Bug#1065481: ITP: pynx -- Python tools for Nano-structures Crystallography

[Picca Frédéric-Emmanuel]

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

[Picca Frédéric-Emmanuel]

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

[Picca Frédéric-Emmanuel]

Package: wnpp
Severity: wishlist
Owner: Picca Frédéric-Emmanuel pi...@debian.org

* Package name: python-qwt
  Version : 6.1.2a3
  Upstream Author : Pierre Raybaut pierre.rayb...@gmail.com
* 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

[Picca Frédéric-Emmanuel]

Package: wnpp
Severity: normal


I am orphaning this package so It can be team maintain by the pkg-java team.

cheers

Frederic


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Bug#759820: ITP: vispy -- OpenGL interactive scientific visualization

[Picca Frédéric-Emmanuel]

Package: wnpp
Severity: wishlist
Owner: Picca Frédéric-Emmanuel pi...@debian.org

* 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


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Bug#741078: ITP: lmfit-py -- Least-Squares Minimization with Constraints

[Picca Frédéric-Emmanuel]

Package: wnpp
Severity: wishlist
Owner: Picca Frédéric-Emmanuel pi...@debian.org

* 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


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Bug#721653: ITP: ssm -- macromolecular superposition library

[Picca Frédéric-Emmanuel]

Package: wnpp
Severity: wishlist
Owner: Picca Frédéric-Emmanuel pi...@debian.org

* Package name: ssm
  Version : 1.3
  Upstream Author : E. Krissinel k...@ebi.ac.uk
* 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.


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Bug#721529: ITP : libccp4 -- CCP4 core functionality

[PICCA Frédéric-Emmanuel]

Package: wnpp
Owner: Picca Frédéric-Emmanuel pi...@debian.org
Severity: wishlist

* Package name : libccp4
  Version : 6.3.1
  Upstream Author : CCP4 c...@ccp4.ac.uk
* 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.


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Bug#679905: RE : Bug#679905: cctbx: changing back from ITP to RFP

[PICCA Frédéric-Emmanuel]

 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

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Bug#717871: ITP: sardana -- sardana control system

[Picca Frédéric-Emmanuel]

Package: wnpp
Severity: wishlist
Owner: Picca Frédéric-Emmanuel pi...@debian.org

* Package name: sardana
  Version : 1.2.0
  Upstream Author : Carlos Pascual-Izarra cpasc...@cells.es
* 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.


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Bug#711554: RE : Bug#711554: ITP: pyhst -- High Speed Tomographic reconstruction controled from Python

[PICCA Frédéric-Emmanuel]

Hello Jerome,

if you want I can sponsorise this package :)

cheers

Fred

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Bug#711554: RE : RE : Bug#711554: ITP: pyhst -- High Speed Tomographic reconstruction controled from Python

[PICCA Frédéric-Emmanuel]

 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

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Bug#517342: collab-maint repository

[Picca Frédéric-Emmanuel]

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


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Bug#660272: RE : Bug#660272: ITP: sift -- predict if an amino acid substitution in a protein has phenotypic effect

[PICCA Frédéric-Emmanuel]

 beware that python-guiqwt containt already a sift binary.
/usr/bin/sift

see you

Frederic


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Bug#642586: ITP: mmtk -- The molecular modeling toolkit

[Picca Frédéric-Emmanuel]

Package: wnpp
Severity: wishlist
Owner: Picca Frédéric-Emmanuel pi...@synchrotron-soleil.fr

Dear Maintainer,

* Package name: mmtk
  Version : 2.7.5
  Upstream Author : Konrad Hinsen konrad.hin...@synchrotron-soleil.fr
* 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/



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Bug#614247: ITP: taurus -- framework for TANGO control system client applications

[Picca Frédéric-Emmanuel]

Package: wnpp
Severity: wishlist
Owner: Picca Frédéric-Emmanuel pi...@synchrotron-soleil.fr


* Package name: taurus
  Version : 2.0.0
  Upstream Author : Tiago Coutinho tcouti...@cells.es
* 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.




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Bug#614245: ITP: pytango -- API for the TANGO control system

[Picca Frédéric-Emmanuel]

Package: wnpp
Severity: wishlist
Owner: Picca Frédéric-Emmanuel pi...@synchrotron-soleil.fr


* Package name: pytango
  Version : 7.1.3
  Upstream Author : Tiago Coutinho tcouti...@cells.es
* 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.




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Bug#569153:

[PICCA Frédéric-Emmanuel]

* Package name: hkl
  Version : 4.0.2
  Upstream Author : Picca Frédéric-Emmanuel  pi...@synchrotorn-soleil.fr
* 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.



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Bug#539375: ITP: remotetea -- ONC/RPC for Java package

[Picca Frédéric-Emmanuel]

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 haraldalbre...@users.sourceforge.net
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





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Bug#349540: still working on jacorb ?

[PICCA Frédéric-Emmanuel]

hello

everythings in the title.

did you solved this licence problem ?

thanks

Frederic

Bug#349540: RE : Bug#349540: still working on jacorb ?

[PICCA Frédéric-Emmanuel]

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