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2021-06-01gnu: rust-cbindgen@0.17: Update to 0.19.0.Jonathan Brielmaier
* gnu/packages/rust-apps.scm (rust-cbindgen-0.17): Update to 0.19.0 and rename to rust-cbindgen-0.19.
2021-06-01tests: hpcguix-web: Fix it.Mathieu Othacehe
* gnu/tests/web.scm (run-hpcguix-web-server-test): Increase the VM memory size and add retries for the http-get test.
2021-06-01gnu: Add bamutils.Roel Janssen
* gnu/packages/bioinformatics.scm (bamutils): New variable.
2021-06-01gnu: sbcl: Update to 2.1.5.Pierre Neidhardt
* gnu/packages/lisp.scm (sbcl): Update to 2.1.5.
2021-06-01gnu: Add python-vedo.Paul Garlick
* gnu/packages/python-science.scm (python-vedo): New variable.
2021-06-01gnu: vtk: Wrap python modules.Paul Garlick
* gnu/packages/image-processing.scm (vtk)[inputs]: Add python. [arguments]: Add VTK_WRAP_PYTHON and VTK_PYTHON_VERSION flags.
2021-06-01gnu: guix: Update to 1.3.0-3.50dfbbf.Mathieu Othacehe
* gnu/packages/package-management.scm (guix): Update to 1.3.0-3.50dfbbf.
2021-06-01gnu: Add python-sinfo.Roel Janssen
* gnu/packages/python-xyz.scm (python-sinfo): New variable.
2021-06-01gnu: Add python-stdlib-list.Roel Janssen
* gnu/packages/python-xyz.scm (python-stdlib-list): New variable.
2021-06-01gnu: guix-build-coordinator: Update to 0-30.f9af463.Christopher Baines
* gnu/packages/package-management.scm (guix-build-coordinator): Update to 0-30.f9af463.
2021-06-01publish: Add keep-alive support when sending nar.Mathieu Othacehe
The default Guile web server implementation supports the keep alive mechanism. However, in our custom http-write implementation, the connection is unconditionally close after sending nar files. To prevent that, when supported, add the client port to the server poll set so that further requests can be handled without closing the connection. * guix/scripts/publish.scm (nar-response-port): Rename it into ... (nar-compressed-port): ... this procedure. Operate directly on a given PORT. (http-write): Add keep-alive support when sending nar files. * guix/scripts/substitute.scm (process-substitution): Pass the download size to the progress-report-port procedure so that it doesn't block reading from the input port when keep-alive is supported.
2021-06-01publish: Preserve the request connection header.Mathieu Othacehe
The Guile web server is reading the response connection header to decide whether to close the connection. However, as the request connection header is not forwarded to the response, this mechanism cannot work. * guix/scripts/publish.scm (add-extra-headers): New procedure. (make-request-handler): Use it to forward the request connection header to the response.
2021-06-01progress: Add a download-size argument to progress-report-port.Mathieu Othacehe
* guix/progress.scm (progress-report-port): Add a download-size argument.
2021-05-31services: dnsmasq: Extend 'activation-service'.Brice Waegeneire
* gnu/services/dns.scm (dnsmasq-activation): New procedure … (dnsmasq-service-type): … use it.
2021-05-31services: hostapd: Use package from configuration.Brice Waegeneire
* gnu/services/networking.scm (hostapd-shepherd-services): Replace 'hostapd' by the package specified in the configuration.
2021-05-31tests: Fix loadable-kernel-modules-service tests.Brice Waegeneire
* gnu/tests/linux-modules.scm (run-loadable-kernel-modules-service-test): Actually load the modules with kernel-module-loader-service-type. Use a singleton service instead of defining a custom one. * doc/guix.texi (Service Reference): To give an example of linux-loadable-module-service-type use a singleton instead of defining a new service.
2021-05-31gnu: emacs-tramp: Update to 2.5.0.5.Nicolas Goaziou
* gnu/packages/emacs-xyz.scm (emacs-tramp): Update to 2.5.0.5.
2021-05-31gnu: emacs-solaire-mode: Update to 2.0.0.Nicolas Goaziou
* gnu/packages/emacs-xyz.scm (emacs-solaire-mode): Update to 2.0.0.
2021-05-31gnu: texmacs: Update to 1.99.21.Nicolas Goaziou
* gnu/packages/text-editors.scm (texmacs): Update to 1.99.21.
2021-05-31gnu: emacs-moody: Update to 0.5.5.Nicolas Goaziou
* gnu/packages/emacs-xyz.scm (emacs-moody): Update to 0.5.5.
2021-05-31gnu: emacs-posframe: Update to 1.0.3.Nicolas Goaziou
* gnu/packages/emacs-xyz.scm (emacs-posframe): Update to 1.0.3.
2021-05-31gnu: lagrange: Update to 1.5.0.Solene Rapenne via Guix-patches via
* gnu/packages/web-browsers.scm (lagrange): Update to 1.5.0. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-05-31gnu: Add emacs-eyebrowse.Stefan Reichör
* gnu/packages/emacs-xyz.scm (emacs-eyebrowse): New variable. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-05-31gnu: Add python-easy-ansi.Stefan Reichör
* gnu/packages/python-xyz.scm (python-easy-ansi): New variable. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-05-31gnu: Add emacs-evil-paredit.Xinglu Chen
* gnu/packages/emacs-xyz.scm (emacs-evil-paredit): New variable. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-05-31gnu: tome4: Update to 1.7.3.Solene Rapenne via Guix-patches via
* gnu/packages/games.scm (tome4): Update to 1.7.3. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-05-31gnu: bits: Use git-version and git-file-name.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bits)[version]: Use git-version. [source]: Use git-file-name.
2021-05-31gnu: piranha: Use git-version.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (piranha)[version]: Use git-version.
2021-05-31gnu: r-chipkernels: Use git-version and git-file-name.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-chipkernels)[version]: Use git-version. [source]: Use git-file-name.
2021-05-31gnu: f-seq: Use git-version and git-file-name.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (f-seq)[version]: Use git-version. [source]: Use git-file-name.
2021-05-31gnu: bismark: Use git-file-name.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bismark)[source]: Use git-file-name.
2021-05-31gnu: filevercmp: Use git-version.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (filevercmp)[version]: Use git-version; bind "revision" in outer let.
2021-05-31gnu: r-chipseeker: Move out of experiment section.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-chipseeker): Move the package from the "experiment" section to the section for regular Bioconductor packages.
2021-05-31gnu: r-spp: Move to (gnu packages bioconductor).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-spp): Move from here... * gnu/packages/bioconductor.scm (r-spp): ...to here.
2021-05-31gnu: r-geneoverlap: Move out of experiment section.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-geneoverlap): Move the package definition out of the "experiment" section into the section for regular Bioconductor packages.
2021-05-31gnu: r-phantompeakqualtools: Let-bind commit, set revision to 1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-phantompeakqualtools): Bind the commit outside of the package value. [version]: Use git-version. [source]: Use git-file-name.
2021-05-31gnu: r-methylkit: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-methylkit): Move from here... * gnu/packages/bioconductor.scm (r-methylkit): ...to here.
2021-05-31gnu: r-copywriter: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-copywriter): Move from here... * gnu/packages/bioconductor.scm (r-copywriter): ...to here.
2021-05-31gnu: r-copyhelper: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-copyhelper): Move from here... * gnu/packages/bioconductor.scm (r-copyhelper): ...to here. [source]: Repalce 'string-append' by 'bioconductor-uri' with 'experiment.
2021-05-31gnu: r-chipseq: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-chipseq): Move from here... * gnu/packages/bioconductor.scm (r-chipseq): ...to here.
2021-05-31gnu: r-rhdf5: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-rhdf5): Move from here... * gnu/packages/bioconductor.scm (r-rhdf5): ...to here.
2021-05-31gnu: r-annotationfilter: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-annotationfilter): Move from here... * gnu/packages/bioconductor.scm (r-annotationfilter): ...to here.
2021-05-31gnu: r-rhdf5filters: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-rhdf5filters): Move from here... * gnu/packages/bioconductor.scm (r-rhdf5filters): ...to here.
2021-05-31gnu: r-tximport: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-tximport): Move from here... * gnu/packages/bioconductor.scm (r-tximport): ...to here.
2021-05-31gnu: r-mutationalpatterns: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Move from here... * gnu/packages/bioconductor.scm (r-mutationalpatterns): ...to here.
2021-05-31gnu: r-rcas: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-rcas): Move from here... * gnu/packages/bioconductor.scm (r-rcas): ...to here.
2021-05-31gnu: r-bamsignals: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-bamsignals): Move from here... * gnu/packages/bioconductor.scm (r-bamsignals): ...to here.
2021-05-31gnu: r-rhtslib: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-rhtslib): Move from here... * gnu/packages/bioconductor.scm (r-rhtslib): ...to here.
2021-05-31gnu: r-zlibbioc: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-zlibbioc): Move from here... * gnu/packages/bioconductor.scm (r-zlibbioc): ...to here.
2021-05-31gnu: r-seqlogo: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-seqlogo): Move from here... * gnu/packages/bioconductor.scm (r-seqlogo): ...to here.
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