Merge branch 'master' into core-updates

substitute: Rename cache directory from "substitute-binary" to "substitute".

* guix/scripts/substitute.scm (%narinfo-cache-directory): Change
  "substitute-binary" to "substitute".
* tests/store.scm ("substitute query"): Likewise.
* tests/substitute.scm (call-with-narinfo): Likewise.

Rename 'guix substitute-binary' to 'guix substitute'.

* guix/scripts/substitute-binary.scm: Rename to...
* guix/scripts/substitute.scm: ... this.  Adjust module name, entry
  point, comments, and help string accordingly.
* nix/scripts/substitute-binary.in: Rename to...
* nix/scripts/substitute.in: ... this.
* pre-inst-env.in (NIX_SUBSTITUTERS): Adjust accordingly.
* tests/substitute-binary.scm: Rename to...
* tests/substitute.scm: ... this.  Adjust references to (guix scripts
  substitute) accordingly.
* guix/ui.scm (show-guix-help)[internal?]: Change "substitute-binary" to
  "substitute".
* Makefile.am (MODULES, SCM_TESTS): Adjust to file renames.
* daemon.am (nodist_pkglibexec_SCRIPTS): Likewise.
* config-daemon.ac: Likewise.
* guix/tests.scm (call-with-derivation-narinfo): Adjust comments and
  docstring.

derivations: 'substitution-oracle' now ignores sub-trees that are valid.

Before that, "guix build qt", when only qt itself is missing, would lead
'substitution-oracle' to call 'substitutable-paths' with 318 items.
Now, this is down to 6 items, because it doesn't ask about prerequisites
that are already valid.

* guix/derivations.scm (substitution-oracle)[valid-input?,
  dependencies]: New procedures.
  Use 'dependencies' and remove call to 'remove'.

derivations: Add a 'cut?' parameter to 'derivation-prerequisites'.

* guix/derivations.scm (valid-derivation-input?): New procedure.
  (derivation-prerequisites): Add 'cut?' parameter and honor it.
* tests/derivations.scm ("derivation-prerequisites and
  derivation-input-is-valid?"): New test.

gnu: python: Do not use patchelf.

* gnu/packages/python.scm (python-2): Add rpath for lib directory of output to
  LDFLAGS.  Remove 'patchelf' from inputs.  Remove #:modules and
  #:imported-modules from arguments.  Remove 'add-lib-to-runpath' phase.
  (python): Do not add #:modules to inherited package arguments.

derivations: Don't invoke the substituter when an item is already in store.

Fixes <http://bugs.gnu.org/20188>.
Reported by Mark H Weaver <mhw@netris.org>.

* guix/derivations.scm (substitution-oracle): Add 'valid?' procedure.
  Remove 'valid?' items from PATHS.

packages: Add zip archive support to 'patch-and-repack'.

Fixes <http://bugs.gnu.org/19830>.

* guix/packages.scm (%standard-patch-inputs): Add "unzip".
  (patch-and-repack)[decompression-type]: Detect zip archive.
  [build]: Invoke "unzip" when appropriate.

gnu: calibre: Add a patch to avoid automatic checking for updates.

* gnu/packages/patches/calibre-no-updates-dialog.patch: New file.
* gnu-system.am (dist_patch_DATA): Register patch.
* gnu/packages/ebook.scm (calibre): Use patch.

gnu: Add pbtranscript-tofu.

* gnu/packages/bioinformatics.scm (pbtranscript-tofu): New variable.

gnu: Add python2-bx-python.

* gnu/packages/bioinformatics.scm (python2-bx-python): New variable.

gnu: Add python2-pbcore.

* gnu/packages/bioinformatics.scm (python2-pbcore): New variable.

gnu: guix: Update snapshot.

* gnu/packages/package-management.scm (guix-devel): Update.

gnu: geiser: Make description more concise and less personal.

* gnu/packages/emacs.scm (geiser)[description]: Tweak.

gnu: geiser: Update to 0.7.

* gnu/packages/emacs.scm (geiser): Update to 0.7.

substitute-binary: Remove thread-safe 'regexp-exec' wrapper.

* guix/scripts/substitute-binary.scm: Remove 'regexp-exec' setting.

substitute-binary: Pipeline HTTP requests instead of using threads.

* guix/scripts/substitute-binary.scm (fetch-narinfo, %lookup-threads,
  n-par-map*): Remove.
  (narinfo-cache-file, cached-narinfo, cache-narinfo!, narinfo-request,
  http-multiple-get, read-to-eof, fetch-narinfos, lookup-narinfos,
  narinfo-from-file): New procedures.
  (lookup-narinfo): Rewrite in terms of 'lookup-narinfos'.
  (guix-substitute-binary): Use 'lookup-narinfos' instead of
  'lookup-narinfo'.

substitute-binary: Allow callers to specify the size of a narinfo.

* guix/scripts/substitute-binary.scm (read-narinfo): Add #:size
  parameter and honor it.

Remove unused patchelf inputs.

* gnu/packages/maths.scm (lapack, gmsh), gnu/packages/ssh.scm (libssh): Remove
  unused patchelf from native-inputs.

gnu: bigloo: Use Emacs with X11 support.

* gnu/packages/scheme.scm (bigloo)[inputs]: Change EMACS-NO-X to EMACS.