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

The patches don't have a stable checksum.

lib/spack/llnl/util/filesystem.py

@@ -16,6 +16,7 @@
 import sys
 import tempfile
 from contextlib import contextmanager
+from sys import platform as _platform
 from typing import Callable, List, Match, Optional, Tuple, Union
 
 from llnl.util import tty
@@ -25,7 +26,9 @@
 from spack.util.executable import Executable, which
 from spack.util.path import path_to_os_path, system_path_filter
 
-if sys.platform != "win32":
+is_windows = _platform == "win32"
+
+if not is_windows:
     import grp
     import pwd
 else:
@@ -151,7 +154,7 @@ def lookup(name):
 
 
 def getuid():
-    if sys.platform == "win32":
+    if is_windows:
         import ctypes
 
         if ctypes.windll.shell32.IsUserAnAdmin() == 0:
@@ -164,7 +167,7 @@ def getuid():
 @system_path_filter
 def rename(src, dst):
     # On Windows, os.rename will fail if the destination file already exists
-    if sys.platform == "win32":
+    if is_windows:
         # Windows path existence checks will sometimes fail on junctions/links/symlinks
         # so check for that case
         if os.path.exists(dst) or os.path.islink(dst):
@@ -193,7 +196,7 @@ def _get_mime_type():
     """Generate method to call `file` system command to aquire mime type
     for a specified path
     """
-    if sys.platform == "win32":
+    if is_windows:
         # -h option (no-dereference) does not exist in Windows
         return file_command("-b", "--mime-type")
     else:
@@ -548,7 +551,7 @@ def get_owner_uid(path, err_msg=None):
     else:
         p_stat = os.stat(path)
 
-    if sys.platform != "win32":
+    if _platform != "win32":
         owner_uid = p_stat.st_uid
     else:
         sid = win32security.GetFileSecurity(
@@ -581,7 +584,7 @@ def group_ids(uid=None):
     Returns:
         (list of int): gids of groups the user is a member of
     """
-    if sys.platform == "win32":
+    if is_windows:
         tty.warn("Function is not supported on Windows")
         return []
 
@@ -601,7 +604,7 @@ def group_ids(uid=None):
 @system_path_filter(arg_slice=slice(1))
 def chgrp(path, group, follow_symlinks=True):
     """Implement the bash chgrp function on a single path"""
-    if sys.platform == "win32":
+    if is_windows:
         raise OSError("Function 'chgrp' is not supported on Windows")
 
     if isinstance(group, str):
@@ -1128,7 +1131,7 @@ def open_if_filename(str_or_file, mode="r"):
 @system_path_filter
 def touch(path):
     """Creates an empty file at the specified path."""
-    if sys.platform == "win32":
+    if is_windows:
         perms = os.O_WRONLY | os.O_CREAT
     else:
         perms = os.O_WRONLY | os.O_CREAT | os.O_NONBLOCK | os.O_NOCTTY
@@ -1190,7 +1193,7 @@ def temp_cwd():
             yield tmp_dir
     finally:
         kwargs = {}
-        if sys.platform == "win32":
+        if is_windows:
             kwargs["ignore_errors"] = False
             kwargs["onerror"] = readonly_file_handler(ignore_errors=True)
         shutil.rmtree(tmp_dir, **kwargs)
@@ -1435,7 +1438,7 @@ def visit_directory_tree(root, visitor, rel_path="", depth=0):
         try:
             isdir = f.is_dir()
         except OSError as e:
-            if sys.platform == "win32" and hasattr(e, "winerror") and e.winerror == 5 and islink:
+            if is_windows and hasattr(e, "winerror") and e.winerror == 5 and islink:
                 # if path is a symlink, determine destination and
                 # evaluate file vs directory
                 link_target = resolve_link_target_relative_to_the_link(f)
@@ -1544,11 +1547,11 @@ def readonly_file_handler(ignore_errors=False):
     """
 
     def error_remove_readonly(func, path, exc):
-        if sys.platform != "win32":
+        if not is_windows:
             raise RuntimeError("This method should only be invoked on Windows")
         excvalue = exc[1]
         if (
-            sys.platform == "win32"
+            is_windows
             and func in (os.rmdir, os.remove, os.unlink)
             and excvalue.errno == errno.EACCES
         ):
@@ -1578,7 +1581,7 @@ def remove_linked_tree(path):
 
     # Windows readonly files cannot be removed by Python
     # directly.
-    if sys.platform == "win32":
+    if is_windows:
         kwargs["ignore_errors"] = False
         kwargs["onerror"] = readonly_file_handler(ignore_errors=True)
 
@@ -2092,7 +2095,7 @@ def names(self):
             # on non Windows platform
             # Windows valid library extensions are:
             # ['.dll', '.lib']
-            valid_exts = [".dll", ".lib"] if sys.platform == "win32" else [".dylib", ".so", ".a"]
+            valid_exts = [".dll", ".lib"] if is_windows else [".dylib", ".so", ".a"]
             for ext in valid_exts:
                 i = name.rfind(ext)
                 if i != -1:
@@ -2240,7 +2243,7 @@ def find_libraries(libraries, root, shared=True, recursive=False, runtime=True):
         message = message.format(find_libraries.__name__, type(libraries))
         raise TypeError(message)
 
-    if sys.platform == "win32":
+    if is_windows:
         static_ext = "lib"
         # For linking (runtime=False) you need the .lib files regardless of
         # whether you are doing a shared or static link
@@ -2272,7 +2275,7 @@ def find_libraries(libraries, root, shared=True, recursive=False, runtime=True):
     # finally search all of root recursively. The search stops when the first
     # match is found.
     common_lib_dirs = ["lib", "lib64"]
-    if sys.platform == "win32":
+    if is_windows:
         common_lib_dirs.extend(["bin", "Lib"])
 
     for subdir in common_lib_dirs:
@@ -2407,7 +2410,7 @@ def _link(self, path, dest_dir):
             # For py2 compatibility, we have to catch the specific Windows error code
             # associate with trying to create a file that already exists (winerror 183)
             except OSError as e:
-                if sys.platform == "win32" and e.winerror == 183:
+                if e.winerror == 183:
                     # We have either already symlinked or we are encoutering a naming clash
                     # either way, we don't want to overwrite existing libraries
                     already_linked = islink(dest_file)

lib/spack/llnl/util/lock.py

@@ -3,14 +3,12 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-import contextlib
 import errno
 import os
 import socket
 import sys
 import time
 from datetime import datetime
-from typing import Callable, Optional, Union
 
 import llnl.util.tty as tty
 from llnl.util.lang import pretty_seconds
@@ -548,11 +546,11 @@ def upgrade_read_to_write(self, timeout=None):
         else:
             raise LockUpgradeError(self.path)
 
-    def release_read(self, release_fn: Callable = None):
+    def release_read(self, release_fn=None):
         """Releases a read lock.
 
         Arguments:
-            release_fn (Callable): function to call *before* the last recursive
+            release_fn (typing.Callable): function to call *before* the last recursive
                 lock (read or write) is released.
 
         If the last recursive lock will be released, then this will call
@@ -588,7 +586,7 @@ def release_write(self, release_fn=None):
         """Releases a write lock.
 
         Arguments:
-            release_fn (Callable): function to call before the last recursive
+            release_fn (typing.Callable): function to call before the last recursive
                 write is released.
 
         If the last recursive *write* lock will be released, then this
@@ -686,6 +684,18 @@ def _status_msg(self, locktype, status):
 class LockTransaction(object):
     """Simple nested transaction context manager that uses a file lock.
 
+    Arguments:
+        lock (Lock): underlying lock for this transaction to be accquired on
+            enter and released on exit
+        acquire (typing.Callable or contextlib.contextmanager): function to be called
+            after lock is acquired, or contextmanager to enter after acquire and leave
+            before release.
+        release (typing.Callable): function to be called before release. If
+            ``acquire`` is a contextmanager, this will be called *after*
+            exiting the nexted context and before the lock is released.
+        timeout (float): number of seconds to set for the timeout when
+            accquiring the lock (default no timeout)
+
     If the ``acquire_fn`` returns a value, it is used as the return value for
     ``__enter__``, allowing it to be passed as the ``as`` argument of a
     ``with`` statement.
@@ -699,27 +709,7 @@ class LockTransaction(object):
 
     """
 
-    def __init__(
-        self,
-        lock: Lock,
-        acquire: Optional[Union[Callable, contextlib.contextmanager]] = None,
-        release: Optional[Callable] = None,
-        timeout: Optional[float] = None,
-    ):
-        """
-        Arguments:
-            lock: underlying lock for this transaction to be accquired on
-                enter and released on exit
-            acquire: function to be called
-                after lock is acquired, or contextmanager to enter after acquire and leave
-                before release.
-            release: function to be called before release. If
-                ``acquire`` is a contextmanager, this will be called *after*
-                exiting the nexted context and before the lock is released.
-            timeout: number of seconds to set for the timeout when
-                accquiring the lock (default no timeout)
-        """
-
+    def __init__(self, lock, acquire=None, release=None, timeout=None):
         self._lock = lock
         self._timeout = timeout
         self._acquire_fn = acquire

lib/spack/llnl/util/symlink.py

@@ -5,13 +5,15 @@
 import errno
 import os
 import shutil
-import sys
 import tempfile
 from os.path import exists, join
+from sys import platform as _platform
 
 from llnl.util import lang
 
-if sys.platform == "win32":
+is_windows = _platform == "win32"
+
+if is_windows:
     from win32file import CreateHardLink
 
 
@@ -21,7 +23,7 @@ def symlink(real_path, link_path):
 
     On Windows, use junctions if os.symlink fails.
     """
-    if sys.platform != "win32":
+    if not is_windows:
         os.symlink(real_path, link_path)
     elif _win32_can_symlink():
         # Windows requires target_is_directory=True when the target is a dir.
@@ -97,7 +99,7 @@ def _win32_is_junction(path):
     if os.path.islink(path):
         return False
 
-    if sys.platform == "win32":
+    if is_windows:
         import ctypes.wintypes
 
         GetFileAttributes = ctypes.windll.kernel32.GetFileAttributesW

lib/spack/llnl/util/tty/__init__.py

@@ -14,7 +14,6 @@
 import traceback
 from datetime import datetime
 from sys import platform as _platform
-from typing import Optional
 
 if _platform != "win32":
     import fcntl
@@ -164,13 +163,14 @@ def get_timestamp(force=False):
         return ""
 
 
-def msg(message, *args, newline=True):
+def msg(message, *args, **kwargs):
     if not msg_enabled():
         return
 
     if isinstance(message, Exception):
         message = "%s: %s" % (message.__class__.__name__, str(message))
 
+    newline = kwargs.get("newline", True)
     st_text = ""
     if _stacktrace:
         st_text = process_stacktrace(2)
@@ -182,18 +182,19 @@ def msg(message, *args, newline=True):
         print(indent + _output_filter(str(arg)))
 
 
-def info(
-    message, *args, format="*b", stream=None, wrap=False, break_long_words=False, countback=3
-):
+def info(message, *args, **kwargs):
     if isinstance(message, Exception):
         message = "%s: %s" % (message.__class__.__name__, str(message))
 
-    if stream is None:
-        stream = sys.stdout
+    format = kwargs.get("format", "*b")
+    stream = kwargs.get("stream", sys.stdout)
+    wrap = kwargs.get("wrap", False)
+    break_long_words = kwargs.get("break_long_words", False)
+    st_countback = kwargs.get("countback", 3)
 
     st_text = ""
     if _stacktrace:
-        st_text = process_stacktrace(countback)
+        st_text = process_stacktrace(st_countback)
     cprint(
         "@%s{%s==>} %s%s"
         % (format, st_text, get_timestamp(), cescape(_output_filter(str(message)))),
@@ -251,7 +252,10 @@ def die(message, *args, **kwargs):
     sys.exit(1)
 
 
-def get_number(prompt, default=None, abort=None):
+def get_number(prompt, **kwargs):
+    default = kwargs.get("default", None)
+    abort = kwargs.get("abort", None)
+
     if default is not None and abort is not None:
         prompt += " (default is %s, %s to abort) " % (default, abort)
     elif default is not None:
@@ -279,12 +283,14 @@ def get_number(prompt, default=None, abort=None):
     return number
 
 
-def get_yes_or_no(prompt, default: Optional[bool] = None):
-    if default is None:
+def get_yes_or_no(prompt, **kwargs):
+    default_value = kwargs.get("default", None)
+
+    if default_value is None:
         prompt += " [y/n] "
-    elif default is True:
+    elif default_value is True:
         prompt += " [Y/n] "
-    elif default is False:
+    elif default_value is False:
         prompt += " [y/N] "
     else:
         raise ValueError("default for get_yes_no() must be True, False, or None.")
@@ -294,7 +300,7 @@ def get_yes_or_no(prompt, default: Optional[bool] = None):
         msg(prompt, newline=False)
         ans = input().lower()
         if not ans:
-            result = default
+            result = default_value
             if result is None:
                 print("Please enter yes or no.")
         else:
@@ -305,13 +311,20 @@ def get_yes_or_no(prompt, default: Optional[bool] = None):
     return result
 
 
-def hline(label=None, char="-", max_width=64):
+def hline(label=None, **kwargs):
     """Draw a labeled horizontal line.
 
     Keyword Arguments:
         char (str): Char to draw the line with.  Default '-'
         max_width (int): Maximum width of the line.  Default is 64 chars.
     """
+    char = kwargs.pop("char", "-")
+    max_width = kwargs.pop("max_width", 64)
+    if kwargs:
+        raise TypeError(
+            "'%s' is an invalid keyword argument for this function." % next(kwargs.iterkeys())
+        )
+
     rows, cols = terminal_size()
     if not cols:
         cols = max_width

lib/spack/llnl/util/tty/color.py

@@ -326,7 +326,8 @@ def __init__(self, stream, color=None):
         self._stream = stream
         self._color = color
 
-    def write(self, string, raw=False):
+    def write(self, string, **kwargs):
+        raw = kwargs.get("raw", False)
         raw_write = getattr(self._stream, "write")
 
         color = self._color
@@ -337,6 +338,7 @@ def write(self, string, raw=False):
                 color = get_color_when()
         raw_write(colorize(string, color=color))
 
-    def writelines(self, sequence, raw=False):
+    def writelines(self, sequence, **kwargs):
+        raw = kwargs.get("raw", False)
         for string in sequence:
-            self.write(string, raw=raw)
+            self.write(string, self.color, raw=raw)

lib/spack/spack/cmd/unit_test.py

@@ -26,6 +26,7 @@
 description = "run spack's unit tests (wrapper around pytest)"
 section = "developer"
 level = "long"
+is_windows = sys.platform == "win32"
 
 
 def setup_parser(subparser):
@@ -211,7 +212,7 @@ def unit_test(parser, args, unknown_args):
     # mock configuration used by unit tests
     # Note: skip on windows here because for the moment,
     # clingo is wholly unsupported from bootstrap
-    if sys.platform != "win32":
+    if not is_windows:
         with spack.bootstrap.ensure_bootstrap_configuration():
             spack.bootstrap.ensure_core_dependencies()
             if pytest is None:

lib/spack/spack/compiler.py

@@ -28,6 +28,8 @@
 
 __all__ = ["Compiler"]
 
+is_windows = sys.platform == "win32"
+
 
 @llnl.util.lang.memoized
 def _get_compiler_version_output(compiler_path, version_arg, ignore_errors=()):
@@ -596,7 +598,7 @@ def search_regexps(cls, language):
         suffixes = [""]
         # Windows compilers generally have an extension of some sort
         # as do most files on Windows, handle that case here
-        if sys.platform == "win32":
+        if is_windows:
             ext = r"\.(?:exe|bat)"
             cls_suf = [suf + ext for suf in cls.suffixes]
             ext_suf = [ext]

lib/spack/spack/detection/common.py

@@ -29,6 +29,7 @@
 import spack.util.spack_yaml
 import spack.util.windows_registry
 
+is_windows = sys.platform == "win32"
 #: Information on a package that has been detected
 DetectedPackage = collections.namedtuple("DetectedPackage", ["spec", "prefix"])
 
@@ -183,7 +184,7 @@ def library_prefix(library_dir):
     elif "lib" in lowered_components:
         idx = lowered_components.index("lib")
         return os.sep.join(components[:idx])
-    elif sys.platform == "win32" and "bin" in lowered_components:
+    elif is_windows and "bin" in lowered_components:
         idx = lowered_components.index("bin")
         return os.sep.join(components[:idx])
     else:
@@ -259,13 +260,13 @@ def find_windows_compiler_bundled_packages():
 
 
 class WindowsKitExternalPaths(object):
-    if sys.platform == "win32":
+    if is_windows:
         plat_major_ver = str(winOs.windows_version()[0])
 
     @staticmethod
     def find_windows_kit_roots():
         """Return Windows kit root, typically %programfiles%\\Windows Kits\\10|11\\"""
-        if sys.platform != "win32":
+        if not is_windows:
             return []
         program_files = os.environ["PROGRAMFILES(x86)"]
         kit_base = os.path.join(
@@ -358,7 +359,7 @@ def compute_windows_program_path_for_package(pkg):
         pkg (spack.package_base.PackageBase): package for which
                            Program Files location is to be computed
     """
-    if sys.platform != "win32":
+    if not is_windows:
         return []
     # note windows paths are fine here as this method should only ever be invoked
     # to interact with Windows
@@ -378,7 +379,7 @@ def compute_windows_user_path_for_package(pkg):
     installs see:
     https://learn.microsoft.com/en-us/dotnet/api/system.environment.specialfolder?view=netframework-4.8
     """
-    if sys.platform != "win32":
+    if not is_windows:
         return []
 
     # Current user directory

lib/spack/spack/detection/path.py

@@ -31,6 +31,8 @@
     path_to_dict,
 )
 
+is_windows = sys.platform == "win32"
+
 
 def common_windows_package_paths():
     paths = WindowsCompilerExternalPaths.find_windows_compiler_bundled_packages()
@@ -55,7 +57,7 @@ def executables_in_path(path_hints):
         path_hints (list): list of paths to be searched. If None the list will be
             constructed based on the PATH environment variable.
     """
-    if sys.platform == "win32":
+    if is_windows:
         path_hints.extend(common_windows_package_paths())
     search_paths = llnl.util.filesystem.search_paths_for_executables(*path_hints)
     return path_to_dict(search_paths)
@@ -147,7 +149,7 @@ def by_library(packages_to_check, path_hints=None):
 
     path_to_lib_name = (
         libraries_in_ld_and_system_library_path(path_hints=path_hints)
-        if sys.platform != "win32"
+        if not is_windows
         else libraries_in_windows_paths(path_hints)
     )
 

lib/spack/spack/directory_layout.py

@@ -21,6 +21,7 @@
 import spack.util.spack_json as sjson
 from spack.error import SpackError
 
+is_windows = sys.platform == "win32"
 # Note: Posixpath is used here as opposed to
 # os.path.join due to spack.spec.Spec.format
 # requiring forward slash path seperators at this stage
@@ -345,7 +346,7 @@ def remove_install_directory(self, spec, deprecated=False):
 
         # Windows readonly files cannot be removed by Python
         # directly, change permissions before attempting to remove
-        if sys.platform == "win32":
+        if is_windows:
             kwargs = {
                 "ignore_errors": False,
                 "onerror": fs.readonly_file_handler(ignore_errors=False),

lib/spack/spack/fetch_strategy.py

@@ -28,6 +28,7 @@
 import os.path
 import re
 import shutil
+import sys
 import urllib.parse
 from typing import List, Optional
 
@@ -52,6 +53,7 @@
 
 #: List of all fetch strategies, created by FetchStrategy metaclass.
 all_strategies = []
+is_windows = sys.platform == "win32"
 
 CONTENT_TYPE_MISMATCH_WARNING_TEMPLATE = (
     "The contents of {subject} look like {content_type}.  Either the URL"
@@ -860,6 +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/hooks/sbang.py

@@ -30,7 +30,8 @@
 
 #: Groupdb does not exist on Windows, prevent imports
 #: on supported systems
-if sys.platform != "win32":
+is_windows = sys.platform == "win32"
+if not is_windows:
     import grp
 
 #: Spack itself also limits the shebang line to at most 4KB, which should be plenty.

lib/spack/spack/installer.py

@@ -84,6 +84,9 @@
 #: queue invariants).
 STATUS_REMOVED = "removed"
 
+is_windows = sys.platform == "win32"
+is_osx = sys.platform == "darwin"
+
 
 class InstallAction(object):
     #: Don't perform an install
@@ -166,9 +169,9 @@ def _do_fake_install(pkg):
     if not pkg.name.startswith("lib"):
         library = "lib" + library
 
-    plat_shared = ".dll" if sys.platform == "win32" else ".so"
-    plat_static = ".lib" if sys.platform == "win32" else ".a"
-    dso_suffix = ".dylib" if sys.platform == "darwin" else plat_shared
+    plat_shared = ".dll" if is_windows else ".so"
+    plat_static = ".lib" if is_windows else ".a"
+    dso_suffix = ".dylib" if is_osx else plat_shared
 
     # Install fake command
     fs.mkdirp(pkg.prefix.bin)

lib/spack/spack/package_base.py

@@ -92,6 +92,9 @@
 _spack_configure_argsfile = "spack-configure-args.txt"
 
 
+is_windows = sys.platform == "win32"
+
+
 def deprecated_version(pkg, version):
     """Return True if the version is deprecated, False otherwise.
 
@@ -162,7 +165,7 @@ def windows_establish_runtime_linkage(self):
 
         Performs symlinking to incorporate rpath dependencies to Windows runtime search paths
         """
-        if sys.platform == "win32":
+        if is_windows:
             self.win_rpath.add_library_dependent(*self.win_add_library_dependent())
             self.win_rpath.add_rpath(*self.win_add_rpath())
             self.win_rpath.establish_link()
@@ -207,7 +210,7 @@ def to_windows_exe(exe):
                 plat_exe = []
                 if hasattr(cls, "executables"):
                     for exe in cls.executables:
-                        if sys.platform == "win32":
+                        if is_windows:
                             exe = to_windows_exe(exe)
                         plat_exe.append(exe)
                 return plat_exe
@@ -2398,7 +2401,7 @@ def rpath(self):
 
         # on Windows, libraries of runtime interest are typically
         # stored in the bin directory
-        if sys.platform == "win32":
+        if is_windows:
             rpaths = [self.prefix.bin]
             rpaths.extend(d.prefix.bin for d in deps if os.path.isdir(d.prefix.bin))
         else:

lib/spack/spack/spec.py

@@ -54,6 +54,7 @@
 import itertools
 import os
 import re
+import sys
 import warnings
 from typing import Tuple
 
@@ -117,6 +118,7 @@
     "SpecDeprecatedError",
 ]
 
+is_windows = sys.platform == "win32"
 #: Valid pattern for an identifier in Spack
 
 identifier_re = r"\w[\w-]*"

lib/spack/spack/test/cmd/external.py

@@ -16,6 +16,8 @@
 from spack.main import SpackCommand
 from spack.spec import Spec
 
+is_windows = sys.platform == "win32"
+
 
 @pytest.fixture
 def executables_found(monkeypatch):
@@ -37,7 +39,7 @@ def _win_exe_ext():
 
 
 def define_plat_exe(exe):
-    if sys.platform == "win32":
+    if is_windows:
         exe += ".bat"
     return exe
 

lib/spack/spack/test/cmd/resource.py

@@ -7,6 +7,7 @@
 
 from spack.main import SpackCommand
 
+is_windows = sys.platform == "win32"
 resource = SpackCommand("resource")
 
 #: these are hashes used in mock packages
@@ -22,7 +23,7 @@
         "bf07a7fbb825fc0aae7bf4a1177b2b31fcf8a3feeaf7092761e18c859ee52a9c",
         "7d865e959b2466918c9863afca942d0fb89d7c9ac0c99bafc3749504ded97730",
     ]
-    if sys.platform != "win32"
+    if not is_windows
     else [
         "abcd1234abcd1234abcd1234abcd1234abcd1234abcd1234abcd1234abcd1234",
         "1234abcd1234abcd1234abcd1234abcd1234abcd1234abcd1234abcd1234abcd",
@@ -67,7 +68,7 @@ def test_resource_list_only_hashes(mock_packages, capfd):
 def test_resource_show(mock_packages, capfd):
     test_hash = (
         "c45c1564f70def3fc1a6e22139f62cb21cd190cc3a7dbe6f4120fa59ce33dcb8"
-        if sys.platform != "win32"
+        if not is_windows
         else "3c5b65abcd6a3b2c714dbf7c31ff65fe3748a1adc371f030c283007ca5534f11"
     )
     with capfd.disabled():

lib/spack/spack/test/cmd_extensions.py

@@ -14,6 +14,8 @@
 import spack.extensions
 import spack.main
 
+is_windows = sys.platform == "win32"
+
 
 class Extension:
     """Helper class to simplify the creation of simple command extension
@@ -272,7 +274,7 @@ def test_variable_in_extension_path(config, working_env):
     os.environ["_MY_VAR"] = os.path.join("my", "var")
     ext_paths = [os.path.join("~", "${_MY_VAR}", "spack-extension-1")]
     # Home env variable is USERPROFILE on Windows
-    home_env = "USERPROFILE" if sys.platform == "win32" else "HOME"
+    home_env = "USERPROFILE" if is_windows else "HOME"
     expected_ext_paths = [
         os.path.join(os.environ[home_env], os.environ["_MY_VAR"], "spack-extension-1")
     ]

lib/spack/spack/test/concretize.py

@@ -25,6 +25,8 @@
 from spack.spec import Spec
 from spack.version import ver
 
+is_windows = sys.platform == "win32"
+
 
 def check_spec(abstract, concrete):
     if abstract.versions.concrete:
@@ -1136,7 +1138,7 @@ def test_custom_compiler_version(self):
     def test_all_patches_applied(self):
         uuidpatch = (
             "a60a42b73e03f207433c5579de207c6ed61d58e4d12dd3b5142eb525728d89ea"
-            if sys.platform != "win32"
+            if not is_windows
             else "d0df7988457ec999c148a4a2af25ce831bfaad13954ba18a4446374cb0aef55e"
         )
         localpatch = "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855"

lib/spack/spack/test/conftest.py

@@ -54,6 +54,8 @@
 from spack.util.pattern import Bunch
 from spack.util.web import FetchError
 
+is_windows = sys.platform == "win32"
+
 
 def ensure_configuration_fixture_run_before(request):
     """Ensure that fixture mutating the configuration run before the one where
@@ -619,7 +621,7 @@ def ensure_debug(monkeypatch):
     tty.set_debug(current_debug_level)
 
 
-@pytest.fixture(autouse=sys.platform == "win32", scope="session")
+@pytest.fixture(autouse=is_windows, scope="session")
 def platform_config():
     spack.config.add_default_platform_scope(spack.platforms.real_host().name)
 
@@ -631,7 +633,7 @@ def default_config():
     This ensures we can test the real default configuration without having
     tests fail when the user overrides the defaults that we test against."""
     defaults_path = os.path.join(spack.paths.etc_path, "defaults")
-    if sys.platform == "win32":
+    if is_windows:
         defaults_path = os.path.join(defaults_path, "windows")
     with spack.config.use_configuration(defaults_path) as defaults_config:
         yield defaults_config
@@ -688,7 +690,7 @@ def configuration_dir(tmpdir_factory, linux_os):
     tmpdir.ensure("user", dir=True)
 
     # Slightly modify config.yaml and compilers.yaml
-    if sys.platform == "win32":
+    if is_windows:
         locks = False
     else:
         locks = True
@@ -1673,11 +1675,11 @@ def mock_executable(tmpdir):
     """
     import jinja2
 
-    shebang = "#!/bin/sh\n" if sys.platform != "win32" else "@ECHO OFF"
+    shebang = "#!/bin/sh\n" if not is_windows else "@ECHO OFF"
 
     def _factory(name, output, subdir=("bin",)):
         f = tmpdir.ensure(*subdir, dir=True).join(name)
-        if sys.platform == "win32":
+        if is_windows:
             f += ".bat"
         t = jinja2.Template("{{ shebang }}{{ output }}\n")
         f.write(t.render(shebang=shebang, output=output))

lib/spack/spack/test/database.py

@@ -33,6 +33,8 @@
 from spack.schema.database_index import schema
 from spack.util.executable import Executable
 
+is_windows = sys.platform == "win32"
+
 pytestmark = pytest.mark.db
 
 
@@ -449,7 +451,7 @@ def test_005_db_exists(database):
     lock_file = os.path.join(database.root, ".spack-db", "lock")
     assert os.path.exists(str(index_file))
     # Lockfiles not currently supported on Windows
-    if sys.platform != "win32":
+    if not is_windows:
         assert os.path.exists(str(lock_file))
 
     with open(index_file) as fd:

lib/spack/spack/test/installer.py

@@ -24,6 +24,8 @@
 import spack.store
 import spack.util.lock as lk
 
+is_windows = sys.platform == "win32"
+
 
 def _mock_repo(root, namespace):
     """Create an empty repository at the specified root
@@ -526,7 +528,7 @@ def _repoerr(repo, name):
 
     # The call to install_tree will raise the exception since not mocking
     # creation of dependency package files within *install* directories.
-    with pytest.raises(IOError, match=path if sys.platform != "win32" else ""):
+    with pytest.raises(IOError, match=path if not is_windows else ""):
         inst.dump_packages(spec, path)
 
     # Now try the error path, which requires the mock directory structure
@@ -877,7 +879,7 @@ def _chgrp(path, group, follow_symlinks=True):
     metadatadir = spack.store.layout.metadata_path(spec)
     # Regex matching with Windows style paths typically fails
     # so we skip the match check here
-    if sys.platform == "win32":
+    if is_windows:
         metadatadir = None
     # Should fail with a "not a directory" error
     with pytest.raises(OSError, match=metadatadir):

lib/spack/spack/test/link_paths.py

@@ -11,8 +11,9 @@
 import spack.paths
 from spack.compiler import _parse_non_system_link_dirs
 
+is_windows = sys.platform == "win32"
 drive = ""
-if sys.platform == "win32":
+if is_windows:
     match = re.search(r"[A-Za-z]:", spack.paths.test_path)
     if match:
         drive = match.group()
@@ -209,7 +210,7 @@ def test_obscure_parsing_rules():
     ]
 
     # TODO: add a comment explaining why this happens
-    if sys.platform == "win32":
+    if is_windows:
         paths.remove(os.path.join(root, "second", "path"))
 
     check_link_paths("obscure-parsing-rules.txt", paths)

lib/spack/spack/test/llnl/util/file_list.py

@@ -13,6 +13,8 @@
 
 import spack.paths
 
+is_windows = sys.platform == "win32"
+
 
 @pytest.fixture()
 def library_list():
@@ -26,7 +28,7 @@ def library_list():
             "/dir3/libz.so",
             "libmpi.so.20.10.1",  # shared object libraries may be versioned
         ]
-        if sys.platform != "win32"
+        if not is_windows
         else [
             "/dir1/liblapack.lib",
             "/dir2/libpython3.6.dll",
@@ -57,10 +59,10 @@ def header_list():
 
 
 # TODO: Remove below when llnl.util.filesystem.find_libraries becomes spec aware
-plat_static_ext = "lib" if sys.platform == "win32" else "a"
+plat_static_ext = "lib" if is_windows else "a"
 
 
-plat_shared_ext = "dll" if sys.platform == "win32" else "so"
+plat_shared_ext = "dll" if is_windows else "so"
 
 
 plat_apple_shared_ext = "dylib"
@@ -76,8 +78,7 @@ def test_joined_and_str(self, library_list):
         expected = " ".join(
             [
                 "/dir1/liblapack.%s" % plat_static_ext,
-                "/dir2/libpython3.6.%s"
-                % (plat_apple_shared_ext if sys.platform != "win32" else "dll"),
+                "/dir2/libpython3.6.%s" % (plat_apple_shared_ext if not is_windows else "dll"),
                 "/dir1/libblas.%s" % plat_static_ext,
                 "/dir3/libz.%s" % plat_shared_ext,
                 "libmpi.%s.20.10.1" % plat_shared_ext,
@@ -92,8 +93,7 @@ def test_joined_and_str(self, library_list):
         expected = ";".join(
             [
                 "/dir1/liblapack.%s" % plat_static_ext,
-                "/dir2/libpython3.6.%s"
-                % (plat_apple_shared_ext if sys.platform != "win32" else "dll"),
+                "/dir2/libpython3.6.%s" % (plat_apple_shared_ext if not is_windows else "dll"),
                 "/dir1/libblas.%s" % plat_static_ext,
                 "/dir3/libz.%s" % plat_shared_ext,
                 "libmpi.%s.20.10.1" % plat_shared_ext,

lib/spack/spack/test/llnl/util/lock.py

@@ -62,7 +62,8 @@
 import llnl.util.multiproc as mp
 from llnl.util.filesystem import getuid, touch
 
-if sys.platform != "win32":
+is_windows = sys.platform == "win32"
+if not is_windows:
     import fcntl
 
 pytestmark = pytest.mark.skipif(sys.platform == "win32", reason="does not run on windows")
@@ -126,7 +127,7 @@ def make_readable(*paths):
     # stat.S_IREAD constants or a corresponding integer value). All other
     # bits are ignored."
     for path in paths:
-        if sys.platform != "win32":
+        if not is_windows:
             mode = 0o555 if os.path.isdir(path) else 0o444
         else:
             mode = stat.S_IREAD
@@ -135,7 +136,7 @@ def make_readable(*paths):
 
 def make_writable(*paths):
     for path in paths:
-        if sys.platform != "win32":
+        if not is_windows:
             mode = 0o755 if os.path.isdir(path) else 0o744
         else:
             mode = stat.S_IWRITE
@@ -615,7 +616,7 @@ def test_read_lock_read_only_dir_writable_lockfile(lock_dir, lock_path):
             pass
 
 
-@pytest.mark.skipif(False if sys.platform == "win32" else getuid() == 0, reason="user is root")
+@pytest.mark.skipif(False if is_windows else getuid() == 0, reason="user is root")
 def test_read_lock_no_lockfile(lock_dir, lock_path):
     """read-only directory, no lockfile (so can't create)."""
     with read_only(lock_dir):

lib/spack/spack/test/patch.py

@@ -20,6 +20,7 @@
 from spack.spec import Spec
 from spack.stage import Stage
 from spack.util.executable import Executable
+from spack.util.path import is_windows
 
 # various sha256 sums (using variables for legibility)
 # many file based shas will differ between Windows and other platforms
@@ -28,22 +29,22 @@
 # files with contents 'foo', 'bar', and 'baz'
 foo_sha256 = (
     "b5bb9d8014a0f9b1d61e21e796d78dccdf1352f23cd32812f4850b878ae4944c"
-    if sys.platform != "win32"
+    if not is_windows
     else "bf874c7dd3a83cf370fdc17e496e341de06cd596b5c66dbf3c9bb7f6c139e3ee"
 )
 bar_sha256 = (
     "7d865e959b2466918c9863afca942d0fb89d7c9ac0c99bafc3749504ded97730"
-    if sys.platform != "win32"
+    if not is_windows
     else "556ddc69a75d0be0ecafc82cd4657666c8063f13d762282059c39ff5dbf18116"
 )
 baz_sha256 = (
     "bf07a7fbb825fc0aae7bf4a1177b2b31fcf8a3feeaf7092761e18c859ee52a9c"
-    if sys.platform != "win32"
+    if not is_windows
     else "d30392e66c636a063769cbb1db08cd3455a424650d4494db6379d73ea799582b"
 )
 biz_sha256 = (
     "a69b288d7393261e613c276c6d38a01461028291f6e381623acc58139d01f54d"
-    if sys.platform != "win32"
+    if not is_windows
     else "2f2b087a8f84834fd03d4d1d5b43584011e869e4657504ef3f8b0a672a5c222e"
 )
 
@@ -55,7 +56,7 @@
 
 platform_url_sha = (
     "252c0af58be3d90e5dc5e0d16658434c9efa5d20a5df6c10bf72c2d77f780866"
-    if sys.platform != "win32"
+    if not is_windows
     else "ecf44a8244a486e9ef5f72c6cb622f99718dcd790707ac91af0b8c9a4ab7a2bb"
 )
 
@@ -159,17 +160,17 @@ def test_patch_order(mock_packages, config):
 
     mid2_sha256 = (
         "mid21234abcd1234abcd1234abcd1234abcd1234abcd1234abcd1234abcd1234"
-        if sys.platform != "win32"
+        if not is_windows
         else "mid21234abcd1234abcd1234abcd1234abcd1234abcd1234abcd1234abcd1234"
     )
     mid1_sha256 = (
         "0b62284961dab49887e31319843431ee5b037382ac02c4fe436955abef11f094"
-        if sys.platform != "win32"
+        if not is_windows
         else "aeb16c4dec1087e39f2330542d59d9b456dd26d791338ae6d80b6ffd10c89dfa"
     )
     top_sha256 = (
         "f7de2947c64cb6435e15fb2bef359d1ed5f6356b2aebb7b20535e3772904e6db"
-        if sys.platform != "win32"
+        if not is_windows
         else "ff34cb21271d16dbf928374f610bb5dd593d293d311036ddae86c4846ff79070"
     )
 
@@ -218,7 +219,7 @@ def test_patched_dependency(mock_packages, config, install_mockery, mock_fetch):
     # make sure the patch makes it into the dependency spec
     t_sha = (
         "c45c1564f70def3fc1a6e22139f62cb21cd190cc3a7dbe6f4120fa59ce33dcb8"
-        if sys.platform != "win32"
+        if not is_windows
         else "3c5b65abcd6a3b2c714dbf7c31ff65fe3748a1adc371f030c283007ca5534f11"
     )
     assert (t_sha,) == spec["libelf"].variants["patches"].value

lib/spack/spack/test/util/environment.py

@@ -11,6 +11,8 @@
 
 import spack.util.environment as envutil
 
+is_windows = sys.platform == "win32"
+
 
 @pytest.fixture()
 def prepare_environment_for_tests():
@@ -21,14 +23,14 @@ def prepare_environment_for_tests():
 
 
 def test_is_system_path():
-    sys_path = "C:\\Users" if sys.platform == "win32" else "/usr/bin"
+    sys_path = "C:\\Users" if is_windows else "/usr/bin"
     assert envutil.is_system_path(sys_path)
     assert not envutil.is_system_path("/nonsense_path/bin")
     assert not envutil.is_system_path("")
     assert not envutil.is_system_path(None)
 
 
-if sys.platform == "win32":
+if is_windows:
     test_paths = [
         "C:\\Users",
         "C:\\",
@@ -49,7 +51,7 @@ def test_is_system_path():
 
 
 def test_filter_system_paths():
-    nonsense_prefix = "C:\\nonsense_path" if sys.platform == "win32" else "/nonsense_path"
+    nonsense_prefix = "C:\\nonsense_path" if is_windows else "/nonsense_path"
     expected = [p for p in test_paths if p.startswith(nonsense_prefix)]
     filtered = envutil.filter_system_paths(test_paths)
     assert expected == filtered

lib/spack/spack/test/util/executable.py

@@ -14,11 +14,13 @@
 import spack.util.executable as ex
 from spack.hooks.sbang import filter_shebangs_in_directory
 
+is_windows = sys.platform == "win32"
+
 
 def test_read_unicode(tmpdir, working_env):
     script_name = "print_unicode.py"
     # read the unicode back in and see whether things work
-    if sys.platform == "win32":
+    if is_windows:
         script = ex.Executable("%s %s" % (sys.executable, script_name))
     else:
         script = ex.Executable("./%s" % script_name)

lib/spack/spack/test/util/path.py

@@ -13,6 +13,9 @@
 import spack.config
 import spack.util.path as sup
 
+is_windows = sys.platform == "win32"
+
+
 #: Some lines with lots of placeholders
 padded_lines = [
     "==> [2021-06-23-15:59:05.020387] './configure' '--prefix=/Users/gamblin2/padding-log-test/opt/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_pla/darwin-bigsur-skylake/apple-clang-12.0.5/zlib-1.2.11-74mwnxgn6nujehpyyalhwizwojwn5zga",  # noqa: E501
@@ -33,7 +36,7 @@ def test_sanitze_file_path(tmpdir):
     """Test filtering illegal characters out of potential file paths"""
     # *nix illegal files characters are '/' and none others
     illegal_file_path = str(tmpdir) + "//" + "abcdefghi.txt"
-    if sys.platform == "win32":
+    if is_windows:
         # Windows has a larger set of illegal characters
         illegal_file_path = os.path.join(tmpdir, 'a<b>cd?e:f"g|h*i.txt')
     real_path = sup.sanitize_file_path(illegal_file_path)
@@ -43,7 +46,7 @@ def test_sanitze_file_path(tmpdir):
 # This class pertains to path string padding manipulation specifically
 # which is used for binary caching. This functionality is not supported
 # on Windows as of yet.
-@pytest.mark.skipif(sys.platform == "win32", reason="Padding funtionality unsupported on Windows")
+@pytest.mark.skipif(is_windows, reason="Padding funtionality unsupported on Windows")
 class TestPathPadding:
     @pytest.mark.parametrize("padded,fixed", zip(padded_lines, fixed_lines))
     def test_padding_substitution(self, padded, fixed):
@@ -119,7 +122,7 @@ def test_path_debug_padded_filter(debug, monkeypatch):
     string = fmt.format(prefix, os.sep, os.sep.join([sup.SPACK_PATH_PADDING_CHARS] * 2), suffix)
     expected = (
         fmt.format(prefix, os.sep, "[padded-to-{0}-chars]".format(72), suffix)
-        if debug <= 1 and sys.platform != "win32"
+        if debug <= 1 and not is_windows
         else string
     )
 

lib/spack/spack/util/compression.py

@@ -28,6 +28,8 @@
 
 ALLOWED_SINGLE_EXT_ARCHIVE_TYPES = PRE_EXTS + EXTS + NOTAR_EXTS
 
+is_windows = sys.platform == "win32"
+
 try:
     import bz2  # noqa
 
@@ -156,7 +158,7 @@ def _unzip(archive_file):
         archive_file (str): absolute path of the file to be decompressed
     """
     extracted_file = os.path.basename(strip_extension(archive_file, "zip"))
-    if sys.platform == "win32":
+    if is_windows:
         return _untar(archive_file)
     else:
         exe = "unzip"
@@ -168,7 +170,7 @@ def _unzip(archive_file):
 
 
 def _unZ(archive_file):
-    if sys.platform == "win32":
+    if is_windows:
         result = _7zip(archive_file)
     else:
         result = _system_gunzip(archive_file)
@@ -187,7 +189,7 @@ def _lzma_decomp(archive_file):
             with lzma.open(archive_file) as lar:
                 shutil.copyfileobj(lar, ar)
     else:
-        if sys.platform == "win32":
+        if is_windows:
             return _7zip(archive_file)
         else:
             return _xz(archive_file)
@@ -225,7 +227,7 @@ def _xz(archive_file):
     """Decompress lzma compressed .xz files via xz command line
     tool. Available only on Unix
     """
-    if sys.platform == "win32":
+    if is_windows:
         raise RuntimeError("XZ tool unavailable on Windows")
     decompressed_file = os.path.basename(strip_extension(archive_file, "xz"))
     working_dir = os.getcwd()
@@ -308,7 +310,7 @@ def decompressor_for(path, extension=None):
     # Catch tar.xz/tar.Z files here for Windows
     # as the tar utility on Windows cannot handle such
     # compression types directly
-    if ("xz" in extension or "Z" in extension) and sys.platform == "win32":
+    if ("xz" in extension or "Z" in extension) and is_windows:
         return _win_compressed_tarball_handler
 
     return _untar

lib/spack/spack/util/environment.py

@@ -25,12 +25,14 @@
 import spack.util.executable as executable
 from spack.util.path import path_to_os_path, system_path_filter
 
+is_windows = sys.platform == "win32"
+
 system_paths = (
     ["/", "/usr", "/usr/local"]
-    if sys.platform != "win32"
+    if not is_windows
     else ["C:\\", "C:\\Program Files", "C:\\Program Files (x86)", "C:\\Users", "C:\\ProgramData"]
 )
-suffixes = ["bin", "bin64", "include", "lib", "lib64"] if sys.platform != "win32" else []
+suffixes = ["bin", "bin64", "include", "lib", "lib64"] if not is_windows else []
 system_dirs = [os.path.join(p, s) for s in suffixes for p in system_paths] + system_paths
 
 
@@ -136,7 +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/util/lock.py

@@ -21,6 +21,8 @@
 import spack.error
 import spack.paths
 
+is_windows = sys.platform == "win32"
+
 
 class Lock(llnl.util.lock.Lock):
     """Lock that can be disabled.
@@ -32,7 +34,7 @@ class Lock(llnl.util.lock.Lock):
 
     def __init__(self, *args, **kwargs):
         super(Lock, self).__init__(*args, **kwargs)
-        self._enable = spack.config.get("config:locks", sys.platform != "win32")
+        self._enable = spack.config.get("config:locks", not is_windows)
 
     def _lock(self, op, timeout=0):
         if self._enable:

lib/spack/spack/util/path.py

@@ -22,6 +22,8 @@
 
 import spack.util.spack_yaml as syaml
 
+is_windows = sys.platform == "win32"
+
 __all__ = ["substitute_config_variables", "substitute_path_variables", "canonicalize_path"]
 
 
@@ -151,7 +153,7 @@ def sanitize_file_path(pth):
     # instances of illegal characters on join
     pth_cmpnts = pth.split(os.path.sep)
 
-    if sys.platform == "win32":
+    if is_windows:
         drive_match = r"[a-zA-Z]:"
         is_abs = bool(re.match(drive_match, pth_cmpnts[0]))
         drive = pth_cmpnts[0] + os.path.sep if is_abs else ""
@@ -208,7 +210,7 @@ def path_filter_caller(*args, **kwargs):
 def get_system_path_max():
     # Choose a conservative default
     sys_max_path_length = 256
-    if sys.platform == "win32":
+    if is_windows:
         sys_max_path_length = 260
     else:
         try:
@@ -236,7 +238,7 @@ class Path:
 
     unix = 0
     windows = 1
-    platform_path = windows if sys.platform == "win32" else unix
+    platform_path = windows if is_windows else unix
 
 
 def format_os_path(path, mode=Path.unix):
@@ -485,7 +487,7 @@ def debug_padded_filter(string, level=1):
     Returns (str): filtered string if current debug level does not exceed
         level and not windows; otherwise, unfiltered string
     """
-    if sys.platform == "win32":
+    if is_windows:
         return string
 
     return padding_filter(string) if tty.debug_level() <= level else string

lib/spack/spack/util/unparse/unparser.py

@@ -413,7 +413,6 @@ def visit_Try(self, node):
                 self.dispatch(node.finalbody)
 
     def visit_TryExcept(self, node):
-        # this construct only exists in Python < 3.3
         self.fill("try")
         with self.block():
             self.dispatch(node.body)
@@ -426,8 +425,7 @@ def visit_TryExcept(self, node):
                 self.dispatch(node.orelse)
 
     def visit_TryFinally(self, node):
-        # this construct only exists in Python < 3.3
-        if len(node.body) == 1 and isinstance(node.body[0], ast.TryExcept):  # type: ignore
+        if len(node.body) == 1 and isinstance(node.body[0], ast.TryExcept):
             # try-except-finally
             self.dispatch(node.body)
         else:

lib/spack/spack/util/windows_registry.py

@@ -13,7 +13,8 @@
 
 from llnl.util import tty
 
-if sys.platform == "win32":
+is_windows = sys.platform == "win32"
+if is_windows:
     import winreg
 
 
@@ -153,7 +154,7 @@ def __init__(self, key, root_key=HKEY.HKEY_CURRENT_USER):
                          to get an entrypoint, the HKEY constants are always open, or an already
                          open key can be used instead.
         """
-        if sys.platform != "win32":
+        if not is_windows:
             raise RuntimeError(
                 "Cannot instantiate Windows Registry class on non Windows platforms"
             )
@@ -166,7 +167,7 @@ def invalid_reg_ref_error_handler(self):
         try:
             yield
         except FileNotFoundError as e:
-            if sys.platform == "win32" and e.winerror == 2:
+            if e.winerror == 2:
                 tty.debug("Key %s at position %s does not exist" % (self.key, str(self.root)))
             else:
                 raise e
@@ -181,7 +182,7 @@ def _load_key(self):
                 winreg.OpenKeyEx(self.root.hkey, self.key, access=winreg.KEY_READ),
             )
         except FileNotFoundError as e:
-            if sys.platform == "win32" and e.winerror == 2:
+            if e.winerror == 2:
                 self._reg = -1
                 tty.debug("Key %s at position %s does not exist" % (self.key, str(self.root)))
             else:

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:

pyproject.toml

@@ -113,7 +113,6 @@ namespace_packages = true
 # globally, then turn back on in spack and spack submodules
 ignore_errors = true
 ignore_missing_imports = true
-check_untyped_defs = true
 
   [[tool.mypy.overrides]]
   module = 'spack.*'

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")