[Blends-commit] [Git][blends-team/med][master] 3 commits: Recreate d/control and dependency_data

Andreas Tille (@tille) gitlab at salsa.debian.org
Wed Jan 12 20:08:42 GMT 2022



Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
004e6ad2 by Andreas Tille at 2022-01-12T20:41:53+01:00
Recreate d/control and dependency_data

- - - - -
ec1a7db3 by Andreas Tille at 2022-01-12T20:44:16+01:00
Update changelog entry

- - - - -
86a7efe0 by Andreas Tille at 2022-01-12T20:45:19+01:00
Upload to unstable

- - - - -


3 changed files:

- debian/changelog
- debian/control
- + dependency_data/debian-med_3.7.1.json


Changes:

=====================================
debian/changelog
=====================================
@@ -5,7 +5,52 @@ debian-med (3.7.1) unstable; urgency=medium
   * Remove r-other-hms-dbmi-spp since it is r-cran-spp
   * Standards-Version: 4.6.0
 
- -- Andreas Tille <tille at debian.org>  Tue, 23 Nov 2021 08:04:35 +0100
+  * start of automatic changelog entry * 
+  
+  * Changes in metapackage dependencies
+   -med-bio
+    added:
+      Recommends: r-bioc-mofa2, igblast, tipp, haploview, cutesv,
+                  python3-cogent3
+      Suggests:  r-bioc-isoformswitchanalyzer, catfishq, nano-snakemake,
+                 tandem-genotypes, illustrate
+    removed:
+      Recommends: hinge, r-bioc-pcamethods, python3-cogent,
+                  r-other-hms-dbmi-spp, haploview-cran-amap, compclust,
+                  gassst, ccs, ncbi-igblast
+      Suggests:  r-cran-rsgcc, r-bioc-org.ce.eg.db, r-bioc-org.rn.eg.db
+   -med-bio-dev
+    added:
+      Recommends: goby-java, python3-cigar, python3-pangolearn,
+                  python3-compclust
+    removed:
+      Recommends: libgoby-java, r-other-hms-dbmi-spp, pangolearn, libbiod-dev,
+                  python3-hyphy
+      Suggests:  r-cran-rsgcc
+   -med-bio-ngs
+    added:
+      Recommends:  q2cli
+      Suggests:  r-bioc-mofa2, r-bioc-isoformswitchanalyzer
+   -med-covid-19
+    added:
+      Recommends:  tipp, python3-idseq-dag, r-cran-kernelheaping
+    removed:
+      Recommends:  idseq-dag
+   -med-epi
+    added:
+      Recommends:  r-cran-kernelheaping
+   -med-imaging
+    added:
+      Suggests:  illustrate
+   -med-imaging-dev
+    added:
+      Recommends:  libvtk9-dev, libinsighttoolkit5-dev
+      Suggests:  libvtk7-dev
+    removed:
+      Recommends:  libvtk7-dev, libinsighttoolkit4-dev
+      Suggests:  libvtk6-dev
+
+ -- Andreas Tille <tille at debian.org>  Wed, 12 Jan 2022 20:44:28 +0100
 
 debian-med (3.7) unstable; urgency=medium
 


=====================================
debian/control
=====================================
@@ -122,6 +122,7 @@ Recommends: abacas,
             baitfisher,
             bali-phy,
             ballview,
+            bamclipper,
             bamkit,
             bamtools,
             bandage,
@@ -141,6 +142,7 @@ Recommends: abacas,
             bio-rainbow,
             bio-tradis,
             bio-vcf,
+            bioawk,
             biobambam2,
             biosyntax,
             bitseq,
@@ -186,6 +188,7 @@ Recommends: abacas,
             crac,
             csb,
             cutadapt,
+            cutesv,
             daligner,
             damapper,
             datamash,
@@ -221,6 +224,7 @@ Recommends: abacas,
             exonerate,
             fasta3,
             fastahack,
+            fastani,
             fastaq,
             fastdnaml,
             fastlink,
@@ -256,7 +260,6 @@ Recommends: abacas,
             gff2ps,
             gffread,
             ggd-utils,
-            ghemical,
             ghmm,
             glam2,
             gmap,
@@ -278,6 +281,7 @@ Recommends: abacas,
             idba,
             igdiscover,
             igor,
+            igv,
             indelible,
             infernal,
             insilicoseq,
@@ -540,7 +544,6 @@ Recommends: abacas,
             r-cran-webgestaltr,
             r-cran-wgcna,
             r-other-ascat,
-            r-other-hms-dbmi-spp,
             r-other-mott-happy.hbrem,
             r-other-rajewsky-dropbead,
             racon,
@@ -576,7 +579,6 @@ Recommends: abacas,
             saint,
             salmid,
             salmon,
-            sambamba,
             samblaster,
             samclip,
             samtools,
@@ -653,6 +655,7 @@ Recommends: abacas,
             thesias,
             tiddit,
             tigr-glimmer,
+            tipp,
             tm-align,
             tnseq-transit,
             toil,
@@ -711,13 +714,11 @@ Suggests: acacia,
           axpcoords,
           bagpipe,
           bambus,
-          bamclipper,
           bax2bam,
           bcbio,
           biceps,
           big-blast,
           bigsdb,
-          bioawk,
           bismark,
           blat,
           blimps-utils,
@@ -727,13 +728,12 @@ Suggests: acacia,
           cactus,
           caftools,
           card-rgi,
-          ccs,
+          catfishq,
           cdna-db,
           cellprofiler,
           cinema,
           cluster3,
           cmap,
-          compclust,
           conda-package-handling,
           condetri,
           contrafold,
@@ -764,7 +764,6 @@ Suggests: acacia,
           exalt,
           excavator,
           falcon,
-          fastani,
           ffp,
           fieldbioinformatics,
           figaro,
@@ -773,7 +772,6 @@ Suggests: acacia,
           forester,
           forge,
           galaxy,
-          gassst,
           gatk,
           gbrowse-syn,
           genemark,
@@ -783,18 +781,20 @@ Suggests: acacia,
           genographer,
           gerp++,
           getdata,
+          ghemical,
           glimmerhmm,
           gmv,
           gramalign,
           graphbin,
           graphmap2,
-          haploview-cran-amap,
+          haploview,
           hawkeye,
           htqc,
           hts-nim-tools,
           idefix,
           idseq-bench,
-          igv,
+          igblast,
+          illustrate,
           inspect,
           jbrowse,
           jigsaw,
@@ -831,10 +831,10 @@ Suggests: acacia,
           mugsy,
           mummergpu,
           mview,
+          nano-snakemake,
           nanocall,
           nanocomp,
           nanoplot,
-          ncbi-igblast,
           ncbi-magicblast,
           nextsv,
           ngila,
@@ -875,7 +875,7 @@ Suggests: acacia,
           python3-alignlib,
           python3-anndata,
           python3-cgecore,
-          python3-cogent,
+          python3-cogent3,
           python3-cyvcf2,
           python3-deeptools,
           python3-deeptoolsintervals,
@@ -939,10 +939,10 @@ Suggests: acacia,
           r-bioc-go.db,
           r-bioc-grohmm,
           r-bioc-gviz,
-          r-bioc-org.ce.eg.db,
+          r-bioc-isoformswitchanalyzer,
+          r-bioc-mofa2,
           r-bioc-org.hs.eg.db,
           r-bioc-org.mm.eg.db,
-          r-bioc-org.rn.eg.db,
           r-bioc-qusage,
           r-bioc-savr,
           r-bioc-singlecellexperiment,
@@ -965,7 +965,6 @@ Suggests: acacia,
           r-cran-qqman,
           r-cran-rcpphnsw,
           r-cran-rentrez,
-          r-cran-rsgcc,
           r-cran-sctransform,
           r-other-apmswapp,
           r-other-fastbaps,
@@ -982,6 +981,7 @@ Suggests: acacia,
           rose,
           rsat,
           sailfish,
+          sambamba,
           sap,
           science-workflow,
           seq-gen,
@@ -1005,6 +1005,7 @@ Suggests: acacia,
           strelka,
           tab2mage,
           tacg,
+          tandem-genotypes,
           taverna,
           taxinspector,
           tetra,
@@ -1046,6 +1047,7 @@ Recommends: bio-tradis,
             biosquid,
             cwltool,
             gffread,
+            goby-java,
             libace-perl,
             libai-fann-perl,
             libbambamc-dev,
@@ -1075,7 +1077,6 @@ Recommends: bio-tradis,
             libbio-tools-run-remoteblast-perl,
             libbio-variation-perl,
             libbiococoa-dev,
-            libbiod-dev,
             libbiojava-java,
             libbiojava4-java,
             libbioparser-dev,
@@ -1177,6 +1178,7 @@ Recommends: bio-tradis,
             python3-biotools,
             python3-bx,
             python3-cgecore,
+            python3-cigar,
             python3-cobra,
             python3-corepywrap,
             python3-csb,
@@ -1186,7 +1188,6 @@ Recommends: bio-tradis,
             python3-deeptoolsintervals,
             python3-dendropy,
             python3-dnaio,
-            python3-ete3,
             python3-fast5,
             python3-freecontact,
             python3-gfapy,
@@ -1194,6 +1195,7 @@ Recommends: bio-tradis,
             python3-htseq,
             python3-intervaltree-bio,
             python3-kineticstools,
+            python3-loompy,
             python3-mirtop,
             python3-nanoget,
             python3-ngs,
@@ -1218,11 +1220,9 @@ Recommends: bio-tradis,
             python3-ruffus,
             python3-screed,
             python3-shasta,
-            python3-skbio,
             python3-sqt,
             python3-streamz,
             python3-tinyalign,
-            python3-torch,
             python3-treetime,
             python3-wdlparse,
             r-bioc-biobase,
@@ -1232,7 +1232,6 @@ Recommends: bio-tradis,
             r-cran-fitdistrplus,
             r-cran-forecast,
             r-cran-genetics,
-            r-cran-gprofiler,
             r-cran-haplo.stats,
             r-cran-metamix,
             r-cran-phangorn,
@@ -1251,7 +1250,6 @@ Recommends: bio-tradis,
             r-cran-tsne,
             r-cran-vegan,
             r-cran-webgestaltr,
-            r-other-hms-dbmi-spp,
             ruby-bio,
             ruby-crb-blast,
             sbmltoolbox,
@@ -1273,7 +1271,6 @@ Suggests: bioclipse,
           libfreecontact-dev,
           libfreecontact-doc,
           libfreecontact-perl,
-          libgoby-java,
           libmaus2-dev,
           libmilib-java,
           libminimap-dev,
@@ -1292,30 +1289,32 @@ Suggests: bioclipse,
           libtfbs-perl,
           libxxsds-dynamic-dev,
           octace-bioinfo,
-          pangolearn,
           python-biopython-doc,
           python3-alignlib,
           python3-bcbio,
           python3-bel-resources,
           python3-biopython-sql,
           python3-cogent3,
+          python3-compclust,
           python3-consensuscore2,
           python3-cooler,
           python3-ctdopts,
+          python3-ete3,
           python3-galaxy-lib,
-          python3-hyphy,
           python3-intake,
           python3-joypy,
-          python3-loompy,
           python3-mcaller,
           python3-misopy,
           python3-ncls,
           python3-networkx,
+          python3-pangolearn,
           python3-pycosat,
           python3-pyflow,
           python3-roadrunner,
           python3-scanpy,
           python3-seqcluster,
+          python3-skbio,
+          python3-torch,
           python3-unifrac,
           q2-alignment,
           q2-composition,
@@ -1428,6 +1427,7 @@ Suggests: bioclipse,
           r-cran-fastcluster,
           r-cran-future.apply,
           r-cran-future.batchtools,
+          r-cran-gprofiler,
           r-cran-ica,
           r-cran-itertools,
           r-cran-kaos,
@@ -1444,7 +1444,6 @@ Suggests: bioclipse,
           r-cran-robustrankaggreg,
           r-cran-rocr,
           r-cran-rook,
-          r-cran-rsgcc,
           r-cran-rsvd,
           r-cran-shazam,
           r-cran-sitmo,
@@ -1569,7 +1568,6 @@ Recommends: abyss,
             prodigal,
             python3-biomaj3-cli,
             python3-biopython,
-            python3-cogent3,
             qiime,
             r-bioc-edger,
             r-bioc-hilbertvis,
@@ -1607,7 +1605,8 @@ Suggests: bagpipe,
           blast2,
           cufflinks,
           embassy-phylip,
-          giira
+          giira,
+          python3-cogent3
 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
@@ -1649,9 +1648,7 @@ Architecture: all
 Depends: ${misc:Depends},
          med-config (= ${source:Version}),
          med-tasks (= ${source:Version})
-Recommends: epigrass,
-            python3-seirsplus,
-            python3-torch,
+Recommends: python3-seirsplus,
             python3-treetime,
             r-cran-covid19us,
             r-cran-diagnosismed,
@@ -1662,6 +1659,7 @@ Recommends: epigrass,
             r-cran-epir,
             r-cran-epitools,
             r-cran-incidence,
+            r-cran-kernelheaping,
             r-cran-lexrankr,
             r-cran-seroincidence,
             r-cran-sf,
@@ -1669,9 +1667,11 @@ Recommends: epigrass,
             r-cran-surveillance
 Suggests: chime,
           epifire,
+          epigrass,
           netepi-analysis,
           netepi-collection,
           python3-epimodels,
+          python3-torch,
           r-cran-cmprsk,
           r-cran-covid19,
           r-cran-msm,
@@ -1723,7 +1723,6 @@ Recommends: aeskulap,
             bart,
             bart-view,
             biosig-tools,
-            camitk-imp,
             ctn,
             ctsim,
             dcm2niix,
@@ -1732,12 +1731,10 @@ Recommends: aeskulap,
             dicomnifti,
             dicomscope,
             gdf-tools,
-            ginkgocadx,
             gwyddion,
             imagej,
             invesalius,
             ismrmrd-tools,
-            itksnap,
             king,
             libgdcm-tools,
             medcon,
@@ -1759,6 +1756,7 @@ Recommends: aeskulap,
             plastimatch,
             python3-dipy,
             python3-nibabel,
+            python3-nipy,
             python3-nipype,
             python3-nitime,
             python3-pydicom,
@@ -1778,6 +1776,7 @@ Suggests: afni,
           bioimagexd,
           blox,
           brainvisa,
+          camitk-imp,
           caret,
           cdmedicpacs,
           cellprofiler,
@@ -1804,13 +1803,16 @@ Suggests: afni,
           fsl,
           fslview,
           gimias,
+          ginkgocadx,
           hid,
+          illustrate,
           imagemagick,
           imagevis3d,
           imview,
           incf-nidash-oneclick-clients,
           insightapplications,
           isis,
+          itksnap,
           jemris,
           jist,
           kradview,
@@ -1845,7 +1847,6 @@ Suggests: afni,
           pngquant,
           pymeg,
           python3-mvpa2,
-          python3-nipy,
           science-workflow,
           slicer,
           sofa-apps,
@@ -1881,12 +1882,11 @@ Recommends: cimg-dev,
             gmic,
             libbart-dev,
             libbiosig-dev,
-            libcamitk-dev,
             libcifti-dev,
             libedf-dev,
             libgdf-dev,
             libgiftiio-dev,
-            libinsighttoolkit4-dev,
+            libinsighttoolkit5-dev,
             libismrmrd-dev,
             libmaxflow-dev,
             libmdc2-dev,
@@ -1898,15 +1898,13 @@ Recommends: cimg-dev,
             libodil-dev,
             libopenigtlink-dev,
             libopenslide-dev,
-            libopensurgsim-dev,
             libpapyrus3-dev,
             libsight-dev,
             libteem-dev,
-            libvigraimpex-dev,
             libvistaio-dev,
             libvolpack1-dev,
             libvtk-dicom-dev,
-            libvtk7-dev,
+            libvtk9-dev,
             libxdf-dev,
             octave-bart,
             octave-dicom,
@@ -1920,15 +1918,16 @@ Recommends: cimg-dev,
             python3-mia,
             python3-mne,
             python3-nibabel,
+            python3-nipy,
             python3-nipype,
             python3-nitime,
             python3-openslide,
             python3-pydicom,
             python3-pyxnat,
-            python3-vigra,
             r-cran-rniftilib
 Suggests: emokit,
           libbio-formats-java,
+          libcamitk-dev,
           libcamp-dev,
           libctk-dev,
           libcv-dev,
@@ -1941,15 +1940,17 @@ Suggests: emokit,
           libnifti-doc,
           libopenmeeg-dev,
           libopenslide-java,
+          libopensurgsim-dev,
           libsimpleitk1-dev,
           libvia-dev,
+          libvigraimpex-dev,
           libvmtk-dev,
-          libvtk6-dev,
+          libvtk7-dev,
           libxdffileio-dev,
           python-vmtk,
           python3-mvpa2,
-          python3-nipy,
           python3-simpleitk,
+          python3-vigra,
           pytorch-vision,
           tifffile
 Description: Debian Med image processing and visualization packages development
@@ -2035,7 +2036,6 @@ Depends: ${misc:Depends},
          med-config (= ${source:Version}),
          med-tasks (= ${source:Version})
 Recommends: entangle,
-            ginkgocadx,
             gnumed-client,
             gnumed-server,
             libchipcard-tools,
@@ -2052,6 +2052,7 @@ Suggests: clearhealth,
           freemed,
           freemedforms-emr,
           freeshim,
+          ginkgocadx,
           libctapimkt1,
           medintux,
           mirrormed,


=====================================
dependency_data/debian-med_3.7.1.json
=====================================
@@ -0,0 +1 @@
+{"bio-dev": {"depends": [], "suggests": ["conda-package-handling", "cwlformat", "python3-biopython-sql", "python-biopython-doc", "python3-cogent3", "python3-mcaller", "python3-joypy", "python3-ncls", "python3-pycosat", "libtfbs-perl", "libfreecontact-dev", "libfreecontact-perl", "libfreecontact-doc", "qiime", "q2-alignment", "q2-composition", "q2-cutadapt", "q2-dada2", "q2-deblur", "q2-demux", "q2-diversity", "q2-emperor", "q2-feature-classifier", "q2-feature-table", "q2-fragment-insertion", "q2-gneiss", "q2-longitudinal", "q2-metadata", "q2-phylogeny", "q2-quality-control", "q2-quality-filter", "q2-sample-classifier", "q2-shogun", "q2-taxa", "q2-types", "q2-vsearch", "q2cli", "q2cwl", "q2lint", "q2templates", "r-bioc-affxparser", "r-bioc-affy", "r-bioc-affyio", "r-bioc-altcdfenvs", "r-bioc-annotate", "r-bioc-annotationdbi", "r-bioc-annotationhub", "r-bioc-aroma.light", "r-bioc-arrayexpress", "r-bioc-biocgenerics", "r-bioc-biocneighbors", "r-bioc-biomart", "r-bioc-biomformat", "r-bioc-biostrings", "r-bioc-biovizbase", "r-bioc-bitseq", "r-bioc-bridgedbr", "r-bioc-bsgenome", "r-bioc-cager", "r-bioc-cner", "r-bioc-complexheatmap", "r-bioc-cummerbund", "r-bioc-ctc", "r-bioc-dada2", "r-bioc-deseq", "r-bioc-deseq2", "r-bioc-dnacopy", "r-bioc-ebseq", "r-bioc-enrichedheatmap", "r-bioc-ensembldb", "r-bioc-genefilter", "r-bioc-geneplotter", "r-bioc-genomeinfodb", "r-bioc-genomicalignments", "r-bioc-genomicfeatures", "r-bioc-genomicranges", "r-bioc-geoquery", "r-bioc-go.db", "r-bioc-graph", "r-bioc-gseabase", "r-bioc-gsva", "r-bioc-gviz", "r-bioc-hypergraph", "r-bioc-impute", "r-bioc-iranges", "r-bioc-limma", "r-bioc-makecdfenv", "r-bioc-mergeomics", "r-bioc-metagenomeseq", "r-bioc-mofa", "r-bioc-multiassayexperiment", "r-bioc-nanostringqcpro", "r-bioc-oligo", "r-bioc-oligoclasses", "r-bioc-org.hs.eg.db", "r-bioc-pcamethods", "r-bioc-phyloseq", "r-bioc-preprocesscore", "r-bioc-purecn", "r-bioc-qusage", "r-bioc-rbgl", "r-bioc-rsamtools", "r-bioc-rentrez", "r-bioc-rtracklayer", "r-bioc-s4vectors", "r-bioc-savr", "r-bioc-shortread", "r-bioc-snpstats", "r-bioc-structuralvariantannotation", "r-bioc-titancna", "r-bioc-tfbstools", "r-bioc-tximport", "r-bioc-variantannotation", "r-bioc-xvector", "r-cran-adegenet", "r-cran-adephylo", "r-cran-amap", "r-cran-biwt", "r-cran-dt", "r-cran-dynamictreecut", "r-cran-fastcluster", "r-cran-future.apply", "r-cran-future.batchtools", "r-cran-ica", "r-cran-itertools", "r-cran-kaos", "r-cran-metap", "r-cran-minerva", "r-cran-natserv", "r-cran-nmf", "r-cran-optimalcutpoints", "r-cran-parmigene", "r-cran-pcapp", "r-cran-proc", "r-cran-rann", "r-cran-rcpphnsw", "r-cran-robustrankaggreg", "r-cran-rocr", "r-cran-rook", "r-cran-rsvd", "r-cran-shazam", "r-cran-sitmo", "r-cran-venndiagram", "ruby-rgfa", "librostlab-doc", "librostlab-blast-doc", "libswarm2-dev", "python3-networkx", "libbam-dev", "libfast-perl", "libpbcopper-dev", "libminimap-dev", "libdisorder-dev", "cthreadpool-dev", "python3-pyflow", 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["r-cran-msm", "r-cran-cmprsk", "shiny-server", "python3-epimodels", "repast"], "recommends": ["epigrass", "r-cran-covid19", "r-cran-covid19us", "r-cran-epibasix", "r-cran-epitools", "r-cran-surveillance", "r-cran-epi", "r-cran-diagnosismed", "r-cran-epicalc", "r-cran-epir", "r-cran-seroincidence", "r-cran-incidence", "r-cran-epiestim", "r-cran-kernelheaping", "ushahidi", "r-cran-lexrankr", "r-cran-sf", "r-cran-sjplot", "python3-treetime", "python3-torch", "python3-seirsplus", "chime", "netepi-analysis", "netepi-collection", "epifire"], "ignore": [], "avoid": []}}
\ No newline at end of file



View it on GitLab: https://salsa.debian.org/blends-team/med/-/compare/e3424cb2671cf7102de4ca19bd2e5b7100c837a5...86a7efe0e263316c05164d39e1f20971b0e31d2c

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View it on GitLab: https://salsa.debian.org/blends-team/med/-/compare/e3424cb2671cf7102de4ca19bd2e5b7100c837a5...86a7efe0e263316c05164d39e1f20971b0e31d2c
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