The build system expects all Python modules to be on PYTHONPATH.
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww)[arguments]: Set
PYTHONPATH variable in new build phase.
The build system expects all Python modules to be on PYTHONPATH.
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[arguments]: Set PYTHONPATH
variable in new build phase.
The build system expects all Python modules to be on PYTHONPATH.
* gnu/packages/bioinformatics.scm (pigx-bsseq)[arguments]: Set PYTHONPATH
variable in new build phase.
The build system expects all Python modules to be on PYTHONPATH.
* gnu/packages/bioinformatics.scm (pigx-chipseq)[arguments]: Set PYTHONPATH
variable in new build phase.
The build system expects all Python modules to be on PYTHONPATH.
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Set PYTHONPATH
variable in new build phase.
* gnu/packages/patches/jami-libclient-audio-managers.patch: New patch.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/jami.scm (jami)[source]: Move all patches to...
(%jami-sources): here and add the newly added patch.
* guix/inferior.scm (port->inferior): In the inferior, define
'cached-store-connection', 'store-protocol-error?', and
'store-protocol-error-message'.
(inferior-eval-with-store): Use them.
Fixes <https://issues.guix.gnu.org/48007>.
Reported by Ricardo Wurmus <rekado@elephly.net>.
Previously, at each 'inferior-eval-with-store' call, the inferior would
create a new <store-connection> object with empty caches. Consequently,
when repeatedly calling 'inferior-package-derivation', we would not
benefit from any caching and instead recompute all the derivations for
every package. This patch fixes it by caching <store-connection>
objects in the inferior.
* guix/inferior.scm (port->inferior): Define '%store-table' in the inferior.
(inferior-eval-with-store): Cache store connections in %STORE-TABLE.
Remove now unneeded 'dynamic-wind' with 'close-port' call.
Previously, each 'inferior-eval-with-store' would lead the inferior to
connect to the named socket the parent is listening to. With this
change, the connection is established once for all and reused
afterwards.
* guix/inferior.scm (<inferior>)[bridge-file-name]: Remove.
(open-bidirectional-pipe): New procedure.
(inferior-pipe): Use it instead of 'open-pipe*' and return two values.
(port->inferior): Adjust call to 'inferior'.
(open-inferior): Adjust to 'inferior-pipe' changes.
(close-inferior): Remove 'inferior-bridge-file-name' handling.
(open-store-bridge!): Switch back to 'call-with-temporary-directory'.
Define '%bridge-socket' in the inferior, connected to the caller.
(proxy): Change first argument to be an inferior. Add 'reponse-port'
and call to 'drain-input'. Pass 'reponse-port' to 'select' and use it
as a loop termination clause.
(inferior-eval-with-store): Remove 'socket' and 'connect' calls from the
inferior code, and use '%bridge-socket' instead.
Previously, each 'inferior-eval-with-store' call would have the calling
process create a temporary directory with a listening socket in there.
Now that listening socket is created once and reused in subsequent
calls.
* guix/inferior.scm (<inferior>)[bridge-file-name, bridge-socket]: New
fields.
(port->inferior): Adjust accordingly.
(close-inferior): Close 'inferior-bridge-socket' and delete
'inferior-bridge-file-name' if set.
(open-store-bridge!, ensure-store-bridge!): New procedures.
(inferior-eval-with-store): Use them.
* gnu/packages/commencement.scm (%final-inputs-riscv64): New variable.
* guix/build-system/gnu.scm (standard-inputs): Use %final-inputs-riscv64
when targeting riscv64-linux.
This partially reverts commit f15ca337be. What
mattered was the addition of guile-bytestructures.
* gnu/packages/mes.scm (nyacc)[arguments]: Remove phase
'install-system-module.
* gnu/packages/patches/polkit-CVE-2021-4034.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/polkit.scm (polkit-mozjs)[replacement]: New field.
* gnu/packages/polkit.scm (polkit-mozjs/fixed): New variable.
* guix/import/pypi.scm (find-project-url): New function.
(make-pypi-sexp): Use find-project-url.
* tests/pypi.scm (foo-json): New procedure.
(test-json-1, test-json-2): Define in terms of it.
("find-project-url, with numpy", "find-project-url, uWSGI"):
("find-project-url, flake8-array-spacing")
("find-project-url, foo/goo"): New tests.
Co-authored-by: Ludovic Courtès <ludo@gnu.org>
