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Author SHA1 Message Date
Ricardo Wurmus bec6bf64bc
gnu: rust-instant-0.1: Update to 0.1.9. 
* gnu/packages/crates-io.scm (rust-instant-0.1): Update to 0.1.9.
 2022-05-06 15:34:31 +02:00
Ricardo Wurmus 70f6d2302c
gnu: rust-lock-api-0.4: Update to 0.4.5. 
* gnu/packages/crates-io.scm (rust-lock-api-0.4): Update to 0.4.5.
 2022-05-06 15:34:31 +02:00
Ricardo Wurmus f02f8db381
gnu: rust-parking-lot-0.11: Update to 0.11.2. 
* gnu/packages/crates-io.scm (rust-parking-lot-0.11): Update to 0.11.2.
 2022-05-06 15:34:31 +02:00
Ricardo Wurmus d16298196c
gnu: rust-parking-lot-core-0.8: Update to 0.8.4. 
* gnu/packages/crates-io.scm (rust-parking-lot-core-0.8): Update to 0.8.4.
 2022-05-06 15:34:31 +02:00
Ludovic Courtès 8079bd3da8
gnu: tcl-tls: Use a gexp. 
* gnu/packages/tcl.scm (tcl-tls)[arguments]: Use a gexp.
 2022-05-06 15:23:07 +02:00
Ludovic Courtès 4a3f8994f4
gnu: tcl-tls: Add 'release-monitoring-url' and 'upstream-name' properties. 
* gnu/packages/tcl.scm (tcl-tls)[properties]: New field.
 2022-05-06 15:23:07 +02:00
Daniel Lowe 06d244197b
gnu: tcl: Add tcl-tls to packages. 
* gnu/packages/tcl.scm (tcl-tls): Added 1.7.22

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-06 15:23:07 +02:00
Paul A. Patience e606e02844
gnu: python-vedo: Update to 2022.2.0. 
* gnu/packages/python-science.scm (python-vedo): Update to 2022.2.0.
[arguments]: Add 'fix-tests' phase.
[inputs]: Move fenics and python-matplotlib to propagated-inputs.
Move python-pkgconfig from here...
[native-inputs]: ...to here.
[propagated-inputs]: Add python-deprecated (and fenics and
python-matplotlib).
[description]: Make description more accurate.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-06 15:23:06 +02:00
Paul A. Patience 9edc0f3dbb
gnu: python-vedo: Disable sanity check. 
* gnu/packages/python-science.scm (python-vedo)[arguments]: Disable
sanity check.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-06 15:23:06 +02:00
Paul A. Patience a5fec06868
gnu: python-vedo: Remove input labels. 
* gnu/packages/python-science.scm (python-vedo)[inputs]: Remove labels
and sort the inputs.
[propagated-inputs]: Remove labels.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-06 15:23:06 +02:00
Paul A. Patience 34f49d15e6
gnu: python-vedo: Honor #:tests? flag. 
* gnu/packages/python-science.scm (python-vedo)[arguments]: Adjust
custom 'check' phase to honor the #:tests? flag. Also remove its
trailing boolean.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-06 15:23:06 +02:00
Paul A. Patience b7d2644cd0
gnu: fenics: Fix sanity check. 
* gnu/packages/simulation.scm (fenics)[arguments]: Relax pybind11
requirement to appease the sanity check.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-06 15:23:06 +02:00
Paul A. Patience 9d5160bc8a
gnu: fenics: Honor #:tests? flag. 
* gnu/packages/simulation.scm (fenics)[arguments]: Adjust custom 'check'
phase to honor the #:tests? flag.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-06 15:23:06 +02:00
Paul A. Patience 69505bec93
gnu: fenics-dolfin: Honor #:tests? flag. 
* gnu/packages/simulation.scm (fenics-dolfin)[source]: Remove trailing
boolean.
[arguments]: Adjust custom 'check' phase to honor the #:tests? flag. While
here, remove trailing booleans.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-06 15:23:06 +02:00
Ludovic Courtès a2d44231ea
gnu: Add Guix-Modules. 
* gnu/packages/package-management.scm (guix-modules): New variable.
 2022-05-06 15:23:05 +02:00
Guillaume Le Vaillant 5e27c54e08
gnu: monero-gui: Update to 0.17.3.2. 
* gnu/packages/finance.scm (monero-gui): Update to 0.17.3.2.
 2022-05-06 15:08:41 +02:00
Guillaume Le Vaillant 4188d211c7
gnu: monero: Update to 0.17.3.2. 
* gnu/packages/finance.scm (monero): Update to 0.17.3.2.
  [source]: Remove obsolete part of snippet.
  [arguments]: Remove trailing booleans.
 2022-05-06 15:08:41 +02:00
Jan (janneke) Nieuwenhuizen 53628d6e3b
gnu: Add dezyne. 
* gnu/packages/dezyne.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
 2022-05-06 14:39:50 +02:00
Jan (janneke) Nieuwenhuizen 984add419c
gnu: mescc-tools: Update supported-systems. 
* gnu/packages/mes.scm (mescc-tools)[supported-systems]: Add riscv32-linux,
riscv64-linux, remove powerpc64le-linux.
 2022-05-06 14:39:45 +02:00
Efraim Flashner 22b794a4a7
gnu: links: Use gexps. 
* gnu/packages/web-browsers.scm (links)[arguments]: Rewrite using gexps.
 2022-05-06 14:36:08 +03:00
Efraim Flashner d540c6792b
gnu: links: Remove input labels. 
* gnu/packages/web-browsers.scm (links)[inputs]: Remove input labels.
 2022-05-06 14:36:08 +03:00
Efraim Flashner 1123da369d
gnu: links: Use configure-flags. 
* gnu/packages/web-browsers.scm (links)[arguments]: Add configure-flags
field. Adjust custom 'configure phase to use configure-flags.
 2022-05-06 14:36:08 +03:00
Efraim Flashner 5cf81294c0
gnu: links: Update to 2.26. 
* gnu/packages/web-browsers.scm (links): Update to 2.26.
 2022-05-06 14:36:07 +03:00
Efraim Flashner 166e0dfc44
gnu: ncdu-2: Update to 2.1.2. 
* gnu/packages/ncdu.scm (ncdu-2): Update to 2.1.2.
 2022-05-06 14:36:07 +03:00
Ricardo Wurmus 549e478f23
gnu: Add python-ipydatawidgets. 
* gnu/packages/jupyter.scm (python-ipydatawidgets): New variable.
 2022-05-06 13:02:59 +02:00
Ricardo Wurmus 221bf543e8
gnu: Add python-xyzservices. 
* gnu/packages/python-xyz.scm (python-xyzservices): New variable.
 2022-05-06 13:02:59 +02:00
Ricardo Wurmus 0d73287d97
gnu: Add python-mercantile. 
* gnu/packages/python-xyz.scm (python-mercantile): New variable.
 2022-05-06 13:02:59 +02:00
Ricardo Wurmus ea3cfeb665
gnu: Add python-ipympl. 
* gnu/packages/jupyter.scm (python-ipympl): New variable.
 2022-05-06 13:02:58 +02:00
Ricardo Wurmus e47b080474
gnu: Add python-traittypes. 
* gnu/packages/python-science.scm (python-traittypes): New variable.
 2022-05-06 13:02:55 +02:00
Daniel Meißner 27fc4ae397
gnu: cava: Fix build failure 
* gnu/packages/audio.scm (cava)[source]: Remove bundled iniparser.
(cava)[inputs]: Add iniparser.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-06 10:32:06 +02:00
Daniel Meißner de4e4506c1
gnu: cava: Use G-expressions. 
* gnu/packages/audio.scm (cava)[arguments]: Use G-expressions.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-06 10:32:06 +02:00
kiasoc5 253fc14777
gnu: nftables: Update to 1.0.2. 
* gnu/packages/patches/nftables-fix-makefile.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/linux.scm (nftables): Update to 1.0.2.
[source]: Add patch.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-06 10:32:06 +02:00
Vincent Prat 9e630a362d
gnu: Add python-arpeggio. 
* gnu/packages/python-xyz.scm (python-arpeggio): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-06 10:32:06 +02:00
Michael Rohleder 7727757a73
gnu: ytfzf: Update to 2.3. 
* gnu/packages/patches/ytfzf-programs.patch,
* gnu/packages/patches/ytfzf-updates.patch: Delete patches.
* gnu/local.mk (dist_patch_DATA): Unregister them.
* gnu/packages/image-viewers.scm (ytfzf): Update to 2.3.
[source]: Delete patches.
[arguments]: Remove phase 'patch-script. Add phase 'install-addons,
'wrap-program.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-06 10:32:06 +02:00
Ludovic Courtès 3d05105705
gnu: slurm: Add 21.08.8. 
* gnu/packages/parallel.scm (slurm): Update to 21.08.8.
(slurm-20.11): New variable.
 2022-05-06 10:32:05 +02:00
Ludovic Courtès c018871c04
gnu: slurm: Update to 20.11.9 [fixes CVE-2022-{29500,29501,29502}]. 
* gnu/packages/parallel.scm (slurm): Update to 20.11.9.
 2022-05-06 10:32:05 +02:00
Ricardo Wurmus a2fb35e43d
gnu: python-ipython: Add missing input. 
* gnu/packages/python-xyz.scm (python-ipython)[propagated-inputs]: Add
python-decorator.
 2022-05-06 10:15:04 +02:00
Ricardo Wurmus ce1746819b
gnu: python-traitlets: Update to 5.1.1. 
* gnu/packages/python-xyz.scm (python-traitlets): Update to 5.1.1.
[propagated-inputs]: Remove python-ipython-genutils, python-decorator, and
python-six.
 2022-05-06 10:15:04 +02:00
Ricardo Wurmus 471f650498
gnu: Add python-kneed. 
* gnu/packages/python-xyz.scm (python-kneed): New variable.
 2022-05-06 10:15:04 +02:00
Ricardo Wurmus b4da7c2133
gnu: Add python-databases. 
* gnu/packages/databases.scm (python-databases): New variable.
 2022-05-06 10:15:04 +02:00
Ricardo Wurmus 43992cdbea
gnu: python-anyio: Update to 3.5.0. 
* gnu/packages/python-xyz.scm (python-anyio): Update to 3.5.0.
[arguments]: Remove phase 'fix-compatibility; disable one more test.
[propagated-inputs]: Add python-contextvars and python-dataclasses.
[native-inputs]: Add python-contextlib2 and python-trio; remove
python-iniconfig.
 2022-05-06 10:15:04 +02:00
Ricardo Wurmus b95e3dc17c
gnu: python-multipart: Fix test failure due to PyYAML 6. 
* gnu/packages/python-xyz.scm (python-multipart)[arguments]: Patch instance of
yaml.load.
 2022-05-06 10:15:00 +02:00
Foo Chuan Wei 312879fddc
gnu: Add byacc. 
* gnu/packages/c.scm (byacc): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-05 23:56:58 +02:00
Ludovic Courtès 0780164f1f
gnu: b4: Update to 0.8.0. 
* gnu/packages/version-control.scm (b4): Update to 0.8.0.
 2022-05-05 23:56:58 +02:00
Pierre-Antoine Bouttier 6829d61bc5
gnu: Add n2p2. 
* gnu/packages/maths.scm (n2p2): New variable.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-05 23:56:58 +02:00
Jonathan Brielmaier 34dbbb9172
gnu: icedove: Update to 91.9.0 [fixes CVE-2022-1520]. 
* gnu/packages/gnuzilla.scm (icedove): Update to 91.9.0.
 2022-05-05 23:09:48 +02:00
Andreas Enge d809e71df2
gnu: python-pari-jupyter: Update to 1.4.1. 
* gnu/packages/python-xyz.scm (python-pari-jupyter): Update to 1.4.1.
  [home-page]: Update after maintainer change.
 2022-05-05 16:14:43 +02:00
Andreas Enge a1b0fc8133
gnu: cm: Update to 0.4.0. 
* gnu/packages/algebra.scm (cm): Update to 0.4.0.
 2022-05-05 16:10:16 +02:00
Marius Bakke b80ca672de
gnu: ungoogled-chromium: Update to 101.0.4951.54-1. 
* gnu/packages/chromium.scm (%chromium-version): Set to 101.0.4951.54.
(%ungoogled-origin, ungoogled-chromium): Update hashes.
 2022-05-03 22:35:12 +02:00
Mark H Weaver 9916933a04
gnu: icecat: Update to 91.9.0-guix0-preview1 [security fixes]. 
Includes fixes for CVE-2022-29909, CVE-2022-29911, CVE-2022-29912,
CVE-2022-29914, CVE-2022-29916, and CVE-2022-29917.

* gnu/packages/gnuzilla.scm (%icecat-version, %icecat-build-id): Update.
(icecat-source): Update gnuzilla commit, base version, and hashes.
 2022-05-03 14:56:54 -04:00
Paul A. Patience 8b2d266607
gnu: dealii: Update to 9.3.3. 
* gnu/packages/maths.scm (dealii): Update to 9.3.3.
* gnu/packages/patches/dealii-fix-compiliation-with-boost-1.78.patch:
Delete file.
* gnu/packages/patches/dealii-fix-sundials.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-03 18:02:28 +02:00
Paul A. Patience 240b604eda
gnu: dealii: Add SUNDIALS dependency. 
* gnu/packages/maths.scm (dealii)[propagated-inputs]: Add sundials-5.
Reformat list to clarify comment.
(dealii-openmpi)[propagated-inputs]: Add sundials-openmpi-5.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-03 18:02:28 +02:00
Paul A. Patience d34f941c33
gnu: dealii-openmpi: Remove input labels. 
* gnu/packages/maths.scm (dealii-openmpi)[inputs]: Remove labels.
[propagated-inputs]: Same.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-03 18:02:28 +02:00
Paul A. Patience e131f705dd
gnu: dealii: Remove trailing booleans. 
* gnu/packages/maths.scm (dealii)[snippet]: Remove trailing boolean (and
therefore the 'begin').
[native-inputs, inputs]: Reindent.
[arguments]<#:phases>: Remove trailing boolean.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-03 18:02:28 +02:00
Paul A. Patience e648957b7b
gnu: sundials: Add 5.8.0. 
* gnu/packages/maths.scm (sundials-5, sundials-openmpi-5): New
variables.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-03 18:02:27 +02:00
Paul A. Patience d1a6a795b3
gnu: sundials: Update to 6.2.0. 
* gnu/packages/maths.scm (sundials): Update to 6.2.0.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-03 18:02:27 +02:00
Paul A. Patience 4c509a73b7
gnu: sundials-openmpi: Add HYPRE dependency. 
* gnu/packages/maths.scm (sundials-openmpi)[propagated-inputs]: Add
hypre-openmpi.
[arguments]<#:configure-flags>: Add -DENABLE_HYPRE, -DHYPRE_INCLUDE_DIR
and -DHYPRE_LIBRARY_DIR.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-03 18:02:27 +02:00
Paul A. Patience 0d3c2c9543
gnu: sundials: Fix various issues. 
This commit fixes various issues. First, some of SUNDIALS's CMake
variables were renamed at some point between 5.2.0 and 5.7.0, in
particular KLU_ENABLE, which was changed to ENABLE_KLU. Since
sundials-julia is essentially SUNDIALS 5.2.0, its configure flags need
to be different from those of the sundials package. Second, commit
61bcd648ca, which updated SUNDIALS to
6.1.1, accidentally completely disabled PETSc support for
sundials-openmpi (PETSc is supported only with MPI) by removing the
relevant configure flags. Third, SUNDIALS's default index size is
64 bits, but PETSc's is 32 bits, and they need to be the same; this
issue is discussed in the next three paragraphs.

The default index size in SUNDIALS 3.1.1 (which was the sundials
package's version previous to the aforementioned commit) was also
64 bits (though it was configured through the SUNDIALS_INDEX_TYPE CMake
variable, which could take the values INT64_T or INT32_T), but
SUNDIALS's configure script didn't warn of any incompatibility with
PETSc's 32-bit indices. I don't know if this was an accidental omission
from the configure script or if SUNDIALS's index size didn't have to
correspond to PETSc's at the time.

Keeping 64-bit indices in SUNDIALS would require adding a package for
PETSc with 64-bit indices (using the --with-64-bit-indices configure
flag), possibly named petsc64-openmpi (to follow the style of the SCOTCH
packages, i.e., scotch, scotch32, etc., though there the unadorned
package name represents the 64-bit version, unlike the unadorned petsc),
which would in turn require a package for METIS with 64-bit
indices (using IDXTYPEWIDTH=64). However, SUNDIALS is an optional
dependency of deal.II, both of which have PETSc as an optional
dependency, and deal.II's index size (which defaults to 32 bits) must
match PETSc's. In other words, the current deal.II package can build
with SUNDIALS only if SUNDIALS has 32-bit indices.

Furthermore, users needing 64-bit indices in SUNDIALS probably also need
them in PETSc and other libraries. If and when 64-bit indices are deemed
necessary, we can add all the package variations at once (for SUNDIALS,
PETSc, METIS, deal.II and any others).

* gnu/packages/maths.scm (sundials)[source]: Reuse version in URL.
[native-inputs]: Capitalize and punctuate comment.
[inputs]: Remove petsc, now unnecessary gfortran, and obsolete
comment. Move TODO item to sundials-openmpi.
[arguments]<#:configure-flags>: Add -DSUNDIALS_INDEX_SIZE=32 to match
PETSc's 32-bit indices. Remove obsolete -DEXAMPLES_ENABLE_F77,
-DEXAMPLES_ENABLE_F90 and -DFCMIX_ENABLE. Mention new but currently
unusable -DBUILD_FORTRAN_MODULE_INTERFACE and
-DEXAMPLES_ENABLE_F2003. Rename KLU_ENABLE to ENABLE_KLU.
(sundials-openmpi): Use package/inherit.
[inputs]: Move openmpi and petsc-openmpi from here...
[propagated-inputs]: ...to here. Clarify comment.
[arguments]<#:configure-flags>: Add -DENABLE_PETSC and -DPETSC_DIR, the
equivalents of which were accidentally removed in commit
61bcd648ca.
<#:phases>: Replace a tab with spaces.
[synopsis]: Replace OpenMPI with MPI to conform to other package
synopses.
(sundials-julia)[inputs]: Add gfortran.
[arguments]<#:configure-flags>: Set only, and manually, -DCMAKE_C_FLAGS,
-DSUNDIALS_INDEX_SIZE, -DKLU_ENABLE, -DKLU_INCLUDE_DIR,
-DKLU_LIBRARY_DIR and -DLAPACK_ENABLE instead of inheriting from the
sundials package, because some of SUNDIALS's CMake variables have
changed name.
[synopsis]: Capitalize “LAPACK”.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-03 18:02:27 +02:00
Paul A. Patience a3b6a4df6c
gnu: petsc-openmpi: Fix header inclusions. 
* gnu/packages/maths.scm (petsc-openmpi)[arguments]: Add
'patch-header-inclusions' phase.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-03 18:02:27 +02:00
Ludovic Courtès 7855a9366b
services: pipefs: Correctly handle lack of extensions. 
Previously, in the absence of extensions of 'pipefs-service-type', we'd
get a wrong-type-arg exception while folding services:

  In gnu/services/nfs.scm:
     134:37  1 (_ #<<pipefs-configuration> mount-point: "/var/lib/nfs…> …)
  In ice-9/boot-9.scm:
    1685:16  0 (raise-exception _ #:continuable? _)
  In procedure car: Wrong type argument in position 1 (expecting pair): ()

* gnu/services/nfs.scm (pipefs-service-type)[extend]: Gracefully handle
the case where VALUES is the empty list, as done in 'gss-service-type'.
 2022-05-03 18:02:27 +02:00
Leo Famulari 654f878f0b
gnu: Mutt: Update to 2.2.4. 
* gnu/packages/mail.scm (mutt): Update to 2.2.4.
 2022-05-02 19:31:42 -04:00
Leo Famulari 39bdf71db1
gnu: linux-libre 4.19: Update to 4.19.241. 
* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.241.
(linux-libre-4.19-pristine-source): Update hash.
 2022-05-02 18:57:38 -04:00
Leo Famulari ac2857e042
gnu: linux-libre 5.15: Update to 5.15.37. 
* gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.37.
(linux-libre-5.15-pristine-source): Update hash.
 2022-05-02 18:57:38 -04:00
Jan (janneke) Nieuwenhuizen 6b588da368
gnu: mes: Update to 0.24. 
* gnu/packages/mes.scm (mes-next)[source]: Update to 0.24.
[native-inputs]: Add m2-planet.
 2022-05-02 19:07:06 +02:00
Jan (janneke) Nieuwenhuizen c14f1e3195
gnu: m2-planet: Update to 1.9.0. 
* gnu/packages/mes.scm (m2-planet): Update to 1.9.0.
 2022-05-02 19:07:04 +02:00
Jan (janneke) Nieuwenhuizen 954ff74bc8
gnu: mescc-tools: Update to 1.4.0. 
* gnu/packages/mes.scm (mescc-tools): Update to 1.4.0.
 2022-05-02 19:07:02 +02:00
Konstantinos Agiannis f49b1a10f3
gnu: Add xschem. 
* gnu/packages/engineering.scm (xschem): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 18:03:06 +02:00
Ludovic Courtès 2a37f174be
services: Make sure Shepherd destructors match constructors. 
This is a followup to b06ecc5751,
211fe3f66e, and
fd57ce267c.

* gnu/services/base.scm (guix-publish-shepherd-service): Change 'stop'
method to use 'make-systemd-destructor' when 'make-systemd-constructor'
is used.
* gnu/services/dict.scm (dicod-shepherd-service): Change 'stop' method
to use 'make-inetd-destructor' when 'make-inetd-constructor' is used.
* gnu/services/messaging.scm (bitlbee-shepherd-service): Likewise.
 2022-05-02 17:57:30 +02:00
Ricardo Wurmus 39d6c13fda
gnu: python-hic2cool: Fix build. 
* gnu/packages/bioinformatics.scm (python-hic2cool)[arguments]: Fix
incompatibility with h5py 3; disable two tests.
 2022-05-02 17:33:31 +02:00
Mădălin Ionel Patrașcu 7494f4b4ab
gnu: Add r-agimicrorna. 
* gnu/packages/bioconductor.scm (r-agimicrorna): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2022-05-02 15:23:50 +02:00
Mădălin Ionel Patrașcu 9c19db8c1d
gnu: Add r-adductomicsr. 
* gnu/packages/bioconductor.scm (r-adductomicsr): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2022-05-02 15:17:28 +02:00
Mădălin Ionel Patrașcu 495bc9f962
gnu: Add r-orgmassspecr. 
* gnu/packages/cran.scm (r-orgmassspecr): New variable.
 2022-05-02 15:17:28 +02:00
Mădălin Ionel Patrașcu 290934c8fc
gnu: Add r-adductdata. 
* gnu/packages/bioconductor.scm (r-adductdata): New variable.
 2022-05-02 15:17:28 +02:00
Felix Gruber f455c1e313
gnu: Add python-scrapy. 
* gnu/packages/python-web.scm (python-scrapy): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:46 +02:00
Felix Gruber d9a7f652e2
gnu: Add python-itemloaders. 
* gnu/packages/python-xyz.scm (python-itemloaders): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:46 +02:00
Felix Gruber 76b6337650
gnu: Add python-parsel. 
* gnu/packages/python-web.scm (python-parsel): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:46 +02:00
Felix Gruber d219d48cce
gnu: Add python-protego. 
* gnu/packages/python-web.scm (python-protego): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:46 +02:00
Felix Gruber c0c16d6b84
gnu: Add python-itemadapter. 
* gnu/packages/python-xyz.scm (python-itemadapter): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:45 +02:00
Felix Gruber fce913281f
gnu: Add python-queuelib. 
* gnu/packages/python-xyz.scm (python-queuelib): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:45 +02:00
Felix Gruber f728d1dcd2
gnu: Add python-pydispatcher. 
* gnu/packages/python-xyz.scm (python-pydispatcher): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:45 +02:00
Felix Gruber 919fdd6fcc
gnu: Add python-sybil. 
* gnu/packages/python-check.scm (python-sybil): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:45 +02:00
Greg Hogan 8ffd8fc64e
gnu: bear: Update to 3.0.19. 
* gnu/packages/build-tools.scm (bear): Update to 3.0.19.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:45 +02:00
Greg Hogan 9bf9da2571
gnu: spdlog: Update to 1.10.0. 
* gnu/packages/logging.scm (spdlog): Update to 1.10.0.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:45 +02:00
Greg Hogan c152174ca2
gnu: fmt: Update to 8.1.1. 
* gnu/packages/pretty-print.scm (fmt): Update to 8.1.1.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:44 +02:00
Paul A. Patience 67b10f18c7
gnu: apl: Use G-expressions. 
* gnu/packages/apl.scm (apl)[arguments]: Use G-expressions.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:44 +02:00
Paul A. Patience fe6ba5e902
gnu: apl: Remove input labels. 
* gnu/packages/apl.scm (apl)[inputs]: Remove labels and sort.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:44 +02:00
Paul A. Patience 94b1905580
gnu: apl: Update to 1.8-r1550. 
This commit fixes a failing build caused by -Werror (the configure
script no longer sets the -Werror compilation flag).

* gnu/packages/apl.scm (apl): Update to 1.8-r1550.
[arguments]: Add 'fix-configure' phase.
[license]: Prefix with 'license:'.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:44 +02:00
Niklas Eklund 35e5d2ce56
gnu: Add emacs-git-email. 
* gnu/packages/emacs-xyz.scm (emacs-git-email): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:44 +02:00
kiasoc5 75b7f495d0
gnu: ugrep: Update to 3.7.9. 
* gnu/packages/search.scm (ugrep): Update to 3.7.9.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:44 +02:00
Greg Hogan a8fde99e80
gnu: aws-sdk-cpp: Remove openssl input. 
* gnu/packages/cpp.scm (aws-sdk-cpp):
[inputs]: Remove openssl.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:43 +02:00
Greg Hogan af856afb6c
gnu: s2n: Link to aws-lc as libcrypto dependency. 
* gnu/packages/tls.scm (s2n):
[arguments]: Fix for openssl as replacement input for aws-lc.
[propagated-inputs]: Add aws-lc and remove openssl.
[supported-systems]: Only support x86_64-linux.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:43 +02:00
Greg Hogan a5a408c3a7
gnu: aws-lc: Fix checksum and enable tests. 
* gnu/packages/tls.scm (aws-lc):
[source]: Fix checksum.
[arguments]: Enable tests.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:43 +02:00
Greg Hogan fec71efeae
gnu: aws-crt-cpp: Fix comment formatting. 
* gnu/packages/cpp.scm (aws-crt-cpp): Fix comment formatting.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:43 +02:00
Greg Hogan a822f3e2d0
gnu: aws-c-mqtt: Fix comment formatting. 
* gnu/packages/c.scm (aws-c-mqtt): Fix comment formatting.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:43 +02:00
Greg Hogan b62d4872ba
gnu: aws-c-s3: Fix comment formatting. 
* gnu/packages/c.scm (aws-c-s3): Fix comment formatting.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:43 +02:00
Greg Hogan d62c101991
gnu: aws-c-auth: Fix comment formatting. 
* gnu/packages/c.scm (aws-c-auth): Fix comment formatting.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:43 +02:00
Greg Hogan b8c4bb3e0d
gnu: aws-c-compression: Fix comment formatting. 
* gnu/packages/c.scm (aws-c-compression): Fix comment formatting.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:42 +02:00
Greg Hogan d7c8a83549
gnu: aws-c-http: Fix comment formatting. 
* gnu/packages/c.scm (aws-c-http): Fix comment formatting.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:42 +02:00
Greg Hogan e8f2855d73
gnu: aws-c-sdkutils: Fix comment formatting. 
* gnu/packages/c.scm (aws-c-sdkutils): Fix comment formatting.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:42 +02:00
Greg Hogan c7805de435
gnu: aws-c-cal: Fix comment formatting. 
* gnu/packages/c.scm (aws-c-cal): Fix comment formatting.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:42 +02:00
Greg Hogan d230c67068
gnu: aws-c-io: Fix comment formatting. 
* gnu/packages/c.scm (aws-c-io): Fix comment formatting.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:42 +02:00
Greg Hogan 4dbb1520e2
gnu: aws-c-event-stream: Fix comment formatting. 
* gnu/packages/c.scm (aws-c-event-stream): Fix comment formatting.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:42 +02:00
Greg Hogan a9b4d69c9c
gnu: aws-checksums: Fix comment formatting. 
* gnu/packages/c.scm (aws-checksums): Fix comment formatting.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:42 +02:00
Greg Hogan acbf5b1022
gnu: aws-c-common: Only support i686 and x86_64. 
* gnu/packages/c.scm (aws-c-common):
[supported-systems]: Only support i686-linux and x86_64-linux.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-02 15:14:41 +02:00
Ludovic Courtès 6075d25143
services: bitlbee: Preserve 'PURPLE_PLUGIN_PATH'. 
Fixes a regression introduced in
211fe3f66e whereby, in inetd mode, and
when using 'bitlbee-purple', libpurple plugins would not be found.

* gnu/services/messaging.scm (bitlbee-shepherd-service): Pass
 #:preserved-environment-variables to 'least-authority-wrapper'.
 2022-05-02 15:14:41 +02:00
Ricardo Wurmus b1dd32d8e3
gnu: htslib-for-stringtie: Inherit from htslib-1.12. 
* gnu/packages/bioinformatics.scm (htslib-for-stringtie): Inherit from
htslib-1.12.
 2022-05-02 14:35:26 +02:00
Ricardo Wurmus 4571b218b5
gnu: Remove python-xlrd-1. 
* gnu/packages/python-xyz.scm (python-xlrd-1): Remove variable.
 2022-05-02 13:49:57 +02:00
Ricardo Wurmus 4642a50d52
gnu: Remove python-cytoolz-for-cooler. 
* gnu/packages/python-xyz.scm (python-cytoolz-for-cooler): Remove variable.
 2022-05-02 13:35:03 +02:00
Ricardo Wurmus 5caad9f252
gnu: python-cooler: Use more recent cytoolz. 
* gnu/packages/bioinformatics.scm (python-cooler)[propagated-inputs]: Replace
python-cytoolz-for-cooler with python-cytoolz.
 2022-05-02 13:33:16 +02:00
Ricardo Wurmus 9dafaf1635
gnu: python-anndata: Remove python-xlrd-1. 
* gnu/packages/python-xyz.scm (python-anndata)[propagated-inputs]: Remove
python-xlrd-1.
 2022-05-02 12:39:02 +02:00
Marius Bakke 098f2eea33
gnu: ungoogled-chromium: Update to 101.0.4951.41-1. 
* gnu/packages/chromium.scm (%preserved-third-party-files): Include bundled
Vulkan headers.
(%chromium-version): Set to 101.0.4951.41.
(%debian-revision): Set to debian/101.0.4951.41-2.
(%debian-patches): Add one new patch.
(%ungoogled-origin, ungoogled-chromium): Update hashes.
* gnu/packages/patches/ungoogled-chromium-system-nspr.patch: Refresh.
 2022-05-01 22:28:31 +02:00
Ludovic Courtès fee06d5aaa
services: opendht: Use 'least-authority-wrapper'. 
* gnu/services/networking.scm (opendht-configuration->command-line-arguments):
Use 'least-authority-wrapper'.
(opendht-shepherd-service): Use 'make-forkexec-constructor'.
 2022-05-01 21:30:36 +02:00
Ludovic Courtès dac4efc466
services: quassel: Use 'least-authority-wrapper'. 
* gnu/services/messaging.scm (quassel-shepherd-service): Use
'least-authority-wrapper' instead of
'make-forkexec-constructor/container'.
 2022-05-01 21:30:36 +02:00
Ludovic Courtès 53dbc6fd9a
services: wesnothd: Use 'least-authority-wrapper'. 
* gnu/services/games.scm (wesnothd-shepherd-service): Use
'least-authority-wrapper' instead of
'make-forkexec-constructor/container'.
 2022-05-01 21:30:36 +02:00
Ludovic Courtès 19df5f2423
services: wesnothd: Grant write access to /var/run/wesnothd. 
* gnu/services/games.scm (wesnothd-shepherd-service): Augment 'modules'
field.  Pass #:mappings argument to 'make-forkexec-constructor/container'.
(wesnothd-activation): New variable.
(wesnothd-service-type): Extend ACTIVATION-SERVICE-TYPE.
 2022-05-01 21:30:36 +02:00
Ludovic Courtès f5ef68ba98
services: ipfs: Use 'least-authority-wrapper'. 
* gnu/services/networking.scm (ipfs-binary): Call
'least-authority-wrapper'.
(%ipfs-home-mapping): Remove surrounding gexp.
(ipfs-shepherd-service)[exec-command]: New procedure.
[ipfs-config-command, set-config!-gexp, shepherd&co]
[container-gexp, container-script]: Remove.
[inner-gexp]: Use 'exec-command'.
 2022-05-01 21:30:35 +02:00
Ludovic Courtès 211fe3f66e
services: bitlbee: Use 'make-inetd-constructor'. 
* gnu/services/messaging.scm (bitlbee-shepherd-service): Add call to
'least-authority-wrapper'.  In 'start' method, use
'make-inetd-constructor' when available.
* gnu/tests/messaging.scm (run-bitlbee-test)["valid PID"]: Remove test.
 2022-05-01 21:30:35 +02:00
Ludovic Courtès fd57ce267c
services: dicod: Use 'make-inetd-constructor'. 
* gnu/services/dict.scm (dicod-shepherd-service): Use
'make-inetd-constructor' in the 'start' method when available.
 2022-05-01 21:30:35 +02:00
Ludovic Courtès 002bcb7eb0
services: dicod: Rewrite using 'least-authority-wrapper'. 
* gnu/services/dict.scm (dicod-shepherd-service): Rewrite using
'least-authority-wrapper' plus 'make-forkexec-constructor' instead of
'make-forkexec-constructor/container'.
 2022-05-01 21:30:35 +02:00
Ludovic Courtès 3682bd4003
Add (guix least-authority). 
* guix/least-authority.scm: New file.
* Makefile.am (MODULES): Add it.
* gnu/build/shepherd.scm (default-mounts): Make public.
 2022-05-01 21:30:35 +02:00
Ludovic Courtès 391bd14359
linux-container: Add #:child-is-pid1? parameter to 'call-with-container'. 
* gnu/build/linux-container.scm (wait-child-process)
(status->exit-status): New procedures.
(call-with-container): Add #:child-is-pid1? parameter and honor it.
[thunk*]: New variable.  Pass it to 'run-container'.
 2022-05-01 21:30:35 +02:00
Ludovic Courtès f6c9763984
linux-container: Ensure signal-handling asyncs get a chance to run. 
Previously we could enter the blocking 'waitpid' call and miss an
opportunity to run the signal handler async.

* gnu/build/linux-container.scm (call-with-container)
[periodically-schedule-asyncs]: New procedure.
[install-signal-handlers]: Call it.
 2022-05-01 21:30:35 +02:00
Ludovic Courtès a76fa226c8
linux-container: 'call-with-container' relays SIGTERM and SIGINT. 
* gnu/build/linux-container.scm (call-with-container): Add #:relayed-signals.
[install-signal-handlers]: New procedure.
Call it.
 2022-05-01 21:30:34 +02:00
Ludovic Courtès eaebc7f2b7
file-systems: Avoid load-time warnings when attempting to load (guix store). 
This makes sure warnings like "incompatible bytecode version" don't go
through when looking for (guix store).

* gnu/system/file-systems.scm (%store-prefix): Parameterize
'current-warning-port' around 'resolve-module' call.
 2022-05-01 21:30:34 +02:00
Ludovic Courtès 774f8804ba
gexp: Add 'references-file'. 
* gnu/services/base.scm (references-file): Remove.
* guix/gexp.scm (references-file): New procedure.
* tests/gexp.scm ("references-file"): New test.
 2022-05-01 21:30:34 +02:00
Julien Lepiller 674124b1ed
gnu: ocaml-uuidm: Update to 0.9.8. 
* gnu/packages/ocaml.scm (ocaml-uuidm): Update to 0.9.8.
(ocaml4.07-uuidm): New variable.
 2022-05-01 17:05:58 +02:00
Julien Lepiller c34ac580dc
gnu: ocamlformat: Update to 0.21.0. 
* gnu/packages/ocaml.scm (ocamlformat): Update to 0.21.0.
 2022-05-01 17:03:46 +02:00
Julien Lepiller e719135a57
gnu: ocaml-cmdliner: Update to 1.1.0. 
Cmdliner changed its output format, so two packages need to be modified
to accept the new format.

The patch modifies ocaml 4.07 packages to ensure this patch results in the
same derivations for these variants.

* gnu/packages/ocaml.scm (ocaml-cmdliner): Update to 1.1.0.
(ocaml-alcotest, ocaml-mdx)[arguments]: Fix tests.
(ocaml4.07-cmdliner): New variable.
(ocaml4.07-alcotest): Do not fix tests.
 2022-05-01 17:03:02 +02:00
Julien Lepiller 3d5d09abb8
gnu: ocaml-re: Update to 1.10.4. 
* gnu/packages/ocaml.scm (ocaml-re): Update to 1.10.4.
 2022-05-01 13:14:59 +02:00
Julien Lepiller be83b59d31
gnu: ocaml-spawn: Update to 0.15.1. 
* gnu/packages/ocaml.scm (ocaml-spawn): Update to 0.15.1.
 2022-05-01 13:14:59 +02:00
Julien Lepiller a342c32cd5
gnu: ocaml-ppx-fields-conv: Update to 0.15.0. 
* gnu/packages/ocaml.scm (ocaml-ppx-fields-conv): Update to 0.15.0.
 2022-05-01 13:14:59 +02:00
Julien Lepiller 6d97a08525
gnu: ocaml-parsexp: Update to 0.15.0. 
* gnu/packages/ocaml.scm (ocaml-parsexp): Update to 0.15.0.
 2022-05-01 13:14:59 +02:00
Julien Lepiller 88ee602039
gnu: ocaml-ppx-hash: Update to 0.15.0. 
* gnu/packages/ocaml.scm (ocaml-ppx-hash): Update to 0.15.0.
 2022-05-01 13:14:58 +02:00
Julien Lepiller db20b6c133
gnu: ocaml-ppx-sexp-value: Update to 0.15.0. 
* gnu/packages/ocaml.scm (ocaml-ppx-sexp-value): Update to 0.15.0.
 2022-05-01 13:14:58 +02:00
Julien Lepiller 4ce554c6da
gnu: ocaml-jst-config: Update to 0.15.1. 
* gnu/packages/ocaml.scm (ocaml-jst-config): Update to 0.15.1.
 2022-05-01 13:14:58 +02:00
Julien Lepiller ae08819ca5
gnu: ocaml-ppx-stable: Update to 0.15.0. 
* gnu/packages/ocaml.scm (ocaml-ppx-stable): Update to 0.15.0.
 2022-05-01 13:14:58 +02:00
Julien Lepiller 85b23e64e2
gnu: ocaml-ppx-base: Update to 0.15.0. 
* gnu/packages/ocaml.scm (ocaml-ppx-base): Update to 0.15.0.
 2022-05-01 13:14:58 +02:00
Julien Lepiller 72ca35c539
gnu: ocaml-ppx-compare: Update to 0.15.0. 
* gnu/packages/ocaml.scm (ocaml-ppx-compare): Update to 0.15.0.
 2022-05-01 13:14:58 +02:00
Julien Lepiller d1a4653bf6
gnu: ocaml-jane-street-headers: Update to 0.15.0. 
* gnu/packages/ocaml.scm (ocaml-jane-street-headers): Update to 0.15.0.
 2022-05-01 13:14:58 +02:00
Julien Lepiller 0cea8f99aa
gnu: ocaml-base-bigstring: Update to 0.15.0. 
* gnu/packages/ocaml.scm (ocaml-base-bigstring): Update to 0.15.0.
 2022-05-01 13:14:57 +02:00
Julien Lepiller 4fe2489816
gnu: ocaml-core: Update to 0.15.0. 
These packages cannot be updated individually.

* gnu/packages/ocaml.scm (ocaml-ppx-inline-test, ocaml-sexplib0)
(ocaml-sexplib, ocaml-base, ocaml-stdio, ocaml-ppx-sexp-conv)
(ocaml-ppx-expect, ocaml-base-quickcheck, ocaml-core)
(ocaml-core-kernel, ocaml-timezone): Update to 0.15.0.
(ocaml-ppxlib): Fix tests.
(ocaml-int-repr): New variable.
 2022-05-01 13:14:57 +02:00
Julien Lepiller e8a3a1d279
gnu: ocaml-ppxlib: Update to 0.25.0. 
* gnu/packages/ocaml.scm (ocaml-ppxlib): Update to 0.25.0.
 2022-05-01 13:14:57 +02:00
Julien Lepiller 556ccb4ae1
gnu: coq: Update to 8.15.1. 
* gnu/packages/coq.scm (coq): Update to 8.15.1.
 2022-05-01 13:14:57 +02:00
Julien Lepiller b27a2366ab
gnu: ocaml-hex: Update to 1.5.0. 
* gnu/packages/ocaml.scm (ocaml-hex): Update to 1.5.0.
 2022-05-01 13:14:57 +02:00
Julien Lepiller ab8d68cadd
gnu: ocaml-easy-format: Update to 1.3.3. 
* gnu/packages/ocaml.scm (ocaml-easy-format): Update to 1.3.3.
 2022-05-01 13:14:57 +02:00
Julien Lepiller cda4ca0ab5
gnu: ocaml-variantslib: Update to 0.15.0. 
* gnu/packages/ocaml.scm (ocaml-variantslib): Update to 0.15.0.
 2022-05-01 13:14:56 +02:00
Julien Lepiller f076cdba02
gnu: ocaml-ppx-optcomp: Update to 0.15.0. 
* gnu/packages/ocaml.scm (ocaml-ppx-optcomp): Update to 0.15.0.
 2022-05-01 13:14:56 +02:00
Julien Lepiller ffdd749ad5
gnu: ocaml-cstruct: Update to 6.1.0. 
* gnu/packages/ocaml.scm (ocaml-cstruct): Update to 6.1.0.
 2022-05-01 13:14:56 +02:00
Julien Lepiller ae7c2c4b16
gnu: ocaml-ppx-bin-prot: Update to 0.15.0. 
* gnu/packages/ocaml.scm (ocaml-ppx-bin-prot): Update to 0.15.0.
 2022-05-01 13:14:56 +02:00
Julien Lepiller 143b9d3a3d
gnu: ocaml-ppx-jane: Update to 0.15.0. 
* gnu/packages/ocaml.scm (ocaml-ppx-jane): Update to 0.15.0.
 2022-05-01 13:14:56 +02:00