[Blends-commit] [Git][blends-team/pan][master] tasks: update with recent packages
Emmanuel FARHI (@farhi-guest)
gitlab at salsa.debian.org
Tue Jan 30 17:57:49 GMT 2024
Emmanuel FARHI pushed to branch master at Debian Blends Team / pan
Commits:
8e5c41fa by Emmanuel FARHI at 2024-01-30T18:53:34+01:00
tasks: update with recent packages
- - - - -
18 changed files:
- tasks/coherent-diffraction
- tasks/control-systems
- tasks/control-systems-dev
- tasks/data-reduction-frameworks
- tasks/data-reduction-frameworks-dev
- tasks/diffraction
- tasks/grazing-incidence
- tasks/imaging
- tasks/laue
- tasks/machine-learning
- tasks/modelling
- tasks/mx
- tasks/mx-dev
- tasks/powder
- tasks/small-angle-scattering
- tasks/spectroscopy
- tasks/tomography
- tasks/xas
Changes:
=====================================
tasks/coherent-diffraction
=====================================
@@ -1,14 +1,15 @@
Format: https://blends.debian.org/blends/1.1
Task: coherent-diffraction
-Description: coherent diffraction software
+Description: photons-and-neutrons coherent diffraction
This metapackage will install X-ray photons-and-neutrons PAN Blend coherent
diffraction packages.
-Comment: Improve the Description
Recommends: facet-analyser
Recommends: python3-moviepy
+Recommends: pynx, python3-pynx
+
Suggests: bonsu
Homepage: https://cxs.soton.ac.uk/Bonsu
License: GPL3+
@@ -33,11 +34,6 @@ Homepage: https://github.com/FXIhub/hawk
License: GPL-2
Pkg-Description: diffraction pattern reconstruction
-Suggests: pynx
-Homepage: https://gitlab.esrf.fr/favre/PyNX
-License: CeCILL-B
-Pkg-Description: Python tools for Nano-structures Crystallography
-
Suggests: ptypy
Homepage: https://github.com/ptycho/ptypy
License: GPL-2+
=====================================
tasks/control-systems
=====================================
@@ -1,12 +1,15 @@
Format: https://blends.debian.org/blends/1.1
Task: control-systems
-Description: Debian PAN Control Systems
- This metapackage will install Debian PAN packages related to control
+Description: photons-and-neutrons control cystems
+ This metapackage will install X-ray photons-and-neutrons PAN packages related to control
systems acquisition used in the PAN facilities.
-Comment: Improve the description
+
+Recommends: epics-base
Recommends: ghkl
+Recommends: libepics-perl
+
Recommends: python3-tango
Recommends: python3-taurus
@@ -15,6 +18,8 @@ Recommends: python3-taurus-pyqtgraph
Recommends: python3-sardana
+Recommends: python3-pyepics
+
Recommends: tango-db, tango-starter, tango-accesscontrol
Suggests: micromanager
=====================================
tasks/control-systems-dev
=====================================
@@ -1,12 +1,16 @@
Format: https://blends.debian.org/blends/1.1
Task: control-systems-dev
-Description: Debian PAN Control System development packages
- This metapackage will install Debian PAN packages which might be
+Description: photons-and-neutrons control system development packages
+ This metapackage will install X-ray photons-and-neutrons PAN packages which might be
helpful for development of applications related to control system
acquisition.
.
You might also be interested in the control-system metapackage.
+Recommends: epics-dev
+
+Recommends: libepics-perl
+
Recommends: libhkl-dev
Recommends: libtango-dev
@@ -19,6 +23,8 @@ Recommends: python3-taurus
Recommends: python3-taurus-pyqtgraph
+Recommends: python3-pyepics
+
Suggests: libuca
Homepage: http://ufo.kit.edu/software.html#libuca
License: LGPL-2.1
=====================================
tasks/data-reduction-frameworks
=====================================
@@ -1,9 +1,8 @@
Format: https://blends.debian.org/blends/1.1
Task: data-reduction-frameworks
-Description: Data reduction frameworks
+Description: photons-and-neutrons data reduction frameworks
This metapackage will install X-ray photons-and-neutrons PAN frameworks
dedicated to the data reduction
-Comment: improve the description
Recommends: admesh
@@ -181,7 +180,7 @@ Recommends: zstd
-# Jupiter
+# Jupyter
Recommends: jupyterhub
@@ -223,11 +222,11 @@ Recommends: xpython
# R/Julia/Octave
-Recommends: octave
-Recommends: octave-*
-Recommends: r-*
-Recommends: julia-*
-Recommends: libjulia-openblas64
+#Recommends: octave
+#Recommends: octave-*
+#Recommends: r-*
+#Recommends: julia-*
+#Recommends: libjulia-openblas64
=====================================
tasks/data-reduction-frameworks-dev
=====================================
@@ -1,9 +1,8 @@
Format: https://blends.debian.org/blends/1.1
Task: data-reduction-frameworks-dev
-Description: PAN Debian data reduction frameworks dev
+Description: photons-and-neutrons data reduction framework development packages
This metapackage will install X-ray photons-and-neutrons PAN frameworks
dedicated to data reduction development.
-comment: Improve the description
Depends: pan-data-reduction-frameworks
=====================================
tasks/diffraction
=====================================
@@ -1,9 +1,8 @@
Format: https://blends.debian.org/blends/1.1
Task: diffraction
-Description: diffraction software suit
+Description: photons-and-neutrons diffraction
This metapackage will install all X-ray photons-and-neutrons PAN diffraction
software
-Comment: Improve the description
Recommends: binoculars, binoculars-doc, python3-binoculars
=====================================
tasks/grazing-incidence
=====================================
@@ -1,9 +1,8 @@
Format: https://blends.debian.org/blends/1.1
Task: grazing-incidence
-Description: Grazing incidence X-ray photon and neutron diffraction
- This metapackage will install all GID, GIXD, GIND, GISAS, GISAXS, GISANS
- software
-Comment: Improve the description
+Description: photons-and-neutrons grazing incidence diffraction
+ This metapackage will install all X-ray photons-and-neutrons PAN packages for
+ GID, GIXD, GIND, GISAS, GISAXS, GISANS software
Recommends: binoculars
=====================================
tasks/imaging
=====================================
@@ -1,9 +1,8 @@
Format: https://blends.debian.org/blends/1.1
Task: imaging
-Description: imaging software
+Description: photons-and-neutrons imaging
This metapackage will install all X-ray photons-and-neutrons PAN imaging
software
-Comment: Improve the description
Recommends: 3depict
@@ -99,6 +98,8 @@ Recommends: python3-skimage
Recommends: python3-specutils
+Recommends: python3-vispy
+
Recommends: python3-wcsaxes
Recommends: python3-willow
=====================================
tasks/laue
=====================================
@@ -1,8 +1,7 @@
Format: https://blends.debian.org/blends/1.1
Task: laue
-Description: laue software suit
- This metapackage will install all X-ray photons-and-neutrons PAN laue software
-Comment: Improve the description
+Description: photons-and-neutrons Laue diffraction
+ This metapackage will install all X-ray photons-and-neutrons PAN Laue software
Suggests: esmeralda
Homepage: http://lauesuite.com/
=====================================
tasks/machine-learning
=====================================
@@ -1,9 +1,8 @@
Format: https://blends.debian.org/blends/1.1
Task: machine-learning
-Description: machine learning software
+Description: photons-and-neutrons machine learning
This metapackage will install all the machine learning software for
- photons-and-neutrons PAN
-Comment: Improve the description
+ X-ray photons-and-neutrons PAN
Recommends: keras-doc, python3-keras, python3-keras-applications, python3-keras-preprocessing
@@ -35,6 +34,8 @@ Recommends: python3-skorch
Recommends: python3-torch
+Recommends: python3-torch-cuda
+
Recommends: python3-torch-ignite
Recommends: python3-tpot, python-tpot-doc
=====================================
tasks/modelling
=====================================
@@ -1,9 +1,8 @@
Format: https://blends.debian.org/blends/1.1
Task: modelling
-Description: modeling software
+Description: photons-and-neutrons modelling
This metapackage will install all modelling software for X-ray
photons-and-neutrons PAN
-Comment: Improve the description
Recommends: debichem-analytical-biochemistry
@@ -25,6 +24,8 @@ Recommends: debichem-semiempirical
Recommends: debichem-visualisation
+Recommends: quantum-espresso-data-sssp
+
Recommends: python3-phonopy
Recommends: python3-pymatgen
=====================================
tasks/mx
=====================================
@@ -1,18 +1,49 @@
Format: https://blends.debian.org/blends/1.1
Task: mx
-Description: Macro Molecular diffraction
+Description: photons-and-neutrons macro molecular diffraction
This metapackage will install all MX diffraction software for X-ray
photons-and-neutrons PAN.
-Comment: Improve the description
+
+Recommends: apbs
+
+Recommends: autodock
+
+Recommends: clustalw
+
+Recommends: dials
+
+Recommends: gnuplot
+
+Recommends: imagej
+
+Recommends: jmol
+
+Recommends: libmmdb2-0
+
+Recommends: openbabel
+
+Recommends: povray
+
+Recommends: pymol
Recommends: python3-mrcfile
Recommends: python3-cctbx
+Recommends: python3-dials
+
Recommends: python3-dials-data
Recommends: python3-extra-data
+Recommends: python3-nxmx
+
+Recommends: rasmol
+
+Recommends: raster3d
+
+Recommends: theseus
+
Suggests: coot
WNPP: 531904
Homepage: http://biop.ox.ac.uk/coot/
@@ -128,8 +159,6 @@ Homepage: http://www.dectris.ch/software_albula.html
License: ?
Pkg-Description: Dectris diffraction image viewer and analysis tool
-Recommends: apbs
-
Suggests: aplx
Homepage: http://www.microapl.co.uk/apl
License: non-free
@@ -142,8 +171,6 @@ License: ?
Remark: which part of the suite is used ?
Pkg-Description: ?
-Recommends: autodock
-
Suggests: autoproc
Homepage: http://www.globalphasing.com/autoproc
License: ?
@@ -151,8 +178,6 @@ Pkg-Description: MX data processing
Remark: http://www.globalphasing.com/autoproc/licence/index.html ok for non-free ?
needed: mosflm, scala, xds, pointless, ccp4, gnuplot
-Recommends: openbabel
-
Suggests: balbes
Homepage: http://www.ysbl.york.ac.uk/~fei/balbes
License: ?
@@ -232,18 +257,6 @@ Pkg-Description: CCP4 exists to produce and support a world-leading,
techniques and practice.
Remark: this is a suite of software.
-Suggests: cctbx
-WNPP: 679905
-Homepage: http://cctbx.sourceforge.net
-Vcs-Browser: https://salsa.debian.org/science-team/cctbx
-Vcs-Git: https://salsa.debian.org/science-team/cctbx.git
-Pkg-Description: CCTBX is a toolbox for developing crystallographic
- software. It provides fundamental and advanced methods and algorithms
- usefull in the scientific fields of crystallography[1], chemistry,
- physics and biology. It also provides Libraries for general
- scientific computing. The package is organized as a set of ISO C++
- classes with Python bindings.
-
Suggests: chart
Homepage: ?
License: ?
@@ -277,8 +290,6 @@ Pkg-Description: CHOOCH is a program that will automatically determine
MAD or SAD experiments.
Remark: part of ccp4
-Recommends: clustalw
-
Suggests: cn2coot
Homepage: ?
License: ?
@@ -633,8 +644,6 @@ License: ?
Pkg-Description: ?
Comment: ?
-Recommends: gnuplot
-
Suggests: gramm
Homepage: http://vakser.bioinformatics.ku.edu/main/resources_gramm.php
License: ?
@@ -677,8 +686,6 @@ License: ?
Pkg-Description: ?
Comment: ?
-Recommends: imagej
-
Suggests: imosflm
Homepage: ?
License: ?
@@ -703,8 +710,6 @@ License: ?
Pkg-Description: ?
Comment: ?
-Recommends: jmol
-
Suggests: labelit
Homepage: ?
License: ?
@@ -789,8 +794,6 @@ License: ?
Pkg-Description: ?
Comment: ?
-Recommends: libmmdb2-0
-
Suggests: mosflm
Homepage: ?
License: ?
@@ -857,8 +860,6 @@ License: ?
Pkg-Description: ?
Comment: ?
-Recommends: povray
-
Suggests: promotif
Homepage: ?
License: ?
@@ -871,20 +872,12 @@ License: ?
Pkg-Description: ?
Comment: ?
-Recommends: pymol
-
-Recommends: python
-
Suggests: raddose
Homepage: ?
License: ?
Pkg-Description: ?
Comment: ?
-Recommends: rasmol
-
-Recommends: raster3d
-
Suggests: refmac
Homepage: ?
License: ?
@@ -1059,8 +1052,6 @@ License: ?
Pkg-Description: ?
Comment: ?
-Recommends: theseus
-
Suggests: tools
Homepage: ?
License: ?
@@ -1144,35 +1135,6 @@ License: ?
Pkg-Description: ?
Comment: ?
-Suggests: dials
-Homepage: http://cci.lbl.gov/dials2/
-License: BSD-3-clauses
-Vcs-Browser: https://salsa.debian.org/science-team/dials
-Vcs-Git: https://salsa.debian.org/science-team/dials.git
-Pkg-Description: Diffraction Integration for Advance Light Source
- The field of structural biology by X-ray crystallography has
- benefitted greatly from technological advances in recent
- years. Automation, highly brilliant beamlines at 3rd generation
- synchrotron sources and high frame-rate pixel array detectors have
- together enabled extremely rapid collection of most MX datasets. In
- tandem, large area photon-counting detection, microfocus beams and
- high quality X-ray optics have brought more challenging projects
- within reach. At the cutting edge of this technological advance, the
- demonstration of FEL nano-crystallography offers the tantalizing
- prospect of a new era of structural biology at large facilities, with
- a concomitant step change in data rates and requirements for
- computationally intensive processing.
- .
- There is a clear need for new software for diffraction data analysis,
- designed to cope with the ever increasing volumes and rates of data
- collection, and with the developments in experimental methodology,
- from shutterless, fine-sliced rotation scans through to the
- randomly-oriented snapshots of serial crystallography. To keep up
- with these technological advances it is to be expected that this new
- software would utilize techniques of parallel processing using
- multiple CPU and GPU machines, facilitating not just speed, but
- highly accurate analysis based on a comprehensive physical model.
-
Suggests: gemmi
Homepage: https://github.com/project-gemmi/gemmi
License: MPL2 or LGPL3
=====================================
tasks/mx-dev
=====================================
@@ -1,7 +1,7 @@
Format: https://blends.debian.org/blends/1.1
Task: mx-dev
-Description: Debian PAN Macro-Molecular diffraction development packages
- This metapackage will install Debian PAN packages which might be
+Description: photons-and-neutrons macro-molecular diffraction development packages
+ This metapackage will install X-ray photons-and-neutrons PAN packages which might be
helpful for development of applications related to Macro-Molecular
diffraction.
.
=====================================
tasks/powder
=====================================
@@ -1,9 +1,8 @@
Format: https://blends.debian.org/blends/1.1
Task: powder
-Description: powder diffraction
+Description: photons-and-neutrons powder diffraction
This metapackage will install all X-ray photons-and-neutrons PAN powder
diffraction software.
-Comment: Improve the description
Recommends: cif2hkl
=====================================
tasks/small-angle-scattering
=====================================
@@ -1,9 +1,8 @@
Format: https://blends.debian.org/blends/1.1
Task: small-angle-scattering
-Description: small angle scattering
+Description: photons-and-neutrons small angle scattering
This metapackage will install all X-ray photons-and-neutrons PAN Blend
small angle scattering packages.
-Comment: improve the description
Recommends: dioptas
=====================================
tasks/spectroscopy
=====================================
@@ -1,6 +1,6 @@
Format: https://blends.debian.org/blends/1.1
Task: spectroscopy
-Description: X-Rays and Neutron spectroscopy
+Description: photons-and-neutrons spectroscopy
This metapackage will install all X-ray photons-and-neutrons PAN spectroscopy
packages (XPS, ARPES, IXS, ...).
@@ -20,6 +20,8 @@ Recommends: python3-igor
Recommends: python3-navarp
+Recommends: python3-opusfc
+
Recommends: python3-orange-spectroscopy
Recommends: python3-phonopy
=====================================
tasks/tomography
=====================================
@@ -1,9 +1,8 @@
Format: https://blends.debian.org/blends/1.1
Task: tomography
-Description: Photons and Neutrons (PAN) Blend tomography
+Description: photons-and-neutrons tomography
This metapackage will install all X-ray photons-and-neutrons PAN Blend
tomography packages.
-Comment: improve the Description
Recommends: ctsim, ctsim-doc, ctsim-help
@@ -39,6 +38,8 @@ Recommends: python3-tomogui
Recommends: python3-tomopy
+Recommends: python3-tomoscan
+
Recommends: python3-ufo-tofu
Recommends: rheolef
@@ -67,28 +68,11 @@ License: GPL2+
Pkg-Description: gather all information from the user that can be
provided prior to the tomography experiment.
-Recommends: tomopy
-Homepage: https://github.com/tomopy/tomopy
-License: BSD-3
-Pkg-Description: tomographic data processing and image reconstruction toolbox
- TomoPy is a Python toolbox to perform tomographic data processing and
- image reconstruction tasks at the Advanced Photon Sourc
-
Suggests: tomodata
Homepage: http://confluence.synchrotron-soleil.fr/display/ANATOMIX/tomodata.py+documentation
License: ?
Pkg-Description: conversion of files from nexus to edf, parameterization, reconstruction
-Recommends: dioptas
-Homepage: https://github.com/Dioptas/Dioptas
-License: GPL-3.0 License
-Pkg-Description: Dioptas is a Python-based program for on-the-fly data processing and exploration of two-dimensional X-ray diffraction area
- detector data. It is specifically designed for the large amount of data collected at XRD beamlines at synchrotrons.
-
-Suggests: tomogui
-Homepage: https://pypi.org/project/tomogui/
-License: MIT
-Pkg-Description: Tomogui offers a Graphical User Interface to run tomographic reconstruction based on freeart and silx.
Suggests: tomoj
Homepage: https://sourceforge.net/projects/tomoj/
=====================================
tasks/xas
=====================================
@@ -1,9 +1,8 @@
Format: https://blends.debian.org/blends/1.1
Task: xas
-Description: EXAFS and XANES
+Description: photons-and-neutrons EXAFS and XANES
This metapackage will install all X-ray photons-and-neutrons PAN EXAFS and
XANES absorption spectroscopy packages.
-Comment: Improve the description
Recommends: feff85
@@ -17,51 +16,12 @@ Depends: quantum-espresso
Recommends: python3-xraylarch
-Suggests: xraylarch
-Homepage: http://xraypy.github.io/xraylarch/
-Vcs-Browser: https://salsa.debian.org/science-team/xraylarch
-Vcs-Git: https://salsa.debian.org/science-team/xraylarch.git
-License: BSD-3
-Pkg-Description: X-ray Analysis for Synchrotron Applications using Python
- Larch is an open-source library and analysis toolkit for processing
- scientific data. Initially designed for x-ray spectroscopic and
- scattering data collected at modern synchrotrons and x-ray sources,
- Larch also provides many general-purpose processing and analysis
- tools for dealing with arrays of scientific data and organize complex
- data sets.
- .
- Larch is written in Python, making heavy use of the wonderful numpy,
- scipy, h5py, and matplotlib libraries, and can be used directly as a
- Python library or extended using Python. In addition, Larch provides
- a Python-like language (a macro language, or domain specific
- language) that is intended to be very easy to use for novices while
- also being complete enough for advanced data processing and analysis.
- .
- Larch has several related target application areas, including:
- .
- * XAFS analysis, becoming version 2 of the Ifeffit Package.
- * Visualizing and analyzing micro-X-ray fluorescence maps.
- * Quantitative X-ray fluorescence analysis.
- * X-ray standing waves and surface scattering analysis.
- * Data collection software for synchrotron data.
- .
- The essential idea is that having these different areas connected by
- a common macro language will strengthen the analysis tools available
- for all of them, and provide a very shallow barrier for those
- interested in scripting the manipulation and analysis of their data.
- .
- Currently, Larch provides a complete set of XAFS Analysis tools
- (replacing all of the Ifeffit package), has some support for
- visualizing and analyzing XRF maps and spectra, and has many extra
- tools for X-ray spectral analysis, data handling, and general-purpose
- data modeling.
-
Suggests: prestopronto
Homepage: http://code.google.com/p/prestopronto
License: GPL3+
Pkg-Description: Software for analysis of Quick Exafs data
-Suggest: rixs
+Suggests: rixs
Homepage: internal SEXTANTS's beamline repository in Synchrotron SOLEIL
License: ?
Pkg-Description: Sorting and visualization of 1D spectra: XAS, scan positions, etc. (Detailed specifications sent to S. Bac in April 2020)
View it on GitLab: https://salsa.debian.org/blends-team/pan/-/commit/8e5c41fadb3d4205185dcfcf49e156a031f3dbbf
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