diff -Nru debian-science-1.11ubuntu1/debian/changelog debian-science-1.12ubuntu1/debian/changelog --- debian-science-1.11ubuntu1/debian/changelog 2019-10-31 04:24:55.000000000 +0000 +++ debian-science-1.12ubuntu1/debian/changelog 2020-02-01 20:54:10.000000000 +0000 @@ -1,3 +1,23 @@ +debian-science (1.12ubuntu1) focal; urgency=low + + * Merge from Debian unstable. Remaining changes: + - Update libsdformat4 to libsdformat6. + - Remove all polybori binary packages from Recommends, Suggests and the + mathematics-dev tasks as those no longer exist in Ubuntu. + + -- Steve Langasek Sat, 01 Feb 2020 12:54:10 -0800 + +debian-science (1.12) unstable; urgency=medium + + [ Stuart Prescott ] + * Team upload. + * Further Python 3 updates. + + [ Andreas Tille ] + * Standards-Version: 4.4.0 + + -- Stuart Prescott Tue, 21 Jan 2020 00:59:36 +1100 + debian-science (1.11ubuntu1) focal; urgency=low * Merge from Debian unstable. Remaining changes: diff -Nru debian-science-1.11ubuntu1/debian/control debian-science-1.12ubuntu1/debian/control --- debian-science-1.11ubuntu1/debian/control 2019-10-31 04:24:55.000000000 +0000 +++ debian-science-1.12ubuntu1/debian/control 2020-01-20 21:44:03.000000000 +0000 @@ -8,7 +8,7 @@ Ole Streicher Build-Depends-Indep: blends-dev (>= 0.7~), debhelper (>= 12~) -Standards-Version: 4.3.0 +Standards-Version: 4.4.0 Vcs-Browser: https://salsa.debian.org/blends-team/science Vcs-Git: https://salsa.debian.org/blends-team/science.git Homepage: https://wiki.debian.org/DebianScience/ @@ -187,6 +187,7 @@ science-tasks (= ${source:Version}) Recommends: adun.app, apbs, + avogadro, bkchem, bodr, chemeq, @@ -214,39 +215,39 @@ kalzium, katomic, libcdk-java, - mmass, - mmass-modules, mopac7-bin, mpqc, mpqc-support, + msxpertsuite, openbabel, openfoam, pdb2pqr, psi3, pyfai, pymol, + python3-pymzml, qutemol, rasmol, tandem-mass, + v-sim, viewmol, xbs, xdrawchem, xmakemol-gl | xmakemol -Suggests: avogadro, - fdmnes, +Suggests: fdmnes, gcu-plugin, gdpc-examples, libegad, libint, libschroedinger-coordgenlibs-dev, + mmass, + mmass-modules, molden, molekel, - msxpertsuite, openchrom, - python-mzml-doc, + python-pymzml-doc, python3-periodictable, - tinker, - v-sim + tinker Description: Debian Science Chemistry packages This metapackage will install Debian Science packages related to Chemistry. You might also be interested in the field::chemistry @@ -272,6 +273,7 @@ netcdf-bin, python3-pyvisa, segyio-bin, + xlsx2csv, xyscan Suggests: binoculars, comedi-source, @@ -318,6 +320,7 @@ python3-pymeasure, python3-segyio Suggests: libnarval1-dev, + python3-xrayutilities, r-cran-mi, r-cran-ncdf4 Description: Debian Science data acquisition development packages @@ -331,22 +334,22 @@ Depends: ${misc:Depends}, science-config (= ${source:Version}), science-tasks (= ${source:Version}) -Recommends: environment-modules, +Recommends: dmtcp, + environment-modules, gridengine-client, gridengine-exec, gridengine-master, gridengine-qmon, - ipython, + htcondor, + ipython3, mpich, - nordugrid-arc-nox, openmpi-bin, python3-scoop Suggests: coop-computing-tools, - dmtcp, globus-core, hpcc, - htcondor, mpich2python, + nordugrid-arc-nox, octave-mpi, openmpipython, psom, @@ -395,6 +398,7 @@ netlogo, pksfc, python3-pandasdmx, + python3-quantecon, r-cran-ecdat, r-cran-pdfetch, r-cran-rdbnomics, @@ -424,7 +428,8 @@ Depends: ${misc:Depends}, science-config (= ${source:Version}), science-tasks (= ${source:Version}) -Recommends: libgdf-dev +Recommends: libgdf-dev, + sigviewer Suggests: aghermann, bluespike, chronus, @@ -450,7 +455,6 @@ rtxi, science-dataacquisition, science-neuroscience-modeling, - sigviewer, spike, stimfit, trellis-neuro @@ -478,9 +482,13 @@ code-saturne, dime, fenics, + freecad, gerris, + getdp, gmsh, + hdfview, libadios-bin, + librecad, libsilo-bin, lxi-tools, netgen, @@ -488,9 +496,10 @@ openfoam, python3-admesh, python3-dolfin, + python3-escript | python3-escript-mpi, python3-fiat, + python3-openturns, python3-silo, - pythoncad, sailcut, scram, solvespace, @@ -508,17 +517,11 @@ ecs, eficas, feel++-apps, - freecad, - getdp, - hdfview, - librecad, logcentral, logcentral-tools, metis-edf, openmeca, pycgns, - python3-escript | python3-escript-mpi, - python3-openturns, r-cran-spc, salome-gui, salome-jobmanager, @@ -559,6 +562,8 @@ libgetfem++-dev, libhdf5-serial-dev, libitpp-dev, + libjhdf4-java, + libjhdf5-java, liblxi-dev, libmadlib-dev, libmed-dev, @@ -569,11 +574,14 @@ libnlopt-dev, liboce-ocaf-dev, liboce-visualization-dev, + libopenturns-dev, libp4est-dev, libplb-dev, libsilo-dev, + libsis-jhdf5-java, libslicot-dev, libxdmf-dev, + python3-collada, python3-fluids, python3-netcdf4, python3-pygalmesh, @@ -591,13 +599,9 @@ libgismo-dev, libgtkdatabox-dev, libgtkdataboxmm-dev, - libjhdf4-java, - libjhdf5-java, libluminate-dev, libmetis-edf-dev, - libopenturns-dev, libqwt-dev | libqwt5-qt4-dev, - libsis-jhdf5-java, libslepc3.4.2-dev, libtet1.4-dev, libug-dev, @@ -659,11 +663,13 @@ grace, grass, grass-doc, + hyantesite, hydroffice.bag-tools, josm, mapnik-utils, mapserver-bin, ogdi-bin, + openscenegraph, osm2pgsql, osmpbf-bin, pgadmin3, @@ -690,10 +696,8 @@ gosmore, gpsdrive, gpx2shp, - hyantesite, libmseed-dev, openjump, - openscenegraph, python3-pyepsg, sumo Description: Debian Science Geography packages @@ -746,7 +750,9 @@ paw, paw++, pawserv, - sasview, + pythia8-root-interface, + rivet, + rivet-plugins, zftp Suggests: geant321-doc, geant4, @@ -799,9 +805,6 @@ libroot-tree5.34, octave-lhapdf, paw-demos, - pythia8-root-interface, - rivet, - rivet-plugins, rivet-root-converter, root-macro-fastjet, root-plugin-geom-gdml, @@ -862,12 +865,17 @@ libfastjet-fortran-dev, libfastjetplugins-dev, libfastjettools-dev, + libhepmc-dev, + libhepmcfio-dev, + libhepmcinterface8-dev, libooptools-dev, + libpythia8-dev, + librivet-dev, libsiscone-dev, libsiscone-spherical-dev, neuron-dev, python3-neuron, - python3-sasmodels + rivet-plugins-dev Suggests: ckon, clhep-doc, fastjet-doc, @@ -877,12 +885,7 @@ hepmc-user-manual, herwig++-dev, lhapdf-ccwrap-doc, - libhepmc-dev, - libhepmcfio-dev, - libhepmcinterface8-dev, liblhapdf-dev, - libpythia8-dev, - librivet-dev, libroot-bindings-python-dev, libroot-bindings-ruby-dev, libroot-core-dev, @@ -933,7 +936,6 @@ pythia8-doc-html, pythia8-doc-worksheet, pythia8-examples, - rivet-plugins-dev, rivet-plugins-doc, rivet-reference, rivet-user-manual, @@ -957,10 +959,10 @@ science-config (= ${source:Version}), science-tasks (= ${source:Version}) Recommends: gwyddion, - limereg + limereg, + teem-apps Suggests: gpiv, - gpivtools, - teem-apps + gpivtools Description: Debian Science image analysis packages This metapackage will install Debian Science packages related to scientific image acquisition. This might be used in several @@ -978,13 +980,13 @@ liblimereg-dev, libsimage-dev, libvigraimpex-dev, + libvlfeat-dev, python3-imageio, python3-meshio Suggests: lib3ds-dev, libcv-dev, libfreeimage-dev, - libvisad-java, - libvlfeat-dev + libvisad-java Description: Debian Science development of image analysis applications This metapackage will install Debian Science development libraries to develop scientific image analysis applications acquisitions. @@ -1106,6 +1108,7 @@ python3-nltk, python3-snowballstemmer, python3-streamparser, + python3-timbl, r-cran-nlp, r-cran-tm, sequitur-g2p, @@ -1136,13 +1139,14 @@ hol88, lbt, maria, + matita, maude, minisat+, mona, picosat, proofgeneral, - prover9, sat4j, + spass, toulbar2, why3, z3 @@ -1150,8 +1154,7 @@ coinor-libcoinmp-dev, cvc3, mace2, - matita, - spass, + prover9, why Description: Debian Science Logic packages This metapackage is part of the Debian Pure Blend "Debian Science" @@ -1176,6 +1179,8 @@ libvigraimpex-dev, mcl, octave-ga, + python3-genetic, + python3-mdp, python3-opencv, python3-sklearn, python3-statsmodels, @@ -1189,7 +1194,10 @@ r-cran-mnp, r-cran-msm, r-cran-tgp, - weka + scilab-ann, + vowpal-wabbit, + weka, + yap Suggests: flann, libacovea-dev, libcomplearn-dev, @@ -1211,15 +1219,11 @@ lua-torch-xlua, pgapack, pybrain, - python3-mdp, root-system, science-numericalcomputation, science-statistics, science-typesetting, - scilab-ann, - torch-core-free, - vowpal-wabbit, - yap + torch-core-free Description: Debian Science Machine Learning packages This metapackage will install packages useful for machine learning. Included packages range from knowledge-based (expert) inference @@ -1241,6 +1245,7 @@ coinor-cbc, coinor-symphony, coq, + cryptominisat, eclib-tools, fenics, flintqs, @@ -1265,6 +1270,7 @@ geogebra, geomview, gerris, + getdp, gfan, ginac-tools, gmsh, @@ -1277,10 +1283,13 @@ lrcalc, lrslib, magnus, + mathicgb, mathomatic, + matita, maxima-sage, mcl, minisat, + model-builder, mumps-test, nauty, netgen, @@ -1291,11 +1300,11 @@ planarity, polylib-utils, proofgeneral, - prover9, python3-deap, python3-dolfin, python3-ffc, python3-minieigen, + python3-openturns, python3-sagenb-export, python3-ufl, qhull-bin, @@ -1303,6 +1312,7 @@ regina-normal, rheolef, rubiks, + sagemath, sagemath-database-conway-polynomials, sagemath-database-elliptic-curves, sagemath-database-graphs, @@ -1310,9 +1320,9 @@ sagemath-database-polytopes, science-statistics, scilab, + scilab-ann, scotch, singular, - snappea, surf-alggeo, sympow, tachyon, @@ -1320,10 +1330,10 @@ toulbar2, wxmaxima, xcas, - xmaxima + xmaxima, + xmds2 Suggests: ann-tools, cliquer, - cryptominisat, eprover, evolver-ogl | evolver-nox, feel++-apps, @@ -1337,27 +1347,22 @@ gap-small-groups, gap-small-groups-extra, gap-trans-groups, - getdp, gmp-ecm, isabelle, kseg, - mathicgb, - matita, matlab-support, netgen-doc, octaviz, pari-extra, primesieve, proofgeneral-coq, + prover9, pyomo, - python3-openturns, r-cran-evd, - sagemath, sagetex, - scilab-ann, scilab-scimax, - xmds, - xmds2 + snappea, + xmds Description: Debian Science Mathematics packages This metapackage will install Debian Science packages related to Mathematics. You might also be interested in the field::mathematics @@ -1437,6 +1442,7 @@ libmadlib-dev, libmatheval-dev, libmathic-dev, + libmathicgb-dev, libmatio-dev, libmpfi-dev, libmpfrc++-dev, @@ -1446,6 +1452,7 @@ libnfft3-dev, libnglib-dev, libopenblas-dev, + libopenturns-dev, libp4est-dev, libparsington-java, libplb-dev, @@ -1471,12 +1478,14 @@ libtachyon-dev, libtnt-dev, libviennacl-dev, + libxsmm-dev, libzn-poly-dev, minpack-dev, petsc-dev, python3-asteval, python3-brial, python3-bumps, + python3-cryptominisat, python3-cvxopt, python3-cypari2, python3-dolfin, @@ -1487,6 +1496,7 @@ python3-ltfatpy, python3-numexpr, python3-numpy, + python3-openturns, python3-optlang, python3-petsc4py, python3-pynfft, @@ -1516,12 +1526,10 @@ libjlapack-java, liblevmar-dev, liblrs-dev, - libmathicgb-dev, libmkl-full-dev, libmtj-java, libnetlib-java, libntl-dev, - libopenturns-dev, libparmetis-dev, libqrupdate-dev, libsollya-dev, @@ -1531,12 +1539,9 @@ libtet1.4.2-dev, libtrilinos-dev, libug-dev, - libxsmm-dev, openturns-examples, - python3-cryptominisat, python3-linop, python3-msgpack-numpy, - python3-openturns, python3-pyviennacl, sollya Description: Debian Science Mathematics-dev packages @@ -1556,12 +1561,14 @@ cmor-tables, coda, cylc, + dballe, ecaccess, fcm, ferret-vis, flexpart, flextra, grads, + gwyddion, libdap-bin, libdap-doc, libeccodes-tools, @@ -1582,16 +1589,16 @@ python3-iapws, python3-metaconfig, python3-netcdf4, - python3-sphere -Suggests: dballe, - geonetwork, + python3-sphere, + sasview, + vistrails +Suggests: geonetwork, gerris, gnudatalanguage, octave-octcdf, paraview, python3-openturns, r-base, - vistrails, zygrib Description: Debian Science Meteorology packages This metapackage is part of the Debian Pure Blend "Debian Science" @@ -1628,7 +1635,9 @@ libncarg-bin, libnetcdf-dev, liboasis3-dev, + libopenturns-dev, libproj-dev, + librsl-dev, libsphere-dev, libterralib-dev, libudunits2-dev, @@ -1636,6 +1645,8 @@ netcdf-bin, python3-coda, python3-gpyfft, + python3-openturns, + python3-sasmodels, python3-ulmo, r-cran-rnetcdf, sfftw-dev, @@ -1646,13 +1657,10 @@ libcblas-dev, libfeel++-dev, liblas-dev, - libopenturns-dev, - librsl-dev, mpi-defaults-dev, openturns-examples, pkg-config, python3-coards, - python3-openturns, udunits-bin Description: Debian Science Meteorology-dev packages This metapackage will install Debian Science packages which might be @@ -1668,6 +1676,7 @@ science-tasks (= ${source:Version}) Recommends: abinit, ase, + avogadro, binoculars, cadabra, cbflib-bin, @@ -1705,12 +1714,13 @@ python3-sympy, pyxplot, quantum-espresso, + sasview, science-numericalcomputation, scilab, - udav + udav, + v-sim Suggests: ape, atompaw, - avogadro, axiom, bigdft, dx, @@ -1724,8 +1734,6 @@ gpivtools, hdf5-helpers, hdf5-tools, - horae, - ifeffit, libgraphviz-perl, libgsl0ldbl, liblevmar-2-6, @@ -1740,8 +1748,6 @@ scidavis, science-mathematics, science-statistics, - sixpack, - v-sim, wannier90-1, wannier90-2 Description: Debian Science Nanoscale Physics packages @@ -1789,6 +1795,7 @@ liboce-visualization-dev, libopenmpi-dev | libmpich-dev, libscalapack-mpi-dev, + libsis-jhdf5-java, libssm-dev, libsymspg-dev, libxc-dev, @@ -1799,6 +1806,7 @@ python3-gpyfft, python3-periodictable, python3-pycodcif, + python3-sasmodels, r-cran-rnetcdf, scalapack-doc, science-mathematics-dev @@ -1812,7 +1820,6 @@ libroot-math-mlp-dev, libroot-montecarlo-vmc-dev, libroot-tmva-dev, - libsis-jhdf5-java, oce-draw, python3-h5py, python3-netcdf4, @@ -1899,6 +1906,7 @@ moose, nest, pcsim, + python3-brian, xppaut Description: Debian Science packages for modeling of neural systems This metapackage will install Debian packages which might be useful for @@ -1919,6 +1927,7 @@ science-config (= ${source:Version}), science-tasks (= ${source:Version}) Recommends: admesh, + algotutor, calculix-ccx, calculix-cgx, coinor-cbc, @@ -1929,7 +1938,9 @@ iep, ipython, julia, + lammps, libadolc-dev, + libarrayfire-unified-dev, libceres-dev, libclblas-dev, libclfft-dev, @@ -1944,12 +1955,17 @@ octave, pdl, psurface, + python3-arrayfire, python3-bitstring, python3-deap, + python3-escript | python3-escript-mpi, + python3-guiqwt, python3-lmfit, python3-matplotlib, python3-numpy, + python3-pysph, python3-scipy, + python3-sfepy, python3-sparse, python3-tables, python3-theano, @@ -1959,13 +1975,13 @@ r-base, r-cran-nleqslv, scilab, + scilab-ann, spyder, toulbar2, vitables, yade, yorick -Suggests: algotutor, - calculix-ccx-doc, +Suggests: calculix-ccx-doc, calculix-ccx-test, calculix-cgx-examples, ceres-solver-doc, @@ -1975,8 +1991,6 @@ freemat, geneva, hpcc, - lammps, - libarrayfire-unified-dev, libcblas-dev, libclsparse-dev, libcneartree-dev, @@ -1993,20 +2007,17 @@ python3-agatedbf, python3-agateexcel, python3-agatesql, - python3-arrayfire, python3-bcolz, python3-dbfread, - python3-escript | python3-escript-mpi, - python3-guiqwt, python3-leather, + python3-numcodecs, python3-pydap, - python3-pysph, python3-spyder-line-profiler, python3-spyder-memory-profiler, python3-spyder-reports, python3-spyder-unittest, python3-woo, - scilab-ann, + python3-zarr, scilab-jims, scilab-metanet, scilab-scimax, @@ -2042,6 +2053,7 @@ gpaw, gwyddion, maxima, + meshlab, oce-draw, openfoam, opticalraytracer, @@ -2054,7 +2066,8 @@ quantum-espresso, science-electronics, science-numericalcomputation, - toulbar2 + toulbar2, + v-sim Suggests: blzpack, clhep, espresso++, @@ -2065,23 +2078,18 @@ geant4, gpiv, gpivtools, - horae, - ifeffit, jfreemesh, libroot-math-mlp-dev, libroot-montecarlo-vmc-dev, libroot-tmva-dev, - meshlab, octaviz, openctm-tools, paw-demos, root-system, science-mathematics, science-statistics, - sixpack, spis, - tessa | tessa-mpi, - v-sim + tessa | tessa-mpi Description: Debian Science Physics packages This metapackage will install Debian Science packages related to Physics. You might also be interested in the debtag field::physics and, depending on @@ -2144,9 +2152,9 @@ Depends: ${misc:Depends}, science-config (= ${source:Version}), science-tasks (= ${source:Version}) -Recommends: octave-psychtoolbox-3 -Suggests: psychopy, - science-neuroscience-cognitive, +Recommends: octave-psychtoolbox-3, + psychopy +Suggests: science-neuroscience-cognitive, visionegg Description: Debian Science packages for Psychophysics This metapackage will install Debian packages which might be useful for @@ -2227,6 +2235,7 @@ libignition-math4-dev, libignition-msgs-dev, libignition-transport-dev, + libkido-dev, liboctomap-dev, libode-dev, libompl-dev, @@ -2251,7 +2260,6 @@ ros-simulators-dev Suggests: libcnoid-dev, libcv-dev, - libkido-dev, libroboptim-core-dev, libsdformat6-dev, visp-images-data @@ -2270,8 +2278,9 @@ calculix-cgx, esys-particle, gazebo9, + getdp, + lammps, libceres-dev, - libkim-api-v2-models, liggghts, music-bin, neuron, @@ -2279,21 +2288,21 @@ occt-misc, openfoam, python3-deap, + python3-escript | python3-escript-mpi, + python3-pysph, + python3-sfepy, + sumo, yade Suggests: calculix-ccx-doc, calculix-ccx-test, calculix-cgx-examples, ceres-solver-doc, fdmnes, - getdp, - lammps, libgismo-dev, + libkim-api-v2-models, libopensurgsim-dev, - python3-escript | python3-escript-mpi, - python3-pysph, python3-woo, - radiance, - sumo + radiance Description: Debian Science Simulation packages This metapackage will install Debian Science packages that are used to do simulations in different fields of science. @@ -2309,7 +2318,9 @@ elpa-ess, littler, psignifit, + pspp, python3-bayespy, + python3-openturns, python3-pandas, python3-scipy, python3-statsmodels, @@ -2447,8 +2458,6 @@ Suggests: libapophenia2-dev, libtamuanova-dev, node-shiny-server-client, - pspp, - python3-openturns, r-cran-bbmle, r-cran-blockmodeling, r-cran-brglm, @@ -2491,7 +2500,6 @@ science-config (= ${source:Version}), science-tasks (= ${source:Version}) Recommends: biber, - bibus, bibutils, cb2bib, dia, @@ -2513,6 +2521,7 @@ python3-pybtex-docutils, python3-sphinxcontrib.bibtex, r-cran-knitr, + sagetex, sketch, texlive, texlive-bibtex-extra, @@ -2521,7 +2530,8 @@ texmaker | kile | lyx | auctex | vim-latexsuite | texstudio, transfig, xfig -Suggests: csv2latex, +Suggests: bibus, + csv2latex, gpapers, libgtkmathview-bin, libqtexengine-dev, @@ -2536,7 +2546,6 @@ r-cran-shape, r-cran-xtable, referencer, - sagetex, svgtoipe, tellico, texlive-math-extra, @@ -2562,11 +2571,13 @@ geg, gfsview, giza-dev, + gle-graphics, gmsh, gnudatalanguage, gnuplot, grace, graphviz, + gri, gwyddion, imview, kst, @@ -2575,9 +2586,11 @@ mathgl, matlab2tikz, mayavi2, + paraview, pdl, plotdrop, python3-gnuplot, + python3-guiqwt, python3-pyqtgraph, python3-seaborn, pyxplot, @@ -2586,13 +2599,12 @@ trend, udav, veusz, + vistrails, yorick Suggests: cassandra, circos, circos-tools, findimagedupes, - gle-graphics, - gri, ifrit, jeuclid-mathviewer, libcoin-dev, @@ -2609,10 +2621,8 @@ lybniz, med-imaging, ovito, - paraview, pgfplots, pgplot5, - python3-guiqwt, python3-matplotlib, python3-pivy, python3-vtk7, @@ -2632,7 +2642,6 @@ tcl-vtk7, texlive-pictures, visit, - vistrails, vtk7-examples, worldwind Description: Debian Science data visualisation packages @@ -2653,6 +2662,7 @@ libforge-dev, libgl2ps-dev, libglbinding-dev, + libgli-dev, libglm-dev, libglobjects-dev, libgnuplot-iostream-dev, @@ -2675,6 +2685,7 @@ python3-matplotlib-venn, python3-pivy, python3-plplot-qt, + python3-qwt, python3-qwt3d-qt5, python3-skimage, python3-skimage-lib, @@ -2683,11 +2694,9 @@ tcl-vtk7, vtk7-examples Suggests: libcollada-dom2.4-dp-dev, - libgli-dev, libgtkdataboxmm-dev, libqglviewer-dev, - libqtexengine-dev, - python3-qwt + libqtexengine-dev Description: Debian Science development of visualisation applications This metapackage will install Debian Science packages related to the development of applications to visualise scientific data. @@ -2703,10 +2712,10 @@ gearman, gearman-tools, make, - pegasus-wms, snakemake, toil -Suggests: libbenchmark-tools +Suggests: libbenchmark-tools, + pegasus-wms Description: workflow management systems useful for scientific research This task lists some packages providing workflow management systems useful for scientific research. diff -Nru debian-science-1.11ubuntu1/debian/control.stub debian-science-1.12ubuntu1/debian/control.stub --- debian-science-1.11ubuntu1/debian/control.stub 2019-10-01 15:50:42.000000000 +0000 +++ debian-science-1.12ubuntu1/debian/control.stub 2020-01-20 21:44:03.000000000 +0000 @@ -6,7 +6,7 @@ Ole Streicher Build-Depends-Indep: blends-dev (>= 0.7~), debhelper (>= 12~) -Standards-Version: 4.3.0 +Standards-Version: 4.4.0 Vcs-Browser: https://salsa.debian.org/blends-team/science Vcs-Git: https://salsa.debian.org/blends-team/science.git Homepage: https://wiki.debian.org/DebianScience/ diff -Nru debian-science-1.11ubuntu1/dependency_data/debian-science_1.12.json debian-science-1.12ubuntu1/dependency_data/debian-science_1.12.json --- debian-science-1.11ubuntu1/dependency_data/debian-science_1.12.json 1970-01-01 00:00:00.000000000 +0000 +++ debian-science-1.12ubuntu1/dependency_data/debian-science_1.12.json 2020-01-20 13:59:36.000000000 +0000 @@ -0,0 +1 @@ +{"devices": {"depends": [], "suggests": ["libticables-dev", "libticalcs-dev", "libticonv-dev", "libtifiles-dev"], "recommends": ["expeyes", "gfm", "tiemu", "tilem", "tilp2", "bossa", "bossa-cli"], "ignore": [], "avoid": []}, "social": {"depends": [], "suggests": [], "recommends": ["opensesame"], "ignore": [], "avoid": []}, "robotics": {"depends": [], "suggests": ["arduino-mk", "ompl-demos", "libcoin-runtime", "vtk7", "octave", "gnuplot"], "recommends": ["rtai", "xenomai-runtime", "morse-simulator", "choreonoid", "liburdfdom-tools", "solid", "robot-player", "d-collide", "rtnet", "orca", "roboop", "orocos-rtt", "orocos-kdl", "orocos-ocl", "orocos-bfl", "ros-desktop-full", "ros-desktop", "ros-perception", "ros-simulators", "ros-robot", "ros-robot-state-publisher", "ros-opencv-apps", "openrtm", "openhrp", "pcl", "gazebo9", "openrave", "octomap-tools", "octovis", "aseba"], "ignore": [], "avoid": []}, "bci": {"depends": [], "suggests": ["pyff", "pybci", "bcpy2000", "bci2000", "emokit", "openvibe"], "recommends": [], "ignore": [], "avoid": []}, "simulations": {"depends": [], "suggests": ["calculix-ccx-doc", "calculix-ccx-test", "calculix-cgx-examples", "libopensurgsim-dev", "ceres-solver-doc", "libgismo-dev"], "recommends": ["sumo", "esys-particle", "lammps", "liggghts", "yade", "python3-deap", "openfoam", "getdp", "fdmnes", "radiance", "music-bin", "calculix-ccx", "calculix-cgx", "neuron", "python3-sfepy", "python3-pysph", "python3-woo", "libceres-dev", "gazebo9", "python3-escript | python3-escript-mpi", "libkim-api-v2-models", "occt-draw", "occt-misc"], "ignore": [], "avoid": []}, "distributedcomputing": {"depends": [], "suggests": ["hpcc", "coop-computing-tools", "python3-mpi4py", "psom", "octave-mpi"], "recommends": ["ipython3", "nordugrid-arc-nox", "gridengine-client", "gridengine-exec", "gridengine-master", "gridengine-qmon", "globus-core", "openmpi-bin", "mpich", "openmpipython", "mpich2python", "htcondor", "dmtcp", "environment-modules", "python3-scoop"], "ignore": [], "avoid": []}, "chemistry": {"depends": [], "suggests": ["gdpc-examples", "python-pymzml-doc", "python3-periodictable", "libschroedinger-coordgenlibs-dev"], "recommends": ["apbs", "bkchem", "bodr", "libcdk-java", "chemeq", "chemical-mime-data", "chemtool", "easychem", "gabedit", "galculator", "garlic", "gausssum", "gchempaint", "gdis", "ghemical", "gcrystal", "gcu-bin", "gcu-plugin", "gperiodic", "gromacs | gromacs-mpich | gromacs-openmpi", "kalzium", "katomic", "mopac7-bin", "mpqc", "mpqc-support", "openbabel", "psi3", "pymol", "viewmol", "xdrawchem", "xmakemol-gl | xmakemol", "v-sim", "rasmol", "adun.app", "gdpc", "xbs", "gelemental", "avogadro", "gamgi", "msxpertsuite", "drawxtl", "chemical-structures", "openfoam", "pyfai", "libegad", "libint", "molden", "molekel", "tinker", "jmol", "qutemol", "cp2k", "pdb2pqr", "mmass", "mmass-modules", "python3-pymzml", "tandem-mass", "openchrom", "fdmnes"], "ignore": [], "avoid": []}, "mathematics": {"depends": [], "suggests": ["gap-online-help", "gap-gapdoc", "gap-io", "gap-scscp", "netgen-doc", "r-cran-evd", "sagetex", "matlab-support", "ann-tools", "gmp-ecm", "primesieve", "evolver-ogl | evolver-nox"], "recommends": ["axiom", "ginac-tools", "xmaxima", "wxmaxima", "pari-gp", "pari-extra", "gap", "magnus", "gap-small-groups-extra", "gap-trans-groups", "gap-prim-groups", "gap-small-groups", "gap-table-of-marks", "gap-guava", "gap-character-tables", "gap-float", "gap-design", "gap-factint", "gap-laguna", "gap-sonata", "gap-toric", "gap-openmath", "gap-grape", "gerris", "freefem", "freefem3d", "freefem++", "netgen", "gmsh", "getdp", "coq", "proofgeneral", "proofgeneral-coq", "matita", "agda", "prover9", "hol-light", "minisat", "science-statistics", "geomview", "octave", "xmds", "xmds2", "freemat", "mathomatic", "scilab", "scilab-scimax", "scilab-ann", "regina-normal", "snappea", "lp-solve", "qsopt-ex", "libmatheval1", "mumps-test", "nauty", "geogebra", "lrslib", "fenics", "python3-dolfin", "python3-ffc", "python3-ufl", "kseg", "polylib-utils", "rheolef", "scotch", "isabelle", "bliss", "python3-openturns", "python3-deap", "mcl", "sagemath", "maxima-sage", "sagemath-database-conway-polynomials", "sagemath-database-elliptic-curves", "sagemath-database-graphs", "sagemath-database-mutually-combinatorial-designs", "sagemath-database-polytopes", "python3-sagenb-export", "eclib-tools", "gfan", "lcalc", "fplll-tools", "lrcalc", "palp", "sympow", "tachyon", "4ti2", "normaliz", "surf-alggeo", "graphviz", "singular", "julia", "qhull-bin", "mathicgb", "frobby", "geneagrapher", "planarity", "flintqs", "rubiks", "octaviz", "eprover", "python3-minieigen", "coinor-symphony", "coinor-cbc", "tetgen", "feel++-apps", "auto-07p", "toulbar2", "cohomcalg", "cryptominisat", "form", "xcas", "pyomo", "model-builder"], "ignore": [], "avoid": []}, "engineering": {"depends": [], "suggests": ["r-cran-spc", "logcentral", "logcentral-tools", "ann-tools", "salome-kernel", "calculix-ccx-doc", "calculix-ccx-test", "calculix-cgx-examples"], "recommends": ["librecad", "sailcut", "oce-draw", "python3-silo", "libsilo-bin", "gerris", "gmsh", "getdp", "netgen", "z88", "freecad", "feel++-apps", "python3-openturns", "code-aster-gui", "code-aster", "metis-edf", "eficas", "code-saturne", "ecs", "hdfview", "sfc", "cba", "fenics", "python3-dolfin", "python3-fiat", "syrthes", "openfoam", "brlcad", "diet-agent", "tetgen", "dime", "avl", "cgns-convert", "pycgns", "varkon", "tochnog", "salome-gui", "salome-jobmanager", "salome-med", "salome-paravis", "salome-smesh", "salome-yacs", "libadios-bin", "calculix-ccx", "calculix-cgx", "scram", "python3-escript | python3-escript-mpi", "solvespace", "openmeca", "python3-admesh", "lxi-tools"], "ignore": [], "avoid": []}, "nanoscale-physics-dev": {"depends": [], "suggests": ["libcblas-dev", "libfftw3-doc", "libfeel++-dev", "oce-draw", "python3-netcdf4", "python3-h5py"], "recommends": ["abinit-doc", "libblas-dev", "liblapack-dev", "liblapack-doc", "libetsf-io-dev", "libetsf-io-doc", "libfftw3-dev", "python3-gpyfft", "libgsl0-dev", "gsl-bin", "gsl-doc-info", "gsl-ref-html | gsl-ref-psdoc", "libnetcdf-dev", "netcdf-doc", "r-cran-rnetcdf", "libhdf5-dev", "libsis-jhdf5-java", "libxc-dev", "libopenmpi-dev | libmpich-dev", "wannier90-1-dev", "gsl-doc-pdf", "libscalapack-mpi-dev", "scalapack-doc", "science-mathematics-dev", "liboce-visualization-dev", "liboce-ocaf-dev", "libpspio-dev", "libsymspg-dev", "root-system", "libroot-tmva-dev", "libroot-montecarlo-vmc-dev", "libroot-math-mlp-dev", "python3-fabio", "libcbf-dev", "pyfai", "libssm-dev", "libclipper-dev", "python3-binoculars", "python3-pycodcif", "libcod-precision-perl", "libcexceptions-dev", "libccp4-dev", "python3-periodictable", "libxc-dev", "python3-sasmodels"], "ignore": [], "avoid": []}, "physics": {"depends": [], "suggests": ["paw-demos", "science-statistics", "science-mathematics", "openctm-tools", "feel++-apps", "evolver-ogl | evolver-nox"], "recommends": ["cernlib", "geant321", "paw++", "paw", "gpaw", "clhep", "geant4", "abinit | mpqc | openmx | psi3", "gerris", "feynmf", "openfoam", "fityk", "tessa | tessa-mpi", "science-numericalcomputation", "oce-draw", "science-electronics", "v-sim", "gpiv", "gpivtools", "maxima", "python3-sympy", "axiom", "meshlab", "cadabra", "drawxtl", "opticalraytracer", "ghkl", "python3-deap", "etsf-io", "pymca", "quantum-espresso", "gwyddion", "blzpack", "gate", "jfreemesh", "spis", "espresso++", "cp2k", "octaviz", "root-system", "libroot-tmva-dev", "libroot-montecarlo-vmc-dev", "libroot-math-mlp-dev", "fdmnes", "pyfr", "toulbar2"], "ignore": [], "avoid": []}, "neuroscience-datasets": {"depends": [], "suggests": [], "recommends": ["mni-icbm152-nlin-2009", "mni-colin27-nifti", "haxby2001-faceobject", "fsl-harvard-oxford-atlases", "fsl-juelich-histological-atlas", "fsl-jhu-dti-whitematter-atlas", "fsl-mni-structural-atlas", "fsl-talairach-daemon-atlas", "fsl-oxford-thalamic-connectivity-atlas", "fsl-bangor-cerebellar-atlas", "mclaren-rhesus-macaque-atlas", "sri24-atlas"], "ignore": [], "avoid": []}, "linguistics": {"depends": [], "suggests": ["libticcutils2-dev", "frogdata", "libtimbl3-dev", "libtimbl4-dev", "libtimblserver2-dev", "libmbt0-dev", "libucto1-dev", "libfolia-dev", "wnsqlbuilder", "python3-nltk", "apertium-af-nl", "apertium-apy", "apertium-arg", "apertium-arg-cat", "apertium-bel", "apertium-bel-rus", "apertium-br-fr", "apertium-ca-it", "apertium-cat", "apertium-cat-srd", "apertium-crh", "apertium-crh-tur", "apertium-cy-en", "apertium-dan", "apertium-dan-nor", "apertium-en-ca", "apertium-en-es", "apertium-en-gl", "apertium-eo-ca", "apertium-eo-en", "apertium-eo-es", "apertium-eo-fr", "apertium-es-ast", "apertium-es-ca", "apertium-es-gl", "apertium-es-it", "apertium-es-pt", "apertium-es-ro", "apertium-eu-en", "apertium-eu-es", "apertium-fra", "apertium-fra-cat", "apertium-fr-ca", "apertium-fr-es", "apertium-hbs", "apertium-hbs-eng", "apertium-hbs-mkd", "apertium-hbs-slv", "apertium-hin", "apertium-id-ms", "apertium-isl", "apertium-isl-eng", "apertium-is-sv", "apertium-ita", "apertium-kaz", "apertium-kaz-tat", "apertium-mk-bg", "apertium-mk-en", "apertium-mlt-ara", "apertium-nno", "apertium-nno-nob", "apertium-nob", "apertium-oc-ca", "apertium-oc-es", "apertium-oci", "apertium-pol", "apertium-pt-ca", "apertium-pt-gl", "apertium-rus", "apertium-separable", "apertium-sme-nob", "apertium-spa", "apertium-spa-arg", "apertium-srd", "apertium-srd-ita", "apertium-swe", "apertium-swe-dan", "apertium-swe-nor", "apertium-szl", "apertium-tat", "apertium-tur", "apertium-ukr", "apertium-urd", "apertium-urd-hin", "python3-streamparser", "libcg3-dev", "r-cran-nlp", "r-cran-tm", "python3-snowballstemmer"], "recommends": ["wordnet", "apertium", "apertium-lex-tools", "link-grammar", "artha", "sequitur-g2p", "timbl", "timblserver", "mbt", "mbtserver", "ucto", "dimbl", "frog", "collatinus", "python3-timbl", "travatar", "cg3", "libcld2-dev", "python3-pynlpl", "uctodata", "giella-sme", "hfst", "hfst-ospell", "lttoolbox", "r-cran-snowballc", "r-cran-lexrankr", "spacy", "python3-thinc", "irstlm"], "ignore": [], "avoid": []}, "logic": {"depends": [], "suggests": ["coinor-libcoinmp-dev"], "recommends": ["agda", "coq", "hol-light", "hol88", "matita", "proofgeneral", "why", "why3", "depqbf", "picosat", "sat4j", "alt-ergo", "boolector", "cvc3", "cvc4", "z3", "prover9", "mace2", "maude", "spass", "coinor-cbc", "coinor-symphony", "minisat+", "clasp", "coala", "gringo", "lbt", "maria", "mona", "toulbar2"], "ignore": [], "avoid": []}, "engineering-dev": {"depends": [], "suggests": ["libgtkdatabox-dev", "libgtkdataboxmm-dev", "libqwt-dev | libqwt5-qt4-dev", "openturns-examples", "libdiet-sed2.8-dev", "libdiet-client2.8-dev", "libdiet-dagda2.8-dev", "libdiet-admin2.8-dev", "ceres-solver-doc"], "recommends": ["libalberta-dev", "code-saturne-bin", "code-saturne-include", "libcgns-dev", "libitpp-dev", "libadios-dev", "libbox-dev", "libsilo-dev", "libxdmf-dev", "libgetfem++-dev", "libhdf5-serial-dev", "libjhdf5-java", "libjhdf4-java", "libsis-jhdf5-java", "pycgns", "liboce-visualization-dev", "liboce-ocaf-dev", "libdeal.ii-dev", "libfeel++-dev", "libluminate-dev", "libopenturns-dev", "libmadlib-dev", "libtet1.4-dev", "libslepc3.4.2-dev", "libelmer-dev", "libug-dev", "libmed-dev", "libmedc-dev", "libmedimport-dev", "libnetcdf-dev", "python3-netcdf4", "r-cran-rnetcdf", "libnfft3-dev", "libnlopt-dev", "libcoin-dev", "libmetis-edf-dev", "libslicot-dev", "python3-collada", "libann-dev", "libflann-dev", "libdime-dev", "libdxflib-dev", "salome-kernel-dev", "python3-pynfft", "libplb-dev", "libceres-dev", "trilinos-all-dev", "libdeal.ii-dev", "libp4est-dev", "libgismo-dev", "python3-pygalmesh", "python3-fluids", "liblxi-dev"], "ignore": [], "avoid": []}, "viewing": {"depends": [], "suggests": ["libgrits-dev", "worldwind", "med-imaging", "libgtkmathview-bin", "jeuclid-mathviewer", "texlive-pictures", "pgplot5", "r-cran-plotrix", "r-cran-colorspace", "r-cran-labeling", "r-cran-scales", "r-cran-ggplot2", "r-cran-scatterplot3d", "r-cran-vioplot", "r-cran-shape", "r-cran-qqman", "r-cran-aplpack", "r-cran-aplpack", "findimagedupes", "libpuzzle-bin", "python3-matplotlib", "circos", "circos-tools", "libqglviewer-dev", "libcoin-dev", "libsoqt520-dev", "libvtk7-dev", "libvtk7-qt-dev", "tcl-vtk7", "python3-vtk7", "libvtk7-java", "vtk7-examples", "python3-pivy", "libgts-bin"], "recommends": ["vistrails", "pdl", "gnudatalanguage", "kst", "ifrit", "yorick", "fityk", "gnuplot", "grace", "gri", "labplot", "graphviz", "pyxplot", "plotdrop", "qtiplot", "python3-guiqwt", "imview", "mayavi2", "g3data", "gwyddion", "paraview", "visit", "gle-graphics", "gmsh", "giza-dev", "lybniz", "3depict", "mathgl", "udav", "matlab2tikz", "cassandra", "pgfplots", "feedgnuplot", "libgnuplot-iostream-dev", "libqglviewer2", "python3-gnuplot", "ovito", "scidavis", "veusz", "ctioga2", "python3-seaborn", "trend", "python3-pyqtgraph", "rlplot", "solvespace", "gfsview", "r-cran-sjplot", "geg"], "ignore": [], "avoid": []}, "dataacquisition": {"depends": [], "suggests": ["gnudatalanguage", "comedi-source", "rtai", "xenomai-runtime", "linux-image-2.6-rt", "rt-tests", "gpsd", "binoculars", "tango-db", "tango-starter", "tango-accesscontrol", "python3-pytango", "python3-taurus", "hart"], "recommends": ["engauge-digitizer", "qtdmm", "g3data", "ktimetrace", "netcdf-bin", "libgetdata-tools", "jaaa", "ghkl", "narval-utils", "xyscan", "filo", "segyio-bin", "clickhouse-tools", "csvkit", "lxi-tools", "xlsx2csv", "python3-pyvisa", "mx-dataacquisition", "epics", "plot-digitizer", "libfreenect-dev", "opendap"], "ignore": [], "avoid": []}, "viewing-dev": {"depends": [], "suggests": ["libcollada-dom2.4-dp-dev"], "recommends": ["pdl", "gnudatalanguage", "libgrits-dev", "python3-matplotlib", "libgnuplot-iostream-dev", "libqglviewer-dev", "python3-gnuplot", "python3-gnuplotlib", "libcoin-dev", "libsoqt520-dev", "libvtk7-qt-dev", "libvtk7-dev", "tcl-vtk7", "python3-vtk7", "libvtk7-java", "vtk7-examples", "python3-pivy", "libgtkdataboxmm-dev", "libgtkdatabox-dev", "inventor-dev", "libqtexengine-dev", "libqwtplot3d-qt5-dev", "python3-qwt3d-qt5", "python3-qwt", "libchealpix-dev", "python3-skimage", "python3-skimage-lib", "python3-matplotlib-venn", "libplplot-dev", "python3-plplot-qt", "libglm-dev", "libglbinding-dev", "libforge-dev", "libgli-dev", "libglobjects-dev", "libslvs1-dev", "libgts-dev", "python3-vispy", "libgl2ps-dev", "libqglviewer-dev-qt5", "python3-qwt", "liborigin2-dev"], "ignore": [], "avoid": []}, "highenergy-physics": {"depends": [], "suggests": ["paw-demos", "geant321-doc", "lhapdf-pdfsets-minimal", "root-system-doc"], 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"libroot-proof-clarens-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", "libroot-math-matrix-dev", "libroot-math-minuit-dev", "libroot-math-mlp-dev", "libroot-math-physics-dev", "libroot-math-quadp-dev", "libroot-math-smatrix-dev", "libroot-math-splot-dev", "libroot-misc-minicern-dev", "libroot-montecarlo-eg-dev", "libroot-montecarlo-vmc-dev", "libroot-net-dev", "libroot-net-auth-dev", "libroot-proof-dev", "libroot-proof-proofplayer-dev", "libroot-tmva-dev", "libroot-tree-dev", "libroot-tree-treeplayer-dev", "libroot-core-dev", "libroot-static", "librivet-dev", "rivet-plugins-dev", "libthepeg-dev", "herwig++-dev", "neuron-dev", "python3-neuron"], "ignore": [], "avoid": []}, "statistics": {"depends": [], "suggests": ["r-cran-spc", "r-cran-mlmrev", "r-cran-gnm", "r-cran-brglm", "science-mathematics", "libtamuanova-dev", "r-cran-blockmodeling", "r-cran-catools", "r-cran-fastmatch", "r-cran-futile.logger", "r-cran-futile.options", "r-cran-igraph", "r-cran-lambda.r", "r-cran-magrittr", "r-cran-nnls", "r-cran-r.oo", "r-cran-r.utils", "libapophenia2-dev", "r-cran-bbmle", "r-cran-ellipse", "r-cran-irlba", "r-cran-luminescence", "r-cran-minpack.lm", "r-cran-princurve", "r-cran-rngtools", "node-shiny-server-client"], "recommends": ["elpa-ess", "littler", "r-recommended", "rkward", "r-cran-mapproj", "r-cran-abind", "r-cran-arm", "r-cran-bayesm", "r-cran-boot", "r-cran-cairodevice", "r-cran-ca", "r-cran-car", "r-cran-caret", "r-cran-chron", "r-cran-cluster", "r-cran-coda", "r-cran-codetools", "r-cran-date", "r-cran-dbi", "r-cran-eco", "r-cran-effects", "r-cran-erm", "r-cran-fbasics", "r-cran-fcopulae", "r-cran-fecofin", "r-cran-fextremes", "r-cran-fmultivar", "r-cran-foptions", "r-cran-foreign", "r-cran-fportfolio", "r-cran-gam", "r-cran-gdata", "r-cran-geepack", "r-cran-glmnet", "r-cran-gmodels", "r-cran-goftest", "r-cran-gplots", "r-cran-gregmisc", "r-cran-gtools", "r-cran-hdf5", "r-cran-hmisc", "r-cran-its", "r-cran-kernsmooth", "r-cran-lattice", "r-cran-latticeextra", "r-cran-lavaan", "r-cran-lhs", "r-cran-lme4", "r-cran-lmtest", "r-cran-mapdata", "r-cran-maps", "r-cran-maptree", "r-cran-matchit", "r-cran-matrix", "r-cran-mcmcpack", "r-cran-mgcv", "r-cran-misc3d", "r-cran-modelmetrics", "r-cran-mnp", "r-cran-multcomp", "r-cran-mvtnorm", "r-cran-nlme", "r-cran-pscl", "r-cran-psy", "r-cran-qtl", "r-cran-quadprog", "r-cran-qvcalc", "r-cran-randomfieldsutils", "r-cran-raschsampler", "r-cran-rcmdr", "r-cran-relimp", "r-cran-rggobi", "r-cran-rgl", "r-cran-rgtk2", "r-cran-rmpi", "r-cran-rms", "r-cran-rmysql", "r-cran-rodbc", "r-cran-rpart", "r-cran-rpvm", "r-cran-rquantlib", "r-cran-rserve", "r-cran-rsprng", "r-cran-sandwich", "r-cran-sem", "r-cran-sm", "r-cran-snow", "r-cran-strucchange", "r-cran-survival", "r-cran-timedate", "r-cran-tkrplot", "r-cran-tseries", "r-cran-vgam", "r-cran-mass", "r-cran-xml", "r-cran-zelig", "r-cran-zoo", "r-cran-msm", "r-cran-amore", "r-cran-teachingdemos", "r-cran-expm", "r-cran-ggplot2", "r-cran-reshape2", "psignifit", "python3-scipy", "r-cran-vcd", "r-cran-vcdextra", "r-cran-corpcor", "r-cran-bradleyterry2", "r-cran-estimability", "r-cran-elliptic", "r-cran-logspline", "r-cran-lsmeans", "r-cran-modeltools", "r-cran-rinside", "r-cran-pbapply", "r-cran-pbivnorm", "r-cran-contfrac", "r-cran-desolve", "r-cran-hypergeo", "r-cran-coin", "r-cran-bayesfactor", "r-cran-afex", "r-cran-bms", "r-cran-conting", "r-cran-permute", "python3-statsmodels", "r-cran-spam", "r-cran-spatstat", "r-cran-deldir", "r-cran-fastcluster", "r-cran-statmod", "python3-openturns", "python3-pandas", "r-cran-ecodist", "r-cran-energy", "r-cran-mvnormtest", "r-cran-rsdmx", "r-cran-acepack", "r-cran-fcalendar", "rstudio", "apophenia-bin", "r-cran-nmf", "pspp", "datamash", "python3-bayespy"], "ignore": [], "avoid": []}, "neuroscience-modeling": {"depends": [], "suggests": ["moose", "pcsim", "nest", "invt", "xppaut"], "recommends": ["python3-brian", "cnrun", "neuron"], "ignore": [], "avoid": []}, "nanoscale-physics": {"depends": [], "suggests": ["hdf5-helpers", "hdf5-tools", "netcdf-doc", "openmpi-doc | mpich-doc", "axiom", "maxima", "libgraphviz-perl", "python3-pygraphviz", "dx", "dxsamples", "dx-doc", "gpiv", "gpivtools", "feel++-apps", "pymca", "qtiplot", "scidavis", "science-statistics", "science-mathematics"], "recommends": ["abinit", "mpqc", "openmx", "psi3", "quantum-espresso", "drawxtl", "etsf-io", "feynmf", "fityk", "gnuplot", "grace", "libblas3", "liblapack3", "libgsl0ldbl", "gsl-bin", "netcdf-bin", "nco", "ncview", "openmpi-bin | mpich", "science-numericalcomputation", "avogadro", "garlic", "gdis", "ghemical", "v-sim", "gwyddion", "cadabra", "extrema", "ggobi", "mayavi2", "udav", "gperiodic", "graphviz", "python3-scipy", "python3-sympy", "pyxplot", "octave", "scilab", "cbflib-bin", "python3-lmfit", "binoculars", "cod-tools", "libssm-bin", "ape", "atompaw", "bigdft", "cp2k", "exciting", "gpaw", "octopus", "ase", "wannier90-1", "wannier90-2", "octaviz", "fdmnes", "liblevmar-2-6", "sasview"], "ignore": [], "avoid": []}, "financial": {"depends": [], "suggests": [], "recommends": ["r-cran-fasianoptions", "r-cran-fassets", "r-cran-fbasics", "r-cran-fbonds", "r-cran-fcopulae", "r-cran-fexoticoptions", "r-cran-fextremes", "r-cran-fgarch", "r-cran-fimport", "r-cran-fmultivar", "r-cran-fnonlinear", "r-cran-foptions", "r-cran-fregression", "r-cran-ftrading", "r-cran-funitroots", "r-cran-timedate", "r-cran-timeseries", "r-cran-fportfolio"], "ignore": [], "avoid": []}} \ No newline at end of file diff -Nru debian-science-1.11ubuntu1/tasks/chemistry debian-science-1.12ubuntu1/tasks/chemistry --- debian-science-1.11ubuntu1/tasks/chemistry 2019-10-01 15:50:42.000000000 +0000 +++ debian-science-1.12ubuntu1/tasks/chemistry 2020-01-20 21:44:03.000000000 +0000 @@ -49,8 +49,6 @@ Recommends: pyfai -#Recommends: python-mmtk - Recommends: libegad Homepage: http://egad.ucsd.edu/egad/ WNPP: 429693 @@ -165,9 +163,9 @@ Recommends: mmass, mmass-modules -#Recommends: python-mzml +Recommends: python3-pymzml -Suggests: python-mzml-doc +Suggests: python-pymzml-doc Recommends: tandem-mass diff -Nru debian-science-1.11ubuntu1/tasks/dataacquisition debian-science-1.12ubuntu1/tasks/dataacquisition --- debian-science-1.11ubuntu1/tasks/dataacquisition 2019-10-01 15:50:42.000000000 +0000 +++ debian-science-1.12ubuntu1/tasks/dataacquisition 2020-01-20 21:44:03.000000000 +0000 @@ -74,6 +74,8 @@ Recommends: lxi-tools +Recommends: xlsx2csv + Recommends: python3-pyvisa Homepage: http://pyvisa.sourceforge.net/ License: MIT diff -Nru debian-science-1.11ubuntu1/tasks/dataacquisition-dev debian-science-1.12ubuntu1/tasks/dataacquisition-dev --- debian-science-1.11ubuntu1/tasks/dataacquisition-dev 2019-10-01 15:50:43.000000000 +0000 +++ debian-science-1.12ubuntu1/tasks/dataacquisition-dev 2020-01-20 21:44:03.000000000 +0000 @@ -9,7 +9,15 @@ Recommends: libtango-dev, liblog4tango-dev -#Recommends: python-xrayutilities +Recommends: python3-xrayutilities +WNPP: 723017 +Responsible: Eugen Wintersberger +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 diff -Nru debian-science-1.11ubuntu1/tasks/distributedcomputing debian-science-1.12ubuntu1/tasks/distributedcomputing --- debian-science-1.11ubuntu1/tasks/distributedcomputing 2019-10-01 15:50:42.000000000 +0000 +++ debian-science-1.12ubuntu1/tasks/distributedcomputing 2020-01-20 21:44:03.000000000 +0000 @@ -6,7 +6,7 @@ and parallel-computing. -Recommends: ipython +Recommends: ipython3 Why: Provides ipcluster/ipcontroller/ipengine for Python-based distributed computing diff -Nru debian-science-1.11ubuntu1/tasks/economics debian-science-1.12ubuntu1/tasks/economics --- debian-science-1.11ubuntu1/tasks/economics 2019-10-01 15:50:42.000000000 +0000 +++ debian-science-1.12ubuntu1/tasks/economics 2020-01-20 21:44:03.000000000 +0000 @@ -97,10 +97,12 @@ but not large-scale models. For solving large-scale problems, but without complementarity equations, see Dynare or similar toolboxes. -#Recommends: python-quantecon -#Homepage: https://quantecon.org/quantecon-py -#License: BSD-3-clause -#Pkg-Description: high performance, open source Python code library for economics +Recommends: python3-quantecon +Homepage: https://quantecon.org/quantecon-py +License: BSD-3-clause +Pkg-Description: high performance, open source Python code library for economics + QuantEcon provides a high performance, open source Python code library + for economics. Recommends: r-cran-ecdat Homepage: https://CRAN.R-project.org/package=Ecdat diff -Nru debian-science-1.11ubuntu1/tasks/engineering debian-science-1.12ubuntu1/tasks/engineering --- debian-science-1.11ubuntu1/tasks/engineering 2019-10-01 15:50:42.000000000 +0000 +++ debian-science-1.12ubuntu1/tasks/engineering 2020-01-20 21:44:03.000000000 +0000 @@ -25,8 +25,6 @@ Recommends: netgen -Recommends: pythoncad - Recommends: z88 Recommends: freecad diff -Nru debian-science-1.11ubuntu1/tasks/engineering-dev debian-science-1.12ubuntu1/tasks/engineering-dev --- debian-science-1.11ubuntu1/tasks/engineering-dev 2019-10-01 15:50:43.000000000 +0000 +++ debian-science-1.12ubuntu1/tasks/engineering-dev 2020-01-20 21:44:03.000000000 +0000 @@ -77,7 +77,7 @@ Recommends: libslicot-dev -#Recommends: python-collada +Recommends: python3-collada Recommends: libann-dev, libflann-dev diff -Nru debian-science-1.11ubuntu1/tasks/highenergy-physics debian-science-1.12ubuntu1/tasks/highenergy-physics --- debian-science-1.11ubuntu1/tasks/highenergy-physics 2019-10-01 15:50:42.000000000 +0000 +++ debian-science-1.12ubuntu1/tasks/highenergy-physics 2020-01-20 21:44:03.000000000 +0000 @@ -81,5 +81,3 @@ Recommends: geant4 Recommends: neuron - -Recommends: sasview diff -Nru debian-science-1.11ubuntu1/tasks/highenergy-physics-dev debian-science-1.12ubuntu1/tasks/highenergy-physics-dev --- debian-science-1.11ubuntu1/tasks/highenergy-physics-dev 2019-10-01 15:50:42.000000000 +0000 +++ debian-science-1.12ubuntu1/tasks/highenergy-physics-dev 2020-01-20 21:44:03.000000000 +0000 @@ -62,5 +62,3 @@ Suggests: ckon Recommends: neuron-dev, python3-neuron - -Recommends: python3-sasmodels diff -Nru debian-science-1.11ubuntu1/tasks/linguistics debian-science-1.12ubuntu1/tasks/linguistics --- debian-science-1.11ubuntu1/tasks/linguistics 2019-10-01 15:50:42.000000000 +0000 +++ debian-science-1.12ubuntu1/tasks/linguistics 2020-01-20 21:44:03.000000000 +0000 @@ -22,8 +22,29 @@ Recommends: collatinus -#Suggests: python-timbl -#WNPP: 705129 +Recommends: python3-timbl +WNPP: 705129 +Responsible: Maarten van Gompel +Homepage: http://github.com/proycon/python-timbl/ +Pkg-Description: Python bindings for the Tilburg Memory Based Learner (Timbl) + python-timbl is a Python extension module wrapping the full TiMBL C++ + programming interface. With this module, all functionality exposed + through the C++ interface is also available to Python scripts. Being + able to access the API from Python greatly facilitates prototyping + TiMBL-based applications. + . + TiMBL is an open source software package implementing several + memory-based learning algorithms, among which IB1-IG, an + implementation of k-nearest neighbor classification with feature + weighting suitable for symbolic feature spaces, and IGTree, a + decision-tree approximation of IB1-IG. All implemented algorithms have + in common that they store some representation of the training set + explicitly in memory. During testing, new cases are classified by + extrapolation from the most similar stored cases. + . + The Python module offers both a high-level as well as a low-level + interface, the former is very Pythonic and easy to use while the + latter offers the full API. Suggests: wnsqlbuilder Homepage: http://wnsqlbuilder.sf.net diff -Nru debian-science-1.11ubuntu1/tasks/machine-learning debian-science-1.12ubuntu1/tasks/machine-learning --- debian-science-1.11ubuntu1/tasks/machine-learning 2019-10-01 15:50:42.000000000 +0000 +++ debian-science-1.12ubuntu1/tasks/machine-learning 2020-01-20 21:44:03.000000000 +0000 @@ -51,7 +51,9 @@ Recommends: libga-dev, libevocosm-dev, pgapack, octave-ga Comment: Evolutionary algorithm libraries in various languages -#Recommends: python-genetic, python-pyevolve +Recommends: python3-genetic + +#Recommends: python-pyevolve Recommends: flann Homepage: http://www.cs.ubc.ca/~mariusm/index.php/FLANN/FLANN @@ -103,16 +105,16 @@ ; Added by blends-inject 0.0.7. [now official package] #Recommends: python-pebl -#Recommends: python-orange -#License: GPLv3 -#Homepage: http://orange.biolab.si/ -#Pkg-URL: http://orange.biolab.si/debian/ -#Responsible: Mitar -#Pkg-Description: Data mining framework -# Orange is a component-based data mining software. It includes a range -# of data visualization, exploration, preprocessing and modeling -# techniques. It can be used through a nice and intuitive user interface -# or, for more advanced users, as a module for Python programming language. +Recommends: python3-orange +License: GPLv3 +Homepage: http://orange.biolab.si/ +Pkg-URL: http://orange.biolab.si/debian/ +Responsible: Mitar +Pkg-Description: Data mining framework + Orange is a component-based data mining software. It includes a range + of data visualization, exploration, preprocessing and modeling + techniques. It can be used through a nice and intuitive user interface + or, for more advanced users, as a module for Python programming language. #Recommends: python-pymc diff -Nru debian-science-1.11ubuntu1/tasks/mathematics debian-science-1.12ubuntu1/tasks/mathematics --- debian-science-1.11ubuntu1/tasks/mathematics 2019-10-01 15:50:42.000000000 +0000 +++ debian-science-1.12ubuntu1/tasks/mathematics 2020-01-20 21:44:03.000000000 +0000 @@ -223,3 +223,5 @@ Recommends: xcas Recommends: pyomo + +Recommends: model-builder diff -Nru debian-science-1.11ubuntu1/tasks/mathematics-dev debian-science-1.12ubuntu1/tasks/mathematics-dev --- debian-science-1.11ubuntu1/tasks/mathematics-dev 2019-10-31 04:24:55.000000000 +0000 +++ debian-science-1.12ubuntu1/tasks/mathematics-dev 2020-02-01 20:54:10.000000000 +0000 @@ -132,6 +132,8 @@ Recommends: liblevmar-dev +Recommends: python3-brial + Recommends: libquadrule-dev Recommends: libcdd-dev, diff -Nru debian-science-1.11ubuntu1/tasks/meteorology debian-science-1.12ubuntu1/tasks/meteorology --- debian-science-1.11ubuntu1/tasks/meteorology 2019-10-31 04:24:55.000000000 +0000 +++ debian-science-1.12ubuntu1/tasks/meteorology 2020-01-20 21:44:03.000000000 +0000 @@ -109,3 +109,7 @@ when investigating climate data. Recommends: coda + +Recommends: sasview + +Recommends: gwyddion diff -Nru debian-science-1.11ubuntu1/tasks/meteorology-dev debian-science-1.12ubuntu1/tasks/meteorology-dev --- debian-science-1.11ubuntu1/tasks/meteorology-dev 2019-10-01 15:50:43.000000000 +0000 +++ debian-science-1.12ubuntu1/tasks/meteorology-dev 2020-01-20 21:44:03.000000000 +0000 @@ -108,3 +108,5 @@ Recommends: python3-ulmo Recommends: libcoda-dev, libcoda-java, python3-coda + +Recommends: python3-sasmodels diff -Nru debian-science-1.11ubuntu1/tasks/nanoscale-physics debian-science-1.12ubuntu1/tasks/nanoscale-physics --- debian-science-1.11ubuntu1/tasks/nanoscale-physics 2019-10-01 15:50:42.000000000 +0000 +++ debian-science-1.12ubuntu1/tasks/nanoscale-physics 2020-01-20 21:44:03.000000000 +0000 @@ -31,8 +31,6 @@ Recommends: gnuplot, grace -Recommends: horae, ifeffit, sixpack - Recommends: libblas3, liblapack3 Recommends: libgsl0ldbl, gsl-bin @@ -281,3 +279,4 @@ and Tcl. Both unconstrained and constrained (under linear equations, inequality and box constraints) Levenberg-Marquardt variants are included. +Recommends: sasview diff -Nru debian-science-1.11ubuntu1/tasks/nanoscale-physics-dev debian-science-1.12ubuntu1/tasks/nanoscale-physics-dev --- debian-science-1.11ubuntu1/tasks/nanoscale-physics-dev 2019-10-01 15:50:43.000000000 +0000 +++ debian-science-1.12ubuntu1/tasks/nanoscale-physics-dev 2020-01-20 21:44:03.000000000 +0000 @@ -109,3 +109,5 @@ Recommends: python3-periodictable Recommends: libxc-dev + +Recommends: python3-sasmodels diff -Nru debian-science-1.11ubuntu1/tasks/neuroscience-modeling debian-science-1.12ubuntu1/tasks/neuroscience-modeling --- debian-science-1.11ubuntu1/tasks/neuroscience-modeling 2019-10-01 15:50:43.000000000 +0000 +++ debian-science-1.12ubuntu1/tasks/neuroscience-modeling 2020-01-20 21:44:03.000000000 +0000 @@ -12,7 +12,7 @@ metapackages for a variety of additional software that might be useful for neuroscience research. -#Recommends: python-brian +Recommends: python3-brian #Suggests: python-pynn diff -Nru debian-science-1.11ubuntu1/tasks/numericalcomputation debian-science-1.12ubuntu1/tasks/numericalcomputation --- debian-science-1.11ubuntu1/tasks/numericalcomputation 2019-10-01 15:50:43.000000000 +0000 +++ debian-science-1.12ubuntu1/tasks/numericalcomputation 2020-01-20 21:44:03.000000000 +0000 @@ -46,8 +46,6 @@ Suggests: hpcc -#Recommends: python-scitools - Recommends: python3-deap Recommends: python3-lmfit @@ -110,7 +108,7 @@ Suggests: calculix-cgx-examples -#Recommends: python-sfepy +Recommends: python3-sfepy Recommends: python3-bitstring @@ -192,3 +190,8 @@ Recommends: psurface Suggests: libpsurface-dev + +Suggests: python3-numcodecs + +Suggests: python3-zarr + diff -Nru debian-science-1.11ubuntu1/tasks/physics debian-science-1.12ubuntu1/tasks/physics --- debian-science-1.11ubuntu1/tasks/physics 2019-10-01 15:50:42.000000000 +0000 +++ debian-science-1.12ubuntu1/tasks/physics 2020-01-20 21:44:03.000000000 +0000 @@ -34,8 +34,6 @@ Recommends: fityk -Recommends: horae, ifeffit, sixpack - Recommends: tessa | tessa-mpi Recommends: science-numericalcomputation diff -Nru debian-science-1.11ubuntu1/tasks/simulations debian-science-1.12ubuntu1/tasks/simulations --- debian-science-1.11ubuntu1/tasks/simulations 2019-10-31 04:24:55.000000000 +0000 +++ debian-science-1.12ubuntu1/tasks/simulations 2020-01-20 21:44:03.000000000 +0000 @@ -31,7 +31,7 @@ Recommends: neuron -#Recommends: python-sfepy +Recommends: python3-sfepy Suggests: libopensurgsim-dev diff -Nru debian-science-1.11ubuntu1/tasks/statistics debian-science-1.12ubuntu1/tasks/statistics --- debian-science-1.11ubuntu1/tasks/statistics 2019-10-01 15:50:43.000000000 +0000 +++ debian-science-1.12ubuntu1/tasks/statistics 2020-01-20 21:44:03.000000000 +0000 @@ -48,8 +48,6 @@ Recommends: psignifit -#Recommends: python-stats - Recommends: python3-scipy Why: Provides scipy.stats module diff -Nru debian-science-1.11ubuntu1/tasks/viewing debian-science-1.12ubuntu1/tasks/viewing --- debian-science-1.11ubuntu1/tasks/viewing 2019-10-01 15:50:43.000000000 +0000 +++ debian-science-1.12ubuntu1/tasks/viewing 2020-01-20 21:44:03.000000000 +0000 @@ -17,9 +17,6 @@ Recommends: yorick -#Recommends: python-scientific -#Why: Maybe should go in some other metapackage (mathematics?) - Recommends: fityk Recommends: gnuplot, grace, gri, labplot, graphviz, pyxplot, plotdrop, qtiplot @@ -78,8 +75,6 @@ Suggests: python3-matplotlib -#Suggests: python-scitools - Recommends: matlab2tikz Recommends: cassandra diff -Nru debian-science-1.11ubuntu1/tasks/viewing-dev debian-science-1.12ubuntu1/tasks/viewing-dev --- debian-science-1.11ubuntu1/tasks/viewing-dev 2019-10-01 15:50:43.000000000 +0000 +++ debian-science-1.12ubuntu1/tasks/viewing-dev 2020-01-20 21:44:03.000000000 +0000 @@ -7,15 +7,10 @@ Recommends: pdl, gnudatalanguage Why: IDL-like -#Recommends: python-scientific -#Why: Maybe should go in some other metapackage (mathematics?) - Recommends: libgrits-dev Recommends: python3-matplotlib -#Recommends: python-scitools - Recommends: libgnuplot-iostream-dev Recommends: libqglviewer-dev