debian/changelog

+debian-med (3.5) unstable; urgency=medium
+
+  * Python2 packages only suggested
+    Closes: #945659
+  * Remove tophat since deprecated by upstream
+  * giira from Recommends to Suggests since it needs tophat
+  * lintian-override for field-too-long Recommends
+
+  * start of automatic changelog entry * 
+  
+  * Changes in metapackage dependencies
+   -med-bio
+    added:
+      Recommends: idefix, resfinder, purple, pufferfish
+      Suggests:   skewer, giira
+    removed:
+      Recommends: giira, tophat
+      Suggests:   mobyle-programs, mobyle-tutorials, mobyle
+   -med-bio-dev
+    added:
+      Recommends: python3-dnaio, python3-pyani, biobambam2, libcdk-java
+      Suggests:   r-bioc-dada2, python-pbcommand, python-pbh5tools,
+                  r-cran-dt, r-cran-proc, python-kineticstools, libfast-perl,
+                  python-corepywrap, libmaus2-dev, python-pbcore,
+                  r-cran-pcapp, r-cran-dynamictreecut, python-cogent,
+                  r-cran-kaos
+    removed:
+      Recommends: python-pbh5tools, python-pbcommand, python-kineticstools,
+                  python-corepywrap, libmaus2-dev, python-pbcore,
+                  r-cran-dynamictreecut, python-cogent
+   -med-bio-ngs
+    removed:
+      Recommends: tophat
+   -med-cloud
+    added:
+      Recommends: hisat2
+      Suggests:   python-cogent
+    removed:
+      Recommends: python-cogent, tophat
+   -med-imaging
+    added:
+      Suggests:   python-nipype, python-nitime, python-dipy, python-nipy
+    removed:
+      Recommends: python-nipype, python-nitime, python-dipy, python-nipy
+      Suggests:   tifffile
+   -med-imaging-dev
+    added:
+      Suggests:   python-vigra, python-nipype, python-cfflib, python-nitime,
+                  python-pyxnat, python-nipy, python-vmtk, python-dipy
+    removed:
+      Recommends: python-vigra, python-nipype, python-cfflib, python-nitime,
+                  python-pyxnat, python-nipy, python-vmtk, python-dipy
+   -med-psychology
+    added:
+      Suggests:  python-pyepl
+    removed:
+      Recommends:  python-pypsignifit, python-pyepl
+
+ -- Andreas Tille <tille@debian.org>  Thu, 28 Nov 2019 09:25:44 +0100
+
 debian-med (3.4) unstable; urgency=medium
 
   * Standards-Version: 4.4.1

debian/control

@@ -183,7 +183,6 @@ Recommends: abacas,
             dialign-tx,
             diamond-aligner,
             dindel,
-            discosnp,
             disulfinder,
             dnaclust,
             dotter,
@@ -199,6 +198,7 @@ Recommends: abacas,
             embassy-domalign,
             embassy-domsearch,
             emboss,
+            emmax,
             estscan,
             examl,
             exonerate,
@@ -236,7 +236,6 @@ Recommends: abacas,
             gffread,
             ghemical,
             ghmm,
-            giira,
             glam2,
             grabix,
             graphlan,
@@ -313,6 +312,7 @@ Recommends: abacas,
             mipe,
             mira-assembler,
             mlv-smile,
+            mmseqs2,
             mothur,
             mptp,
             mrbayes,
@@ -334,7 +334,6 @@ Recommends: abacas,
             ncoils,
             neobio,
             njplot,
-            norsnet,
             norsp,
             obitools,
             openms,
@@ -346,11 +345,8 @@ Recommends: abacas,
             parsinsert,
             parsnp,
             patman,
-            pbbarcode,
             pbdagcon,
-            pbh5tools,
             pbsim,
-            pdb2pqr,
             perlprimer,
             perm,
             pftools,
@@ -380,7 +376,6 @@ Recommends: abacas,
             poretools,
             prank,
             predictnls,
-            predictprotein,
             prime-phylo,
             primer3,
             proalign,
@@ -389,18 +384,6 @@ Recommends: abacas,
             probcons,
             proda,
             prodigal,
-            profbval,
-            profisis,
-            profnet-bval,
-            profnet-chop,
-            profnet-con,
-            profnet-isis,
-            profnet-md,
-            profnet-norsnet,
-            profnet-prof,
-            profnet-snapfun,
-            profphd,
-            profphd-net,
             profphd-utils,
             proftmb,
             progressivemauve,
@@ -442,15 +425,19 @@ Recommends: abacas,
             r-bioc-impute,
             r-bioc-limma,
             r-bioc-mergeomics,
+            r-bioc-multiassayexperiment,
             r-bioc-pcamethods,
             r-bioc-phyloseq,
             r-bioc-rtracklayer,
             r-bioc-tfbstools,
+            r-cran-adegenet,
+            r-cran-adephylo,
             r-cran-alakazam,
             r-cran-ape,
             r-cran-bio3d,
             r-cran-distory,
             r-cran-genabel,
+            r-cran-kaos,
             r-cran-metamix,
             r-cran-phangorn,
             r-cran-phytools,
@@ -463,6 +450,7 @@ Recommends: abacas,
             r-cran-shazam,
             r-cran-tcr,
             r-cran-tigger,
+            r-cran-treescape,
             r-cran-vegan,
             r-cran-webgestaltr,
             r-other-hms-dbmi-spp,
@@ -515,7 +503,6 @@ Recommends: abacas,
             sim4,
             sim4db,
             skesa,
-            smalr,
             smalt,
             smithwaterman,
             snap,
@@ -558,7 +545,6 @@ Recommends: abacas,
             tm-align,
             tnseq-transit,
             toil,
-            tophat,
             topp,
             toppred,
             trace2dbest,
@@ -574,7 +560,6 @@ Recommends: abacas,
             tvc,
             uc-echo,
             umis,
-            unanimity,
             unicycler,
             varna,
             vcftools,
@@ -638,11 +623,11 @@ Suggests: acacia,
           dazzle,
           deepbinner,
           dendroscope,
+          discosnp,
           e-hive,
           ecell,
           embassy-phylip,
           emboss-explorer,
-          emmax,
           emperor,
           ensembl,
           estferret,
@@ -669,6 +654,7 @@ Suggests: acacia,
           genezilla,
           genographer,
           getdata,
+          giira,
           glimmerhmm,
           gmap,
           gmv,
@@ -676,6 +662,7 @@ Suggests: acacia,
           haploview,
           hawkeye,
           htqc,
+          idefix,
           igdiscover,
           igv,
           inspect,
@@ -710,10 +697,6 @@ Suggests: acacia,
           minimus,
           mirbase,
           mirtop,
-          mmseqs2,
-          mobyle,
-          mobyle-programs,
-          mobyle-tutorials,
           modeller,
           molekel,
           mosaik-aligner,
@@ -731,6 +714,7 @@ Suggests: acacia,
           nextsv,
           ngila,
           ngsqctoolkit,
+          norsnet,
           nw-align,
           oases,
           obo-edit,
@@ -744,11 +728,14 @@ Suggests: acacia,
           partitionfinder,
           patristic,
           pbalign,
+          pbbarcode,
           pbgenomicconsensus,
+          pbh5tools,
           pbhoney,
           pbjelly,
           pbsuite,
           pcma,
+          pdb2pqr,
           pfaat,
           phagefinder,
           phpphylotree,
@@ -761,11 +748,26 @@ Suggests: acacia,
           pipasic,
           pizzly,
           plato,
+          predictprotein,
+          profbval,
+          profisis,
           profit,
+          profnet-bval,
+          profnet-chop,
+          profnet-con,
+          profnet-isis,
+          profnet-md,
+          profnet-norsnet,
+          profnet-prof,
+          profnet-snapfun,
+          profphd,
+          profphd-net,
           prokka,
           prot4est,
           psipred,
           pssh2,
+          pufferfish,
+          purple,
           pyrophosphate-tools,
           python3-alignlib,
           python3-cogent,
@@ -785,12 +787,9 @@ Suggests: acacia,
           r-bioc-go.db,
           r-bioc-metagenomeseq,
           r-bioc-mofa,
-          r-bioc-multiassayexperiment,
           r-bioc-qusage,
           r-bioc-savr,
           r-bioc-tximport,
-          r-cran-adegenet,
-          r-cran-adephylo,
           r-cran-boolnet,
           r-cran-corrplot,
           r-cran-drinsight,
@@ -798,13 +797,11 @@ Suggests: acacia,
           r-cran-fitdistrplus,
           r-cran-forecast,
           r-cran-gprofiler,
-          r-cran-kaos,
           r-cran-pheatmap,
           r-cran-qqman,
           r-cran-rentrez,
           r-cran-sctransform,
           r-cran-seurat,
-          r-cran-treescape,
           r-cran-tsne,
           r-other-apmswapp,
           r-other-wgcna,
@@ -813,6 +810,7 @@ Suggests: acacia,
           raxml-ng,
           rbs-finder,
           repeatmasker,
+          resfinder,
           rmblast,
           roadtrips,
           roche454ace2caf,
@@ -831,6 +829,8 @@ Suggests: acacia,
           sina,
           sistr,
           situs,
+          skewer,
+          smalr,
           smrtanalysis,
           snpeff,
           solvate,
@@ -859,6 +859,7 @@ Suggests: acacia,
           twain,
           ugene,
           umap,
+          unanimity,
           unc-fish,
           uniprime,
           varmatch,
@@ -895,7 +896,6 @@ Recommends: bio-tradis,
             libbio-coordinate-perl,
             libbio-das-lite-perl,
             libbio-eutilities-perl,
-            libbio-graphics-perl,
             libbio-mage-perl,
             libbio-mage-utils-perl,
             libbio-primerdesigner-perl,
@@ -917,6 +917,7 @@ Recommends: bio-tradis,
             libbpp-raa-dev,
             libbpp-seq-dev,
             libbpp-seq-omics-dev,
+            libcdk-java,
             libchado-perl,
             libconsensuscore-dev,
             libdivsufsort-dev,
@@ -987,11 +988,6 @@ Recommends: bio-tradis,
             libzerg-perl,
             libzerg0-dev,
             mcl,
-            pyfai,
-            python-cogent,
-            python-corepywrap,
-            python-pbcore,
-            python-pbh5tools,
             python3-airr,
             python3-bcbio,
             python3-biom-format,
@@ -1005,6 +1001,7 @@ Recommends: bio-tradis,
             python3-cutadapt,
             python3-cyvcf2,
             python3-dendropy,
+            python3-dnaio,
             python3-fast5,
             python3-freecontact,
             python3-gfapy,
@@ -1027,8 +1024,11 @@ Recommends: bio-tradis,
             python3-sqt,
             python3-treetime,
             r-bioc-biobase,
+            r-cran-adegenet,
+            r-cran-adephylo,
             r-cran-boolnet,
             r-cran-distory,
+            r-cran-fitdistrplus,
             r-cran-forecast,
             r-cran-genetics,
             r-cran-gprofiler,
@@ -1054,13 +1054,16 @@ Recommends: bio-tradis,
             seqan-dev,
             snakemake,
             toil
-Suggests: bioclipse,
+Suggests: biobambam2,
+          bioclipse,
           ctdconverter,
           galaxy-lib,
           libbam-dev,
           libbigwig-dev,
+          libbio-graphics-perl,
           libbiod-dev,
           libdisorder-dev,
+          libfast-perl,
           libforester-java,
           libfreecontact-doc,
           libgclib,
@@ -1082,9 +1085,14 @@ Suggests: bioclipse,
           mgltools-pybabel,
           mgltools-vision,
           octace-bioinfo,
+          pyfai,
           python-biopython-doc,
+          python-cogent,
+          python-corepywrap,
           python-kineticstools,
           python-pbcommand,
+          python-pbcore,
+          python-pbh5tools,
           python3-alignlib,
           python3-biopython-sql,
           python3-consensuscore2,
@@ -1097,6 +1105,7 @@ Suggests: bioclipse,
           python3-loompy,
           python3-mirtop,
           python3-misopy,
+          python3-pyani,
           python3-pycosat,
           python3-pyflow,
           python3-roadrunner,
@@ -1117,6 +1126,7 @@ Suggests: bioclipse,
           r-bioc-bsgenome,
           r-bioc-cner,
           r-bioc-cummerbund,
+          r-bioc-dada2,
           r-bioc-deseq2,
           r-bioc-dnacopy,
           r-bioc-ebseq,
@@ -1154,17 +1164,18 @@ Suggests: bioclipse,
           r-bioc-tximport,
           r-bioc-variantannotation,
           r-bioc-xvector,
-          r-cran-adegenet,
-          r-cran-adephylo,
           r-cran-corrplot,
           r-cran-drinsight,
+          r-cran-dt,
           r-cran-dynamictreecut,
-          r-cran-fitdistrplus,
           r-cran-future.apply,
           r-cran-future.batchtools,
           r-cran-ica,
+          r-cran-kaos,
           r-cran-metap,
           r-cran-natserv,
+          r-cran-pcapp,
+          r-cran-proc,
           r-cran-rann,
           r-cran-rocr,
           r-cran-rsvd,
@@ -1221,7 +1232,6 @@ Recommends: abyss,
             datamash,
             dialign,
             dialign-tx,
-            discosnp,
             disulfinder,
             dnaclust,
             dssp,
@@ -1247,6 +1257,7 @@ Recommends: abyss,
             grinder,
             gromacs,
             hhsuite,
+            hisat2,
             hmmer,
             idba,
             infernal,
@@ -1275,7 +1286,6 @@ Recommends: abyss,
             neobio,
             paraclu,
             parsinsert,
-            pdb2pqr,
             perm,
             phyml,
             phyutility,
@@ -1290,7 +1300,6 @@ Recommends: abyss,
             proda,
             prodigal,
             pynast,
-            python-cogent,
             python3-biomaj3-cli,
             python3-biopython,
             qiime,
@@ -1320,7 +1329,6 @@ Recommends: abyss,
             tabix,
             theseus,
             tigr-glimmer,
-            tophat,
             tree-puzzle | tree-ppuzzle,
             vcftools,
             velvet,
@@ -1328,8 +1336,11 @@ Recommends: abyss,
             zalign
 Suggests: bagpipe,
           cufflinks,
+          discosnp,
           embassy-phylip,
-          gmap
+          gmap,
+          pdb2pqr,
+          python-cogent
 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
@@ -1382,6 +1393,7 @@ Recommends: epigrass,
             r-cran-epitools,
             r-cran-lexrankr,
             r-cran-seroincidence,
+            r-cran-sf,
             r-cran-sjplot,
             r-cran-surveillance
 Suggests: epifire,
@@ -1389,7 +1401,6 @@ Suggests: epifire,
           netepi-collection,
           r-cran-cmprsk,
           r-cran-msm,
-          r-cran-sf,
           repast,
           shiny-server,
           ushahidi
@@ -1459,15 +1470,12 @@ Recommends: aeskulap,
             mriconvert,
             mricron,
             mrtrix,
-            mrtrix3,
             nifti-bin,
             odil,
             openslide-tools,
             orthanc,
             orthanc-wsi,
             pixelmed-apps,
-            python-nipy,
-            python-nitime,
             python3-dicom,
             python3-nibabel,
             tifffile,
@@ -1534,6 +1542,7 @@ Suggests: afni,
           mni-icbm152-nlin-2009,
           mni-n3,
           mrisim,
+          mrtrix3,
           odin,
           omero,
           opendicom.net,
@@ -1552,7 +1561,9 @@ Suggests: afni,
           pngquant,
           pymeg,
           python-dipy,
+          python-nipy,
           python-nipype,
+          python-nitime,
           python-pyxid,
           python3-mvpa2,
           python3-surfer,
@@ -1597,6 +1608,7 @@ Recommends: cimg-dev,
             libgdcm2-dev,
             libgdf-dev,
             libgiftiio-dev,
+            libinsighttoolkit4-dev,
             libismrmrd-dev,
             libmaxflow-dev,
             libmdc2-dev,
@@ -1618,11 +1630,6 @@ Recommends: cimg-dev,
             octave-bart,
             octave-dicom,
             octave-gdf,
-            python-cfflib,
-            python-nipy,
-            python-nitime,
-            python-pyxnat,
-            python-vigra,
             python3-dicom,
             python3-gdcm,
             python3-imageio,
@@ -1640,7 +1647,6 @@ Suggests: emokit,
           libeegdev-dev,
           libfreeimage-dev,
           libics-dev,
-          libinsighttoolkit4-dev,
           liblimereg-dev,
           libmni-perllib-perl,
           libnifti-doc,
@@ -1654,8 +1660,13 @@ Suggests: emokit,
           libvtk6-dev,
           libxdffileio-dev,
           odin,
+          python-cfflib,
           python-dipy,
+          python-nipy,
           python-nipype,
+          python-nitime,
+          python-pyxnat,
+          python-vigra,
           python-vmtk,
           python3-biosig,
           python3-mne,
@@ -1673,9 +1684,9 @@ Architecture: all
 Depends: ${misc:Depends},
          med-config (= ${source:Version}),
          med-tasks (= ${source:Version})
-Recommends: opencfu,
-            orthanc-wsi
+Recommends: orthanc-wsi
 Suggests: catissuesuite,
+          opencfu,
           openelis,
           openfreezer
 Description: Debian Med suggestions for medical laboratories
@@ -1786,12 +1797,11 @@ Depends: ${misc:Depends},
          med-tasks (= ${source:Version})
 Recommends: praat,
             psignifit,
-            python-pyepl,
             r-cran-foreign,
             r-cran-psy,
             r-cran-psych
 Suggests: psychopy,
-          python-pypsignifit,
+          python-pyepl,
           r-cran-psychometric,
           r-cran-psychotree,
           r-cran-psyphy,

debian/med-bio.lintian-overrides

+# We really have a lot of recommends
+med-bio: field-too-long Recommends (* chars > 5000)

tasks/bio

@@ -427,7 +427,8 @@ Recommends: fitgcp
 
 Recommends: gasic
 
-Recommends: giira
+Suggests: giira
+Comment: Needs deprecated tophat
 
 Recommends: ipig
 

tasks/bio-dev

@@ -20,7 +20,8 @@ Recommends: python3-biopython
 
 Suggests: python3-biopython-sql, python-biopython-doc
 
-Recommends: python-cogent
+Suggests: python-cogent
+Comment: py2removal
 
 Suggests: python3-pycosat
 
@@ -67,7 +68,10 @@ Recommends: libzerg0-dev, libzerg-perl
 
 Recommends: librg-reprof-bundle-perl
 
-Recommends: python-corepywrap, librcsb-core-wrapper0-dev
+Suggests: python-corepywrap
+Comment: py2removal
+
+Recommends: librcsb-core-wrapper0-dev
 
 Recommends: libsbml5-dev, sbmltoolbox
 
@@ -332,7 +336,8 @@ Recommends: libgff-dev
 
 Recommends: python3-pysam
 
-Recommends: python-pbcore, python-pbh5tools
+Suggests: python-pbcore, python-pbh5tools
+Comment: py2removal
 
 Recommends: python3-cobra
 
@@ -350,7 +355,8 @@ Recommends: python3-pbconsensuscore
 
 Recommends: python3-consensuscore2, libconsensuscore-dev
 
-Recommends: python-pbcommand
+Suggests: python-pbcommand
+Comment: py2removal
 
 Recommends: python3-pyvcf
 
@@ -358,7 +364,8 @@ Recommends: python3-pyfaidx
 
 Recommends: python3-sqt
 
-Recommends: python-kineticstools
+Suggests: python-kineticstools
+Comment: py2removal
 
 Suggests: libbam-dev
 

tasks/cloud

@@ -59,8 +59,11 @@ X-Begin-Category: Tools for the molecular biologist.
 Recommends: melting, mipe, ncbi-epcr, primer3
 Comment: Oligonucleotides and PCR
 
-Recommends: acedb-other, disulfinder, ncbi-tools-bin, ncoils, python-cogent,
+Recommends: acedb-other, disulfinder, ncbi-tools-bin, ncoils,
             readseq, tigr-glimmer, seqan-apps, staden-io-lib-utils
+
+Suggests: python-cogent
+Comment: py2removal
 X-End-Category: Tools for the molecular biologist.
 
 X-Begin-Category: Others

tasks/imaging

@@ -42,15 +42,18 @@ Recommends: sofa-apps
 Recommends: python3-mvpa2
 Why: Suggested by maintainer Michael Hanke <michael.hanke@gmail.com>
 
-Recommends: python-nipy
+Suggests: python-nipy
+Comment: py2removal
 Why: Although listed in -dev task, it also has a strong focus on interactive
  data analysis.
 
-Recommends: python-nipype
+Suggests: python-nipype
+Comment: py2removal
 Why: Although listed in -dev task, it also has a strong focus on interactive
  data analysis.
 
-Recommends: python-nitime
+Suggests: python-nitime
+Comment: py2removal
 Why: Although listed in -dev task, it also has a strong focus on interactive
  data analysis.
 
@@ -635,7 +638,9 @@ Registration: http://sccn.ucsd.edu/eeglab/install.html
 Suggests: elastix
 
 Suggests: python-pyxid
-Recommends: python-dipy
+
+Suggests: python-dipy
+Comment: py2removal
 Why: Although listed in -dev task, it also has a strong focus on interactive
  data analysis.
 

tasks/imaging-dev

@@ -33,11 +33,14 @@ Suggests: liblimereg-dev
 Recommends: python3-mvpa2
 Why: Suggested by maintainer Michael Hanke <michael.hanke@gmail.com>
 
-Recommends: python-nipy
+Suggests: python-nipy
+Comment: py2removal
 
-Recommends: python-nipype
+Suggests: python-nipype
+Comment: py2removal
 
-Recommends: python-nitime
+Suggests: python-nitime
+Comment: py2removal
 
 Recommends: libvia-dev
 
@@ -92,15 +95,18 @@ Vcs-Git: git://github.com/daeken/Emokit.git
 Pkg-Description: Emotiv EPOC headset Python interface
  Emotive is an interface to a budget Emotiv EPOC EEG headset.
 
-Recommends: python-pyxnat
+Suggests: python-pyxnat
+Comment: py2removal
 
-Recommends: python-dipy
+Suggests: python-dipy
+Comment: py2removal
 
 Recommends: libbiosig-dev, python3-biosig
 
 Recommends: libctk-dev
 
-Recommends: python-cfflib
+Suggests: python-cfflib
+Comment: py2removal
 
 Recommends: libopenslide-dev
 
@@ -126,9 +132,15 @@ Recommends: python3-mne
 
 Suggests: tifffile
 
-Recommends: python-vmtk, libvmtk-dev
+Recommends: libvmtk-dev
 
-Recommends: libvigraimpex-dev, python-vigra
+Suggests: python-vmtk
+Comment: py2removal
+
+Recommends: libvigraimpex-dev
+
+Suggests: python-vigra
+Comment: py2removal
 
 Recommends: libvtk-dicom-dev
 

tasks/psychology

@@ -6,12 +6,12 @@ Description: Debian Med packages for psychology
 Suggests: science-psychophysics
 Meta-Suggests: svn://svn.debian.org/blends/projects/science/trunk/debian-science/tasks/psychophysics
 
-Recommends: python-pyepl
+Suggests: python-pyepl
+Comment: py2removal
 
 Recommends: praat
 
-Recommends: r-cran-foreign, psignifit, python-pypsignifit
-Why: analysis packages of particular relevance for psych. data
+Recommends: r-cran-foreign, psignifit
 
 Recommends: r-cran-psy
 Remark: r-cran-psy is orphaned upstream.