gnu: Remove python-setuptools and python2-setuptools from inputs (part 2)

This patch contains the changes where removing setuptools from the inputs
affected some code-lines beside.

* gnu/packages/admin.scm (ansible): Remove all [inputs], [native-inputs] and
  [propagated-inputs] where python-setuptools or python2-setuptools are the
  sole entries. Remove python-setuptools and python2-setuptools listed on a
  line by its own from [inputs], [native-inputs] and [propagated-inputs].

* gnu/packages/backup.scm (duplicity): Likewise.
* gnu/packages/bioinformatics.scm (bamm, python2-pybedtools,
  python2-bx-python, python2-dendropy, python-pysam, python2-pysam, clipper,
  crossmap, cutadapt, deeptools, grit, idr, python2-warpedlmm,
  pbtranscript-tofu, seqmagick): Likewise.
* gnu/packages/docbook.scm (dblatex): Likewise.
* gnu/packages/freedesktop.scm (python-pyxdg, python2-pyxdg): Likewise.
* gnu/packages/lirc.scm (python2-lirc): Likewise.
* gnu/packages/mp3.scm (eyed3): Likewise.
* gnu/packages/nutrition.scm (gourmet): Likewise.
* gnu/packages/openstack.scm (python-hacking, python2-hacking,
  python-os-testr, python2-os-testr,
  python-stevedore, python2-stevedore,
  python-tempest-lib, python2-tempest-lib,
  python-oslo.log, python2-oslo.log,
  python-keystoneclient, python2-keystoneclient): Likewise.
* gnu/packages/password-utils.scm (assword): Likewise.
* gnu/packages/python.scm (python-passlib, python2-passlib,
  python-babel, python2-babel,
  python-parse-type,
  python-pytest, python2-pytest,
  python-scripttest, python2-scripttest,
  python-testtools, python2-testtools,
  python-testscenarios, python2-testscenarios,
  python-subunit, python2-subunit,
  python-pbr-0.11,
  python-pbr, python2-pbr,
  python-testrepository, python2-testrepository,
  behave,
  python-wheel, python2-wheel,
  python-requests, python2-requests,
  python-jsonschema, python2-jsonschema,
  python-pyjwt, python2-pyjwt,
  python-virtualenv, python2-virtualenv,
  python-jinja2, python2-jinja2,
  python-joblib, python2-joblib,
  python-sphinx, python2-sphinx,
  python-feedgenerator, python2-feedgenerator,
  python-scikit-image, python2-scikit-image,
  python-redis, python2-redis,
  python2-fastlmm,
  python-numpydoc, python2-numpydoc,
  python-matplotlib, python2-matplotlib,
  python2-pysnptools,
  python-rpy2, python2-rpy2,
  python-pillow, python2-pillow,
  python-pycparser, python2-pycparser,
  python-cffi, python2-cffi,
  python-cairocffi, python2-cairocffi,
  python-drmaa, python2-drmaa,
  python-pathpy, python2-pathpy,
  python-simplegeneric, python2-simplegeneric,
  python-ipython, python2-ipython,
  python-apsw, python2-apsw,
  python-lxml, python2-lxml,
  python-networkx, python2-networkx,
  python-pyzmq, python2-pyzmq,
  python-mccabe, python2-mccabe,
  python-mccabe-0.2.1,
  python-flake8, python2-flake8,
  python-flake8-2.2.4,
  python-mistune, python2-mistune,
  python-ptyprocess, python2-ptyprocess,
  python-llfuse, python2-llfuse,
  python-webob, python2-webob,
  python-xlrd, python2-xlrd,
  python-tables, python2-tables,
  python-pip, python2-pip,
  python-libarchive-c, python2-libarchive-c,
  python-docopt, python2-docopt,
  python-pyrfc3339, python2-pyrfc3339,
  python-configobj, python2-configobj,
  python-clint, python2-clint,
  python-rply, python2-rply,
  python2-rpython,
  python-widgetsnbextension, python2-widgetsnbextension
  jupyter,
  python-jupyter-console, python2-jupyter-console,
  python-hy, python2-hy,
  python-urllib3, python2-urllib3,
  python-rsa, python2-rsa,
  python-tox, python2-tox,
  python2-hypothesis,
  python-paste, python2-paste,
  python-pastescript, python2-pastescript,
  python2-unicodecsv,
  python-pkgconfig, python2-pkgconfig,
  python2-rope,
  python-sqlparse, python2-sqlparse,
  python-gevent, python2-gevent,
  python-tabulate, python2-tabulate,
  python-arrow, python2-arrow,
  python-cleo, python2-cleo,
  python-fake-factory, python2-fake-factory,
  ptpython): Likewise.
* gnu/packages/rdf.scm (python-rdflib, python2-rdflib): Likewise.
* gnu/packages/terminals.scm (asciinema): Likewise.
* gnu/packages/version-control.scm (git-annex-remote-hubic): Likewise.
* gnu/packages/xdisorg.scm (arandr): Likewise.

gnu/packages/bioinformatics.scm

@@ -215,8 +215,7 @@ structure of the predicted RNA.")
        ("libtool" ,libtool)
        ("zlib" ,zlib)
        ("python-nose" ,python2-nose)
-       ("python-pysam" ,python2-pysam)
-       ("python-setuptools" ,python2-setuptools)))
+       ("python-pysam" ,python2-pysam)))
     (inputs
      `(("htslib" ,htslib)
        ("samtools" ,samtools)
@@ -530,8 +529,7 @@ intended to behave exactly the same as the original BWK awk.")
        ("samtools" ,samtools)))
     (native-inputs
      `(("python-pyyaml" ,python2-pyyaml)
-       ("python-nose" ,python2-nose)
-       ("python-setuptools" ,python2-setuptools)))
+       ("python-nose" ,python2-nose)))
     (home-page "https://pythonhosted.org/pybedtools/")
     (synopsis "Python wrapper for BEDtools programs")
     (description
@@ -1342,8 +1340,7 @@ well as many of the command line options.")
      `(("python-numpy" ,python2-numpy)
        ("zlib" ,zlib)))
     (native-inputs
-     `(("python-nose" ,python2-nose)
-       ("python-setuptools" ,python2-setuptools)))
+     `(("python-nose" ,python2-nose)))
     (home-page "http://bitbucket.org/james_taylor/bx-python/")
     (synopsis "Tools for manipulating biological data")
     (description
@@ -1407,7 +1404,6 @@ multiple sequence alignments.")
        ("zlib"              ,zlib)))
     (native-inputs
      `(("python-cython"     ,python-cython)
-       ("python-setuptools" ,python-setuptools)
        ;; Dependencies below are are for tests only.
        ("samtools"          ,samtools)
        ("bcftools"          ,bcftools)
@@ -1583,9 +1579,8 @@ databases.")
        ("python-numpy" ,python2-numpy)
        ("python-scipy" ,python2-scipy)))
     (native-inputs
-     `(("python-mock" ,python2-mock) ; for tests
-       ("python-pytz" ,python2-pytz) ; for tests
-       ("python-setuptools" ,python2-setuptools)))
+     `(("python-mock" ,python2-mock)   ; for tests
+       ("python-pytz" ,python2-pytz))) ; for tests
     (home-page "https://github.com/YeoLab/clipper")
     (synopsis "CLIP peak enrichment recognition")
     (description
@@ -1758,8 +1753,7 @@ time.")
        ("zlib" ,zlib)))
     (native-inputs
      `(("python-cython" ,python2-cython)
-       ("python-nose" ,python2-nose)
-       ("python-setuptools" ,python2-setuptools)))
+       ("python-nose" ,python2-nose)))
     (home-page "http://crossmap.sourceforge.net/")
     (synopsis "Convert genome coordinates between assemblies")
     (description
@@ -1857,8 +1851,7 @@ preparation protocols.")
                  (alist-delete 'check %standard-phases))))
     (native-inputs
      `(("python-cython" ,python-cython)
-       ("python-nose" ,python-nose)
-       ("python-setuptools" ,python-setuptools)))
+       ("python-nose" ,python-nose)))
     (home-page "https://code.google.com/p/cutadapt/")
     (synopsis "Remove adapter sequences from nucleotide sequencing reads")
     (description
@@ -2000,8 +1993,7 @@ trees (phylogenies) and characters.")
                ;; There is currently a test failure that only happens on some
                ;; systems, and only using "setup.py test"
                (lambda _ (zero? (system* "nosetests")))))))
-      (native-inputs `(("python2-setuptools" ,python2-setuptools)
-                       ("python2-nose" ,python2-nose)
+      (native-inputs `(("python2-nose" ,python2-nose)
                        ,@(package-native-inputs base))))))
 
 
@@ -2029,9 +2021,8 @@ trees (phylogenies) and characters.")
        ("python-pysam" ,python2-pysam)
        ("python-pybigwig" ,python2-pybigwig)))
     (native-inputs
-     `(("python-mock" ,python2-mock) ;for tests
-       ("python-pytz" ,python2-pytz) ;for tests
-       ("python-setuptools" ,python2-setuptools)))
+     `(("python-mock" ,python2-mock)   ;for tests
+       ("python-pytz" ,python2-pytz))) ;for tests
     (home-page "https://github.com/fidelram/deepTools")
     (synopsis "Tools for normalizing and visualizing deep-sequencing data")
     (description
@@ -2687,8 +2678,7 @@ comment or quality sections.")
        ("python-pysam" ,python2-pysam)
        ("python-networkx" ,python2-networkx)))
     (native-inputs
-     `(("python-cython" ,python2-cython)
-       ("python-setuptools" ,python2-setuptools)))
+     `(("python-cython" ,python2-cython)))
     (home-page "http://grit-bio.org")
     (synopsis "Tool for integrative analysis of RNA-seq type assays")
     (description
@@ -2934,8 +2924,7 @@ data.  It also provides the bgzip, htsfile, and tabix utilities.")
        ("python-numpy" ,python-numpy)
        ("python-matplotlib" ,python-matplotlib)))
     (native-inputs
-     `(("python-cython" ,python-cython)
-       ("python-setuptools" ,python-setuptools)))
+     `(("python-cython" ,python-cython)))
     (home-page "https://github.com/nboley/idr")
     (synopsis "Tool to measure the irreproducible discovery rate (IDR)")
     (description
@@ -3423,9 +3412,8 @@ linker_so='gcc -shared'); defines")))))
        ("python-scipy" ,python2-scipy)
        ("python-matplotlib" ,python2-matplotlib)))
     (native-inputs
-     `(("python-mock" ,python2-mock) ;for tests
-       ("python-pytz" ,python2-pytz) ;for tests
-       ("python-setuptools" ,python2-setuptools)))
+     `(("python-mock" ,python2-mock)   ;for tests
+       ("python-pytz" ,python2-pytz))) ;for tests
     (home-page "http://genes.mit.edu/burgelab/miso/index.html")
     (synopsis "Mixture of Isoforms model for RNA-Seq isoform quantitation")
     (description
@@ -3562,8 +3550,7 @@ files and writing bioinformatics applications.")
        ("python-pandas" ,python2-pandas)
        ("python-pysnptools" ,python2-pysnptools)))
     (native-inputs
-     `(("python-setuptools" ,python2-setuptools)
-       ("python-mock" ,python2-mock)
+     `(("python-mock" ,python2-mock)
        ("python-nose" ,python2-nose)
        ("unzip" ,unzip)))
     (home-page "https://github.com/PMBio/warpedLMM")
@@ -3625,8 +3612,7 @@ the phenotype as it models the data.")
          ("python-h5py" ,python2-h5py)))
       (native-inputs
        `(("python-cython" ,python2-cython)
-         ("python-nose" ,python2-nose)
-         ("python-setuptools" ,python2-setuptools)))
+         ("python-nose" ,python2-nose)))
       (home-page "https://github.com/PacificBiosciences/cDNA_primer")
       (synopsis "Analyze transcriptome data generated with the Iso-Seq protocol")
       (description
@@ -4750,8 +4736,7 @@ bioinformatics file formats, sequence alignment, and more.")
      ;; should be removed.
      `(("python-biopython" ,python2-biopython-1.66)))
     (native-inputs
-     `(("python-setuptools" ,python2-setuptools)
-       ("python-nose" ,python2-nose)))
+     `(("python-nose" ,python2-nose)))
     (home-page "http://github.com/fhcrc/seqmagick")
     (synopsis "Tools for converting and modifying sequence files")
     (description