debian/changelog

+debian-med (3.4) unstable; urgency=medium
+
+  * Standards-Version: 4.4.1
+  * Use debhelper-compat
+  * Re-render dependencies without Python2 packages
+
+  * start of automatic changelog entry * 
+  
+  * Changes in metapackage dependencies
+   -med-bio
+    added:
+      Recommends:  python3-deeptoolsintervals, skesa, python3-orange, vg,
+                   mmseqs2, mindthegap, kaptive, r-cran-tsne,
+                   python3-deeptools, r-cran-seurat, python3-cogent,
+                   kleborate, python3-reaper, python3-treetime, pizzly,
+                   trim-galore, pigx-scrnaseq, pigx-rnaseq,
+                   r-bioc-multiassayexperiment, wham-align, r-other-wgcna,
+                   r-bioc-mofa, seqcluster, r-cran-kaos, r-cran-drinsight
+      Suggests:  r-bioc-tximport, r-bioc-qusage, python3-pyflow,
+                 python3-alignlib, r-cran-corrplot, r-cran-fitdistrplus,
+                 r-cran-dynamictreecut, python3-loompy, strelka,
+                 r-cran-gprofiler, python3-py2bit, r-cran-sctransform
+    removed:
+      Recommends:  python-orange, python-treetime, python-reaper, python-cogent
+   -med-bio-dev
+    added:
+      Recommends:  python3-roadrunner, python3-deeptoolsintervals,
+                   r-other-hms-dbmi-spp, python3-loompy, python3-py2bit,
+                   r-cran-rotl, r-cran-seqinr, libseqan2-dev, r-cran-boolnet,
+                   r-other-apmswapp, r-cran-vegan, r-cran-tsne, gffread,
+                   python3-deeptools, r-cran-seurat, r-cran-corrplot,
+                   r-cran-fitdistrplus, r-cran-qqman, r-cran-metamix,
+                   r-cran-pscbs, r-cran-pheatmap, r-cran-sctransform,
+                   r-cran-adephylo, r-cran-phangorn, r-cran-distory,
+                   python3-htseq, libmaus2-dev, python3-rdkit, r-cran-samr,
+                   r-cran-webgestaltr, python3-freecontact, libseqan3-dev,
+                   r-cran-rentrez, r-cran-adegenet, r-cran-dynamictreecut,
+                   r-cran-gprofiler, r-cran-forecast, libgclib,
+                   python3-biom-format, r-cran-drinsight
+      Suggests:  r-cran-rann, r-bioc-biostrings, r-bioc-deseq2,
+                 r-bioc-mergeomics, r-cran-metap, r-bioc-qusage,
+                 python3-pyflow, python3-pycosat, r-bioc-metagenomeseq,
+                 r-bioc-annotate, r-bioc-cner, r-bioc-geneplotter,
+                 r-bioc-ensembldb, r-bioc-rentrez, r-bioc-tximport,
+                 r-bioc-rtracklayer, r-bioc-annotationhub, r-bioc-ebseq,
+                 r-bioc-go.db, r-bioc-limma, r-cran-ica, r-bioc-pcamethods,
+                 r-bioc-savr, r-cran-rsvd, python3-alignlib,
+                 r-cran-future.batchtools, r-bioc-tfbstools, r-bioc-bitseq,
+                 r-bioc-cummerbund, r-bioc-multiassayexperiment, r-bioc-gviz,
+                 r-bioc-genefilter, r-bioc-phyloseq, r-bioc-impute,
+                 r-bioc-aroma.light, r-cran-future.apply, r-bioc-mofa,
+                 r-bioc-dnacopy
+    removed:
+      Recommends:  python-htseq, python-mmtk, python-rdkit, python-screed,
+                   python-biom-format, python-roadrunner, python-freecontact
+      Suggests:  python-pyflow, r-cran-rentrez
+   -med-bio-ngs
+    added:
+      Recommends:  wham-align
+   -med-cloud
+    removed:
+      Recommends:  python-biopython
+   -med-data
+    added:
+      Recommends:  python3-hl7
+      Suggests:  oscar
+    removed:
+      Recommends:  python-hl7
+   -med-epi
+    added:
+      Recommends:  python3-treetime
+    removed:
+      Recommends:  python-treetime
+   -med-imaging
+    added:
+      Recommends:  python3-nibabel, python3-mvpa2, python3-dicom,
+                   python3-surfer, tifffile
+    removed:
+      Recommends:  python-surfer, python-mvpa2, python-dicom,
+                   python-nibabel, python-tifffile
+   -med-imaging-dev
+    added:
+      Recommends:  python3-mia, python3-mvpa2, python3-dicom,
+                   python3-openslide, python3-gdcm, python3-imageio,
+                   python3-mne, python3-nibabel
+      Suggests:  tifffile
+    removed:
+      Recommends:  python-mia | python3-mia, python-gdcm, python-mne,
+                   python-mvpa2, python-dicom, python-nibabel,
+                   python-imageio, python-openslide
+      Suggests:  python-libavg, python-tifffile
+   -med-physics
+    added:
+      Suggests:  python3-multipletau
+    removed:
+      Suggests:  python-multipletau
+   -med-practice
+    added:
+      Recommends:  oscar
+   -med-psychology
+    removed:
+      Suggests:  python-visionegg
+   -med-tools
+    added:
+      Recommends:  python3-fitbit
+      Suggests:  oscar
+    removed:
+      Recommends:  python-clips, python-fitbit
+
+ -- Andreas Tille <tille@debian.org>  Sat, 05 Oct 2019 12:02:38 +0200
+
 debian-med (3.3) unstable; urgency=medium
 
   * Re-render tasks with Buster release state

debian/compat

-12

debian/control.stub

@@ -4,8 +4,8 @@ Uploaders: Andreas Tille <tille@debian.org>
 Section: misc
 Priority: optional
 Build-Depends-Indep: blends-dev (>= 0.7.2~),
-                     debhelper (>= 12~)
-Standards-Version: 4.3.0
+Build-Depends: debhelper-compat (= 12)
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/blends-team/med
 Vcs-Git: https://salsa.debian.org/blends-team/med.git
 

tasks/imaging

@@ -862,5 +862,3 @@ Recommends: dcm2niix
 Recommends: orthanc-wsi
 
 Recommends: odil
-
-Suggests: tifffile