Re: [ITP] biosig [was: Re: newcomer issues when packaging biosig, stimfit, etc.]
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
Re: [ITP] biosig [was: Re: newcomer issues when packaging biosig, stimfit, etc.]
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.]
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
--- origsrc/biosig-2.3.3/biosig4c++/Makefile.in 2021-08-13 11:17:15.0 +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) ${SONAME_PREFIX}"$@" $^
Re: [ITP] biosig [was: Re: newcomer issues when packaging biosig, stimfit, etc.]
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--- origsrc/biosig-2.3.3/biosig4c++/Makefile.in 2021-08-13 11:17:15.0
+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)
Re: [ITP] biosig [was: Re: newcomer issues when packaging biosig, stimfit, etc.]
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 C3NzaC1lZDI1NTE5ILKBmNf1QN3lStTwpn46QIip7sS6zNKy0rG8WCYHv/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.]
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 C3NzaC1lZDI1NTE5ILKBmNf1QN3lStTwpn46QIip7sS6zNKy0rG8WCYHv/ZU END SSH2 PUBLIC KEY Cheers, Alois
Re: [ITP] biosig [was: Re: newcomer issues when packaging biosig, stimfit, etc.]
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.]
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.]
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
# 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
Re: [ITP] biosig [was: Re: newcomer issues when packaging biosig, stimfit, etc.]
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.]
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# 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.]
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
# 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"
}
# 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),
Re: [ITP] biosig [was: Re: newcomer issues when packaging biosig, stimfit, etc.]
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.]
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.]
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.]
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
[ITP] biosig [was: Re: newcomer issues when packaging biosig, stimfit, etc.]
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
# 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
#
