Bug#1018887: ITP: cwl-utils -- Python Utilities and Autogenerated Classes for CWL v1.0 - v1.2

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
X-Debbugs-Cc: cru...@debian.org

Subject: ITP: cwl-utils -- Python Utilities and Autogenerated Classes for CWL 
v1.0 - v1.2
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: cwl-utils
  Version : 0.16
  Upstream Author : Copyright: Common workflow language working group 

* URL : https://github.com/common-workflow-language/cwl-utils
* License : Apache-2.0
  Programming Lang: Python
  Description : Python Utilities and Autogenerated Classes for CWL v1.0 - 
v1.2
 The autogenerated classes can create, load, and save objects based upon CWL
 (the Common Workflow Language open standards for executable descriptions of
 comandline tools and workflows made from them).
 .
 See the 'cwl-utils' package for command line utilities that use these classes.

Remark: This package is maintained by Debian Python Team at
   https://salsa.debian.org/python-team/packages/cwl-utils

Bug#1022044: ITP: pytest-httpserver -- HTTP server for pytest to test HTTP clients

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
X-Debbugs-Cc: cru...@debian.org

Subject: ITP: pytest-httpserver -- HTTP server for pytest to test HTTP clients
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: pytest-httpserver
  Version : 1.0.6
  Upstream Author : Zsolt Cserna
* URL : https://github.com/csernazs/pytest-httpserver
* License : Expat
  Programming Lang: Python
  Description : HTTP server for pytest to test HTTP clients
 This library is designed to help to test HTTP clients without contacting the
 real HTTP server. In other words, it is a fake HTTP server which is accessible
 via localhost can be started with the pre-defined expected HTTP requests and
 their responses.

Remark: This package is maintained by Debian Python Team at
   https://salsa.debian.org/python-team/packages/pytest-httpserver

Bug#1022057: ITP: seqan-raptor -- pre-filter for querying very large collections of nucleotide sequences

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
X-Debbugs-Cc: cru...@debian.org

Subject: ITP: seqan-raptor -- pre-filter for querying very large collections of 
nucleotide sequences
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: seqan-raptor
  Version : 2.0.0.0.git.fecfbca+ds
  Upstream Author : Enrico Seiler
* URL : https://github.com/seqan/raptor
* License : BSD-3-clause
  Programming Lang: C
  Description : pre-filter for querying very large collections of 
nucleotide sequences
 Raptor is a system for approximately searching many queries such as
 next-generation sequencing reads or transcripts in large collections of
 nucleotide sequences. Raptor uses winnowing minimizers to define a set of
 representative k-mers, an extension of the interleaved Bloom filters (IBFs) as
 a set membership data structure and probabilistic thresholding for minimizers.
 Our approach allows compression and partitioning of the IBF to enable the
 effective use of secondary memory. We test and show the performance and
 limitations of the new features using simulated and real datasets. Our data
 structure can be used to accelerate various core bioinformatics applications.

Remark: This package is maintained by Debian Med Packaging Team at
   https://salsa.debian.org/med-team/seqan-raptor

Bug#1079678: ITP: r-bioc-golubesets -- exprSets for golub leukemia data

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
X-Debbugs-Cc: debia...@lists.debian.org, cru...@debian.org

Subject: ITP: r-bioc-golubesets -- exprSets for golub leukemia data
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: r-bioc-golubesets
  Version : 1.46.0
  Upstream Author : Todd Golub 
* URL : https://bioconductor.org/packages/golubEsets/
* License : LGPL-2
  Programming Lang: GNU R
  Description : exprSets for golub leukemia data
 representation of public golub data with some covariate
 data of provenance unknown to the maintainer at present; now
 employs ExpressionSet format

Remark: This package is maintained by Debian R Packages Maintainers at
   https://salsa.debian.org/r-pkg-team/r-bioc-golubesets

This package will enabled us to run the entire testsuite for r-bioc-biobase


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Bug#1037201: ITP: cwltest -- Common Workflow Language testing framework

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
X-Debbugs-Cc: cru...@debian.org

Subject: ITP: cwltest -- Common Workflow Language testing framework
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: cwltest
  Version : 2.3.20230607140609
  Upstream Author : CWL, a project of Software Freedom Conservancy
* URL : https://www.commonwl.org
* License : Apache-2.0
  Programming Lang: Python
  Description : Common Workflow Language testing framework


Remark: This package is maintained by Debian Med Packaging Team at
   https://salsa.debian.org/med-team/cwltest

Bug#1039956: ITP: subarch-select -- Select among binaries based upon x86 microarchitecture support

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
X-Debbugs-Cc: cru...@debian.org

Subject: ITP: subarch-select -- Select among binaries based upon x86 
microarchitecture support
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: subarch-select
  Version : 0.1
  Upstream Author : Erik Garrison 
* URL : https://github.com/ekg/subarch-select/
* License : Expat
  Programming Lang: C++
  Description : Select among binaries based upon x86 microarchitecture 
support
 Pick an executable based on CPU capabilities.
 .
 Call subarch-select with argument pairs that list CPU features
 (as in /proc/cpuinfo "flags"), and a path to execute if the flags are all
 matched. The first set of flags that match the system capabilities will select
 the given path. Arguments to the program should be passed after "--".
 .
 Also supports the x86-64 microarchitectures: x86-64-v2, x86-64-v3, v86-64-v4

Remark: This package is maintained by Debian Med Packaging Team at
   https://salsa.debian.org/med-team/subarch-select

Bug#1051798: ITP: python-pcre2 -- Python bindings for the PCRE2 regular expression library

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
X-Debbugs-Cc: cru...@debian.org

Subject: ITP: python-pcre2 -- Python bindings for the PCRE2 regular 
expression library

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

* Package name : python-pcre2
Version : 0.2.0+ds
Upstream Author : grtetrault
* URL : https://github.com/grtetrault/pcre2.py
* License : BSD-3-clause
Programming Lang: Python
Description : Python bindings for the PCRE2 regular expression library
This package contains Python bindings for PCRE2. PCRE2 is the revised 
API for
the Perl-compatible regular expressions (PCRE) library created by Philip 
Hazel.

.
For original source code, see the official PCRE2 repository:
https://github.com/PCRE2Project/pcre2

Upstream publishes to https://pypi.org/project/pcre2/ and has made 
recent releases.


--
Michael R. Crusoe



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Bug#1023322: ITP: seqan-needle -- pre-filter for the counting of very large collections of nucleotide sequences

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
X-Debbugs-Cc: cru...@debian.org

Subject: ITP: seqan-needle -- pre-filter for the counting of very large 
collections of nucleotide sequences
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: seqan-needle
  Version : 1.0.1.0.0.git.3011926+ds
  Upstream Author : Mitra Darvish
* URL : https://github.com/seqan/needle
* License : BSD-3-clause
  Programming Lang: C
  Description : pre-filter for the counting of very large collections of 
nucleotide sequences
 Needle is a tool for semi-quantitative analysis of very large collections of
 nucleotide sequences.
 .
 Needle stores its data in multiple interleaved Bloom filter, a fast and space
 efficient probabilistic data structure and uses a windowing scheme (also called
 minimisers) to reduce the amount of data to store. How many interleaved Bloom
 filter are used is defined by the user. Each interleaved Bloom filter has a so
 called expression threshold and stores minimisers with an occurrence greater
 than or equal to its own expression threshold and smaller than the next biggest
 expression threshold (if there is no bigger expression threshold, all greater
 than or equal to the threshold are stored). These expression thresholds are
 then used during the query (called estimate) to approximate the expression
 values of given transcripts.

Remark: This package is maintained by Debian Med Packaging Team at
   https://salsa.debian.org/med-team/seqan-needle

Bug#1061293: ITP: python-spython -- Command line python tool for working with Singularity

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
X-Debbugs-Cc: cru...@debian.org

Subject: ITP: python-spython -- Command line python tool for working 
with Singularity

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

* Package name : python-spython
Version : 0.3.13
Upstream Author : , Vanessa Sochat
* URL : https://github.com/singularityhub/singularity-cli
* License : MPL-2.0
Programming Lang: Python
Description : Command line python tool for working with Singularity
Singularity Python (spython) is the Python API for working with Singularity
software containers.
.
This library does not support Singularity 2.x! It won't work and we no 
longer

support it.

Remark: This package is maintained by Debian Python Team at
https://salsa.debian.org/python-team/packages/python-spython

--
Michael R. Crusoe



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Bug#1066026: ITP: python-pytest-retry -- Adds the ability to retry flaky tests in pytest

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
X-Debbugs-Cc: cru...@debian.org

Subject: ITP: python-pytest-retry -- Adds the ability to retry flaky 
tests in pytest

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

* Package name : python-pytest-retry
Version : 1.6.2
Upstream Author : Copyright: (c) 2022 Silas
* URL : https://github.com/str0zzapreti/pytest-retry
* License : expat
Programming Lang: Python
Description : Adds the ability to retry flaky tests in pytest
A plugin for Pytest which adds the ability to retry flaky tests,
thereby improving the consistency of the test suite results.

Remark: This package is maintained by Debian Python Team at
https://salsa.debian.org/python-team/packages/python-pytest-retry

--
Michael R. Crusoe



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Bug#1067114: ITP: python-sphinx-codeautolink -- Automatic links from code examples to reference documentation

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
X-Debbugs-Cc: cru...@debian.org

Subject: ITP: python-sphinx-codeautolink -- Automatic links from code examples 
to reference documentation
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name : python-sphinx-codeautolink
Version : 0.15.0
Upstream Author : Copyright: (c) 2021-2023 Felix Hildén 
* URL : https://sphinx-codeautolink.rtfd.io/
* License : expat
Programming Lang: Python
Description : Automatic links from code examples to reference documentation
This plugin for the Sphinx documenation tool makes code examples clickable by
inserting links from individual code elements to the corresponding reference
documentation. We aim for a minimal setup assuming your examples are already
valid Python.
.
For a live demo, see our online documentation on
`Read The Docs <https://sphinx-codeautolink.rtfd.org>`_.

Remark: This package is maintained by Debian Python Team at
https://salsa.debian.org/python-team/packages/python-sphinx-codeautolink

--
Michael R. Crusoe



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Bug#994403: ITP: python-types-toml -- Typing stubs for toml

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
X-Debbugs-Cc: cru...@debian.org

Subject: ITP: python-types-toml -- Typing stubs for toml
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: python-types-toml
  Version : 0.1.5
  Upstream Author : 
* URL : https://github.com/python/typeshed
* License : Apache-2.0
  Programming Lang: Python
  Description : Typing stubs for toml
 This is a PEP 561 type stub package for the toml package. It can be used by
 type-checking tools like mypy, PyCharm, pytype etc. to check code that uses
 toml. The source for this package can be found at
 https://github.com/python/typeshed/tree/master/stubs/toml.
 All fixes for types and metadata should be contributed there.
 . 
 See https://github.com/python/typeshed/blob/master/README.md for more details.

Remark: This package is maintained by Debian Python Team at
   https://salsa.debian.org/python-team/packages/python-toml-types

Bug#994404: ITP: python-types-typed-ast -- Typing stubs for typed-ast

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
X-Debbugs-Cc: cru...@debian.org

Subject: ITP: python-types-typed-ast -- Typing stubs for typed-ast
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: python-types-typed-ast
  Version : 1.4.4
  Upstream Author : 
* URL : https://github.com/python/typeshed
* License : Apache-2.0
  Programming Lang: Python
  Description : Typing stubs for typed-ast
 This is a PEP 561 type stub package for the typed-ast package. It can be used 
by
 type-checking tools like mypy, PyCharm, pytype etc. to check code that uses
 typed-ast. The source for this package can be found at
 https://github.com/python/typeshed/tree/master/stubs/typed-ast.
 All fixes for types and metadata should be contributed there.
 .
 See https://github.com/python/typeshed/blob/master/README.md for more details.

Remark: This package is maintained by Debian Python Team at
   https://salsa.debian.org/python-team/packages/python-types-typed-ast

Bug#994599: ITP: python-tomli -- lil' TOML parser for Python

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
X-Debbugs-Cc: cru...@debian.org

Subject: ITP: python-tomli -- lil' TOML parser for Python
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: python-tomli
  Version : 1.2.1
  Upstream Author : Taneli Hukkinen
* URL : https://github.com/hukkin/tomli
* License : Expat
  Programming Lang: Python
  Description : lil' TOML parser for Python
 Tomli is a Python library for parsing TOML. https://toml.io/
 Tomli is fully compatible with TOML v1.0.0. https://toml.io/en/v1.0.0

Remark: This package is maintained by Debian Python Team at
   https://salsa.debian.org/python-team/packages/python-tomli

Bug#994830: ITP: python-types-dataclasses -- Typing stubs for dataclasses

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
X-Debbugs-Cc: cru...@debian.org

Subject: ITP: python-types-dataclasses -- Typing stubs for dataclasses
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: python-types-dataclasses
  Version : 0.1.7
  Upstream Author : Gary van der Merwe 
* URL : https://github.com/python/typeshed
* License : Apache-2.0
  Programming Lang: Python
  Description : Typing stubs for dataclasses
 This is a PEP 561 type stub package for the dataclasses package. It can be
 used by type-checking tools like mypy, PyCharm, pytype etc. to check
 code that uses dataclasses. The source for this package can be found at
 https://github.com/python/typeshed/tree/master/stubs/dataclasses. All
 fixes for types and metadata should be contributed there.
 .
 See https://github.com/python/typeshed/blob/master/README.md for
 more details.

Remark: This package is maintained by Debian Python Team at
   https://salsa.debian.org/python-team/packages/python-types-dataclasses

Bug#1069568: ITP: python-hatch-mypyc -- Hatch build hook plugin for Mypyc

[Michael R. Crusoe]

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

* Package name : python-hatch-mypyc
Version : 0.16.0
Upstream Author : Ofek Lev 
* URL : https://github.com/ofek/hatch-mypyc
* License : Expat
Programming Lang: Python
Description : Hatch build hook plugin for Mypyc
Provides a build hook plugin for Hatch build system for Python that compiles
code with Mypyc.

Remark: This package is Team Maintained by Michael R. Crusoe and the Debian 
Python Team at
https://salsa.debian.org/python-team/packages/python-hatch-mypyc



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Bug#1076018: ITP: r-bioc-alabaster.schemas -- Schemas for the Alabaster Framework

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
X-Debbugs-Cc: debia...@lists.debian.org, cru...@debian.org

Subject: ITP: r-bioc-alabaster.schemas -- Schemas for the Alabaster Framework
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name : r-bioc-alabaster.schemas
Version : 1.4.0+ds
Upstream Author : Aaron Lun
* URL : https://bioconductor.org/packages/alabaster.schemas/
* License : MIT
Programming Lang: GNU R
Description : Schemas for the Alabaster Framework
Stores all schemas required by various alabaster.* packages.
No computation should be performed by this package, as that is handled by 
alabaster.base.
We use a separate package instead of storing the schemas in alabaster.base 
itself,
to avoid conflating management of the schemas with code maintenence.

Remark: This package is maintained by Debian R Packages Maintainers at
https://salsa.debian.org/r-pkg-team/r-bioc-alabaster.schemas

This package is a build-dep for r-bioc-alabaster.base & Bioconductor 3.19



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Bug#1076020: ITP: r-bioc-alabaster.base -- Save Bioconductor Objects To File

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
X-Debbugs-Cc: debia...@lists.debian.org, cru...@debian.org

Subject: ITP: r-bioc-alabaster.base -- Save Bioconductor Objects To File
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name : r-bioc-alabaster.base
Version : 1.4.2
Upstream Author : Copyright: FIXME-2024 Aaron Lun
* URL : https://bioconductor.org/packages/alabaster.base/
* License : MIT
Programming Lang: GNU R
Description : Save Bioconductor Objects To File
Save Bioconductor data structures into file artifacts, and load them back into 
memory.
This is a more robust and portable alternative to serialization of such objects 
into RDS files.
Each artifact is associated with metadata for further interpretation;
downstream applications can enrich this metadata with context-specific 
properties.

Remark: This package is maintained by Debian R Packages Maintainers at
https://salsa.debian.org/r-pkg-team/r-bioc-alabaster.base

This package is needed for Bioconductor 3.19



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Bug#1076024: ITP: r-bioc-ucsc.utils -- Low-level utilities to retrieve data from the UCSC Genome

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
X-Debbugs-Cc: debia...@lists.debian.org, cru...@debian.org

Subject: ITP: r-bioc-ucsc.utils -- Low-level utilities to retrieve data from 
the UCSC Genome
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name : r-bioc-ucsc.utils
Version : 1.0.0+ds
Upstream Author : Hervé Pagès
* URL : https://bioconductor.org/packages/UCSC.utils
* License : Artistic-2.0
Programming Lang: GNU R
Description : Low-level utilities to retrieve data from the UCSC Genome
Browser
A set of low-level utilities to retrieve data from the UCSC
Genome Browser. Most functions in the package access the data via
the UCSC REST API but some of them query the UCSC MySQL server
directly. Note that the primary purpose of the package is to support
higher-level functionalities implemented in downstream packages
like GenomeInfoDb or txdbmaker.

Remark: This package is maintained by Debian R Packages Maintainers at
https://salsa.debian.org/r-pkg-team/r-bioc-ucsc.utils

This package is a build-dep for r-bioc-genomeinfodb & Bioconductor 3.19




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Bug#1076033: ITP: r-bioc-gypsum -- Interface to the gypsum REST API

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
X-Debbugs-Cc: debia...@lists.debian.org, cru...@debian.org

Subject: ITP: r-bioc-gypsum -- Interface to the gypsum REST API
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name : r-bioc-gypsum
Version : 1.0.1+ds
Upstream Author : Aaron Lun
* URL : https://bioconductor.org/packages/gypsum/
* License : MIT
Programming Lang: GNU R
Description : Interface to the gypsum REST API
Client for the gypsum REST API (https://gypsum.artifactdb.com), a cloud-based 
file store in the ArtifactDB ecosystem.
This package provides functions for uploads, downloads, and various 
adminstrative and management tasks.
Check out the documentation at https://github.com/ArtifactDB/gypsum-worker for 
more details.

Remark: This package is maintained by Debian R Packages Maintainers at
https://salsa.debian.org/r-pkg-team/r-bioc-gypsum

This package is need by Bioconductor 3.19



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Bug#1076039: ITP: r-bioc-pwalign -- Perform pairwise sequence alignments

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
X-Debbugs-Cc: debia...@lists.debian.org, cru...@debian.org

Subject: ITP: r-bioc-pwalign -- Perform pairwise sequence alignments
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name : r-bioc-pwalign
Version : 1.0.0
Upstream Author : Patrick Aboyoun,
* URL : https://bioconductor.org/packages/pwalign
* License : Artistic-2.0
Programming Lang: GNU R
Description : Perform pairwise sequence alignments
The two main functions in the package are pairwiseAlignment() and
stringDist(). The former solves (Needleman-Wunsch) global alignment,
(Smith-Waterman) local alignment, and (ends-free) overlap alignment
problems. The latter computes the Levenshtein edit distance or pairwise
alignment score matrix for a set of strings.

Remark: This package is maintained by Debian R Packages Maintainers at

https://salsa.debian.org/r-pkg-team/r-bioc-pwalign

This package is a build-dep for r-bioc-shortread & Bioconductor 3.19




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Bug#1076055: ITP: r-cran-httptest2 -- Test Helpers for 'httr2'

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
X-Debbugs-Cc: debia...@lists.debian.org, cru...@debian.org

Subject: ITP: r-cran-httptest2 -- Test Helpers for 'httr2'
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name : r-cran-httptest2
Version : 1.1.0+ds
Upstream Author : Neal Richardson,
* URL : https://cran.r-project.org/package=httptest2
* License : MIT
Programming Lang: GNU R
Description : Test Helpers for 'httr2'
Testing and documenting code that communicates with remote servers
can be painful. This package helps with writing tests for packages that
use 'httr2'. It enables testing all of the logic
on the R sides of the API without requiring access to the
remote service, and it also allows recording real API responses to use as
test fixtures. The ability to save responses and load them offline also
enables writing vignettes and other dynamic documents that can be
distributed without access to a live server.

Remark: This package is maintained by Debian R Packages Maintainers at

https://salsa.debian.org/r-pkg-team/r-cran-httptest2

This package is a test-dep for r-bioc-biomart & Bioconductor 3.19



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Bug#1076066: ITP: r-bioc-txdbmaker -- Tools for making TxDb objects from genomic annotations

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
X-Debbugs-Cc: debia...@lists.debian.org, cru...@debian.org

Subject: ITP: r-bioc-txdbmaker -- Tools for making TxDb objects from genomic 
annotations
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name : r-bioc-txdbmaker
Version : 1.0.1+ds
Upstream Author : H. Pagès,
* URL : https://bioconductor.org/packages/txdbmaker
* License : Artistic-2.0
Programming Lang: GNU R
Description : Tools for making TxDb objects from genomic annotations
A set of tools for making TxDb objects from genomic annotations
from various sources (e.g. UCSC, Ensembl, and GFF files). These tools
allow the user to download the genomic locations of transcripts,
exons, and CDS, for a given assembly, and to import them in a TxDb
object. TxDb objects are implemented in the GenomicFeatures package,
together with flexible methods for extracting the desired features in
convenient formats.

Remark: This package is maintained by Debian R Packages Maintainers at
https://salsa.debian.org/r-pkg-team/r-bioc-txdbmaker

This package is a build-dep for r-bioc-tximeta & Bioconductor 3.19



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Bug#1076073: ITP: r-bioc-alabaster.sce -- Load and Save SingleCellExperiment from File

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
X-Debbugs-Cc: debia...@lists.debian.org, cru...@debian.org

Subject: ITP: r-bioc-alabaster.sce -- Load and Save SingleCellExperiment from 
File
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name : r-bioc-alabaster.sce
Version : 1.4.0+ds
Upstream Author : Aaron Lun
* URL : https://bioconductor.org/packages/alabaster.sce/
* License : MIT
Programming Lang: GNU R
Description : Load and Save SingleCellExperiment from File
Save SingleCellExperiment into file artifacts, and load them back into memory.
This is a more portable alternative to serialization of such objects into RDS 
files.
Each artifact is associated with metadata for further interpretation;
downstream applications can enrich this metadata with context-specific 
properties.

Remark: This package is maintained by Debian R Packages Maintainers at
https://salsa.debian.org/r-pkg-team/r-bioc-alabaster.sce

Build-dep for r-bioc-scrnaseq 2.18.0 & bioc-3.19



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Bug#1076074: ITP: r-bioc-alabaster.se -- Load and Save SummarizedExperiments from File

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
X-Debbugs-Cc: debia...@lists.debian.org, cru...@debian.org

Subject: ITP: r-bioc-alabaster.se -- Load and Save SummarizedExperiments from 
File
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name : r-bioc-alabaster.se
Version : 1.4.1+ds
Upstream Author : Aaron Lun
* URL : https://bioconductor.org/packages/alabaster.se
* License : MIT
Programming Lang: GNU R
Description : Load and Save SummarizedExperiments from File
Save SummarizedExperiments into file artifacts, and load them back into memory.
This is a more portable alternative to serialization of such objects into RDS 
files.
Each artifact is associated with metadata for further interpretation;
downstream applications can enrich this metadata with context-specific 
properties.

Remark: This package is maintained by Debian R Packages Maintainers at
https://salsa.debian.org/r-pkg-team/r-bioc-alabaster.se

This package is a build-dep for r-bioc-alabaster.sce 1.4.0 & bioc-3.19



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Bug#1076075: ITP: r-bioc-alabaster.matrix -- Load and Save Artifacts from File

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
X-Debbugs-Cc: debia...@lists.debian.org, cru...@debian.org

Subject: ITP: r-bioc-alabaster.matrix -- Load and Save Artifacts from File
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name : r-bioc-alabaster.matrix
Version : 1.4.2+ds
Upstream Author : Aaron Lun
* URL : https://bioconductor.org/packages/alabaster.matrix
* License : MIT
Programming Lang: GNU R
Description : Load and Save Artifacts from File
Save matrices, arrays and similar objects into file artifacts, and load them 
back into memory.
This is a more portable alternative to serialization of such objects into RDS 
files.
Each artifact is associated with metadata for further interpretation;
downstream applications can enrich this metadata with context-specific 
properties.

Remark: This package is maintained by Debian R Packages Maintainers at
https://salsa.debian.org/r-pkg-team/r-bioc-alabaster.matrix

This package is a build-dep for r-bioc-scrnaseq 2.18.0 & bioc-3.19



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Bug#1076077: ITP: r-bioc-alabaster.ranges -- Load and Save Ranges-related Artifacts from File

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
X-Debbugs-Cc: debia...@lists.debian.org, cru...@debian.org

Subject: ITP: r-bioc-alabaster.ranges -- Load and Save Ranges-related Artifacts 
from File
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name : r-bioc-alabaster.ranges
Version : 1.4.2+ds
Upstream Author : Aaron Lun
* URL : https://bioconductor.org/packages/alabaster.ranges
* License : MIT
Programming Lang: GNU R
Description : Load and Save Ranges-related Artifacts from File
Save GenomicRanges, IRanges and related data structures into file artifacts, 
and load them back into memory.
This is a more portable alternative to serialization of such objects into RDS 
files.
Each artifact is associated with metadata for further interpretation;
downstream applications can enrich this metadata with context-specific 
properties.

Remark: This package is maintained by Debian R Packages Maintainers at
https://salsa.debian.org/r-pkg-team/r-bioc-alabaster.ranges

This package is build-dep for r-bioc-alabaster.se & bioc-3.19



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Bug#1076092: ITP: r-bioc-spatialexperiment -- S4 Class for Spatially Resolved -omics Data

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
X-Debbugs-Cc: debia...@lists.debian.org, cru...@debian.org

Subject: ITP: r-bioc-spatialexperiment -- S4 Class for Spatially Resolved 
-omics Data
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name : r-bioc-spatialexperiment
Version : 1.14.0+ds
Upstream Author : Dario Righelli,
* URL : https://bioconductor.org/packages/SpatialExperiment
* License : GPL-3
Programming Lang: GNU R
Description : S4 Class for Spatially Resolved -omics Data
Defines an S4 class for storing data from spatial -omics experiments.
The class extends SingleCellExperiment to
support storage and retrieval of additional information from spot-based and
molecule-based platforms, including spatial coordinates, images, and
image metadata. A specialized constructor function is included for data
from the 10x Genomics Visium platform.

Remark: This package is maintained by Debian R Packages Maintainers at
https://salsa.debian.org/r-pkg-team/r-bioc-spatialexperiment

This package is needed for the upgrade to bioc-3.19



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Bug#1076191: ITP: r-cran-rmariadb -- Database Interface and 'MariaDB' Driver

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
X-Debbugs-Cc: debia...@lists.debian.org, cru...@debian.org

Subject: ITP: r-cran-rmariadb -- Database Interface and 'MariaDB' Driver
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name : r-cran-rmariadb
Version : 1.3.2+ds
Upstream Author : Kirill Müller,
* URL : https://cran.r-project.org/package=RMariaDB
* License : MIT
Programming Lang: GNU R
Description : Database Interface and 'MariaDB' Driver
Implements a 'DBI'-compliant interface to 'MariaDB'
(<https://mariadb.org/>) and 'MySQL' (<https://www.mysql.com/>)
databases.

Remark: This package is maintained by Debian R Packages Maintainers at
https://salsa.debian.org/r-pkg-team/r-cran-rmariadb

This package is a test dependency for the new version of r-bioc-ucsc.utils, and 
thus needed for the bioc-3.19 transition



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Bug#1076277: ITP: r-bioc-hgu95a.db -- Affymetrix Affymetrix HG_U95A Array annotation data (chip

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
X-Debbugs-Cc: debia...@lists.debian.org, cru...@debian.org

Subject: ITP: r-bioc-hgu95a.db -- Affymetrix Affymetrix HG_U95A Array 
annotation data (chip
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name : r-bioc-hgu95a.db
Version : 3.13.0
Upstream Author : Marc Carlson
* URL : https://bioconductor.org/packages/data/experiment/hgu95a.db/
* License : Artistic-2.0
Programming Lang: GNU R
Description : Affymetrix Affymetrix HG_U95A Array annotation data (chip
hgu95a) Affymetrix Affymetrix HG_U95A Array annotation data (chip
hgu95a) assembled using data from public repositories

Remark: This package is maintained by Debian R Packages Maintainers at
https://salsa.debian.org/r-pkg-team/r-bioc-hgu95a.db

This package is a build-dependency for r-bioc-gsvadata, and thus needed for the 
bioc-3.19 transition



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Bug#1076276: ITP: r-bioc-gsvadata -- Data employed in the vignette of the GSVA package

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
X-Debbugs-Cc: debia...@lists.debian.org, cru...@debian.org

Subject: ITP: r-bioc-gsvadata -- Data employed in the vignette of the GSVA 
package
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name : r-bioc-gsvadata
Version : 1.40.0
Upstream Author : Robert Castelo 
* URL : https://bioconductor.org/packages/GSVAdata
* License : Artistic-2.0
Programming Lang: GNU R
Description : Data employed in the vignette of the GSVA package
This package stores the data employed in the vignette of the GSVA package.
These data belong to the following publications:
- Armstrong et al. Nat Genet 30:41-47, 2002
- Cahoy et al. J Neurosci 28:264-278, 2008
- Carrel and Willard, Nature, 434:400-404, 2005
- Huang et al. PNAS, 104:9758-9763, 2007
- Pickrell et al. Nature, 464:768-722, 2010
- Skaletsky et al. Nature, 423:825-837
- Verhaak et al. Cancer Cell 17:98-110, 2010

Remark: This package is maintained by Debian R Packages Maintainers at
https://salsa.debian.org/r-pkg-team/r-bioc-gsvadata

This package is a test dependency for the new version of r-bioc-gsva, and thus 
needed for the bioc-3.19 transition



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Bug#800412: ITP: transrate-tools -- command line tool used by transrate to process BAM files

[Michael R. Crusoe]

Package: wnpp
Owner: "Debian Med Team" 
Severity: wishlist
X-Debbugs-CC:  debian-...@lists.debian.org

* Package name: transrate-tools
  Version : 1.0.0
  Upstream Author : Richard Smith-Unna & Chris Boursnell 
* URL : https://github.com/Blahah/transrate-tools
* License : MIT
  Programming Lang: C++
  Description : command line tool used by transrate to process BAM files

Transrate is a library and command-line tool for quality assessment of
de-novo transcriptome assemblies.

This program is a dependency for transrate and provides command line tools
used to process BAM files.

This package will be maintained as part of the Debian Med packaging team.

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#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#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#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#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.

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#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#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#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#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]

See
https://www.python.org/dev/peps/pep-0484/#suggested-syntax-for-python-2-7-and-straddling-code
Pe 8 mar. 2016 06:24, "Brian May"  a scris:

> "Michael R. Crusoe"  writes:
>
> >  This is a backport of the standard library typing module to Python
> >  versions older than 3.5.
>
> Not sure what the point of this is; doesn't typing hinting require PEP
> 3107, which isn't in Python 2.x?
> --
> Brian May 
>

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#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.

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#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#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#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#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#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#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#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#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#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#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#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#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#974999: ITP: r-bioc-glmgampoi -- GNU R fit a Gamma-Poisson generalized linear model

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Subject: ITP: r-bioc-glmgampoi -- GNU R fit a Gamma-Poisson generalized linear 
model
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: r-bioc-glmgampoi
  Version : 1.2.0
  Upstream Author : Constantin Ahlmann-Eltze,
* URL : https://bioconductor.org/packages/glmGamPoi/
* License : GPL-3
  Programming Lang: GNU R
  Description : GNU R fit a Gamma-Poisson generalized linear model
 Fit linear models to overdispersed count data.
 The package can estimate the overdispersion and fit repeated models
 for matrix input. It is designed to handle large input datasets as they
 typically occur in single cell RNA-seq experiments.

Remark: This package is maintained by Debian R Packages Maintainers at
   https://salsa.debian.org/r-pkg-team/r-bioc-glmgampoi


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Bug#975439: ITP: r-bioc-bluster -- Clustering Algorithms for Bioconductor

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Subject: ITP: r-bioc-bluster -- Clustering Algorithms for Bioconductor
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: r-bioc-bluster
  Version : 1.0.0
  Upstream Author : Aaron Lun
* URL : https://bioconductor.org/packages/bluster/
* License : GPL-3
  Programming Lang: GNU R
  Description : Clustering Algorithms for Bioconductor
 Wraps common clustering algorithms in an easily extended S4 framework.
 Backends are implemented for hierarchical, k-means and graph-based clustering.
 Several utilities are also provided to compare and evaluate clustering results.

Remark: This package is maintained by Debian R Packages Maintainers at
   https://salsa.debian.org/r-pkg-team/r-bioc-bluster

This package is a precondition for r-bioc-scran

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Bug#975625: ITP: r-cran-profmem -- Simple Memory Profiling for R

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Subject: ITP: r-cran-profmem -- Simple Memory Profiling for R
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: r-cran-profmem
  Version : 0.5.0
  Upstream Author : Henrik Bengtsson
* URL : https://cran.r-project.org/package=profmem
* License : LGPL-2.1
  Programming Lang: GNU R
  Description : Simple Memory Profiling for R
 A simple and light-weight API for memory profiling of R expressions. The
 profiling is built on top of R's built-in memory profiler
 ('utils::Rprofmem()'), which records every memory allocation done by R
 (also native code).

Remark: This package is maintained by Debian R Packages Maintainers at
   https://salsa.debian.org/r-pkg-team/r-cran-profmem

This package is a precondition for r-cran-bench

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Bug#975629: ITP: r-cran-bench -- High Precision Timing of R Expressions

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Subject: ITP: r-cran-bench -- High Precision Timing of R Expressions
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: r-cran-bench
  Version : 1.1.1
  Upstream Author : Jim Hester,
* URL : https://cran.r-project.org/package=bench
* License : GPL-3
  Programming Lang: GNU R
  Description : High Precision Timing of R Expressions
 Tools to accurately benchmark and analyze execution times for R expressions.

Remark: This package is maintained by Debian R Packages Maintainers at
   https://salsa.debian.org/r-pkg-team/r-cran-bench


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Bug#981116: ITP: python-wdlparse -- Workflow Description Language (WDL) parser for Python

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
X-Debbugs-Cc: cru...@debian.org

Subject: ITP: python-wdlparse -- Workflow Description Language (WDL) parser for 
Python
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: python-wdlparse
  Version : 0.1.0
  Upstream Author : , Regents of the University of California
* URL : https://github.com/DataBiosphere/wdl-parsers
* License : Apache-2.0
  Programming Lang: Python
  Description : Workflow Description Language (WDL) parser for Python
 A Python package that provides the generated Hermes and Antlr4 WDL parsers for
 Python.

Remark: This package is maintained by Debian Med Packaging Team at
   https://salsa.debian.org/med-team/python-wdlparse

Bug#981866: ITP: python-stubserver -- mock tester of external web dependencies for Python

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
X-Debbugs-Cc: cru...@debian.org

Subject: ITP: python-stubserver -- mock tester of external web dependencies for 
Python
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: python-stubserver
  Version : 1.1
  Upstream Author : Copyright: (C) 2015 - Chris Tarttelin for PyRuby LTD
* URL : https://pypi.org/project/stubserver/
* License : BSD-2-clause
  Programming Lang: Python
  Description : mock tester of external web dependencies for Python
 Testing external web dependencies in a mock objects style. This library
 includes the tests at the bottom of the stubserver.py file, which serve both
 as the TDD tests written while creating this library, and as examples /
 documentation.  It supports any HTTP method, i.e. GET, PUT, POST and DELETE.
 It supports chunked encoding, but currently the developers have no use cases
 for multipart support etc, so it doesn't do it.
 .
 There is also an FTPStubServer for your FTP testing needs, but that is NOT
 bug free at the moment.  All assistance gratefully received.

Remark: This package is maintained by Debian Med Packaging Team at
   https://salsa.debian.org/med-team/python-stubserver

Bug#982082: ITP: r-bioc-scrnaseq -- Collection of Public Single-Cell RNA-Seq Datasets

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
X-Debbugs-Cc: cru...@debian.org

Subject: ITP: r-bioc-scrnaseq -- Collection of Public Single-Cell RNA-Seq 
Datasets
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: r-bioc-scrnaseq
  Version : 2.4.0+ds
  Upstream Author : Davide Risso,
* URL : https://bioconductor.org/packages/data/experiment/scRNAseq/
* License : CC0
  Programming Lang: GNU R
  Description : Collection of Public Single-Cell RNA-Seq Datasets
 Gene-level counts for a collection of public scRNA-seq datasets,
 provided as SingleCellExperiment objects with cell- and gene-level metadata.

Remark: This package is maintained by Debian R Packages Maintainers at
   https://salsa.debian.org/r-pkg-team/r-bioc-scrnaseq

This package is suggested by r-bioc-{scuttle,scater,scran,singler,bluster}

Bug#982142: ITP: uncalled -- Utility for Nanopore Current Alignment to Large Expanses of DNA

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
X-Debbugs-Cc: cru...@debian.org

Subject: ITP: uncalled -- Utility for Nanopore Current Alignment to Large 
Expanses of DNA
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: uncalled
  Version : 2.2+ds
  Upstream Author : , Sam Kovaka 
* URL : https://github.com/skovaka/UNCALLED
* License : expat
  Programming Lang: C++
  Description : Utility for Nanopore Current Alignment to Large Expanses of 
DNA
 Streaming algorithm for mapping raw nanopore signal to DNA references
 .
 Enables real-time enrichment or depletion on Oxford Nanopore Technologies
 (ONT) MinION runs via ReadUntil.
 .
 Also supports standalone signal mapping of fast5 reads

Remark: This package is maintained by Debian Med Packaging Team at
   https://salsa.debian.org/med-team/uncalled

Bug#982417: Python louvain packages naming confusion.

[Michael R. Crusoe]

On Tue, 9 Feb 2021 at 23:53, Diane Trout  wrote:

> Hello,
>
> The fairly popular (in the world of bioinformatics) ScanPy package uses
> a Python version of the louvain clustering algorithm implemented by:
>
> https://github.com/vtraag/louvain-igraph
> https://pypi.org/project/louvain/
>
> which installs into the "louvain" dist-packages directory.
> (from debc)
> ./usr/lib/python3/dist-packages/louvain/
>
> I have it mostly packaged
>
> However currently in the Debian archive there's a different louvain
> package
>
> https://github.com/taynaud/python-louvain
> https://pypi.org/project/python-louvain/
> https://salsa.debian.org/python-team/packages/python-louvain
>
> It installs into (according to debc)
> ./usr/lib/python3/dist-packages/community/
>
> Unfortunately for this package we now automatically run autodep8 which
> fails because the import name is community and not louvain.
>

In the short term I recommend fixing this by adding a file to the Debian
python-louvain package named "debian/tests/autopkgtest-pkg-python.conf"
with the contents "import_name = community"


-- 
Michael R. Crusoe

Bug#984815: ITP: libbiosoup-dev -- C++ header-only support library for bioinformatics tools

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
X-Debbugs-Cc: cru...@debian.org

Subject: ITP: libbiosoup-dev -- C++ header-only support library for 
bioinformatics tools
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: libbiosoup-dev
  Version : 0.10.0
  Upstream Author : Robert Vaser
* URL : https://github.com/rvaser/biosoup/
* License : MIT
  Programming Lang: C++
  Description : C++ header-only support library for bioinformatics tools
 Biosoup is a c++ collection of header only data structures used for storage
 and logging in bioinformatics tools.

Remark: This package is maintained by Debian Med Packaging Team at
   https://salsa.debian.org/med-team/libbiosoup-dev

Bug#986236: ITP: r-cran-visnetwork -- Network Visualization using 'vis.js' Library

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
X-Debbugs-Cc: cru...@debian.org

Subject: ITP: r-cran-visnetwork -- Network Visualization using 'vis.js' Library
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: r-cran-visnetwork
  Version : 2.0.9+ds
  Upstream Author : Almende B.V. (vis.js library in htmlwidgets/lib,
* URL : https://cran.r-project.org/package=visNetwork
* License : MIT
  Programming Lang: GNU R
  Description : Network Visualization using 'vis.js' Library
 Provides an R interface to the 'vis.js' JavaScript charting
 library. It allows an interactive visualization of networks.

Remark: This package is maintained by Debian R Packages Maintainers at
   https://salsa.debian.org/r-pkg-team/r-cran-visnetwork

This package is a precondition for r-cran-diagrammer

Bug#986237: ITP: r-cran-influencer -- Software Tools to Quantify Structural Importance of Nodes in a

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
X-Debbugs-Cc: cru...@debian.org

Subject: ITP: r-cran-influencer -- Software Tools to Quantify Structural 
Importance of Nodes in a
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: r-cran-influencer
  Version : 0.1.0
  Upstream Author : Jacobs Simon,
* URL : https://cran.r-project.org/package=influenceR
* License : GPL-2
  Programming Lang: GNU R
  Description : Software Tools to Quantify Structural Importance of Nodes 
in a
   Network Provides functionality to compute various node centrality
   measures on networks. Included are functions to compute
   betweenness centrality (by utilizing Madduri and Bader's SNAP
   library), implementations of Burt's constraint and effective
   network size (ENS) metrics, Borgatti's algorithm to identify key
   players, and Valente's bridging metric. On Unix systems, the
   betweenness, Key Players, and bridging implementations are
   parallelized with OpenMP, which may run faster on systems which
   have OpenMP configured.

Remark: This package is maintained by Debian R Packages Maintainers at
   https://salsa.debian.org/r-pkg-team/r-cran-influencer

This package is a precondition for r-cran-diagrammer

Bug#986241: ITP: r-cran-diagrammer -- Graph/Network Visualization

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
X-Debbugs-Cc: cru...@debian.org

Subject: ITP: r-cran-diagrammer -- Graph/Network Visualization
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: r-cran-diagrammer
  Version : 1.0.6.1+ds
  Upstream Author : Richard Iannone
* URL : https://cran.r-project.org/package=DiagrammeR
* License : MIT
  Programming Lang: GNU R
  Description : Graph/Network Visualization
 Build graph/network structures using functions for stepwise addition and
 deletion of nodes and edges. Work with data available in tables for bulk
 addition of nodes, edges, and associated metadata. Use graph selections
 and traversals to apply changes to specific nodes or edges. A wide
 selection of graph algorithms allow for the analysis of graphs. Visualize
 the graphs and take advantage of any aesthetic properties assigned to
 nodes and edges.

Remark: This package is maintained by Debian R Packages Maintainers at
   https://salsa.debian.org/r-pkg-team/r-cran-diagrammer

Bug#986621: ITP: r-bioc-rcwl -- An R interface to the Common Workflow Language

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
X-Debbugs-Cc: cru...@debian.org

Subject: ITP: r-bioc-rcwl -- An R interface to the Common Workflow Language
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: r-bioc-rcwl
  Version : 1.6.0+ds
  Upstream Author : Qiang Hu,
* URL : https://bioconductor.org/packages/Rcwl/
* License : GPL-2
  Programming Lang: GNU R
  Description : An R interface to the Common Workflow Language
 The Common Workflow Language (CWL) is an open standard for development
 of data analysis workflows that is portable and scalable across
 different tools and working environments. Rcwl provides a simple way to
 wrap command line tools and build CWL data analysis pipelines
 programmatically within R. It increases the ease of usage, development,
 and maintenance of CWL pipelines.

Remark: This package is maintained by Debian R Packages Maintainers at
   https://salsa.debian.org/r-pkg-team/r-bioc-rcwl

Bug#924246: 12

[Michael R. Crusoe]

Package: wnpp
Severity: normal

test

Bug#932003: ITP: mypyc -- Mypy to Python C Extension Compile

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist

Subject: ITP: mypyc -- Mypy to Python C Extension Compile
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: mypyc
  Version : 0.0.git.20190713T1002.833151a+ds1
  Upstream Author : Copyright: © 2017-2018 Jukka Lehtosalo and contributors
* URL : http://www.mypy-lang.org/
* License : Expat
  Programming Lang: C
  Description : Mypy to Python C Extension Compile
 *Mypyc is (mostly) not yet useful for general Python development.*
 .
 Mypyc is a compiler that compiles mypy-annotated, statically typed
 Python modules into CPython C extensions. Currently our primary focus
 is on making mypy faster through compilation -- the default mypy wheels
 are compiled with mypyc.  Compiled mypy is about 4x faster than
 without compilation.
 .
 Mypyc compiles what is essentially a Python language variant using "strict"
 semantics. This means (among some other things):
 .
  * Most type annotations are enforced at runtime (raising ``TypeError`` on
mismatch)
 .
  * Classes are compiled into extension classes without ``__dict__``
(much, but not quite, like if they used ``__slots__``)
 .
  * Monkey patching doesn't work
 .
  * Instance attributes won't fall back to class attributes if undefined
 .
  * Metaclasses not supported
 .
  * Also there are still a bunch of bad bugs and unsupported features :)
 .
 Compiled modules can import arbitrary Python modules, and compiled modules
 can be used from other Python modules.  Typically mypyc is used to only
 compile modules that contain performance bottlenecks.
 .
 You can run compiled modules also as normal, interpreted Python
 modules, since mypyc targets valid Python code. This means that
 all Python developer tools and debuggers can be used.
 .
 This package provides the command-line interface.

Remark: This package is maintained by Debian Med Packaging Team at
   https://salsa.debian.org/med-team/mypy

Bug#934629: ITP: seqan3 -- C++ library for the analysis of biological sequences (development)

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist

Subject: ITP: seqan3 -- C++ library for the analysis of biological sequences 
(development)
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: seqan3
  Version : 3.0.0+ds
  Upstream Author : , Knut Reinert, FU Berlin
* URL : http://www.seqan.de/
* License : BSD-3-clause
  Programming Lang: C
  Description : C++ library for the analysis of biological sequences 
(development)
 SeqAn is a C++ template library of efficient algorithms and data
 structures for the analysis of sequences with the focus on
 biological data. This library applies a unique generic design that
 guarantees high performance, generality, extensibility, and
 integration with other libraries. SeqAn is easy to use and
 simplifies the development of new software tools with a minimal loss
 of performance.
 .
 This package contains the developer files.

Remark: This package is maintained by Debian Med Packaging Team at
   https://salsa.debian.org/med-team/seqan2

Bug#939537: ITP: vg -- tools for working with genome variation graphs

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist

Subject: ITP: vg -- tools for working with genome variation graphs
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: vg
  Version : 1.18.0+ds
  Upstream Author : Copyright: © 2014 Erik Garrison
* URL : https://github.com/vgteam/vg#vg
* License : MIT
  Programming Lang: C
  Description : tools for working with genome variation graphs
 variation graph data structures, interchange formats, alignment, genotyping,
 and variant calling methods
 .
 Variation graphs provide a succinct encoding of the sequences of many genomes.
 A variation graph (in particular as implemented in vg) is composed of:
 .
 - nodes, which are labeled by sequences and ids
 - edges, which connect two nodes via either of their respective ends
 - paths, describe genomes, sequence alignments, and annotations (such as gene
   models and transcripts) as walks through nodes connected by edges
 .
 This model is similar to a number of sequence graphs that have been used in
 assembly and multiple sequence alignment. Paths provide coordinate systems
 relative to genomes encoded in the graph, allowing stable mappings to be
 produced even if the structure of the graph is changed.

Remark: This package is maintained by Debian Med Packaging Team at
   https://salsa.debian.org/med-team/vg

Bug#939933: ITP: megadock -- ultra-high-performance protein-protein docking for heterogeneous supercomputers

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist

Subject: ITP: megadock -- ultra-high-performance protein-protein docking for 
heterogeneous supercomputers
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: megadock
  Version : 4.1.1
  Upstream Author : Copyright: © 2014-2018 Akiyama Laboratory, Tokyo Institute 
of Technology, All Rights Reserved.
* URL : http://www.bi.cs.titech.ac.jp/megadock/
* License : GPL-3+
  Programming Lang: C
  Description : ultra-high-performance protein-protein docking for 
heterogeneous supercomputers
 MEGADOCK is an ultra-high-performance protein-protein prediction software for 
heterogeneous supercomputers using FFT-grid-based docking with MPI/OpenMP/GPU 
parallelization

Remark: This package is maintained by Debian Med Packaging Team at
   https://salsa.debian.org/med-team/megadock

Bug#940180: ITP: libbio-searchio-hmmer-perl -- perl parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam)

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist

Subject: ITP: libbio-searchio-hmmer-perl -- perl parser for HMMER2 and HMMER3 
output (hmmscan, hmmsearch, hmmpfam)
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: libbio-searchio-hmmer-perl
  Version : 1.7.3
  Upstream Author : Copyright: Balamurugan Kumarasamy , 
Ewan Birney , Jason Stajich , Josh 
Lauricha , Kai Blin 
, Mauricio Herrera Cuadra 
, Sendu Bala , Thomas Sharpton 

* URL : https://metacpan.org/release/Bio-SearchIO-hmmer
* License : Artistic
  Programming Lang: Perl
  Description : perl parser for HMMER2 and HMMER3 output (hmmscan, 
hmmsearch, hmmpfam)
 This object implements a parser for hmmpfam hsp output, a program in the
 HMMER package.

Remark: This package is maintained by Michael R. Crusoe at
   https://salsa.debian.org/med-team/libbio-searchio-hmmer-perl

Bug#940244: ITP: libbio-alignio-stockholm-perl -- stockholm sequence input/output stream

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist

Subject: ITP: libbio-alignio-stockholm-perl -- stockholm sequence input/output 
stream
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: libbio-alignio-stockholm-perl
  Version : 1.7.3
  Upstream Author : Copyright: Peter Schattner , Chris 
Fields 
* URL : https://metacpan.org/release/Bio-AlignIO-stockholm
* License : Artistic
  Programming Lang: Perl
  Description : stockholm sequence input/output stream
 Indexes Stockholm format alignments such as those from Pfam and Rfam. Returns
 raw stream data using the ID or a Bio::SimpleAlign object (via Bio::AlignIO).
 .
 Bio::AlignIO::stockholm also allows for ID parsing using a callback:

Remark: This package is maintained by Michael R. Crusoe at
   https://salsa.debian.org/med-team/libbio-alignio-stockholm-perl

Bug#940248: ITP: libbio-db-biofetch-perl -- Database object interface to BioFetch retrieval

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist

Subject: ITP: libbio-db-biofetch-perl -- Database object interface to BioFetch 
retrieval
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: libbio-db-biofetch-perl
  Version : 1.7.3
  Upstream Author : Copyright: Lincoln Stein 
* URL : https://metacpan.org/release/Bio-DB-BioFetch
* License : Artistic
  Programming Lang: Perl
  Description : Database object interface to BioFetch retrieval
 Bio::DB::BioFetch is a guaranteed best effort sequence entry fetching method.
 It goes to the Web-based dbfetch server located at the EBI
 (http://www.ebi.ac.uk/Tools/dbfetch/dbfetch) to retrieve sequences in the
 EMBL or GenBank sequence repositories.
 .
 Bio::DB::BioFetch implements all the Bio::DB::RandomAccessI interface, plus
 the get_Stream_by_id() and get_Stream_by_acc() methods that are found in the
 Bio::DB::SwissProt interface.

Remark: This package is maintained by Michael R. Crusoe at
   https://salsa.debian.org/med-team/libbio-db-biofetch-perl

Bug#940252: ITP: libbio-db-gff-perl -- Storage and retrieval of sequence annotation data

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist

Subject: ITP: libbio-db-gff-perl -- Storage and retrieval of sequence 
annotation data
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: libbio-db-gff-perl
  Version : 1.7.3
  Upstream Author : Copyright: (c) 2001-2003, 2005, 2008 Cold Spring Harbor 
Laboratory
* URL : https://metacpan.org/release/Bio-DB-GFF
* License : Artistic
  Programming Lang: Perl
  Description : Storage and retrieval of sequence annotation data
 Bio::DB::GFF provides fast indexed access to a sequence annotation database.
 It supports multiple database types (ACeDB, relational), and multiple schemas
 through a system of adaptors and aggregators.
 .
 The following operations are supported by this module:
 .
  - retrieving a segment of sequence based on the ID of a landmark
 .
  - retrieving the DNA from that segment
 .
  - finding all annotations that overlap with the segment
 .
  - finding all annotations that are completely contained within the
 segment
 .
  - retrieving all annotations of a particular type, either within a
 segment, or globally
 .
  - conversion from absolute to relative coordinates and back again,
 using any arbitrary landmark for the relative coordinates
 .
  - using a sequence segment to create new segments based on relative
 offsets

Remark: This package is maintained by Michael R. Crusoe at
   https://salsa.debian.org/med-team/libbio-db-gff-perl

Bug#940253: ITP: libbio-db-ace-perl -- Database object interface to ACeDB servers

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist

Subject: ITP: libbio-db-ace-perl -- Database object interface to ACeDB servers
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: libbio-db-ace-perl
  Version : 1.7.3
  Upstream Author : Copyright: Ewan Birney , Lincoln Stein 

* URL : https://metacpan.org/release/Bio-DB-Ace
* License : Artistic
  Programming Lang: Perl
  Description : Database object interface to ACeDB servers
 This provides a standard BioPerl database access to Ace, using Lincoln Steins
 excellent AcePerl module.
 .
 This interface is designed at the moment to work through a
 aceclient/aceserver type mechanism

Remark: This package is maintained by Michael R. Crusoe at
   https://salsa.debian.org/med-team/libbio-db-ace-perl

--help

Bug#940254: ITP: libbio-db-embl-perl -- Database object interface for EMBL entry retrieval

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist

Subject: ITP: libbio-db-embl-perl -- Database object interface for EMBL entry 
retrieval
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: libbio-db-embl-perl
  Version : 1.7.4
  Upstream Author : Copyright: Heikki Lehvaslaiho 
* URL : https://metacpan.org/release/Bio-DB-EMBL
* License : Artistic
  Programming Lang: Perl
  Description : Database object interface for EMBL entry retrieval
 Allows the dynamic retrieval of sequence objects Bio::Seq from the EMBL
 database using the dbfetch script at EBI:
 http://www.ebi.ac.uk/Tools/dbfetch/dbfetch.
 .
 In order to make changes transparent we have host type (currently only ebi)
 and location (defaults to ebi) separated out. This allows later additions of
 more servers in different geographical locations.
 .
 The functionality of this module is inherited from Bio::DB::DBFetch which
 implements Bio::DB::WebDBSeqI.

Remark: This package is maintained by Michael R. Crusoe at
   https://salsa.debian.org/med-team/libbio-db-embl-perl

Bug#940255: ITP: libbio-db-seqfeature-perl -- Normalized feature for use with Bio::DB::SeqFeature::Store

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist

Subject: ITP: libbio-db-seqfeature-perl -- Normalized feature for use with 
Bio::DB::SeqFeature::Store
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: libbio-db-seqfeature-perl
  Version : 1.7.3
  Upstream Author : Copyright: Lincoln Stein , Nathan Weeks 

* URL : https://metacpan.org/release/Bio-DB-SeqFeature
* License : Artistic
  Programming Lang: Perl
  Description : Normalized feature for use with Bio::DB::SeqFeature::Store
 The Bio::DB::SeqFeature object is the default SeqFeature class stored in
 Bio::DB::SeqFeature databases. It implements both the
 Bio::DB::SeqFeature::NormalizedFeatureI and
 Bio::DB::SeqFeature::NormalizedTableFeatureI interfaces, which means that its
 subfeatures, if any, are stored in the database in a normalized fashion, and
 that the parent/child hierarchy of features and subfeatures are also stored
 in the database as set of tuples. This provides efficiencies in both storage
 and retrieval speed.
 .
 Typically you will not create Bio::DB::SeqFeature directly, but will ask the
 database to do so on your behalf, as described in Bio::DB::SeqFeature::Store.

Remark: This package is maintained by Michael R. Crusoe at
   https://salsa.debian.org/med-team/libbio-db-seqfeature-perl

Bug#940256: ITP: libbio-cluster-perl -- BioPerl cluster modules

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist

Subject: ITP: libbio-cluster-perl -- BioPerl cluster modules
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: libbio-cluster-perl
  Version : 1.7.3
  Upstream Author : Copyright: Allen Day , Andrew Macgregor 
, David Green, Hilmar Lapp , Jo-Ann 
Stanton, Shawn Hoon , Stan Nelson 
* URL : https://metacpan.org/release/Bio-Cluster
* License : Artistic
  Programming Lang: Perl
  Description : BioPerl cluster modules
 The ClusterIO module works with the ClusterIO format module to read various
 cluster formats such as NCBI UniGene.
 .
 This description was automagically extracted from the module by dh-make-perl.

Remark: This package is maintained by Michael R. Crusoe at
   https://salsa.debian.org/med-team/libbio-cluster-perl

Bug#940257: ITP: libbio-tools-run-remoteblast-perl -- Object for remote execution of the NCBI Blast via HTTP

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist

Subject: ITP: libbio-tools-run-remoteblast-perl -- Object for remote execution 
of the NCBI Blast via HTTP
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: libbio-tools-run-remoteblast-perl
  Version : 1.7.3
  Upstream Author : Copyright: Jason Stajich 
* URL : https://metacpan.org/release/Bio-Tools-Run-RemoteBlast
* License : Artistic
  Programming Lang: Perl
  Description : Object for remote execution of the NCBI Blast via HTTP
 Class for remote execution of the NCBI Blast via HTTP.
 .
 For a description of the many CGI parameters see:
 https://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html
 .
 Various additional options and input formats are available.
 .
 This description was automagically extracted from the module by dh-make-perl.

Remark: This package is maintained by Michael R. Crusoe at
   https://salsa.debian.org/med-team/libbio-tools-run-remoteblast

Bug#940258: ITP: libbio-db-ncbihelper-perl -- collection of routines useful for queries to NCBI databases.

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist

Subject: ITP: libbio-db-ncbihelper-perl -- collection of routines useful for 
queries to NCBI databases.
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: libbio-db-ncbihelper-perl
  Version : 1.7.4
  Upstream Author : Copyright: Aaron Mackey , Brian 
Osborne , Jason Stajich , Lincoln 
Stein 
* URL : https://metacpan.org/release/Bio-DB-NCBIHelper
* License : Artistic
  Programming Lang: Perl
  Description : collection of routines useful for queries to NCBI databases.
 Provides a single place to setup some common methods for querying NCBI web
 databases. Bio::DB::NCBIHelper just centralizes the methods for constructing
 a URL for querying NCBI GenBank and NCBI GenPept and the common HTML
 stripping done in postprocess_data().
 .
 The base NCBI query URL used is:
 https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi

Remark: This package is maintained by Michael R. Crusoe at
   https://salsa.debian.org/med-team/libbio-db-ncbihelper-perl

Bug#944785: ITP: pufferfish -- An efficient index for the colored, compacted, de Bruijn graph

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist

Subject: ITP: pufferfish -- An efficient index for the colored, compacted, de 
Bruijn graph 
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: pufferfish
  Version : 1.0.0
  Upstream Author : , 2016 Rob Patro, Avi Srivastava, Hirak Sarkar
* URL : https://github.com/COMBINE-lab/pufferfish
* License : GPL-3+
  Programming Lang: C
  Description : An efficient index for the colored, compacted, de Bruijn 
graph 
 Pufferfish is a new time and memory-efficient data structure for indexing a
 compacted, colored de Bruijn graph (ccdBG). 
 .
 Though the de Bruijn Graph (dBG) has enjoyed tremendous popularity as an
 assembly and sequence comparison data structure, it has only relatively
 recently begun to see use as an index of the reference sequences (e.g. deBGA,
 kallisto). Particularly, these tools index the compacted dBG (cdBG), in which
 all non-branching paths are collapsed into individual nodes and labeled with
 the string they spell out. This data structure is particularly well-suited for
 representing repetitive reference sequences, since a single contig in the cdBG
 represents all occurrences of the repeated sequence. The original positions in
 the reference can be recovered with the help of an auxiliary "contig table"
 that maps each contig to the reference sequence, position, and orientation
 where it appears as a substring. The deBGA paper has a nice description how
 this kind of index looks (they call it a unipath index, because the contigs we
 index are unitigs in the cdBG), and how all the pieces fit together to be able
 to resolve the queries we care about.  Moreover, the cdBG can be built on
 multiple reference sequences (transcripts, chromosomes, genomes), where each
 reference is given a distinct color (or colour, if you're of the British
 persuasion). The resulting structure, which also encodes the relationships
 between the cdBGs of the underlying reference sequences, is called the
 compacted, colored de Bruijn graph (ccdBG).  This is not, of course, the only
 variant of the dBG that has proven useful from an indexing perspective. The
 (pruned) dBG has also proven useful as a graph upon which to build a path
 index of arbitrary variation / sequence graphs, which has enabled very
 interesting and clever indexing schemes like that adopted in GCSA2. Also,
 thinking about sequence search in terms of the dBG has led to interesting
 representations for variation-aware sequence search backed by indexes like the
 vBWT (implemented in the excellent gramtools package).

Remark: This package is maintained by Debian Med Packaging Team at
   https://salsa.debian.org/med-team/pufferfish

This package will be team maintained by Debian-Med

Bug#946266: ITP: libbio-db-swissprot-perl -- Database object interface to SwissProt retrieval

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist

Subject: ITP: libbio-db-swissprot-perl -- Database object interface to 
SwissProt retrieval
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: libbio-db-swissprot-perl
  Version : 1.7.3
  Upstream Author : Copyright: Jason Stajich 
* URL : https://metacpan.org/release/Bio-DB-SwissProt
* License : Artistic
  Programming Lang: Perl
  Description : Database object interface to SwissProt retrieval
 SwissProt is a curated database of proteins managed by the Swiss
 Bioinformatics Institute. Additional tools for parsing and manipulating
 swissprot files can be found at
 ftp://ftp.ebi.ac.uk/pub/software/swissprot/Swissknife/.
 .
 Allows the dynamic retrieval of Sequence objects (Bio::Seq) from the
 SwissProt database via an Expasy retrieval.
 .
 In order to make changes transparent we have host type (currently only
 expasy) and location (default to Switzerland) separated out. This allows the
 user to pick the closest Expasy mirror for running their queries.
 .
 This description was automagically extracted from the module by dh-make-perl.

Remark: This package is maintained by Debian Med team at
   https://salsa.debian.org/med-team/libbio-db-swissprot-perl

Bug#946269: ITP: libbio-db-refseq-perl -- Database object interface for RefSeq retrieval

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist

Subject: ITP: libbio-db-refseq-perl -- Database object interface for RefSeq 
retrieval
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: libbio-db-refseq-perl
  Version : 1.7.3
  Upstream Author : Copyright: Heikki Lehvaslaiho 
* URL : https://metacpan.org/release/Bio-DB-RefSeq
* License : Artistic
  Programming Lang: Perl
  Description : Database object interface for RefSeq retrieval
 Allows the dynamic retrieval of sequence objects Bio::Seq from the RefSeq
 nucleotide database using the dbfetch script at EBI:
 .
 http://www.ebi.ac.uk/Tools/dbfetch/dbfetch
 .
 At this time the module specifically retrieves nucleotide sequences only.
 .
 In order to make changes transparent we have host type (currently only ebi)
 and location (defaults to ebi) separated out. This allows later additions of
 more servers in different geographical locations.
 .
 The functionality of this module is inherited from Bio::DB::DBFetch which
 implements Bio::DB::WebDBSeqI.

Remark: This package is maintained by Debian Med team at
   https://salsa.debian.org/med-team/libbio-db-refseq-perl

Bug#946272: ITP: libbio-procedural-perl -- Simple low-dependency procedural interfaces to BioPerl

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist

Subject: ITP: libbio-procedural-perl -- Simple low-dependency procedural 
interfaces to BioPerl
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: libbio-procedural-perl
  Version : 1.7.4
  Upstream Author : Copyright: Ewan Birney 
* URL : https://metacpan.org/release/Bio-Procedural
* License : Artistic
  Programming Lang: Perl
  Description : Simple low-dependency procedural interfaces to BioPerl
 The code in this distribution focuses on simple low-dependency procedural
 interfaces to BioPerl that don't require knowledge of BioPerl classes and
 methods.

Remark: This package is maintained by Debian Med team at
   https://salsa.debian.org/med-team/libbio-procedural-perl

Bug#946299: ITP: simde -- Implementations of SIMD instructions for all systems

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist

Subject: ITP: simde -- Implementations of SIMD instructions for all systems
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: simde
  Version : 0.0.0.git.20191205.c2e740c
  Upstream Author : , Evan Nemerson 
* URL : https://github.com/nemequ/simde
* License : MIT
  Programming Lang: C
  Description : Implementations of SIMD instructions for all systems
 SIMDe provides fast, portable implementations of SIMD intrinsics on hardware
 which doesn't natively support them, such as calling SSE functions on ARM.
 There is no performance penalty if the hardware supports the native
 implementation (e.g., SSE/AVX runs at full speed on x86, NEON on ARM, etc.).
 .
 This makes porting code to other architectures much easier in a few key ways:
 .
 First, instead of forcing you to rewrite everything for each architecture,
 SIMDe lets you get a port up and running almost effortlessly. You can then
 start working on switching the most performance-critical sections to native
 intrinsics, improving performance gradually. SIMDe lets (for example) SSE/AVX
 and NEON code exist side-by-side, in the same implementation.
 .
 Second, SIMDe makes it easier to write code targeting ISA extensions you don't
 have convenient access to. You can run NEON code on your x86 machine without an
 emulator. Obviously you'll eventually want to test on the actual hardware
 you're targeting, but for most development, SIMDe can provide a much easier
 path.
 .
 SIMDe takes a very different approach from most other SIMD abstraction layers
 in that it aims to expose the entire functionality of the underlying
 instruction set. Instead of limiting functionality to the lowest common
 denominator, SIMDe tries to minimize the amount of effort required to port
 while still allowing you the space to optimize as needed.
 .
 The current focus is on writing complete portable implementations, though a
 large number of functions already have accelerated implementations using one
 (or more) of the following:
 .
 SIMD intrinsics from other ISA extensions (e.g., using NEON to implement
 SSE).
 Compiler-specific vector extensions and built-ins such as
 __builtin_shufflevector and __builtin_convertvector
 Compiler auto-vectorization hints, using:
OpenMP 4 SIMD
Cilk Plus
GCC loop-specific pragmas
clang pragma loop hint directives

Remark: This package is maintained by Debian Med Packaging Team at
   https://salsa.debian.org/med-team/simde

Bug#946468: ITP: libbio-variation-perl -- BioPerl variation-related functionality

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist

Subject: ITP: libbio-variation-perl -- BioPerl variation-related functionality
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: libbio-variation-perl
  Version : 1.7.4
  Upstream Author : Copyright: Allen Day , Heikki 
Lehvaslaiho 
* URL : https://metacpan.org/release/Bio-Variation
* License : Artistic
  Programming Lang: Perl
  Description : BioPerl variation-related functionality
  The code in this distribution focuses on simple low-dependency variant-related
 functionality for BioPerl.
 .
 Bio::Variation name space contains modules to store sequence variation
 information as differences between the reference sequence and changes
 sequences. Also included are classes to write out and recrete objects
 from EMBL-like flat files and XML. Lastly, there are simple classes to
 calculate values for sequence change objects.

Remark: This package is maintained by Debian Med Team at
   https://salsa.debian.org/med-team/libbio-variation-perl

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#946638: ITP: hopscotch-map -- C++ fast hash map and hash set using hopscotch hashing

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist

Subject: ITP: hopscotch-map -- C++ fast hash map and hash set using hopscotch 
hashing
Package: wnpp
Owner: Michael R. Crusoe 
Severity: wishlist

* Package name: hopscotch-map
  Version : 2.2.1
  Upstream Author : Tessil
* URL : https://github.com/Tessil/hopscotch-map/
* License : MIT
  Programming Lang: C
  Description : C++ fast hash map and hash set using hopscotch hashing
 The hopscotch-map library is a C++ implementation of a fast hash map and hash
 set using open-addressing and hopscotch hashing to resolve collisions. It is a
 cache-friendly data structure offering better performances than
 `std::unordered_map` in most cases and is closely similar to
 `google::dense_hash_map` while using less memory and providing more
 functionalities.
 .
 The library provides the following main classes: `tsl::hopscotch_map`,
 `tsl::hopscotch_set`, `tsl::hopscotch_pg_map` and `tsl::hopscotch_pg_set`. The
 first two are faster and use a power of two growth policy, the last two use a
 prime growth policy instead and are able to cope better with a poor hash
 function. Use the prime version if there is a chance of repeating patterns in
 the lower bits of your hash (e.g. you are storing pointers with an identity
 hash function).
 .
 In addition to these classes the library also provides `tsl::bhopscotch_map`,
 `tsl::bhopscotch_set`, `tsl::bhopscotch_pg_map` and `tsl::bhopscotch_pg_set`.
 These classes have an additional requirement for the key, it must be
 `LessThanComparable`, but they provide a better asymptotic upper bound.
 Nonetheless if you don't have specific requirements (risk of hash DoS attacks),
 `tsl::hopscotch_map` and `tsl::hopscotch_set` should be sufficient in most
 cases and should be your default pick as they perform better in general.

Remark: This package is maintained by Debian Med Packaging Team at
   https://salsa.debian.org/med-team/hopscotch-map

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#915829: ITP: arcp -- (Archive and Package) URI parser and generator

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist

Subject: ITP: arcp -- (Archive and Package) URI parser and generator
Package: wnpp
Owner: Debian Med team 
Severity: wishlist

* Package name: arcp
  Version : 0.2.0
  Upstream Author : Stian Soiland-Reyes 
* URL : http://arcp.readthedocs.io/
* License : Apache-2.0
  Programming Language: Python
  Description : (Archive and Package) URI parser and generator


 arcp provides functions for creating arcp URIs, 
 which can be used for identifying or parsing hypermedia 
 files packaged in an archive or package, like a ZIP file.
 .
 arcp URIs can be used to consume or reference hypermedia resources 
 bundled inside a file archive or an application package, as well as 
 to resolve URIs for archive resources within a programmatic framework.
 .
 This URI scheme provides mechanisms to generate a unique base URI 
 to represent the root of the archive, so that relative URI references 
 in a bundled resource can be resolved within the archive without having to
 extract the archive content on the local file system.
 .
 An arcp URI can be used for purposes of isolation (e.g. when consuming 
 multiple archives), security constraints (avoiding “climb out” from the
 archive), or for externally identiyfing sub-resources referenced by
 hypermedia formats.
 .
 Examples:
  - ``arcp://uuid,32a423d6-52ab-47e3-a9cd-54f418a48571/doc.html``
  - ``arcp://uuid,b7749d0b-0e47-5fc4-999d-f154abe68065/pics/``
  - ``arcp://ni,sha-256;F-34D4TUeOfG0selz7REKRDo4XePkewPeQYtjL3vQs0/``
  - ``arcp://name,gallery.example.org/``
 .
 The different forms of URI authority_ in arcp URIs can be used depending
 on which uniqueness constraints to apply when addressing an archive.
 See the arcp specification
 (https://tools.ietf.org/html/draft-soilandreyes-arcp-02) for details.
 .
 Note that this library only provides mechanisms to 
  *generate* and *parse* arcp URIs, and do *not* integrate with any 
 particular archive or URL handling modules like 
 "zipfile" or "urllib.request".

Needed for latest cwltool. 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#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#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