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

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Adrien Bernede 2023-02-27 16:15:46 +01:00 committed by GitHub
commit b2e526678a
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27 changed files with 747 additions and 55 deletions
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95
lib/spack/llnl/util/tty/colify.py
View File

@ -11,6 +11,7 @@
import io
import os
import sys
from typing import IO, Any, List, Optional
from llnl.util.tty import terminal_size
from llnl.util.tty.color import cextra, clen
@ -97,7 +98,16 @@ def config_uniform_cols(elts, console_width, padding, cols=0):
return config
def colify(elts, **options):
def colify(
elts: List[Any],
cols: int = 0,
output: Optional[IO] = None,
indent: int = 0,
padding: int = 2,
tty: Optional[bool] = None,
method: str = "variable",
console_cols: Optional[int] = None,
):
"""Takes a list of elements as input and finds a good columnization
of them, similar to how gnu ls does. This supports both
uniform-width and variable-width (tighter) columns.
@ -106,31 +116,21 @@ def colify(elts, **options):
using ``str()``.
Keyword Arguments:
output (typing.IO): A file object to write to. Default is ``sys.stdout``
indent (int): Optionally indent all columns by some number of spaces
padding (int): Spaces between columns. Default is 2
width (int): Width of the output. Default is 80 if tty not detected
cols (int): Force number of columns. Default is to size to terminal, or
output: A file object to write to. Default is ``sys.stdout``
indent: Optionally indent all columns by some number of spaces
padding: Spaces between columns. Default is 2
width: Width of the output. Default is 80 if tty not detected
cols: Force number of columns. Default is to size to terminal, or
single-column if no tty
tty (bool): Whether to attempt to write to a tty. Default is to autodetect a
tty: Whether to attempt to write to a tty. Default is to autodetect a
tty. Set to False to force single-column output
method (str): Method to use to fit columns. Options are variable or uniform.
method: Method to use to fit columns. Options are variable or uniform.
Variable-width columns are tighter, uniform columns are all the same width
and fit less data on the screen
console_cols: number of columns on this console (default: autodetect)
"""
# Get keyword arguments or set defaults
cols = options.pop("cols", 0)
output = options.pop("output", sys.stdout)
indent = options.pop("indent", 0)
padding = options.pop("padding", 2)
tty = options.pop("tty", None)
method = options.pop("method", "variable")
console_cols = options.pop("width", None)
if options:
raise TypeError(
"'%s' is an invalid keyword argument for this function." % next(options.iterkeys())
)
if output is None:
output = sys.stdout
# elts needs to be an array of strings so we can count the elements
elts = [str(elt) for elt in elts]
@ -153,10 +153,11 @@ def colify(elts, **options):
cols = 1
# Specify the number of character columns to use.
if not console_cols:
if console_cols is None:
console_rows, console_cols = terminal_size()
elif type(console_cols) != int:
elif not isinstance(console_cols, int):
raise ValueError("Number of columns must be an int")
console_cols = max(1, console_cols - indent)
# Choose a method. Variable-width colums vs uniform-width.
@ -192,7 +193,13 @@ def colify(elts, **options):
return (config.cols, tuple(config.widths))
def colify_table(table, **options):
def colify_table(
table: List[List[Any]],
output: Optional[IO] = None,
indent: int = 0,
padding: int = 2,
console_cols: Optional[int] = None,
):
"""Version of ``colify()`` for data expressed in rows, (list of lists).
Same as regular colify but:
@ -218,20 +225,38 @@ def transpose():
for row in table:
yield row[i]
if "cols" in options:
raise ValueError("Cannot override columsn in colify_table.")
options["cols"] = columns
# don't reduce to 1 column for non-tty
options["tty"] = True
colify(transpose(), **options)
colify(
transpose(),
cols=columns, # this is always the number of cols in the table
tty=True, # don't reduce to 1 column for non-tty
output=output,
indent=indent,
padding=padding,
console_cols=console_cols,
)
def colified(elts, **options):
def colified(
elts: List[Any],
cols: int = 0,
output: Optional[IO] = None,
indent: int = 0,
padding: int = 2,
tty: Optional[bool] = None,
method: str = "variable",
console_cols: Optional[int] = None,
):
"""Invokes the ``colify()`` function but returns the result as a string
instead of writing it to an output string."""
sio = io.StringIO()
options["output"] = sio
colify(elts, **options)
colify(
elts,
cols=cols,
output=sio,
indent=indent,
padding=padding,
tty=tty,
method=method,
console_cols=console_cols,
)
return sio.getvalue()

2
lib/spack/spack/util/environment.py
View File

@ -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(

42
var/spack/repos/builtin/packages/celeritas/package.py
View File

@ -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")

1
var/spack/repos/builtin/packages/go/package.py
View File

@ -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.

1
var/spack/repos/builtin/packages/hdf5-vol-cache/package.py
View File

@ -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")

91
var/spack/repos/builtin/packages/hpctoolkit/411d62544717873432c49ef45c7cb99cc5de2fb8.patch Normal file
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@ -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

130
var/spack/repos/builtin/packages/hpctoolkit/511afd95b01d743edc5940c84e0079f462b2c23e.patch Normal file
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@ -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

10
var/spack/repos/builtin/packages/hpctoolkit/package.py
View File

@ -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

4
var/spack/repos/builtin/packages/ompss-2/package.py
View File

@ -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",

7
var/spack/repos/builtin/packages/openmpi/package.py
View File

@ -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

21
var/spack/repos/builtin/packages/py-nbqa/package.py Normal file
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@ -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"))

4
var/spack/repos/builtin/packages/py-warpx/package.py
View File

@ -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",

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# 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:")

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# 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"))

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# 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"))

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# 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"))

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# 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"))

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@ -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"))

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@ -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"))

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# 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"))

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@ -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"))

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@ -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"))

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@ -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")

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@ -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")

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@ -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"))

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@ -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"))

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@ -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")