[Blends-commit] [Git][blends-team/pan][master] 2 commits: updates the pan tasks
Frédéric-Emmanuel Picca
gitlab at salsa.debian.org
Thu Apr 23 16:08:22 BST 2020
Frédéric-Emmanuel Picca pushed to branch master at Debian Blends Team / pan
Commits:
19f37c86 by Picca Frédéric-Emmanuel at 2020-04-23T16:42:27+02:00
updates the pan tasks
- - - - -
de252b3a by Picca Frédéric-Emmanuel at 2020-04-23T17:07:56+02:00
updated all the tasks
- - - - -
13 changed files:
- debian/control
- tasks/control-systems
- tasks/control-systems-dev
- tasks/data-reduction-frameworks
- tasks/data-reduction-frameworks-dev
- tasks/diffraction
- tasks/gid
- tasks/microscopy
- tasks/mx
- tasks/powder
- tasks/small-angle-scattering
- tasks/tomography
- tasks/xas
Changes:
=====================================
debian/control
=====================================
@@ -1,4 +1,4 @@
-# This file is autogenerated via make -f debian/rules dist. Do not edit!
+# This file is autogenerated. Do not edit!
Source: debian-pan
Section: science
Priority: extra
@@ -29,37 +29,41 @@ Description: PAN Blend config package
.
* pan-something do something # FIXME
-Package: pan-coherent-diffraction
-Architecture: all
-Depends: pan-tasks (= ${binary:Version}), pan-config (= ${binary:Version})
-Suggests: hawk,
- pynx
-Description: coherent diffraction software
- This metapackage will install PAN Blend coherent diffraction packages.
-
Package: pan-control-systems
+Section: metapackages
Architecture: all
-Depends: pan-tasks (= ${binary:Version}), pan-config (= ${binary:Version})
+Depends: ${misc:Depends},
+ pan-config (= ${source:Version}),
+ pan-tasks (= ${source:Version})
Recommends: ghkl,
- python-pytango,
- python-taurus,
- tango-accesscontrol,
- tango-db,
- tango-starter
+ python3-sardana,
+ python3-tango,
+ python3-taurus,
+ python3-taurus-pyqtgraph,
+ tango-accesscontrol,
+ tango-db,
+ tango-starter
Suggests: micromanager,
- opengda,
- tomographie-preexperiment-data-collector
-Description:
+ opengda,
+ tomographie-preexperiment-data-collector
+Description: Debian PAN Control Systems
+ This metapackage will install Debian PAN packages related to control
+ systems acquisition used in the PAN facilities.
Package: pan-control-systems-dev
+Section: metapackages
Architecture: all
-Depends: pan-tasks (= ${binary:Version}), pan-config (= ${binary:Version})
+Depends: ${misc:Depends},
+ pan-config (= ${source:Version}),
+ pan-tasks (= ${source:Version})
Recommends: libhkl-dev,
- libtango8-dev,
- python-pytango,
- python-taurus
+ libtango-dev,
+ python3-sardana,
+ python3-tango,
+ python3-taurus,
+ python3-taurus-pyqtgraph
Suggests: libuca,
- lima
+ lima
Description: Debian PAN Control System development packages
This metapackage will install Debian PAN packages which might be
helpful for development of applications related to control system
@@ -68,271 +72,298 @@ Description: Debian PAN Control System development packages
You might also be interested in the control-system metapackage.
Package: pan-data-reduction-frameworks
+Section: metapackages
Architecture: all
-Depends: pan-tasks (= ${binary:Version}), pan-config (= ${binary:Version})
+Depends: ${misc:Depends},
+ pan-config (= ${source:Version}),
+ pan-tasks (= ${source:Version})
Recommends: fityk,
- gnuplot,
- imagej,
- libxy-bin,
- ngraph-gtk,
- octave,
- pymca,
- qtiplot,
- qtoctave,
- scilab,
- spyder,
- vistrails,
- xmaxima
+ gnuplot,
+ imagej,
+ libxy-bin,
+ ngraph-gtk,
+ octave,
+ pymca,
+ scilab,
+ silx,
+ spyder3,
+ vistrails,
+ xmaxima
Suggests: dawn,
- disp,
- edna,
- graphlab,
- gumtree,
- mantid,
- thredds
+ disp,
+ edna,
+ graphlab,
+ gumtree,
+ mantid,
+ nexpy,
+ thredds
Description: Data reduction frameworks
This metapackage will install framework dedicated to the data reduction
Package: pan-data-reduction-frameworks-dev
+Section: metapackages
Architecture: all
-Depends: pan-tasks (= ${binary:Version}), pan-config (= ${binary:Version})
-Recommends: libnexus0,
- libnexus0-java,
- nexus-tools,
- python-fabio,
- python-guidata,
- python-guiqwt
+Depends: ${misc:Depends},
+ libmgl-dev,
+ libnexus-dev,
+ pan-config (= ${source:Version}),
+ pan-data-reduction-framework,
+ pan-tasks (= ${source:Version})
Suggests: cdma,
- comete,
- libnexus0-python
+ comete
Description: PAN Debian data reduction framework dev
This metapackage will install all PAN Blend packages. This is
a temporary package until we sorted all packages into the right
categories.
+Package: pan-diffraction
+Section: metapackages
+Architecture: all
+Depends: ${misc:Depends},
+ pan-config (= ${source:Version}),
+ pan-tasks (= ${source:Version})
+Recommends: binoculars,
+ xrayutilities
+Suggests: nebula
+Description: diffraction software suit
+ This metapackage will install all diffraction softwares
+
Package: pan-gid
+Section: metapackages
Architecture: all
-Depends: pan-tasks (= ${binary:Version}), pan-config (= ${binary:Version})
+Depends: ${misc:Depends},
+ pan-config (= ${source:Version}),
+ pan-tasks (= ${source:Version})
+Recommends: xrayutilities
Suggests: fitgisaxs,
- gsas,
- isgisaxs
+ gsas,
+ isgisaxs
Description: Grazing incidence X-ray and neutron diffraction
- This metapackage will install all GID, GIXD, GIND, GISAS, GISAXS, GISANS softwares
+ This metapackage will install all GID, GIXD, GIND, GISAS, GISAXS, GISANS softwares
Package: pan-microscopy
+Section: metapackages
Architecture: all
-Depends: pan-tasks (= ${binary:Version}), pan-config (= ${binary:Version})
+Depends: ${misc:Depends},
+ pan-config (= ${source:Version}),
+ pan-tasks (= ${source:Version})
Recommends: gwyddion
Suggests: threeb
Description: microscopy IR
This metapackage will install all microscopy softwares.
Package: pan-mx
+Section: metapackages
Architecture: all
-Depends: pan-tasks (= ${binary:Version}), pan-config (= ${binary:Version})
+Depends: ${misc:Depends},
+ pan-config (= ${source:Version}),
+ pan-tasks (= ${source:Version})
Recommends: apbs,
- autodock,
- clustalw,
- default-jdk,
- dino,
- gnuplot,
- imagej,
- jmol,
- openbabel,
- pymol,
- python,
- rasmol,
- raster3d,
- scsh,
- theseus
+ autodock,
+ clustalw,
+ gnuplot,
+ imagej,
+ jmol,
+ libmmdb2-0,
+ openbabel,
+ povray,
+ pymol,
+ python,
+ rasmol,
+ raster3d,
+ theseus
Suggests: 3dna,
- adxv,
- aimless,
- albula,
- aplx,
- atsas,
- autoproc,
- balbes,
- best,
- biox-xds,
- bioxhit,
- bobscript,
- bp3_old,
- c3d,
- cath,
- ccp4,
- cctbx,
- chart,
- chimera,
- chooch,
- cn2coot,
- cns,
- coot,
- crank,
- crystfel,
- das,
- dna,
- domain-finder,
- dps2ar,
- dviewer,
- dyndom3d,
- edna,
- elves,
- epmr,
- escet,
- evrouter,
- fit2d,
- fobscom,
- gramm,
- grasp,
- ha_ncs,
- harker,
- hbplus,
- hca,
- hkl2map,
- hyss,
- imosflm,
- induced-rad-dam,
- ipymol,
- ispyb-client,
- labelit,
- lam,
- laue,
- liged,
- ligplot,
- ligplus,
- lscale,
- maid,
- main,
- mar345,
- marutils,
- mercury,
- mgltools-pmv,
- mlfsom,
- mmdb,
- molscriptmolscript-2.1.2,
- mosflm,
- msi,
- nmoldyn,
- nuccyl,
- nucplot,
- onoono80ono90,
- pgplot_5.2,
- phaser,
- phaser_sad,
- phases,
- phenix,
- pirate,
- plotmtv,
- pointless,
- povray,
- promotif,
- pxpy,
- raddose,
- refmac,
- replace,
- ribbons,
- ringer,
- rmerge,
- rosetta,
- rtools,
- saxs,
- scala_mpi,
- shakerr,
- sharp,
- shelx,
- sir,
- sir2002,
- snb2.2,
- snow,
- solvesolve-2.08,
- stac-stac2,
- strategy,
- surfnet,
- tcltkblt,
- test_exec,
- testcase,
- textal,
- tools,
- tops,
- usf,
- viewhkl,
- wink,
- workflow-ds,
- workflow-executor,
- xds,
- xdsme,
- xiaxia2,
- xprep,
- xrec,
- xtalview
+ adxv,
+ aimless,
+ albula,
+ aplx,
+ atsas,
+ autoproc,
+ balbes,
+ best,
+ biox-xds,
+ bioxhit,
+ bobscript,
+ bp3_old,
+ c3d,
+ cath,
+ ccp4,
+ cctbx,
+ chart,
+ chimera,
+ chooch,
+ cn2coot,
+ cns,
+ coot,
+ crank,
+ crystfel,
+ das,
+ dials,
+ dna,
+ domain-finder,
+ dps2ar,
+ dviewer,
+ dyndom3d,
+ edna,
+ elves,
+ epmr,
+ escet,
+ evrouter,
+ fit2d,
+ fobscom,
+ gemmi,
+ gramm,
+ grasp,
+ ha_ncs,
+ harker,
+ hbplus,
+ hca,
+ hkl2map,
+ hyss,
+ imosflm,
+ induced-rad-dam,
+ ipymol,
+ ispyb-client,
+ labelit,
+ lam,
+ laue,
+ liged,
+ ligplot,
+ ligplus,
+ lscale,
+ maid,
+ main,
+ mar345,
+ marutils,
+ mercury,
+ mlfsom,
+ molscriptmolscript-2.1.2,
+ mosflm,
+ msi,
+ nmoldyn,
+ nuccyl,
+ nucplot,
+ onoono80ono90,
+ pgplot_5.2,
+ phaser,
+ phaser_sad,
+ phases,
+ phenix,
+ pirate,
+ plotmtv,
+ pointless,
+ powder,
+ promotif,
+ pxpy,
+ raddose,
+ refmac,
+ replace,
+ ribbons,
+ ringer,
+ rmerge,
+ rosetta,
+ rtools,
+ saxs,
+ scala_mpi,
+ shakerr,
+ sharp,
+ shelx,
+ sir,
+ sir2002,
+ snb2.2,
+ snow,
+ solvesolve-2.08,
+ stac-stac2,
+ strategy,
+ surfnet,
+ tcltkblt,
+ test_exec,
+ testcase,
+ textal,
+ tools,
+ tops,
+ usf,
+ viewhkl,
+ wink,
+ workflow-ds,
+ workflow-executor,
+ xds,
+ xdsme,
+ xiaxia2,
+ xprep,
+ xrec,
+ xtalview
Description: Macro Molecular diffraction
This metapackage will install all MX diffraction softwares.
-Package: pan-mx-dev
-Architecture: all
-Depends: pan-tasks (= ${binary:Version}), pan-config (= ${binary:Version})
-Suggests: ccif,
- ccp4,
- clipper,
- mmdb
-Description: Debian PAN Macro-Molecular diffraction development packages
- This metapackage will install Debian PAN packages which might be
- helpful for development of applications related to Macro-Molecular
- diffraction.
- .
- You might also be interested in the mx metapackage.
-
Package: pan-powder
+Section: metapackages
Architecture: all
-Depends: pan-tasks (= ${binary:Version}), pan-config (= ${binary:Version})
+Depends: ${misc:Depends},
+ pan-config (= ${source:Version}),
+ pan-tasks (= ${source:Version})
Recommends: fityk,
- libxy-bin,
- objcryst-fox,
- pyfai,
- spd
+ libxy-bin,
+ objcryst-fox,
+ pyfai,
+ spd
Suggests: fullprof,
- jpowder,
- xrdua
+ jpowder,
+ pyGSAS,
+ pyXRD,
+ xrdua
Description: powder diffraction
This metapackage will install all powder diffraction softwares.
Package: pan-small-angle-scattering
+Section: metapackages
Architecture: all
-Depends: pan-tasks (= ${binary:Version}), pan-config (= ${binary:Version})
+Depends: ${misc:Depends},
+ pan-config (= ${source:Version}),
+ pan-tasks (= ${source:Version})
Recommends: fityk,
- pyfai,
- python-mmtk,
- spd
+ pyfai,
+ sasview,
+ spd
Suggests: bsl,
- diffraction-ring-profiler,
- sastbx,
- saxsview
+ diffraction-ring-profiler,
+ sastbx,
+ saxsview
Description: small angle scattering
This metapackage will install all PAN Blend small angle scattering.
Package: pan-tomography
+Section: metapackages
Architecture: all
-Depends: pan-tasks (= ${binary:Version}), pan-config (= ${binary:Version})
-Suggests: astra,
- freeart,
- imagej-pluggins-tomo,
- rabbitct,
- tomographie-preexperiment-data-collector,
- ufo-code ufo-filters
+Depends: ${misc:Depends},
+ pan-config (= ${source:Version}),
+ pan-tasks (= ${source:Version})
+Recommends: libufo-bin,
+ mayavi2,
+ paraview,
+ python3-skimage,
+ ufo-filters
+Suggests: astra-toolbox,
+ freeart,
+ imagej-pluggins-tomo,
+ pyastra-toolbox,
+ python3-pyhst2-cuda,
+ rabbitct,
+ tomographie-preexperiment-data-collector,
+ tomopy
Description: PAN Blend tomography
This metapackage will install all PAN Blend tomography packages.
Package: pan-xas
+Section: metapackages
Architecture: all
-Depends: pan-tasks (= ${binary:Version}), pan-config (= ${binary:Version})
-Recommends: pymca,
- quantum-espresso
-Suggests: horae,
- ifeffit,
- prestopronto,
- python-ifeffit,
- sixpack
+Depends: ${misc:Depends},
+ pan-config (= ${source:Version}),
+ pan-tasks (= ${source:Version}),
+ pymca,
+ quantum-espresso
+Suggests: prestopronto,
+ xraylarch
Description: EXAFS and XANES
This metapackage will install all EXAFS and XANES softwares.
=====================================
tasks/control-systems
=====================================
@@ -1,19 +1,21 @@
+Format: https://blends.debian.org/blends/1.1
Task: control-systems
-Description:Debian PAN Control Systems
+Description: Debian PAN Control Systems
This metapackage will install Debian PAN packages related to control
systems acquisition used in the PAN facilities.
Comment: Improve the description
-Depends: ghkl
+Recommends: ghkl
-Depends: python-pytango
+Recommends: python3-tango
-Depends: python-taurus
+Recommends: python3-taurus
-Depends: python-sardana
+Recommends: python3-taurus-pyqtgraph
-Depends: tango-db, tango-starter, tango-accesscontrol
+Recommends: python3-sardana
+Recommends: tango-db, tango-starter, tango-accesscontrol
Suggests: micromanager
WNPP: 646853
=====================================
tasks/control-systems-dev
=====================================
@@ -1,3 +1,4 @@
+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
@@ -6,20 +7,22 @@ Description: Debian PAN Control System development packages
.
You might also be interested in the control-system metapackage.
-Depends: libhkl-dev
+Recommends: libhkl-dev
-Depends: libtango8-dev
+Recommends: libtango-dev
-Depends: python-pytango
+Recommends: python3-tango
-Depends: python-sardana
+Recommends: python3-sardana
-Depends: python-taurus
+Recommends: python3-taurus
+
+Recommends: python3-taurus-pyqtgraph
Suggests: libuca
Homepage: http://ufo.kit.edu/software.html#libuca
License: LGPL-2.1
-Pkg-Description: generic solution to access two-dimensional detectors
+Pkg-Description: generic solution to access two-dimensional detectors
libuca is an open source, generic solution to access two-dimensional
detectors under POSIX operating systems.
.
@@ -29,4 +32,4 @@ Pkg-Description: generic solution to access two-dimensional detectors
Suggests: lima
Homepage: http://lima.blissgarden.org/index.html
License: GPL-3
-Pkg-Description: Library for Image Acquisition
\ No newline at end of file
+Pkg-Description: Library for Image Acquisition
=====================================
tasks/data-reduction-frameworks
=====================================
@@ -1,33 +1,32 @@
+Format: https://blends.debian.org/blends/1.1
Task: data-reduction-frameworks
Description: Data reduction frameworks
This metapackage will install framework dedicated to the data reduction
Comment: improve the description
-Depends: fityk
+Recommends: fityk
-Depends: gnuplot
+Recommends: gnuplot
-Depends: imagej
+Recommends: imagej
-Depends: libxy-bin
+Recommends: libxy-bin
-Depends: ngraph-gtk
+Recommends: ngraph-gtk
-Depends: octave
+Recommends: octave
-Depends: pymca
+Recommends: pymca
-Depends: qtiplot
+Recommends: scilab
-Depends: qtoctave
+Recommends: silx
-Depends: scilab
+Recommends: spyder3
-Depends: spyder
+Recommends: vistrails
-Depends: vistrails
-
-Depends: xmaxima
+Recommends: xmaxima
Suggests: dawn
Homepage: http://www.dawb.org/
=====================================
tasks/data-reduction-frameworks-dev
=====================================
@@ -1,3 +1,4 @@
+Format: https://blends.debian.org/blends/1.1
Task: data-reduction-framework-dev
Description: PAN Debian data reduction framework dev
This metapackage will install all PAN Blend packages. This is
@@ -5,13 +6,11 @@ Description: PAN Debian data reduction framework dev
categories.
comment: Improve the description
-Depends: python-fabio
+Depends: pan-data-reduction-framework
-Depends: python-guidata
+Depends: libmgl-dev
-Depends: python-guiqwt
-
-Depends: libnexus0, libnexus0-java, libnexus0-python, nexus-tools
+Depends: libnexus-dev
Suggests: cdma
Homepage: http://code.google.com/p/cdma/
=====================================
tasks/diffraction
=====================================
@@ -3,6 +3,10 @@ Description: diffraction software suit
This metapackage will install all diffraction softwares
Comment: Improve the description
+Depends: binoculars
+
+Depends: xrayutilities
+
Suggests: nebula
Homepage: https://github.com/Natnux/nebula
License: GPL-2+
=====================================
tasks/gid
=====================================
@@ -1,9 +1,9 @@
Task: gid
Description: Grazing incidence X-ray and neutron diffraction
- This metapackage will install all GID, GIXD, GIND, GISAS, GISAXS, GISANS softwares
+ This metapackage will install all GID, GIXD, GIND, GISAS, GISAXS, GISANS softwares
Comment: Improve the description
-Depends: python-xrayutilities
+Depends: xrayutilities
Suggest: x-socs
Homepage: http://sourceforge.net/projects/xsocs/?source=directory
=====================================
tasks/microscopy
=====================================
@@ -1,8 +1,10 @@
+Format: https://blends.debian.org/blends/1.1
Task: microscopy
Description: microscopy IR
This metapackage will install all microscopy softwares.
Comment: Improve the description
-Depends: gwyddion
+Recommends: gwyddion
+
+Suggests: threeb
-Suggests: threeb
\ No newline at end of file
=====================================
tasks/mx
=====================================
@@ -1,3 +1,4 @@
+Format: https://blends.debian.org/blends/1.1
Task: mx
Description: Macro Molecular diffraction
This metapackage will install all MX diffraction softwares.
@@ -5,8 +6,10 @@ Comment: Improve the description
Suggests: coot
WNPP: 531904
-Homepage:http://biop.ox.ac.uk/coot/
+Homepage: http://biop.ox.ac.uk/coot/
License: GPLv3 GPLv2+ LGPLv3
+Vcs-Browser: https://salsa.debian.org/science-team/coot
+Vcs-Git: https://salsa.debian.org/science-team/coot.git
Pkg-Description: Crystallographic Object-Oriented Toolkit
Suggests: edna
@@ -16,8 +19,8 @@ Pkg-Description: Framework to build online data analysis programs
Suggests: nmoldyn
Homepage: http://dirac.cnrs-orleans.fr/plone/software/nmoldyn/
-Vcs-Browser: http://anonscm.debian.org/git/debian-science/packages/nmoldyn.git
-Vcs-Git: git://anonscm.debian.org/debian-science/packages/nmoldyn.git
+Vcs-Browser: https://salsa.debian.org/science-team/nmoldyn
+Vcs-Git: https://salsa.debian.org/science-team/nmoldyn.git
Pkg-Description: ?
Suggests: phenix
@@ -116,7 +119,7 @@ Homepage: http://www.dectris.ch/software_albula.html
License: ?
Pkg-Description: Dectris diffraction image viewer and analysis tool
-Depends: apbs
+Recommends: apbs
Suggests: aplx
Homepage: http://www.microapl.co.uk/apl
@@ -130,7 +133,7 @@ License: ?
Remark: which part of the suite is used ?
Pkg-Description: ?
-Depends: autodock
+Recommends: autodock
Suggests: autoproc
Homepage: http://www.globalphasing.com/autoproc
@@ -139,7 +142,7 @@ 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
-Depends: openbabel
+Recommends: openbabel
Suggests: balbes
Homepage: http://www.ysbl.york.ac.uk/~fei/balbes
@@ -153,7 +156,7 @@ Pkg-Description: BALBES is a system for solving protein structures
intervention when running complicated combination of jobs such as
model searching, molecular replacement and refinement.
.
- F.Long, A.Vagin, P.Young and G.N.Murshudov "BALBES: a Molecular Replacement Pipeline " Acta Cryst. D64 125-132(2008)
+ F.Long, A.Vagin, P.Young and G.N.Murshudov "BALBES: a Molecular Replacement Pipeline " Acta Cryst. D64 125-132(2008)
Remark: need ccp4
Suggests: best
@@ -182,16 +185,14 @@ Remark: ESRF can you gives more information about this software
Suggests: bp3_old
Homepage: ?
-Remark: old means useless ?
-Pkg-Description: ?
Remark: ESRF can you gives more information about this software
+Pkg-Description: ?
Suggests: c3d
Homepage: ?
License: ?
-Remark: file format ?
-Pkg-Description: ?
Remark: ESRF can you gives more information about this software
+Pkg-Description: ?
Suggests: cath
Homepage: http://www.cathdb.info
@@ -225,8 +226,8 @@ Remark: this is a suite of software.
Suggests: cctbx
WNPP: 679905
Homepage: http://cctbx.sourceforge.net
-Vcs-Browser: http://anonscm.debian.org/git/debian-science/packages/cctbx.git
-Vcs-Git: git://anonscm.debian.org/debian-science/packages/cctbx.git
+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,
@@ -267,7 +268,7 @@ Pkg-Description: CHOOCH is a program that will automatically determine
MAD or SAD experiments.
Remark: part of ccp4
-Depends: clustalw
+Recommends: clustalw
Suggests: cn2coot
Homepage: ?
@@ -376,8 +377,6 @@ Pkg-Description: The Distributed Annotation System (DAS) defines a
sequence and structure communities.
Remark: ESRF can you gives more information about this software
-Depends: dino
-
Suggests: dna
Homepage: ?
License: ?
@@ -579,7 +578,7 @@ Pkg-Description: EPMR is a general-purpose molecular replacement
between Fo and Fc, even if by the slimmest of margins, the algorithm
will eventually find it.
.
- EPMR includes the following features:
+ EPMR includes the following features:
* the ability to automatically search for multiple copies of a
molecule in the asymmetric unit, either sequentially or
concurrently
@@ -625,7 +624,7 @@ License: ?
Pkg-Description: ?
Comment: ?
-Depends: gnuplot
+Recommends: gnuplot
Suggests: gramm
Homepage: http://vakser.bioinformatics.ku.edu/main/resources_gramm.php
@@ -633,14 +632,12 @@ License: ?
Pkg-Description: ?
Comment: ?
-
Suggests: grasp
Homepage: http://www.doe-mbi.ucla.edu/Software/GRASP.html
License: ?
Pkg-Description: ?
Comment: ?
-
Suggests: ha_ncs
Homepage: ?
License: ?
@@ -677,8 +674,7 @@ License: ?
Pkg-Description: ?
Comment: ?
-
-Depends: imagej
+Recommends: imagej
Suggests: imosflm
Homepage: ?
@@ -698,16 +694,13 @@ License: ?
Pkg-Description: ?
Comment: ?
-
Suggests: ispyb-client
Homepage: ?
License: ?
Pkg-Description: ?
Comment: ?
-
-Depends: default-jdk
-Depends: jmol
+Recommends: jmol
Suggests: labelit
Homepage: ?
@@ -775,15 +768,12 @@ License: ?
Pkg-Description: ?
Comment: ?
-
Suggests: mercury
Homepage: http://www.ccdc.cam.ac.uk/free_services/mercury
License: ?
Pkg-Description: ?
Comment: ?
-Depends: mgltools-pmv
-
Suggests: mlfsom
Homepage: ?
License: ?
@@ -796,24 +786,7 @@ License: ?
Pkg-Description: ?
Comment: ?
-Suggests: mmdb
-WNPP: 679982
-Homepage: http://www.ncbi.nlm.nih.gov/Structure/MMDB/mmdb.shtml
-Vcs-Browser: http://anonscm.debian.org/git/debian-science/packages/mmdb.git
-Vcs-Git: git://anonscm.debian.org/debian-science/packages/mmdb.git
-Pkg-Description: MMDB is designed to assist developers in working with macromolecular coordinate
- files. The library handles both PDB and mmCIF format files.
- .
- The Library also features an internal binary format, portable between different
- platforms. This is achieved at uniformity of the Library's interface functions,
- so that there is no difference in handling different formats.
- .
- MMDB provides various high-level tools for working with coordinate files,
- including reading and writing, orthogonal-fractional transforms, generation of
- symmetry mates, editing the molecular structure and more.
- .
- MMDB is previously written by Eugene Krissinel, and is distributed as a part of
- the CCP4 suite. This project maintains a current stand-alone version of the library.
+Recommends: libmmdb2-0
Suggests: mosflm
Homepage: ?
@@ -893,8 +866,7 @@ License: ?
Pkg-Description: ?
Comment: ?
-
-Depends: povray
+Recommends: povray
Suggests: powder
Homepage: ?
@@ -914,9 +886,9 @@ License: ?
Pkg-Description: ?
Comment: ?
-Depends: pymol
+Recommends: pymol
-Depends: python
+Recommends: python
Suggests: raddose
Homepage: ?
@@ -924,9 +896,9 @@ License: ?
Pkg-Description: ?
Comment: ?
-Depends: rasmol
+Recommends: rasmol
-Depends: raster3d
+Recommends: raster3d
Suggests: refmac
Homepage: ?
@@ -953,13 +925,11 @@ Pkg-Description: ?
Comment: ?
Suggests: rmerge
-Comment: hugins-tools ?
+Comment: ?
Homepage: ?
License: ?
Pkg-Description: ?
-Comment: ?
-
Suggests: rosetta
Homepage: ?
License: ?
@@ -979,14 +949,10 @@ Pkg-Description: ?
Comment: ?
Suggests: scala_mpi
-Comment: scala packages ?
+Comment: ?
Homepage: ?
License: ?
Pkg-Description: ?
-Comment: ?
-
-Depends: scsh
-Remark: Usefull ?
Suggests: shakerr
Homepage: ?
@@ -1027,7 +993,7 @@ Pkg-Description: ?SHELX is a set of programs for crystal structure
using SHELXS (and recently SHELXD and SHELXE), and the refinement of
proteins against high-resolution data (2.5A or better) using SHELXL.
.
- SHELX-97 consists of the following programs:
+ SHELX-97 consists of the following programs:
.
* SHELXS - Structure solution by Patterson and direct methods
* SHELXC - Preparations of files for macromolecular phasing with SHELXD and SHELXE
@@ -1037,7 +1003,7 @@ Pkg-Description: ?SHELX is a set of programs for crystal structure
* CIFTAB - Tables for publication via (small molecule) CIF format
* SHELXA - Post-absorption corrections (for emergency use only)
* SHELXPRO - Protein interface to SHELX
- * SHELXWAT - Automatic water divining for macromolecules
+ * SHELXWAT - Automatic water divining for macromolecules
.
The program SHELXA was kindly donated by an anonymous user. It
applies "absorption corrections" by fitting the observed to the
@@ -1120,7 +1086,7 @@ License: ?
Pkg-Description: ?
Comment: ?
-Depends: theseus
+Recommends: theseus
Suggests: tools
Homepage: ?
@@ -1207,7 +1173,9 @@ Comment: ?
Suggests: dials
Homepage: http://cci.lbl.gov/dials2/
-License: ?
+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
@@ -1230,4 +1198,35 @@ Pkg-Description: Diffraction Integration for Advance Light Source
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.
\ No newline at end of file
+ highly accurate analysis based on a comprehensive physical model.
+
+Suggests: gemmi
+Homepage: https://github.com/project-gemmi/gemmi
+License: MPL2 or LGPL3
+Pkg-Description:
+ Gemmi is a library, accompanied by a set of programs, developed
+ primarily for use in macromolecular crystallography (MX). For working
+ with:
+ - macromolecular models (content of PDB, PDBx/mmCIF and mmJSON files),
+ - refinement restraints (CIF files),
+ - reflection data (MTZ and mmCIF formats),
+ - data on a 3D grid (electron density maps, masks, MRC/CCP4 format)
+ - crystallographic symmetry.
+ .
+ Parts of this library can be useful in structural bioinformatics (for
+ symmetry-aware analysis of protein models), and in other
+ molecular-structure sciences that use CIF files (we have the fastest
+ open-source CIF parser).
+ .
+ Gemmi is open-source (MPL) and portable – it runs on Linux, Windows,
+ MacOS and even inside a web browser if compiled to WebAssembly. It is
+ written in C++11, with Python (2 and 3) bindings, and with partial C
+ and Fortran 2003 interface.
+ .
+ Occasionally, the project gets sidetracked into visualization of the
+ PDB data.
+ .
+ Gemmi is a joint project of Global Phasing Ltd and CCP4.
+ .
+ The project is named after Gemmi Pass. The name can also be expanded
+ as GEneral MacroMolecular I/o.
=====================================
tasks/powder
=====================================
@@ -1,17 +1,18 @@
+Format: https://blends.debian.org/blends/1.1
Task: powder
Description: powder diffraction
This metapackage will install all powder diffraction softwares.
Comment: Improve the description
-Depends: fityk
+Recommends: fityk
-Depends: libxy-bin
+Recommends: libxy-bin
-Depends: objcryst-fox
+Recommends: objcryst-fox
-Depends: pyfai
+Recommends: pyfai
-Depends: spd
+Recommends: spd
Suggests: fullprof
Homepage: http://www.ill.eu/sites/fullprof
@@ -116,3 +117,4 @@ Pkg-Description: matrix algorithm for X-ray diffraction patterns
* Covariation Matrix Adapation Evolutionary Strategy (CMA-ES; using DEAP)
* Multiple Particle Swarm Optimization (MPSO; using DEAP)
* scripting support
+
=====================================
tasks/small-angle-scattering
=====================================
@@ -1,16 +1,16 @@
+Format: https://blends.debian.org/blends/1.1
Task: small-angle-scattering
Description: small angle scattering
This metapackage will install all PAN Blend small angle scattering.
Comment: improve the description
-Depends: fityk
+Recommends: fityk
-Depends: pyfai
+Recommends: pyfai
-Depends: python-mmtk
-
-Depends: spd
+Recommends: sasview
+Recommends: spd
Suggests: bsl
Homepage: http://www.small-angle.ac.uk/dms/small-angle/linux/bsl-tar/bsl.tar.gz
@@ -28,18 +28,8 @@ Homepage: http://sastbx.als.lbl.gov/wiki/index.php/Main_Page
License: ?
Pkg-Description: Small angle scattering
-Suggests: sasview
-Homepage: http://www.sasview.org/about.html
-License: PSF
-Pkg-Description: Small Angle Scattering Analysis Software
- SasView is a Small Angle Scattering Analysis Software Package,
- originally developed as part of the NSF DANSE project under the name
- SansView, now managed by an international collaboration of
- facilities. Feedback and contributions are welcome and encouraged.
-
Suggests: saxsview
Homepage: http://saxsview.sourceforge.net
-License: GPL3+
License: ?
Pkg-Description: ?
Comment: ?
=====================================
tasks/tomography
=====================================
@@ -3,13 +3,17 @@ Description: PAN Blend tomography
This metapackage will install all PAN Blend tomography packages.
Comment: improve the Description
-Depends; volview
+Depends: libufo-bin
+
+Depends: mayavi2
Depends: paraview
-Depends: mayavi2
+Suggests: python3-pyhst2-cuda
+
+Depends: python3-skimage
-Depends: python-skimage
+Depends: ufo-filters
Suggests: astra-toolbox
Homepage: http://sourceforge.net/p/astra-toolbox/wiki/Home/
@@ -62,27 +66,3 @@ 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: ufo-code
-Homepage: http://ufo.kit.edu/software.html
-License: LGPL-3
-Pkg-Description: fast X-ray radiography, tomography and laminography processing
- The UFO framework is a C library for fast X-ray radiography,
- tomography and laminography processing. Due to the provided bindings,
- it comes with a simple, scriptable user interface.
- .
- The source consists of a small managing core and a filter suite built
- on top of the core. The filters are laid out in a graph-structure and
- executed on the GPU, if possible, for maximum performance.
-
-Suggests: ufo-filters
-Homepage: http://ufo.kit.edu/software.html
-License: LGPL-3
-Pkg-Description: fast X-ray radiography, tomography and laminography processing
- The UFO framework is a C library for fast X-ray radiography,
- tomography and laminography processing. Due to the provided bindings,
- it comes with a simple, scriptable user interface.
- .
- The source consists of a small managing core and a filter suite built
- on top of the core. The filters are laid out in a graph-structure and
- executed on the GPU, if possible, for maximum performance.
=====================================
tasks/xas
=====================================
@@ -1,22 +1,17 @@
+Format: https://blends.debian.org/blends/1.1
Task: xas
Description: EXAFS and XANES
This metapackage will install all EXAFS and XANES softwares.
Comment: Improve the description
-Depends: horae
-
-Depends: ifeffit
-
Depends: pymca
-Depends: python-ifeffit
-
Depends: quantum-espresso
-Depends: sixpack
-
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
@@ -54,5 +49,5 @@ Pkg-Description: X-ray Analysis for Synchrotron Applications using Python
Suggests: prestopronto
Homepage: http://code.google.com/p/prestopronto
-License:GPL3+
-Pkg-Description: Software for analysis of Quick Exafs data
\ No newline at end of file
+License: GPL3+
+Pkg-Description: Software for analysis of Quick Exafs data
View it on GitLab: https://salsa.debian.org/blends-team/pan/-/compare/d053f45a61d9d648885fbc64fb41e94465a54c4b...de252b3a2e8ebc8ccb4ca0579b5dfe633c9e9716
--
View it on GitLab: https://salsa.debian.org/blends-team/pan/-/compare/d053f45a61d9d648885fbc64fb41e94465a54c4b...de252b3a2e8ebc8ccb4ca0579b5dfe633c9e9716
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