAGS) c-example2.c -L../src -lb64 -o $@
 
 clean: 
 	rm -f *.exe* *.o $(TARGETS) $(DEBRIS) *.bak *~
@@ -33,10 +37,10 @@ depend: $(SOURCES)
 	makedepend -f- $(CFLAGS) $(SOURCES) 2> /dev/null 1> depend
 
 test-c-example1: c-example1
-	./c-example1
+	PATH=$(PWD)/src:$(PATH) ./c-example1
 
 test-c-example2: c-example2
-	./c-example2 loremgibson.txt encoded.txt decoded.txt
+	PATH=$(PWD)/src:$(PATH) ./c-example2 loremgibson.txt encoded.txt decoded.txt
 	diff -q loremgibson.txt decoded.txt
 
 test: test-c-example1 test-c-example2
--- origsrc/libb64-1.2.1/src/Makefile	2013-06-18 14:49:36.000000000 +0200
+++ src/libb64-1.2.1/src/Makefile	2022-01-08 19:39:12.010457300 +0100
@@ -1,4 +1,4 @@
-LIBRARIES = libb64.a
+LIBRARIES = cygb64.dll
 
 # Build flags (uncomment one)
 #############################
@@ -24,11 +24,9 @@ vpath %.h ../include/b64
 
 all: $(TARGETS) #strip
 
-libb64.a: cencode.o cdecode.o
-	$(AR) $(ARFLAGS) $@ $^
-
-strip:
-	strip $(BINARIES) *.exe
+cygb64.dll: cencode.o cdecode.o
+	gcc -shared -Wl,--enable-auto-import -Wl,--enable-auto-image-base  \
+	-o $@  -Wl,--out-implib=libb64.dll.a  $^ 
 
 clean:
 	rm -f *.exe* *.o $(TARGETS) *.bak *~

Re: newcomer issues when packaging biosig,stimfit, etc.

[Marco Atzeri]

On 08.01.2022 20:15, Marco Atzeri wrote:
> following on cygwin-apps
> 
> On 08.01.2022 18:41, Marco Atzeri wrote:
>> On 08.01.2022 18:34, Alois Schlögl wrote:
>>> Dear Cygwin community,
>>>
>>
>> Hi Alois,
>>
>>> I intend to package Stimfit [1] and Biosig [2] (and perhaps 
>>> libb64,libbiosig,sigviewer) for cygwin. The packages are already 
>>> available in Debian, but when trying to package them for cygwin, I 
>>> run into some difficulties.
>>> I read the documentation [3-5], but I got stuck, and I'd appreciate 
>>> your help on this. Attached are my current versions of  *.cygports 
>>> and *.hint files
>>
>> please subscribe to cygwin-apps.
>> The discussion about maintainership and packaging are handled there
>>
> 
> I looked on libb64, as it is not using autoconf/automake
> you can not use the default src_* but you need to define them.
> 
> As the Makefile is building only static lib and has no install
> procedure I modified to build only shared and I used
> cygport for the installation.
> I also separated the test.
> 
> See attached update cygport and patch.
> 


as we have already base64

$ cygcheck -l coreutils | grep base64
/usr/bin/base64.exe
/usr/share/man/man1/base64.1.gz

I wonder if is it really useful.
Otherwise you need to change name to the binary


Regards
Marco

Re: newcomer issues when packaging biosig,stimfit, etc.

[Marco Atzeri]

On 11.01.2022 12:33, Alois Schlögl wrote:
> 
> Dear Marco,
> 
> 
> Yesterday, I've tried to subscribe to the cygwin-apps mailinglist, but 
> so far I did not get any confirmation email. When trying to send to the 
> mailinglist, it fails with " Your message has been rejected, probably 
> because you are not ...".
> Do you know how long it typically takes until the mailing list 
> subscription is confirmed ?

sorry I don't.
I am subscripted by so long.


Jon,
could you check ?

> In the meantime, please find below the status for the libb64 and biosig 
> packages.

> Thanks that was helpful. Attached is an updated version for biosig and 
> libb64.
> 
> cygport libb64.cygport all
> cygport biosig.cygport all
> 
> runs now w/o error. How can I test whether result can be installed and 
> used ?

One major problem.
Never build in the source directory, the final src.patch
must fit with you desired patch.
So only what you patched should come out.

For this package that does not respect the build in a
different directory than source, you shoud start
with something like:

src_compile() {
         cd ${S}
         lndirs
         cd ${B}
         cygautoreconf
         cygconf
         cygmake
}

unfortunately I have no time to dig further
short term

Regards
Marco

Re: newcomer issues when packaging biosig,stimfit, etc.

[Brian Inglis]

On 11.01.2022 12:33, Alois Schlögl wrote:
> Yesterday, I've tried to subscribe to the cygwin-apps mailinglist, but 
> so far I did not get any confirmation email. When trying to send to 
> the mailinglist, it fails with " Your message has been rejected, 
> probably because you are not ...".
> Do you know how long it typically takes until the mailing list 
> subscription is confirmed?

You need to configure email to cygwin, sourceware, and other lists as 
plain text only, otherwise the server may reject your messages.

To subscribe quickly use:

	https://cygwin.com/mailman/listinfo/cygwin-apps/

fill out your email address, name, "password", and click [Subscribe].

You should get a confirmation email in a few minutes, where you click on 
the embedded link to enable the subscription.

-- 
Take care. Thanks, Brian Inglis, Calgary, Alberta, Canada

This email may be disturbing to some readers as it contains
too much technical detail. Reader discretion is advised.
[Data in binary units and prefixes, physical quantities in SI.]

[ITP] biosig [was: Re: newcomer issues when packaging biosig, stimfit, etc.]

[Alois Schlögl]

[-- Attachment #1: Type: text/plain, Size: 1612 bytes --]



Am 1/12/22 um 06:47 schrieb Marco Atzeri:
>> In the meantime, please find below the status for the libb64 and 
>> biosig packages.
>
>> Thanks that was helpful. Attached is an updated version for biosig 
>> and libb64.
>>
>> cygport libb64.cygport all
>> cygport biosig.cygport all
>>
>> runs now w/o error. How can I test whether result can be installed 
>> and used ?
>
> One major problem.
> Never build in the source directory, the final src.patch
> must fit with you desired patch.
> So only what you patched should come out.
>
> For this package that does not respect the build in a
> different directory than source, you shoud start
> with something like:
>
> src_compile() {
>         cd ${S}
>         lndirs
>         cd ${B}
>         cygautoreconf
>         cygconf
>         cygmake
> } 



I've adapted biosig.cygport accordingly and addressed this in the 
attached version. It runs fine when doing

    cygport biosig.cygport all

runs w/o error. Also testing the package with

tar -C / -xvf 
biosig-2.3.3-1.x86_64/dist/biosig/biosig-tools/biosig-tools-2.3.3-1.tar.xz
tar -C / -xvf 
biosig-2.3.3-1.x86_64/dist/biosig/libbiosig/libbiosig-2.3.3-1.tar.xz
tar -C / -xvf 
biosig-2.3.3-1.x86_64/dist/biosig/libbiosig-devel/libbiosig-devel-2.3.3-1.tar.xz

and running
    save2gdf -h
works fine.

Moreover, I understand now why my libb64.cygport file is not ready. 
ecause libb64 is not necessary for libbiosig's support of Stimfit, I'll 
omit libb64 for now.
Would you please check whether Biosig is ready to be included in cygwin ?


Cheers,
    Alois

[-- Attachment #2: biosig.cygport --]
[-- Type: text/plain, Size: 3379 bytes --]

# package name
NAME="biosig"
VERSION=2.3.3
RELEASE=1

# .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="biosig-2.3.3-fix-build.patch"

# use the standard src_compile, src_install and src_test


PKG_NAMES="libbiosig libbiosig-devel biosig-tools"

biosig_tools_CONTENTS="
  usr/bin/save2gdf.exe
  usr/bin/physicalunits.exe
  usr/bin/biosig2gdf.exe
  usr/share/man/man1/save2gdf.1.gz  
  usr/share/man/man1/biosig2gdf.1.gz
  usr/share/man/man1/biosig_fhir.1.gz  
  usr/share/man/man1/physicalunits.1.gz

  usr/share/doc/biosig/COPYING
  usr/share/doc/biosig/README
"
# not included yet
# usr/share/man/biosig_fhir.1  usr/share/man/sigviewer.1


libbiosig_CONTENTS="
  usr/bin/libbiosig.dll
  usr/bin/libphysicalunits.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
"

DIFF_EXCLUDES="depend"

# use not standard src_compile, src_install and src_test

src_compile() {
        cd ${S}
        lndirs
        cd ${B}
        cygautoreconf
        cygconf  # --prefix=/usr
	# libbiosig
	cygmake lib
	# biosig-tools w/o biosig_fhir
	cygmake -C biosig4c++ save2gdf physicalunits biosig2gdf
	# python3-biosig
}

src_install() {
	cd ${S}

	doinclude ${S}/biosig4c++/*.h
	
	dobin ${B}/biosig4c++/save2gdf.exe 
        # dobin ${B}/biosig4c++/biosig_fhir.exe
	dobin ${B}/biosig4c++/biosig2gdf.exe 
	dobin ${B}/biosig4c++/physicalunits.exe 
	dobin ${B}/biosig4c++/libbiosig.dll 
	dobin ${B}/biosig4c++/libphysicalunits.dll 

	dolib ${B}/biosig4c++/libbiosig.dll.a 
	dolib ${B}/biosig4c++/libbiosig.a 
	dolib ${B}/biosig4c++/libphysicalunits.dll.a 
	dolib ${B}/biosig4c++/libphysicalunits.a 

        dopkgconfig ${B}/biosig4c++/libbiosig.pc

	# doman ${S}/biosig4c++/doc/bin2rec.1
        doman ${S}/biosig4c++/doc/biosig2gdf.1
        doman ${S}/biosig4c++/doc/biosig_fhir.1
        doman ${S}/biosig4c++/doc/physicalunits.1
        doman ${S}/biosig4c++/doc/save2gdf.1

}

src_test() {
    cd ${S}
    biosig4c++/physicalunits.exe
    biosig4c++/save2gdf.exe  --help
    # biosig4c++/biosig_fhir.exe --help
}


[-- Attachment #3: biosig-2.3.3-1.hint --]
[-- Type: text/plain, Size: 1293 bytes --]

# comment
sdesc: "Tools for biomedical signal processing"
ldesc: "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, etc. Major application areas are: Neuroinformatics, 
brain-computer interfaces, neurophysiology, psychology, 
cardiovascular 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 addressed 
in this scientific field. BioSig handles this by providing solutions for 
data acquisition, artifact processing, quality control, feature extraction, 
classification, modeling, data visualization, etc. "
category: Libs,Science,Utils
requires: libb64 libcholmod tinyxml cygwin
# depends: version-relation[, version-relation...]
# obsoletes: version-relation[, version-relation...]
# provides: package[, package...]
# conflicts: version-relation[, version-relation...]
external-source: release/biosig/biosig-2.3.3-1-src.tar.xz
# message: id "some text"
test:
version: 2.3.3
# disable-check: check-name [check-name...]






[-- Attachment #4: biosig-2.3.3-1.src.patch --]
[-- Type: text/x-patch, Size: 4871 bytes --]

--- origsrc/biosig-2.3.3/Makefile	2021-08-13 11:17:24.000000000 +0200
+++ src/biosig-2.3.3/Makefile	2022-01-12 21:54:44.813446500 +0100
@@ -30,13 +30,13 @@ R: lib
 
 install ::
 	$(MAKE) -C biosig4c++ install
-	install -d $(DESTDIR)/usr/local/share/biosig/matlab
-	cp -r biosig4matlab/* $(DESTDIR)/usr/local/share/biosig/matlab/
-	-rm -rf $(DESTDIR)/usr/local/share/biosig/matlab/maybe-missing
+	install -d $(DESTDIR)/usr/share/biosig/matlab
+	cp -r biosig4matlab/* $(DESTDIR)/usr/share/biosig/matlab/
+	-rm -rf $(DESTDIR)/usr/share/biosig/matlab/maybe-missing
 
 uninstall ::
 	$(MAKE) -C biosig4c++ uninstall
-	-rm -rf $(DESTDIR)/usr/local/share/biosig
+	-rm -rf $(DESTDIR)/usr/share/biosig
 
 clean ::
 	$(MAKE) -C biosig4c++/mma clean
@@ -52,8 +52,8 @@ distclean : clean
 		biosig4c++/python/setup.py \
 		biosig4c++/R/DESCRIPTION
 
-ifneq (:,/usr/bin/java)
-ifneq (:,/usr/bin/javac)
+ifneq (:,:)
+ifneq (:,:)
 first :: lib
 	-$(MAKE) -C biosig4c++/java
 endif
@@ -92,11 +92,11 @@ biosig4octave ::
 	ln -sf biosig4c++/mex/biosig4octave-2.3.3.src.tar.gz
 
 ifneq (:,/usr/bin/octave)
-ifneq (:,/usr/bin/mkoctfile)
+ifneq (:,:)
 BIOSIG_MEX_DIR = $(DESTDIR)$(shell octave-config -p LOCALOCTFILEDIR)/biosig
 BIOSIG_DIR     = $(DESTDIR)$(shell octave-config -p LOCALFCNFILEDIR)/biosig
 first ::
-	MKOCTFILE="/usr/bin/mkoctfile" $(MAKE) -C biosig4c++/mex mex4o
+	MKOCTFILE=":" $(MAKE) -C biosig4c++/mex mex4o
 install ::
 	# mexbiosig
 	#-/usr/bin/octave --no-gui --eval "pkg install -global biosig4c++/mex/mexbiosig-2.3.3.src.tar.gz"
@@ -145,7 +145,7 @@ clean ::
 	$(MAKE) -C biosig4c++/python clean
 endif
 
-ifneq (:,/usr/bin/R)
+ifneq (:,:)
 first ::
 	-$(MAKE) -C biosig4c++/R build
 install ::
--- origsrc/biosig-2.3.3/biosig4c++/Makefile	2021-08-13 11:17:24.000000000 +0200
+++ src/biosig-2.3.3/biosig4c++/Makefile	2022-01-12 21:54:45.047825000 +0100
@@ -94,8 +94,8 @@ CFLAGS       += -pipe -fPIC -fno-builtin
 CFLAGS       += -Wno-deprecated
 CFLAGS       += -fvisibility=hidden
 
-prefix        = /usr/local
-exec_prefix  ?= /usr/local
+prefix        = /usr
+exec_prefix  ?= /usr
 libdir        = ${exec_prefix}/lib
 includedir    = ${prefix}/include
 bindir        = ${exec_prefix}/bin
@@ -241,7 +241,7 @@ ifeq (1,1)
 	  LDLIBS     += -lsuitesparseconfig
 	endif
 endif
-ifeq (1,1)
+ifeq (1,)
 	DEFINES      += -D=WITH_DCMTK
 	LDLIBS       += -ldcmdata -loflog -lofstd
 	SOURCES      += t210/sopen_dcmtk_read.cpp
@@ -257,7 +257,7 @@ endif
 ifeq (1,1)
 	LDLIBS     += -lm
 endif
-ifeq (1,1)
+ifeq (1,)
 	DEFINES    += -D=WITH_LIBTINYXML
 	LDLIBS     += -ltinyxml
 endif
@@ -370,7 +370,7 @@ SOURCES      += biosig.c \
 		biosig_client.c \
 		biosig_server.c
 
-ifneq (1,1)
+ifneq (1,)
   ## build with internal TinyXML when libtinyxml is not available
   SOURCES    +=	XMLParser/tinyxml.cpp \
 		XMLParser/tinyxmlparser.cpp \
@@ -790,7 +790,7 @@ win64mma: mma/biosig.tm mma/biosig.c
 #############################################################
 
 mex4o mex4m oct mex:
-	MKOCTFILE="/usr/bin/mkoctfile" $(MAKE) -C mex $@
+	MKOCTFILE=":" $(MAKE) -C mex $@
 
 mexw32 mexw64:
 	CROSS=$(CROSS) CROSS64=$(CROSS64) $(MAKE) -C mex $@
--- origsrc/biosig-2.3.3/biosig4c++/java/Makefile	2021-08-13 11:17:24.000000000 +0200
+++ src/biosig-2.3.3/biosig4c++/java/Makefile	2022-01-12 21:54:45.719726700 +0100
@@ -9,7 +9,7 @@
 ### JNI ###
 # https://stackoverflow.com/questions/5963266/call-c-function-from-java
 
-JAVA_HOME ?= $(realpath $(dir $(realpath $(shell which /usr/bin/javac )))/..)
+JAVA_HOME ?= $(realpath $(dir $(realpath $(shell which : )))/..)
 
 CLASS_PATH ?= $(JAVA_HOME)/bin
 
@@ -21,13 +21,13 @@ libBiosig.so: Biosig.h Biosig.c
 		Biosig.c -L.. -lbiosig -o libBiosig.so
 
 Biosig.h: Biosig.class
-	/usr/bin/javac -h . Biosig.java
+	: -h . Biosig.java
 
 Biosig.class: Biosig.java
-	/usr/bin/javac Biosig.java
+	: Biosig.java
 
 test: libBiosig.so
-	LD_LIBRARY_PATH=.. /usr/bin/java -Djava.library.path=. Biosig "../data/Newtest17-256.bdf"
+	LD_LIBRARY_PATH=.. : -Djava.library.path=. Biosig "../data/Newtest17-256.bdf"
 
 clean: 
 	-rm *.h
--- origsrc/biosig-2.3.3/biosig4c++/mex/Makefile	2021-08-13 11:17:24.000000000 +0200
+++ src/biosig-2.3.3/biosig4c++/mex/Makefile	2022-01-12 21:54:46.157222500 +0100
@@ -116,7 +116,7 @@ else
 	SONAME_POSTFIX = .$(DLEXT).${MAJOR_VERSION}.${MINOR_VERSION}
 endif
 
-exec_prefix ?= /usr/local
+exec_prefix ?= /usr
 
 DEFINES_ALL   = #-D=NDEBUG
 
--- origsrc/biosig-2.3.3/biosig4c++/mma/Makefile	2021-08-13 11:17:24.000000000 +0200
+++ src/biosig-2.3.3/biosig4c++/mma/Makefile	2022-01-12 21:54:46.375982200 +0100
@@ -13,7 +13,7 @@
 CROSS   ?= /home/schloegl/src/mxe.github.schloegl/usr/bin/i686-w64-mingw32.static
 CROSS64 ?= /home/schloegl/src/mxe.github.schloegl/usr/bin/x86_64-w64-mingw32.static
 
-exec_prefix ?= /usr/local
+exec_prefix ?= /usr
 
 ###########################################
 ## set Mathematica variables

[-- Attachment #5: biosig-2.3.3-1-src.hint --]
[-- Type: text/plain, Size: 1071 bytes --]

# comment
sdesc: "Tools for biomedical signal processing"
ldesc: "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, etc. Major application areas are: Neuroinformatics, 
brain-computer interfaces, neurophysiology, psychology, 
cardiovascular 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 addressed 
in this scientific field. BioSig handles this by providing solutions for 
data acquisition, artifact processing, quality control, feature extraction, 
classification, modeling, data visualization, etc. "
category: Libs,Science,Utils
homepage: http://biosig.sourceforge.net/
build-depends: libb64 libcholmod-dev libtinyxml libz 
test:
skip:
version: 2.3.3
# disable-check: check-name [check-name...]

[-- Attachment #6: libbiosig-2.3.3-1.hint --]
[-- Type: text/plain, Size: 445 bytes --]

# comment
sdesc: "Libary for biomedical signal processing"
ldesc: "Libary for biomedical signal processing"
category: Libs
requires: cholmod cygwin
# depends: version-relation[, version-relation...]
# obsoletes: version-relation[, version-relation...]
provides: libbiosig
# conflicts: version-relation[, version-relation...]
external-source: biosig
# message: id "some text"
test:
version: 2.3.3
# disable-check: check-name [check-name...]






[-- Attachment #7: libbiosig_devel-2.3.3-1.hint --]
[-- Type: text/plain, Size: 453 bytes --]

# comment
sdesc: "Libary for biomedical signal processing"
ldesc: "Libary for biomedical signal processing"
category: Libs
requires: cholmod-devel cygwin
# depends: version-relation[, version-relation...]
# obsoletes: version-relation[, version-relation...]
# provides: libbiosig
# conflicts: version-relation[, version-relation...]
external-source: biosig
# message: id "some text"
test:
version: 2.3.3
# disable-check: check-name [check-name...]

Re: [ITP] biosig [was: Re: newcomer issues when packaging biosig, stimfit, etc.]

[Marco Atzeri]

On 12.01.2022 23:59, Alois Schlögl wrote:
> 
> 
> Am 1/12/22 um 06:47 schrieb Marco Atzeri:
>>> In the meantime, please find below the status for the libb64 and 
>>> biosig packages.
>>
>>> Thanks that was helpful. Attached is an updated version for biosig 
>>> and libb64.
>>>
>>> cygport libb64.cygport all
>>> cygport biosig.cygport all
>>>
>>> runs now w/o error. How can I test whether result can be installed 
>>> and used ?
>>
>> One major problem.
>> Never build in the source directory, the final src.patch
>> must fit with you desired patch.
>> So only what you patched should come out.
>>
>> For this package that does not respect the build in a
>> different directory than source, you shoud start
>> with something like:
>>
>> src_compile() {
>>         cd ${S}
>>         lndirs
>>         cd ${B}
>>         cygautoreconf
>>         cygconf
>>         cygmake
>> } 
> 
> 
> 
> I've adapted biosig.cygport accordingly and addressed this in the 
> attached version. It runs fine when doing
> 
>     cygport biosig.cygport all
> 
> runs w/o error. Also testing the package with
> 
> tar -C / -xvf 
> biosig-2.3.3-1.x86_64/dist/biosig/biosig-tools/biosig-tools-2.3.3-1.tar.xz
> tar -C / -xvf 
> biosig-2.3.3-1.x86_64/dist/biosig/libbiosig/libbiosig-2.3.3-1.tar.xz
> tar -C / -xvf 
> biosig-2.3.3-1.x86_64/dist/biosig/libbiosig-devel/libbiosig-devel-2.3.3-1.tar.xz 
> 
> 
> and running
>     save2gdf -h
> works fine.
> 
> Moreover, I understand now why my libb64.cygport file is not ready. 
> ecause libb64 is not necessary for libbiosig's support of Stimfit, I'll 
> omit libb64 for now.
> Would you please check whether Biosig is ready to be included in cygwin ?
> 
> 
> Cheers,
>     Alois


Hi Alois.

it is almost fine

the only problem I see is that the shared library are build as

   libbiosig.dll while they should be called cygbiosig.dll
   (probably better cygbiosig-3.dll to handle the SOMANE)

please also run the test in the ${B} directory


I was playing with the CMakeList.txt to see if that was more easy
than your deep patch of the upstream Makefile's

src_compile() {
     cd ${B}
     CYGCMAKE_SOURCE="${S}/biosig4c++"
     cygcmake
     cygmake


I see however that also the CMakeLists.txt need some patching as
it builds only the shared lib withouh the SONAME and it is not updated 
to include all the needed file in the t40x directory
and does not build the utility.

Sorry for slow response, but I have little time in this moment

Regards
Marco

Re: [ITP] biosig [was: Re: newcomer issues when packaging biosig, stimfit, etc.]

[Alois Schlögl]

Am 1/14/22 um 11:09 schrieb Marco Atzeri:
> On 12.01.2022 23:59, Alois Schlögl wrote:
>>
>>
>> Am 1/12/22 um 06:47 schrieb Marco Atzeri:
>>>> In the meantime, please find below the status for the libb64 and 
>>>> biosig packages.
>>>
>>>> Thanks that was helpful. Attached is an updated version for biosig 
>>>> and libb64.
>>>>
>>>> cygport libb64.cygport all
>>>> cygport biosig.cygport all
>>>>
>>>> runs now w/o error. How can I test whether result can be installed 
>>>> and used ?
>>>
>>> One major problem.
>>> Never build in the source directory, the final src.patch
>>> must fit with you desired patch.
>>> So only what you patched should come out.
>>>
>>> For this package that does not respect the build in a
>>> different directory than source, you shoud start
>>> with something like:
>>>
>>> src_compile() {
>>>         cd ${S}
>>>         lndirs
>>>         cd ${B}
>>>         cygautoreconf
>>>         cygconf
>>>         cygmake
>>> } 
>>
>>
>>
>> I've adapted biosig.cygport accordingly and addressed this in the 
>> attached version. It runs fine when doing
>>
>>     cygport biosig.cygport all
>>
>> runs w/o error. Also testing the package with
>>
>> tar -C / -xvf 
>> biosig-2.3.3-1.x86_64/dist/biosig/biosig-tools/biosig-tools-2.3.3-1.tar.xz
>> tar -C / -xvf 
>> biosig-2.3.3-1.x86_64/dist/biosig/libbiosig/libbiosig-2.3.3-1.tar.xz
>> tar -C / -xvf 
>> biosig-2.3.3-1.x86_64/dist/biosig/libbiosig-devel/libbiosig-devel-2.3.3-1.tar.xz 
>>
>>
>> and running
>>     save2gdf -h
>> works fine.
>>
>> Moreover, I understand now why my libb64.cygport file is not ready. 
>> ecause libb64 is not necessary for libbiosig's support of Stimfit, 
>> I'll omit libb64 for now.
>> Would you please check whether Biosig is ready to be included in 
>> cygwin ?
>>
>>
>> Cheers,
>>     Alois
>
>
> Hi Alois.
>
> it is almost fine


Hi Marco,

thanks for the feedback.


>
> the only problem I see is that the shared library are build as
>
>   libbiosig.dll while they should be called cygbiosig.dll
>   (probably better cygbiosig-3.dll to handle the SOMANE)
>

I tried to do that, but run into issue. The exe-files still expect 
libbbiosig.dll, and do not recognise cygbiosig-3.dll
It seems this would require significant changes by upstream, also by 
other projects that would make use of libbiosig (e.g. stimfit, 
sigviewer, python-biosig, etc.)
Since I do not under stand the purpose of renaming libbiosig to 
cygbiosig, I'm reluctant to go that route.
What kind of problems is this renaming supposed to solve ?

Concerning SONAME-versioning, I'd like to avoid this for now, and 
introduce versioning only when its really needed.
In the foreseeable future, I do not expect any changes will be needed 
that would break the API

> please also run the test in the ${B} directory

Done, this works without error. Please adapt that change accordingly.

>
>
> I was playing with the CMakeList.txt to see if that was more easy
> than your deep patch of the upstream Makefile's
>

I'm afraid that this "deep patch" is just an accidental artifact.
When running configure, all Makefile are rebuild from Makefile.in,
The Makefile(s) were packaged just by accident in v2.3.3.
But in fact these Makefiles should not have part of the released package.



Cheers,
   Alois

Re: [ITP] biosig [was: Re: newcomer issues when packaging biosig, stimfit, etc.]

[Marco Atzeri]

On 14.01.2022 22:48, Alois Schlögl wrote:
> 
> 
> Am 1/14/22 um 11:09 schrieb Marco Atzeri:
>> On 12.01.2022 23:59, Alois Schlögl wrote:

>>
>> I was playing with the CMakeList.txt to see if that was more easy
>> than your deep patch of the upstream Makefile's
>>
> 
> I'm afraid that this "deep patch" is just an accidental artifact.
> When running configure, all Makefile are rebuild from Makefile.in,
> The Makefile(s) were packaged just by accident in v2.3.3.
> But in fact these Makefiles should not have part of the released package.
> 

add DIFF_EXCLUDES="Makefile" to avoid the artifact


> Cheers,
>    Alois

Re: [ITP] biosig [was: Re: newcomer issues when packaging biosig, stimfit, etc.]

[Achim Gratz]

Marco Atzeri writes:
> add DIFF_EXCLUDES="Makefile" to avoid the artifact

DISTCLEANFILES would be more appropriate it seems.


Regards,
Achim.
-- 
+<[Q+ Matrix-12 WAVE#46+305 Neuron microQkb Andromeda XTk Blofeld]>+

SD adaptation for Waldorf microQ V2.22R2:
http://Synth.Stromeko.net/Downloads.html#WaldorfSDada

Re: [ITP] biosig [was: Re: newcomer issues when packaging biosig, stimfit, etc.]

[Alois Schlögl]

[-- Attachment #1: Type: text/plain, Size: 888 bytes --]



Am 1/15/22 um 19:01 schrieb Marco Atzeri:
> On 14.01.2022 22:48, Alois Schlögl wrote:
>>
>>
>> Am 1/14/22 um 11:09 schrieb Marco Atzeri:
>>> On 12.01.2022 23:59, Alois Schlögl wrote:
>
>>>
>>> I was playing with the CMakeList.txt to see if that was more easy
>>> than your deep patch of the upstream Makefile's
>>>
>>
>> I'm afraid that this "deep patch" is just an accidental artifact.
>> When running configure, all Makefile are rebuild from Makefile.in,
>> The Makefile(s) were packaged just by accident in v2.3.3.
>> But in fact these Makefiles should not have part of the released 
>> package.
>>
>
> add DIFF_EXCLUDES="Makefile" to avoid the artifact
>
>
>> Cheers,
>>    Alois


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











[-- Attachment #2: biosig.cygport --]
[-- Type: text/plain, Size: 3792 bytes --]

# package name
NAME="biosig"
VERSION=2.3.3
RELEASE=1

# .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="biosig-2.3.3-fix-build.patch"

# use the standard src_compile, src_install and src_test


PKG_NAMES="libbiosig libbiosig-devel biosig-tools python39-biosig"
# PKG_NAMES="libbiosig libbiosig-devel biosig-tools"

biosig_tools_CONTENTS="
  usr/bin/save2gdf.exe
  usr/bin/physicalunits.exe
  usr/bin/biosig2gdf.exe
  usr/share/man/man1/save2gdf.1.gz  
  usr/share/man/man1/biosig2gdf.1.gz
  usr/share/man/man1/biosig_fhir.1.gz  
  usr/share/man/man1/physicalunits.1.gz

  usr/share/doc/biosig/COPYING
  usr/share/doc/biosig/README
"
# not included yet
# usr/share/man/biosig_fhir.1  usr/share/man/sigviewer.1


libbiosig_CONTENTS="
  usr/bin/libbiosig.dll
  usr/bin/libphysicalunits.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
"

#python3-biosig_CONTENTS="
#	dist/Biosig-2.3.3-cp39-cp39-cygwin_3_3_3_x86_64.whl
#"

DIFF_EXCLUDES="depend Makefile"

# use not standard src_compile, src_install and src_test

src_compile() {
        cd ${S}
        lndirs
        cd ${B}
        cygautoreconf
        cygconf  # --prefix=/usr
	# libbiosig
	cygmake lib
	# biosig-tools w/o biosig_fhir
	cygmake -C biosig4c++ save2gdf physicalunits biosig2gdf
	# python3-biosig
	cygmake -C biosig4c++/python wheel
	# cd ${B}/biosig4c++/python/
	# python3_distutils_compile bdist_wheel
	# python3_wheel_compile

}

src_install() {
	cd ${S}

	doinclude ${S}/biosig4c++/*.h
	
	dobin ${B}/biosig4c++/save2gdf.exe 
        # dobin ${B}/biosig4c++/biosig_fhir.exe
	dobin ${B}/biosig4c++/biosig2gdf.exe 
	dobin ${B}/biosig4c++/physicalunits.exe 
	dobin ${B}/biosig4c++/libbiosig.dll 
	dobin ${B}/biosig4c++/libphysicalunits.dll 

	dolib ${B}/biosig4c++/libbiosig.dll.a 
	dolib ${B}/biosig4c++/libbiosig.a 
	dolib ${B}/biosig4c++/libphysicalunits.dll.a 
	dolib ${B}/biosig4c++/libphysicalunits.a 

        dopkgconfig ${B}/biosig4c++/libbiosig.pc

	# doman ${S}/biosig4c++/doc/bin2rec.1
        doman ${S}/biosig4c++/doc/biosig2gdf.1
        doman ${S}/biosig4c++/doc/biosig_fhir.1
        doman ${S}/biosig4c++/doc/physicalunits.1
        doman ${S}/biosig4c++/doc/save2gdf.1

	# dowheel ${B}/biosig4c++/python/dist/Biosig-2.3.3-cp39-cp39-cygwin_3_3_3_x86_64.whl

}

src_test() {
    cd ${B}
    biosig4c++/physicalunits.exe
    biosig4c++/save2gdf.exe  --help
    # biosig4c++/biosig_fhir.exe --help
    python -c "import biosig"
}


[-- Attachment #3: biosig-2.3.3-1-src.hint --]
[-- Type: text/plain, Size: 1090 bytes --]

# comment
sdesc: "Tools for biomedical signal processing"
ldesc: "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, etc. Major application areas are: Neuroinformatics, 
brain-computer interfaces, neurophysiology, psychology, 
cardiovascular 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 addressed 
in this scientific field. BioSig handles this by providing solutions for 
data acquisition, artifact processing, quality control, feature extraction, 
classification, modeling, data visualization, etc. "
category: Libs,Science,Utils
homepage: http://biosig.sourceforge.net/
build-depends: libb64 libcholmod-dev libtinyxml libz python-wheel-wheel 
test:
skip:
version: 2.3.3
# disable-check: check-name [check-name...]

[-- Attachment #4: biosig-2.3.3-1.hint --]
[-- Type: text/plain, Size: 1293 bytes --]

# comment
sdesc: "Tools for biomedical signal processing"
ldesc: "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, etc. Major application areas are: Neuroinformatics, 
brain-computer interfaces, neurophysiology, psychology, 
cardiovascular 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 addressed 
in this scientific field. BioSig handles this by providing solutions for 
data acquisition, artifact processing, quality control, feature extraction, 
classification, modeling, data visualization, etc. "
category: Libs,Science,Utils
requires: libb64 libcholmod tinyxml cygwin
# depends: version-relation[, version-relation...]
# obsoletes: version-relation[, version-relation...]
# provides: package[, package...]
# conflicts: version-relation[, version-relation...]
external-source: release/biosig/biosig-2.3.3-1-src.tar.xz
# message: id "some text"
test:
version: 2.3.3
# disable-check: check-name [check-name...]






[-- Attachment #5: libbiosig-2.3.3-1.hint --]
[-- Type: text/plain, Size: 445 bytes --]

# comment
sdesc: "Libary for biomedical signal processing"
ldesc: "Libary for biomedical signal processing"
category: Libs
requires: cholmod cygwin
# depends: version-relation[, version-relation...]
# obsoletes: version-relation[, version-relation...]
provides: libbiosig
# conflicts: version-relation[, version-relation...]
external-source: biosig
# message: id "some text"
test:
version: 2.3.3
# disable-check: check-name [check-name...]






[-- Attachment #6: libbiosig_devel-2.3.3-1.hint --]
[-- Type: text/plain, Size: 453 bytes --]

# comment
sdesc: "Libary for biomedical signal processing"
ldesc: "Libary for biomedical signal processing"
category: Libs
requires: cholmod-devel cygwin
# depends: version-relation[, version-relation...]
# obsoletes: version-relation[, version-relation...]
# provides: libbiosig
# conflicts: version-relation[, version-relation...]
external-source: biosig
# message: id "some text"
test:
version: 2.3.3
# disable-check: check-name [check-name...]






[-- Attachment #7: python39-biosig-2.3.3-1.hint --]
[-- Type: text/plain, Size: 563 bytes --]

# comment
sdesc: "Biosig for Python"
ldesc: "Python-bindings to libbiosig, can be use
to load all biosig dataformats in to Python. 
category: Libs,Science,Utils
requires: libbiosig-devel python39 python39-numpy cygwin
# depends: version-relation[, version-relation...]
# obsoletes: version-relation[, version-relation...]
# provides: package[, package...]
# conflicts: version-relation[, version-relation...]
external-source: release/biosig/biosig-2.3.3-1-src.tar.xz
# message: id "some text"
test:
version: 2.3.3
# disable-check: check-name [check-name...]

Re: [ITP] biosig [was: Re: newcomer issues when packaging biosig, stimfit, etc.]

[Alois Schlögl]

[-- Attachment #1: Type: text/plain, Size: 293 bytes --]



Am 1/15/22 um 21:44 schrieb Achim Gratz:
> Marco Atzeri writes:
>> add DIFF_EXCLUDES="Makefile" to avoid the artifact
> DISTCLEANFILES would be more appropriate it seems.
>
>
> Regards,
> Achim.


I tried this (see attachment), but I'm not sure this is what you meant.


Regards,
    Alois

[-- Attachment #2: biosig.cygport --]
[-- Type: text/plain, Size: 3878 bytes --]

# package name
NAME="biosig"
VERSION=2.3.3
RELEASE=1

# .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="biosig-2.3.3-fix-build.patch"

# use the standard src_compile, src_install and src_test


PKG_NAMES="libbiosig libbiosig-devel biosig-tools python3-biosig"
# PKG_NAMES="libbiosig libbiosig-devel biosig-tools"

biosig_tools_CONTENTS="
  usr/bin/save2gdf.exe
  usr/bin/physicalunits.exe
  usr/bin/biosig2gdf.exe
  usr/share/man/man1/save2gdf.1.gz  
  usr/share/man/man1/biosig2gdf.1.gz
  usr/share/man/man1/biosig_fhir.1.gz  
  usr/share/man/man1/physicalunits.1.gz

  usr/share/doc/biosig/COPYING
  usr/share/doc/biosig/README
"
# not included yet
# usr/share/man/biosig_fhir.1  usr/share/man/sigviewer.1


libbiosig_CONTENTS="
  usr/bin/libbiosig.dll
  usr/bin/libphysicalunits.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
"

#python3-biosig_CONTENTS="
#	dist/Biosig-2.3.3-cp39-cp39-cygwin_3_3_3_x86_64.whl
#"

DIFF_EXCLUDES="depend"

# CYGPORT_USE_UNSTABLE_API=1
# use not standard src_compile, src_install and src_test

src_prep() {
	DISTCLEANFILES
}

src_compile() {
        cd ${S}
        lndirs
        cd ${B}
        cygautoreconf
        cygconf  # --prefix=/usr
	# libbiosig
	cygmake lib
	# biosig-tools w/o biosig_fhir
	cygmake -C biosig4c++ save2gdf physicalunits biosig2gdf
	# python3-biosig
	cygmake -C biosig4c++/python wheel
	# cd ${B}/biosig4c++/python/
	# python3_distutils_compile bdist_wheel
	# python3_wheel_compile

}

src_install() {
	cd ${S}

	doinclude ${S}/biosig4c++/*.h
	
	dobin ${B}/biosig4c++/save2gdf.exe 
        # dobin ${B}/biosig4c++/biosig_fhir.exe
	dobin ${B}/biosig4c++/biosig2gdf.exe 
	dobin ${B}/biosig4c++/physicalunits.exe 
	dobin ${B}/biosig4c++/libbiosig.dll 
	dobin ${B}/biosig4c++/libphysicalunits.dll 

	dolib ${B}/biosig4c++/libbiosig.dll.a 
	dolib ${B}/biosig4c++/libbiosig.a 
	dolib ${B}/biosig4c++/libphysicalunits.dll.a 
	dolib ${B}/biosig4c++/libphysicalunits.a 

        dopkgconfig ${B}/biosig4c++/libbiosig.pc

	# doman ${S}/biosig4c++/doc/bin2rec.1
        doman ${S}/biosig4c++/doc/biosig2gdf.1
        doman ${S}/biosig4c++/doc/biosig_fhir.1
        doman ${S}/biosig4c++/doc/physicalunits.1
        doman ${S}/biosig4c++/doc/save2gdf.1

	# dowheel ${B}/biosig4c++/python/dist/Biosig-2.3.3-cp39-cp39-cygwin_3_3_3_x86_64.whl

}

src_test() {
    cd ${B}
    biosig4c++/physicalunits.exe
    biosig4c++/save2gdf.exe  --help
    # biosig4c++/biosig_fhir.exe --help
    python -c "import biosig"
    check_python3_module biosigABC
}

Re: [ITP] biosig [was: Re: newcomer issues when packaging biosig, stimfit, etc.]

[Brian Inglis]

On 2022-01-17 14:44, Alois Schlögl wrote:
> Am 1/15/22 um 21:44 schrieb Achim Gratz:
>> Marco Atzeri writes:

>>> add DIFF_EXCLUDES="Makefile" to avoid the artifact

>> DISTCLEANFILES would be more appropriate it seems.

DISTCLEANFILES is deleted immediately after downloading and unpacking 
the *UPSTREAM* source:

	https://cygwin.github.io/cygport/src_prep_cygpart.html#robo112

"A list of files to be deleted immediately upon unpacking sources, 
relative to $S. This is intended to be used with buildsystem-generated 
files which are incorrectly included in the source tarball."

> I tried this (see attachment), but I'm not sure this is what you meant.

DIFF_EXCLUDES is a list of files generated in $S not automatically 
excluded from the source package:

	https://cygwin.github.io/cygport/pkg_pkg_cygpart.html#robo384

"A list of file names, directory names, or glob patterns in $S which 
will be excluded when creating the .src.patch file. This should be used 
for files automatically generated in $S to avoid polluting the patch.
NOTE
Files generated by various buildsystem infrastructures, such as 
autoconf, automake, gettext, and libtool are already excluded 
automatically and need not be listed here."

Add to DIFF_EXCLUDES the names of any files you see after the output 
header:

>>> Creating source patches

-- 
Take care. Thanks, Brian Inglis, Calgary, Alberta, Canada

This email may be disturbing to some readers as it contains
too much technical detail. Reader discretion is advised.
[Data in binary units and prefixes, physical quantities in SI.]

Re: [ITP] biosig [was: Re: newcomer issues when packaging biosig, stimfit, etc.]

[Alois Schlögl]

[-- Attachment #1: Type: text/plain, Size: 1782 bytes --]



Am 1/18/22 um 06:32 schrieb Brian Inglis:
> On 2022-01-17 14:44, Alois Schlögl wrote:
>> Am 1/15/22 um 21:44 schrieb Achim Gratz:
>>> Marco Atzeri writes:
>
>>>> add DIFF_EXCLUDES="Makefile" to avoid the artifact
>
>>> DISTCLEANFILES would be more appropriate it seems.
>
> DISTCLEANFILES is deleted immediately after downloading and unpacking 
> the *UPSTREAM* source:
>
>     https://cygwin.github.io/cygport/src_prep_cygpart.html#robo112
>
> "A list of files to be deleted immediately upon unpacking sources, 
> relative to $S. This is intended to be used with buildsystem-generated 
> files which are incorrectly included in the source tarball."
>
>> I tried this (see attachment), but I'm not sure this is what you meant.
>
> DIFF_EXCLUDES is a list of files generated in $S not automatically 
> excluded from the source package:
>
>     https://cygwin.github.io/cygport/pkg_pkg_cygpart.html#robo384
>
> "A list of file names, directory names, or glob patterns in $S which 
> will be excluded when creating the .src.patch file. This should be 
> used for files automatically generated in $S to avoid polluting the 
> patch.
> NOTE
> Files generated by various buildsystem infrastructures, such as 
> autoconf, automake, gettext, and libtool are already excluded 
> automatically and need not be listed here."
>


> Add to DIFF_EXCLUDES the names of any files you see after the output 
> header:
>
>>>> Creating source patches
>


Ok, thanks for these clear hints. I've now added these files as 
suggested. The revised version is attached.
Moreover, I've removed (commented) all aspects for building of 
python-biosig bindings, in order not to delay the inclusion of Biosig in 
Cygwin.
Is there anything else that need to be considered ?



Cheers,
    Alois







[-- Attachment #2: biosig.cygport --]
[-- Type: text/plain, Size: 3981 bytes --]

# package name
NAME="biosig"
VERSION=2.3.3
RELEASE=1

# .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="biosig-2.3.3-fix-build.patch"

# use the standard src_compile, src_install and src_test

# PKG_NAMES="libbiosig libbiosig-devel biosig-tools python3-biosig"
PKG_NAMES="libbiosig libbiosig-devel biosig-tools"

biosig_tools_CONTENTS="
  usr/bin/save2gdf.exe
  usr/bin/physicalunits.exe
  usr/bin/biosig2gdf.exe
  usr/share/man/man1/save2gdf.1.gz  
  usr/share/man/man1/biosig2gdf.1.gz
  usr/share/man/man1/biosig_fhir.1.gz  
  usr/share/man/man1/physicalunits.1.gz

  usr/share/doc/biosig/COPYING
  usr/share/doc/biosig/README
"
# not included yet, would require libb64
# usr/share/man/biosig_fhir.1  usr/share/man/sigviewer.1


libbiosig_CONTENTS="
  usr/bin/libbiosig.dll
  usr/bin/libphysicalunits.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
"

#python3-biosig_CONTENTS="
#	dist/Biosig-2.3.3-cp39-cp39-cygwin_3_3_3_x86_64.whl
#"

DIFF_EXCLUDES="depend
  Makefile                
  biosig4c++/Makefile     
  biosig4c++/java/Makefile
  biosig4c++/mex/Makefile 
  biosig4c++/mma/Makefile 
"

# use not standard src_compile, src_install and src_test

src_compile() {
        cd ${S}
        lndirs
        cd ${B}
        cygautoreconf
        cygconf  # --prefix=/usr
	### libbiosig
	cygmake lib
	### biosig-tools w/o biosig_fhir
	cygmake -C biosig4c++ save2gdf physicalunits biosig2gdf
	### python3-biosig
	# cygmake -C biosig4c++/python wheel
	# cd ${B}/biosig4c++/python/
	# python3_distutils_compile bdist_wheel
	# python3_wheel_compile
}

src_install() {
	cd ${S}

	doinclude ${S}/biosig4c++/*.h
	
	dobin ${B}/biosig4c++/save2gdf.exe 
        # dobin ${B}/biosig4c++/biosig_fhir.exe
	dobin ${B}/biosig4c++/biosig2gdf.exe 
	dobin ${B}/biosig4c++/physicalunits.exe 
	dobin ${B}/biosig4c++/libbiosig.dll 
	dobin ${B}/biosig4c++/libphysicalunits.dll 

	dolib ${B}/biosig4c++/libbiosig.dll.a 
	dolib ${B}/biosig4c++/libbiosig.a 
	dolib ${B}/biosig4c++/libphysicalunits.dll.a 
	dolib ${B}/biosig4c++/libphysicalunits.a 

        dopkgconfig ${B}/biosig4c++/libbiosig.pc

	# doman ${S}/biosig4c++/doc/bin2rec.1
        doman ${S}/biosig4c++/doc/biosig2gdf.1
        doman ${S}/biosig4c++/doc/biosig_fhir.1
        doman ${S}/biosig4c++/doc/physicalunits.1
        doman ${S}/biosig4c++/doc/save2gdf.1

	# dowheel ${B}/biosig4c++/python/dist/Biosig-2.3.3-cp39-cp39-cygwin_3_3_3_x86_64.whl
}

src_test() {
    cd ${B}
    biosig4c++/physicalunits.exe
    biosig4c++/save2gdf.exe  --help
    # biosig4c++/biosig_fhir.exe --help
    # python -c "import biosig"
    # check_python3_module biosig
}

Re: [ITP] biosig [was: Re: newcomer issues when packaging biosig, stimfit, etc.]

[Brian Inglis]

On 2022-01-18 14:50, Alois Schlögl wrote:
> Am 1/18/22 um 06:32 schrieb Brian Inglis:
>> On 2022-01-17 14:44, Alois Schlögl wrote:
>>> Am 1/15/22 um 21:44 schrieb Achim Gratz:
>>>> Marco Atzeri writes:
>>
>>>>> add DIFF_EXCLUDES="Makefile" to avoid the artifact
>>
>>>> DISTCLEANFILES would be more appropriate it seems.
>>
>> DISTCLEANFILES is deleted immediately after downloading and unpacking 
>> the *UPSTREAM* source:
>>
>>     https://cygwin.github.io/cygport/src_prep_cygpart.html#robo112
>>
>> "A list of files to be deleted immediately upon unpacking sources, 
>> relative to $S. This is intended to be used with buildsystem-generated 
>> files which are incorrectly included in the source tarball."
>>
>>> I tried this (see attachment), but I'm not sure this is what you meant.
>>
>> DIFF_EXCLUDES is a list of files generated in $S not automatically 
>> excluded from the source package:
>>
>>     https://cygwin.github.io/cygport/pkg_pkg_cygpart.html#robo384
>>
>> "A list of file names, directory names, or glob patterns in $S which 
>> will be excluded when creating the .src.patch file. This should be 
>> used for files automatically generated in $S to avoid polluting the 
>> patch.
>> NOTE
>> Files generated by various buildsystem infrastructures, such as 
>> autoconf, automake, gettext, and libtool are already excluded 
>> automatically and need not be listed here."

>> Add to DIFF_EXCLUDES the names of any files you see after the output 
>> header:
>>
>>>>> Creating source patches

> Ok, thanks for these clear hints. I've now added these files as 
> suggested. The revised version is attached.
> Moreover, I've removed (commented) all aspects for building of 
> python-biosig bindings, in order not to delay the inclusion of Biosig in 
> Cygwin.
> Is there anything else that need to be considered ?

CATEGORY is a *space* separated list in quotes.

Before SRC_URI and PATCH_URI normally comes:

	HOMEPAGE=https://sourceforge.net/projects/biosig/files/

you don't need to add quotes for nonspaced strings.

You may also test your cygport and any other source patches and files 
you require by creating and committing them into a local git repo named 
the same as the package (preferably all lower case) and pushing to the 
git-cygwin-packages playground repo and branch:

git push --set-upstream ssh://cygwin/git/cygwin-packages/playground.git
playground -f

which will submit the build to the Cygwin GitHub Action CI and print the 
link for you to monitor the CI job, view the build logs for noarch, x86, 
and x86_64, and download them.

-- 
Take care. Thanks, Brian Inglis, Calgary, Alberta, Canada

This email may be disturbing to some readers as it contains
too much technical detail. Reader discretion is advised.
[Data in binary units and prefixes, physical quantities in SI.]

Re: [ITP] biosig [was: Re: newcomer issues when packaging biosig, stimfit, etc.]

[Brian Inglis]

On 2022-01-18 15:56, Brian Inglis wrote:
> On 2022-01-18 14:50, Alois Schlögl wrote:
>> Am 1/18/22 um 06:32 schrieb Brian Inglis:
>>> On 2022-01-17 14:44, Alois Schlögl wrote:
>>>> Am 1/15/22 um 21:44 schrieb Achim Gratz:
>>>>> Marco Atzeri writes:
>>>
>>>>>> add DIFF_EXCLUDES="Makefile" to avoid the artifact
>>>
>>>>> DISTCLEANFILES would be more appropriate it seems.
>>>
>>> DISTCLEANFILES is deleted immediately after downloading and unpacking 
>>> the *UPSTREAM* source:
>>>
>>>     https://cygwin.github.io/cygport/src_prep_cygpart.html#robo112
>>>
>>> "A list of files to be deleted immediately upon unpacking sources, 
>>> relative to $S. This is intended to be used with 
>>> buildsystem-generated files which are incorrectly included in the 
>>> source tarball."
>>>
>>>> I tried this (see attachment), but I'm not sure this is what you meant.
>>>
>>> DIFF_EXCLUDES is a list of files generated in $S not automatically 
>>> excluded from the source package:
>>>
>>>     https://cygwin.github.io/cygport/pkg_pkg_cygpart.html#robo384
>>>
>>> "A list of file names, directory names, or glob patterns in $S which 
>>> will be excluded when creating the .src.patch file. This should be 
>>> used for files automatically generated in $S to avoid polluting the 
>>> patch.
>>> NOTE
>>> Files generated by various buildsystem infrastructures, such as 
>>> autoconf, automake, gettext, and libtool are already excluded 
>>> automatically and need not be listed here."
> 
>>> Add to DIFF_EXCLUDES the names of any files you see after the output 
>>> header:
>>>
>>>>>> Creating source patches
> 
>> Ok, thanks for these clear hints. I've now added these files as 
>> suggested. The revised version is attached.
>> Moreover, I've removed (commented) all aspects for building of 
>> python-biosig bindings, in order not to delay the inclusion of Biosig 
>> in Cygwin.
>> Is there anything else that need to be considered ?
> 
> CATEGORY is a *space* separated list in quotes.
> 
> Before SRC_URI and PATCH_URI normally comes:
> 
>      HOMEPAGE=https://sourceforge.net/projects/biosig/files/
> 
> you don't need to add quotes for nonspaced strings.
> 
> You may also test your cygport and any other source patches and files 
> you require by creating and committing them into a local git repo named 
> the same as the package (preferably all lower case) and pushing to the 
> git-cygwin-packages playground repo and branch:
> 
> git push --set-upstream ssh://cygwin/git/cygwin-packages/playground.git
> playground -f
> 
> which will submit the build to the Cygwin GitHub Action CI and print the 
> link for you to monitor the CI job, view the build logs for noarch, x86, 
> and x86_64, and download them.

I just noticed that your description is badly wrapped: to avoid this, 
run the text through fmt or your editor equivalent (e.g. gvim :set tw=72 
then gqq to wrap the lines) and paste between the quotes after 
DESCRIPTION="...
...".

Forgot to mention BUILD_REQUIRES which lists all the packages and 
libraries which need installed to build the package(s) using cygport.

 From your README for Debian, on Cygwin those packages would probably be:

BUILD_REQUIRES="libtinyxml2-devel octave-devel python-devel"
BUILD_REQUIRES+=" gawk python-numpy python3-numpy R"

and your runtime dependencies should be reported by cygport at the end 
of the packaging stage as:

 >>> biosig requires: cygwin libtinyxml2_6 octave-nan octave-tsa R

If any are missing, you may add them using REQUIRES similar to 
BUILD_REQUIRES, however specifying all the packages with REQUIRES 
results in confusing duplication in cygport output and the setup.ini 
biosig requires: line entry.

-- 
Take care. Thanks, Brian Inglis, Calgary, Alberta, Canada

This email may be disturbing to some readers as it contains
too much technical detail. Reader discretion is advised.
[Data in binary units and prefixes, physical quantities in SI.]

Re: [ITP] biosig [was: Re: newcomer issues when packaging biosig, stimfit, etc.]

[Alois Schlögl]

Am 1/18/22 um 23:56 schrieb Brian Inglis:
> On 2022-01-18 14:50, Alois Schlögl wrote:
>> Am 1/18/22 um 06:32 schrieb Brian Inglis:
>>> On 2022-01-17 14:44, Alois Schlögl wrote:
>>>> Am 1/15/22 um 21:44 schrieb Achim Gratz:
>>>>> Marco Atzeri writes:
>>>
>>>>>> add DIFF_EXCLUDES="Makefile" to avoid the artifact
>>>
>>>>> DISTCLEANFILES would be more appropriate it seems.
>>>
>>> DISTCLEANFILES is deleted immediately after downloading and 
>>> unpacking the *UPSTREAM* source:
>>>
>>>     https://cygwin.github.io/cygport/src_prep_cygpart.html#robo112
>>>
>>> "A list of files to be deleted immediately upon unpacking sources, 
>>> relative to $S. This is intended to be used with 
>>> buildsystem-generated files which are incorrectly included in the 
>>> source tarball."
>>>
>>>> I tried this (see attachment), but I'm not sure this is what you 
>>>> meant.
>>>
>>> DIFF_EXCLUDES is a list of files generated in $S not automatically 
>>> excluded from the source package:
>>>
>>>     https://cygwin.github.io/cygport/pkg_pkg_cygpart.html#robo384
>>>
>>> "A list of file names, directory names, or glob patterns in $S which 
>>> will be excluded when creating the .src.patch file. This should be 
>>> used for files automatically generated in $S to avoid polluting the 
>>> patch.
>>> NOTE
>>> Files generated by various buildsystem infrastructures, such as 
>>> autoconf, automake, gettext, and libtool are already excluded 
>>> automatically and need not be listed here."
>
>>> Add to DIFF_EXCLUDES the names of any files you see after the output 
>>> header:
>>>
>>>>>> Creating source patches
>
>> Ok, thanks for these clear hints. I've now added these files as 
>> suggested. The revised version is attached.
>> Moreover, I've removed (commented) all aspects for building of 
>> python-biosig bindings, in order not to delay the inclusion of Biosig 
>> in Cygwin.
>> Is there anything else that need to be considered ?
>
> CATEGORY is a *space* separated list in quotes.
>
> Before SRC_URI and PATCH_URI normally comes:
>
>     HOMEPAGE=https://sourceforge.net/projects/biosig/files/
>
> you don't need to add quotes for nonspaced strings.
>
> You may also test your cygport and any other source patches and files 
> you require by creating and committing them into a local git repo 
> named the same as the package (preferably all lower case) and pushing 
> to the git-cygwin-packages playground repo and branch:
>
> git push --set-upstream ssh://cygwin/git/cygwin-packages/playground.git
> playground -f
>
> which will submit the build to the Cygwin GitHub Action CI and print 
> the link for you to monitor the CI job, view the build logs for 
> noarch, x86, and x86_64, and download them.
>


In order to use the playgroun, I guess I need to provide my ssh key. 
Here it is:

Name: Alois Schloegl
---- BEGIN SSH2 PUBLIC KEY ----
AAAAC3NzaC1lZDI1NTE5AAAAILKBmNf1QN3lStTwpn46QIip7sS6zNKy0rG8WCYHv/ZU
---- END SSH2 PUBLIC KEY ----


Cheers,
   Alois

Re: [ITP] biosig [was: Re: newcomer issues when packaging biosig, stimfit, etc.]

[Jon Turney]

On 20/01/2022 20:48, Alois Schlögl wrote:
> 
> In order to use the playgroun, I guess I need to provide my ssh key. 
> Here it is:
> 
> Name: Alois Schloegl
> ---- BEGIN SSH2 PUBLIC KEY ----
> AAAAC3NzaC1lZDI1NTE5AAAAILKBmNf1QN3lStTwpn46QIip7sS6zNKy0rG8WCYHv/ZU
> ---- END SSH2 PUBLIC KEY ----

Done.

> Updating ssh key for Alois Schloegl
> Fingerprint: 256 SHA256:bvMkxeY5KcLLESayAW43ZPOiYI9owtf0UKKWIWmue00 no comment (ED25519)

Re: [ITP] biosig [was: Re: newcomer issues when packaging biosig, stimfit, etc.]

[Marco Atzeri]

[-- Attachment #1: Type: text/plain, Size: 1752 bytes --]

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

[-- Attachment #2: 2.3.3-1.Makefilein.patch --]
[-- Type: text/plain, Size: 9144 bytes --]

--- 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}
 
 
 #############################################################

[-- Attachment #3: biosig.cygport --]
[-- Type: text/plain, Size: 2918 bytes --]

# 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"
}

Re: [ITP] biosig [was: Re: newcomer issues when packaging biosig, stimfit, etc.]

[Alois Schlögl]

[-- Attachment #1: Type: text/plain, Size: 2178 bytes --]



Am 1/22/22 um 18:52 schrieb Marco Atzeri:
> 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


Hi  Marco,


thanks for the improvements (especially, libb64 which enables 
biosig_fhir, and python-biosig).
Attached is a revised version. Check on playground was successful [1].


Regards,
    Alois


[1] https://github.com/cygwin/scallywag/actions/runs/1748211333


[-- Attachment #2: 2.3.3-1.Makefilein.patch --]
[-- Type: text/x-patch, Size: 9144 bytes --]

--- 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}
 
 
 #############################################################

[-- Attachment #3: biosig.cygport --]
[-- Type: text/plain, Size: 3572 bytes --]

# 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. "

HOMEPAGE=https://biosig.sourceforge.io

# 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"

BUILD_REQUIRES="libiconv-devel libcholmod-devel zlib-devel pkg-config"
BUILD_REQUIRES+=" gawk python39-numpy python39-devel"

REQUIRES="libcholmod libconv zlib python39-numpy"

PKG_NAMES="libbiosig3 libbiosig-devel biosig-tools python39-biosig"

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/man1/save2gdf.1.gz
  usr/share/man/man1/physicalunits.1.gz
  usr/share/man/man1/biosig2gdf.1.gz
  usr/share/man/man1/biosig_fhir.1.gz

  usr/share/man/man1/sigviewer.1.gz
  usr/share/man/man1/mexSLOAD.1.gz
  usr/share/man/man1/bin2rec.1.gz
  usr/share/man/man1/heka2itx.1.gz
  usr/share/man/man1/rec2bin.1.gz
  usr/share/man/man1/save2aecg.1.gz
  usr/share/man/man1/save2scp.1.gz

  usr/share/doc/biosig/COPYING
  usr/share/doc/biosig/README
"
# not included yet
# usr/share/man/sigviewer.1
# usr/share/man/man1/mexSLOAD.1.gz


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
  biosig4c++/Makefile
  biosig4c++/java/Makefile
  biosig4c++/mex/Makefile
  biosig4c++/mma/Makefile
"

# use not standard src_compile, src_install and src_test

src_compile() {
	cd ${S}
	lndirs
	cd ${B}
	cygautoreconf
	export DESTDIR="${D}"
	cygconf
	# libbiosig and biosig-tools
	# cygmake -C biosig4c++ lib tools
	cygmake lib 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++/biosig2gdf.exe  --help
    biosig4c++/biosig_fhir.exe --help
    # python -c "import biosig"
}

Re: [ITP] biosig [was: Re: newcomer issues when packaging biosig, stimfit, etc.]

[Marco Atzeri]

On 26.01.2022 00:50, Alois Schlögl wrote:
> 

> 
> Hi  Marco,
> 
> 
> thanks for the improvements (especially, libb64 which enables 
> biosig_fhir, and python-biosig).
> Attached is a revised version. Check on playground was successful [1].
> 
> 
> Regards,
>     Alois
> 
> 
> [1] https://github.com/cygwin/scallywag/actions/runs/1748211333
> 

GTG for me.

I added the package on the package list

  $ grep biosig cygwin-pkg-maint
biosig                                       Alois Schloegl


you should be able to upload.
https://cygwin.com/package-upload.html

Regards
Marco

Re: [ITP] biosig [was: Re: newcomer issues when packaging biosig, stimfit, etc.]

[Marco Atzeri]

On 26.01.2022 05:52, Marco Atzeri wrote:
> On 26.01.2022 00:50, Alois Schlögl wrote:
>>
> 
>>
>> Hi  Marco,
>>
>>
>> thanks for the improvements (especially, libb64 which enables 
>> biosig_fhir, and python-biosig).
>> Attached is a revised version. Check on playground was successful [1].
>>
>>
>> Regards,
>>     Alois
>>
>>
>> [1] https://github.com/cygwin/scallywag/actions/runs/1748211333
>>
> 
> GTG for me.
> 
> I added the package on the package list
> 
>   $ grep biosig cygwin-pkg-maint
> biosig                                       Alois Schloegl
> 
> 
> you should be able to upload.
> https://cygwin.com/package-upload.html
> 
> Regards
> Marco
> 

Alois,
do not forget to Announce on the proper mailing list

https://cygwin.com/mailman/listinfo/cygwin-announce

Regards
Marco