r-deseq2: add new versions (#48157 )

py-netcdf4: add v1.7.2 and fix variant (#47824 )
r-sparsematrixstats: add new versions (#48154 )
2025-01-10 14:36:53 -08:00 · 2025-01-10 21:52:42 +01:00 · 2025-01-10 10:50:04 -08:00 · 2025-01-10 10:12:41 -08:00 · 2025-01-10 19:00:51 +01:00 · 2025-01-10 09:18:12 -08:00
9432 changed files with 12001 additions and 20778 deletions
--- a/.github/workflows/bin/setup_git.ps1
+++ b/.github/workflows/bin/setup_git.ps1
@@ -1,5 +1,3 @@
-# (c) 2022 Lawrence Livermore National Laboratory
-
 git config --global user.email "spack@example.com"
 git config --global user.name "Test User"
 git config --global core.longpaths true
--- a/.github/workflows/coverage.yml
+++ b/.github/workflows/coverage.yml
@@ -29,7 +29,7 @@ jobs:
    - run: coverage xml

    - name: "Upload coverage report to CodeCov"
-      uses: codecov/codecov-action@05f5a9cfad807516dbbef9929c4a42df3eb78766
+      uses: codecov/codecov-action@1e68e06f1dbfde0e4cefc87efeba9e4643565303
      with:
        verbose: true
        fail_ci_if_error: false
--- a/.github/workflows/requirements/style/requirements.txt
+++ b/.github/workflows/requirements/style/requirements.txt
@@ -2,6 +2,6 @@ black==24.10.0
 clingo==5.7.1
 flake8==7.1.1
 isort==5.13.2
-mypy==1.8.0
+mypy==1.11.2
 types-six==1.17.0.20241205
 vermin==1.6.0
--- a/.github/workflows/valid-style.yml
+++ b/.github/workflows/valid-style.yml
@@ -20,7 +20,7 @@ jobs:
    - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
    - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b
      with:
-        python-version: '3.11'
+        python-version: '3.13'
        cache: 'pip'
    - name: Install Python Packages
      run: |
@@ -39,7 +39,7 @@ jobs:
        fetch-depth: 0
    - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b
      with:
-        python-version: '3.11'
+        python-version: '3.13'
        cache: 'pip'
    - name: Install Python packages
      run: |
@@ -58,7 +58,7 @@ jobs:
    secrets: inherit
    with:
      with_coverage: ${{ inputs.with_coverage }}
-      python_version: '3.11'
+      python_version: '3.13'
  # Check that spack can bootstrap the development environment on Python 3.6 - RHEL8
  bootstrap-dev-rhel8:
    runs-on: ubuntu-latest
--- a/5
+++ b/5
@@ -8,8 +8,9 @@ or http://www.apache.org/licenses/LICENSE-2.0) or the MIT license,
 Copyrights and patents in the Spack project are retained by contributors.
 No copyright assignment is required to contribute to Spack.

-Spack was originally distributed under the LGPL-2.1 license. Consent from
-contributors to relicense to Apache-2.0/MIT is documented at
+Spack was originally developed in 2013 by Lawrence Livermore National
+Security, LLC. It was originally distributed under the LGPL-2.1 license.
+Consent from contributors to relicense to Apache-2.0/MIT is documented at
 https://github.com/spack/spack/issues/9137.


--- a/2
+++ b/2
@@ -1,6 +1,6 @@
 MIT License

-Copyright (c) 2013-2024 LLNS, LLC and other Spack Project Developers.
+Copyright (c) Spack Project Developers.

 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
--- a/bin/haspywin.py
+++ b/bin/haspywin.py
@@ -1,5 +1,4 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 import subprocess
--- a/bin/sbang
+++ b/bin/sbang
@@ -1,7 +1,6 @@
 #!/bin/sh
 #
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# sbang project developers. See the top-level COPYRIGHT file for details.
+# Copyright sbang project developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/bin/spack
+++ b/bin/spack
@@ -1,8 +1,7 @@
 #!/bin/sh
 # -*- python -*-
 #
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/bin/spack-python
+++ b/bin/spack-python
@@ -1,7 +1,6 @@
 #!/bin/sh
 #
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/bin/spack.bat
+++ b/bin/spack.bat
@@ -1,5 +1,4 @@
-:: Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-:: Spack Project Developers. See the top-level COPYRIGHT file for details.
+:: Copyright Spack Project Developers. See COPYRIGHT file for details.
 ::
 :: SPDX-License-Identifier: (Apache-2.0 OR MIT)
 ::#######################################################################
--- a/bin/spack.ps1
+++ b/bin/spack.ps1
@@ -1,5 +1,4 @@
-#  Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-#  Spack Project Developers. See the top-level COPYRIGHT file for details.
+#  Copyright Spack Project Developers. See COPYRIGHT file for details.

 #  SPDX-License-Identifier: (Apache-2.0 OR MIT)
 # #######################################################################
--- a/bin/spack_pwsh.ps1
+++ b/bin/spack_pwsh.ps1
@@ -1,5 +1,4 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/etc/spack/defaults/packages.yaml
+++ b/etc/spack/defaults/packages.yaml
@@ -65,6 +65,7 @@ packages:
      unwind: [libunwind]
      uuid: [util-linux-uuid, libuuid]
      wasi-sdk: [wasi-sdk-prebuilt]
+      xkbdata-api: [xkeyboard-config, xkbdata]
      xxd: [xxd-standalone, vim]
      yacc: [bison, byacc]
      ziglang: [zig]
--- a/lib/spack/docs/_pygments/style.py
+++ b/lib/spack/docs/_pygments/style.py
@@ -1,5 +1,4 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/basic_usage.rst
+++ b/lib/spack/docs/basic_usage.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/binary_caches.rst
+++ b/lib/spack/docs/binary_caches.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/bootstrapping.rst
+++ b/lib/spack/docs/bootstrapping.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/build_settings.rst
+++ b/lib/spack/docs/build_settings.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/build_systems.rst
+++ b/lib/spack/docs/build_systems.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/build_systems/autotoolspackage.rst
+++ b/lib/spack/docs/build_systems/autotoolspackage.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/build_systems/bundlepackage.rst
+++ b/lib/spack/docs/build_systems/bundlepackage.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/build_systems/cachedcmakepackage.rst
+++ b/lib/spack/docs/build_systems/cachedcmakepackage.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/build_systems/cmakepackage.rst
+++ b/lib/spack/docs/build_systems/cmakepackage.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/build_systems/cudapackage.rst
+++ b/lib/spack/docs/build_systems/cudapackage.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/build_systems/custompackage.rst
+++ b/lib/spack/docs/build_systems/custompackage.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/build_systems/inteloneapipackage.rst
+++ b/lib/spack/docs/build_systems/inteloneapipackage.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/build_systems/intelpackage.rst
+++ b/lib/spack/docs/build_systems/intelpackage.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/build_systems/luapackage.rst
+++ b/lib/spack/docs/build_systems/luapackage.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/build_systems/makefilepackage.rst
+++ b/lib/spack/docs/build_systems/makefilepackage.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/build_systems/mavenpackage.rst
+++ b/lib/spack/docs/build_systems/mavenpackage.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/build_systems/mesonpackage.rst
+++ b/lib/spack/docs/build_systems/mesonpackage.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/build_systems/octavepackage.rst
+++ b/lib/spack/docs/build_systems/octavepackage.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/build_systems/perlpackage.rst
+++ b/lib/spack/docs/build_systems/perlpackage.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/build_systems/pythonpackage.rst
+++ b/lib/spack/docs/build_systems/pythonpackage.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/build_systems/qmakepackage.rst
+++ b/lib/spack/docs/build_systems/qmakepackage.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/build_systems/racketpackage.rst
+++ b/lib/spack/docs/build_systems/racketpackage.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/build_systems/rocmpackage.rst
+++ b/lib/spack/docs/build_systems/rocmpackage.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/build_systems/rpackage.rst
+++ b/lib/spack/docs/build_systems/rpackage.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/build_systems/rubypackage.rst
+++ b/lib/spack/docs/build_systems/rubypackage.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/build_systems/sconspackage.rst
+++ b/lib/spack/docs/build_systems/sconspackage.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/build_systems/sippackage.rst
+++ b/lib/spack/docs/build_systems/sippackage.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/build_systems/sourceforgepackage.rst
+++ b/lib/spack/docs/build_systems/sourceforgepackage.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/build_systems/wafpackage.rst
+++ b/lib/spack/docs/build_systems/wafpackage.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/chain.rst
+++ b/lib/spack/docs/chain.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/conf.py
+++ b/lib/spack/docs/conf.py
@@ -1,5 +1,4 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/config_yaml.rst
+++ b/lib/spack/docs/config_yaml.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

@@ -26,14 +25,23 @@ These settings can be overridden in ``etc/spack/config.yaml`` or
 The location where Spack will install packages and their dependencies.
 Default is ``$spack/opt/spack``.

---------------------------------------------------
-``install_hash_length`` and ``install_path_scheme``
---------------------------------------------------
+---------------
+``projections``
+---------------

-The default Spack installation path can be very long and can create problems
-for scripts with hardcoded shebangs. Additionally, when using the Intel
-compiler, and if there is also a long list of dependencies, the compiler may
-segfault. If you see the following:
+.. warning::
+
+   Modifying projections of the install tree is strongly discouraged.
+
+By default Spack installs all packages into a unique directory relative to the install
+tree root with the following layout:
+
+.. code-block::
+
+   {architecture}/{compiler.name}-{compiler.version}/{name}-{version}-{hash}
+
+In very rare cases, it may be necessary to reduce the length of this path. For example,
+very old versions of the Intel compiler are known to segfault when input paths are too long:

     .. code-block:: console

@@ -41,36 +49,25 @@ segfault. If you see the following:
       ** Segmentation violation signal raised. **
       Access violation or stack overflow. Please contact Intel Support for assistance.

-it may be because variables containing dependency specs may be too long. There
-are two parameters to help with long path names. Firstly, the
-``install_hash_length`` parameter can set the length of the hash in the
-installation path from 1 to 32. The default path uses the full 32 characters.
+Another case is Python and R packages with many runtime dependencies, which can result
+in very large ``PYTHONPATH`` and ``R_LIBS`` environment variables. This can cause the
+``execve`` system call to fail with ``E2BIG``, preventing processes from starting.

-Secondly, it is also possible to modify the entire installation
-scheme. By default Spack uses
-``{architecture}/{compiler.name}-{compiler.version}/{name}-{version}-{hash}``
-where the tokens that are available for use in this directive are the
-same as those understood by the :meth:`~spack.spec.Spec.format`
-method. Using this parameter it is possible to use a different package
-layout or reduce the depth of the installation paths. For example
+For this reason, Spack allows users to modify the installation layout through custom
+projections. For example

     .. code-block:: yaml

       config:
-         install_path_scheme: '{name}/{version}/{hash:7}'
+         install_tree:
+           root: $spack/opt/spack
+           projections:
+             all: "{name}/{version}/{hash:16}"

-would install packages into sub-directories using only the package
-name, version and a hash length of 7 characters.
+would install packages into sub-directories using only the package name, version and a
+hash length of 16 characters.

-When using either parameter to set the hash length it only affects the
-representation of the hash in the installation directory. You
-should be aware that the smaller the hash length the more likely
-naming conflicts will occur. These parameters are independent of those
-used to configure module names.
-
-.. warning:: Modifying the installation hash length or path scheme after
-   packages have been installed will prevent Spack from being
-   able to find the old installation directories.
+Notice that reducing the hash length increases the likelihood of hash collisions.

 --------------------
 ``build_stage``
--- a/lib/spack/docs/configuration.rst
+++ b/lib/spack/docs/configuration.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/containers.rst
+++ b/lib/spack/docs/containers.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/contribution_guide.rst
+++ b/lib/spack/docs/contribution_guide.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/developer_guide.rst
+++ b/lib/spack/docs/developer_guide.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/environments.rst
+++ b/lib/spack/docs/environments.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/extensions.rst
+++ b/lib/spack/docs/extensions.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/features.rst
+++ b/lib/spack/docs/features.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/frequently_asked_questions.rst
+++ b/lib/spack/docs/frequently_asked_questions.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/getting_started.rst
+++ b/lib/spack/docs/getting_started.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/gpu_configuration.rst
+++ b/lib/spack/docs/gpu_configuration.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/index.rst
+++ b/lib/spack/docs/index.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/mirrors.rst
+++ b/lib/spack/docs/mirrors.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/module_file_support.rst
+++ b/lib/spack/docs/module_file_support.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/packages_yaml.rst
+++ b/lib/spack/docs/packages_yaml.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/packaging_guide.rst
+++ b/lib/spack/docs/packaging_guide.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

@@ -237,8 +236,7 @@ for details):
 .. code-block:: python
   :linenos:

-   # Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   # Spack Project Developers. See the top-level COPYRIGHT file for details.
+   # Copyright Spack Project Developers. See COPYRIGHT file for details.
   #
   # SPDX-License-Identifier: (Apache-2.0 OR MIT)

@@ -4900,15 +4898,15 @@ If your package has a virtual dependency like ``mpi``, then referring to
 ``spec["mpi"]`` within ``install()`` will get you the concrete ``mpi``
 implementation in your dependency DAG.  That is a spec object just like
 the one passed to install, only the MPI implementations all set some
-additional properties on it to help you out.  E.g., in mvapich2, you'll
+additional properties on it to help you out.  E.g., in openmpi, you'll
 find this:

-.. literalinclude:: _spack_root/var/spack/repos/builtin/packages/mvapich2/package.py
-   :pyobject: Mvapich2.setup_dependent_package
+.. literalinclude:: _spack_root/var/spack/repos/builtin/packages/openmpi/package.py
+   :pyobject: Openmpi.setup_dependent_package

-That code allows the mvapich2 package to associate an ``mpicc`` property
-with the ``mvapich2`` node in the DAG, so that dependents can access it.
-``openmpi`` and ``mpich`` do similar things.  So, no matter what MPI
+That code allows the ``openmpi`` package to associate an ``mpicc`` property
+with the ``openmpi`` node in the DAG, so that dependents can access it.
+``mvapich2`` and ``mpich`` do similar things.  So, no matter what MPI
 you're using, spec["mpi"].mpicc gets you the location of the MPI
 compilers. This allows us to have a fairly simple polymorphic interface
 for information about virtual dependencies like MPI.
--- a/lib/spack/docs/pipelines.rst
+++ b/lib/spack/docs/pipelines.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/replace_conda_homebrew.rst
+++ b/lib/spack/docs/replace_conda_homebrew.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/repositories.rst
+++ b/lib/spack/docs/repositories.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/requirements.txt
+++ b/lib/spack/docs/requirements.txt
@@ -4,7 +4,7 @@ sphinx_design==0.6.1
 sphinx-rtd-theme==3.0.2
 python-levenshtein==0.26.1
 docutils==0.21.2
-pygments==2.18.0
+pygments==2.19.1
 urllib3==2.3.0
 pytest==8.3.4
 isort==5.13.2
--- a/lib/spack/docs/signing.rst
+++ b/lib/spack/docs/signing.rst
@@ -1,5 +1,4 @@
-.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/docs/spack.yaml
+++ b/lib/spack/docs/spack.yaml
@@ -1,5 +1,4 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -1,8 +1,7 @@
 #!/bin/sh -f
 # shellcheck disable=SC2034  # evals in this script fool shellcheck
 #
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/external/init.py
+++ b/lib/spack/external/init.py
@@ -1,5 +1,4 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/llnl/init.py
+++ b/lib/spack/llnl/init.py
@@ -1,4 +1,3 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
--- a/lib/spack/llnl/path.py
+++ b/lib/spack/llnl/path.py
@@ -1,5 +1,4 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 """Path primitives that just require Python standard library."""
--- a/lib/spack/llnl/string.py
+++ b/lib/spack/llnl/string.py
@@ -1,5 +1,4 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 """String manipulation functions that do not have other dependencies than Python
--- a/lib/spack/llnl/url.py
+++ b/lib/spack/llnl/url.py
@@ -1,5 +1,4 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 """URL primitives that just require Python standard library."""
--- a/lib/spack/llnl/util/init.py
+++ b/lib/spack/llnl/util/init.py
@@ -1,4 +1,3 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
--- a/lib/spack/llnl/util/argparsewriter.py
+++ b/lib/spack/llnl/util/argparsewriter.py
@@ -1,5 +1,4 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/llnl/util/filesystem.py
+++ b/lib/spack/llnl/util/filesystem.py
@@ -1,5 +1,4 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 import collections
--- a/lib/spack/llnl/util/lang.py
+++ b/lib/spack/llnl/util/lang.py
@@ -1,5 +1,4 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/llnl/util/link_tree.py
+++ b/lib/spack/llnl/util/link_tree.py
@@ -1,5 +1,4 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/llnl/util/lock.py
+++ b/lib/spack/llnl/util/lock.py
@@ -1,5 +1,4 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/llnl/util/multiproc.py
+++ b/lib/spack/llnl/util/multiproc.py
@@ -1,5 +1,4 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/llnl/util/symlink.py
+++ b/lib/spack/llnl/util/symlink.py
@@ -1,5 +1,4 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 import os
--- a/lib/spack/llnl/util/tty/init.py
+++ b/lib/spack/llnl/util/tty/init.py
@@ -1,5 +1,4 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/llnl/util/tty/colify.py
+++ b/lib/spack/llnl/util/tty/colify.py
@@ -1,5 +1,4 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/llnl/util/tty/color.py
+++ b/lib/spack/llnl/util/tty/color.py
@@ -1,5 +1,4 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/llnl/util/tty/log.py
+++ b/lib/spack/llnl/util/tty/log.py
@@ -1,5 +1,4 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/llnl/util/tty/pty.py
+++ b/lib/spack/llnl/util/tty/pty.py
@@ -1,5 +1,4 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/spack/init.py
+++ b/lib/spack/spack/init.py
@@ -1,5 +1,4 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)

--- a/lib/spack/spack/audit.py
+++ b/lib/spack/spack/audit.py
@@ -1,5 +1,4 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 """Classes and functions to register audit checks for various parts of
--- a/lib/spack/spack/binary_distribution.py
+++ b/lib/spack/spack/binary_distribution.py
@@ -1,5 +1,4 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)

@@ -592,32 +591,18 @@ def file_matches(f: IO[bytes], regex: llnl.util.lang.PatternBytes) -> bool:
        f.seek(0)


-def deps_to_relocate(spec):
-    """Return the transitive link and direct run dependencies of the spec.
-
-    This is a special traversal for dependencies we need to consider when relocating a package.
-
-    Package binaries, scripts, and other files may refer to the prefixes of  dependencies, so
-    we need to rewrite those locations when dependencies are in a different place at install time
-    than they were at build time.
-
-    This traversal covers transitive link dependencies and direct run dependencies because:
-
-    1. Spack adds RPATHs for transitive link dependencies so that packages can find needed
-       dependency libraries.
-    2. Packages may call any of their *direct* run dependencies (and may bake their paths into
-       binaries or scripts), so we also need to search for run dependency prefixes when relocating.
-
-    This returns a deduplicated list of transitive link dependencies and direct run dependencies.
-    """
-    deps = [
+def specs_to_relocate(spec: spack.spec.Spec) -> List[spack.spec.Spec]:
+    """Return the set of specs that may be referenced in the install prefix of the provided spec.
+    We currently include non-external transitive link and direct run dependencies."""
+    specs = [
        s
        for s in itertools.chain(
-            spec.traverse(root=True, deptype="link"), spec.dependencies(deptype="run")
+            spec.traverse(root=True, deptype="link", order="breadth", key=traverse.by_dag_hash),
+            spec.dependencies(deptype="run"),
        )
        if not s.external
    ]
-    return llnl.util.lang.dedupe(deps, key=lambda s: s.dag_hash())
+    return list(llnl.util.lang.dedupe(specs, key=lambda s: s.dag_hash()))


 def get_buildinfo_dict(spec):
@@ -631,7 +616,7 @@ def get_buildinfo_dict(spec):
        # "relocate_binaries": [],
        # "relocate_links": [],
        "hardlinks_deduped": True,
-        "hash_to_prefix": {d.dag_hash(): str(d.prefix) for d in deps_to_relocate(spec)},
+        "hash_to_prefix": {d.dag_hash(): str(d.prefix) for d in specs_to_relocate(spec)},
    }


@@ -1113,7 +1098,7 @@ def _exists_in_buildcache(spec: spack.spec.Spec, tmpdir: str, out_url: str) -> E


 def prefixes_to_relocate(spec):
-    prefixes = [s.prefix for s in deps_to_relocate(spec)]
+    prefixes = [s.prefix for s in specs_to_relocate(spec)]
    prefixes.append(spack.hooks.sbang.sbang_install_path())
    prefixes.append(str(spack.store.STORE.layout.root))
    return prefixes
@@ -2190,7 +2175,12 @@ def relocate_package(spec):
    old_spack_prefix = str(buildinfo.get("spackprefix"))
    old_rel_prefix = buildinfo.get("relative_prefix")
    old_prefix = os.path.join(old_layout_root, old_rel_prefix)
-    rel = buildinfo.get("relative_rpaths", False)
+
+    # Warn about old style tarballs created with the now removed --rel flag.
+    if buildinfo.get("relative_rpaths", False):
+        tty.warn(
+            f"Tarball for {spec} uses relative rpaths, " "which can cause library loading issues."
+        )

    # In the past prefix_to_hash was the default and externals were not dropped, so prefixes
    # were not unique.
@@ -2230,7 +2220,7 @@ def relocate_package(spec):
    # An analog in this algorithm is any spec that shares a name or provides the same virtuals
    # in the context of the relevant root spec. This ensures that the analog for a spec s
    # is the spec that s replaced when we spliced.
-    relocation_specs = deps_to_relocate(spec)
+    relocation_specs = specs_to_relocate(spec)
    build_spec_ids = set(id(s) for s in spec.build_spec.traverse(deptype=dt.ALL & ~dt.BUILD))
    for s in relocation_specs:
        analog = s
@@ -2268,19 +2258,11 @@ def relocate_package(spec):

    tty.debug("Relocating package from", "%s to %s." % (old_layout_root, new_layout_root))

-    # Old archives maybe have hardlinks repeated.
+    # Old archives may have hardlinks repeated.
    dedupe_hardlinks_if_necessary(workdir, buildinfo)

-    def is_backup_file(file):
-        return file.endswith("~")
-
    # Text files containing the prefix text
-    text_names = list()
-    for filename in buildinfo["relocate_textfiles"]:
-        text_name = os.path.join(workdir, filename)
-        # Don't add backup files generated by filter_file during install step.
-        if not is_backup_file(text_name):
-            text_names.append(text_name)
+    text_names = [os.path.join(workdir, f) for f in buildinfo["relocate_textfiles"]]

    # If we are not installing back to the same install tree do the relocation
    if old_prefix != new_prefix:
@@ -2291,29 +2273,11 @@ def is_backup_file(file):
        # do the relocation of path in binaries
        platform = spack.platforms.by_name(spec.platform)
        if "macho" in platform.binary_formats:
-            relocate.relocate_macho_binaries(
-                files_to_relocate,
-                old_layout_root,
-                new_layout_root,
-                prefix_to_prefix_bin,
-                rel,
-                old_prefix,
-                new_prefix,
-            )
-        elif "elf" in platform.binary_formats and not rel:
+            relocate.relocate_macho_binaries(files_to_relocate, prefix_to_prefix_bin)
+        elif "elf" in platform.binary_formats:
            # The new ELF dynamic section relocation logic only handles absolute to
            # absolute relocation.
-            relocate.new_relocate_elf_binaries(files_to_relocate, prefix_to_prefix_bin)
-        elif "elf" in platform.binary_formats and rel:
-            relocate.relocate_elf_binaries(
-                files_to_relocate,
-                old_layout_root,
-                new_layout_root,
-                prefix_to_prefix_bin,
-                rel,
-                old_prefix,
-                new_prefix,
-            )
+            relocate.relocate_elf_binaries(files_to_relocate, prefix_to_prefix_bin)

        # Relocate links to the new install prefix
        links = [os.path.join(workdir, f) for f in buildinfo.get("relocate_links", [])]
--- a/lib/spack/spack/bootstrap/init.py
+++ b/lib/spack/spack/bootstrap/init.py
@@ -1,5 +1,4 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 """Function and classes needed to bootstrap Spack itself."""
--- a/lib/spack/spack/bootstrap/_common.py
+++ b/lib/spack/spack/bootstrap/_common.py
@@ -1,5 +1,4 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 """Common basic functions used through the spack.bootstrap package"""
--- a/lib/spack/spack/bootstrap/clingo.py
+++ b/lib/spack/spack/bootstrap/clingo.py
@@ -1,5 +1,4 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 """Bootstrap concrete specs for clingo
--- a/lib/spack/spack/bootstrap/config.py
+++ b/lib/spack/spack/bootstrap/config.py
@@ -1,5 +1,4 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 """Manage configuration swapping for bootstrapping purposes"""
--- a/lib/spack/spack/bootstrap/core.py
+++ b/lib/spack/spack/bootstrap/core.py
@@ -1,5 +1,4 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 """Bootstrap Spack core dependencies from binaries.
@@ -549,10 +548,9 @@ def ensure_winsdk_external_or_raise() -> None:
            missing_packages_lst.append("win-sdk")
        missing_packages = " & ".join(missing_packages_lst)
        raise RuntimeError(
-            f"Unable to find the {missing_packages}, please install these packages \
-via the Visual Studio installer \
-before proceeding with Spack or provide the path to a non standard install with \
-'spack external find --path'"
+            f"Unable to find the {missing_packages}, please install these packages via the Visual "
+            "Studio installer before proceeding with Spack or provide the path to a non standard "
+            "install with 'spack external find --path'"
        )
    # wgl/sdk are not required for bootstrapping Spack, but
    # are required for building anything non trivial
--- a/lib/spack/spack/bootstrap/environment.py
+++ b/lib/spack/spack/bootstrap/environment.py
@@ -1,5 +1,4 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 """Bootstrap non-core Spack dependencies from an environment."""
--- a/lib/spack/spack/bootstrap/status.py
+++ b/lib/spack/spack/bootstrap/status.py
@@ -1,5 +1,4 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 """Query the status of bootstrapping on this machine"""
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -1,5 +1,4 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)

@@ -924,7 +923,9 @@ def effective_deptypes(
    in reverse so that dependents override dependencies, not the other way around."""
    topo_sorted_edges = traverse.traverse_topo_edges_generator(
        traverse.with_artificial_edges(specs),
-        visitor=EnvironmentVisitor(*specs, context=context),
+        visitor=traverse.CoverEdgesVisitor(
+            EnvironmentVisitor(*specs, context=context), key=traverse.by_dag_hash
+        ),
        key=traverse.by_dag_hash,
        root=True,
        all_edges=True,
--- a/lib/spack/spack/build_systems/init.py
+++ b/lib/spack/spack/build_systems/init.py
@@ -1,4 +1,3 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
--- a/lib/spack/spack/build_systems/_checks.py
+++ b/lib/spack/spack/build_systems/_checks.py
@@ -1,5 +1,4 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 import os
--- a/Show More
+++ b/Show More