Bug#1069970: ITP: libeddsa-java -- implementation of EdDSA in Java
Package: wnpp Severity: wishlist Owner: Debian-Java team X-Debbugs-Cc: debian-devel@lists.debian.org, debian-j...@lists.debian.org * Package name: libeddsa-java Version : 0.3.0 Upstream Contact: str4d * URL : https://github.com/str4d/ed25519-java * License : CC0-1.0 Programming Lang: Java Description : implementation of EdDSA in Java This package is needed as a dependency of libmina-sshd-java and of new upstream versions of jgit. I plan to maintain it in the Debian-Java team and to be its first uploader. This implementation of EdDSA is based on the ref10 implementation in SUPERCOP. There are two internal implementations: - A port of the radix-2^51 operations in ref10 - fast and constant-time, but only useful for Ed25519; - A generic version using BigIntegers for calculation - a bit slower and not constant-time, but compatible with any EdDSA parameter specification.
Bug#1050556: ITP: libfailsafe-java -- fault tolerance and resilience patterns Java library
Package: wnpp Severity: wishlist Owner: Debian Java Maintainers X-Debbugs-Cc: debian-devel@lists.debian.org * Package name: libfailsafe-java Version : 3.3.2 Upstream Contact: Jonathan Halterman * URL : Jonathan Halterman * License : Apache-2.0 Programming Lang: Java Description : fault tolerance and resilience patterns Java library Failsafe is a lightweight, zero-dependency library for handling failures in Java 8+, with a concise API for handling everyday use cases and the flexibility to handle everything else. It works by wrapping executable logic with one or more resilience policies, which can be combined and composed as needed. Policies include Retry, CircuitBreaker, RateLimiter, Timeout, Bulkhead, and Fallback. Additional modules include OkHttp. This package is needed as a dependency of nextflow. It will be team-maintained by the Debian-Java team.
Bug#1050170: ITP: libconcurrentunit-java -- simple toolkit for testing multi-threaded Java code
Package: wnpp Severity: wishlist Owner: Debian Java Maintainers X-Debbugs-Cc: debian-devel@lists.debian.org * Package name: libconcurrentunit-java Version : 0.4.6 Upstream Contact: Jonathan Halterman * URL : https://github.com/jhalterman/concurrentunit * License : Apache-2.0 Programming Lang: Java Description : simple toolkit for testing multi-threaded Java code ConcurrentUnit was created to help developers test multi-threaded or asynchronous code. It allows one to perform assertions and wait for operations in any thread, with failures being properly reported back to the main test thread. If an assertion fails, the test fails, regardless of which thread the assertion came from. This package is needed as a (transitive) dependency of nextflow. It will be team-maintained by the Debian-Java team.
Bug#1027277: ITP: glgrib -- geophysical GRIB2-encoded fields displayer using OpenGL
Package: wnpp Severity: wishlist Owner: Pierre Gruet User: debian-scie...@lists.debian.org Usertags: field..geography X-Debbugs-Cc: debian-devel@lists.debian.org, debian-scie...@lists.debian.org * Package name: glgrib Version : 1.0.0 Upstream Contact: Philippe Marguinaud * URL : https://github.com/pmarguinaud/glgrib * License : GPL-3 Programming Lang: C++ Description : geophysical GRIB2-encoded fields displayer using OpenGL This is an interactive executable, based on GLFW, displaying GRIB2 fields with OpenGL. It offers a GLFW backend for interactive display or an EGL backend for batch processing without X11 display. The interface is written in Perl/Tk. This software is packaged as an useful geographical data visualization tool, comfortable and eye-appealing. We plan to maintain it under the Debian-science team umbrella.
Bug#1022258: ITP: libmjson-java -- lean JSON Library for Java with a compact API
Package: wnpp Severity: wishlist Owner: Debian-med team X-Debbugs-Cc: debian-devel@lists.debian.org, debian-...@lists.debian.org * Package name: libmjson-java Version : 1.4.0 Upstream Author : Miami-Dade County * URL : https://bolerio.github.io/mjson/ * License : Apache-2.0 Programming Lang: Java Description : lean JSON Library for Java with a compact API mJson is an extremely lightweight Java JSON library with a very concise API. Unlike other JSON libraries, it focuses on manipulating JSON structures in Java without necessarily mapping them to/from strongly typed Java objects. Because of its tiny size, it is well-suited for any application aiming at a small footprint such as mobile applications. mjson is needed as a dependency of htsjdk, which is an important software in the Debian-med ecosystem.
Bug#1021934: ITP: biojava6-live -- Java API to biological data and applications (version 6)
Package: wnpp Severity: wishlist Owner: Debian-med team X-Debbugs-Cc: debian-devel@lists.debian.org, debian-...@lists.debian.org * Package name: biojava6-live Version : 6.0.5 Upstream Author : BioJava Developers * URL : https://biojava.org * License : LGPL-2.1 Programming Lang: Java Description : Java API to biological data and applications (version 6) This package presents the Open Source Java API to biological databases and a series of mostly sequence-based algorithms. BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It includes objects for manipulating sequences, file parsers, server support, access to BioSQL and Ensembl databases, and powerful analysis and statistical routines including a dynamic programming toolkit. Important changes in the API at each major version have made it necesssary to have a new source package for every major version of the library. In the Debian-med team, we have already started seeing packages depending on biojava 6 and it would be a very valuable addition to have it into Debian. The package will be team-maintained by the Debian-med team.
Bug#1016046: ITP: genomicsdb -- sparse array storage library for genomics
Package: wnpp Severity: wishlist Owner: Debian-med team X-Debbugs-Cc: debian-devel@lists.debian.org, debian-...@lists.debian.org * Package name: genomicsdb Version : 1.4.3 Upstream Author : Intel Health and Lifesciences * URL : https://www.genomicsdb.org/ * License : Expat Programming Lang: C++, Java Description : sparse array storage library for genomics GenomicsDB is built on top of a htslib fork and an internal array storage system for importing, querying and transforming variant data. Variant data is sparse by nature (sparse relative to the whole genome) and using sparse array data stores is a perfect fit for storing such data. The GenomicsDB stores variant data in a 2D array where: - Each column corresponds to a genomic position (chromosome + position); - Each row corresponds to a sample in a VCF (or CallSet in the GA4GH terminology); - Each cell contains data for a given sample/CallSet at a given position; data is stored in the form of cell attributes; - Cells are stored in column major order - this makes accessing cells with the same column index (i.e. data for a given genomic position over all samples) fast. - Variant interval/gVCF interval data is stored in a cell at the start of the interval. The END is stored as a cell attribute. For variant intervals (such as deletions and gVCF REF blocks), an additional cell is stored at the END value of the variant interval. When queried for a given genomic position, the query library performs an efficient sweep to determine all intervals that intersect with the queried position. There is a C++ library and a Java library, we plan to ship both of them. This library is needed as a dependency of gatk, which is a packaging target of the Debian-med team.
Bug#1015926: ITP: persalys -- GUI for uncertainty treatment and variabilities management
Package: wnpp Severity: wishlist Owner: Pierre Gruet User: debian-scie...@lists.debian.org Usertags: field..science X-Debbugs-Cc: debian-devel@lists.debian.org, debian-scie...@lists.debian.org * Package name: persalys Version : 12.0.1 Upstream Author : Airbus-EDF-Phimeca * URL : https://persalys.fr/ * License : LGPL-3+ Programming Lang: C++ Description : GUI for uncertainty treatment and variabilities management Persalys is a graphical user interface for OpenTURNS, dedicated to the treatment of uncertainty and the management of variabilities. The software is a tool between the computer simulation, probabilistic analyses and the data sciences. The interface is available in French or in English. Persalys allows one to: - create mathematical models: analytical, coupling with an external model (finite elements, ...), FMU; - analyse the variability of one's parameters thanks to many methods and visualisation tools; - statistically analyse one's measuring data, infer probability distributions or create metamodels. I am an user of Persalys. I plan to maintain in in the Debian-science team.
Bug#1014504: ITP: ojalgo -- Java library to do mathematics, linear algebra and optimisation
Package: wnpp Severity: wishlist Owner: Debian-math team X-Debbugs-Cc: debian-devel@lists.debian.org * Package name: ojalgo Version : 51.3.0 Upstream Author : Optimatika * URL : https://www.ojalgo.org/ * License : Expat Programming Lang: Java Description : Java library to do mathematics, linear algebra and optimisation ojAlgo is a fast pure Java linear algebra library. It features: - Optimisation (mathematical programming) tools including LP, QP and MIP solvers – again this is pure Java with zero dependencies; - A collection of "array" classes that can be sparse or dense and arbitrarily large. They can be used as 1-, 2- or N/Any-dimensional arrays, and may contain/handle a multitude of different number types including complex numbers, rational numbers and quaternions. The memory for the arrays can alternatively be allocated off heap or in a file. The linear algebra part of ojAlgo builds on these arrays – they’re fast and efficient; - Artificial Neural Networks; - Various other things like time series, random numbers, stochastic processes, descriptive statistics... ojAlgo is needed as a dependency of gatk. It will be team-maintained inside the Debian-math team.
Bug#1014344: ITP: gatk-bwamem -- interface to call Heng Li's bwa mem aligner from Java code
Package: wnpp Severity: wishlist Owner: Debian-med team X-Debbugs-Cc: debian-devel@lists.debian.org, debian-...@lists.debian.org * Package name: gatk-bwamem Version : 1.0.4 Upstream Author : Broad Institute * URL : https://github.com/broadinstitute/gatk-bwamem-jni/ * License : BSD-3-Clause Programming Lang: Java Description : interface to call Heng Li's bwa mem aligner from Java code BWA (Burrows-Wheeler Aligner) is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It is written in C. gatk-bwamem provides a Java library and a shared library to allow one to use BWA from Java code.
Bug#1011557: ITP: pagmo -- library for massively parallel optimisation
Package: wnpp Severity: wishlist Owner: Pierre Gruet User: debian-scie...@lists.debian.org Usertags: field..science X-Debbugs-Cc: debian-devel@lists.debian.org, debian-scie...@lists.debian.org * Package name: pagmo Version : 2.18.0 Upstream Author : Francesco Biscani * URL : https://github.com/esa2/pagmo * License : GPL-3+ or LGPL-3+ Programming Lang: C++ Description : library for massively parallel optimisation pagmo is a C++ scientific library built around the idea of providing an unified interface to optimization algorithms and to optimization problems and to make their deployment in massively parallel environments easy. This package is needed as a dependency of openturns, which is maintained in the Debian science team -- which I also plan to do with pagmo.
Bug#1011068: ITP: spectra -- library for large scale eigenvalue problems
Package: wnpp Severity: wishlist Owner: Pierre Gruet X-Debbugs-Cc: debian-devel@lists.debian.org, team+m...@tracker.debian.org * Package name: spectra Version : 1.0.1 Upstream Author : Yixuan Qiu * URL : https://spectralib.org/ * License : MPL-2.0 Programming Lang: C++ Description : library for large scale eigenvalue problems Spectra stands for Sparse Eigenvalue Computation Toolkit as a Redesigned ARPACK. It is a C++ library for large scale eigenvalue problems, built on top of Eigen, an open source linear algebra library. Spectra is implemented as a header-only C++ library, whose only dependency, Eigen, is also header-only. Hence Spectra can be easily embedded in C++ projects that require calculating eigenvalues of large matrices. Spectra is designed to calculate a specified number of eigenvalues of a large square matrix. Usually this number of eigenvalues is much smaller than the size of the matrix, so that only a few eigenvalues and eigenvectors are computed, which in general is more efficient than calculating the whole spectral decomposition. Users can choose eigenvalue selection rules to pick the eigenvalues of interest, such as the largest k eigenvalues, or eigenvalues with largest real parts, etc. The library is needed as a dependency of openturns. It will be maintained inside the Debian-math team.
Bug#1008572: ITP: xgboost-predictor-java -- Java implementation of XGBoost predictor for online prediction tasks
Package: wnpp Severity: wishlist Owner: Pierre Gruet User: debian-scie...@lists.debian.org Usertags: field..science X-Debbugs-Cc: debian-devel@lists.debian.org, debian-scie...@lists.debian.org * Package name: xgboost-predictor-java Version : 0.3.1 Upstream Author : KOMIYA Atsushi * URL : https://github.com/komiya-atsushi/xgboost-predictor-java * License : Apache-2.0 Programming Lang: Java Description : Java implementation of XGBoost predictor for online prediction tasks XGBoost is an optimized distributed gradient boosting library designed to be highly efficient, flexible and portable. It implements machine learning algorithms under the Gradient Boosting framework. XGBoost provides a parallel tree boosting (also known as GBDT, GBM) that solve many data science problems in a fast and accurate way. The same code runs on major distributed environment (Kubernetes, Hadoop, SGE, MPI, Dask) and can solve problems beyond billions of examples. This is the Java implementation of XGBoost. Right now it is needed as a dependency of gatk, but it should be useful more broadly for scientists or people from machine learning. It will be team-maintained in Debian Science team.
Re: Bug#1008304: ITP: http-nio -- http/s file system provider for Java NIO.2
Hi Guillem, Le 28/03/2022 à 13:43, Guillem Jover a écrit : Hi! On Sat, 2022-03-26 at 14:59:17 +0100, Pierre Gruet wrote: Package: wnpp Severity: wishlist Owner: Debian-med team X-Debbugs-Cc: debian-devel@lists.debian.org, debian-...@lists.debian.org * Package name: http-nio Version : 0.1.0 Upstream Author : Daniel Gomez-Sanchez * URL : https://github.com/lbergelson/http-nio * License : BSD-3-Clause Programming Lang: Java Description : http/s file system provider for Java NIO.2 This package provides a http or https file system that can be used in conjunction with Java NIO.2. This lightweight library provides a few classes related to file systems and paths. It is provided by the developers of gatk, which is a long-term packaging target of Debian-med team. I am packaging it as a reverse dependency of gatk. For this reason, it will be team-maintained inside Debian-med team. The http-nio name seems rather generic to be used as either source or binary package name. Could you namespace it? I don't see a very clear naming convention in the archive for Java packages, but then I have not checked the java-policy, TBH. What I see is either -jave or lib-java, either would work here. Thanks for your advice on this; the lib-java pattern seems wholly appropriate here, as it matches the name of the binary package that will be built by this source package. I will make the change as you suggest. Thanks, Guillem Best regards, -- Pierre OpenPGP_signature Description: OpenPGP digital signature
Bug#1008304: ITP: http-nio -- http/s file system provider for Java NIO.2
Package: wnpp Severity: wishlist Owner: Debian-med team X-Debbugs-Cc: debian-devel@lists.debian.org, debian-...@lists.debian.org * Package name: http-nio Version : 0.1.0 Upstream Author : Daniel Gomez-Sanchez * URL : https://github.com/lbergelson/http-nio * License : BSD-3-Clause Programming Lang: Java Description : http/s file system provider for Java NIO.2 This package provides a http or https file system that can be used in conjunction with Java NIO.2. This lightweight library provides a few classes related to file systems and paths. It is provided by the developers of gatk, which is a long-term packaging target of Debian-med team. I am packaging it as a reverse dependency of gatk. For this reason, it will be team-maintained inside Debian-med team.
Bug#1008128: ITP: gatk-fermilite -- interface to call Heng Li's fermi-lite assembler from Java code
Package: wnpp Severity: wishlist Owner: Debian-med team X-Debbugs-Cc: debian-devel@lists.debian.org, debian-...@lists.debian.org * Package name: gatk-fermilite Version : 1.2.1 Upstream Author : Broad Institute * URL : https://github.com/broadinstitute/gatk-fermilite-jni * License : BSD-3-clause Programming Lang: Java, C Description : interface to call Heng Li's fermi-lite assembler from Java code Fml-asm (fermi-lite assembler) is a command-line tool for assembling Illumina short reads in regions from 100bp to 10 million bp in size, based on the fermi-lite library. gatk-fermilite provides a Java library and a shared library to allow one to use fermilite from Java code. The package will be team-maintained inside Debian-med team. It is needed as a dependency of the packaging target gatk.
Bug#1006834: ITP: aeonbits-owner -- API to handle application configuration through Java properties file
Package: wnpp Severity: wishlist Owner: Debian med team X-Debbugs-Cc: debian-devel@lists.debian.org, debian-...@lists.debian.org * Package name: aeonbits-owner Version : 1.0.12 Upstream Author : Luigi R. Viggiano * URL : http://owner.aeonbits.org/ * License : BSD-3-clause Programming Lang: Java Description : API to handle application configuration through Java properties file OWNER was written because the code dealing with the configuration is frequently repetitive, redundant, it’s made of static classes, singletons, long list of methods just doing conversion from a string property to a named method returning a Java primitive or a basic Java object. OWNER solves the problem providing an interface object that - is easy to mock, easy to pass to other objects (via dependency injection); - declaratively maps the configuration without any redundancy; - can easily expand the loading logic in order to have multiple configuration files, multiple level of overriding (global configuration, user-level, defaults, etc); - doesn’t need to have an actual properties file backing the configuration, if one uses @DefaultValue. - provides a lot of features, like hot reloading, variables expansion, etc; - leaves one free to do everything one is already doing with java.util.Properties; - does support a super powerful type conversion, which includes arrays, collections, many standard Java objects, and even the possibility to plug one's own conversion logic. The package is needed as a dependency of gatk, which is a packaging target of Debian-med team. It will be maintained in this team.
Bug#1006501: ITP: snpsift -- tool to annotate and manipulate genome variants
Package: wnpp Severity: wishlist Owner: Debian-med team X-Debbugs-Cc: debian-devel@lists.debian.org, debian-...@lists.debian.org * Package name: snpsift Version : 5.1 Upstream Author : Pablo Cingolani * URL : https://pcingola.github.io/SnpEff/ss_introduction/ * License : Expat Programming Lang: Java Description : tool to annotate and manipulate genome variants SnpSift is a toolbox that allows one to filter and manipulate annotated files. Once the genomic variants have been annotated, one needs to filter them out in order to find the "interesting / relevant variants". Given the large data files, this is not a trivial task (e.g. one cannot load all the variants into XLS spreadsheet). SnpSift helps to perform this VCF file manipulation and filtering required at this stage in data processing pipelines. The package will be team-maintained by Debian-med team.
Bug#1005356: ITP: rockhopper -- system for analyzing bacterial RNA-seq data
Package: wnpp Severity: wishlist Owner: Debian-med team X-Debbugs-Cc: debian-devel@lists.debian.org, debian-...@lists.debian.org * Package name: rockhopper Version : 2.0.3 Upstream Author : Brian Tjaden * URL : https://cs.wellesley.edu/~btjaden/Rockhopper * License : GPL-3+ Programming Lang: Java Description : system for analyzing bacterial RNA-seq data Rockhopper is a comprehensive and user-friendly system for computational analysis of bacterial RNA-seq data. As input, Rockhopper takes RNA sequencing reads output by high-throughput sequencing technology (FASTQ, QSEQ, FASTA, SAM, or BAM files). Rockhopper supports the following tasks: * Reference based transcript assembly (when one or more reference genomes are available) - Aligning reads to genomes - Assembling transcripts - Identifying transcript boundaries and novel transcripts such as small RNAs * De novo transcript assembly (when reference genomes are unavailable) * Normalizing data from different experiments * Quantifying transcript abundance * Testing for differential gene expression * Characterizing operon structures * Visualizing results in a genome browser The package will be team-maintained by Debian-med team.
Bug#1004554: ITP: libpdfbox-graphics2d-java -- Java library to embed graphics as vector drawing in a PDF
Package: wnpp Severity: wishlist Owner: Debian Java team X-Debbugs-Cc: debian-devel@lists.debian.org, pkg-java-maintain...@lists.alioth.debian.org * Package name: libpdfbox-graphics2d-java Version : 0.34 Upstream Author : Emmeran Seehuber * URL : https://github.com/rototor/pdfbox-graphics2d/ * License : Apache-2.0 Programming Lang: Java Description : Java library to embed graphics as vector drawing in a PDF Using this library one can use any Graphics2D API based SVG / graph / chart library to embed those graphics as vector drawing in a PDF. In combination with PDFBox PDFRenderer/PageDrawer one can also "rerender" PDF pages and change certain aspects (e.g. change the color mapping and perform an overfill) . The following features are supported: * Drawing any shape using draw...() and fill...() methods from Graphics2D. * Drawing images. The default is to always lossless compress them. One could plugin one's own Image -> PDImageXObject conversion if one wants to encode the images as jpeg. * All BasicStroke attributes. * Paint: - Color. One can specify one's own color mapping implementation to special map the (RGB) colors to PDColor. Beside using CMYK colors one can also use spot colors. - GradientPaint, LinearGradientPaint and RadialGradientPaint. There are some restrictions. - TexturePaint. * Drawing text. By default all text is drawn as vector shapes, so no fonts are embedded. RTL languages are supported. It's possible to use fonts, but this loses some features (especially RTL support) and one must provide the TTF files of the fonts if the default PDF fonts are not enough. The package will be team-maintained in the Debian Java team.
Bug#1004152: ITP: malt -- sequence alignment and analysis tool to process sequencing data
Package: wnpp Severity: wishlist Owner: Debian-med team X-Debbugs-Cc: debian-devel@lists.debian.org, debian-...@lists.debian.org * Package name: malt Version : 0.5.2 Upstream Author : Daniel Huson * URL : https://github.com/danielhuson/malt * License : GPL-3+ Programming Lang: Java Description : sequence alignment and analysis tool to process sequencing data MALT, an acronym for MEGAN alignment tool, is a sequence alignment and analysis tool designed for processing high-throughput sequencing data, especially in the context of metagenomics. It is an extension of MEGAN6, the MEGenome Analyzer and is designed to provide the input for MEGAN6, but can also be used independently of MEGAN6. The core of the program is a sequence alignment engine that aligns DNA or protein sequences to a DNA or protein reference database in either BLASTN (DNA queries and DNA references), BLASTX (DNA queries and protein references) or BLASTP (protein queries and protein references) mode. The engine uses a banded-alignment algorithm with ane gap scores and BLOSUM substitution matrices (in the case of protein alignments). The program can compute both local alignments (Smith-Waterman) or semi-global alignments (in which reads are aligned end-to-end into reference sequences), the latter being more appropriate for aligning metagenomic reads to references. The package will be team-maintained in Debian-med team.
Bug#1003782: ITP: megan-ce -- interactive tool to explore and analyse microbiome sequencing data
Package: wnpp Severity: wishlist Owner: Debian-med team X-Debbugs-Cc: debian-devel@lists.debian.org, debian-...@lists.debian.org * Package name: megan-ce Version : 6.21.1 Upstream Author : Daniel Huson * URL : https://github.com/danielhuson/megan-ce * License : GPL-3+ Programming Lang: Java Description : interactive tool to explore and analyse microbiome sequencing data MEGAN Community Edition is a shotgun sequencer to analyze microbiome samples. It is a rewrite and extension of the widely-used microbiome analysis tool MEGAN so as to facilitate the interactive analysis of the taxonomic and functional content of very large microbiome datasets. Other new features include a functional classifier called InterPro2GO, gene-centric read assembly, principal coordinate analysis of taxonomy and function, and support for metadata. By integrating MEGAN CE with the high-throughput DNA-to-protein alignment tool DIAMOND a powerful and complete pipeline for the analysis of metagenome shotgun sequences can be provided. megan-ce will be team-maintained by Debian-med team.
Bug#1001099: ITP: stopt -- library for stochastic optimization problems
Package: wnpp Severity: wishlist Owner: Pierre Gruet X-Debbugs-Cc: debian-devel@lists.debian.org * Package name: stopt Version : 4.2 Upstream Author : Xavier Warin * URL : https://gitlab.com/stochastic-control/StOpt/ * License : LGPL-3 Programming Lang: C++ Description : library for stochastic optimization problems The STochastic OPTimization library (StOpt) aims at providing tools in C++ for solving some stochastic optimization problems encountered in finance or in the industry. Different methods are available: - dynamic programming methods based on Monte Carlo with regressions (global, local, kernel and sparse regressors), for underlying states following some uncontrolled Stochastic Differential Equations; - dynamic programming with a representation of uncertainties with a tree: transition problems are here solved by some discretizations of the commands, resolution of LP with cut representation of the Bellman values; - Semi-Lagrangian methods for Hamilton Jacobi Bellman general equations for underlying states following some controlled Stochastic Differential Equations; - Stochastic Dual Dynamic Programming methods to deal with stochastic stock management problems in high dimension. Uncertainties can be given by Monte Carlo and can be represented by a state with a finite number of values (tree); - Some branching nesting methods to solve very high dimensional non linear PDEs and some appearing in HJB problems. Besides some methods are provided to solve by Monte Carlo some problems where the underlying stochastic state is controlled. For each method, a framework is provided to optimize the problem and then simulate it out of the sample using the optimal commands previously computed. Parallelization methods based on OpenMP and MPI are provided in this framework permitting to solve high dimensional problems on clusters. The library should be flexible enough to be used at different levels depending on the user's willingness. The package will be team-maintained in the Debian-math team. The upstream developer is part of the packaging effort.
Bug#999424: ITP: geners -- generic serialization library for C++
Package: wnpp Severity: wishlist Owner: Pierre Gruet X-Debbugs-Cc: debian-devel@lists.debian.org * Package name: geners Version : 1.12.0 Upstream Author : Igor Volobouev * URL : https://geners.hepforge.org/ * License : Expat Programming Lang: C++ Description : generic serialization library for C++ The Generic Serialization library is designed to address the problem of C++ object persistence in situations where the most typical data access pattern is "write once read many" (WORM). "Geners" is a set of tools and conventions which allows its users to develop C++ classes that can be converted to and from a storable stream of bytes in a well-organized and type-safe manner. Serialization of STL containers is supported, including the ones added in the C++11 standard. Independent versioning of each class definition is allowed. Among others, compared to the boost serialization package, Geners archives provide random access to stored objects and can be used to create and serialize very large archive-based objects. Yet, only binary archives are implemented, and implementing non-intrusive serialization is less transparent. I am packaging this software as a dependency of stopt, which is a packaging target of mine. I plan to maintain it myself.
Bug#996993: ITP: biojava5-live -- Java API to biological data and applications (version 5)
Package: wnpp Severity: wishlist Owner: Debian-med team X-Debbugs-Cc: debian-devel@lists.debian.org, debian-...@lists.debian.org * Package name: biojava5-live Version : 5.4.0 Upstream Author : BioJava Developers * URL : https://www.biojava.org/ * License : LGPL-2.1 Programming Lang: Java Description : Java API to biological data and applications (version 5) This package presents the Open Source Java API to biological databases and a series of mostly sequence-based algorithms. BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It includes objects for manipulating sequences, file parsers, server support, access to BioSQL and Ensembl databases, and powerful analysis and statistical routines including a dynamic programming toolkit. This is the version 5 of biojava, which brings several changes compared to version 4, packaged in biojava4-live. It will be maintained by the Debian-med team.
Bug#996991: ITP: jgrapht -- Java library of graph theory data structures and algorithms
Package: wnpp Severity: wishlist Owner: Pierre Gruet User: debian-scie...@lists.debian.org Usertags: field..science X-Debbugs-Cc: debian-devel@lists.debian.org, debian-scie...@lists.debian.org * Package name: jgrapht Version : 1.5.1 Upstream Author : Abdallah Atouani and collaborators * URL : https://jgrapht.org/ * License : LGPL-2.1 or EPL-2.0 Programming Lang: Java Description : Java library of graph theory data structures and algorithms JGraphT is a free Java class library that provides mathematical graph-theory objects and algorithms. In JGraphT, a graph is defined as a set of vertices connected by a set of edges. It is possible to define graphs, to modify, compare or generate them, to run many algorithms through them. One may also import or export graphs. The library is needed for the packaging of biojava5, which is an aim of the Debian med team. It is also a nice adddition to Debian to have this Java library to tackle graph theory problems. Many years ago, libgrapht0.6-java and libjgrapht0.8-java have been packaged because new upstream versions of jgrapht generally incorporated ABI changes. Now this seems not to be the case, hence this unversioned package name. The packaging will be done in the Debian-science team.
Bug#996865: ITP: jheaps -- Java library with various heap implementations
Package: wnpp Severity: wishlist Owner: Debian-java team X-Debbugs-Cc: debian-devel@lists.debian.org, debian-j...@lists.debian.org * Package name: jheaps Version : 0.14 Upstream Author : Dimitrios Michail * URL : https://github.com/d-michail/jheaps * License : Apache-2.0 Programming Lang: Java Description : Java library with various heap implementations This library contains various heap implementations written in Java. A heap is a priority queue data type which contains elements with keys (duplicate keys are permitted) from a totally-ordered universe. The library is easy to use, its data structures have a well defined interface, it is fast and well documented, and the heaps are written in a similar way as in the JDK. jheaps is needed as a dependency of JGraphT, which will also soon be packaged as a dependency of biojava5-live, needed in Debian-med activities. JGraphtT will also be a nice addition to scientific software in Debian-science. The package will be team-maintained in the Debian-java team.
Bug#996727: ITP: ciftools-java -- Java library to read and write CIF files
Package: wnpp Severity: wishlist Owner: Debian java team X-Debbugs-Cc: debian-devel@lists.debian.org, debian-j...@lists.debian.org * Package name: ciftools-java Version : 3.0.0 Upstream Author : Sebastian Bittrich * URL : https://github.com/rcsb/ciftools-java * License : Expat Programming Lang: Java Description : Java library to read and write CIF files CIFTools implements reading and writing of CIF files as well as their efficiently encoded counterpart, called BinaryCIF. The idea is to have a robust, type-safe implementation for the handling of CIF files which does not care about the origin of the data: both conventional text-based and binary files should be handled the same way. This library is needed as a dependency for biojava5-live, which is a packaging aim of Debian med team. It will be team-maintained inside the Debian java team.
Bug#995294: ITP: tipp -- taxonomic identification and abundance profiling tool
Package: wnpp Severity: wishlist Owner: Debian-med team X-Debbugs-Cc: debian-devel@lists.debian.org, debian-...@lists.debian.org * Package name: tipp Version : 1.0 Upstream Author : Siavash Mirarab * URL : https://github.com/TeraTrees/TIPP * License : GPL-3 Programming Lang: Python, Java Description : taxonomic identification and abundance profiling tool TIPP is a modification of SEPP for classifying query sequences (i.e. reads) using phylogenetic placement. TIPP inserts each read into a taxonomic tree and uses the insertion location to identify the taxonomic lineage of the read. The novel idea behind TIPP is that rather than using the single best alignment and placement for taxonomic identification, it uses a collection of alignments and placements and considers statistical support for each alignment and placement. TIPP can also be used for abundance estimation by computing an abundance profile on the reads binned to marker genes in a reference dataset. sepp is already packaged in Debian, and up to now, the binaries of tipp were provided by sepp. Now the sources of sepp and tipp have been separated, which is the reason for making this package. tipp will be team-maintained by Debian-med team.
Bug#992044: ITP: libgoby-java -- next-generation sequencing data and results analysis tool
Package: wnpp Severity: wishlist Owner: Debian-med team X-Debbugs-Cc: debian-devel@lists.debian.org, debian-...@lists.debian.org * Package name: libgoby-java Version : 3.3.1 Upstream Author : Institute for Computational Biomedicine * URL : https://github.com/CampagneLaboratory/goby3 * License : GPL-3 Programming Lang: Java Description : next-generation sequencing data and results analysis tool Goby is a next-gen data management framework designed to facilitate the implementation of efficient data analysis pipelines. Goby provides very efficient file formats to store next-generation sequencing data and intermediary analysis results. It also provides utilities that implement common next-gen data computations. These utilities are designed to be relatively easy to use, yet very efficient. One binary package will contain the Goby IO API, useful to read and write Goby file formats. The related source code is licensed under LGPL-3. The other binary package will contain the whole goby software, released under GPL-3. The package is long-needed by the Debian-med team as a dependency of igv, which is currently in non-free. It will be maintained inside the Debian-med team.
Bug#988879: ITP: grengine -- engine for running and embedding Groovy in a Java virtual machine
Package: wnpp Severity: wishlist Owner: Debian-java team X-Debbugs-Cc: debian-devel@lists.debian.org, debian-j...@lists.debian.org * Package name: grengine Version : 3.0.0 Upstream Author : Alain Stalder * URL : https://www.artecat.ch/grengine * License : Apache-2.0 Programming Lang: Java Description : engine for running and embedding Groovy in a Java virtual machine Grengine allows one to run Groovy code in a Java VM, in a way that is quick, highly configurable and thread-safe. When the default behavior does not suit the users' needs, classes can be overridden to change the way the framework behaves. Even without writing new classes, there are ways to configure the engine quite a lot. This package will be team-maintained inside the Debian-java team. Right now it is needed as a dependency of nextflow.
Bug#988531: ITP: libpf4j-update-java -- update mechanism for Java modular applications
Package: wnpp Severity: wishlist Owner: Debian-java team X-Debbugs-Cc: debian-devel@lists.debian.org, debian-j...@lists.debian.org * Package name: libpf4j-update-java Version : 2.3.0 Upstream Author : Decebal Suiu * URL : https://pf4j.org * License : Apache-2.0 Programming Lang: Java Description : update mechanism for Java modular applications This package allows one to inspect repositories to check the availability of updates for Java plugins. The available updates can then be installed, updated or uninstalled using the classes in this package. Plugins are containers for extension points (defining where, in the application, custom code may be called), for extensions (which implement extension points) and for optional life-cycle methods to start, load and stop extensions. This package will be team-maintained inside the Debian-java team. Right now it is needed as a dependency of nextflow.
Bug#988279: ITP: libpf4j-java -- framework to turn monolithic Java applications into modular ones
Package: wnpp Severity: wishlist Owner: Debian-java team X-Debbugs-Cc: debian-devel@lists.debian.org, debian-j...@lists.debian.org * Package name: libpf4j-java Version : 3.6.0 Upstream Author : Decebal Suiu * URL : https://pf4j.org/ * License : Apache-2.0 Programming Lang: Java Description : framework to turn monolithic Java applications into modular ones PF4J is a lightweight framework which helps one to build a modular application by defining plugins, which are containers for extension points (defining where, in the application, custom code may be called), for extensions (which implement extension points) and for optional lifecycle methods to start, load and stop extensions. A plugin is similar to modules in other programming languages. This package will be team-maintained inside the Debian-java team. Right now it is needed as a dependency of nextflow.
Bug#987946: ITP: capsule-maven-nextflow -- packaging tool for Java applications with Maven coordinates
Package: wnpp Severity: wishlist Owner: Debian-med team X-Debbugs-Cc: debian-devel@lists.debian.org, debian-...@lists.debian.org * Package name: capsule-maven-nextflow Version : 1.0.3.1 Upstream Author : Paolo di Tommaso * URL : https://github.com/nextflow-io/capsule-maven * License : EPL-1.0 Programming Lang: Java Description : packaging tool for Java applications with Maven coordinates A capsule is a single executable JAR that contains everything an application needs to run either in the form of embedded files or as declarative metadata. Maven Capsule is a capsule that allows the creations of capsules that, instead of embedding their dependencies, download all or some of them from a Maven repository. The dependencies are downloaded, cached locally, and shared among other capsules that also depend on them. In addition, this capsule allows specifying capsule metadata in a POM file in addition to the manifest. A capsule with the Maven caplet that has all (or almost all) of its dependencies downloaded rather than embedded is known as a "thin" capsule (as opposed to a "fat" capsule, which embeds all of its dependencies). In fact, a capsule may not contain any of the application's classes/JARs at all. Instead, the capsule's manifest may contain these attributes alone (and no files in the capsule JAR besides the manifest). When the capsule is launched, the newest available version of the application will be downloaded, cached and launched. This package contains a fork of the original capsule-maven project. This fork is suited as a dependency of nextflow.
Bug#987771: ITP: capsule-nextflow -- packaging and deployment tool for Java applications
Package: wnpp Severity: wishlist Owner: Debian-med team X-Debbugs-Cc: debian-devel@lists.debian.org, debian-...@lists.debian.org * Package name: capsule-nextflow Version : 1.1.0 Upstream Author : Paolo di Tommaso * URL : https://github.com/nextflow-io/capsule * License : EPL-1.0 Programming Lang: Java Description : packaging and deployment tool for Java applications A capsule is a single executable JAR that contains everything an application needs to run either in the form of embedded files or as declarative metadata. It can contain JAR artifacts, dependencies and resources, native libraries, the required Java Runtime Environment version, the Java Virtual Machine flags required to run the application well, Java or native agents and more. In short, a capsule is a self-contained JAR that knows everything there is to know about how to run the application the way it is meant to run. One way of thinking about a capsule is as a fat JAR on steroids (that also allows native libraries and never interferes with your dependencies) and a declarative startup script rolled into one; another, is to see it is as the deploy-time counterpart to your build tool. Just as a build tool manages your build, Capsule manages the launching of your application. This package contains a fork of the original capsule project. This fork is suited as a dependency of nextflow, which is a workflow engine needed in the Debian-med team. It will thus be maintained inside this team.
Bug#986141: ITP: snpeff -- genetic variant annotation and effect prediction toolbox
Package: wnpp Severity: wishlist Owner: Debian-med team X-Debbugs-Cc: debian-devel@lists.debian.org, debian-...@lists.debian.org * Package name: snpeff Version : 4.3t Upstream Author : Pablo Cingolani * URL : https://pcingola.github.io/SnpEff/ * License : LGPL-3 Programming Lang: Java Description : genetic variant annotation and effect prediction toolbox SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes (such as amino acid changes). The inputs are predicted variants (SNPs, insertions, deletions and MNPs). The input file is usually obtained as a result of a sequencing experiment, and it is usually in variant call format (VCF). SnpEff analyzes the input variants. It annotates the variants and calculates the effects they produce on known genes (e.g. amino acid changes). This software is needed in many workflows in the Debian-med team. It will be maintained inside the team.
Bug#974879: ITP: intervalstorej -- Java implementation of the Nested Containment List data structure
Package: wnpp Severity: wishlist Owner: Debian Java team X-Debbugs-Cc: debian-devel@lists.debian.org, debian-j...@lists.debian.org * Package name: intervalstorej Version : 1.2 Upstream Author : Mungo Carstairs, Barton Group * URL : https://github.com/bartongroup/IntervalStoreJ/ * License : BSD-3-clause Programming Lang: Java Description : Java implementation of the Nested Containment List data structure NCList provides efficient lookup of intervals overlapping a given range in time O(M log N) where N is the number of intervals stored, and M the number of overlaps found. IntervalStore: - is parameterised by ; - so can store any Java type that implements IntervalI, that is, has methods getBegin() and getEnd() (where begin <= end); - extends java.util.AbstractCollection; - may be referred to as Collection in code; - exposes methods for add, contains, remove, iterator, size etc; - has a 'bulk load' constructor, and methods to add or remove entries, while retaining lookup efficiency; - optimises storage and search of sparsely nested intervals by storing non-nested intervals separately; - incorporates NCList to store any properly nested intervals. This package is needed as a dependency of jalview, which is currently updated as we have a quite old version of it in Debian. jalview now relies on it. It will be maintained inside the Debian Java team.
Bug#973568: ITP: libpj-java -- API and middleware for parallel programming in Java
Package: wnpp Severity: wishlist Owner: Debian-med project X-Debbugs-Cc: debian-devel@lists.debian.org, debian-...@lists.debian.org * Package name: libpj-java Version : 20150107 Upstream Author : Alan Kaminsky * URL : https://www.cs.rit.edu/~ark/pj.shtml * License : GPL-3+ Programming Lang: Java Description : API and middleware for parallel programming in Java Parallel Java (PJ) is for parallel programming in 100% Java on shared memory multiprocessor (SMP) parallel computers, cluster parallel computers, and hybrid SMP cluster parallel computers. PJ was developed in the Department of Computer Science at the Rochester Institute of Technology. libpj-java is needed as a dependency of goby, which is itself needed in the ongoing efforts in Debian-med to package igv in the main section. It will be maintained inside the Debian-med team.
Bug#972554: ITP: icb-utils -- Java library of utilities to manage files and compute statistics
Package: wnpp Severity: wishlist Owner: Debian-med project X-Debbugs-Cc: debian-devel@lists.debian.org, debian-...@lists.debian.org * Package name: icb-utils Version : 2.0.1+git20161002.afee1d9 Upstream Author : Fabien Campagne * URL : https://github.com/CampagneLaboratory/icb-utils * License : Apache-2.0 Programming Lang: Java Description : Java library of utilities to manage files and compute statistics icb-utils is a group of tools originally designed by the Campagne laboratory for computational biomedicine software. They include extensions of standard Java to manage io, extended iterator classes, hashtables, network-related classes, as well as a set of classes allowing for the computation of statistics. This software is needed as a predependency for igv, currently in non-free. It is also a dependency of several software Debian-med is willing to package. The package will be taken care of in Debian-med team.
Bug#971870: ITP: sepp -- methods using ensembles of Hidden Markov Models (HMM)
Package: wnpp Severity: wishlist Owner: Debian-med project X-Debbugs-Cc: debian-devel@lists.debian.org, debian-...@lists.debian.org * Package name: sepp Version : 4.3.10 Upstream Author : Siavash Mirarab * URL : https://github.com/smirarab/sepp/ * License : GPL-3 Programming Lang: Python, Java Description : methods using ensembles of Hidden Markov Models (HMM) The tools SEPP and TIPP implementing these methods use ensembles of Hidden Markov Models (HMMs) in different ways, each focusing on a different problem. SEPP stands for "SATe-enabled Phylogenetic Placement", and addresses the problem of phylogenetic placement of short reads into reference alignments and trees. TIPP stands for "Taxonomic Identification and Phylogenetic Profiling", and addresses the problem of taxonomic identification and abundance profiling of metagenomic data. This package is useful to treat genomic data and will be maintained by Debian-med.
Bug#969186: ITP: libreflections-java -- Java runtime metadata analysis library
Package: wnpp Severity: wishlist Owner: Debian Java team X-Debbugs-Cc: debian-devel@lists.debian.org, debian-j...@lists.debian.org * Package name: libreflections-java Version : 0.9.12 Upstream Author : ronmamo * URL : https://github.com/ronmamo/reflections * License : WTFPL Programming Lang: Java Description : Java runtime metadata analysis library Reflections scans a classpath, indexes the metadata, allows one to query it on runtime and may save and collect that information for many modules within a project. Using Reflections one can query metadata such as: - get all subtypes of some type; - get all types/members annotated with some annotation; - get all resources matching a regular expression; - get all methods with specific signature including parameters, parameter annotations and return type. This package is needed as a predependency of igv, which the Debian med team would like to package out of non-free. I am personnally aiming at this. The package will be maintained in the Debian Java team.
Bug#969176: ITP: libdsiutils-java -- Java library of statistical and text data handling tools
Package: wnpp Severity: wishlist Owner: Debian Java team X-Debbugs-Cc: debian-devel@lists.debian.org, debian-j...@lists.debian.org * Package name: libdsiutils-java Version : 2.6.6 Upstream Author : Sebastiano Vigna * URL : http://dsiutils.di.unimi.it * License : LGPL-3 Programming Lang: Java Description : Java library of statistical and text data handling tools The library contains: - Implementations of pseudorandom number generators; - BitVector and its implementations -- a high-performance but flexible set of bit vector classes; - A it.unimi.dsi.compression package containing codecs for several types of encodings; - ProgressLogger, a flexible logger with statistics marking the progress of the classes that are used and that require hours of computation; - ObjectParser, a class making it easy to specify complex objects on the command line; - MutableString, an alternative to the immutable Java String class; - The I/O package, containing fast version of several classes existing in java.io, many useful classes to read easily text data (e.g., FileLinesCollection), bit streams, classes providing large-size memory mapping such as ByteBufferInputStream, and OfflineIterable -- the easy & fast way to store large sequences of objects on disk and iterate on them; - The it.unimi.dsi.util package, containing pseudorandom number generators, tries, immutable prefix maps, Bloom filters, a very comfortable Properties class and more; - The it.unimi.dsi.stat package, containing a lightweight class for computing basic statistics and an arbitrary-precision implementation of the Jackknife method; - Lots of utility methods in Util; - Big versions of I/O and utility classes in it.unimi.dsi.big.io and it.unimi.dsi.big.util; - The BulletParser, used to parse HTML and XML. This package is needed as a predependency of igv, which the Debian med team would like to package out of non-free. I am personnally aiming at this. The package will be maintained in the Debian Java team.
Bug#966299: ITP: libapfloat-java -- high performance arbitrary precision arithmetic library for Java
Package: wnpp Severity: wishlist Owner: Debian Java team X-Debbugs-Cc: debian-devel@lists.debian.org, debian-j...@lists.debian.org * Package name: libapfloat-java Version : 1.9.1 Upstream Author : Mikko Tommila * URL : http://www.apfloat.org/apfloat_java * License : LGPL-2.1 Programming Lang: Java Description : high performance arbitrary precision arithmetic library for Java Apfloat is a high performance arbitrary precision arithmetic library. You can perform calculations with a precision of millions of digits with it. It's as simple to use as Java's BigDecimal or BigInteger classes, but performs a lot better with extreme precision numbers (more than a few hundred digits). Also, a full suite of mathematical functions for arbitrary precision numbers are available: all those existing in java.lang.Math and more. This package is needed as a dependency of snpeff, which the Debian Med team would like to package. I am personnally aiming at this. It will be maintained in the Debian Java team.
Bug#966192: ITP: libcharts4j-java -- free, lightweight charts and graphs Java API
Package: wnpp Severity: wishlist Owner: Debian Java team X-Debbugs-Cc: debian-devel@lists.debian.org, debian-j...@lists.debian.org * Package name: libcharts4j-java Version : 1.3 Upstream Author : Julien Chastang * URL : https://github.com/julienchastang/charts4j * License : MIT Programming Lang: Java Description : free, lightweight charts and graphs Java API charts4j enables developers to programmatically create the charts available in the Google Chart API through a straightforward and intuitive Java API. This package is needed as a dependency of snpeff, which the Debian med team would like to package. I am personnally aiming at this. The package will be maintained in the Debian Java team.
Bug#963630: ITP: libaparapi-java -- framework for executing native Java code on the GPU
Package: wnpp Severity: wishlist Owner: Debian-med project * Package name: libaparapi-java Version : 2.0.0 Upstream Author : Gary Frost, Syncleus, Inc. * URL : http://aparapi.com/ * License : Apache-2.0 Programming Lang: Java Description : framework for executing native Java code on the GPU This framework converts Java bytecode to an OpenCL kernel dynamically at runtime, to allow Java code to be executed on a graphics card GPU. This allows developers to take profit from GPU architecture while writing Java programs. This package will be taken care of in Debian-med team, where it is needed as a dependency of apfloat, which is itself a dependency of SnpEff.
Re: Bug#961158: ITP: distlib -- Java library of statistical distribution functions
Control: retitle -1 ITP: libdistlib-java -- Java library of statistical distribution functions Hi Scott and Andreas, Le 21/05/2020 à 06:44, Scott Kitterman a écrit : > On Thursday, May 21, 2020 12:08:44 AM EDT Andreas Tille wrote: >> At least the name of the binary package should be >> >> libdistlib-java >> >> Choosing the same name for the source package as the binary package is >> frequently done. > > That would certainly resolve my concern. > > Thanks, > > Scott K > Thanks for your reactions and suggestions, this looks fine. I am therefore renaming the ITP bug and changing the identification block for this new package to the following. * Package name: libdistlib-java Version : 0.9.1 Upstream Author : Peter N. Steinmetz * URL : https://sourceforge.net/projects/statdistlib * License : GPL-2 Programming Lang: Java Description : Java library of statistical distribution functions Best regards, Pierre
Bug#961158: ITP: distlib -- Java library of statistical distribution functions
Package: wnpp Severity: wishlist Owner: Debian-med project * Package name: distlib Version : 0.9.1 Upstream Author : Peter N. Steinmetz * URL : https://sourceforge.net/projects/statdistlib * License : GPL-2 Programming Lang: Java Description : Java library of statistical distribution functions This is a library written in Java, providing probability density function, cumulative distribution function, quantiles and random variate generation for several common statistical distributions. This package will be taken care of in Debian-med team, where it is needed as a dependency of SnpEff.
