<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Dear Andreas,<div class=""><br class=""></div><div class="">thanks for the work. I have had the looming Python 2.7 demise on my radar for a long time, but as typical in academic environments always too much on my plate.</div><div class=""><br class=""></div><div class="">Gato provides the basis for the graphical editor HMMEd, so it is *not* necessary to run ghmm either from C or Python.</div><div class=""><br class=""></div><div class="">- I started to port Gato to Python 3.x and can ping you when I am done</div><div class=""><br class=""></div><div class="">- I will incorporate your patches </div><div class=""><br class=""></div><div class="">- Lapack: No idea, but it looks like a GSL issue? Or maybe our use of GSL</div><div class=""><br class=""></div><div class="">Best,</div><div class="">Alexander</div><div class=""><br class=""></div><div class="">PS: I’ll also update contact information – <a href="mailto:alexander@schlieplab.org" class="">alexander@schlieplab.org</a> is my permanent work email.</div><div class=""><br class=""></div><div class=""><div><br class=""><blockquote type="cite" class=""><div class="">On 11 Sep 2019, at 17:34, Andreas Tille <<a href="mailto:andreas@an3as.eu" class="">andreas@an3as.eu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Control: tags -1 pending, help<br class=""><br class="">Hi,<br class=""><br class="">as you can read below Python2 is EOL. The Debian Med team has packaged<br class="">ghmm for Debian and craftet a Python3 patch which you could use (and<br class="">possibly test more deeply than we did).<br class=""><br class=""> <a href="https://salsa.debian.org/med-team/ghmm/blob/master/debian/patches/2to3.patch" class="">https://salsa.debian.org/med-team/ghmm/blob/master/debian/patches/2to3.patch</a><br class=""><br class="">When trying HMMEd I've got<br class=""><br class=""> ModuleNotFoundError: No module named 'Gato'<br class=""><br class="">but in setup.py I read only a comment:<br class=""><br class=""> #requires = ['GATO', 'ghmm'],<br class=""><br class="">Could you please clarify whether <a href="http://gato.sf.net" class="">http://gato.sf.net</a> is really needed<br class="">to run ghmm in full functionality? The other tools (ghmm-cluster,<br class="">ghmm-config, probdist, scluster, smix_hmm) are all issuing<br class=""><br class=""> ... is obsolete. If you need it rebuild the GHMM with "GHMM_OBSOLETE".<br class=""><br class=""><br class="">Finally I have a question about building with lapack. I get:<br class=""><br class="">...<br class="">libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-fdebug-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong - Wformat -Werror=format-security -I/usr/include -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c rng.c -fPIC -DPIC -o .libs/rng.o<br class="">In file included from /usr/include/x86_64-linux-gnu/clapack.h:4,<br class=""> from matrixop.c:48:<br class="">/usr/include/x86_64-linux-gnu/cblas.h:5:9: error: nested redefinition of 'enum CBLAS_ORDER'<br class=""> 5 | enum CBLAS_ORDER {CblasRowMajor=101, CblasColMajor=102 };<br class=""> | ^~~~~~~~~~~<br class="">/usr/include/x86_64-linux-gnu/cblas.h:5:9: error: redeclaration of 'enum CBLAS_ORDER'<br class="">In file included from /usr/include/gsl/gsl_blas_types.h:28,<br class=""> from /usr/include/gsl/gsl_blas.h:29,<br class=""> from /usr/include/gsl/gsl_linalg.h:30,<br class=""> from matrixop.c:44:<br class="">/usr/include/gsl/gsl_cblas.h:46:6: note: originally defined here<br class=""> 46 | enum CBLAS_ORDER {CblasRowMajor=101, CblasColMajor=102};<br class=""> | ^~~~~~~~~~~<br class="">In file included from /usr/include/x86_64-linux-gnu/clapack.h:4,<br class=""> from matrixop.c:48:<br class="">/usr/include/x86_64-linux-gnu/cblas.h:5:22: error: redeclaration of enumerator 'CblasRowMajor'<br class=""> 5 | enum CBLAS_ORDER {CblasRowMajor=101, CblasColMajor=102 };<br class=""> | ^~~~~~~~~~~~~<br class="">In file included from /usr/include/gsl/gsl_blas_types.h:28,<br class=""> from /usr/include/gsl/gsl_blas.h:29,<br class=""> from /usr/include/gsl/gsl_linalg.h:30,<br class=""> from matrixop.c:44:<br class="">/usr/include/gsl/gsl_cblas.h:46:19: note: previous definition of 'CblasRowMajor' was here<br class=""> 46 | enum CBLAS_ORDER {CblasRowMajor=101, CblasColMajor=102};<br class=""> | ^~~~~~~~~~~~~<br class="">In file included from /usr/include/x86_64-linux-gnu/clapack.h:4,<br class=""> from matrixop.c:48:<br class="">/usr/include/x86_64-linux-gnu/cblas.h:5:41: error: redeclaration of enumerator 'CblasColMajor'<br class=""> 5 | enum CBLAS_ORDER {CblasRowMajor=101, CblasColMajor=102 };<br class=""> | ^~~~~~~~~~~~~<br class=""><br class=""><br class="">Do you have any idea how to fix this? I could just build without lapack<br class="">to get ghmm working but I'd consider it a good idea to gain performance<br class="">for our users.<br class=""><br class="">Kind regards<br class=""><br class=""> Andreas.<br class=""><br class=""><br class="">On Fri, Aug 30, 2019 at 07:18:48AM +0000, Matthias Klose wrote:<br class=""><blockquote type="cite" class="">Package: src:ghmm<br class="">Version: 0.9~rc3-2<br class="">Severity: normal<br class="">Tags: sid bullseye<br class="">User: <a href="mailto:debian-python@lists.debian.org" class="">debian-python@lists.debian.org</a><br class="">Usertags: py2removal<br class=""><br class="">Python2 becomes end-of-live upstream, and Debian aims to remove<br class="">Python2 from the distribution, as discussed in<br class=""><a href="https://lists.debian.org/debian-python/2019/07/msg00080.html" class="">https://lists.debian.org/debian-python/2019/07/msg00080.html</a><br class=""><br class="">Your package either build-depends, depends on Python2, or uses Python2<br class="">in the autopkg tests. Please stop using Python2, and fix this issue<br class="">by one of the following actions.<br class=""><br class="">- Convert your Package to Python3. This is the preferred option. In<br class=""> case you are providing a Python module foo, please consider dropping<br class=""> the python-foo package, and only build a python3-foo package. Please<br class=""> don't drop Python2 modules, which still have reverse dependencies,<br class=""> just document them.<br class=""><br class=""> This is the preferred option.<br class=""><br class="">- If the package is dead upstream, cannot be converted or maintained<br class=""> in Debian, it should be removed from the distribution. If the<br class=""> package still has reverse dependencies, raise the severity to<br class=""> "serious" and document the reverse dependencies with the BTS affects<br class=""> command. If the package has no reverse dependencies, confirm that<br class=""> the package can be removed, reassign this issue to ftp.debian.org,<br class=""> make sure that the bug priority is set to normal and retitle the<br class=""> issue to "RM: PKG -- removal triggered by the Python2 removal".<br class=""><br class="">- If the package has still many users (popcon >= 300), or is needed to<br class=""> build another package which cannot be removed, document that by<br class=""> adding the "py2keep" user tag (not replacing the py2remove tag),<br class=""> using the debian-python@lists.debian.org user. Also any<br class=""> dependencies on an unversioned python package (python, python-dev)<br class=""> must not be used, same with the python shebang. These have to be<br class=""> replaced by python2/python2.7 dependencies and shebang.<br class=""><br class=""> This is the least preferred option.<br class=""><br class="">If the conversion or removal needs action on another package first,<br class="">please document the blocking by using the BTS affects command, like<br class=""><br class=""> affects <bug number of blocking py2removal bug> + src:ghmm<br class=""><br class="">If there is no py2removal bug for that reverse-dependency, please file<br class="">a bug on this package (similar to this bug report).<br class=""><br class="">If there are questions, please refer to the wiki page for the removal:<br class="">https://wiki.debian.org/Python/2Removal, or ask for help on IRC<br class="">#debian-python, or the debian-python@lists.debian.org mailing list.<br class=""><br class="">_______________________________________________<br class="">Debian-med-packaging mailing list<br class="">Debian-med-packaging@alioth-lists.debian.net<br class="">https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging<br class=""></blockquote><br class="">-- <br class=""><a href="http://fam-tille.de" class="">http://fam-tille.de</a><br class=""></div></div></blockquote></div><br class=""></div><br class=""><br class=""><div class="">
<div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class=""><span style="orphans: 2; widows: 2;" class="">--</span></div><div class=""><div style="orphans: 2; widows: 2; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Dr. Alexander Schliep, Associate Professor</div><div style="orphans: 2; widows: 2; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Data Science & AI Division, <a href="http://dsai.se" class="">http://dsai.se</a>, Computer Science & Engineering, Göteborgs Universitet | Chalmers </div><div style="orphans: 2; widows: 2; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><a href="mailto:alexander@schlieplab.org" class="">alexander@schlieplab.org</a>, Lab:<span class="Apple-converted-space"> </span><a href="http://schlieplab" class="">https://schlieplab</a>.org Tel: +46 76-608 69 63<br class=""><br class=""></div></div></div></div></div></div></div></div></div>
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