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22. By Andreas Tille on 2015-09-01

* Moved to Git

* start of automatic changelog entry *

* Changes in metapackage dependencies
 -med-tools
  removed:
    Depends: python3-fitbitscraper
 -med-bio
  added:
    Depends: sortmerna, r-bioc-limma, r-cran-metamix, iqtree,
              relion-bin+gui | relion-bin+mpi+gui, berkeley-express,
              daligner, mhap, sumatra, hyphy-mpi | hyphy-pt,
              python-pbalign, bio-rainbow, python-kineticstools,
              ea-utils, suitename, wgsim, r-bioc-annotate, r-bioc-edger,
              adun-core, r-bioc-genefilter, hyphygui, sumtrees, blasr,
              repeatmasker-recon, pbdagcon, relion-bin | relion-bin+mpi,
              axe-demultiplexer, tantan
    Suggests: adun.app
  removed:
    Depends: relion-bin | relion-bin-mpi, express, relion-gui, hyphy,
              adun.app
 -med-imaging-dev
  added:
    Depends: libvtk-dicom-java, libmaxflow-dev, libvtk-dicom0.5-dev
    Suggests: liblimereg-dev
  removed:
    Depends: libvtk-dicom0.4-dev
    Suggests: limereg-dev
 -med-bio-dev
  added:
    Depends: libdivsufsort-dev, python3-cutadapt | python-cutadapt,
              python3-skbio | python-skbio, python3-dendropy |
              python-dendropy, python3-ruffus | python-ruffus,
              python3-hyphy | python-hyphy
  removed:
    Depends: librdp-readseq-java, librdp-alignment-java

21. By Andreas Tille on 2015-07-02

* Build-Depends: blends-dev (>= 0.6.92.3) to enable respecting user PATH
  /usr/lib/debian-med/bin
* Fix bashism issue since fixed in blends-dev
  Closes: #772308
* Rebuild in Jessie
* Updated descriptions for his and laboratory
* Introduce /usr/lib/debian-med/bin as PATH for Debian Med users

20. By Andreas Tille on 2015-03-29

* Fixed syntax of med-cloud and rerender dependencies
* Versioned Build-Depends: blends-dev (>= 0.6.92.2) to ensure no packages
  from non-free or unstable will be included by accident
* Since last metapackage creation (and before freeze) the following
  packages made it into testing:
   fastaq,
   relion-bin + librelion-dev
  These were adde to the list of Recommends
* After the freeze the package
   psychopy
  was removed from testing and thus it is removed from Recommends

19. By Andreas Tille on 2014-10-23

* debian/control.stub:
   - Build-Depends: blends-dev (>= 0.6.92) to get Section: metapackage entries
   - cme fix dpkg-control
   - debhelper 9
* d/source/format: 3.0 (native)

* start of automatic changelog entry *

* Changes in metapackage dependencies
 -med-pharmacy
  added:
    Depends: r-cran-dosefinding
 -med-tools
  added:
    Depends: cronometer, python-fitbit, python3-fitbitscraper, nut-nutrition
    Suggests: goldencheetah
  removed:
    Suggests: cl-pubmed
 -med-cloud
  added:
    Depends: bagpipe, fitgcp, fastqc, biomaj, sibsim4, biosquid, pdb2pqr,
              soapdenovo, clonalframe, kissplice, conservation-code, mummer,
              gasic, datamash, t-coffee, ampliconnoise, cassiopee, snap,
              tabix, flexbar, zalign, parsinsert, smalt, melting,
              r-cran-vegan, autodock-vina, cufflinks, mafft, dialign, glam2,
              freecontact, probabel, mustang, amap-align, gromacs, anfo,
              sigma-align, giira, blast2, bowtie, phyutility, poa, dialign-tx,
              arden, qiime, squizz, theseus, gmap, autogrid, r-bioc-edger,
              cd-hit, dnaclust, idba, probcons, discosnp, prodigal, cain,
              sra-toolkit, clearcut, gff2ps, genometools, neobio, mrbayes,
              pynast, sim4, bioperl, prank, perm, prime-phylo,
              mira-assembler, bowtie2, vcftools, mapsembler2, r-cran-pvclust,
              hmmer, cdbfasta, clustalw, wise, kalign, soapdenovo2, boxshade,
              clustalo, python3-biopython, proda, abyss, primer3, grinder,
              fastx-toolkit, rtax, minia, mlv-smile, concavity,
              r-other-mott-happy.hbrem, ncbi-epcr, gff2aplot, macs, mothur,
              hhsuite, fasttree, mipe, bamtools, aragorn, bioperl-run,
              exonerate, jellyfish, aevol, circos, paraclu, python-biopython,
              muscle, dssp
  removed:
    Depends: clustalw | clustalw-mpi, r-other-mott-happy, bagphenotype
 -med-psychology
  added:
    Depends: python-pypsignifit
    Suggests: python-visionegg
  removed:
    Depends: psignifit3
    Suggests: visionegg
 -med-bio
  added:
    Depends: bagpipe, minia, emmax, clearcut, metastudent, cassiopee,
              freebayes, relion-gui, r-cran-vegan, uc-echo, spades, pdb2pqr,
              probabel, relion-bin | relion-bin-mpi, mrs, acacia, staden,
              snp-sites, r-bioc-rtracklayer, kissplice, giira, aragorn, rtax,
              gasic, fitgcp, chimeraslayer, perm, prime-phylo,
              velvetoptimiser, saint, crac, grabix, phyutility, r-bioc-gviz,
              ray, spread-phy, r-other-mott-happy.hbrem, pycorrfit,
              rate4site, varscan, mapsembler2, flexbar, trimmomatic,
              blimps-utils, nast-ier, blat, bitseq, mach-haplotyper,
              ngsqctoolkit, discosnp, emperor, dnaclust, unc-fish, idba,
              r-cran-ape, openms, topp, parsinsert, aevol, fsa, biceps,
              ipig, kclust, circos, strap-base, freecontact, wigeon, fastaq,
              soapdenovo2, r-bioc-biostrings, seqan-apps, eigensoft,
              prodigal, modeller, arden, paraclu, situs, pyscanfcs
    Suggests: biomaj-watcher, mobyle-tutorials, r-cran-boolnet,
              mobyle-programs
    Ignore: mozilla-biofox
  removed:
    Depends: r-ape, sra-sdk, ray-denovoassembler, phy-spread | spread-phy,
              fas, vegan, dotur, r-other-mott-happy, bagphenotype
    Suggests: circos, pdb2pqr, seqan-apps, eigensoft, blimps-utils,
              python-rdkit, mozilla-biofox
 -med-his
  added:
    Depends: vista-foia
  removed:
    Depends: vista
 -med-bio-ngs
  added:
    Depends: kissplice
  removed:
    Depends: ssaha2
 -med-practice
  added:
    Suggests: libctapimkt1
  removed:
    Depends: freeicd
    Suggests: libctapimkt0
 -med-imaging-dev
  added:
    Depends: libedf-dev, libpapyrus3-dev, libmialm-dev, r-cran-rniftilib,
              libvmtk-dev, libvtk-dicom0.4-dev,
              libinsighttoolkit3-dev | libinsighttoolkit4-dev,
              python-mia | python3-mia, octave-gdf, python-vmtk,
              python-mvpa2, libvigraimpex-dev, libteem-dev, python-vigra,
              libmia-2.2-dev, libmiaviewit-dev, python-mne
    Suggests: libics-dev, python-tifffile, libvtkedge-dev
  removed:
    Depends: libmia-2.0-dev, python-mvpa, libteem1-dev,
              libinsighttoolkit3-dev
 -med-imaging
  added:
    Depends: mia-viewit, vtk-dicom-tools, pixelmed-apps, conquest-common,
              teem-apps, gdf-tools, python-surfer, python-mvpa2,
              python-dicom, python-nibabel
    Suggests: conquest-mysql, trimage, conquest-dbase, openwalnut-qt4,
              conquest-sqlite, python-pyxid, conquest-postgres
  removed:
    Depends: conquest-dicom-server, python-mvpa, pixelmed-java, python-nifti
    Suggests: pysurfer, pyxid, openwalnut
 -med-bio-phylogeny
  added:
    Depends: spread-phy
  removed:
    Depends: phy-spread | spread-phy
 -med-bio-dev
  added:
    Depends: python-rdkit, libbambamc-dev, libgenome-1.3-dev,
              libfreecontact-perl, libhts-dev,
              libgenome-model-tools-music-perl, python-corepywrap, pyfai,
              libsnp-sites1-dev, libgenome-perl, libfreecontact0-dev,
              libssm-dev, python-biopython | python3-biopython, sbmltoolbox,
              python-csb | python3-csb, python-htseq, python-freecontact,
              libopenms-dev, librelion-dev
    Suggests: r-bioc-iranges, r-bioc-variantannotation, r-bioc-bsgenome,
              r-bioc-preprocesscore, r-bioc-shortread, r-bioc-affy,
              python-biopython-sql | python3-biopython-sql,
              python-biopython-doc, r-bioc-makecdfenv, libfreecontact-doc,
              libgtextutils-dev, r-bioc-affyio, librostlab-doc,
              r-bioc-hypergraph, r-bioc-biovizbase, r-bioc-genomeinfodb,
              librostlab-blast-doc, r-bioc-graph, r-bioc-xvector,
              r-bioc-genomicfeatures, r-bioc-annotationdbi, r-bioc-snpstats,
              r-bioc-rsamtools, r-bioc-altcdfenvs, r-bioc-genomicranges,
              r-bioc-genomicalignments, r-bioc-biomart
  removed:
    Depends: libqsearch-dev, iranges, libopenmm4-dev, librostlab-blast-doc,
              libgenome-1.3-0-dev, biostrings, librostlab-doc,
              python-biopython, python-librcsb-core-wrapper, octave-bioinfo
 -med-epi
  added:
    Depends: ushahidi
 -med-physics
  added:
    Depends: gdf-tools, biosig-tools
    Suggests: python-biosig, octave-biosig, python-multipletau, libbiosig-dev
  removed:
    Depends: biosig

18. By Andreas Tille on 2012-12-20

* Build-Depends: blends-dev (>= 0.6.16.2)
* Added dependency in imaging-dev: libopenigtlink1-dev

17. By Andreas Tille on 2012-11-27

Revert name change from med-pharmacy -> med-pharma
Closes: #694424

16. By Andreas Tille on 2012-11-07

* med-rehabilitation: sitplus is back to testing - regenerate dependencies
* Some new prospective packages in tasks

15. By Andreas Tille on 2012-11-05

* debian/control:
  Usual changes of dependency based on the resolving of new packages
  in Debian as specified in the tasks files
* config/control: Enhanced readability and spelling of long description
* Added dependencies due to packages progressing to testing after last upload
   Bio: r-cran-genabel, gentle, dssp, neobio, fasttree
   Bio-dev: libbiojava3-java, libai-fann-perl, librg-blast-parser-perl,
            libsort-key-top-perl, libhmsbeagle-dev
   Imaging: ants, king
   Practice: freediams, freemedforms-freedata, freemedforms-emr
* Removed dependencies due to packages removed from testing
   Bio: gassst (removed in #689957)
   Rehabilitation: sitplus (lacking build-depends in testing, see #680798)
* Renamed metapackages: med-pharmacy -> med-pharma
* Add debian/med-*.lintian-overrides to prevent false positives about
  homepage links

14. By Andreas Tille on 2012-04-05

* debian/control(.stub):
  Standards-Version: 3.9.3 (no changes needed)
* debian/control:
  Usual changes of dependency based on the resolving of new packages
  in Debian as specified in the tasks files
* tasks/physics: s/octave3.2/octave/
  Closes: #667588

13. By Andreas Tille on 2011-12-16

* tasks/oncology: Fix typo
  Closes: #647987
* tasks/dental: Fullfilled dependency imagetooth results in new
  metapackage med-dental