gnu: python: Replace PYTHONPATH by GUIX_PYTHONPATH.

Using PYTHONPATH as a mean to discover the Python packages had the following
issues:

        1. It is not versioned, so different versions of Python would clash if
        installed in a shared profile.

        2. It would interfere with the host Python site on foreign
        distributions, sometimes preventing a a user to login their GDM
        session (!).

        3. It would take precedence over user installed Python packages
        installed through pip.

        4. It would leak into Python virtualenvs, which are supposed to create
        isolated Python environments.

This changes fixes the above issues by making use of a sitecustomize.py
module.  The newly introduced GUIX_PYTHONPATH environment variable is read
from the environment, filtered for the current Python version of the
interpreter, and spliced in 'sys.path' just before Python's own site location,
which provides the expected behavior.

* gnu/packages/aux-files/python/sitecustomize.py: New file.
* Makefile.am: Register it.
* gnu/packages/python.scm (customize-site)
(guix-pythonpath-search-path): New procedures.
(python-2.7)[phases]{install-sitecustomize.py}: New phase.
[native-inputs]{sitecustomize.py}: New input.
[native-search-paths]: Replace PYTHONPATH with GUIX_PYTHONPATH.
(python-3.9)[native-search-paths]: Likewise.
[phases]{install-sitecustomize}: Override with correct version.
[native-search-paths]: Replace PYTHONPATH with GUIX_PYTHONPATH.
* gnu/packages/commencement.scm (python-boot0):
[phases]{install-sitecustomize}: Likewise.
[native-inputs]{sitecustomize.py}: New input.
[native-search-paths]: Replace PYTHONPATH with GUIX_PYTHONPATH.
* guix/build/python-build-system.scm (site-packages): Do not add a trailing
'/'.

squash! gnu: python: Replace PYTHONPATH by GUIX_PYTHONPATH.

gnu: pixman: Update to 0.40.0.

* gnu/packages/xdisorg.scm (pixman) [version]: Update to 0.40.0.
[license]: Change from X11 to expat.

Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: pixman: Enable some features.

* gnu/packages/xdisorg.scm (pixman) [arguments] Pass --enable-timers and
--enable-gnuplot to #:configure-flags.

Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: openjpeg: Enable tests.

* gnu/packages/image.scm (openjpeg)[arguments]: Enable the test suite.
Pass -DBUILD_UNIT_TESTS, -DBUILD_TESTING, and -DOPJ_DATA_ROOT
to #:configure-flags. Add a new 'disable-failing-tests' phase.
[native-inputs]: Add openjpeg-data.

Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: fontconfig: Update to 2.13.93.

* gnu/packages/patches/fontconfig-hurd-path-max.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Un-register file.
* gnu/packages/fontutils.scm (fontconfig)[source]
{uri}: Use the .tar.xz archive.
{patches}: Remove field.  The patch was merged upstream.
[native-inputs]: Add python-minimal.
[phases]{skip-problematic-tests}: Add phase.
[configure-flags]: Do not set PYTHON to false.
* gnu/packages/fontutils.scm (fontconfig-with-documentation)
[native-inputs]: Add docbook-utils.

gnu: fontconfig-with-documentation: New variable.

In what will become fontconfig 2.14, the complete documentation of fontconfig
requires multiple dependencies that would be problematic to add to this core
package; instead, keep the 'fontconfig' variable package lean and create a new
'fontconfig-with-documentation' package that will be known as "fontconfig" to
the users.

* gnu/packages/fontutils.scm (fontconfig): Hide package.
[outputs]: Remove doc output.
[configure-flags]: Add "--disable-docs" argument.
[phases]{remove-pdf-files}: Remove phase.
{move-man-sections}: Move to...
(fontconfig-with-documentation): ... this new variable with a doc output.

gnu: Replace all uses of texlive-union by texlive-updmap.cfg.

* doc/build.scm (pdf-manual) Replace texlive-union by texlive-updmap.cfg.
* gnu/packages/algebra.scm (pari-gp): Likewise.
* gnu/packages/bioinformatics.scm (discrover, velvet): Likewise.
* gnu/packages/chez.scm (chez-scheme, chez-web, chez-sockets): Likewise.
* gnu/packages/docbook.scm (dblatex): Likewise.
* gnu/packages/emacs-xyz.scm (emacs-auctex): Likewise.
* gnu/packages/engineering.scm (fastcap): Likewise.
* gnu/packages/guile-xyz.scm (emacsy, guile-cv): Likewise.
* gnu/packages/lisp.scm (sbcl): Likewise.
* gnu/packages/maths.scm (octave, hypre): Likewise.
* gnu/packages/music.scm (lilypond): Likewise.
* gnu/packages/plotutils.scm (asymptote): Likewise.
* gnu/packages/python-xyz.scm (python-numpy-documentation)
(python-matplotlib-documentation, python-ipython-documentation)
(python-pypandoc): Likewise.
* gnu/packages/radio.scm (gnuradio, libosmo-dsp): Likewise.
* gnu/packages/scheme.scm (mit-scheme): Likewise.
* gnu/packages/statistics.scm (r-with-tests): Likewise.
* gnu/packages/tex.scm (simple-texlive-package)
(texlive-xmltex, texlive-tiny, texlive-jadetex, teximpatient, lyx): Likewise.

gnu: texlive-amsfonts: Adjust to build with texlive-updmap.cfg.

* gnu/packages/tex.scm (texlive-amsfonts)[phases]
{build-fonts}: Do not set SOURCE_DATE_EPOCH, already done by the build
system.  Let resources be auto-discovered by TeX Live machinery by simply
setting GUIX_TEXMF.  Remove references to the texlive-union input.  Remove
trailing #t.
{install-generated-fonts}: Remove trailing #t.
[native-inputs]: Replace texlive-union by texlive-updmap.cfg.  Remove the
texlive-cm and texlive-metafont arguments of texlive-updmap.cfg.

gnu: texlive-bin: Enable the use of multiple TeX Live trees.

Attempting to compose multiple TeX Live trees (such as can happen when using a
texlive-union generated package) proved problematic; only the texmf.cnf
configuration file from the union would be honored, causing other TeX Live
components to be ignored.

This change does away with TeX Live unions, instead relying on the default
texmf.cnf configuration file provided by the texlive-bin package to honor
individual TeX Live trees referred to via the newly introduced GUIX_TEXMF
variable, and replacing the texlive-union procedure by texlive-updmap.cfg, to
explicit that generating the fonts map configuration is now its sole purpose.

* gnu/packages/tex.scm (texlive-bin)[phases]{customize-texmf}: New phase.
{postint}: Move the patching of the texmf.cnf file to the new above phase.
Patch the updmap.pl script to find its Perl modules.
[native-search-paths]: Rename the TEXMF variable to GUIX_TEXMF.  Remove the
TEXMFCNF variable.
* guix/profiles.scm (texlive-configuration): Remove procedure.
(%default-profile-hooks)[texlive-configuration]: Unregister hook.
(texlive-union): Alias to what has moved to...
(texlivke-updmap.cfg): ... here.  Update doc.  Do not provide a different
texmf.cnf configuration.
[inherit]: Do not inherit from texlive-base.
[build-system]: Switch to the copy-build-system.
[arguments]{install-plan}: New argument.
[phases]{regenerate-updmap.cfg}: New phase, which keeps only the fonts map
generating code from the previous builder code.
[inputs]: Remove bash, and move to ...
[propagated-inputs]: ... here.
[native-inputs]: Remove field, and move the source of the base updmap.cfg file
to...
[source]: ... here.
[synopsis]: Update.
[description]: Likewise.
[license]: Delete duplicates.

gnu: libsigsegv: Update to 2.13.

* gnu/packages/libsigsegv.scm (libsigsegv): Update to 2.13.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: libsndfile: Add opus support.

* gnu/packages/pulseaudio.scm (libsndfile)[inputs]: Move libvorbis,
libogg, flac ...
[propagated-inputs]: ... to here. Add opus.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: postgresql: Set default socket directory.

* gnu/packages/databases.scm (postgresql)[arguments]: Add 'set-socket-dir
phase.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>

gnu: certdata2pem: Fix cross compiling.

* gnu/packages/certs.scm (certdata2pem)[arguments]: Use cc-for-target.

gnu: certdata2pem: Fix source URI.

* gnu/packages/certs.scm (certdata2pem)[source]: Download just the source.

gnu: certs.scm: Add missing import.

* gnu/packages/certs.scm: Use (gnu packages perl).

gnu: nss-certs: Remove Python 2 and Perl build dependencies.

* gnu/packages/certs.scm (certdata2pem): Swap package to a C variant.
(nss-certs): Use 'openssl rehash' instead of the Perl 'c_rehash' script.
Adjust for the new certdata2pem program.  The number of certificates installed
compared to when using the previous script remains unchanged (139 at the time
of this commit).

gnu: nss-certs: Sync with the sources used for nss.

* gnu/packages/certs.scm (nss-certs)[version]: Reuse nss version.
[source]: Reuse nss source.
[phases]{install}: Adjust for the new NSS source files hierarchy.  Remove
trailing #t.

build-systems/gnu: Allow unpacking/repacking more kind of files.

Before this change, only plain directories, tar or zip archives were supported
as the source of a package for the GNU build system; anything else would cause
the unpack phase to fail.  Origins relying on snippets would suffer from the
same problem.

This change adds the support to use files of the following extensions: .gz,
.Z, .bz2, .lz, and .xz, even when they are not tarballs.  Files of unknown
extensions are treated as uncompressed files and supported as well.

* guix/packages.scm (patch-and-repack): Only add the compressor utility to the
PATH when the file is compressed.  Bind more inputs in the mlet, and use them
for decompressing single files.  Adjust the decompression and compression
routines.
[decompression-type]: Remove nested variable.
* guix/build/utils.scm (compressor, tarball?): New procedures.  Move
%xz-parallel-args to the new 'compression helpers' section.
* tests/packages.scm: Add tests.  Add missing copyright year for Jan.
* guix/build/gnu-build-system.scm (first-subdirectory): Return #f when no
sub-directory was found.
(unpack): Support more file types, including uncompressed plain files.

utils: Add NIX_STORE_DIR as a candidate for the value of the store directory.

On the daemon side, nixStore gets set to the environment variable
NIX_STORE_DIR, else the environment variable NIX_STORE else the compile time
macro NIX_STORE_DIR (see the Settings::processEnvironment method in
nix/libstore/globals.cc).  When creating a build environment, it sets
NIX_STORE with the value computed as described above.  Hence, it's safer to
look for both NIX_STORE_DIR and NIX_STORE in (guix build utils), so that it
works in any context (build context or external context).

* guix/build/utils.scm (%store-directory): Consider both NIX_STORE_DIR and
NIX_STORE as environment variables.

gnu: boost: Patch transitive linking bug.

* gnu/packages/patches/boost-fix-transitive-linking.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/boost.scm (boost)[source]: Use it.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>