[Blends-commit] [Git][blends-team/science][master] Cleanup tasks from inconsistencies
Andreas Tille (@tille)
gitlab at salsa.debian.org
Thu Mar 2 14:28:38 GMT 2023
Andreas Tille pushed to branch master at Debian Blends Team / science
Commits:
7d6c6600 by Andreas Tille at 2023-03-02T15:28:10+01:00
Cleanup tasks from inconsistencies
- - - - -
23 changed files:
- tasks/biology
- tasks/chemistry
- tasks/dataacquisition
- tasks/dataacquisition-dev
- tasks/datamanagement
- tasks/distributedcomputing
- tasks/electrophysiology
- tasks/engineering
- tasks/engineering-dev
- tasks/geography
- tasks/highenergy-physics
- tasks/highenergy-physics-dev
- tasks/linguistics
- tasks/mathematics-dev
- tasks/meteorology-dev
- tasks/nanoscale-physics-dev
- tasks/numericalcomputation
- tasks/physics
- tasks/physics-dev
- tasks/simulations
- tasks/tools
- tasks/typesetting
- tasks/viewing-dev
Changes:
=====================================
tasks/biology
=====================================
@@ -23,10 +23,12 @@ Remark: Maintained by Debian Med Blend
Recommends: bauble
-Recommends: genesis, avida-base
+Recommends: genesis
Recommends: critterding
Recommends: nmodl, nrn-mod2c
Suggests: python3-nmodl, libinterviews-dev
+
+Suggests: siconos, siconos-mechanics-tools
=====================================
tasks/chemistry
=====================================
@@ -53,6 +53,8 @@ Recommends: python3-mpiplus
Suggests: refmac-dictionary
+Suggests: libcoordgen-dev, libmaeparser-dev
+
Recommends: libegad
Homepage: http://egad.ucsd.edu/egad/
WNPP: 429693
=====================================
tasks/dataacquisition
=====================================
@@ -17,14 +17,8 @@ X-Suggests: libgpib-bin
Comment: Removed from Debian see
http://snapshot.debian.org/package/gpib/3.2.11-2.1/
-Recommends: ktimetrace
-
Recommends: netcdf-bin
-Suggests: comedi-source
-
-Suggests: rtai
-
Suggests: xenomai-runtime
Recommends: python3-sardana
@@ -58,8 +52,6 @@ Recommends: jaaa
Recommends: ghkl
-Recommends: narval-utils
-
Recommends: xyscan
Recommends: filo
@@ -81,20 +73,6 @@ Recommends: xlsx2csv
Recommends: open3d-tools, open3d-gui
Recommends: python3-pyvisa
-Homepage: http://pyvisa.sourceforge.net/
-License: MIT
-Pkg-Description: control measurement devices and test equipment via GPIB, RS232, or USB
- A Python package with bindings to the "Virtual Instrument Softwares
- Architecture" VISA library, in order to control measurement devices
- and test equipment via GPIB, RS232, or USB.
- .
- Articles about pyvisa:
- * G. Varoquaux has written an interesting article describing the
- use of python and pyvisa for experimental control. Agile computer
- control of a complex experiment. Computing in Science and
- Engineering 10(2), 55 (2008).
- * Writing a graphical application for scientific programming using
- TraitsUI
Suggests: tango-db, tango-starter, tango-accesscontrol, python3-pytango, python3-taurus
=====================================
tasks/dataacquisition-dev
=====================================
@@ -5,19 +5,9 @@ Description: Debian Science data acquisition development packages
to develop applications related to data acquisition. This might be
used in several sciences.
-Recommends: libnarval1-dev
-
Recommends: libtango-dev, liblog4tango-dev, python3-tango
Recommends: python3-xrayutilities
-WNPP: 723017
-Responsible: Eugen Wintersberger <eugen.wintersberger at gmail.com>
-Homepage: http://xrayutilities.sourceforge.net/
-Pkg-Description: Python package for xray data reduction and analysis
- xrayutilities is a collection of scripts used to reduce and analyze x-ray
- diffraction data. It consists of a python package and several routines written
- in C. It especially useful for the reciprocal space conversion of diffraction
- data taken with linear and area detectors.
Recommends: libsdsl-dev
=====================================
tasks/datamanagement
=====================================
@@ -12,7 +12,7 @@ Recommends: datalad
Recommends: datalad-container
-Recommends: hdf5-filter-plugin, hdf5-filter-plugin-blosc, hdf5-filter-plugin-zfp-serial
+Recommends: hdf5-filter-plugin, hdf5-filter-plugin-blosc-serial, hdf5-filter-plugin-zfp-serial
Recommends: nexus-tools
@@ -31,3 +31,5 @@ Suggests: python3-plfit, libplfit-dev
Recommends: python3-jdata
Recommends: python3-pyzoltan
+
+Recommends: virtuoso-opensource
=====================================
tasks/distributedcomputing
=====================================
@@ -10,7 +10,7 @@ Recommends: ipython3
Why: Provides ipcluster/ipcontroller/ipengine for Python-based distributed
computing
-Recommends: nordugrid-arc-nox
+Recommends: nordugrid-arc-client
Recommends: gridengine-client, gridengine-exec, gridengine-master, gridengine-qmon
=====================================
tasks/electrophysiology
=====================================
@@ -16,7 +16,6 @@ Suggests: science-dataacquisition
Recommends: openelectrophy
- ; Added by blends-inject 0.0.3. [Please note here if modified manually]
Suggests: spike
Homepage: http://neuroanalysis.org
Language: C++, Octave/Matlab
@@ -32,17 +31,10 @@ Published-In: Neuroinformatics, 7, 165–178
Published-Title: Spike Train Analysis Toolkit: Enabling Wider Application of Information-Theoretic Techniques to Neurophysiology
Published-Year: 2009
- ; Added by blends-inject 0.0.7. [Please note here if modified manually]
Suggests: klustakwik
-Published-Authors: Kenneth D. Harris, Darrell A. Henze, Jozsef Csicsvari, Hajime Hirase, and György Buzsáki
-Published-In: Journal of Neurophysiology, 84, 401-414
-Published-Title: Accuracy of Tetrode Spike Separation as Determined by Simultaneous Intracellular and Extracellular Measurements
-Published-Year: 2000
- ; Added by blends-inject 0.0.2. [Removed extra information because accepted inside Debian]
Recommends: libgdf-dev
- ; Added by blends-inject 0.0.3. [Please note here if modified manually]
Suggests: neurodata
Homepage: http://sourceforge.net/projects/neurodata/
Language: C++, Octave/Matlab, Perl
@@ -52,7 +44,6 @@ Pkg-Description: suite to analyze data acquired from electrophysiology experimen
electroneurogram traces of coupled oscillators, and a Perl library
for the analysis of voltage trace data.
- ; Added by blends-inject 0.0.3. [Please note here if modified manually]
Suggests: qrtailab
Why: Useful and used in acquisition/analysis setups
Homepage: http://qrtailab.sourceforge.net/
@@ -62,10 +53,8 @@ Pkg-Description: Qt-GUI for RTAI
RTAI project. It can be used as virtual oscilloscope and monitoring
application for interacting with the real-time external.
- ; Added by blends-inject 0.0.7. [now official package]
Suggests: stimfit
- ; Added by blends-inject 0.0.3. [Please note here if modified manually]
Suggests: trellis-neuro
Homepage: http://sourceforge.net/projects/trellis-neuro/
Language: C, C++
@@ -76,7 +65,6 @@ Pkg-Description: interface to neurophysiology data acquisition and stimulation i
instruments. It is based on the eXtensible Instrument Processing
Protocol (XIPP), QT 4, and C/C++.
- ; Added by blends-inject 0.0.4. [Please note here if modified manually]
Suggests: relacs
Homepage: http://www.relacs.net
Language: C++
@@ -110,7 +98,6 @@ Pkg-Description: framework for closed-loop neurophysiological experiments
drivers and they allow you to implement research protocols, filters,
spike detectors, etc.
- ; Added by blends-inject 0.0.4. [Please note here if modified manually]
Suggests: chronus
Homepage: http://www.chronux.org/
Language: C, Matlab/Octave
@@ -129,10 +116,8 @@ Remark: last release more than 2 years ago, and no major vital signs since then
Suggests: libbiosig-dev
- ; Added by blends-inject 0.0.7. [Package available in Debian - extra information removed]
Recommends: sigviewer
- ; Added by blends-inject 0.0.5. [Please note here if modified manually]
Suggests: nspike
Homepage: http://nspike.sourceforge.net
Language: C++
@@ -144,7 +129,6 @@ Pkg-Description: electrophysiological and behavioral data collection
system.
Remark: Last vital signs from 2 years ago
- ; Added by blends-inject 0.0.5. [Please note here if modified manually]
Suggests: rtxi
Homepage: http://www.rtxi.org
Language: C++
@@ -162,7 +146,6 @@ Pkg-Description: real-time data acquisition and control applications in biologic
- Phase Response Curve
- Signal processing
- ; Added by blends-inject 0.0.7. [Please note here if modified manually]
Suggests: bluespike
Homepage: https://github.com/globalvariable/BlueSpike
Language: C
@@ -183,7 +166,6 @@ Published-In: SfN2010, Poster 818.22/OOO43
Published-Title: Real-time experimental interface for electrophysiology experiments
Published-Year: 2010
- ; Added by blends-inject 0.0.7. [Please note here if modified manually]
Suggests: meabench
Homepage: http://www.its.caltech.edu/~daw/meabench/
Language: C++
@@ -209,7 +191,6 @@ Published-URL: http://www.its.caltech.edu/~daw/abstracts/05-WDP.html
Published-Year: 2005
Remark: 64-bit port is not yet fully tested/supported
- ; Added by blends-inject 0.0.7. [Please note here if modified manually]
Suggests: mclust
Homepage: http://redishlab.neuroscience.umn.edu/MClust/MClust.html
Language: C/C++, Matlab
@@ -222,7 +203,6 @@ Pkg-Description: Matlab toolbox for clustering of electrophysiologic recordings
of timestamps in binary format. Timestamps are 32-bit longs at a
resolution of 10 timestamps/ms.
- ; Added by blends-inject 0.0.7. [Please note here if modified manually]
Suggests: neo
Homepage: http://neuralensemble.org/trac/neo
Language: Python
@@ -246,7 +226,6 @@ Remark: Upstream says not worth packaging before v0.2 is released.
Suggests: python3-neo
- ; Added by blends-inject 0.0.7. [Please note here if modified manually]
Suggests: pymeg
Homepage: https://github.com/badbytes/pymeg/wiki
Language: Python
@@ -275,7 +254,6 @@ Suggests: aghermann
Suggests: python3-bioxtasraw
- ; Added by blends-inject 0.0.7. [Please note here if modified manually]
Suggests: eeglab
Homepage: http://sccn.ucsd.edu/eeglab
Language: C, Matlab/Octave
@@ -295,10 +273,8 @@ Published-Title: EEGLAB: an open source toolbox for analysis of single-trial EEG
Published-Year: 2004
Registration: http://sccn.ucsd.edu/eeglab/install.html
- ; Added by blends-inject 0.0.7. [Removed extra information about now official package]
#Suggests: python-neuroshare
- ; Added by blends-inject 0.0.7. [Please note here if modified manually]
Suggests: patchclamp
Homepage: http://sourceforge.net/projects/patchclamp
Language: C/C++
@@ -309,7 +285,6 @@ Pkg-Description: recorder of single-channel and whole-cell currents
perform the most common tasks of recording single channels and
whole-cell currents
- ; Added by blends-inject 0.0.7. [Please note here if modified manually]
Suggests: spykeview
Homepage: https://github.com/rproepp/spykeviewer
Language: Python
=====================================
tasks/engineering
=====================================
@@ -39,7 +39,7 @@ Recommends: metis-edf
Recommends: eficas
-Recommends: code-saturne, ecs
+Recommends: code-saturne
Recommends: hdfview
=====================================
tasks/engineering-dev
=====================================
@@ -51,7 +51,7 @@ Recommends: libopenturns-dev
Suggests: openturns-examples
-Recommends: libmadlib-dev, libtet1.4-dev
+Recommends: libmadlib-dev, libtet1.5-dev
Why: Mesh adaptation
Recommends: libslepc3.4.2-dev
=====================================
tasks/geography
=====================================
@@ -23,11 +23,9 @@ Recommends: mapserver-bin,
gpsbabel,
gpx2shp,
gpsd,
- gpsdrive,
gpsman,
earth3d,
openscenegraph,
- drawmap,
gpstrans,
geoip-bin,
gpsd-clients,
@@ -71,14 +69,6 @@ Recommends: pgadmin3
Suggests: libmseed-dev
-Recommends: openjump
-Pkg-URL: http://snapshot.debian.org/package/openjump/
-Remark: Removed from Debian
- This package was removed from Debian but some versions are available
- from http://snapshot.debian.org/
- .
- Reasons are given here: http://bugs.debian.org/626716
-
Recommends: grace
X-Depends: renderathome, osm-tools
@@ -92,3 +82,5 @@ Recommends: python3-cartopy
Suggests: python3-pyepsg
Recommends: sac2mseed
+
+Recommends: python3-spaghetti
=====================================
tasks/highenergy-physics
=====================================
@@ -49,7 +49,7 @@ Recommends: pythia8-root-interface
Recommends: libroot-bindings-python5.34, libroot-bindings-ruby5.34, libroot-graf3d-gl5.34, libroot-io-xmlparser5.34, \
libroot-math-mathmore5.34, libroot-math-unuran5.34, libroot-misc-memstat5.34, libroot-misc-table5.34, \
- libroot-net-bonjour5.34, libroot-net-ldap5.34, libroot-proof-clarens5.34, libroot-roofit5.34, libroot-geom5.34, \
+ libroot-net-bonjour5.34, libroot-net-ldap5.34, libroot-roofit5.34, libroot-geom5.34, \
libroot-graf2d-gpad5.34, libroot-graf2d-graf5.34, libroot-graf2d-postscript5.34, libroot-graf3d-eve5.34, \
libroot-graf3d-g3d5.34, libroot-gui5.34, libroot-gui-ged5.34, libroot-hist5.34, libroot-hist-spectrum5.34, \
libroot-html5.34, libroot-io5.34, libroot-math-foam5.34, libroot-math-genvector5.34, libroot-math-mathcore5.34, \
@@ -61,7 +61,7 @@ Recommends: libroot-bindings-python5.34, libroot-bindings-ruby5.34, libroot-graf
Recommends: root-plugin-graf2d-asimage, root-plugin-geom-gdml, root-plugin-gui-qt, root-plugin-graf2d-qt, \
root-plugin-math-fftw3, root-plugin-math-minuit2, root-plugin-montecarlo-pythia8, root-plugin-net-globus, \
- root-plugin-net-krb5, root-plugin-proof-peac, root-plugin-sql-mysql, root-plugin-sql-odbc, \
+ root-plugin-net-krb5, root-plugin-sql-mysql, root-plugin-sql-odbc, \
root-plugin-sql-pgsql, root-plugin-geom-geombuilder, root-plugin-geom-geompainter, root-plugin-graf2d-x11, \
root-plugin-graf3d-x3d, root-plugin-gui-fitpanel, root-plugin-gui-guibuilder, root-plugin-gui-sessionviewer, \
root-plugin-hist-hbook, root-plugin-hist-histpainter, root-plugin-hist-spectrumpainter, root-plugin-io-sql, \
@@ -83,3 +83,5 @@ Recommends: geant4
Recommends: neuron
Recommends: dials
+
+Recommends: sdpb
=====================================
tasks/highenergy-physics-dev
=====================================
@@ -39,7 +39,7 @@ Recommends: fcc, libooptools-dev
Recommends: libroot-bindings-python-dev, libroot-bindings-ruby-dev, libroot-graf3d-gl-dev, libroot-io-xmlparser-dev, \
libroot-math-mathmore-dev, libroot-math-unuran-dev, libroot-misc-memstat-dev, libroot-misc-table-dev, \
- libroot-net-bonjour-dev, libroot-net-ldap-dev, libroot-proof-clarens-dev, libroot-roofit-dev, libroot-geom-dev, \
+ libroot-net-bonjour-dev, libroot-net-ldap-dev, libroot-roofit-dev, libroot-geom-dev, \
libroot-graf2d-gpad-dev, libroot-graf2d-graf-dev, libroot-graf2d-postscript-dev, libroot-graf3d-eve-dev, \
libroot-graf3d-g3d-dev, libroot-gui-dev, libroot-gui-ged-dev, libroot-hist-dev, libroot-hist-spectrum-dev, \
libroot-html-dev, libroot-io-dev, libroot-math-foam-dev, libroot-math-genvector-dev, libroot-math-mathcore-dev, \
=====================================
tasks/linguistics
=====================================
@@ -18,7 +18,11 @@ Suggests: libticcutils2-dev
Suggests: frogdata
-Suggests: libtimbl3-dev, libtimbl4-dev, libtimblserver2-dev, libmbt0-dev, libucto1-dev, libfolia-dev
+Suggests: libtimbl-dev, libtimblserver-dev, libmbt-dev, libucto-dev, libfolia-dev
+
+Suggests: tfdocgen
+
+Suggests: libticcutils-dev
Recommends: collatinus
@@ -190,3 +194,7 @@ Suggests: libfasttext-dev, python3-fasttext
Suggests: python3-gensim
Suggests: libopennlp-maxent-java
+
+Recommends: sentencepiece
+
+Suggests: libsentencepiece-dev, python3-sentencepiece
=====================================
tasks/mathematics-dev
=====================================
@@ -31,10 +31,14 @@ Suggests: libcblas-dev
Recommends: libsuperlu-dev
Why: solver
+Recommends: libsuperlu-dist-dev
+
Recommends: libglpk-dev, libglpk-java,
libqsopt-ex-dev
Why: linear programming
+Recommends: python3-swiglpk
+
Recommends: libcgal-dev
Why: computational geometry
@@ -174,6 +178,8 @@ Recommends: python3-gpyfft
Recommends: python3-mpi4py-fft
+Recommends: libspfft-dev
+
Recommends: liblbfgs-dev
Why: solver
@@ -329,3 +335,5 @@ Recommends: libopenmesh-dev
Recommends: libortools-dev, python3-ortools
Recommends: python3-pyemd
+
+Recommends: libsleef-dev
=====================================
tasks/meteorology-dev
=====================================
@@ -77,6 +77,8 @@ Recommends: libfftw3-dev, fftw-dev, sfftw-dev, python3-pyfftw
Recommends: python3-gpyfft
+Recommends: libspfft-dev
+
Recommends: liblapack-doc, libfftw3-doc
Recommends: liblas-dev
=====================================
tasks/nanoscale-physics-dev
=====================================
@@ -25,6 +25,8 @@ Recommends: libfftw3-dev, python3-pyfftw
Recommends: python3-gpyfft
+Recommends: libspfft-dev
+
Recommends: libgsl0-dev, gsl-bin, gsl-doc-info, gsl-ref-html|gsl-ref-psdoc
Recommends: libnetcdf-dev, netcdf-doc, r-cran-rnetcdf
@@ -135,3 +137,7 @@ Recommends: libnexus-dev, libnexus-java
Recommends: python3-nxs
Recommends: python3-qutip
+
+Recommends: python3-sasdata
+
+Recommends: libcoordgen-dev, libmaeparser-dev
=====================================
tasks/numericalcomputation
=====================================
@@ -14,6 +14,8 @@ Why: numerical programming environment similar to Matlab
Recommends: python3-matplotlib, python3-scipy, ipython3, python3-numpy, spyder, python3-guiqwt
Why: Python based numerical programming environment similar to Matlab
+Suggests: python3-spyder-kernels
+
Suggests: python3-lazyarray
Suggests: python3-bcolz
@@ -221,3 +223,9 @@ Suggests: python3-libpysal
Suggests: libmagma-dev
Recommends: python3-pyswarms
+
+Recommends: sdpb
+
+Recommends: libsleef-dev
+
+Recommends: libtoon-dev, libtoontag-dev
=====================================
tasks/physics
=====================================
@@ -189,3 +189,5 @@ Recommends: pyfr
Suggests: evolver-ogl | evolver-nox
Recommends: toulbar2
+
+Recommends: siconos, siconos-mechanics-tools
=====================================
tasks/physics-dev
=====================================
@@ -14,9 +14,9 @@ Recommends: libfftw3-dev, fftw-dev, sfftw-dev, python3-pyfftw
Recommends: python3-gpyfft
-Recommends: libopenctm-dev
+Recommends: libspfft-dev
-#Recommends: python-openctm
+Recommends: libopenctm-dev
Suggests: libtriangle-dev
Comment: Source triangle seems to be unmaintained - it might make sense to team-highjack this package
=====================================
tasks/simulations
=====================================
@@ -65,3 +65,7 @@ Suggests: libopm-common-dev, python3-opm-common, libopm-grid-dev, libopm-materia
Suggests: python3-pyswarms
Recommends: python3-qutip
+
+Recommends: siconos, siconos-mechanics-tools
+
+Recommends: tkgate
=====================================
tasks/tools
=====================================
@@ -43,3 +43,7 @@ Recommends: mrcal
Suggests: libmrcal-dev, python3-mrcal
Suggests: python3-opcodes
+
+Suggests: tiemu-skinedit
+
+Suggests: spacenavd
=====================================
tasks/typesetting
=====================================
@@ -19,7 +19,7 @@ Recommends: dia
Suggests: tellico
-Recommends: texmaker | kile | lyx | texmacs | auctex | vim-latexsuite | texstudio
+Recommends: texmaker, kile, lyx, texmacs, auctex, vim-latexsuite, texstudio, setzer
Recommends: pandoc, pandoc-citeproc
=====================================
tasks/viewing-dev
=====================================
@@ -70,3 +70,5 @@ Recommends: liborigin2-dev
Recommends: libopen3d-dev, python3-open3d
Suggests: python3-opentsne
+
+Recommends: python3-symfit
View it on GitLab: https://salsa.debian.org/blends-team/science/-/commit/7d6c6600c00117e95adb6a8ff0af1963432f7aa7
--
View it on GitLab: https://salsa.debian.org/blends-team/science/-/commit/7d6c6600c00117e95adb6a8ff0af1963432f7aa7
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