Merge branch 'develop' into woptim/extend-commit-fetch

The patches don't have a stable checksum.

lib/spack/spack/fetch_strategy.py

@@ -862,6 +862,9 @@ def clone(self, dest=None, commit=None, branch=None, tag=None, bare=False):
                 )
 
             with working_dir(dest):
+                # By defaults, on all references are fetched by the clone
+                fetch_args = ["fetch", "origin", commit]
+                git(*fetch_args)
                 checkout_args = ["checkout", commit]
                 if not debug:
                     checkout_args.insert(1, "--quiet")

lib/spack/spack/util/environment.py

@@ -138,7 +138,7 @@ def dump_environment(path, environment=None):
     use_env = environment or os.environ
     hidden_vars = set(["PS1", "PWD", "OLDPWD", "TERM_SESSION_ID"])
 
-    fd = os.open(path, os.O_WRONLY | os.O_CREAT, 0o600)
+    fd = os.open(path, os.O_WRONLY | os.O_CREAT | os.O_TRUNC, 0o600)
     with os.fdopen(fd, "w") as env_file:
         for var, val in sorted(use_env.items()):
             env_file.write(

lib/spack/spack/version.py

@@ -1336,6 +1336,10 @@ def lookup_ref(self, ref):
             # won't properly update the local rev-list)
             self.fetcher.git("fetch", "--tags", output=os.devnull, error=os.devnull)
 
+            # We need to do an attempt at fetching the commit in order to
+            # be sure to get it in case it comes from a PR in a fork.
+            self.fetcher.git("fetch", "origin", "%s" % ref, output=os.devnull, error=os.devnull)
+
             # Ensure ref is a commit object known to git
             # Note the brackets are literals, the ref replaces the format string
             try:

var/spack/repos/builtin/packages/celeritas/package.py

@@ -17,12 +17,38 @@ class Celeritas(CMakePackage, CudaPackage, ROCmPackage):
 
     maintainers("sethrj")
 
-    version("0.2.0", sha256="12af28fda0e482a9eba89781b4ead445cf6f170bc1b8d88cc814e49b1ec09e9f")
-    version("0.1.4", sha256="ea82a03fc750a2a805f87afd9ac944109dd7537edb5c0c370f93d332d4cd47db")
-    version("0.1.3", sha256="992c49a48adba884fe3933c9624da5bf480ef0694809430ae98903f2c28cc881")
-    version("0.1.2", sha256="d123ea2e34267adba387d46bae8c9a1146a2e047f87f2ea5f823878c1684678d")
-    version("0.1.1", sha256="a1d58e29226e89a2330d69c40049d61e7c885cf991824e60ff8c9ccc95fc5ec6")
-    version("0.1.0", sha256="46692977b9b31d73662252cc122d7f016f94139475788bca7fdcb97279b93af8")
+    version("0.2.1", sha256="b3717b43f70dd0da848139da4171ca7a887bb6777908845b6d953d47b1f4db41")
+    version(
+        "0.2.0",
+        sha256="12af28fda0e482a9eba89781b4ead445cf6f170bc1b8d88cc814e49b1ec09e9f",
+        deprecated=True,
+    )
+    version("0.1.5", sha256="5e63b9ce7fcfe34a8938565b84453bce51fa6639d1ede13bb59d41de6431cef4")
+    version(
+        "0.1.4",
+        sha256="ea82a03fc750a2a805f87afd9ac944109dd7537edb5c0c370f93d332d4cd47db",
+        deprecated=True,
+    )
+    version(
+        "0.1.3",
+        sha256="992c49a48adba884fe3933c9624da5bf480ef0694809430ae98903f2c28cc881",
+        deprecated=True,
+    )
+    version(
+        "0.1.2",
+        sha256="d123ea2e34267adba387d46bae8c9a1146a2e047f87f2ea5f823878c1684678d",
+        deprecated=True,
+    )
+    version(
+        "0.1.1",
+        sha256="a1d58e29226e89a2330d69c40049d61e7c885cf991824e60ff8c9ccc95fc5ec6",
+        deprecated=True,
+    )
+    version(
+        "0.1.0",
+        sha256="46692977b9b31d73662252cc122d7f016f94139475788bca7fdcb97279b93af8",
+        deprecated=True,
+    )
 
     _cxxstd_values = ("14", "17")
 
@@ -49,7 +75,8 @@ class Celeritas(CMakePackage, CudaPackage, ROCmPackage):
     depends_on("cmake@3.22:", type="build", when="+rocm")
 
     depends_on("nlohmann-json")
-    depends_on("geant4@10.6:", when="+geant4")
+    depends_on("geant4@10.7:11.0", when="@:0.2.0 +geant4")
+    depends_on("geant4@10.6:11.0", when="@0.2.1: +geant4")
     depends_on("hepmc3", when="+hepmc3")
     depends_on("root", when="+root")
     depends_on("swig", when="+swig")
@@ -68,6 +95,7 @@ class Celeritas(CMakePackage, CudaPackage, ROCmPackage):
     depends_on("vecgeom +gdml@1.1.17:", when="+vecgeom")
     depends_on("vecgeom +cuda", when="+vecgeom +cuda")
 
+    conflicts("cxxstd=14", when="@0.3:")
     conflicts("+rocm", when="+cuda", msg="AMD and NVIDIA accelerators are incompatible")
     conflicts("+rocm", when="+vecgeom", msg="HIP support is only available with ORANGE")
     conflicts("^vecgeom+shared@1.2.0", when="+vecgeom +cuda")

var/spack/repos/builtin/packages/go/package.py

@@ -116,6 +116,7 @@ def setup_build_environment(self, env):
         # internal Spack wrappers and fail.
         env.set("CC_FOR_TARGET", self.compiler.cc)
         env.set("CXX_FOR_TARGET", self.compiler.cxx)
+        env.set("GOMAXPROCS", make_jobs)
 
     def setup_dependent_package(self, module, dependent_spec):
         """Called before go modules' install() methods.

var/spack/repos/builtin/packages/hdf5-vol-cache/package.py

@@ -14,6 +14,7 @@ class Hdf5VolCache(CMakePackage):
     maintainers("hyoklee", "lrknox")
 
     version("default", branch="develop")
+    version("v1.1", tag="v1.1")
     version("v1.0", tag="v1.0")
 
     depends_on("hdf5-vol-async")

var/spack/repos/builtin/packages/hpctoolkit/411d62544717873432c49ef45c7cb99cc5de2fb8.patch

@@ -0,0 +1,91 @@
+From 411d62544717873432c49ef45c7cb99cc5de2fb8 Mon Sep 17 00:00:00 2001
+From: "Mark W. Krentel" <krentel@rice.edu>
+Date: Thu, 15 Dec 2022 16:43:43 -0600
+Subject: [PATCH] Add a temporary hack to allow both ROCM 5.2/5.3 to build
+ cleanly.
+
+There were some corner cases (build 5.3 pieces from spack and feed
+into autotools) that didn't work.  After the next release, I will want
+to rework ROCM configure more extensively.
+---
+ configure    | 21 +++++++++++++--------
+ configure.ac | 17 +++++++++++------
+ 2 files changed, 24 insertions(+), 14 deletions(-)
+
+diff --git a/configure b/configure
+index 1760e678e8..814376b3bd 100755
+--- a/configure
++++ b/configure
+@@ -23891,10 +23891,13 @@ $as_echo "$as_me: found $ROCM/rocprofiler/lib/librocprofiler64.so" >&6;}
+     fi
+ 
+     # HSA
+-    if test -f "$ROCM/include/hsa/hsa.h" ; then
+-      { $as_echo "$as_me:${as_lineno-$LINENO}: found $ROCM/include/hsa/hsa.h" >&5
+-$as_echo "$as_me: found $ROCM/include/hsa/hsa.h" >&6;}
+-      ROCM_HSA_IFLAGS="-I$ROCM/include/hsa"
++    # FIXME: as of rocm 5.2/5.3, this was not fully switched over,
++    # so temporarily use both paths.
++    if test -f "$ROCM/include/hsa/hsa.h" || test -f "$ROCM/include/hsa.h"
++    then
++      { $as_echo "$as_me:${as_lineno-$LINENO}: found $ROCM: hsa.h" >&5
++$as_echo "$as_me: found $ROCM: hsa.h" >&6;}
++      ROCM_HSA_IFLAGS="-I$ROCM/include -I$ROCM/include/hsa"
+       ROCM_HSA_INC_MESG="$ROCM/hsa"
+       found=yes
+     fi
+@@ -24020,10 +24023,12 @@ case "$ROCM_HSA" in
+     require_rocm=yes
+     found=no
+ 
+-    if test -f "$ROCM_HSA/include/hsa/hsa.h" ; then
+-      { $as_echo "$as_me:${as_lineno-$LINENO}: found $ROCM_HSA/include/hsa/hsa.h" >&5
+-$as_echo "$as_me: found $ROCM_HSA/include/hsa/hsa.h" >&6;}
+-      ROCM_HSA_IFLAGS="-I$ROCM_HSA/include/hsa"
++    # FIXME: again, temporarily use both paths
++    if test -f "$ROCM_HSA/include/hsa/hsa.h" || test -f "$ROCM_HSA/include/hsa.h"
++    then
++      { $as_echo "$as_me:${as_lineno-$LINENO}: found $ROCM_HSA: hsa.h" >&5
++$as_echo "$as_me: found $ROCM_HSA: hsa.h" >&6;}
++      ROCM_HSA_IFLAGS="-I$ROCM_HSA/include -I$ROCM_HSA/include/hsa"
+       ROCM_HSA_INC_MESG="$ROCM_HSA"
+       found=yes
+     fi
+diff --git a/configure.ac b/configure.ac
+index a14b15835f..9d5ed46134 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -4885,9 +4885,12 @@ case "$ROCM" in
+     fi
+ 
+     # HSA
+-    if test -f "$ROCM/include/hsa/hsa.h" ; then
+-      AC_MSG_NOTICE([found $ROCM/include/hsa/hsa.h])
+-      ROCM_HSA_IFLAGS="-I$ROCM/include/hsa"
++    # FIXME: as of rocm 5.2/5.3, this was not fully switched over,
++    # so temporarily use both paths.
++    if test -f "$ROCM/include/hsa/hsa.h" || test -f "$ROCM/include/hsa.h"
++    then
++      AC_MSG_NOTICE([found $ROCM: hsa.h])
++      ROCM_HSA_IFLAGS="-I$ROCM/include -I$ROCM/include/hsa"
+       ROCM_HSA_INC_MESG="$ROCM/hsa"
+       found=yes
+     fi
+@@ -5002,9 +5005,11 @@ case "$ROCM_HSA" in
+     require_rocm=yes
+     found=no
+ 
+-    if test -f "$ROCM_HSA/include/hsa/hsa.h" ; then
+-      AC_MSG_NOTICE([found $ROCM_HSA/include/hsa/hsa.h])
+-      ROCM_HSA_IFLAGS="-I$ROCM_HSA/include/hsa"
++    # FIXME: again, temporarily use both paths
++    if test -f "$ROCM_HSA/include/hsa/hsa.h" || test -f "$ROCM_HSA/include/hsa.h"
++    then
++      AC_MSG_NOTICE([found $ROCM_HSA: hsa.h])
++      ROCM_HSA_IFLAGS="-I$ROCM_HSA/include -I$ROCM_HSA/include/hsa"
+       ROCM_HSA_INC_MESG="$ROCM_HSA"
+       found=yes
+     fi
+-- 
+GitLab
+

var/spack/repos/builtin/packages/hpctoolkit/511afd95b01d743edc5940c84e0079f462b2c23e.patch

@@ -0,0 +1,130 @@
+From 511afd95b01d743edc5940c84e0079f462b2c23e Mon Sep 17 00:00:00 2001
+From: "Mark W. Krentel" <krentel@rice.edu>
+Date: Tue, 18 May 2021 14:54:41 -0500
+Subject: [PATCH] Cleanup some usage for gcc/g++ 11.x (#413)
+
+1. Change epsilon to hpc_epsilon in prof/Metric header files.  This
+ conflicted with using epsilon in some STL template libraries.
+
+ 2. Add const to some comparison operators that are used in some STL
+ maps.
+---
+ src/lib/banal/Struct-Inline.hpp   | 6 +++---
+ src/lib/prof/Metric-AExpr.cpp     | 4 ++--
+ src/lib/prof/Metric-AExpr.hpp     | 2 +-
+ src/lib/prof/Metric-AExprIncr.hpp | 6 +++---
+ src/lib/support/StringTable.hpp   | 2 +-
+ 5 files changed, 10 insertions(+), 10 deletions(-)
+
+diff --git a/src/lib/banal/Struct-Inline.hpp b/src/lib/banal/Struct-Inline.hpp
+index ffb93355fd..0099ad112d 100644
+--- a/src/lib/banal/Struct-Inline.hpp
++++ b/src/lib/banal/Struct-Inline.hpp
+@@ -150,14 +150,14 @@ public:
+     pretty_index = strTab.str2index(node.getPrettyName());
+   }
+ 
+-  bool operator == (const FLPIndex rhs)
++  bool operator == (const FLPIndex rhs) const
+   {
+     return file_index == rhs.file_index
+       && line_num == rhs.line_num
+       && pretty_index == rhs.pretty_index;
+   }
+ 
+-  bool operator != (const FLPIndex rhs)
++  bool operator != (const FLPIndex rhs) const
+   {
+     return ! (*this == rhs);
+   }
+@@ -167,7 +167,7 @@ public:
+ // Compare (file, line, proc) indices lexigraphically.
+ class FLPCompare {
+ public:
+-  bool operator() (const FLPIndex t1, const FLPIndex t2)
++  bool operator() (const FLPIndex t1, const FLPIndex t2) const
+   {
+     if (t1.file_index < t2.file_index) { return true; }
+     if (t1.file_index > t2.file_index) { return false; }
+diff --git a/src/lib/prof/Metric-AExpr.cpp b/src/lib/prof/Metric-AExpr.cpp
+index 2ce43e6d39..5b32ff67d1 100644
+--- a/src/lib/prof/Metric-AExpr.cpp
++++ b/src/lib/prof/Metric-AExpr.cpp
+@@ -483,7 +483,7 @@ CoefVar::eval(const Metric::IData& mdata) const
+   double sdev = sqrt(v_m.first); // always non-negative
+   double mean = v_m.second;
+   double z = 0.0;
+-  if (mean > epsilon) {
++  if (mean > hpc_epsilon) {
+     z = sdev / mean;
+   }
+ 
+@@ -522,7 +522,7 @@ RStdDev::eval(const Metric::IData& mdata) const
+   double sdev = sqrt(v_m.first); // always non-negative
+   double mean = v_m.second;
+   double z = 0.0;
+-  if (mean > epsilon) {
++  if (mean > hpc_epsilon) {
+     z = (sdev / mean) * 100;
+   }
+ 
+diff --git a/src/lib/prof/Metric-AExpr.hpp b/src/lib/prof/Metric-AExpr.hpp
+index 56359cc9df..d75189f763 100644
+--- a/src/lib/prof/Metric-AExpr.hpp
++++ b/src/lib/prof/Metric-AExpr.hpp
+@@ -97,7 +97,7 @@
+ 
+ //****************************************************************************
+ 
+-#define epsilon  (0.000001)
++#define hpc_epsilon  (0.000001)
+ 
+ namespace Prof {
+ 
+diff --git a/src/lib/prof/Metric-AExprIncr.hpp b/src/lib/prof/Metric-AExprIncr.hpp
+index f1b38d7f74..d0c0feb7e6 100644
+--- a/src/lib/prof/Metric-AExprIncr.hpp
++++ b/src/lib/prof/Metric-AExprIncr.hpp
+@@ -97,7 +97,7 @@
+ 
+ //****************************************************************************
+ 
+-#define epsilon  (0.000001)
++#define hpc_epsilon  (0.000001)
+ 
+ namespace Prof {
+ 
+@@ -841,7 +841,7 @@ public:
+     double sdev = finalizeStdDev(mdata);
+     double mean = accumVar(1, mdata);
+     double z = 0.0;
+-    if (mean > epsilon) {
++    if (mean > hpc_epsilon) {
+       z = sdev / mean;
+     }
+     accumVar(0, mdata) = z;
+@@ -927,7 +927,7 @@ public:
+     double sdev = finalizeStdDev(mdata);
+     double mean = accumVar(1, mdata);
+     double z = 0.0;
+-    if (mean > epsilon) {
++    if (mean > hpc_epsilon) {
+       z = (sdev / mean) * 100;
+     }
+     accumVar(0, mdata) = z;
+diff --git a/src/lib/support/StringTable.hpp b/src/lib/support/StringTable.hpp
+index 9930bc5649..36ce5b7fa9 100644
+--- a/src/lib/support/StringTable.hpp
++++ b/src/lib/support/StringTable.hpp
+@@ -75,7 +75,7 @@ namespace HPC {
+ // compare the strings, not the pointers
+ class StringCompare {
+ public:
+-  bool operator() (const std::string *s1, const std::string *s2)
++  bool operator() (const std::string *s1, const std::string *s2) const
+   {
+     return *s1 < *s2;
+   }
+-- 
+GitLab
+

var/spack/repos/builtin/packages/hpctoolkit/package.py

@@ -162,17 +162,11 @@ class Hpctoolkit(AutotoolsPackage):
     # Fix the build for old revs with gcc 10.x.
     patch("gcc10-enum.patch", when="@2020.01.01:2020.08 %gcc@10.0:")
 
-    patch(
-        "https://gitlab.com/hpctoolkit/hpctoolkit/-/commit/511afd95b01d743edc5940c84e0079f462b2c23e.patch",
-        sha256="8da18df88a80847c092da8d0892de51ea2bf2523124148b6305ab8717707d897",
-        when="@2019.08.01:2021.03 %gcc@11.0:",
-    )
+    patch("511afd95b01d743edc5940c84e0079f462b2c23e.patch", when="@2019.08.01:2021.03 %gcc@11.0:")
 
     # Update configure for rocm 5.3.0
     patch(
-        "https://gitlab.com/hpctoolkit/hpctoolkit/-/commit/411d62544717873432c49ef45c7cb99cc5de2fb8.patch",
-        sha256="484045891a665cdba3b0f141540c89f0d691ed32c5912ef62a93670d44c2786c",
-        when="@2022.04:2022.10 +rocm ^hip@5.3.0:",
+        "411d62544717873432c49ef45c7cb99cc5de2fb8.patch", when="@2022.04:2022.10 +rocm ^hip@5.3.0:"
     )
 
     # Change python to python3 for some old revs that use a script

var/spack/repos/builtin/packages/ompss-2/package.py

@@ -31,6 +31,8 @@ class Ompss2(Package):
     depends_on("python", type="build")
     depends_on("cmake", type="build")
     depends_on("extrae", when="+extrae")
+    depends_on("boost@1.59.0:")
+    depends_on("numactl")
 
     resource(
         name="jemalloc",
@@ -105,6 +107,8 @@ def install_nanos6(self, spec, prefix):
             "--prefix=%s" % prefix,
             "--with-jemalloc=%s" % prefix,
             "--with-hwloc=%s" % spec["hwloc"].prefix,
+            "--with-boost=%s" % spec["boost"].prefix,
+            "--with-libnuma=%s" % spec["numactl"].prefix,
             "--disable-stats-instrumentation",
             "--disable-verbose-instrumentation",
             "--disable-lint-instrumentation",

var/spack/repos/builtin/packages/openmpi/package.py

@@ -42,10 +42,13 @@ class Openmpi(AutotoolsPackage, CudaPackage):
 
     # Current
     version(
-        "4.1.4", sha256="92912e175fd1234368c8730c03f4996fe5942e7479bb1d10059405e7f2b3930d"
-    )  # libmpi.so.40.30.4
+        "4.1.5", sha256="a640986bc257389dd379886fdae6264c8cfa56bc98b71ce3ae3dfbd8ce61dbe3"
+    )  # libmpi.so.40.30.5
 
     # Still supported
+    version(
+        "4.1.4", sha256="92912e175fd1234368c8730c03f4996fe5942e7479bb1d10059405e7f2b3930d"
+    )  # libmpi.so.40.30.4
     version(
         "4.1.3", sha256="3d81d04c54efb55d3871a465ffb098d8d72c1f48ff1cbaf2580eb058567c0a3b"
     )  # libmpi.so.40.30.3

var/spack/repos/builtin/packages/py-nbqa/package.py

@@ -0,0 +1,21 @@
+# 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 PyNbqa(PythonPackage):
+    """Run any standard Python code quality tool on a Jupyter Notebook."""
+
+    homepage = "https://github.com/nbQA-dev/nbQA"
+    pypi = "nbqa/nbqa-1.6.3.tar.gz"
+
+    version("1.6.3", sha256="5394a29fc6d27b9a950c0a36d2d9de25de980be9acfe2a3f3aea0d27b5f7fec1")
+
+    depends_on("python@3.8:", type=("build", "run"))
+    depends_on("py-setuptools", type="build")
+    depends_on("py-ipython@7.8:", type=("build", "run"))
+    depends_on("py-tokenize-rt@3.2:", type=("build", "run"))
+    depends_on("py-tomli", type=("build", "run"))

var/spack/repos/builtin/packages/py-warpx/package.py

@@ -18,7 +18,7 @@ class PyWarpx(PythonPackage):
     """
 
     homepage = "https://ecp-warpx.github.io"
-    url = "https://github.com/ECP-WarpX/WarpX/archive/refs/tags/23.01.tar.gz"
+    url = "https://github.com/ECP-WarpX/WarpX/archive/refs/tags/23.02.tar.gz"
     git = "https://github.com/ECP-WarpX/WarpX.git"
 
     maintainers("ax3l", "dpgrote", "RemiLehe")
@@ -27,6 +27,7 @@ class PyWarpx(PythonPackage):
 
     # NOTE: if you update the versions here, also see warpx
     version("develop", branch="development")
+    version("23.02", sha256="a6c63ebc38cbd224422259a814be501ac79a3b734dab7f59500b6957cddaaac1")
     version("23.01", sha256="e853d01c20ea00c8ddedfa82a31a11d9d91a7f418d37d7f064cf8a241ea4da0c")
     version("22.12", sha256="96019902cd6ea444a1ae515e8853048e9074822c168021e4ec1687adc72ef062")
     version("22.11", sha256="528f65958f2f9e60a094e54eede698e871ccefc89fa103fe2a6f22e4a059515e")
@@ -53,6 +54,7 @@ class PyWarpx(PythonPackage):
     variant("mpi", default=True, description="Enable MPI support")
 
     for v in [
+        "23.02",
         "23.01",
         "22.12",
         "22.11",

var/spack/repos/builtin/packages/r-arrangements/package.py

@@ -0,0 +1,27 @@
+# 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 RArrangements(RPackage):
+    """Fast Generators and Iterators for Permutations, Combinations, Integer
+    Partitions and Compositions.
+
+    Fast generators and iterators for permutations, combinations, integer
+    partitions and compositions. The arrangements are in lexicographical order
+    and generated iteratively in a memory efficient manner. It has been
+    demonstrated that 'arrangements' outperforms most existing packages of
+    similar kind. Benchmarks could be found at
+    <https://randy3k.github.io/arrangements/articles/benchmark.html>."""
+
+    cran = "arrangements"
+
+    version("1.1.9", sha256="e9b5dcb185ec9b28201b196384b04a8d5a15f4ddb9e0b0b2a0c718635ff7345b")
+
+    depends_on("r@3.4.0:", type=("build", "run"))
+    depends_on("r-gmp", type=("build", "run"))
+    depends_on("r-r6", type=("build", "run"))
+    depends_on("gmp@4.2.3:")

var/spack/repos/builtin/packages/r-googleauthr/package.py

@@ -0,0 +1,28 @@
+# 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 RGoogleauthr(RPackage):
+    """Authenticate and Create Google APIs.
+
+    Create R functions that interact with OAuth2 Google APIs
+    <https://developers.google.com/apis-explorer/> easily, with auto-refresh
+    and Shiny compatibility."""
+
+    cran = "googleAuthR"
+
+    version("2.0.0", sha256="ba504baf3bde2e1b3e988bee7602df5765cc6ca542cf0ab76a782c4e60966feb")
+
+    depends_on("r@3.3.0:", type=("build", "run"))
+    depends_on("r-assertthat", type=("build", "run"))
+    depends_on("r-cli", type=("build", "run"))
+    depends_on("r-digest", type=("build", "run"))
+    depends_on("r-gargle@1.2.0:", type=("build", "run"))
+    depends_on("r-httr@1.4.0:", type=("build", "run"))
+    depends_on("r-jsonlite@1.6:", type=("build", "run"))
+    depends_on("r-memoise@1.1.0:", type=("build", "run"))
+    depends_on("r-rlang", type=("build", "run"))

var/spack/repos/builtin/packages/r-ieugwasr/package.py

@@ -0,0 +1,26 @@
+# 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 RIeugwasr(RPackage):
+    """R Interface to the OpenGWAS Database API.
+
+    R interface to the OpenGWAS database API. Includes a wrapper
+    to make generic calls to the API, plus convenience functions for
+    specific queries."""
+
+    homepage = "https://github.com/MRCIEU/ieugwasr"
+    url = "https://github.com/MRCIEU/ieugwasr/archive/refs/tags/0.1.5.tar.gz"
+
+    version("0.1.5", sha256="8d900d5a780f23836c80191f9635fbf48a0ca94f828452948c0f445e3217f422")
+
+    depends_on("r@3.6.0:", type=("build", "run"))
+    depends_on("r-magrittr", type=("build", "run"))
+    depends_on("r-googleauthr", type=("build", "run"))
+    depends_on("r-dplyr", type=("build", "run"))
+    depends_on("r-httr", type=("build", "run"))
+    depends_on("r-jsonlite", type=("build", "run"))

var/spack/repos/builtin/packages/r-iterpc/package.py

@@ -0,0 +1,29 @@
+# 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 RIterpc(RPackage):
+    """Efficient Iterator for Permutations and Combinations.
+
+    Iterator for generating permutations and combinations. They can be either
+    drawn with or without replacement, or with distinct/ non-distinct items
+    (multiset). The generated sequences are in lexicographical order
+    (dictionary order). The algorithms to generate permutations and
+    combinations are memory efficient. These iterative algorithms enable users
+    to process all sequences without putting all results in the memory at the
+    same time. The algorithms are written in C/C++ for faster performance.
+    Note: 'iterpc' is no longer being maintained. Users are recommended to
+    switch to 'arrangements'."""
+
+    cran = "iterpc"
+
+    version("0.4.2", sha256="38bd464042a27536f676e889263eb2c257a431b59083f58cb54473f42ba2071b")
+
+    depends_on("r@3.0.0:", type=("build", "run"))
+    depends_on("r-iterators", type=("build", "run"))
+    depends_on("r-gmp@0.5-12:", type=("build", "run"))
+    depends_on("r-arrangements@1.0.0:", type=("build", "run"))

var/spack/repos/builtin/packages/r-mendelianrandomization/package.py

@@ -0,0 +1,32 @@
+# 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 RMendelianrandomization(RPackage):
+    """Mendelian Randomization Package.
+
+    Encodes several methods for performing Mendelian randomization analyses
+    with summarized data. Summarized data on genetic associations with the
+    exposure and with the outcome can be obtained from large consortia. These
+    data can be used for obtaining causal estimates using instrumental variable
+    methods."""
+
+    cran = "MendelianRandomization"
+
+    version("0.7.0", sha256="cad7cc1b6964fc7d299864378694c5fd947caa83796a1958e581299796b854c7")
+
+    depends_on("r@3.0.1:", type=("build", "run"))
+    depends_on("r-knitr", type=("build", "run"))
+    depends_on("r-rmarkdown", type=("build", "run"))
+    depends_on("r-plotly@3.6.0:", type=("build", "run"))
+    depends_on("r-ggplot2@1.0.1:", type=("build", "run"))
+    depends_on("r-robustbase@0.92-6:", type=("build", "run"))
+    depends_on("r-matrix@1.2:", type=("build", "run"))
+    depends_on("r-iterpc@0.3:", type=("build", "run"))
+    depends_on("r-quantreg@5.01:", type=("build", "run"))
+    depends_on("r-rjson", type=("build", "run"))
+    depends_on("r-glmnet", type=("build", "run"))

var/spack/repos/builtin/packages/r-meta/package.py

@@ -0,0 +1,33 @@
+# 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 RMeta(RPackage):
+    """General Package for Meta-Analysis.
+
+    User-friendly general package providing standard methods for meta-analysis
+    and supporting Schwarzer, Carpenter, and Rücker
+    <doi:10.1007/978-3-319-21416-0>, "Meta-Analysis with R" (2015): - common
+    effect and random effects meta-analysis; - several plots (forest, funnel,
+    Galbraith / radial, L'Abbe, Baujat, bubble); - three-level meta-analysis
+    model; - generalised linear mixed model; - Hartung-Knapp method for random
+    effects model; - Kenward-Roger method for random effects model; -
+    prediction interval; - statistical tests for funnel plot asymmetry; -
+    trim-and-fill method to evaluate bias in meta-analysis; - meta-regression;
+    - cumulative meta-analysis and leave-one-out meta-analysis; - import data
+    from 'RevMan 5'; - produce forest plot summarising several (subgroup)
+    meta-analyses."""
+
+    cran = "meta"
+
+    version("6.2-0", sha256="8ec8fb412996bbe17d3ca073f15c191a77bad486b08f39d7b8c2d07360ad5781")
+
+    depends_on("r@4.0.0:", type=("build", "run"))
+    depends_on("r-metafor@3.0-0:", type=("build", "run"))
+    depends_on("r-lme4", type=("build", "run"))
+    depends_on("r-compquadform", type=("build", "run"))
+    depends_on("r-xml2", type=("build", "run"))

var/spack/repos/builtin/packages/r-metadat/package.py

@@ -0,0 +1,21 @@
+# 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 RMetadat(RPackage):
+    """Meta-Analysis Datasets.
+
+    A collection of meta-analysis datasets for teaching purposes,
+    illustrating/testing meta-analytic methods, and validating published
+    analyses."""
+
+    cran = "metadat"
+
+    version("1.2-0", sha256="f0cce5e30c3d256eaf5a41e4f52ffc7108e195016a4b99409e0ab4c2ef58f5b8")
+
+    depends_on("r@4.0.0:", type=("build", "run"))
+    depends_on("r-mathjaxr", type=("build", "run"))

var/spack/repos/builtin/packages/r-metafor/package.py

@@ -0,0 +1,39 @@
+# 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 RMetafor(RPackage):
+    """Meta-Analysis Package for R.
+
+    A comprehensive collection of functions for conducting meta-analyses in R.
+    The package includes functions to calculate various effect sizes or outcome
+    measures, fit equal-, fixed-, random-, and mixed-effects models to such
+    data, carry out moderator and meta-regression analyses, and create various
+    types of meta-analytical plots (e.g., forest, funnel, radial, L'Abbe,
+    Baujat, bubble, and GOSH plots). For meta-analyses of binomial and
+    person-time data, the package also provides functions that implement
+    specialized methods, including the Mantel-Haenszel method, Peto's method,
+    and a variety of suitable generalized linear (mixed-effects) models (i.e.,
+    mixed-effects logistic and Poisson regression models). Finally, the package
+    provides functionality for fitting meta-analytic multivariate/multilevel
+    models that account for non-independent sampling errors and/or true effects
+    (e.g., due to the inclusion of multiple treatment studies, multiple
+    endpoints, or other forms of clustering). Network meta-analyses and
+    meta-analyses accounting for known correlation structures (e.g., due to
+    phylogenetic relatedness) can also be conducted. An introduction to the
+    package can be found in Viechtbauer (2010) <doi:10.18637/jss.v036.i03>."""
+
+    cran = "metafor"
+
+    version("3.8-1", sha256="d694577f954144d8a5eeab6521fe1c87e68ddf9ecfd7ccc915d01533371b0514")
+
+    depends_on("r@4.0.0:", type=("build", "run"))
+    depends_on("r-matrix", type=("build", "run"))
+    depends_on("r-metadat", type=("build", "run"))
+    depends_on("r-nlme", type=("build", "run"))
+    depends_on("r-mathjaxr", type=("build", "run"))
+    depends_on("r-pbapply", type=("build", "run"))

var/spack/repos/builtin/packages/r-mr-raps/package.py

@@ -0,0 +1,24 @@
+# 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 RMrRaps(RPackage):
+    """Two Sample Mendelian Randomization using Robust Adjusted Profile Score.
+
+    Mendelian randomization is a method of identifying and estimating a
+    confounded causal effect using genetic instrumental variables. This
+    packages implements methods for two-sample Mendelian randomization with
+    summary statistics by using Robust Adjusted Profile Score (RAPS).
+    References: Qingyuan Zhao, Jingshu Wang, Jack Bowden, Dylan S. Small.
+    Statistical inference in two-sample summary-data Mendelian randomization
+    using robust adjusted profile score. <arXiv:1801.09652>."""
+
+    cran = "mr.raps"
+
+    version("0.2", sha256="c899f6143dac99e1232ff0a8d9f5fe099d4f69960782e6843db5b0d7f4f63b19")
+
+    depends_on("r-nortest", type=("build", "run"))

var/spack/repos/builtin/packages/r-mrinstruments/package.py

@@ -0,0 +1,19 @@
+# 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 RMrinstruments(RPackage):
+    """Data sources for genetic instruments to be used in MR.
+
+    Datasets of eQTLs, GWAS catalogs, etc."""
+
+    homepage = "https://github.com/MRCIEU/MRInstruments"
+    url = "https://github.com/MRCIEU/MRInstruments/archive/refs/tags/0.3.3.tar.gz"
+
+    version("0.3.3", sha256="4ddbaf6335133e8f7baef469d6bc1f89212462b9f4062c9e4ddda37b12eb3486")
+
+    depends_on("r@2.10:", type=("build", "run"))

var/spack/repos/builtin/packages/r-mrmix/package.py

@@ -0,0 +1,18 @@
+# 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 RMrmix(RPackage):
+    """Mendelian Randomization Analysis Using Mixture Models (MRMix).
+
+    This package gives robust estimation of causal effects by conducting
+    Mendelian randomization analysis using a mixture model approach."""
+
+    homepage = "https://github.com/gqi/MRMix"
+    git = "https://github.com/gqi/MRMix"
+
+    version("0.1.0", commit="56afdb2bc96760842405396f5d3f02e60e305039")

var/spack/repos/builtin/packages/r-mrpresso/package.py

@@ -0,0 +1,21 @@
+# 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 RMrpresso(RPackage):
+    """Performs the Mendelian Randomization Pleiotropy RESidual Sum and Outlier
+    (MR-PRESSO) test.
+
+    MR-PRESSO (Mendelian Randomization Pleiotropy RESidual Sum and Outlier) is
+    a framework that allows for the evaluation of pleiotropy in
+    multi-instrument Mendelian Randomization utilizing genome-wide summary
+    association statistics."""
+
+    homepage = "https://github.com/rondolab/MR-PRESSO"
+    git = "https://github.com/rondolab/MR-PRESSO"
+
+    version("1.0", commit="cece763b47e59763a7916974de43c7cb93843e41")

var/spack/repos/builtin/packages/r-radialmr/package.py

@@ -0,0 +1,23 @@
+# 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 RRadialmr(RPackage):
+    """RadialMR.
+
+    A package for implementing radial inverse variance weighted and MR-Egger
+    methods."""
+
+    homepage = "https://github.com/WSpiller/RadialMR"
+    git = "https://github.com/WSpiller/RadialMR"
+
+    version("1.0", commit="d63d3fc8270836ab441b9e14a5ba3eeb2795d7cb")
+
+    depends_on("r@3.5.0:", type=("build", "run"))
+    depends_on("r-ggplot2", type=("build", "run"))
+    depends_on("r-magrittr", type=("build", "run"))
+    depends_on("r-plotly", type=("build", "run"))

var/spack/repos/builtin/packages/r-twosamplemr/package.py

@@ -0,0 +1,51 @@
+# 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 RTwosamplemr(RPackage):
+    """Two Sample MR functions and interface to MR Base database.
+
+    A package for performing Mendelian randomization using GWAS summary data.
+    It uses the IEU GWAS database to obtain data automatically, and a wide
+    range of methods to run the analysis. You can use the MR-Base web app to
+    try out a limited range of the functionality in this package, but for any
+    serious work we strongly recommend using this R package."""
+
+    homepage = "https://mrcieu.github.io/TwoSampleMR/"
+    url = "https://github.com/MRCIEU/TwoSampleMR/archive/refs/tags/v0.5.6.tar.gz"
+
+    version("0.5.6", sha256="c63eb008ab7ed08a6f30ccbf0c299beb31b2f5835e5e2aa1b59c5e4fe284a30c")
+
+    depends_on("r@3.6.0:", type=("build", "run"))
+    depends_on("r-ieugwasr@0.1.5:", type=("build", "run"))
+    depends_on("r-ggplot2", type=("build", "run"))
+    depends_on("r-gridextra", type=("build", "run"))
+    depends_on("r-cowplot", type=("build", "run"))
+    depends_on("r-plyr", type=("build", "run"))
+    depends_on("r-reshape2", type=("build", "run"))
+    depends_on("r-stringr", type=("build", "run"))
+    depends_on("r-knitr", type=("build", "run"))
+    depends_on("r-markdown", type=("build", "run"))
+    depends_on("r-gtable", type=("build", "run"))
+    depends_on("r-rmarkdown", type=("build", "run"))
+    depends_on("r-mendelianrandomization", type=("build", "run"))
+    depends_on("r-dplyr", type=("build", "run"))
+    depends_on("r-mr-raps", type=("build", "run"))
+    depends_on("r-psych", type=("build", "run"))
+    depends_on("r-magrittr", type=("build", "run"))
+    depends_on("r-car", type=("build", "run"))
+    depends_on("r-randomforest", type=("build", "run"))
+    depends_on("r-meta", type=("build", "run"))
+    depends_on("r-data-table", type=("build", "run"))
+    depends_on("r-mrpresso", type=("build", "run"))
+    depends_on("r-mrinstruments", type=("build", "run"))
+    depends_on("r-radialmr", type=("build", "run"))
+    depends_on("r-mrmix", type=("build", "run"))
+    depends_on("r-glmnet", type=("build", "run"))
+    depends_on("r-lattice", type=("build", "run"))
+    depends_on("r-pbapply", type=("build", "run"))
+    depends_on("r-mass", type=("build", "run"))

var/spack/repos/builtin/packages/warpx/package.py

@@ -17,7 +17,7 @@ class Warpx(CMakePackage):
     """
 
     homepage = "https://ecp-warpx.github.io"
-    url = "https://github.com/ECP-WarpX/WarpX/archive/refs/tags/23.01.tar.gz"
+    url = "https://github.com/ECP-WarpX/WarpX/archive/refs/tags/23.02.tar.gz"
     git = "https://github.com/ECP-WarpX/WarpX.git"
 
     maintainers("ax3l", "dpgrote", "MaxThevenet", "RemiLehe")
@@ -25,6 +25,7 @@ class Warpx(CMakePackage):
 
     # NOTE: if you update the versions here, also see py-warpx
     version("develop", branch="development")
+    version("23.02", sha256="a6c63ebc38cbd224422259a814be501ac79a3b734dab7f59500b6957cddaaac1")
     version("23.01", sha256="e853d01c20ea00c8ddedfa82a31a11d9d91a7f418d37d7f064cf8a241ea4da0c")
     version("22.12", sha256="96019902cd6ea444a1ae515e8853048e9074822c168021e4ec1687adc72ef062")
     version("22.11", sha256="528f65958f2f9e60a094e54eede698e871ccefc89fa103fe2a6f22e4a059515e")