Re: RFS: python-jdata and python-bjdata - JData/BJData encoders and decoders for python
On 7/22/20 4:33 PM, Anton Gladky wrote: > Hi, > > > forgive me, what are ods-files? > > https://salsa.debian.org/science-team/pybj/-/blob/master/test/perf_results.ods > > Please fix the binary inclusion (do not forget to rename the tarball > then). I see. it looks like this file came from the upstream repo that I forked from https://github.com/Iotic-Labs/py-ubjson/tree/dev-contrib/test I can make a new release to get rid of this file, is that ok? or I need to do a repack? thanks, let me know Qianqian > > Best regards > > Anton > > > Am Mi., 22. Juli 2020 um 01:41 Uhr schrieb Qianqian Fang > mailto:fan...@gmail.com>>: > > On 7/21/20 4:39 PM, Anton Gladky wrote: >> Hi Qianqian, >> >> some general notes to both packages: > > > thanks, see my below updates > > >> - Please go through ALL files and put licenses/copyrights into >> the d/copyright. > > done > > >> - Remove python2-binaries. This python version is not supported >> any more. > > > done > > >> - Remove all binaries from the code (ods-files) > > > forgive me, what are ods-files? > > >> - pysdate - empty clean file is not needed > > > removed. > > >> - Add DEP-8 autopkgstests > > > can you point me to an example project how this is done? > > I currently have "|Testsuite: autopkgtest-pkg-python|" in control > and "|export PYBUILD_TEST_ARGS=test/|" in rules, the CI pipeline > seems to be ok with autopkgtest for pybj > > https://salsa.debian.org/science-team/pybj/-/pipelines/158112 > > > for pyjdata, two tests were failed due to the dependency to > python3-bjdata (which I believe can be fixed once both packages > are uploaded) > > https://salsa.debian.org/science-team/pyjdata/-/pipelines/158115 > > >> Please pay attention, I did not compile and test your packages. >> Please fix all lintian >> errors and warnings, if they exist. > > > most of those should have been fixed, let me know if you see > something that worth fixing. > > thanks > > > Qianqian > > >> >> Best regards >> >> Anton >> >> >> Am Fr., 17. Juli 2020 um 17:34 Uhr schrieb Qianqian Fang >> mailto:fan...@gmail.com>>: >> >> hi Anton >> >> just to let you know that I've fixed the numpy-abi error for pybj >> >> >> https://salsa.debian.org/science-team/pybj/-/commit/818484c1eb462fa1abd80951132a95dcd048641d >> >> https://mentors.debian.net/package/pybj >> >> I also updated pyjdata dependency list: >> >> https://mentors.debian.net/package/pyjdata >> >> let me know if you have any additional questions regarding >> these two packages. >> >> Qianqian >> >> On 7/14/20 6:07 PM, Qianqian Fang wrote: >>> On 7/14/20 5:11 PM, Anton Gladky wrote: Hi. Thanks for your contribution to Debian. I have just some doubts about usefulness for Debian and possible popularity of those two projects. >>> >>> >>> hi Anton >>> >>> thanks for your comment. happy to explain. Changed message >>> title from "JSON/..." to "JData/BJData encoders and >>> decoders" to avoid further confusions. >>> >>> see my self-introduction in a previous thread >>> >>> https://lists.debian.org/debian-science/2020/06/msg6.html >>> >>> https://bugs.debian.org/cgi-bin/pkgreport.cgi?submitter=fangqq%40gmail.com >>> >>> I am working on packaging a number research software >>> produced from my lab and research projects. I have already >>> submitted 5 octave-related projects, mentored by Rafael >>> Laboissière (CCed) via the Debian Octave Group. I intend to >>> maintain these packages in the future (already doing so for >>> Fedora). >>> >>> These two python modules are part of a bigger project that I >>> initiated last year (http://openjdata.org). They allow >>> python users to read/write JData-annotated data files >>> produced by my MATLAB toolbox JSONLab >>> (https://github.com/fangq/jsonlab , about 46000 downloads on >>> Matlab file exchange and ~1000 clones/week on github). This >>> work is partly funded by my NIH (National Institute of >>> Health) grants and broader dissemination is part of the >>> project goals. >>> >>> Do you know how many people can be interested in these two libraries? It looks like at least one of them duplicates the functionality of the built-in JSON module. Could you please shortly describe the benefits of both of them before we start to evaluate it technically? >>> >>> >>> The *python-bjdata* project was extended from >>> *python-ubjson* - an existing Debian package. Unfortunately, >>> the UBJSON spec (http://ubjson.org), despite
Re: RFS: python-jdata and python-bjdata - JData/BJData encoders and decoders for python
Hi, > forgive me, what are ods-files? https://salsa.debian.org/science-team/pybj/-/blob/master/test/perf_results.ods > can you point me to an example project how this is done? > I currently have "Testsuite: autopkgtest-pkg-python" in control and "export PYBUILD_TEST_ARGS=test/" in rules, the CI pipeline seems to be ok with autopkgtest for pybj Ah, OK. I missed it. Please fix the binary inclusion (do not forget to rename the tarball then). Best regards Anton Am Mi., 22. Juli 2020 um 01:41 Uhr schrieb Qianqian Fang : > On 7/21/20 4:39 PM, Anton Gladky wrote: > > Hi Qianqian, > > some general notes to both packages: > > > thanks, see my below updates > > > - Please go through ALL files and put licenses/copyrights into the > d/copyright. > > done > > > - Remove python2-binaries. This python version is not supported any more. > > > done > > > - Remove all binaries from the code (ods-files) > > > forgive me, what are ods-files? > > > - pysdate - empty clean file is not needed > > > removed. > > > - Add DEP-8 autopkgstests > > > can you point me to an example project how this is done? > > I currently have "Testsuite: autopkgtest-pkg-python" in control and "export > PYBUILD_TEST_ARGS=test/" in rules, the CI pipeline seems to be ok with > autopkgtest for pybj > > https://salsa.debian.org/science-team/pybj/-/pipelines/158112 > > > for pyjdata, two tests were failed due to the dependency to python3-bjdata > (which I believe can be fixed once both packages are uploaded) > > https://salsa.debian.org/science-team/pyjdata/-/pipelines/158115 > > > Please pay attention, I did not compile and test your packages. Please fix > all lintian > errors and warnings, if they exist. > > > most of those should have been fixed, let me know if you see something > that worth fixing. > > thanks > > > Qianqian > > > > Best regards > > Anton > > > Am Fr., 17. Juli 2020 um 17:34 Uhr schrieb Qianqian Fang >: > >> hi Anton >> >> just to let you know that I've fixed the numpy-abi error for pybj >> >> >> https://salsa.debian.org/science-team/pybj/-/commit/818484c1eb462fa1abd80951132a95dcd048641d >> >> https://mentors.debian.net/package/pybj >> >> I also updated pyjdata dependency list: >> >> https://mentors.debian.net/package/pyjdata >> >> let me know if you have any additional questions regarding these two >> packages. >> >> Qianqian >> >> On 7/14/20 6:07 PM, Qianqian Fang wrote: >> >> On 7/14/20 5:11 PM, Anton Gladky wrote: >> >> Hi. >> >> Thanks for your contribution to Debian. I have just some doubts about >> usefulness for Debian and possible popularity of those two projects. >> >> >> hi Anton >> >> thanks for your comment. happy to explain. Changed message title from >> "JSON/..." to "JData/BJData encoders and decoders" to avoid further >> confusions. >> >> see my self-introduction in a previous thread >> >> https://lists.debian.org/debian-science/2020/06/msg6.html >> https://bugs.debian.org/cgi-bin/pkgreport.cgi?submitter=fangqq%40gmail.com >> >> I am working on packaging a number research software produced from my lab >> and research projects. I have already submitted 5 octave-related projects, >> mentored by Rafael Laboissière (CCed) via the Debian Octave Group. I intend >> to maintain these packages in the future (already doing so for Fedora). >> >> These two python modules are part of a bigger project that I initiated >> last year (http://openjdata.org). They allow python users to read/write >> JData-annotated data files produced by my MATLAB toolbox JSONLab ( >> https://github.com/fangq/jsonlab , about 46000 downloads on Matlab file >> exchange and ~1000 clones/week on github). This work is partly funded by my >> NIH (National Institute of Health) grants and broader dissemination is part >> of the project goals. >> >> >> Do you know how many people can be interested in these two libraries? >> It looks like at least one of them duplicates the functionality of the >> built-in >> JSON module. Could you please shortly describe the benefits of both >> of them before we start to evaluate it technically? >> >> >> The *python-bjdata* project was extended from *python-ubjson* - an >> existing Debian package. Unfortunately, the UBJSON spec ( >> http://ubjson.org), despite being broadly used, is no longer actively >> maintained. I started a fork earlier this year to continue the development >> of this specification, and python-bjdata is a parser that is compliant to >> the BJData spec. >> >> The jdata/bjdata framework is not a duplication to JSON - instead, it >> defines a systematic way to encode basic data structures into >> JSON/UBJSON/BJData serializable forms. >> >> The detailed specifications, examples and rationales can be found at >> >> http://openjdata.org/wiki/ >> >> in a way, the jdata module is similar to *json-tricks* but aimed at a >> more systematic/standardized way to annotate complex data (such as graphs, >> maps, ND arrays ...) for sharing, exchange and reuse. >> >>
Bug#966019: RFP: python-gsd -- native file format for HOOMD-blue
Package: wnpp Severity: wishlist X-Debbugs-Cc: debichem-de...@lists.alioth.debian.org, debian-science@lists.debian.org, debian-pyt...@lists.debian.org Control: block 962440 by -1 * Package name: python-gsd Version : 2.1.2 Upstream Author : Joshua A. Anderson et al, University of Michigan * URL : https://gsd.readthedocs.io * License : BSD-2 Programming Lang: Python Description : native file format for HOOMD-blue The GSD file format is the native file format for HOOMD-blue. GSD files store trajectories of the HOOMD-blue system state in a binary file with efficient random access to frames. GSD allows all particle and topology properties to vary from one frame to the next. Use the GSD Python API to specify the initial condition for a HOOMD-blue simulation or analyze trajectory output with a script. Read a GSD trajectory with a visualization tool to explore the behavior of the simulation. Required by mdanalysis. Suitable for package within the Debichem team, but the Debian Science Team or Debian Python Module Team could also maintain it.
