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2024-10-11gnu: Add ghdl-clang.csantosb/masterCayetano Santos1-0/+58
* guix-science/packages/electronics.scm (ghdl-clang): New variable.
2024-10-11gnu: Add gnat.Cayetano Santos1-0/+125
* guix-science/packages/electronics.scm (gnat): New variable.
2024-09-10tensorflow: Depend on Flatbuffers 23.1.Ludovic Courtès1-1/+1
Fixes a regression introduced with the upgrade of ‘flatbuffers-next’ in Guix commit fe38c1018284e5190ba4904a729ee3e3714a09d7. * guix-science/packages/python.scm (tensorflow)[inputs]: Change FLATBUFFERS-NEXT to FLATBUFFERS-23.1.
2024-07-18rstudio: rstudio: Adjust to refer to Qt 5.x libraries.Ludovic Courtès1-1/+1
This is a followup to Guix commit 47be97c731afeebea459b1a58aea2bc0b56054a4. * guix-science/packages/rstudio.scm (rstudio)[inputs]: Refer to ‘qtlocation-5’ and ‘qtsensors-5’.
2024-05-22cran: r-shinywidgets: Update to 0.8.6.Ricardo Wurmus1-2/+2
* guix-science/packages/cran.scm (r-shinywidgets): Update to 0.8.6.
2024-05-22bioinformatics: Add r-mcview.Marco Baggio1-0/+77
* guix-science/packages/bioinformatics.scm (r-mcview): New variable.
2024-05-22cran: Add r-shinybusy.Marco Baggio1-1/+25
* guix-science/packages/cran.scm (r-shinybusy): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2024-05-22cran: Remove r-waiter.Ricardo Wurmus1-24/+0
This is now available in Guix proper. * guix-science/packages/cran.scm (r-waiter): Remove variable.
2024-05-22cran: Remove r-shinydashboardplus.Ricardo Wurmus1-85/+0
This is now available in Guix proper. * guix-science/packages/cran.scm (r-shinydashboardplus): Remove variable.
2024-04-18rstudio: rstudio: Use qtsensors from Qt5.Ricardo Wurmus1-2/+2
* guix-science/packages/rstudio.scm (rstudio)[inputs]: Replace qtsensors with qtsensors-5.
2024-04-16cloud: google-cloud-sdk: Update to 465.0.0.Ryan1-2/+2
* guix-science/packages/cloud.csm (google-cloud-sdk): Update to 465.0.0. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2024-03-27gnu: r-shinywidgets: Update to 0.8.3.Ricardo Wurmus1-2/+2
* guix-science/packages/cran.scm (r-shinywidgets): Update to 0.8.3.
2024-03-14machine-learning: python-tensorstore: Do not embed store file names.Ricardo Wurmus1-6/+37
* guix-science/packages/machine-learning.scm (python-tensorstore) [source]: Avoid embedding /gnu/store locations by expecting numpy headers in /tmp. [arguments]: Place numpy headers where they are expected.
2024-03-14python: python-tensorflow: Relax requirement on typing-extensions.Ricardo Wurmus1-0/+1
* guix-science/packages/python.scm (python-tensorflow)[arguments]: Remove upper bound on typing-extensions.
2024-02-20rstudio: rstudio-server: Use G-expressions.Ricardo Wurmus1-99/+98
* guix-science/packages/rstudio.scm (rstudio-server)[arguments]: Use G-expression. (rstudio)[arguments]: Adjust to modify inherited G-expression arguments.
2024-02-20cran: r-bs4dash: Update to 2.3.3.Ricardo Wurmus1-3/+3
* guix-science/packages/cran.scm (r-bs4dash): Update to 2.3.3. [native-inputs]: Add esbuild.
2024-02-20cran: r-diagrammer: Update to 1.0.11.Ricardo Wurmus1-4/+4
* guix-science/packages/cran.scm (r-diagrammer): Update to 1.0.11. [propagated-inputs]: Remove r-downloader and r-viridis; add r-cli and r-viridislite.
2024-02-20cran: r-lavaanplot: Update to 0.8.1.Ricardo Wurmus1-2/+5
* guix-science/packages/cran.scm (r-lavaanplot): Update to 0.8.1. [propagated-inputs]: Add r-dplyr, r-purrr, and r-rlang.
2024-02-13machine-learning: Add python-alphafold.Navid Afkhami1-0/+82
* guix-science/packages/machine-learning.scm (python-alphafold): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2024-02-12bazel: Add bazel-6.1.Ricardo Wurmus1-0/+157
* guix-science/packages/bazel.scm (bazel-6.1): New variable.
2024-02-12gnu: bazel: Do not use proot.Ricardo Wurmus1-15/+6
* guix-science/packages/bazel.scm (bazel)[arguments]: Do not invoke proot; add phase to replace Python shebang. [native-inputs]: Remove proot, add python-wrapper. Co-authored-by: Emmanuel Medernach.
2024-02-07machine-learning: Add python-dm-haiku.Navid Afkhami1-0/+48
* guix-science/packages/machine-learning.scm (python-dm-haiku): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2024-02-07machine-learning: python-flax: Disable some more tests.Navid Afkhami1-0/+7
* guix-science/packages/machine-learning.scm (python-flax)[arguments]: Disable tests that can might depend on CPU micro-architecture.
2024-01-25bioinformatics: Add python-scvi-tools.Ricardo Wurmus1-1/+103
* guix-science/packages/bioinformatics.scm (python-scvi-tools): New variable.
2024-01-25python: python-numpyro: Disable test_mean_var test.Ricardo Wurmus1-0/+3
* guix-science/packages/python.scm (python-numpyro)[arguments]: Disable test_mean_var.
2024-01-25bioinformatics: Add rsat.Ricardo Wurmus1-0/+94
* guix-science/packages/bioinformatics.scm (rsat): New variable.
2024-01-25python: python-jax: Update to 0.4.20.Ricardo Wurmus1-8/+23
* guix-science/packages/python.scm (python-jaxlib/wheel): Update to 0.4.20. [arguments]: Pass bazel arguments to override included platforms repo; disable patching of xla protobuf. [native-inputs]: Add bazel-platforms. (python-jax): Update to 0.4.20.
2024-01-25machine-learning: python-flax: Update to 0.8.0.Ricardo Wurmus1-5/+2
* guix-science/packages/machine-learning.scm (python-flax): Update to 0.8.0.
2024-01-25machine-learning: python-orbax-checkpoint: Update to 0.4.5.Ricardo Wurmus1-15/+6
* guix-science/packages/machine-learning.scm (python-orbax-checkpoint): Update to 0.4.5. [arguments]: Remove 'jax-compatibility phase; add 'chdir phase.
2024-01-25machine-learning: Add python-flax.Ricardo Wurmus1-0/+62
* guix-science/packages/machine-learning.scm (python-flax): New variable.
2024-01-25machine-learning: python-tensorstore: Fix version.Ricardo Wurmus1-1/+3
* guix-science/packages/machine-learning.scm (python-tensorstore)[arguments]: Patch fallback version string.
2024-01-25machine-learning: Add python-orbax-checkpoint.Ricardo Wurmus1-0/+63
* guix-science/packages/machine-learning.scm (python-orbax-checkpoint): New variable.
2024-01-24python: Add python-etils.Ricardo Wurmus1-0/+62
* guix-science/packages/python.scm (python-etils): New variable.
2024-01-24python: Add python-simple-parsing.Ricardo Wurmus1-0/+28
* guix-science/packages/python.scm (python-simple-parsing): New variable.
2024-01-24python: Add python-optree.Ricardo Wurmus1-0/+33
* guix-science/packages/python.scm (python-optree): New variable.
2024-01-24python: Add python-jmp.nafkhamdc1-0/+28
* guix-science/packages/python.scm (python-jmp): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2024-01-24cran: Move r-papaja to Guix.Ricardo Wurmus1-107/+0
* guix-science/packages/cran.scm (r-papaja, r-rmdfiltr, r-tinylabels): Remove variables.
2024-01-24cran: r-shinydashboardplus: Process all JavaScript.Ricardo Wurmus1-29/+51
* guix-science/packages/cran.scm (r-shinydashboardplus)[source]: Delete all minified JavaScript. [arguments]: Use minify-build-system; change 'process-javascript phase to process two more files. [native-inputs]: Add clone of MaterialAdminLTE repository.
2024-01-23machine-learning: python-tensorstore: Build and install Python parts.Ricardo Wurmus1-2/+37
* guix-science/packages/machine-learning.scm (python-tensorstore): [arguments]: Add phases from pyproject-build-system to build and install Python bindings. [native-inputs]: Add python-setuptools, python-setuptools-scm, and python-wheel.
2024-01-18machine-learning: Add python-tensorstore.Ricardo Wurmus1-0/+390
* guix-science/packages/machine-learning.scm (python-tensorstore): New variable.
2024-01-18bazel-build-system: Accept overrides for bazel and jdk.Ricardo Wurmus1-3/+3
* guix-science/build-system/bazel.scm (bazel-build): Mark bazel and jdk as private keywords.
2024-01-18bazel-build-system: Pass bazel arguments to build.Ricardo Wurmus2-8/+11
* guix-science/build/bazel-build-system.scm (build): Accept bazel-arguments. * guix-science/build-system/bazel.scm (bazel-build): Pass bazel-arguments.
2024-01-18bazel: Add bazel-6.4.Ricardo Wurmus1-0/+28
* guix-science/packages/bazel.scm (bazel-6.4): New variable.
2024-01-17cran: r-reactr: Update to 0.5.0.Ricardo Wurmus1-2/+2
* guix-science/packages/cran.scm (r-reactr): Update to 0.5.0.
2024-01-17cran: r-shinywidgets: Update to 0.8.1.Ricardo Wurmus1-2/+2
* guix-science/packages/cran.scm (r-shinywidgets): Update to 0.8.1.
2024-01-16python: Remove python-pydoc-markdow.Ricardo Wurmus1-218/+0
This package is now in Guix proper. Also remove the suite of python-nr.* packages that were only needed for this package. * guix-science/packages/python.scm (python-pydoc-markdown, python-nr.databind.core, python-nr.collections, python-nr.metaclass, python-nr.interface, python-nr.pylang.utils, python-nr.databind.json, python-nr.parsing.date, python-nr.utils.re, python-nr.fs): Remove variables.
2024-01-16python: Remove python-docspec-python.Ricardo Wurmus1-21/+0
This package is now available in Guix proper. * guix-science/packages/python.scm (python-docspec-python): Remove variable.
2024-01-16python: Remove python-docspec.Ricardo Wurmus1-22/+0
This package lives in Guix proper now. * guix-science/packages/python.scm (python-docspec): Remove variable.
2024-01-15python: python-nr.stream: Declare as deprecated alias.Ricardo Wurmus1-19/+1
* guix-science/packages/python.scm (python-nr.stream): Declare as deprecated package alias of python-nr-stream, which is now in Guix proper.
2024-01-15machine-learning: Add python-tslearn.Ricardo Wurmus1-0/+40
* guix-science/packages/machine-learning.scm (python-tslearn): New variable.
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