new packages: r-cmdstanr and cmdstan (#32364)

2 files changed, 117 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/cmdstan/package.py b/var/spack/repos/builtin/packages/cmdstan/package.py
new file mode 100644
index 0000000000..a4e182a657
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cmdstan/package.py
@@ -0,0 +1,83 @@
+# Copyright 2013-2022 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 Cmdstan(MakefilePackage):
+    """CmdStan is the command line interface to Stan."""
+
+    homepage = "https://mc-stan.org/users/interfaces/cmdstan"
+    url = "https://github.com/stan-dev/cmdstan/releases/download/v2.30.1/cmdstan-2.30.1.tar.gz"
+
+    version("2.30.1", sha256="bab76dcefa7f4c955595c0bf0496770507fc6ab0df5896e8cf8c2db0a17eedb9")
+
+    variant("threads", default=True, description="enable thread support")
+    variant("opencl", default=False, description="enable OpenCl support")
+    variant("mpi", default=False, description="enable MPI support")
+
+    depends_on("opencl", when="+opencl")
+    depends_on("mpi", when="+mpi")
+
+    build_targets = ["build"]
+
+    filter_compiler_wrappers("local", relative_root="make")
+
+    def edit(self, spec, prefix):
+        if spec.compiler.name == "intel":
+            cxx_type = "icc"
+        else:
+            cxx_type = spec.compiler.name
+
+        if "+mpi" in spec:
+            cxx = spec["mpi"].mpicxx
+        else:
+            cxx = spack_cxx
+
+        make_options = [
+            "CXX={0}\n".format(cxx),
+            "CXXFLAGS+= -O2 -funroll-loops\n",
+            "LDFLAGS+={0}{1}\n".format(
+                self.compiler.cc_rpath_arg,
+                join_path(prefix, "stan", "lib", "stan_math", "lib", "tbb"),
+            ),
+            "STANCFLAGS+= --warn-pedantic\n",
+            "TBB_CXX_TYPE={0}\n".format(cxx_type),
+        ]
+
+        if "+threads" in spec:
+            make_options.append("STAN_THREADS=true\n")
+
+        if "+opencl" in spec:
+            make_options.append("STAN_OPENCL=true\n")
+
+        if "+mpi" in spec:
+            make_options.append("STAN_MPI=true\n")
+
+        filepath = join_path(self.stage.source_path, "make", "local")
+        with open(filepath, "w") as make_file:
+            make_file.writelines(make_options)
+
+    def install(self, spec, prefix):
+        make(join_path("examples", "bernoulli", "bernoulli"))
+
+        mkdir(prefix.bin)
+
+        with working_dir(self.build_directory):
+            copy("makefile", prefix)
+            copy_tree("make", prefix.make)
+            copy_tree("examples", prefix.examples)
+            copy_tree("lib", prefix.lib)
+            copy_tree("src", prefix.src)
+            copy_tree("stan", prefix.stan)
+
+        with working_dir(join_path(self.build_directory, "bin")):
+            install("diagnose", prefix.bin)
+            install("print", prefix.bin)
+            install("stanc", prefix.bin)
+            install("stansummary", prefix.bin)
+
+    def setup_run_environment(self, env):
+        env.set("CMDSTAN", self.prefix)
diff --git a/var/spack/repos/builtin/packages/r-cmdstanr/package.py b/var/spack/repos/builtin/packages/r-cmdstanr/package.py
new file mode 100644
index 0000000000..d55dc23360
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-cmdstanr/package.py
@@ -0,0 +1,34 @@
+# Copyright 2013-2022 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 RCmdstanr(RPackage):
+    """R Interface to 'CmdStan'.
+
+    A lightweight interface to 'Stan' <https://mc-stan.org>.  The 'CmdStanR'
+    interface is an alternative to 'RStan' that calls the command line
+    interface for compilation and running algorithms instead of interfacing
+    with C++ via 'Rcpp'. This has many benefits including always being
+    compatible with the latest version of Stan, fewer installation errors,
+    fewer unexpected crashes in RStudio, and a more permissive license."""
+
+    homepage = "https://mc-stan.org/cmdstanr/"
+    url = "https://github.com/stan-dev/cmdstanr/archive/refs/tags/v0.5.3.tar.gz"
+
+    version("0.5.3", sha256="dafd5808e1a17d2e4ae4048437235b4399464a7c65de68ba4af0ab2b03e27871")
+    version("0.5.2", sha256="5bc2e164e7cce3bfb93d592df5e3059157c8d510b136535bdb6d09c3ef060f64")
+    version("0.5.1", sha256="5b3e83d48c19d309ccca720979449a8ac130ba7e443e70992b1771a1dd9124c9")
+
+    depends_on("r@3.5.0:", type=("build", "run"))
+    depends_on("r-checkmate", type=("build", "run"))
+    depends_on("r-data-table", type=("build", "run"))
+    depends_on("r-jsonlite@1.2.0:", type=("build", "run"))
+    depends_on("r-posterior@1.1.0:", type=("build", "run"))
+    depends_on("r-processx@3.5.0:", type=("build", "run"))
+    depends_on("r-r6@2.4.0:", type=("build", "run"))
+    depends_on("r-withr@2.5.0:", type=("build", "run"), when="@0.5.2:")
+    depends_on("cmdstan", type="run")