debian-med-tasks.desc

@@ -162,15 +162,6 @@ Description: Debian Med packages for psychology
 Key:
  med-psychology
 
-Task: med-rehabilitation
-Parent: debian-med
-Section: debian-med
-Description: Debian Med packages for rehabilitation technologies
- This metapackage will install tools that are useful for
- rehabilitation and therapy.
-Key:
- med-rehabilitation
-
 Task: med-statistics
 Parent: debian-med
 Section: debian-med

debian/changelog

-debian-med (3.1) UNRELEASED; urgency=medium
+debian-med (3.1) unstable; urgency=medium
 
   * Versioned Build-Depends bumped to 0.6.99 to enable Recommends in tasks
     files
@@ -6,8 +6,11 @@ debian-med (3.1) UNRELEASED; urgency=medium
     (leave out list of changed metapackage dependencies which is messed up
      due to this change)
   * Moved to Salsa
+  * Standards-Version: 4.1.4
+  * Bumped versioned Build-Depends blends-dev to >= 0.7~
+  * Priotity: optional (as per policy 4.0.1.0 - see #759260)
 
- -- Andreas Tille <tille@debian.org>  Wed, 19 Apr 2017 21:09:03 +0200
+ -- Andreas Tille <tille@debian.org>  Thu, 26 Apr 2018 22:33:08 +0200
 
 debian-med (3.0.1) unstable; urgency=medium
 

debian/control

@@ -3,9 +3,9 @@ Source: debian-med
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Uploaders: Andreas Tille <tille@debian.org>
 Section: misc
-Priority: extra
-Build-Depends-Indep: blends-dev (>= 0.6.99)
-Standards-Version: 3.9.8
+Priority: optional
+Build-Depends-Indep: blends-dev (>= 0.7~)
+Standards-Version: 4.1.4
 Vcs-Browser: https://salsa.debian.org/blends-team/med
 Vcs-Git: https://salsa.debian.org/blends-team/med.git
 
@@ -73,7 +73,6 @@ Suggests: med-cloud,
           med-physics,
           med-practice,
           med-psychology,
-          med-rehabilitation,
           med-tools,
           med-typesetting
 Description: Default selection of tasks for Debian Med
@@ -104,7 +103,6 @@ Recommends: abacas,
             arden,
             ariba,
             art-nextgen-simulation-tools,
-            artemis,
             artfastqgenerator,
             assemblytics,
             atac,
@@ -116,14 +114,12 @@ Recommends: abacas,
             axe-demultiplexer,
             baitfisher,
             bali-phy,
-            ballview,
             bamtools,
             barrnap,
             bcftools,
             beads,
             beagle,
             beast-mcmc,
-            beast2-mcmc,
             bedops,
             bedtools,
             belvu,
@@ -131,9 +127,11 @@ Recommends: abacas,
             bio-eagle,
             bio-rainbow,
             bio-tradis,
+            biosyntax-gedit,
             bitseq,
             blasr,
             blixem,
+            bolt-lmm,
             bowtie,
             bowtie2,
             boxshade,
@@ -148,6 +146,8 @@ Recommends: abacas,
             centrifuge,
             cgview,
             chimeraslayer,
+            chromhmm,
+            chromimpute,
             circlator,
             circos,
             clearcut,
@@ -214,6 +214,7 @@ Recommends: abacas,
             gasic,
             gbrowse,
             gdpc,
+            gemma,
             genometools,
             gentle,
             gff2aplot,
@@ -221,6 +222,7 @@ Recommends: abacas,
             ghemical,
             giira,
             glam2,
+            grabix,
             graphlan,
             grinder,
             gromacs,
@@ -242,7 +244,6 @@ Recommends: abacas,
             iqtree,
             iva,
             jaligner,
-            jalview,
             jellyfish,
             jmodeltest,
             jmol,
@@ -261,7 +262,7 @@ Recommends: abacas,
             lefse,
             librg-utils-perl,
             libvcflib-tools,
-            logol-bin,
+            logol,
             loki,
             ltrsift,
             macs,
@@ -311,7 +312,7 @@ Recommends: abacas,
             njplot,
             norsnet,
             norsp,
-            openms,
+            pal2nal,
             paleomix,
             paml,
             paraclu,
@@ -378,6 +379,8 @@ Recommends: abacas,
             progressivemauve,
             proteinortho,
             prottest,
+            pscan-chip,
+            pscan-tfbs,
             psortb,
             pycorrfit,
             pymol,
@@ -387,11 +390,11 @@ Recommends: abacas,
             python-treetime,
             python3-biomaj3,
             qcumber,
-            qiime,
             qtltools,
             quorum,
             r-bioc-annotate,
             r-bioc-biostrings,
+            r-bioc-bitseq,
             r-bioc-cummerbund,
             r-bioc-deseq2,
             r-bioc-dnacopy,
@@ -426,7 +429,6 @@ Recommends: abacas,
             radiant,
             rambo-k,
             rapmap,
-            rasmol,
             raster3d,
             rate4site,
             raxml,
@@ -436,8 +438,6 @@ Recommends: abacas,
             rdp-readseq,
             readseq,
             reapr,
-            relion-bin | relion-bin+mpi,
-            relion-bin+gui | relion-bin+mpi+gui,
             repeatmasker-recon,
             reprof,
             rna-star,
@@ -456,6 +456,7 @@ Recommends: abacas,
             seaview,
             seer,
             seqan-apps,
+            seqmagick,
             seqprep,
             seqsero,
             seqtk,
@@ -474,8 +475,10 @@ Recommends: abacas,
             sniffles,
             snp-sites,
             snpomatic,
+            soapaligner,
             soapdenovo,
             soapdenovo2,
+            soapsnp,
             sortmerna,
             spaced,
             spades,
@@ -505,7 +508,6 @@ Recommends: abacas,
             tm-align,
             tnseq-transit,
             tophat,
-            topp,
             toppred,
             transdecoder,
             transrate-tools,
@@ -532,18 +534,20 @@ Suggests: acacia,
           apollo,
           arachne,
           arb,
+          artemis,
           asap,
           autodocktools,
           axparafit,
           axpcoords,
           bagpipe,
+          ballview,
           bambus,
           bandage,
           bcbio,
+          beast2-mcmc,
           biceps,
           big-blast,
           bigsdb,
-          biosyntax-gedit,
           blat,
           blimps-utils,
           blobology,
@@ -555,7 +559,6 @@ Suggests: acacia,
           ccs,
           cdna-db,
           cellprofiler,
-          chromhmm,
           cinema,
           cluster3,
           cmap,
@@ -590,7 +593,6 @@ Suggests: acacia,
           exabayes,
           exalt,
           excavator,
-          fasta,
           fasta3,
           ffp,
           figaro,
@@ -608,11 +610,12 @@ Suggests: acacia,
           genetrack,
           genezilla,
           genographer,
+          genometester,
           getdata,
+          ghmm,
           glimmerhmm,
           gmap,
           gmv,
-          grabix,
           haploview,
           hawkeye,
           hexamer,
@@ -620,6 +623,7 @@ Suggests: acacia,
           htqc,
           igv,
           inspect,
+          jalview,
           jbrowse,
           jigsaw,
           jstreeview,
@@ -671,8 +675,8 @@ Suggests: acacia,
           obo-edit,
           oligoarrayaux,
           omegamap,
+          openms,
           operondb,
-          pal2nal,
           partigene,
           partitionfinder,
           patristic,
@@ -684,26 +688,28 @@ Suggests: acacia,
           phylophlan,
           phyloviz-core,
           phylowin,
+          phyx,
+          pilon,
           pipasic,
           plato,
           porechop,
           profit,
           prokka,
           prot4est,
-          pscan-tfbs,
           psipred,
           pssh2,
           pyrophosphate-tools,
           python-orange,
           python-reaper,
+          qiime,
           qtlcart,
           qualimap,
           r-bioc-annotationhub,
           r-bioc-aroma.light,
-          r-bioc-bitseq,
           r-bioc-ensembldb,
           r-bioc-go.db,
           r-bioc-savr,
+          r-bioc-tfbstools,
           r-cran-boolnet,
           r-cran-metamix,
           r-cran-pheatmap,
@@ -712,8 +718,13 @@ Suggests: acacia,
           r-cran-samr,
           r-other-apmswapp,
           raccoon,
+          racon,
+          rampler,
+          rasmol,
           raxml-ng,
           rbs-finder,
+          relion-bin | relion-bin+mpi,
+          relion-bin+gui | relion-bin+mpi+gui,
           repeatmasker,
           rmblast,
           roadtrips,
@@ -731,12 +742,11 @@ Suggests: acacia,
           sistr,
           situs,
           snpeff,
-          soapaligner,
-          soapsnp,
           solvate,
           sparta,
           spice,
           splitstree,
+          spoa,
           ssaha,
           strap,
           strap-base,
@@ -749,6 +759,7 @@ Suggests: acacia,
           tigr-glimmer-mg,
           tn-seqexplorer,
           toil,
+          topp,
           trace2dbest,
           tracetuner,
           treebuilder3d,
@@ -760,6 +771,7 @@ Suggests: acacia,
           ugene,
           umap,
           unc-fish,
+          unicycler,
           uniprime,
           varmatch,
           varscan,
@@ -781,6 +793,7 @@ Recommends: bio-tradis,
             bioperl,
             bioperl-run,
             biosquid,
+            cwltool,
             libace-perl,
             libai-fann-perl,
             libbambamc-dev,
@@ -836,7 +849,6 @@ Recommends: bio-tradis,
             libngs-java,
             libngs-sdk-dev,
             libnhgri-blastall-perl,
-            libopenms-dev,
             libpal-java,
             libpbbam-dev,
             libpbdata-dev,
@@ -845,7 +857,6 @@ Recommends: bio-tradis,
             libqes-dev,
             librcsb-core-wrapper0-dev,
             librdp-taxonomy-tree-java,
-            librelion-dev,
             librg-blast-parser-perl,
             librg-reprof-bundle-perl,
             librostlab-blast0-dev,
@@ -881,7 +892,6 @@ Recommends: bio-tradis,
             python-pbcore,
             python-pbh5tools,
             python-pysam,
-            python-rdkit,
             python3-biomaj3,
             python3-biopython | python-biopython,
             python3-biotools | python-biotools,
@@ -904,24 +914,29 @@ Recommends: bio-tradis,
             r-cran-phylobase,
             r-cran-rncl,
             r-cran-rnexml,
-            ruby-bio,
             sbmltoolbox,
             seqan-dev
 Suggests: bioclipse,
           libbam-dev,
+          libbioparser-dev,
           libdisorder-dev,
+          libedlib-dev,
           libforester-java,
           libfreecontact-doc,
           libgatbcore-dev,
           libgff-perl,
           libgoby-java,
           libgtextutils-dev,
+          libopenms-dev,
           libpbcopper-dev,
           libqcpp-dev,
+          librelion-dev,
           libroadrunner-dev,
           librostlab-blast-doc,
           librostlab-doc,
+          libspoa-dev,
           libswarm2-dev,
+          libthread-pool-dev,
           mgltools-networkeditor,
           mgltools-pybabel,
           mgltools-vision,
@@ -931,6 +946,7 @@ Suggests: bioclipse,
           python-biopython-doc,
           python-mmtk,
           python-pyflow,
+          python-rdkit,
           python-roadrunner,
           python-screed,
           python3-biopython-sql | python-biopython-sql,
@@ -969,6 +985,7 @@ Suggests: bioclipse,
           r-cran-natserv,
           r-cran-rentrez,
           r-cran-rocr,
+          ruby-bio,
           ruby-crb-blast,
           ruby-rgfa
 Description: Debian Med packages for development of bioinformatics applications
@@ -1091,7 +1108,6 @@ Recommends: abyss,
             python-cogent,
             python3-biomaj3-cli,
             python3-biopython,
-            qiime,
             r-bioc-hilbertvis,
             r-cran-pvclust,
             r-cran-qtl,
@@ -1127,7 +1143,8 @@ Recommends: abyss,
 Suggests: bagpipe,
           cufflinks,
           embassy-phylip,
-          gmap
+          gmap,
+          qiime
 Description: Debian Med bioinformatics applications usable in cloud computing
  This metapackage will install Debian packages related to molecular biology,
  structural biology and bioinformatics for use in life sciences, that do not
@@ -1169,8 +1186,7 @@ Architecture: all
 Depends: ${misc:Depends},
          med-config (= ${source:Version}),
          med-tasks (= ${source:Version})
-Recommends: epigrass,
-            python-treetime,
+Recommends: python-treetime,
             r-cran-diagnosismed,
             r-cran-epi,
             r-cran-epibasix,
@@ -1180,10 +1196,13 @@ Recommends: epigrass,
             r-cran-lexrankr,
             r-cran-seroincidence,
             r-cran-surveillance
-Suggests: netepi-analysis,
+Suggests: epigrass,
+          netepi-analysis,
           netepi-collection,
           r-cran-cmprsk,
           r-cran-msm,
+          r-cran-sf,
+          r-cran-sjplot,
           repast,
           shiny-server,
           ushahidi
@@ -1229,7 +1248,6 @@ Depends: ${misc:Depends},
          med-tasks (= ${source:Version})
 Recommends: aeskulap,
             amide,
-            ants,
             bart,
             bart-view,
             biosig-tools,
@@ -1241,7 +1259,6 @@ Recommends: aeskulap,
             dicom3tools,
             dicomnifti,
             dicomscope,
-            fw4spl,
             gdf-tools,
             ginkgocadx,
             gwyddion,
@@ -1261,28 +1278,22 @@ Recommends: aeskulap,
             mricron,
             mrtrix,
             nifti-bin,
-            odin,
             openslide-tools,
             orthanc,
             orthanc-wsi,
-            pixelmed-apps,
             plastimatch,
             python-dicom,
-            python-dipy,
-            python-mvpa2,
             python-nibabel,
             python-nipy,
             python-nipype,
             python-nitime,
-            python-surfer,
             python-tifffile,
             sigviewer,
             sofa-apps,
-            teem-apps,
-            voxbo,
             vtk-dicom-tools,
             xmedcon
 Suggests: afni,
+          ants,
           bioimagesuite,
           bioimagexd,
           blox,
@@ -1312,6 +1323,7 @@ Suggests: afni,
           freesurfer,
           fsl,
           fslview,
+          fw4spl,
           gimias,
           hid,
           imagemagick,
@@ -1336,6 +1348,7 @@ Suggests: afni,
           mni-icbm152-nlin-2009,
           mni-n3,
           mrisim,
+          odin,
           omero,
           opendicom.net,
           openelectrophy,
@@ -1348,18 +1361,24 @@ Suggests: afni,
           orthanc-webviewer,
           paraview,
           piano,
+          pixelmed-apps,
           pngquant,
           pymeg,
+          python-dipy,
+          python-mvpa2,
           python-pyxid,
+          python-surfer,
           science-workflow,
           slicer,
           stabilitycalc,
           stir,
+          teem-apps,
           tempo,
           trimage,
           via-bin,
           visit,
           vmtk,
+          voxbo,
           xnat
 Description: Debian Med image processing and visualization packages
  This metapackage will install Debian packages which might be useful in
@@ -1402,9 +1421,7 @@ Recommends: cimg-dev,
             libodil0-dev,
             libopenigtlink-dev,
             libopenslide-dev,
-            libopensurgsim-dev,
             libpapyrus3-dev,
-            libteem-dev,
             libvigraimpex-dev,
             libvistaio-dev,
             libvolpack1-dev,
@@ -1412,16 +1429,10 @@ Recommends: cimg-dev,
             libvtk6-dev,
             octave-bart,
             octave-gdf,
-            odin,
-            python-casmoothing,
-            python-cfflib,
             python-dicom,
-            python-dipy,
             python-gdcm,
             python-imageio,
             python-mia | python3-mia,
-            python-mne,
-            python-mvpa2,
             python-nibabel,
             python-nipy,
             python-nipype,
@@ -1443,11 +1454,18 @@ Suggests: emokit,
           libnifti-doc,
           libopenmeeg-dev,
           libopenslide-java,
+          libopensurgsim-dev,
+          libteem-dev,
           libvia-dev,
           libvmtk-dev,
           libxdffileio-dev,
           octave-dicom,
+          odin,
+          python-cfflib,
+          python-dipy,
           python-libavg,
+          python-mne,
+          python-mvpa2,
           python-tifffile,
           python-vmtk
 Description: Debian Med image processing and visualization packages development
@@ -1572,15 +1590,15 @@ Depends: ${misc:Depends},
          med-tasks (= ${source:Version})
 Recommends: praat,
             psignifit,
-            psychopy,
-            python-pyepl,
             r-cran-foreign,
             r-cran-psy
 Suggests: miscpsycho,
           psych,
           psychometric,
+          psychopy,
           psychotree,
           psyphy,
+          python-pyepl,
           python-pypsignifit,
           python-visionegg,
           science-psychophysics
@@ -1588,18 +1606,6 @@ Description: Debian Med packages for psychology
  This metapackage contains dependencies for a collection of software
  which might be helpful for psychological research.
 
-Package: med-rehabilitation
-Section: metapackages
-Architecture: all
-Depends: ${misc:Depends},
-         med-config (= ${source:Version}),
-         med-tasks (= ${source:Version})
-Recommends: sitplus
-Suggests: aghermann
-Description: Debian Med packages for rehabilitation technologies
- This metapackage will install tools that are useful for
- rehabilitation and therapy.
-
 Package: med-statistics
 Section: metapackages
 Architecture: all

debian/control.stub

@@ -2,9 +2,9 @@ Source: debian-med
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Uploaders: Andreas Tille <tille@debian.org>
 Section: misc
-Priority: extra
-Build-Depends-Indep: blends-dev (>= 0.6.99)
-Standards-Version: 3.9.8
+Priority: optional
+Build-Depends-Indep: blends-dev (>= 0.7~)
+Standards-Version: 4.1.4
 Vcs-Browser: https://salsa.debian.org/blends-team/med
 Vcs-Git: https://salsa.debian.org/blends-team/med.git