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* gnu: xl2tpd: Fix build.Mathieu Othacehe2020-06-22
| | | | | * gnu/packages/vpn.scm (xl2tpd)[arguments]: Substitute hardcoded pppd path instead of trying to set CFLAGS variable.
* gnu: python-plotly: Update to 4.8.1.Pierre Langlois2020-06-22
| | | | | | | | | | | | | | | | But keep version 2.4.1 around for packages that still need it and for python2 support. * gnu/packages/graph.scm (python-plotly): Update to 4.8.1. [source]: Use git-fetch so that tests are also included. [arguments]: Enable tests. [home-page]: Follow redirect. (python-plotly-2.4.1): New variable. (python2-plotly): Inherit from python-plotly-2.4.1. * gnu/packages/bioinformatics.scm (python-deeptools)[native-inputs]: Depend on python-plotly-2.4.1. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add python-xarray.Pierre Langlois2020-06-22
| | | | | | | | | | | From 27ec21904f769c1e8114f767972d9037e1e9f68a Mon Sep 17 00:00:00 2001 From: Pierre Langlois <pierre.langlois@gmx.com> Date: Thu, 18 Jun 2020 00:58:02 +0200 Subject: [PATCH 4/5] gnu: Add python-xarray. * gnu/package/python-science.scm (python-xarray): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add python-retrying.Pierre Langlois2020-06-22
| | | | | | * gnu/packages/python-xyz.scm (python-retrying): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: python-pandas: Update to 1.0.5.Pierre Langlois2020-06-22
| | | | | | | | | | | | | | | | | | But also keep version 0.25.3 around for packages requiring an earlier versions, as well as version 0.24.2 for a version with python2. * gnu/packages/python-science.scm (python-pandas): Update to 1.0.5. [arguments]: Adapt 'patch-which phase. Add new 'prepare-x phase. Do not delete tests that depend on "moto", they are skipped automatically. [propagated-inputs]: Add python-jinja2. [inputs]: Add xsel and xclip. [native-inputs]: Add xorg-server-for-tests so we can test clipboard support. (python-pandas-0.24): New variable. (python2-pandas): Inherit from python-pandas-0.25. * gnu/packages/bioinformatics.scm (python-biom-format)[propagated-inputs]: Switch to python-pandas-0.25. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: deeptools: Deprecate in favor of python-deeptools.Pierre Langlois2020-06-22
| | | | | | | | | | And make sure python-deeptools's tests are running. * gnu/packages/bioinformatics.scm (python-deeptools): Fetch source using git. [native-inputs]: Add python-mock and python-nose. (deeptools): Mark as deprecated. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* self: Build with Guile 3.0.3.Ludovic Courtès2020-06-22
| | | | * gnu/packages/guile.scm (guile-3.0/libgc-7): Inherit from GUILE-3.0.3.
* deduplicate: Avoid traversing directories twice.Ludovic Courtès2020-06-22
| | | | | | | | | | | | | Until now, we'd call (nar-sha256 file) unconditionally. Thus, if FILE was a directory, we would traverse it for no reason, and then call 'deduplicate' on FILE, which would again traverse it. This change also removes redundant (mkdir-p store) calls from the loop, and avoids 'lstat' calls by using 'scandir*'. * guix/store/deduplication.scm (deduplicate): Add named loop. Move 'mkdir-p' outside the loop. Use 'scandir*' instead of 'scandir'. Do not call 'nar-sha256' when FILE has type 'directory.
* compile: Build gnu/{packages,tests}/* with '-O1'.Ludovic Courtès2020-06-22
| | | | | * guix/build/compile.scm (optimization-options): Use '-O1' for the simple case.
* gnu: emacs-helm: Update to 3.6.3.Pierre Neidhardt2020-06-22
| | | | * gnu/packages/emacs-xyz.scm (emacs-helm): Update to 3.6.3.
* gnu: emacs-helm-fish-completion: Update to 0.5.Pierre Neidhardt2020-06-22
| | | | * gnu/packages/emacs-xyz.scm (emacs-helm-fish-completion): Update to 0.5.
* gnu: js8call: Fix build.Guillaume Le Vaillant2020-06-22
| | | | * gnu/packages/radio.scm (js8call)[inputs]: Use regular hamlib.
* gnu: wsjtx: Update to 2.2.1.Guillaume Le Vaillant2020-06-22
| | | | | | * gnu/packages/radio.scm (wsjtx-hamlib): Update to 2.2.1. [arguments]: Add a 'fix-tests' phase. (wsjtx): Update to 2.2.1.
* gnu: qgis: Disable some failing tests.Guillaume Le Vaillant2020-06-22
| | | | * gnu/packages/geo.scm (qgis)[arguments]: Disable a few more failing tests.
* gnu: Add r-rgreat.Ricardo Wurmus2020-06-22
| | | | * gnu/packages/bioconductor.scm (r-rgreat): New variable.
* gnu: rust-libc-0.2: Don't skip build.Efraim Flashner2020-06-22
| | | | | * gnu/packages/crates-io.scm (rust-libc-0.2)[arguments]: Don't skip build.
* gnu: rust-libc-0.2: Update to 0.2.71.Efraim Flashner2020-06-22
| | | | * gnu/packages/crates-io.scm (rust-libc-0.2): Update to 0.2.71.
* gnu: rust-rayon-1.3: Rename to rust-rayon-1.Efraim Flashner2020-06-22
| | | | | | | | | | | * gnu/packages/crates-io.scm (rust-rayon-1.3): Rename to rust-rayon-1. (rust-criterion-0.3, rust-criterion-0.2, rust-gimli-0.18, rust-hashbrown-0.5, rust-indexmap-1.3, rust-jpeg-decoder-0.1, rust-nasm-rs-0.1, rust-scroll-0.9, rust-syn-1.0, rust-syn-0.15) [arguments]: Adjust accordingly. * gnu/packages/gnome.scm (librsvg-next)[arguments]: Same. * gnu/packages/rust-apps.scm (tokei)[arguments]: Same. * gnu/packages/video.scm (rav1e)[arguments]: Same.
* gnu: Remove rust-rayon-1.1.Efraim Flashner2020-06-22
| | | | | | | * gnu/packages/crates-io.scm (rust-rayon-1.1): Remove variable. (rust-criterion-0.2, rust-gimli-0.18, rust-hashbrown-0.5, rust-jpeg-decoder-0.1, rust-scroll-0.9, rust-syn-0.15) [arguments]: Replace rust-rayon-1.1 with 1.3.
* gnu: rust-rayon-core-1.7: Rename to rust-rayon-core-1.Efraim Flashner2020-06-22
| | | | | | | * gnu/packages/crates-io.scm (rust-rayon-core-1.7): Rename to rust-rayon-core-1. (rust-criterion-0.2, rust-rayon-1.3, rust-rayon-1.1, rust-rayon-0.8) [arguments]: Adjust accordingly.
* gnu: Remove rust-rayon-core-1.5.Efraim Flashner2020-06-22
| | | | | | * gnu/packages/crates-io.scm (rust-rayon-core-1.5): Remove variable. (rust-criterion-0.2, rust-rayon-1.1) [arguments]: Replace rust-rayon-core-1.5 with 1.7.
* gnu: sequoia: Fix typos.Efraim Flashner2020-06-22
| | | | | * gnu/packages/sequoia.scm (sequoia)[arguments]: Move unquote next to the expression it applies to.
* gnu: rust-regex-1.3: Rename to rust-regex-1.Efraim Flashner2020-06-22
| | | | | | | | | | | | | | | | | | | | * gnu/packages/crates-io.scm (rust-regex-1.3): Rename to rust-regex-1. (rust-ansi-term-0.12, rust-bindgen-0.52, rust-bindgen-0.51, rust-bindgen-0.50, rust-bindgen-0.37, rust-bindgen-0.49, rust-clap-2, rust-compiletest-rs-0.3, rust-console-0.9, rust-console-0.7, rust-docopt-1.1, rust-env-logger-0.7, rust-env-logger-0.6, rust-env-logger-0.5, rust-gimli-0.18, rust-globset-0.4, rust-grep-cli-0.1, rust-grep-matcher-0.1, rust-grep-regex-0.1, rust-grep-searcher-0.1, rust-ignore-0.4, rust-lalrpop-0.17, rust-lalrpop-util-0.17, rust-locale-config-0.3, rust-localeconfig-0.2, rust-nom-5, rust-nom-4.2, rust-once-cell-1.2, rust-proptest-0.9, rust-proptest-0.8, rust-pulldown-cmark-0.4, rust-regex-automata-0.1, rust-rusqlite-0.19, rust-scan-fmt-0.2, rust-syn-1.0, rust-syn-0.15, rust-ucd-parse-0.1, rust-version-sync-0.8) [arguments]: Adjust accordingly. * gnu/packages/gnome.scm (librsvg-next)[arguments]: Same. * gnu/packages/rust-apps.scm (fd, ripgrep, tokei, rust-cargo-c) [arguments]: Same. * gnu/packages/sequoia.scm (sequoia)[arguments]: Same.
* gnu: Remove rust-regex-1.1.Efraim Flashner2020-06-22
| | | | | | | | | | | | | | | * gnu/packages/crates-io.scm (rust-regex-1.1): Remove variable. (rust-bindgen-0.50, rust-bindgen-0.49, rust-clap-2, rust-compiletest-rs-0.2, rust-console-0.7, rust-docopt-1.1, rust-env-logger-0.7, rust-env-logger-0.6, rust-env-logger-0.5, rust-gimli-0.18, rust-globset-0.4, rust-grep-cli-0.1, rust-grep-matcher-0.1, rust-grep-regex-0.1, rust-grep-searcher-0.1, rust-ignore-0.4, rust-nom-5, rust-nom-4.2, rust-once-cell-1.2, rust-proptest-0.9, rust-proptest-0.8, rust-pulldown-cmark-0.4, rust-regex-automata-0.1, rust-rusqlite-0.19, rust-syn-0.15, rust-ucd-parse-0.1, rust-version-sync-0.8) [arguments]: Replace rust-regex-1.1 with 1.3. * gnu/packages/rust-apps.scm (ripgrep)[arguments]: Same.
* gnu: Add rust-once-cell-0.1.Efraim Flashner2020-06-22
| | | | * gnu/packages/crates-io.scm (rust-once-cell-0.1): New variable.
* gnu: Add rust-gettext-rs-0.4.Efraim Flashner2020-06-22
| | | | * gnu/packages/crates-io.scm (rust-gettext-rs-0.4): New variable.
* gnu: Add rust-gettext-sys-0.19.Efraim Flashner2020-06-22
| | | | * gnu/packages/crates-io.scm (rust-gettext-sys-0.19): New variable.
* gnu: Add rust-locale-config-0.2.Efraim Flashner2020-06-22
| | | | * gnu/packages/crates-io.scm (rust-locale-config-0.2): New variable.
* gnu: Add rust-proptest-0.7.Efraim Flashner2020-06-22
| | | | * gnu/packages/crates-io.scm (rust-proptest-0.7): New variable.
* gnu: Add rust-regex-syntax-0.4.Efraim Flashner2020-06-22
| | | | * gnu/packages/crates-io.scm (rust-regex-syntax-0.4): New variable.
* gnu: Add rust-section-testing-0.0.Efraim Flashner2020-06-22
| | | | * gnu/packages/crates-io.scm (rust-section-testing-0.0): New variable.
* gnu: rust-tempfile-3.1: Rename to rust-tempfile-3.Efraim Flashner2020-06-22
| | | | | | | | | | | | | | | | | | | * gnu/packages/crates-io.scm (rust-tempfile-3.1): Rename to ... (rust-tempfile-3): .. this. (rust-cairo-rs-0.8, rust-cairo-rs-0.7, rust-cc-1.0, rust-compiletest-rs-0.3, rust-filetime-0.2, rust-gdk-pixbuf-sys-0.9, rust-gio-sys-0.9, rust-git2-0.11, rust-glib-0.9, rust-glib-0.8, rust-glib-sys-0.9, rust-gobject-sys-0.9, rust-handlebars-2.0, rust-lscolors-0.6, rust-native-tls-0.2, rust-nix-0.15, rust-nix-0.14, rust-no-panic-0.1, rust-pango-sys-0.9, rust-pangocairo-0.10, rust-proptest-0.9, rust-proptest-0.8, rust-rustdoc-stripper-0.1, rust-rustls-0.16, rust-rusty-fork-0.2, rust-sourcefile-0.1, rust-tiff-0.2, rust-tokio-0.2, rust-tokio-fs-0.1, rust-tokio-uds-0.2, rust-wayland-client-0.23, rust-wayland-client-0.21, rust-xattr-0.2) [arguments]: Adjust accordingly. * gnu/packages/rust-apps.scm (rust-cbindgen, tokei)[arguments]: Same. * gnu/packages/sequoia.scm (sequoia)[arguments]: Same. * gnu/packages/terminals.scm (alacritty)[arguments]: Same.
* gnu: Remove rust-tempfile-3.0.Efraim Flashner2020-06-22
| | | | | | | | | | * gnu/packages/crates-io.scm (rust-tempfile-3.0): Remove variable. (rust-compiletest-rs-0.3, rust-filetime-0.2, rust-handlebars-2.0, rust-nix-0.15, rust-nix-0.14, rust-proptest-0.9, rust-proptest-0.8, rust-rustls-0.16, rust-rusty-fork-0.2, rust-tiff-0.2, rust-tokei-fs-0.1, rust-tokio-uds-0.2, rust-xattr-0.2) [arguments]: Replace rust-tempfile-3.0 with 3.1. * gnu/packages/rust-apps.scm (tokei)[arguments]: Same.
* gnu: rust-proptest-0.9: Update to 0.9.6.Efraim Flashner2020-06-22
| | | | | | * gnu/packages/crates-io.scm (rust-proptest-0.9): Update to 0.9. [arguments]: Don't skip build. In cargo-inputs replace rust-rand-0.4 with 0.6, rust-rand-chacha-0.2 with 0.1, rust-rand-xorshift-0.2 with 0.1.
* gnu: r-zoo: Move to (gnu packages cran).Ricardo Wurmus2020-06-22
| | | | | * gnu/packages/statistics.scm (r-zoo): Move this variable from here... * gnu/packages/cran.scm (r-zoo): ...to here.
* gnu: r-directlabels: Move to (gnu packages cran).Ricardo Wurmus2020-06-22
| | | | | * gnu/packages/statistics.scm (r-directlabels): Move this variable from here... * gnu/packages/cran.scm (r-directlabels): ...to here.
* gnu: r-boruta: Move to (gnu packages cran).Ricardo Wurmus2020-06-22
| | | | | * gnu/packages/statistics.scm (r-boruta): Move this variable from here... * gnu/packages/cran.scm (r-boruta): ...to here.
* gnu: r-boruta: Fix indentation and description.Ricardo Wurmus2020-06-22
| | | | | * gnu/packages/statistics.scm (r-boruta)[description]: Fix indentation, add line breaks, and complete the first sentence fragment.
* gnu: r-fit-models: Update to 0.63.Ricardo Wurmus2020-06-22
| | | | * gnu/packages/statistics.scm (r-fit-models): Update to 0.63.
* gnu: r-glmnet: Update to 4.0-2.Ricardo Wurmus2020-06-22
| | | | | * gnu/packages/statistics.scm (r-glmnet): Update to 4.0-2. [propagated-inputs]: Add r-survival.
* gnu: r-rmarkdown: Update to 2.3.Ricardo Wurmus2020-06-22
| | | | * gnu/packages/statistics.scm (r-rmarkdown): Update to 2.3.
* gnu: r-backports: Update to 1.1.8.Ricardo Wurmus2020-06-22
| | | | * gnu/packages/statistics.scm (r-backports): Update to 1.1.8.
* gnu: r-ggplot2: Update to 3.3.2.Ricardo Wurmus2020-06-22
| | | | * gnu/packages/statistics.scm (r-ggplot2): Update to 3.3.2.
* gnu: r-isoband: Update to 0.2.2.Ricardo Wurmus2020-06-22
| | | | | * gnu/packages/cran.scm (r-isoband): Update to 0.2.2. [propagated-inputs]: Remove r-rcpp.
* gnu: r-zvcv: Update to 2.1.0.Ricardo Wurmus2020-06-22
| | | | | * gnu/packages/cran.scm (r-zvcv): Update to 2.1.0. [propagated-inputs]: Remove r-partitions; add r-bh, r-dplyr, r-magrittr, and r-rlinsolve.
* gnu: r-umap: Update to 0.2.6.0.Ricardo Wurmus2020-06-22
| | | | * gnu/packages/cran.scm (r-umap): Update to 0.2.6.0.
* gnu: r-ldheatmap: Update to 0.99-8.Ricardo Wurmus2020-06-22
| | | | * gnu/packages/cran.scm (r-ldheatmap): Update to 0.99-8.
* gnu: r-nonnest2: Update to 0.5-4.Ricardo Wurmus2020-06-22
| | | | * gnu/packages/cran.scm (r-nonnest2): Update to 0.5-4.
* gnu: r-rcppgsl: Update to 0.3.8.Ricardo Wurmus2020-06-22
| | | | | * gnu/packages/cran.scm (r-rcppgsl): Update to 0.3.8. [native-inputs]: Remove r-knitr.
* gnu: r-ggeffects: Update to 0.15.0.Ricardo Wurmus2020-06-22
| | | | * gnu/packages/cran.scm (r-ggeffects): Update to 0.15.0.
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