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Re: RFS: python-jdata and python-bjdata - JData/BJData encoders and decoders for python

On 7/29/20 5:18 PM, Anton Gladky wrote:
Hi,

uploaded yesterday. Now it is waiting for review in NEW queue.


hi Anton

yes, I saw the email message. thank you so much for the help!

Qianqian



Best regards

Anton


Am Mo., 27. Juli 2020 um 22:15 Uhr schrieb Qianqian Fang <fangqq@gmail.com>:
On 7/22/20 4:33 PM, Anton Gladky wrote:

> 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).


hi Anton

I noticed that although the auto-test did run for the pyjdata package, it reported 0 test. I migrated my test unit to use unittest, and now it runs properly.

to make this update, I created a new upstream release (v0.3.6), and imported it to salsa, see new commits here

https://salsa.debian.org/science-team/pyjdata/-/commits/master

let em know if you see anything else worth fixing.

Qianqian



Best regards

Anton


Am Mi., 22. Juli 2020 um 01:41 Uhr schrieb Qianqian Fang <fangqq@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 <fangqq@gmail.com>:
hi Anton

just to let you know that I've fixed the numpy-abi error for pybj



I also updated pyjdata dependency list:


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/msg00006.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.

https://packages.debian.org/buster/python/python3-json-tricks

the bjdata module is a binary JSON format (similar to UBJSON, and msgpack) to store binary and strongly typed hierarchical data. The differences are highlighted in this github tracker

https://github.com/ubjson/universal-binary-json/issues/109

Although these two modules were recently developed, we are beginning to integrate those in my other tools including iso2mesh, jsonlab and mcx (~10,000 registered users combined). So packaging and maintaining these tools will greatly facilitate the data exchange among the user communities.

let me know if I can provide any additional explanations.

thanks

Qianqian



Best regards


Anton


Am Di., 14. Juli 2020 um 06:35 Uhr schrieb Qianqian Fang <fangqq@gmail.com>:
Dear Science team,

I just submitted two python module packages and wonder if anyone is
willing to take a look and sponsor these packages

The python-jdata and python-bjdata packages aim to enable sharing python
data with other programming environments (like MATLAB, C/C++) via
JSON/binary JSON encoded data files (i.e. the JData/Binary JData
specifications).

The RFS and mentors links can be found in the below two links

https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=964993
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=964994

both packaging files can be found at

https://salsa.debian.org/science-team/pybj
https://salsa.debian.org/science-team/pyjdata

Also need some input on removing the missing-dependency-on-numpy-abi error.

thanks

Qianqian



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