* guix/import/cran.scm (%bioconductor-packages-list-url): Replace variable...
(bioconductor-packages-list-url): ...with this procedure.
(bioconductor-packages-list): Accept optional TYPE argument.
(latest-bioconductor-package-version): Same.
(fetch-description): Determine package type and use it in calls to
LATEST-BIOCONDUCTOR-PACKAGE-VERSION and BIOCONDUCTOR-URI.
(description->package): Pass package type to URI helper procedure; include
package type in annotation or experiment packages from Bioconducter.
* guix/ssh.scm (remote-authorize-signing-key): New variable.
* gnu/machine/ssh.scm (deploy-managed-host): Authorize coordinator's
signing key before any invocations of 'remote-eval'.
(deploy-managed-host): Display an error if a signing key does not exist.
* doc/guix.texi (Invoking guix deploy): Remove section describing manual
signing key authorization.
(Invoking guix deploy): Add section describing the 'authorize?' field.
* gnu/machine.scm (roll-back-machine, &deploy-error, deploy-error?)
(deploy-error-should-roll-back)
(deploy-error-captured-args): New variable.
* gnu/machine/ssh.scm (roll-back-managed-host): New variable.
* guix/scripts/deploy.scm (guix-deploy): Roll-back systems when a
deployment fails.
* doc/guix.texi (Invoking guix deploy): Add section describing
prerequisites for deploying as a non-root user.
* guix/remote.scm (remote-pipe-for-gexp): New optional 'become-command'
argument.
(%remote-eval): New optional 'become-command' argument.
(remote-eval): New 'become-command' keyword argument.
* guix/ssh.scm (remote-inferior): New optional 'become-command'
argument.
(inferior-remote-eval): New optional 'become-command' argument.
(remote-authorize-signing-key): New optional 'become-command' argument.
* gnu/machine/ssh.scm (machine-become-command): New variable.
(managed-host-remote-eval): Invoke 'remote-eval' with the
'#:become-command' keyword.
(deploy-managed-host): Invoke 'remote-authorize-signing-key' with the
'#:become-command' keyword.
* gnu/services.scm (activation-script): Return a <program-file> rather
than a <scheme-file>.
* gnu/deploy.scm (guix-deploy): Remove handling for '--system'.
(show-help): Remove documentation for '--system'.
(%default-options): Remove default setting for 'system'.
* gnu/machine/ssh.scm (machine-ssh-configuration): Add 'system' field.
(managed-host-remote-eval): Pass 'system' field to 'remote-eval'.
(machine-check-building-for-appropriate-system): New variable.
(check-deployment-sanity): Add call to
'machine-check-building-for-appropriate-system'.
* doc/guix.texi (Invoking guix deploy): Describe new 'system' field.
* guix/ssh.scm (remote-system): New variable.
* guix/remote.scm (remote-eval): Use result of 'remote-system' when
lowering the G-Expression.
(remote-eval): Add 'system' keyword argument.
(trampoline): Return a <program-file> rather than a <scheme-file>.
It turns out the list in the release notes is incomplete.
This updates the list from /gnu/store/<hash>-ghc-8.4.3/lib/ghc-8.4.3.
* guix/import/hackage.scm (ghc-standard-libraries): Update list.
* guix/scripts/deploy.scm (load-source-file): Enumerate and include all
submodules of (gnu machine) when loading the provided deployment
specification.
Fixes <https://bugs.gnu.org/36942>.
Reported by ison <ison@airmail.cc>.
guix/scripts/system/reconfigure.scm (install-bootloader-program): Switch
new symlink to the canonical bootloader configuration file.
Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
* guix/build/cargo-build-system.scm (generate-all-checksums): New
procedure.
(update-cargo-lock, patch-cargo-checksums): New phases.
(%standard-phases): Add 'update=cargo-lock after 'configure and
'patch-cargo-checksums after 'patch-generated-file-shebangs.
* doc/guix.texi (Build System)[cargo-build-system]: Mention how
Cargo.lock files are handled.
Fixes <https://bugs.gnu.org/36878>.
Reported by Robert Vollmert <rob@vllmrt.net>.
* guix/scripts/system/reconfigure.scm (upgrade-shepherd-services): Load
all service files, rather than just those of services to be started.
Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
Fixes <https://bugs.gnu.org/36813>.
Reported by Jakob L. Kreuze <zerodaysfordays.sdf.org@sdf.org>.
* guix/gexp.scm (program-file-compiler): Pass #:system and #:target to
'gexp->script'.
(load-path-expression): Add #:system and #:target and honor them.
(gexp->script): Likewise.
* tests/gexp.scm ("program-file #:system"): New test.
* doc/guix.texi (G-Expressions): Adjust accordingly.
Without this, ant reported error messages like
Target "tests" does not exist in the project "null".
Simple using the jar-name is a good compromise.
* guix/build/ant-build-system.scm (default-build.xml): Add attribute
to sxml expression.
Guile-JSON 3.x is incompatible with Guile-JSON 1.x, which we relied on
until now: it maps JSON dictionaries to alists (instead of hash tables),
and JSON arrays to vectors (instead of lists). This commit is about
adjusting all the existing code to this new mapping.
* m4/guix.m4 (GUIX_CHECK_GUILE_JSON): New macro.
* configure.ac: Use it.
* doc/guix.texi (Requirements): Mention the Guile-JSON version.
* guix/git-download.scm (git-fetch)[guile-json]: Use GUILE-JSON-3.
* guix/import/cpan.scm (string->license): Expect vectors instead of
lists.
(module->dist-name): Use 'json-fetch' instead of 'json-fetch-alist'.
(cpan-fetch): Likewise.
* guix/import/crate.scm (crate-fetch): Likewise, and call 'vector->list'
for DEPS.
* guix/import/gem.scm (rubygems-fetch): Likewise.
* guix/import/json.scm (json-fetch-alist): Remove.
* guix/import/pypi.scm (pypi-fetch): Use 'json-fetch' instead of
'json-fetch-alist'.
(latest-source-release, latest-wheel-release): Call 'vector->list' on
RELEASES.
* guix/import/stackage.scm (stackage-lts-info-fetch): Use 'json-fetch'
instead of 'json-fetch-alist'.
(lts-package-version): Use 'vector->list'.
* guix/import/utils.scm (hash-table->alist): Remove.
(alist->package): Pass 'vector->list' on the inputs fields, and default
to the empty vector.
* guix/scripts/import/json.scm (guix-import-json): Remove call to
'hash-table->alist'.
* guix/swh.scm (define-json-reader): Expect pair? or null? instead of
hash-table?.
[extract-field]: Use 'assoc-ref' instead of 'hash-ref'.
(json->branches): Use 'map' instead of 'hash-map->list'.
(json->checksums): Likewise.
(json->directory-entries, origin-visits): Call 'vector->list' on the
result of 'json->scm'.
* tests/import-utils.scm ("alist->package with dependencies"): New test.
* gnu/installer.scm (build-compiled-file)[builder]: Use GUILE-JSON-3.
* gnu/installer.scm (installer-program)[installer-builder]: Likewise.
* gnu/installer/locale.scm (iso639->iso639-languages): Use 'assoc-ref'
instead of 'hash-ref', and pass vectors through 'vector->list'.
(iso3166->iso3166-territories): Likewise.
* gnu/system/vm.scm (system-docker-image)[build]: Use GUILE-JSON-3.
* guix/docker.scm (manifest, config): Adjust for Guile-JSON 3.
* guix/scripts/pack.scm (docker-image)[build]: Use GUILE-JSON-3.
* guix/import/github.scm (fetch-releases-or-tags): Update docstring.
(latest-released-version): Use 'assoc-ref' instead of 'hash-ref'. Pass
the result of 'fetch-releases-or-tags' to 'vector->list'.
* guix/import/launchpad.scm (latest-released-version): Likewise.
* guix/svn-download.scm (<svn-multi-reference>): New record type.
(svn-multi-reference-url, svn-multi-reference-revision,
svn-multi-reference-locations, svn-multi-reference-user-name,
svn-multi-reference-password, svn-multi-fetch): New procedures.
* guix/build/svn.scm (svn-fetch): Use "svn export" instead of "svn checkout"
because it does not include the .svn directory and allows us to fetch single
files.
This restores the behavior of 'guix lint' prior to commit
50fc2384fe.
* guix/lint.scm (check-source)[warnings-for-uris]: Rewrite to stop as
soon as one of URIS is valid.
Fixes a regression introduced in
50fc2384fe.
Previously, 'guix lint -c source coreutils' would complain if one of the
mirrors was unavailable. This is no longer the case.
* guix/lint.scm (check-source)[warnings-for-uris]: Use 'filter-map'.
Remove 'append-map' call.
Use 'append-map' here so that we can meaningfull compare the length or
URIS and that of WARNINGS.
Use '=' to compare lengths.
* guix/discovery.scm (scheme-modules): Rename the inner 'file' to
'relative'. Pass FILE as an addition argument to WARN.
* guix/ui.scm (warn-about-load-error): Add 'module' argument (actually,
what was called 'file' really contained a module name.) Call
'check-module-matches-file' in the catch-all error case.
(check-module-matches-file): New procedure.
* tests/guix-build.sh: Test it.
This simplifies the code since one no longer needs to think about
whether '.guix-channel' was present.
* guix/channels.scm (read-channel-metadata): Always pass a string as the
first argument to 'channel-metadata'.
(read-channel-metadata-from-source): Always return a <channel-metadata>
record.
(channel-instance-dependencies): Remove now unneeded 'match'.
(standard-module-derivation): Assume DIRECTORY is never #f and contains
a leading slash.
* tests/channels.scm (channel-metadata-directory)
(channel-metadata-dependencies): New procedures.
("channel-instance-metadata returns #f if .guix-channel does not
exist"): Remove.
("channel-instance-metadata returns default if .guix-channel does not
exist"): New test.
(make-instance): Use 'write' instead of 'display' when creating
'.guix-channel'.
(instance--no-deps): Remove dependencies.
(instance--sub-directory): New variable.
("channel-instance-metadata and default dependencies")
("channel-instance-metadata and directory"): New tests.
("latest-channel-instances excludes duplicate channel dependencies"):
Expect 'channel-commit' to return a string and adjust accordingly.
The idea is that 'read-channel-metadata' will take care of converting
possibly older versions to the current data type. Thus, storing the
version number is unnecessary.
* guix/channels.scm (<channel-metadata>)[version]: Remove.
(read-channel-metadata, channel-instance-dependencies): Adjust
accordingly.
Until now the 'version' field in '.guix-channel' could be omitted, or it
could be any value.
* guix/channels.scm (read-channel-metadata): Rename to...
(channel-instance-metadata): ... this.
(channel-instance-dependencies): Adjust accordingly.
(read-channel-metadata): New procedure. Use 'match'
to require a 'version' field. Provide proper error handling when the
channel sexp is malformed or when given an unsupported version number.
(read-channel-metadata-from-source): Use 'catch' and
'system-error-errno' instead of 'file-exists?'.
* tests/channels.scm (instance--unsupported-version): New variable.
(read-channel-metadata): Rename to...
(channel-instance-metadata): ... this. Rename tests accordingly.
("channel-instance-metadata rejects unsupported version"): New test.
Ricardo Wurmus