Merge branch 'add-r-uqsa' into 'master'

Add r uqsa

See merge request technical-coordination/project-internal/devops/platform/ebrains-spack-builds!271

packages/r-uqsa/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 RUqsa(RPackage):
+    """This package will solve an initial value problem (given an ordinary
+    differential equation) for a list of simulation experiments. The
+    simulations will be compared to data, repeatedly.  The package can
+    sample the parameters of the model via ABC (approximate Bayesian
+    computation) and by doing so quantify the uncertainty that remains
+    within the model even after considering the data. Experiments are
+    evaluated in a sequence, intermediate probability densities are
+    modeled using the VineCopua package."""
+
+    # FIXME: Add a proper url for your package's homepage here.
+    homepage = "https://github.com/icpm-kth/uqsa"
+    url = "https://github.com/icpm-kth/uqsa/archive/refs/tags/v2.2.tar.gz"
+
+    version("2.2", sha256="df15d20c0cd466083181ec8f37cd331f409dcd23838553cd46a7a7305bdcfc7f")
+
+    depends_on("r-vinecopula")
+    depends_on("r-mass")
+    depends_on("r-r-utils")
+    depends_on("r-ks")
+

packages/r-vinecopula/package.py

-# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
+# 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 import *
+from spack.package import *
 
 
 class RVinecopula(RPackage):
-    """Provides tools for the statistical analysis of regular vine copula models."""
+    """Provides tools for the statistical analysis of regular vine copula 
+    models, see Aas et al. (2009) <doi:10.1016/j.insmatheco.2007.02.001> and 
+    Dissman et al. (2013) <doi:10.1016/j.csda.2012.08.010>.
+    The package includes tools for parameter estimation, model selection,
+    simulation, goodness-of-fit tests, and visualization. Tools for estimation,
+    selection and exploratory data analysis of bivariate copula models are also
+    provided."""
 
     homepage = "https://cran.r-project.org/package=VineCopula"
-    cran     = "VineCopula"
+    url = "https://github.com/tnagler/VineCopula/archive/refs/tags/v2.4.5.tar.gz"
 
-    version('2.4.5', sha256='06b9f67d14d525cbf04c991cedbd2e4f58bbb1f24ec10947aeed1efef91c33cd')
-    version('2.4.4', sha256='8449b1181fd7f325a2f0539cdaa4a4ff895c41424f462f52258729436078c90a')
-    version('2.4.3', sha256='42727aa7345ab544242182222eb97476f5dc04bc837f94f6fd3ea6ccac93ea17')
-    version('2.4.2', sha256='468a4aa80feaa8b285ba596430b963b2f9f5e1f64254dcd63baf2fb0059e9a90')
-    version('2.4.1', sha256='b19640d91a0d6608355c6fe9a32c0d1bc6c1993047cba440617d07b5b389de30')
+    version("2.4.5", sha256="2255a2a0f2644e447f33c7fa3562cb1ad109aa7809ea250fe82b67b35cc2d23d")
 
-    depends_on('r-mass', type=('build', 'run'))
-    depends_on('r-mvtnorm', type=('build', 'run'))
-    depends_on('r-adgoftest', type=('build', 'run'))
-    depends_on('r-lattice', type=('build', 'run'))
+    depends_on("r-mass")
+    depends_on("r-mvtnorm")
+    depends_on("r-r-methodss3")
+    depends_on("r-adgoftest")
+    depends_on("r-lattice")

spack.yaml

@@ -64,6 +64,7 @@ spack:
     - biobb-gromacs
     - apbs
     - py-pdb2pqr
+    - r-uqsa
     - sda
     - r-rgsl
     - r-sbtabvfgen