gnu: python-numpydoc: Correct inputs.

This does what 213d1745c6adbfd274b1edc575529e026b0ab743 was
supposed to do.

* gnu/packages/python.scm (python-numpydoc, python-numpydoc)
Change first of the duplicate [native-inputs] definitions to
[propagated-inputs].

gnu: calibre: Do not use python setuptools for building.

* gnu/packages/ebook.scm (calibre)[arguments]: Set #:use-setuptools?
to false.

gnu: file-system-shepherd-service: Use mount-file-system.

* gnu/services/base.scm (file-system-shepherd-service): Use
  mount-file-system instead of manually mounting the file system.

gnu: Add dnscrypt-proxy.

* gnu/packages/dns.scm (dnscrypt-proxy): New variable.

gnu: Add dnscrypt-wrapper.

* gnu/packages/dns.scm (dnscrypt-wrapper): New variable.

gnu: virt-manager: Do not use python setuptools for building.

* gnu/packages/qemu.scm (virt-manager)[arguments]: Set #use-setuptools? to #f.

gnu: dblatex: Update to 0.3.9.

* gnu/packages/docbook.scm (dblatex): Update to 0.3.9.

gnu: libsigc++: Update to 2.10.0.

* gnu/packages/glib.scm (libsigc++): Update to 2.10.0.

gnu: go-1.7: Update to 1.7.4 [security fixes].

* gnu/packages/golang.scm (go-1.7): Update to 1.7.4.

gnu: vtk: Build with more system libraries.

* gnu/packages/vtk.scm (vtk)[inputs]: Add expat, freetype, hdf5, jpeg,
png, tiff, jsoncpp, libogg, libtheora, and zlib.
[arguments]: Use #:build-type keyword.  Add cmake flags for system
libraries.

gnu: vtk: Upgrade to 7.1.0.

* gnu/packages/vtk.scm (vtk): Upgrade to 7.1.0.
[source]: Remove patches.  Use version-major+minor.
* gnu/packages/patches/vtk-mesa-10.patch: Delete patch.
* gnu/local.mk (dist_patch_DATA): Remove it.

gnu: jsoncpp: Build shared libraries.

* gnu/packages/serialization.scm (jsoncpp)[arguments]: New field.

gnu: netcdf: Upgrade to 4.4.1.1.

* gnu/packages/maths.scm (netcdf, netcdf-parallel-openmpi): Upgrade to
4.4.1.1.
[source]: Adjust patch name, add netcdf-tst_h_par.patch
* gnu/packages/patches/netcdf-config.date.patch: Rename to...
* gnu/packages/patches/netcdf-date-time.patch: ...this.  Adjust for
latest source.
* gnu/packages/patches/netcdf-tst_h_par.patch: New patch.
* gnu/local.mk (dist_patch_DATA): Adjust patches.

gnu: offlineimap: Update to 7.0.12.

* gnu/packages/mail.scm (offlineimap): Update to 7.0.12.

gnu: dblatex: Do not use python setuptools for building.

* gnu/packages/docbook.scm (dblatex)[arguments]: Set #:use-setuptools?
to false.

offload: Do not abort when a machine is unreachable.

* guix/scripts/offload.scm (machine-load): Wrap 'open-ssh-session' call
in 'false-if-exception'; return +inf.0 if it returns #f.

offload: Gracefully report connection failures.

* guix/scripts/offload.scm (open-ssh-session): Check the return value of
'connect!'.  Call 'leave' when it's not 'ok.

store: Increase buffering for the '%stderr-write' upcall.

* guix/store.scm (process-stderr) <%stderr-write>: Pass #:buffer-size to
'dump-port'.

daemon: Buffer data sent to clients by the 'export-path' RPC.

Before that we'd have STDERR_WRITE round trips for very small amounts of
data, ranging from a few bytes for the metadata of nars to the size of
one file being exported.

With this change, something like:

  guix archive --export /gnu/store/5rrsbaghh5ix1vjcicsl60gsxilhjnf2-coreutils-8.25 | dd of=/dev/null

reports a throughput of 35 MB/s instead of 25 MB/s before.

* nix/nix-daemon/nix-daemon.cc (TunnelSink): Inherit from 'BufferedSink'
rather than 'Sink'.  Rename 'operator ()' to 'write'.
(performOp) <wopExportPath>: Add 'sink.flush' call.

offload: Warn about the lack of zlib support.

* guix/scripts/offload.scm (guix-offload): Print a warning when
'zlib-support?' returns false.