Merge branch 'master' into 'test-spacktests-workaround'

update branch

See merge request technical-coordination/project-internal/devops/platform/ebrains-spack-builds!277

packages/nest/package.py

@@ -21,13 +21,12 @@ class Nest(CMakePackage):
         #
         #'https://github.com/nest/nest-simulator/releases/download/v2.12.0/nest-2.12.0.tar.gz',
         'https://github.com/nest/nest-simulator/archive/refs/tags/v2.12.0.tar.gz',
-
         'https://github.com/nest/nest-simulator/archive/refs/tags/v3.0.tar.gz'
     ]
     git      = "https://github.com/nest/nest-simulator.git"
 
     version('master', branch='master')
-    version('3.4_rc2',sha256='037012200489ad4f800ed5dc6279917e89c831d101a4b852b5c42278923566a3')
+    version('3.4',    sha256='c56699111f899045ba48e55e87d14eca8763b48ebbb3648beee701a36aa3af20')
     version('3.3',    sha256='179462b966cc61f5785d2fee770bc36f86745598ace9cd97dd620622b62043ed')
     version('3.2',    sha256='583d5725882ad5e8fd4fc7ffab425da97cbbb91fadbc327e940c184e8892b958')
     patch('nest-simulator-3.2-p1-VersionNumber.patch', when='@3.2')

packages/r-dynutils/package.py

+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class RDynutils(RPackage):
+    """Provides common functionality for the 'dynverse' packages. 'dynverse' is created to support the development, execution, and benchmarking of trajectory inference methods. For more information, check out <https://dynverse.org>."""
+
+    homepage = "https://cran.r-project.org/package=dynutils"
+    cran = "dynutils"
+
+    version("1.0.11", sha256="09ce9efda019e5c345ad6a7131f41f7fe9c8458c1b105191d8618416ea125619")
+
+    depends_on("r-assertthat")
+    depends_on("r-crayon")
+    depends_on("r-desc")
+    depends_on("r-dplyr")
+    depends_on("r-magrittr")
+    depends_on("r-matrix")
+    depends_on("r-proxyc")
+    depends_on("r-purrr")
+    depends_on("r-rcpp")
+    depends_on("r-remotes")
+    depends_on("r-stringr")
+    depends_on("r-tibble")
+
+
+

packages/r-gillespiessa2/package.py

+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class RGillespiessa2(RPackage):
+    """A fast, scalable, and versatile framework for simulating large systems with Gillespie's Stochastic Simulation Algorithm ('SSA'). This package is the spiritual successor to the 'GillespieSSA' package originally written by Mario Pineda-Krch. Benefits of this package include major speed improvements (>100x), easier to understand documentation, and many unit tests that try to ensure the package works as intended. Cannoodt and Saelens et al. (2021) <doi:10.1038/s41467-021-24152-2>."""
+
+    homepage = "https://cran.r-project.org/package=GillespieSSA2"
+    cran = "GillespieSSA2"
+
+    version("0.3.0", sha256="206497ae7be8ff88a5edafe81b0295eb4b14109c546878ace16a7396a0035f72")
+
+    depends_on("r-assertthat")
+    depends_on("r-dplyr")
+    depends_on("r-dynutils")
+    depends_on("r-matrix")
+    depends_on("r-purrr")
+    depends_on("r-rcpp")
+    depends_on("r-rcppxptrutils")
+    depends_on("r-readr")
+    depends_on("r-rlang")
+    depends_on("r-stringr")
+    depends_on("r-tidyr")
+

packages/r-proxyc/package.py

+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class RProxyc(RPackage):
+    """Computes proximity between rows or columns of large matrices efficiently in C++. Functions are optimised for large sparse matrices using the Armadillo and Intel TBB libraries. Among several built-in similarity/distance measures, computation of correlation, cosine similarity and Euclidean distance is particularly fast."""
+
+    homepage = "https://cran.r-project.org/package=proxyC"
+    cran = "proxyC"
+
+    version("0.3.3", sha256="3e25da94633da0b5c6cdac03f5b6d8205d078f60c5a09073e90a1b6f0930e302")
+
+    depends_on("r-rcpp")
+    depends_on("r-rcppparallel")
+    depends_on("r-rcpparmadillo")
+    depends_on("r-matrix")

packages/r-rcppxptrutils/package.py

+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class RRcppxptrutils(RPackage):
+    """Provides the means to compile user-supplied C++ functions with 'Rcpp' and retrieve an 'XPtr' that can be passed to other C++ components."""
+
+    homepage = "https://cran.r-project.org/package=RcppXPtrUtils"
+    cran = "RcppXPtrUtils"
+
+    version("0.1.2", sha256="34d0cab1891c95453c357cf93ab97b6ea42ef98cdc4809c9abfafd469c3da542")
+
+    depends_on("r-rcpp")

packages/r-uqsa/package.py

@@ -27,4 +27,4 @@ class RUqsa(RPackage):
     depends_on("r-mass")
     depends_on("r-r-utils")
     depends_on("r-ks")
-
+    depends_on("r-gillespiessa2")

spack.yaml

@@ -20,7 +20,7 @@ spack:
     - py-lazyarray
     #- py-version-query
     # EBRAINS simulators
-    - nest@3.4_rc2
+    - nest@3.4
     - arbor +python +mpi
     - neuron +mpi
     - py-pynn@0.10.1 +mpi