Bug#1065481: ITP: pynx -- Python tools for Nano-structures Crystallography
Package: wnpp Severity: wishlist Owner: Picca Frédéric-Emmanuel X-Debbugs-Cc: debian-de...@lists.debian.org, debian-pan-maintain...@alioth-lists.debian.net, pi...@debian.org * Package name: pynx Version : 2023.1.2-1 Upstream Contact: fa...@esrf.fr * URL : https://gitlab.esrf.fr/favre/PyNX * License : CeCILL-B Programming Lang: (OpenCL, Python) Description : Python tools for Nano-structures Crystallography PyNX stands for *Python tools for Nano-structures Crystallography*. It is a python library with the following main modules: . 1) pynx.scattering: *X-ray scattering computing using graphical processing units*, allowing up to 2.5x10^11 reflections/atoms/seconds (single nVidia Titan X). The sub-module``pynx.scattering.gid`` can be used for *Grazing Incidence Diffraction* calculations, using the Distorted Wave Born Approximation . 2) pynx.ptycho : simulation and analysis of experiments using the *ptychography* technique, using either CPU (deprecated) or GPU using OpenCL. Examples are available in the pynx/Examples directory. Scripts for analysis of raw data from beamlines are also available, as well as using or producing ptychography data sets in CXI (Coherent X-ray Imaging) format. . 3) pynx.wavefront: *X-ray wavefront propagation* in the near, far field, or continuous (examples available at the end of ``wavefront.py``). Also provided are sub-modules for Fresnel propagation and simulation of the illumination from a Fresnel Zone Plate, both using OpenCL for high performance computing. . 4) pynx.cdi: *Coherent Diffraction Imaging* reconstruction algorithms using GPU. . In addition, it includes :doc:`scripts ` for command-line processing of ptychography data from generic CXI data (pynx-ptycho-cxi) or specific to beamlines (pynx-ptycho-id01, pynx-ptycho-id13,...). This package will be naintain in the Debian-Science repository by the Debian-PAN team
Bug#871637: ITP: silx -- Toolbox for X-Ray data analysis
Package: wnpp Severity: wishlist Owner: =?utf-8?q?Picca_Fr=C3=A9d=C3=A9ric-Emmanuel?= * Package name: silx Version : 0.5.0 Upstream Author : European Synchrotron Radiation Facility Data analysis unit (s...@esrf.fr) * URL : https://github.com/silx-kit/silx * License : LGPL, MIT Programming Lang: Python Description : Toolbox for X-Ray data analysis The silx project aims at providing a collection of Python packages to support the development of data assessment, reduction and analysis applications at synchrotron radiation facilities. It aims at providing reading/writing different file formats, data reduction routines and a set of Qt widgets to browse and visualize data. . The current version provides : . * reading HDF5 file format (with support of SPEC file format) * histogramming * fitting * 1D and 2D visualization using multiple backends (matplotlib or OpenGL) * image plot widget with a set of associated tools (See changelog file). * Unified browser for HDF5, SPEC and image file formats supporting inspection and visualization of n-dimensional datasets. * Unified viewer (silx view filename) for HDF5, SPEC and image file formats * OpenGL-based widget to display 3D scalar field with isosurface and cutting plane. I need to package this because it is a new dependency for PyFAI and the next Pymca
Bug#796955: ITP: python-qwt -- Pure Python implementation of Qwt
Package: wnpp Severity: wishlist Owner: "Picca Frédéric-Emmanuel" * Package name: python-qwt Version : 6.1.2a3 Upstream Author : Pierre Raybaut * URL : https://github.com/PierreRaybaut/qwt * License : Expat Programming Lang: Python Description : Pure Python implementation of Qwt The qwt package is a pure Python implementation of Qwt C++ library with the following limitations. . The following `Qwt` classes won't be reimplemented in `qwt` because most powerful features already exist in `guiqwt`: * QwtPlotZoomer * QwtCounter * QwtEventPattern * QwtPicker * QwtPlotPicker . QwtClipper is not implemented yet (and it will probably be very difficult or impossible to implement it in pure Python without performance issues). As a consequence, when zooming in a plot curve, the entire curve is still painted (in other words, when working with large amount of data, there is no performance gain when zooming in). This package will be maintain under the debian-science umbrella. It is a requiered dependency for the new guiqwt package.
Bug#770595: O: remotetea
Package: wnpp Severity: normal I am orphaning this package so It can be team maintain by the pkg-java team. cheers Frederic -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20141122133530.25431.55747.reportbug@mordor
Bug#759820: ITP: vispy -- OpenGL interactive scientific visualization
Package: wnpp Severity: wishlist Owner: "Picca Frédéric-Emmanuel" * Package name: vispy Version : 0.3.0 Upstream Author : Vispy Development Team * URL : http://vispy.org * License : BSD, MIT/X Programming Lang: Python Description : OpenGL interactive scientific visualization Vispy is an OpenGL-based interactive visualization library in Python. Its goal is to make it easy to create beautiful and fast dynamic visualizations. For example, scientific plotting of tens of millions of points, interacting with complex polygonial models, and (dynamic) volume rendering. All thanks to the graphics card’s hardware acceleration. . Vispy will eventually offer graphical APIs at multiple levels, including a matplotlib-like scientific plotting library. Currently, only the lowest-level API is implemented: it brings an easy-to-use Pythonic object-oriented interface to OpenGL. This layer requires you to have basic knowledge of modern OpenGL (notably the OpenGL shading language, GLSL). . We are currently working on higher level layers. They will hide most OpenGL concepts and let you create beautiful visualizations in a few lines of code. Stay tuned! This package will be maintained under the debian-science team umbrella Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-science/packages/vispy.git Vcs-Git: git://anonscm.debian.org/debian-science/packages/vispy.git -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20140830173406.27479.57233.reportbug@mordor
Bug#741078: ITP: lmfit-py -- Least-Squares Minimization with Constraints
Package: wnpp Severity: wishlist Owner: "Picca Frédéric-Emmanuel" * Package name: lmfit-py Version : 0.7.4 Upstream Author : matt.newvi...@gmail.com * URL : http://lmfit.github.io/lmfit-py/ * License : EXPAT Programming Lang: Python Description : Least-Squares Minimization with Constraints The lmfit Python package provides a simple, flexible interface to non-linear optimization or curve fitting problems. The package extends the optimization capabilities of scipy.optimize by replacing floating pointing values for the variables to be optimized with Parameter objects. These Parameters can be fixed or varied, have upper and/or lower bounds placed on its value, or written as an algebraic expression of other Parameters. . The principal advantage of using Parameters instead of simple variables is that the objective function does not have to be rewritten to reflect every change of what is varied in the fit, or what relationships or constraints are placed on the Parameters. This means a scientific programmer can write a general model that encapsulates the phenomenon to be optimized, and then allow user of that model to change what is varied and fixed, what range of values is acceptable for Parameters, and what constraints are placed on the model. The ease with which the model can be changed also allows one to easily test the significance of certain Parameters in a fitting model. . The lmfit package allows a choice of several optimization methods available from scipy.optimize. The default, and by far best tested optimization method used is the Levenberg-Marquardt algorithm from from MINPACK-1 as implemented in scipy.optimize.leastsq. This method is by far the most tested and best support method in lmfit, and much of this document assumes this algorithm is used unless explicitly stated. An important point for many scientific analysis is that this is only method that automatically estimates uncertainties and correlations between fitted variables from the covariance matrix calculated during the fit. . A few other optimization routines are also supported, including Nelder-Mead simplex downhill, Powell's method, COBYLA, Sequential Least Squares methods as implemented in scipy.optimize.fmin, and several others from scipy.optimize. In their native form, some of these methods setting allow upper or lower bounds on parameter variables, or adding constraints on fitted variables. By using Parameter objects, lmfit allows bounds and constraints for all of these methods, and makes it easy to swap between methods without hanging the objective function or set of Parameters. . Finally, because the approach derived from MINPACK-1 usin the covariance matrix to determine uncertainties is sometimes questioned (and sometimes rightly so), lmfit supports methods to do a brute force search of the confidence intervals and correlations for sets of parameters. This package will be maintained under the debian-science umbrella Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-science/packages/lmfit- py.git Vcs-Git: git://anonscm.debian.org/debian-science/packages/lmfit-py.git -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20140308082407.6853.62179.reportbug@mordor
Bug#721653: ITP: ssm -- macromolecular superposition library
Package: wnpp Severity: wishlist Owner: "Picca Frédéric-Emmanuel" * Package name: ssm Version : 1.3 Upstream Author : E. Krissinel * URL : http://www.ccp4.ac.uk/ * License : (LGPL-2.1) Programming Lang: (C++) Description : macromolecular superposition library SSM is a macromolecular coordinate superposition library, written by Eugene Krissinel of the EBI. . The library implements the SSM algorithm of protein structure comparison in three dimensions, which includes an original procedure of matching graphs built on the protein's secondary-structure elements, followed by an iterative three-dimensional alignment of protein backbone Calpha atoms. . The algorithm implemented by the software is described in: E. Krissinel & K. Henrick (2004) Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr D Biol Crystallogr. 60, 2256-68. -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20130902185447.6966.82641.reportbug@mordor
Bug#721529: ITP : libccp4 -- CCP4 core functionality
Package: wnpp Owner: "Picca Frédéric-Emmanuel" Severity: wishlist * Package name : libccp4 Version : 6.3.1 Upstream Author : CCP4 * URL : http://www.ccp4.ac.uk/ * License : (GPL, LGPL) Programming Lang: (C, C++, Fortran) Description : CCP4 core functionality The CCP4 software suite is based around a library of routines which cover common tasks, such as file opening, parsing keyworded input, reading and writing of standard data formats, applying symmetry operations, etc. Programs in the suite call these routines which, as well as saving the programmer some effort, ensure that the varied programs in the suite have a similar look-and-feel. . The library contains several sub components: . * CMTZ library -- Contains a variety of functions for manipulating the data structure, for example adding crystals, datasets or columns. The data structure can be dumped to an output MTZ data file. . * CMAP library -- Functions defining the C-level API for accessing CCP4 map files. . * CSYM library -- a collection of functions centered around a data file syminfo.lib which is auto-generated from sgtbx (the Space Group Toolbox of cctbx). . * CCP4 utility library -- many utility functions which either give specific CCP4 or platform independent functionality. . * CCP4 Parser library -- provides CCP4-style parsing, as used for processing keywords of CCP4 programs, MTZ header records, etc. . * CCP4 resizable arrays -- defines an object and methods which looks just like a simple C array, but can be resized at will without incurring excessive overheads. This package contains the shared library components needed for programs that have been compiled with the libccp4 library. -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/a2a20ec3b8560d408356cac2fc148e53b1cab...@sun-dag1.synchrotron-soleil.fr
Bug#679905: RE : Bug#679905: cctbx: changing back from ITP to RFP
> Hi all, Hello Baptiste > it makes me sad to see cctbx going back to RFP, unfortunately this is > closer to the truth as far as I'm concerned. this is the standard procedure, cctbx is not yet ready for inclusion after one year, so ITP -> RFP. now , I did not managed to work on cctbx since I need first to tackle the ccp4 part... Once his will be done, I think that it will be easyer to work on cctbx. > I still have interest in the package, but interest is not enough. Due to > real life problems (moving homes, unforseen difficulties with a paid > assignment), I have not been able to work on it at all since last february. Yes I understand, so I hope that your problems will find solutions. thanks for the great work you already done on cctbx > I can't tell yet when I've got more time available. For this reason, I > won't change the bug back to ITP until I've got some work done. If > anybody else feels like working on it before I do, go for it. And if you > have any questions, feel free to ask me. Indeed the gir repository of the cctbx packaging is still available in Debian science. Cheers Frederic -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/a2a20ec3b8560d408356cac2fc148e53b1ca6...@sun-dag1.synchrotron-soleil.fr
Bug#717871: ITP: sardana -- sardana control system
Package: wnpp Severity: wishlist Owner: "Picca Frédéric-Emmanuel" * Package name: sardana Version : 1.2.0 Upstream Author : Carlos Pascual-Izarra * URL : http://packages.python.org/sardana * License : LGPL3+ Programming Lang: Python Description : sardana control system SARDANA, is a TANGO based control system designed for instrument control and data acquisition, mainly developed by CELLS Alba Synchrotron Controls Section. SARDANA framework is designed to hide the complexity and heterogeneity of the control system (some internal control of a group of devices), while providing a wide, rich, and extensible set of operations that a user may need. -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20130725201350.1706.75958.reportbug@mordor
Bug#711554: RE : RE : Bug#711554: ITP: pyhst -- High Speed Tomographic reconstruction controled from Python
> The code was just (officially) freed ... but I am sure there is still > plenty of work on the packaging side. Great news. so we can work togheter to package it :). I will discuss about this with my boss :) Fred -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/a2a20ec3b8560d408356cac2fc148e5358ec4...@sun-dag1.synchrotron-soleil.fr
Bug#711554: RE : Bug#711554: ITP: pyhst -- High Speed Tomographic reconstruction controled from Python
Hello Jerome, if you want I can sponsorise this package :) cheers Fred -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/a2a20ec3b8560d408356cac2fc148e5358ec4...@sun-dag1.synchrotron-soleil.fr
Bug#517342: collab-maint repository
Hello, I set up a git repository for the packaging of asymptote [1] tell me if it is ok for you. I already imported the brand new 2.21 version into the repository. Cheers Frederic [1] http://anonscm.debian.org/gitweb/?p=collab-maint/asymptote.git;a=summary -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/878v6fgxs5@synchrotron-soleil.fr
Bug#660272: RE : Bug#660272: ITP: sift -- predict if an amino acid substitution in a protein has phenotypic effect
beware that python-guiqwt containt already a sift binary. /usr/bin/sift see you Frederic -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/a2a20ec3b8560d408356cac2fc148e5325126...@sun-dag1.synchrotron-soleil.fr
Bug#642586: ITP: mmtk -- The molecular modeling toolkit
Package: wnpp Severity: wishlist Owner: "Picca Frédéric-Emmanuel" Dear Maintainer, * Package name: mmtk Version : 2.7.5 Upstream Author : Konrad Hinsen * URL : http://dirac.cnrs-orleans.fr/MMTK/ * License : CeCILL-C Programming Lang: C, Python Description : The molecular modeling toolkit The Molecular Modeling Toolkit (MMTK) is a library for molecular simulation applications. It provides the most common methods in molecular simulations (molecular dynamics, energy minimization, normal mode analysis) and several force fields used for biomolecules (Amber 94, Amber 99, several elastic network models). MMTK also serves as a code basis that can be easily extended and modified to deal with non-standard situations in molecular simulations. this will be a dependency for nMOLDYN http://dirac.cnrs-orleans.fr/plone/software/nmoldyn/ -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110924080513.16311.23811.reportbug@mordor
Bug#614245: ITP: pytango -- API for the TANGO control system
Package: wnpp Severity: wishlist Owner: "Picca Frédéric-Emmanuel" * Package name: pytango Version : 7.1.3 Upstream Author : Tiago Coutinho * URL : http://packages.python.org/PyTango * License : LGPL3+ Programming Lang: C++, Python Description : API for the TANGO control system TANGO is an object oriented distributed control system using CORBA, mainly developed by the Controls Section of the ALBA Synchrotron. PyTango provides bindings for its client- and server-side C++ APIs. With PyTango, you can write TANGO device servers and TANGO applications (scripts, CLIs, GUIs) that access TANGO device servers in pure Python. -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110220171023.29991.94839.reportbug@mordor
Bug#614247: ITP: taurus -- framework for TANGO control system client applications
Package: wnpp Severity: wishlist Owner: "Picca Frédéric-Emmanuel" * Package name: taurus Version : 2.0.0 Upstream Author : Tiago Coutinho * URL : http://packages.python.org/taurus * License : LGPL3+ Programming Lang: Python Description : framework for TANGO control system client applications TANGO is an object oriented distributed control system using CORBA, mainly developed by the Controls Section of the ALBA Synchrotron. TAURUS is a library for connecting graphical or commandline clients to TANGO device servers, built on top of the PyTango bindings and the graphical library PyQt. It provides an abstraction layer for accessing TANGO in a pythonic, object oriented way. . The goals of this library are to: * provide a simple TANGO API to the end-user application; * speed up development of TANGO-based applications; * provide a standardized look-and-feel. . In many aspects, TAURUS follows the same approach as the TANGO Java Application Tool Kit: Tango ATK. If you know ATK, TAURUS will look familiar. . The TAURUS library is divided into two parts: the core module which handles all interaction with PyTango, and the Qt module which provides a collection of widgets that can be used inside any PyQt GUI. -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110220171506.30298.49550.reportbug@mordor
Bug#569153:
* Package name: hkl Version : 4.0.2 Upstream Author : Picca Frédéric-Emmanuel * URL : http://repo.or.cz/w/hkl.git * License : (GPL) Programming Lang: (C) Description : diffractometer computation control library The hkl library is a framework for diffraction computation and diffractometer control, heavily used at the SOLEIL synchrotron. It supports various types of diffractometer geometry: Eulerian 4-circle, Eulerian 6-circle, kappa 4-circle, kappa 6-circle, and z-axis geometry. For each of these it provides several numerically computed modes, such as bisector and constant psi. -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/606cc410b038e34cb97646a32d0ec0bf03888...@venusbis.synchrotron-soleil.fr
Bug#539375: ITP: remotetea -- ONC/RPC for Java package
Package: wnpp Severity: wishlist X-Debbugs-CC: debian-de...@lists.debian.org --- Please fill out the fields below. --- Package name: remotetea Version: 1.0.7 Upstream Author: Harald Albrecht URL: http://remotetea.sourceforge.net/ License: LGPL Description: ONC/RPC for Java package This package implements Sun's ONC/RPC Remote Procedure Call specification (see RFC 1831, RFC 1832, RFC 1833). . Functionality currently supported: - RPC calls over TCP/IP as well as UDP/IP. - RPC client functionality. - RPC server functionality org.acplt.oncrpc.server - Querying the ONC/RPC potmapper - jrpcgen-utility for converting x-files into Java classes. - Support for authentication types AUTH_NONE, AUTH_UNIX and AUTH_SHORT on both the client and server side. Hello you can find a first version of almost working package on debian mentors. I did not use pbuild to be sur all the build depenendy are ok. Your upload of the package 'remotetea' to mentors.debian.net was successful. Sponsors can now download it. The URL of your package is: http://mentors.debian.net/debian/pool/main/r/remotetea The respective dsc file can be found at: http://mentors.debian.net/debian/pool/main/r/remotetea/remotetea_1.0.7-1.dsc - While checking your package we found these issues: You uploaded files which already exists in the repository: - remotetea_1.0.7-1.dsc - remotetea_1.0.7-1.diff.gz - remotetea_1.0.7.orig.tar.gz We have overwritten the files in the repository by those from your new upload. Please note that this is allowed when uploading to mentors.debian.net. But in the official Debian repository you cannot change the upstream tarball (.orig.tar.gz). Processing your upload took 3.4 seconds. - If you do not yet have a sponsor for your package you may want to go to http://mentors.debian.net/cgi-bin/maintainer-packages?action=details;package=remotetea and set the "Seeking a sponsor" option to hilight your package on the welcome page. You can also send an RFS (request for sponsorship) to the debian-mentors mailing list. Your package page will give your suggestions on how to send that mail. Good luck finding a sponsor! And thanks for using mentors.debian.net The mentors.debian.net team -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
Bug#349540: RE : Bug#349540: still working on jacorb ?
Hello > I have not, but I'm still interested in seing JacORB in Debian. > Your interest for JacORB is quite motivating, and as we have set up a > Debian CORBA Team, would you be interested in stepping in and joining > the team? In fact in my institut we are using a control system based on CORBA. you can find information on http://www.tango-controls.org The GUI interface is based on java so my JacORB interest. Did you spoke with the jacorb upstream about this licence issue ? Do you think that tango could be included in the Debian CORBA Team. Frederic
Bug#349540: still working on jacorb ?
hello everythings in the title. did you solved this licence problem ? thanks Frederic