Bug#966302: RFS: dukpy [ITP]
Hi, I'm looking for a sponsor for the package: * dukpy (#966302) The package is on: https://salsa.debian.org/med-team/dukpy The package is the last dependency of benten[1,2]. [1] https://github.com/rabix/benten [2] https://bugs.debian.org/963743 The package has 4 lintian-overrides, which is for ignoring the minified JavaScript source-is-missing.The package does have autopkgtest and passed well. Please consider to review and sponsor this. Any kind of suggestions are appreciated. Thank you! Sincerely, Sao I Kuan saoik...@gmail.com
Bug#966302: ITP: dukpy -- Simple JavaScript interpreter for Python
Package: wnpp Severity: wishlist Owner: Sao I Kuan * Package name: dukpy Version : 0.2.3 Upstream Author : Alessandro Molina * URL : https://github.com/amol-/dukpy * License : Expat Programming Lang: Python Description : Simple JavaScript interpreter for Python A simple javascript interpreter for Python built on top of duktape engine without any external dependency. It comes with a bunch of common transpilers built-in for convenience.
Bug#956033: RFS: idseq-bench [ITP]
On Sun, Jul 5, 2020 at 12:24 AM Andreas Tille wrote: > > Hi Sao, > > On Sat, Jul 04, 2020 at 04:26:36PM +0900, Sao I Kuan wrote: > > Hi, > > > > I'm looking for a sponsor for the package: > > * idseq-bench (#956033) > > > > The package is on: > > https://salsa.debian.org/med-team/idseq-bench > > ... > > Please consider to review and sponsor this. Any kind of suggestions > > are appreciated. > > I've build the package and started the executables in /usr/bin with > --help option. These issue a warning: > > unable to import 'smart_open.gcs', disabling that module > > Do you know what this means? Thanks for figuring this out. This warning is shown by the dependency: smart-open. I disabled gcs from smart-open[1,2,3], because idseq-bench does not use gcs. I missed some code while excluding gcs from smart-open, now I updated and pushed the patch[4]. Could you please consider to upload smart-open first? Thank you! [1] https://salsa.debian.org/med-team/smart-open [2] https://salsa.debian.org/med-team/smart-open/-/blob/master/debian/README.source [3] https://salsa.debian.org/med-team/smart-open/-/blob/master/debian/patches/exclude-gcs.patch [4] https://salsa.debian.org/med-team/smart-open/-/commit/fbb01c5775eb7066edf485b9dcd7c32b2c11b9b7 Sincerely, Sao I Kuan saoik...@gmail.com
Bug#963480:
Control: block 963743 by -1
Bug#963234:
Control: block 963743 by -1
Bug#963234: RFS: cwlformat [ITP]
Hi, I'm looking for a sponsor for the package: cwlformat (#963234) The package is on: https://salsa.debian.org/med-team/cwlformat The package is dependency of benten[1,2]. [1] https://github.com/rabix/benten [2] https://bugs.debian.org/963743 The package is lintian-clean. The package does have autopkgtest and passed well. Please consider to review and sponsor this. Any kind of suggestions are appreciated. Thank you! Sincerely, Sao I Kuan saoik...@gmail.com
Bug#963480: RFS: python-duckpy [ITP]
Hi, I'm looking for a sponsor for the package: *python-duckpy (#963480) The package is on: https://salsa.debian.org/med-team/python-duckpy The package is dependency of benten[1,2]. [1] https://github.com/rabix/benten [2] https://bugs.debian.org/963743 The package is lintian-clean. Please consider to review and sponsor this. Any kind of suggestions are appreciated. Thank you! Sincerely, Sao I Kuan saoik...@gmail.com
Bug#963480:
Control: retitle -1 ITP: python-duckpy -- A simple Python library for searching on DuckDuckGo
Bug#963480:
Control: retitile -1 ITP: python-duckpy -- A simple Python library for searching on DuckDuckGo
Bug#956033: RFS: idseq-bench [ITP]
Hi, I'm looking for a sponsor for the package: * idseq-bench (#956033) The package is on: https://salsa.debian.org/med-team/idseq-bench The package has a dependency which is waiting in NEW queue: insilicoseq[1,2]. [1] https://bugs.debian.org/961331 [2] https://ftp-master.debian.org/new/insilicoseq_1.4.6-1.html Please consider to review and sponsor this. Any kind of suggestions are appreciated. Thank you! Sincerely, Sao I Kuan saoik...@gmail.com
Bug#961331:
Control: block 956033 by -1 thanks
Bug#961331:
block 956033 by -1 thanks
Bug#963743: ITP: benten -- Language server for Common Workflow Language documents
Package: wnpp Severity: wishlist Owner: Sao I Kuan * Package name: benten Version : 2020.06.03 Upstream Author : Kaushik Ghose * URL : http://github.com/rabix/benten * License : Apache-2.0 Programming Lang: Python Description : Language server for Common Workflow Language documents Benten is written using Python3 and developed against VS Code. The language server component will work with any editor/IDE that offers language server support. Syntax highlighting is currently only available for the VS Code extension. The VS Code extension is written in Typescript. This package is a work which is part of COVID-19 hackathon[1]. The package will be team maintained (med-team). [1] https://lists.debian.org/debian-med/2020/06/msg00071.html
Bug#963234: ITP: cwlformat -- opinionated code formatter for CWL
Dear Jonas, > A package description should be helpful for someone not already > knowledgeable about the topic of what the package covers. Please > consider adding a brief explanation for what "CWL" is. Certainly, I would modify this[1]. [1] https://salsa.debian.org/med-team/cwlformat/-/commit/f93c5f455aeaa8e341e941f69bd45e1498525d00 Thanks for reviewing. Sincerely, Sao I Kuan saoik...@gmail.com
Bug#963480: ITP: duckpy -- A simple Python library for searching on DuckDuckGo
Package: wnpp Severity: wishlist Owner: Sao I Kuan * Package name: duckpy Version : 2.1.1 Upstream Author : Alisson Lauffe * URL : https://github.com/AmanoTeam/duckpy * License : Expat Programming Lang: Python Description : A simple Python library for searching on DuckDuckGo A simple Python module for searching on DuckDuckGo. And also provide an asynchronous version inside the duckpy.aio package. . Can also set up proxies and/or enable or disable random User-Agents depending on your needs. This package is a dependency of upcoming package Benton[1]. The package will be team maintained (med-team). [1] https://github.com/rabix/benten
Bug#963234: ITP: cwlformat -- opinionated code formatter for CWL
Package: wnpp Severity: wishlist Owner: Sao I Kuan * Package name: cwlformat Version : 2020.05.19 Upstream Author : Kaushik Ghose * URL : https://github.com/rabix/cwl-format * License : Apache-2.0 Programming Lang: Python Description : opinionated code formatter for CWL CWL Format is a specification and a reference implementation for a very opinionated CWL code formatter. . It outputs CWL in a standardized YAML format. It has no settings or options because you have better things to do with your time. And because CWL Format is always correct. This package is a dependency work which is part of COVID-19 hackathon [1]. The package will be team maintained (med-team). [1] https://lists.debian.org/debian-med/2020/06/msg00071.html
Bug#962942: RFS: seirsplus [ITP]
Hi, I'm looking for a sponsor for the package: * seirsplus (#962942) The package is on: https://salsa.debian.org/med-team/seirsplus The package is lintian-clean. Please consider reviewing and sponsoring this. Any kind of suggestions are appreciated. Thank you! Sincerely, Sao I Kuan saoik...@gmail.com
Bug#961331: RFS: insilicoseq [ITP]
Hi, Andreas, Thanks for your careful review. On Thu, Jun 11, 2020 at 2:16 AM Andreas Tille wrote: > > Ahhh and please check calling /usr/bin/iss without any > argument throws a strange warning... I patched argument error and forwarded the bug to upstream[1]. [1] https://github.com/HadrienG/InSilicoSeq/issues/177 > On Wed, Jun 10, 2020 at 07:11:54PM +0200, Andreas Tille wrote: > > Hi, > > Very short notice since I'm busy with real life: > > I've added a primitive manpage. Would you be able to > > check whether you can write a simple autopkgtest using > > the provided data? I browsed the README quickly and > > it should be possible (at least at first sight) Thanks a lot :) and I have added autopkgtest and it worked. Sincerely, Sao I Kuan saoik...@gmail.com
Bug#962942: ITP: seirsplus -- Models of SEIRS epidemic dynamics with extensions
Package: wnpp Severity: wishlist Owner: Sao I Kuan * Package name: seirsplus Version : 0.0~git20200528.5c04080 Upstream Author : Ryan Seamus McGee * URL : https://github.com/ryansmcgee/seirsplus * License : Expat Programming Lang: Python Description : Models of SEIRS epidemic dynamics with extensions This package implements generalized SEIRS infectious disease dynamics models with extensions that model the effect of factors including population structure, social distancing, testing, contact tracing, and quarantining detected cases. . Notably, this package includes stochastic implementations of these models on dynamic networks. This package is a work which is part of COVID-19 hackathon [1]. The package will be team maintained (med-team). [1] https://lists.debian.org/debian-med/2020/06/msg00071.html
Bug#961319: RFS: ncbi-acc-download [ITP]
Hi, I'm looking for a sponsor for the package: * ncbi-acc-download (#961319) The package is on: https://salsa.debian.org/med-team/ncbi-acc-download The package is dependency of idseq-bench[1,2]. [1] https://github.com/chanzuckerberg/idseq-bench [2] https://bugs.debian.org/956033 The package does have autopkgtest and passed well. The package does have two lintian warnings: W: ncbi-acc-download: binary-without-manpage usr/bin/nad W: ncbi-acc-download: binary-without-manpage usr/bin/ncbi-acc-download Please consider to review and sponsor this. Any kind of suggestions are appreciated. Thank you! Sincerely, Sao I Kuan saoik...@gmail.com
Bug#961331: RFS: insilicoseq [ITP]
Hi, I'm looking for a sponsor for the package: * insilicoseq (#961331) The package is on: https://salsa.debian.org/med-team/insilicoseq The package is dependency of idseq-bench[1,2]. [1] https://github.com/chanzuckerberg/idseq-bench [2] https://bugs.debian.org/956033 The package does have one lintian warning: W: insilicoseq: binary-without-manpage usr/bin/iss Please consider to review and sponsor this. Any kind of suggestions are appreciated. Thank you! Sincerely, Sao I Kuan saoik...@gmail.com
Bug#961331: ITP: insilicoseq -- A sequencing simulator producing realistic illumina reads
Package: wnpp Severity: wishlist Owner: Sao I Kuan * Package name: insilicoseq Version : 1.4.6 Upstream Author : Hadrien Gourle * URL : http://github.com/HadrienG/InSilicoSeq * License : Expat Programming Lang: Python Description : A sequencing simulator producing realistic illumina reads Primarily intended for simulating metagenomic samples, it can also be used to produce sequencing data from a single genome. . InSilicoSeq is written in python, and use kernel density estimators to model the read quality of real sequencing data. . InSilicoSeq support substitution, insertion and deletion errors. If you don't have the use for insertion and deletion error a basic error model is provided. This package is a dependency of idseq-bench (#956033) and will be team-maintained with Debian Med Packaging Team.
Bug#961319: ITP: ncbi-acc-download -- Download genome files from NCBI by accession
Package: wnpp Severity: wishlist Owner: Sao I Kuan * Package name: ncbi-acc-download Version : 0.2.6 Upstream Author : Kai Blin * URL : https://github.com/kblin/ncbi-acc-download * License : Apache-2.0 Programming Lang: Python Description : Download genome files from NCBI by accession This package provides a script to download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API. This package is a dependency of idseq-bench (#956033) and will be team-maintained with Debian Med Packaging Team.
Bug#956455: RFS: smart-tools [ITP]
Hi, Andreas. On Sun, Apr 12, 2020 at 1:37 PM Andreas Tille wrote: > > On Sat, Apr 11, 2020 at 10:02:18PM +0200, Andreas Tille wrote: > > Hi, > > > > just a short notice. Somehow the pristine-tar branch is broken. > > The original tarball can not be extracted by `gbp buildpackage`. > > I tried to fix this bit the watch file is not properly crafted. > > If I try > > > > uscan --verbose --force-download > > > > I get > > > > uscan warn: In debian/watch no matching files for watch line > > I've fixed the watch file (please compare with Debian Med > package_template in case of trouble) and re-downloaded the source > tarball to include it into pristine-tar branch. It was just wrongly > named. For your next package I would recommend to *first* create > the watch file and download your target tarball with uscan. Than > you can be really sure that it will work. ;-) > I have reviewed that. Learn something new. Thanks. ^^ > > May be somebody else can help - but I need some rest now and may > > be the next two days. Since we have lots of new contributors I > > guess you can get some help here. Sorry for leaving you alone > > for some time with this issue and thanks for your contribution > > anyway > > I just took the needed time and uploaded to new. Please add it > to > > > https://salsa.debian.org/med-team/community/2020-covid19-hackathon/-/wikis/NEW-Requests > > to make sure ftpmaster will realise it in connection with the > sprint. Done~ Thanks for your help. Sincerely, Sao I Kuan saoik...@gmail.com
Bug#956455: RFS: smart-tools [ITP]
Hi, I'm looking for a sponsor for the package: * smart-open (#956455) The packages are on: https://salsa.debian.org/med-team/smart-open The package is dependency of idseq-bench[1,2]. [1] https://github.com/chanzuckerberg/idseq-bench [2] https://bugs.debian.org/956033 The package does have two issues: * GCS: runtime dependencies are not packaged (google-cloud-storage and its deps). - I disabled the GCS related codes, and all the other tests are works well. - d/patches/exclude-gcs.patch * S3: test dependencies not packaged (moto and its deps). - I disabled the S3 related tests. - d/patches/exclude-moto-s3-test.patch Because of reverse dependency of this package (specially idseq-bench) is only using the feature for local filesystems, GCS and S3 related codes are unnecessary for now. So I disabled them. I mentioned this issue in d/README.source. I enabled all the tests not related with GCS and S3, are all passed well. The package was tested on both gbp and sbuild, and lintian-clean. Please consider to review and sponsor this. Any kind of suggestions are appreciated. Thank you! Sincerely, Sao I Kuan saoik...@gmail.com
Bug#956455: ITP: smart-open -- utils for streaming large files
Package: wnpp Severity: wishlist Owner: Sao I Kuan * Package name: smart-open Version : 1.11.1 Upstream Author : Radim Rehurek * URL : https://github.com/piskvorky/smart_open * License : Expat Programming Lang: Python Description : utils for streaming large files smart-open is a library for efficient streaming of very large files from/to storages such as HDFS, WebHDFS, HTTP, HTTPS, SFTP, or local filesystem. It supports transparent, on-the-fly (de-)compression for a variety of different formats (gzip, bz2, etc.). This package is a dependency of idseq-bench (#956033)[0]. [0] https://bugs.debian.org/956033 This package is a work which is part of COVID-19 BioHackathon[1,2]. The package will be team maintained (med-team). [1] https://salsa.debian.org/med-team/community/2020-covid19-hackathon/-/wikis/Covid-19-hackathon [2] https://salsa.debian.org/med-team/community/2020-covid19-hackathon/-/wikis/COVID-19-Hackathon-packages-needing-work
Bug#956089: ITP: recan -- genetic distance plotting for recombination events analysis
Package: wnpp Severity: wishlist Owner: Sao I Kuan * Package name: recan Version : 0.1.2 Upstream Author : Yuriy Babin * URL : https://github.com/babinyurii/recan * License : Expat Programming Lang: Python Description : genetic distance plotting for recombination events analysis recan is a Python package which allows to construct genetic distance plots to explore and discover recombination events in viral genomes. . This method has been previously implemented in desktop software tools: RAT, Simplot and RDP4. This package is a work which is part of COVID-19 BioHackathon [1,2]. The package will be team maintained (med-team). [1] https://salsa.debian.org/med-team/community/2020-covid19-hackathon/-/wikis/Covid-19-hackathon [2] https://salsa.debian.org/med-team/community/2020-covid19-hackathon/-/wikis/COVID-19-Hackathon-packages-needing-work
Bug#956033: ITP: idseq-bench -- Benchmark generator for the IDseq Portal
Package: wnpp Severity: wishlist Owner: Sao I Kuan * Package name: idseq-bench Version : 0.0~git20191121.9623264 Upstream Author : Chan Zuckerberg Initiative * URL : https://github.com/chanzuckerberg/idseq-bench * License : Expat Programming Lang: Python Description : Benchmark generator for the IDseq Portal IDseq (Infectious Disease Sequencing Platform) is an unbiased global software platform that helps scientists identify pathogens in metagenomic sequencing data. . * Discover - Identify the pathogen landscape * Detect - Monitor and review potential outbreaks * Decipher - Find potential infecting organisms in large datasets . This package provides the benchmark generator for the IDseq Portal. This package is a work which is part of COVID-19 BioHackathon [1,2]. The package will be team maintained (med-team). [1] https://salsa.debian.org/med-team/community/2020-covid19-hackathon/-/wikis/Covid-19-hackathon [2] https://salsa.debian.org/med-team/community/2020-covid19-hackathon/-/wikis/COVID-19-Hackathon-packages-needing-work
