Re: Moving libdeflate from Debian-Med to a more appropriate team

[Michael R. Crusoe]

On 08/08/2024 07.02, nick black wrote:

Michael R. Crusoe left as an exercise for the reader:

Please create a new group on salsa and then we can move the repo[0] from the 
debian-med namespace.


done: https://salsa.debian.org/deflate-team


Thank you Nick, I've moved the libdeflate Salsa repo from the Debian-Med 
namespace to that one: https://salsa.debian.org/deflate-team/libdeflate

Anyone else who is interested in volunteering, please contact Nick and Andrea.

Thanks again!


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Re: Moving libdeflate from Debian-Med to a more appropriate team

[Michael R. Crusoe]

On 06/08/2024 20.36, Andrea Pappacoda wrote:

Il giorno mar 6 ago 2024 alle 11:32:15 -04:00:00, nick black 
 ha scritto:

I maintain it for Fedora, and would be happy to handle it in
Debian; it's a dependency for one of my other packages (notcurses).
Happy to enter into a team maintainership as well.


Hi Nick and Michael, I'd be happy to join this hypothetical team as well. I 
already maintain multiple C++/CMake packages, and I'm looking into using 
libdeflate in Pistache, a library which I maintain both upstream and in Debian.


Thank you Andrea and Nick for volunteering!

Please create a new group on salsa and then we can move the repo[0] from the 
debian-med namespace.

Then you can formalize the change by uploading the new version[1] of libdeflate with the 
new "Maintainer".

[0] https://salsa.debian.org/med-team/libdeflate
[1] https://github.com/ebiggers/libdeflate/releases/tag/v1.21


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Moving libdeflate from Debian-Med to a more appropriate team

[Michael R. Crusoe]

libdeflate-dev has 3304 reverse-dependencies in "unstable"[0].

I would like to move it from Debian-Med to a more appropriate team.

Are there any volunteers?

Some history: libzstd-dev (3020 reverse build-depends) was also first packaged 
by Debian-Med but is now under the RPM packaging team.

liblzma-dev (from xz-utils, 4381 reverse build-depend) has never been under 
team maintainership as far as I can tell.

Thanks!

[0] According to `build-rdeps --distribution unstable libdeflate-dev`

--
Michael R. Crusoe


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Re: Videoconference Saturday 2020-10-17 18:00 UTC (Was: For those who want to keep on contributing (Was: Debian @ COVID-19 Biohackathon (April 5-11, 2020))

[Michael R. Crusoe]

On Fri, Oct 16, 2020 at 3:50 PM Andreas Tille  wrote:

> Hi,
>
> the video conferences of the Debian Med team have shifted to two
> meetings per month now.  Do enable different people joing we shift
> weekdays by simply meeting on every
>
>2th  and  17th
>
> of a month.  So the next meeting is tomorrow 18:00 UTC
>
> For those who would like to join our next videomeeting it will happen at
> Friday
>
>
> https://www.timeanddate.com/worldclock/fixedtime.html?msg=Debian+CoViD-19+Biohackathon+Video+Conference&iso=20201017T20&p1=37&ah=1
>

Notes are at
https://storm.debian.net/shared/SlUYTQlMWDJUfhR7J2PIiDaMDa_e28was0bsjELz77k

Thanks to the attendees!


> The meeting is on the Debian Social channel
>
>  https://jitsi.debian.social/DebianMedCovid19
>
> These video meetings were started in the Debian Med Biohackathon[1].
> The topic is what contributors have done in the past week and to
> coordinate the work for next week.  Here are the reports of some past
> meetings:
>
>  https://wiki.debian.org/DebianMed/Meeting/WeeklyCovid19
>
> To repeat myself: Newcomers are always welcome.
>
> Most probably I will not be able to attend myself the meeting
> tomorrow - but I wish all attendees a lot of fun
>
>Andreas.
>
> [1] https://lists.debian.org/debian-devel-announce/2020/03/msg00010.html
>
> --
> http://fam-tille.de
>
>

Re: Videoconference today Friday 2020-06-12 18:00 UTC (Was: For those who want to keep on contributing (Was: Debian @ COVID-19 Biohackathon (April 5-11, 2020)))

[Michael R. Crusoe]

Thank you Andreas for announcing the meeting, and thanks to the attendees
for their participation. Our meeting notes are at
https://storm.debian.net/shared/6NfKT87njAmCg3tr_uhkE2Qp9SQhVxy8mwD1fQUzfMy

On Fri, Jun 12, 2020 at 1:07 PM Andreas Tille  wrote:

> Hi,
>
> for those who would like to join our next videomeeting it will happen at
>
>
> https://www.timeanddate.com/worldclock/fixedtime.html?msg=Debian+CoViD-19+Biohackathon+Video+Conference&iso=20200612T20&p1=37&ah=1
>
> As last week we will use
>
>  https://jitsi.debian.social/DebianMedCovid19
>
> These weekly video meetings were started in the Debian Med
> Biohackathon[1].  The topic is what contributors have done in the past
> week and to coordinate the work for next week.  Despite the one week of
> hackathon is over Covid-19 is not and there is a lot of remaining work
> to do.  Newcomers are always welcome.
>
> See you
>
>Andreas.
>
> [1] https://lists.debian.org/debian-devel-announce/2020/03/msg00010.html
>
> --
> http://fam-tille.de
>
>

Bug#946611: ITP: golang-github-abeconnelly-autoio -- Golang io functions that provide standard scanner interfaces for compressed files.

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist

Package: wnpp
Severity: wishlist
Owner: Michael R. Crusoe 

* Package name: golang-github-abeconnelly-autoio
  Version : 0.0~git20150803.989b7b0-1
  Upstream Author : Abram Connelly
* URL : https://github.com/abeconnelly/autoio
* License : AGPL-3
  Programming Lang: Go
  Description : Golang IO functions that provide standard scanner 
interfaces for compressed files.

 autoio.go A lightweight (and work in progress) Go library to provide
 a simple interface to use compressed files like you use normal files.

 Needed for packaging https://github.com/arvados/l7g

Bug#919681: ITP: sourmash -- tools for comparing DNA sequences with MinHash sketches

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
Owner: Debian Med team 

* Package name: sourmash
  Version : 2.0.0~a11
  Upstream Author : C. Titus Brown , Luiz C. Irber, Jr 

* URL : http://sourmash.readthedocs.io/en/latest/
* License : BSD-3-Clause
  Programming Lang: Python, C++
  Description : tools for comparing DNA sequences with MinHash sketches

 Compute MinHash signatures for nucleotide (DNA/RNA) and protein sequences.
 .
 MinHash sketches provide a lightweight way to store “signatures” of large DNA
 or RNA sequence collections, and then compare or search them using a Jaccard
 index. MinHash sketches can be used to identify samples, find similar samples,
 identify data sets with shared sequences, and build phylogenetic trees
 (Ondov et al. 2015).
 .
 sourmash provides a command line script, a Python library, and a CPython
 module for MinHash sketches

Sourmash is team maintained by Debian-Med at 
https://salsa.debian.org/med-team/sourmash

Bug#919570: ITP: python-mypy-extensions -- Experimental type system extensions for mypy typechecker (Python 3)

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
Owner: Debian Med team 

* Package name: python-mypy-extensions
  Version : 0.4.1
  Upstream Author : Jukka Lehtosalo and contributors
* URL : https://github.com/python/mypy_extensions/
* License : Expat
  Programming Lang: Python
  Description : Experimental type system extensions for mypy typechecker 
(Python 3)

(Include the long description here.
 Add type annotations to your Python programs, and use mypy to type check them.
 Mypy is essentially a Python linter on steroids, and it can catch many
 programming errors by analyzing your program, without actually having to run
 it. Mypy has a powerful type system with features such as type inference,
 gradual typing, generics and union types.
 .
 The "mypy_extensions" module defines experimental extensions to the
 standard "typing" module that are supported by the mypy typechecker.
 .
 This package provides the modules for Python 3.

This python module was previously part of the python3-mypy binary package from
the mypy source package as it came from the same PyPI source distribution. Now
it has been split into its own sdist/GitHub repo as of mypy v 0.660, so this
separate package is needed.

As with mypy, python-mypy-extensions will be team maintained by Debian Med.

Bug#915852: ITP: bagit -- Create and validate BagIt packages

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
Owner: Debian Med team 

* Package name: bagit
  Version : 1.7.0
  Upstream Author : Ed Summers 
* URL : https://libraryofcongress.github.io/bagit-python/
* License : CC0
  Programming Lang: Python
  Description : Create and validate BagIt packages

bagit is a Python library and command line utility for working with
 `BagIt `__ style data packages.

A new dependency of cwltool. Will be team maintained by Debian-Med.

Bug#914928: ITP: python-typing-extensions -- Backported and Experimental Type Hints for Python

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
Owner: Debian Med team 

* Package name: python-typing-extensions
  Version : 3.6.6
  Upstream Author : Guido van Rossum, Jukka Lehtosalo, Lukasz Langa, Michael 
Lee 
* URL : 
https://github.com/python/typing/blob/master/typing_extensions/README.rst
* License : PSF
  Programming Lang: Python
  Description : Backported and Experimental Type Hints for Python

 The typing module was added to the standard library in Python 3.5 on a
 provisional basis and will no longer be provisional in Python 3.7. However,
 this means users of Python 3.5 - 3.6 who are unable to upgrade will not be
 able to take advantage of new types added to the typing module, such as
 typing.Text or typing.Coroutine.
 .
 The typing_extensions module contains both backports of these changes as well
 as experimental types that will eventually be added to the typing module, such
 as Protocol.
 .
 Users of other Python versions should continue to install and use the typing
 module from PyPi instead of using this one unless specifically writing code
 that must be compatible with multiple Python versions or requires experimental
 types.

A dependency of the latest release of python-schema-salad. This package will be
team-maintained by Debian Med

Bug#911076: ITP: libdeflate -- fast, whole-buffer DEFLATE-based compression and decompression

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
Owner: Debian Med team 

* Package name: libdeflate
  Version : 1.0
  Upstream Author : Eric Biggers 
* URL : https://github.com/ebiggers/libdeflate
* License : MIT
  Programming Lang: C
  Description : fast, whole-buffer DEFLATE-based compression and 
decompression

The supported formats are:
 . 
 DEFLATE (raw)
 zlib (a.k.a. DEFLATE with a zlib wrapper)
 gzip (a.k.a. DEFLATE with a gzip wrapper)
 libdeflate is heavily optimized. It is significantly faster than the zlib
 library, both for compression and decompression, and especially on x86
 processors. In addition, libdeflate provides optional high compression modes
 that provide a better compression ratio than the zlib's "level 9".

libdeflate is a recommended dependency of htslib and will be team-maintained by
Debian Med

Bug#890755: ITP: ctdconverter -- Convert CTD files into Galaxy tool and CWL CommandLineTool files

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
Owner: Debian Med team 

* Package name: ctdconverter
  Version : 2.0
  Upstream Author : WorkflowConversion
* URL : https://github.com/WorkflowConversion/CTDConverter/
* License : GPL-3 / Apache-2.0
  Programming Lang: Python
  Description : Convert CTD files into Galaxy tool and CWL CommandLineTool 
files

Common Tool Descriptors (CTDs) are XML documents that represent the inputs,
outputs, parameters of command line tools in a platform-independent way.

CTDConverter, given one or more Common Tool Descriptors (CTD) XML files,
generates Galaxy tool wrappers and Common Workflow Language (CWL) Command
Line Tool v1.0 standard descriptions from CTD files.

Will assist in including CWL descriptions in the seqan-apps, openms/topp,
flexbar, and lambda-align packages

Will be team-maintained by Debian Med

Bug#890752: ITP: ctdopts -- Gives your Python tools a CTD-compatible interface

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
Owner: Debian Med team 

* Package name: ctdopts
  Version : 1.2
  Upstream Author : Andras Szolek et al.
* URL : https://github.com/WorkflowConversion/CTDopts
* License : GPL-3+
  Programming Lang: Python
  Description : Gives your Python tools a CTD-compatible interface

Common Tool Descriptors (CTDs) are XML documents that represent the inputs,
outputs, parameters of command line tools in a platform-independent way.

CTDopts is a module for enabling tools with CTD reading/writing, argument
parsing, validating and manipulating capabilities.

Needed for CTDConverter to convert CTD to CWL (and Galaxy) as part of including
CWL descriptions in the seqan-apps, openms/topp, flexbar, and lambda-align
packages

Will be team-maintained by Debian Med

Bug#890061: ITP: galaxy-lib -- Subset of Galaxy core code base designed to be used

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
Owner: Debian Med team 

* Package name: galaxy-lib
  Version : 17.9.10
  Upstream Author : Galaxy Project and Community 
* URL : https://github.com/galaxyproject/galaxy-lib
* License : AFL
  Programming Lang: Python
  Description : Subset of Galaxy core code base designed to be used


Dependency for the Toil workflow system; group maintained by Debian-Med

Bug#860746: ITP: easel -- a library of C functions for biological sequence analysis

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
Owner: Debian Med team 

* Package name: easel
  Version : 0.43
  Upstream Author : Sean R. Eddy 
* URL : https://github.com/EddyRivasLab/easel
* License : BSD-3-clause
  Programming Lang: C
  Description : a library of C functions for biological sequence analysis

 Easel is an ANSI C code library for computational analysis of
 biological sequences using probabilistic models. Easel is used by
 HMMER, the profile hidden Markov model software that underlies the
 Pfam protein families database, and by Infernal, the profile
 stochastic context-free grammar software that underlies the Rfam RNA
 family database. Easel aims to make similar applications more robust
 and easier to develop, by providing a set of reusable, documented, and
 well-tested functions.

Several existing packages contain code copies and it is high time this and the 
example
apps were seperately packaged.

This will be team maintained by Debian Med

Bug#851488: ITP: python-gffutils -- Work with GFF and GTF files in a flexible database framework

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
Owner: Debian Med team 

* Package name: python-gffutils
  Version : 0.8.7.1
  Upstream Author : Ryan Dale 
* URL : http://daler.github.io/gffutils/
* License : MIT
  Programming Lang: Python
  Description : Work with GFF and GTF files in a flexible database framework

 A Python package for working with and manipulating the GFF and GTF format
  files typically used for genomic annotations.  Files are loaded into a
   sqlite3 database, allowing much more complex manipulation of hierarchical
features (e.g., genes, transcripts, and exons) than is possible with
 plain-text methods alone.

Dependency of bcbio, to be team maintained by Debian Med

Bug#851358: ITP: python-pybedtools -- Python wrapper around BEDTools for bioinformatics work

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
Owner: Debian Med team 

* Package name: python-pybedtools
  Version : 0.7.8
  Upstream Author : Ryan Dale 
* URL : https://github.com/daler/pybedtools
* License : GPL 2+
  Programming Lang: Python, Cython, 
  Description : Python wrapper around BEDTools for bioinformatics work


The BEDTools suite of programs is widely used for genomic interval
 manipulation or “genome algebra”. pybedtools wraps and extends BEDTools and
  offers feature-level manipulations from within Python.

Dependency for bcbio; and will be team maintained by Debian Med

Bug#841047: ITP: r-hms-dbmi-spp -- GNU R package for processing ChIP-seq & other functional sequencing data

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
Owner: Debian Med team 

* Package name: r-hms-dbmi-spp
  Version : 1.14
  Upstream Author : peterK 
* URL : http://compbio.med.harvard.edu/Supplements/ChIP-seq/
* License : GPL-2
  Programming Lang: R, C++
  Description : GNU R package for processing ChIP-seq & other functional 
sequencing data

A set of routines for reading short sequence alignments, calculating tag
density, estimates of statistically significant enrichment/depletion
along the chromosome, identifying point binding positions (peaks), and
characterizing saturation properties related to sequencing depth.

Dependency of phantompeakqualtools, a dependency of the new pRSEM feature in
rsem. Will be group maintained by the Debian Med team.

Bug#834592: ITP: hisat2 -- graph-based alignment of short nucleotide reads to many genomes

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
Owner: Debian Med team 

* Package name: hisat2
  Version : 2.0.4
  Upstream Author : HISAT2 team 
* URL : https://ccb.jhu.edu/software/hisat2/index.shtml
* License : GPL-3+
  Programming Lang: Perl, Python, C++
  Description : graph-based alignment of short nucleotide reads to many 
genomes

 HISAT2 is a fast and sensitive alignment program for mapping next-generation
 sequencing reads (both DNA and RNA) to a population of human genomes (as well
 as against a single reference genome). Based on an extension of BWT for graphs
 a graph FM index (GFM) was designed and implementd. In addition to using
 one global GFM index that represents a population of human genomes, HISAT2
 uses a large set of small GFM indexes that collectively cover the whole genome
 (each index representing a genomic region of 56 Kbp, with 55,000 indexes
 needed to cover the human population). These small indexes (called local
 indexes), combined with several alignment strategies, enable rapid and
 accurate alignment of sequencing reads. This new indexing scheme is called a
 Hierarchical Graph FM index (HGFM).

hisat2 will be team-maintained by the Debian Med team.

Bug#834590: ITP: python3-typed-ast -- AST with PEP 484 type comments support

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
Owner: Debian Med team 

* Package name: python3-typed-ast
  Version : 0.5.5
  Upstream Author : David Fisher 
* URL : https://pypi.python.org/pypi/typed-ast
* License : Python, Apache-2.0
  Programming Lang: Python, C
  Description : AST with PEP 484 type comments support

A fork of the CPython 2.7 and 3.5 ast modules with the ability to parse
PEP 484 type comments. The primary goals of this package are correctness and
speed.

This enhances the package mypy which is team-maintained by Debian Med, as will
this package.

Bug#828850: ITP: r-bioc-deseq2 -- R package for RNA-Seq Differential Expression Analysis

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
Owner: Debian Med team 

* Package name: r-bioc-deseq2
  Version : 1.12.3
  Upstream Author : Michael Love 
* URL : https://bioconductor.org/packages/DESeq2
* License : LGPL-3+
  Programming Lang: R
  Description : R package for RNA-Seq Differential Expression Analysis

Differential gene expression analysis based on the negative binomial
distribution. Estimate variance-mean dependence in count data from
high-throughput sequencing assays and test for differential expression based
on a model using the negative binomial distribution.

Popular bioinformatics tool/library; team maintained by Debian Med

Bug#828796: ITP: r-bioc-geneplotter -- R package of functions for plotting genomic data

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
Owner: Debian Med team 

* Package name: r-bioc-geneplotter
  Version : 1.50.0
  Upstream Author : Bioconductor Package Maintainer 

* URL : http://bioconductor.org/packages/geneplotter/
* License : Artistic-2.0
  Programming Lang: R
  Description : R package of functions for plotting genomic data

geneplotter contains plotting functions for microarrays

Dependency for r-bioc-deseq2; team mainted by Debian Med

Bug#828690: ITP: r-cran-pscbs -- R package: Analysis of Parent-Specific DNA Copy Numbers

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
Owner: Debian Med team 

* Package name: r-cran-pscbs
  Version : 0.61.0
  Upstream Author : Henrik Bengtsson 
* URL : https://github.com/HenrikBengtsson/PSCBS
* License : GPL-2+
  Programming Lang: R
  Description : R package: Analysis of Parent-Specific DNA Copy Numbers

Segmentation of allele-specific DNA copy number data and detection of regions
 with abnormal copy number within each parental chromosome. Both tumor-normal
 paired and tumoronly analyses are supported.

Prerequisite for cnvkit, to be maintained by Debian Med

Bug#828197: ITP: r-cran-future -- R package: A Future API for R

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
Owner: Debian Med team 

* Package name: r-cran-future
  Version : 1.0.0
  Upstream Author : Henrik Bengtsson 
* URL : https://github.com/HenrikBengtsson/future
* License : LGPL-2.1+
  Programming Lang: R
  Description : R package: A Future API for R

In programming, a future is an abstraction for a value that may be available
 at some point in the future. The state of a future can either be unresolved or
 resolved. As soon as it is resolved, the value is available. Futures are
 useful constructs in for instance concurrent evaluation, e.g. parallel
 processing and distributed processing on compute clusters. The purpose of this
 package is to provide a lightweight interface for using futures in R.

A dependency of r-cran-pscbs, team maintained by Debian Med

Bug#828196: ITP: r-cran-globals -- R package: Identify Global Objects in R Expressions

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
Owner: Debian Med team 

* Package name: r-cran-globals
  Version : 0.6.1
  Upstream Author : Henrik Bengtsson 
* URL : https://github.com/HenrikBengtsson/globals
* License : LGPL-2.1+
  Programming Lang: R
  Description : R package: Identify Global Objects in R Expressions

 Identifies global ("unknown") objects in R expressions by code inspection
 using various strategies, e.g. conservative or liberal. The objective of this
 package is to make it as simple as possible to identify global objects for the
 purpose of exporting them in distributed compute environments.

Dependency of r-cran-future, will be team maintained by Debian Med

Bug#828194: ITP: r-cran-listenv -- R package: Environments Behaving (Almost) as Lists

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
Owner: Debian Med team 

* Package name: r-cran-listenv
  Version : 0.6.0
  Upstream Author : Henrik Bengtsson 
* URL : https://github.com/HenrikBengtsson/listenv
* License : LGPL 2.1+
  Programming Lang: R
  Description : R package: Environments Behaving (Almost) as Lists

List environments are environments that have list-like properties. For
 instance, the elements of a list environment are ordered and can be accessed
 and iterated over using index subsetting, e.g. 'x <- listenv(a=1, b=2); for (i
 in seq_along(x)) x[[i]] <- x[[i]]^2; y <- as.list(x)'.

A dependency of r-cran-pscbs, will be team maintained by Debian Med.

Bug#828189: ITP: r-bioc-dnacopy -- R package: DNA copy number data analysis

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
Owner: Debian Med team 

* Package name: r-bioc-dnacopy
  Version : 1.46.0
  Upstream Author : Venkatraman E. Seshan 
* URL : 
http://www.bioconductor.org/packages/release/bioc/html/DNAcopy.html
* License : GPL-2.0+
  Programming Lang: R
  Description : R package: DNA copy number data analysis

 Implements the circular binary segmentation (CBS) algorithm to segment DNA
 copy number data and identify genomic regions with abnormal copy number.
 .
 This package is for analyzing array DNA copy number data, which is usually
 (but not always) called array Comparative Genomic Hybridization (array CGH)
 data It implements a methodology for finding change-points in these data which
 are points after which the (log) test over reference ratios have changed
 location. This model is that the change-points correspond to positions where
 the underlying DNA copy number has changed. Therefore, change-points can be
 used to identify regions of gained and lost copy number. We also provide a
 function for making relevant plots of these data.

This is a dependency for r-cran-pscbs and will be team maintained by the Debian 
Med team

Bug#828184: ITP: r-cran-r.cache -- R package: Fast and Light-Weight Caching of Objects and Results

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
Owner: Debian Med team 

* Package name: r-cran-r.cache
  Version : 0.12.0
  Upstream Author : Henrik Bengtsson 
* URL : https://github.com/HenrikBengtsson/R.cache
* License : LGPL (>= 2.1)
  Programming Lang: R
  Description : R package: Fast and Light-Weight Caching of Objects and 
Results

Memoization can be used to speed up repetitive and computational expensive
function calls.  The first time a function that implements memoization is
called the results are stored in a cache memory.  The next time the function is
called with the same set of parameters, the results are momentarily retrieved
from the cache avoiding repeating the calculations.  With this package, any R
object can be cached in a key-value storage where the key can be an arbitrary
set of R objects.  The cache memory is persistent (on the file system).

Dependency of r-cran-pscbs, will be team maintained by the Debian Med team

Bug#828176: ITP: cnvkit -- Copy number variant detection from targeted DNA sequencing

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
Owner: Debian Med team 

* Package name: cnvkit
  Version : 0.7.11
  Upstream Author : Eric Talevich 
* URL : http://cnvkit.readthedocs.io/
* License : Apache-2.0
  Programming Lang: Python
  Description : Copy number variant detection from targeted DNA sequencing

A command-line toolkit and Python library for detecting copy number variants
and alterations genome-wide from targeted DNA sequencing. It is designed for
use with hybrid capture, including both whole-exome and custom target panels,
and short-read sequencing platforms such as Illumina and Ion Torrent.

Will be team maintained by the Debian Med team

Bug#823512: ITP: mypy -- Optional static typing for Python

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
Owner: Debian Med team 

* Package name: mypy
  Version : 0.3.1
  Upstream Author : Jukka Lehtosalo 
* URL : http://www.mypy-lang.org/
* License : MIT
  Programming Lang: Python
  Description : Optional static typing for Python

Add type annotations to your Python programs, and use mypy to type check them.
Mypy is essentially a Python linter on steroids, and it can catch many
programming errors by analyzing your program, without actually having to run
it. Mypy has a powerful type system with features such as type inference,
gradual typing, generics and union types.

This package is useful for every Python developer. It will be group maintained
by the Debain Med team.

Re: Bug#817056: ITP: python-typing -- Type Hints for Python

[Michael R. Crusoe]

That was my plan. Though I just realized that I don't need this if I switch
to building only the Python 3 version of schema-salad-tool so I am likely
to close this ITP.

The package is at git+ssh://git.debian.org/git/debian-med/python-typing.git
if anyone is interested.

On Mon, Mar 7, 2016 at 7:38 PM, Scott Kitterman 
wrote:

> On Monday, March 07, 2016 09:01:30 AM Michael R. Crusoe wrote:
> > Package: wnpp
> > Severity: wishlist
> > Owner: Debian Med team 
> >
> > * Package name: python-typing
> >   Version : 3.5.0.1
> >   Upstream Author : Guido van Rossum, Jukka Lehtosalo, Łukasz Langa
> >  * URL :
> > https://docs.python.org/3.5/library/typing.html * License :
> Python
> > 2.0
> >   Programming Lang: Python
> >   Description : Type Hints for Python
> >
> >  This is a backport of the standard library typing module to Python
> >  versions older than 3.5.
> >
> >  Typing defines a standard notation for Python function and variable
> >  type annotations. The notation can be used for documenting code in a
> >  concise, standard format, and it has been designed to also be used by
> >  static and runtime type checkers, static analyzers, IDEs and other
> >  tools.
> >
> > This is a new dependency for python-schema-salad, and will be for any
> other
> > Py2/Py3 package that contains typing hints. It will be maintained by the
> > Debian-Med team but I'm happy to hand it over to other interested
> parties.
>
> Please only package this for python(2).  We are in the process of dropping
> python3.4, so a python3 package isn't needed.
>
> Scott K
>



-- 
Michael R. Crusoe CWL Community Engineer cru...@ucdavis.edu
Common Workflow Language projectUniversity of California, Davis
https://impactstory.org/MichaelRCrusoe http://twitter.com/biocrusoe

Bug#817056: ITP: python-typing -- Type Hints for Python

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
Owner: Debian Med team 

* Package name: python-typing
  Version : 3.5.0.1
  Upstream Author : Guido van Rossum, Jukka Lehtosalo, Łukasz Langa 

* URL : https://docs.python.org/3.5/library/typing.html
* License : Python 2.0
  Programming Lang: Python
  Description : Type Hints for Python

 This is a backport of the standard library typing module to Python
 versions older than 3.5.
 
 Typing defines a standard notation for Python function and variable
 type annotations. The notation can be used for documenting code in a
 concise, standard format, and it has been designed to also be used by
 static and runtime type checkers, static analyzers, IDEs and other
 tools.

This is a new dependency for python-schema-salad, and will be for any other
Py2/Py3 package that contains typing hints. It will be maintained by the
Debian-Med team but I'm happy to hand it over to other interested parties.

Bug#814050: ITP: varna -- Visualization Applet for RNA

[Michael R. Crusoe]

Package: wnpp
Owner: Debian Med team 

Severity: wishlist

* Package name: varna
  Version : 3-93
  Upstream Author : Kevin Darty, Alain Denise and Yann Ponty 
* URL : http://varna.lri.fr/
* License : GPL-3
  Programming Lang: Java
  Description : Visualization Applet for RNA

VARNA is Java lightweight Applet dedicated to drawing the secondary structure
 of RNA. It is also a Swing component that can be very easily included in an
 existing Java code working with RNA secondary structure to provide a fast and
 interactive visualization.
 .
 Being free of fancy external library dependency and/or network access, the
 VARNA Applet can be used as a base for a standalone applet. It looks
 reasonably good and scales up or down nicely to adapt to the space available
 on a web page, thanks to the anti-aliasing drawing primitives of Swing.

This package is required to update jalview to version 2.9; it will be team 
maintained by the Debian Med group.

Bug#814000: ITP: cwltool -- Common workflow language reference implementation

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
Owner: Debian Med team 

* Package name: cwltool
  Version : 1.0.20160203221531
  Upstream Author : Common Workflow Language working group 

* URL : http://www.commonwl.org
* License : Apache-2.0
  Programming Lang: Python
  Description : Common workflow language reference implementation

This is the reference implementation of the Common Workflow Language. It is
intended to be feature complete and provide comprehensive validation of CWL
files as well as provide other tools related to working with CWL.

This is written and tested for Python 2.7.

The reference implementation consists of two packages. The "cwltool" package
is the primary Python module containing the reference implementation in the
"cwltool" module and console executable by the same name.

The "cwl-runner" package is optional and provides an additional entry point
under the alias "cwl-runner", which is the implementation-agnostic name for the
default CWL interpreter installed on a host.

The Debian Med team will be maintaining this package. I am also the CWL
Community Engineer.

Bug#813839: ITP: python-schema-salad -- rdflib extension adding JSON-LD parser and serializer

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
Owner: Debian Med team 

* Package name: python-schema-salad
  Version : 1.6.2016020448
  Upstream Author : Common workflow language working group 

* URL : https://pypi.python.org/pypi/schema-salad
* License : Apache-2.0
  Programming Lang: Python
  Description : Schema Annotations for Linked Avro Data (SALAD)

Salad is a schema language for describing JSON or YAML structured linked data
documents. Salad is based originally on JSON-LD and the Apache Avro data
serialization system.

Salad schema describes rules for preprocessing, structural validation, and link
checking for documents described by a Salad schema. Salad features for rich
data modeling such as inheritance, template specialization, object identifiers,
object references, documentation generation, and transformation to RDF. Salad
provides a bridge between document and record oriented data modeling and the
Semantic Web.

A dependency of cwltool; will be co-maintained by the debian-med team.

Bug#813827: ITP: python-rdflib-jsonld -- rdflib extension adding JSON-LD parser and serializer

[Michael R. Crusoe]

Package: wnpp
Owner: Debian Med team 
Severity: wishlist

* Package name: python-rdflib-jsonld
  Version : 0.3
  Upstream Author : RDFLib Team
* URL : https://github.com/RDFLib/rdflib-jsonld
* License : BSD
  Programming Lang: Python
  Description : rdflib extension adding JSON-LD parser and serializer

 This parser/serialiser will
 .
 - read in an JSON-LD formatted document and create an RDF graph
 - serialize an RDF graph to JSON-LD formatted output

This package is in the dependency chain for the cwltool and will be
co-maintained by the debian-med team.