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Pierre Langlois 3417a25156
gnu: Add python-xarray. 
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>
 2020-06-22 15:44:14 +02:00
Pierre Langlois 7fd33283df
gnu: Add python-retrying. 
* gnu/packages/python-xyz.scm (python-retrying): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2020-06-22 15:44:12 +02:00
Pierre Langlois 20b545f768
gnu: python-pandas: Update to 1.0.5. 
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>
 2020-06-22 15:44:08 +02:00
Pierre Langlois 3a79adab41
gnu: deeptools: Deprecate in favor of python-deeptools. 
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>
 2020-06-22 15:43:59 +02:00
Ludovic Courtès 955caaab26
self: Build with Guile 3.0.3. 
* gnu/packages/guile.scm (guile-3.0/libgc-7): Inherit from GUILE-3.0.3.
 2020-06-22 15:42:56 +02:00
Ludovic Courtès fe5de925aa
deduplicate: Avoid traversing directories twice. 
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.
 2020-06-22 15:42:55 +02:00
Ludovic Courtès a0d419e639
compile: Build gnu/{packages,tests}/* with '-O1'. 
* guix/build/compile.scm (optimization-options): Use '-O1' for the
simple case.
 2020-06-22 15:42:55 +02:00
Pierre Neidhardt a0dccc71a6
gnu: emacs-helm: Update to 3.6.3. 
* gnu/packages/emacs-xyz.scm (emacs-helm): Update to 3.6.3.
 2020-06-22 15:05:46 +02:00
Pierre Neidhardt 561aeefb0b
gnu: emacs-helm-fish-completion: Update to 0.5. 
* gnu/packages/emacs-xyz.scm (emacs-helm-fish-completion): Update to 0.5.
 2020-06-22 15:01:09 +02:00
Guillaume Le Vaillant 69b82c6078
gnu: js8call: Fix build. 
* gnu/packages/radio.scm (js8call)[inputs]: Use regular hamlib.
 2020-06-22 14:50:50 +02:00
Guillaume Le Vaillant 09e27115d6
gnu: wsjtx: Update to 2.2.1. 
* gnu/packages/radio.scm (wsjtx-hamlib): Update to 2.2.1.
  [arguments]: Add a 'fix-tests' phase.
  (wsjtx): Update to 2.2.1.
 2020-06-22 14:50:50 +02:00
Guillaume Le Vaillant 0213f0940e
gnu: qgis: Disable some failing tests. 
* gnu/packages/geo.scm (qgis)[arguments]: Disable a few more failing tests.
 2020-06-22 14:50:50 +02:00
Ricardo Wurmus c89afe7516
gnu: Add r-rgreat. 
* gnu/packages/bioconductor.scm (r-rgreat): New variable.
 2020-06-22 14:39:03 +02:00
Efraim Flashner 277ac1f242
gnu: rust-libc-0.2: Don't skip build. 
* gnu/packages/crates-io.scm (rust-libc-0.2)[arguments]: Don't skip
build.
 2020-06-22 14:15:34 +03:00
Efraim Flashner a1b79c09ee
gnu: rust-libc-0.2: Update to 0.2.71. 
* gnu/packages/crates-io.scm (rust-libc-0.2): Update to 0.2.71.
 2020-06-22 14:15:34 +03:00
Efraim Flashner a56305539f
gnu: rust-rayon-1.3: Rename to rust-rayon-1. 
* 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.
 2020-06-22 14:15:34 +03:00
Efraim Flashner 6c2189c858
gnu: Remove rust-rayon-1.1. 
* 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.
 2020-06-22 14:15:34 +03:00
Efraim Flashner 8781c8edd2
gnu: rust-rayon-core-1.7: Rename to rust-rayon-core-1. 
* 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.
 2020-06-22 14:15:34 +03:00
Efraim Flashner 4f76fbfcd9
gnu: Remove rust-rayon-core-1.5. 
* 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.
 2020-06-22 14:15:33 +03:00
Efraim Flashner df4d2ddaee
gnu: sequoia: Fix typos. 
* gnu/packages/sequoia.scm (sequoia)[arguments]: Move unquote next to
the expression it applies to.
 2020-06-22 14:15:33 +03:00
Efraim Flashner 6cd7b35544
gnu: rust-regex-1.3: Rename to rust-regex-1. 
* 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.
 2020-06-22 14:15:33 +03:00
Efraim Flashner 9c13497df4
gnu: Remove rust-regex-1.1. 
* 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.
 2020-06-22 14:15:33 +03:00
Efraim Flashner 80cfe5458c
gnu: Add rust-once-cell-0.1. 
* gnu/packages/crates-io.scm (rust-once-cell-0.1): New variable.
 2020-06-22 14:15:33 +03:00
Efraim Flashner f4022d8549
gnu: Add rust-gettext-rs-0.4. 
* gnu/packages/crates-io.scm (rust-gettext-rs-0.4): New variable.
 2020-06-22 14:15:32 +03:00
Efraim Flashner e1240cb249
gnu: Add rust-gettext-sys-0.19. 
* gnu/packages/crates-io.scm (rust-gettext-sys-0.19): New variable.
 2020-06-22 14:15:32 +03:00
Efraim Flashner b3987cd3d2
gnu: Add rust-locale-config-0.2. 
* gnu/packages/crates-io.scm (rust-locale-config-0.2): New variable.
 2020-06-22 14:15:32 +03:00
Efraim Flashner d77146e9fe
gnu: Add rust-proptest-0.7. 
* gnu/packages/crates-io.scm (rust-proptest-0.7): New variable.
 2020-06-22 14:15:32 +03:00
Efraim Flashner eba1524df2
gnu: Add rust-regex-syntax-0.4. 
* gnu/packages/crates-io.scm (rust-regex-syntax-0.4): New variable.
 2020-06-22 14:15:32 +03:00
Efraim Flashner 5247f79db6
gnu: Add rust-section-testing-0.0. 
* gnu/packages/crates-io.scm (rust-section-testing-0.0): New variable.
 2020-06-22 14:15:31 +03:00
Efraim Flashner 7c6948c71e
gnu: rust-tempfile-3.1: Rename to rust-tempfile-3. 
* 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.
 2020-06-22 14:15:31 +03:00
Efraim Flashner 0c9bca4ffe
gnu: Remove rust-tempfile-3.0. 
* 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.
 2020-06-22 14:15:31 +03:00
Efraim Flashner 9f2bb42bee
gnu: rust-proptest-0.9: Update to 0.9.6. 
* 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.
 2020-06-22 14:15:28 +03:00
Ricardo Wurmus fae72ebb49
gnu: r-zoo: Move to (gnu packages cran). 
* gnu/packages/statistics.scm (r-zoo): Move this variable from here...
* gnu/packages/cran.scm (r-zoo): ...to here.
 2020-06-22 12:46:03 +02:00
Ricardo Wurmus d30ab75a7d
gnu: r-directlabels: Move to (gnu packages cran). 
* gnu/packages/statistics.scm (r-directlabels): Move this variable from here...
* gnu/packages/cran.scm (r-directlabels): ...to here.
 2020-06-22 12:42:19 +02:00
Ricardo Wurmus 5c1aab1dc1
gnu: r-boruta: Move to (gnu packages cran). 
* gnu/packages/statistics.scm (r-boruta): Move this variable from here...
* gnu/packages/cran.scm (r-boruta): ...to here.
 2020-06-22 12:39:51 +02:00
Ricardo Wurmus 6c9834f59f
gnu: r-boruta: Fix indentation and description. 
* gnu/packages/statistics.scm (r-boruta)[description]: Fix indentation, add
line breaks, and complete the first sentence fragment.
 2020-06-22 12:38:41 +02:00
Ricardo Wurmus 62648f4ae3
gnu: r-fit-models: Update to 0.63. 
* gnu/packages/statistics.scm (r-fit-models): Update to 0.63.
 2020-06-22 12:15:51 +02:00
Ricardo Wurmus 913eaa619c
gnu: r-glmnet: Update to 4.0-2. 
* gnu/packages/statistics.scm (r-glmnet): Update to 4.0-2.
[propagated-inputs]: Add r-survival.
 2020-06-22 12:15:51 +02:00
Ricardo Wurmus 15bee10afe
gnu: r-rmarkdown: Update to 2.3. 
* gnu/packages/statistics.scm (r-rmarkdown): Update to 2.3.
 2020-06-22 12:15:50 +02:00
Ricardo Wurmus 55e89c6aa6
gnu: r-backports: Update to 1.1.8. 
* gnu/packages/statistics.scm (r-backports): Update to 1.1.8.
 2020-06-22 12:15:50 +02:00
Ricardo Wurmus 3c37c67224
gnu: r-ggplot2: Update to 3.3.2. 
* gnu/packages/statistics.scm (r-ggplot2): Update to 3.3.2.
 2020-06-22 12:15:50 +02:00
Ricardo Wurmus c68914aa15
gnu: r-isoband: Update to 0.2.2. 
* gnu/packages/cran.scm (r-isoband): Update to 0.2.2.
[propagated-inputs]: Remove r-rcpp.
 2020-06-22 12:15:50 +02:00
Ricardo Wurmus ad85d0d536
gnu: r-zvcv: Update to 2.1.0. 
* 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.
 2020-06-22 12:15:50 +02:00
Ricardo Wurmus 22f8260ba1
gnu: r-umap: Update to 0.2.6.0. 
* gnu/packages/cran.scm (r-umap): Update to 0.2.6.0.
 2020-06-22 12:15:50 +02:00
Ricardo Wurmus 4a55cc48b8
gnu: r-ldheatmap: Update to 0.99-8. 
* gnu/packages/cran.scm (r-ldheatmap): Update to 0.99-8.
 2020-06-22 12:15:50 +02:00
Ricardo Wurmus 0319196561
gnu: r-nonnest2: Update to 0.5-4. 
* gnu/packages/cran.scm (r-nonnest2): Update to 0.5-4.
 2020-06-22 12:15:50 +02:00
Ricardo Wurmus 3995c50878
gnu: r-rcppgsl: Update to 0.3.8. 
* gnu/packages/cran.scm (r-rcppgsl): Update to 0.3.8.
[native-inputs]: Remove r-knitr.
 2020-06-22 12:15:50 +02:00
Ricardo Wurmus 2d916665ce
gnu: r-ggeffects: Update to 0.15.0. 
* gnu/packages/cran.scm (r-ggeffects): Update to 0.15.0.
 2020-06-22 12:15:50 +02:00
Ricardo Wurmus 71017346ad
gnu: r-bayestestr: Update to 0.7.0. 
* gnu/packages/cran.scm (r-bayestestr): Update to 0.7.0.
 2020-06-22 12:15:50 +02:00
Ricardo Wurmus 13141c667b
gnu: r-rstatix: Update to 0.6.0. 
* gnu/packages/cran.scm (r-rstatix): Update to 0.6.0.
[propagated-inputs]: Add r-generics.
 2020-06-22 12:15:50 +02:00