tests: refactor for robustness, avoid dependence on path parsing

Signed-off-by: Gregory Becker <becker33@llnl.gov>

.github/workflows/audit.yaml

@@ -66,7 +66,7 @@ jobs:
           ./share/spack/qa/validate_last_exit.ps1
           spack -d audit externals
           ./share/spack/qa/validate_last_exit.ps1
-    - uses: actions/upload-artifact@6f51ac03b9356f520e9adb1b1b7802705f340c2b
+    - uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882
       if: ${{ inputs.with_coverage == 'true' && runner.os != 'Windows' }}
       with:
         name: coverage-audits-${{ matrix.system.os }}

.github/workflows/bin/setup_git.ps1

@@ -1,3 +1,5 @@
+# (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

.github/workflows/bootstrap.yml

@@ -161,7 +161,11 @@ jobs:
           source share/spack/setup-env.sh
           spack -d gpg list
           tree $HOME/.spack/bootstrap/store/
-
+      - name: Bootstrap File
+        run: |
+          source share/spack/setup-env.sh
+          spack -d python share/spack/qa/bootstrap-file.py
+          tree $HOME/.spack/bootstrap/store/
 
   windows:
     runs-on: "windows-latest"
@@ -192,3 +196,9 @@ jobs:
           spack -d gpg list
           ./share/spack/qa/validate_last_exit.ps1
           tree $env:userprofile/.spack/bootstrap/store/
+      - name: Bootstrap File
+        run: |
+          ./share/spack/setup-env.ps1
+          spack -d python share/spack/qa/bootstrap-file.py
+          ./share/spack/qa/validate_last_exit.ps1
+          tree $env:userprofile/.spack/bootstrap/store/

.github/workflows/build-containers.yml

@@ -94,7 +94,7 @@ jobs:
           fi
 
       - name: Upload Dockerfile
-        uses: actions/upload-artifact@6f51ac03b9356f520e9adb1b1b7802705f340c2b
+        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882
         with:
           name: dockerfiles_${{ matrix.dockerfile[0] }}
           path: dockerfiles
@@ -103,7 +103,7 @@ jobs:
         uses: docker/setup-qemu-action@49b3bc8e6bdd4a60e6116a5414239cba5943d3cf
 
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@6524bf65af31da8d45b59e8c27de4bd072b392f5
+        uses: docker/setup-buildx-action@c47758b77c9736f4b2ef4073d4d51994fabfe349
 
       - name: Log in to GitHub Container Registry
         uses: docker/login-action@9780b0c442fbb1117ed29e0efdff1e18412f7567
@@ -120,7 +120,7 @@ jobs:
           password: ${{ secrets.DOCKERHUB_TOKEN }}
 
       - name: Build & Deploy ${{ matrix.dockerfile[0] }}
-        uses: docker/build-push-action@48aba3b46d1b1fec4febb7c5d0c644b249a11355
+        uses: docker/build-push-action@4f58ea79222b3b9dc2c8bbdd6debcef730109a75
         with:
           context: dockerfiles/${{ matrix.dockerfile[0] }}
           platforms: ${{ matrix.dockerfile[1] }}
@@ -133,7 +133,7 @@ jobs:
     needs: deploy-images
     steps:
       - name: Merge Artifacts
-        uses: actions/upload-artifact/merge@6f51ac03b9356f520e9adb1b1b7802705f340c2b
+        uses: actions/upload-artifact/merge@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882
         with:
           name: dockerfiles
           pattern: dockerfiles_*

.github/workflows/coverage.yml

@@ -29,7 +29,6 @@ jobs:
     - run: coverage xml
 
     - name: "Upload coverage report to CodeCov"
-      uses: codecov/codecov-action@1e68e06f1dbfde0e4cefc87efeba9e4643565303
+      uses: codecov/codecov-action@05f5a9cfad807516dbbef9929c4a42df3eb78766
       with:
         verbose: true
-        fail_ci_if_error: false

.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==1.11.2
-types-six==1.17.0.20241205
+mypy==1.8.0
+types-six==1.16.21.20241105
 vermin==1.6.0

.github/workflows/unit_tests.yaml

@@ -15,17 +15,17 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11', '3.12']
         on_develop:
         - ${{ github.ref == 'refs/heads/develop' }}
         include:
         - python-version: '3.6'
           os: ubuntu-20.04
           on_develop: ${{ github.ref == 'refs/heads/develop' }}
-        - python-version: '3.7'
-          os: ubuntu-22.04
-          on_develop: ${{ github.ref == 'refs/heads/develop' }}
         exclude:
+        - python-version: '3.7'
+          os: ubuntu-latest
+          on_develop: false
         - python-version: '3.8'
           os: ubuntu-latest
           on_develop: false
@@ -52,13 +52,7 @@ jobs:
           # Needed for unit tests
           sudo apt-get -y install \
               coreutils cvs gfortran graphviz gnupg2 mercurial ninja-build \
-              cmake bison libbison-dev subversion
-    # On ubuntu 24.04, kcov was removed. It may come back in some future Ubuntu
-    - name: Set up Homebrew
-      id: set-up-homebrew
-      uses: Homebrew/actions/setup-homebrew@40e9946c182a64b3db1bf51be0dcb915f7802aa9
-    - name: Install kcov with brew
-      run: "brew install kcov"
+              cmake bison libbison-dev kcov
     - name: Install Python packages
       run: |
           pip install --upgrade pip setuptools pytest pytest-xdist pytest-cov
@@ -86,7 +80,7 @@ jobs:
           UNIT_TEST_COVERAGE: ${{ matrix.python-version == '3.11' }}
       run: |
           share/spack/qa/run-unit-tests
-    - uses: actions/upload-artifact@6f51ac03b9356f520e9adb1b1b7802705f340c2b
+    - uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882
       with:
         name: coverage-${{ matrix.os }}-python${{ matrix.python-version }}
         path: coverage
@@ -105,13 +99,7 @@ jobs:
       run: |
           sudo apt-get -y update
           # Needed for shell tests
-          sudo apt-get install -y coreutils csh zsh tcsh fish dash bash subversion
-    # On ubuntu 24.04, kcov was removed. It may come back in some future Ubuntu
-    - name: Set up Homebrew
-      id: set-up-homebrew
-      uses: Homebrew/actions/setup-homebrew@40e9946c182a64b3db1bf51be0dcb915f7802aa9
-    - name: Install kcov with brew
-      run: "brew install kcov"
+          sudo apt-get install -y coreutils kcov csh zsh tcsh fish dash bash
     - name: Install Python packages
       run: |
           pip install --upgrade pip setuptools pytest coverage[toml] pytest-xdist
@@ -125,7 +113,7 @@ jobs:
           COVERAGE: true
       run: |
           share/spack/qa/run-shell-tests
-    - uses: actions/upload-artifact@6f51ac03b9356f520e9adb1b1b7802705f340c2b
+    - uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882
       with:
         name: coverage-shell
         path: coverage
@@ -140,13 +128,13 @@ jobs:
     - name: Install dependencies
       run: |
           dnf install -y \
-              bzip2 curl gcc-c++ gcc gcc-gfortran git gnupg2 gzip \
+              bzip2 curl file gcc-c++ gcc gcc-gfortran git gnupg2 gzip \
               make patch tcl unzip which xz
     - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
     - name: Setup repo and non-root user
       run: |
           git --version
-          git config --global --add safe.directory '*'
+          git config --global --add safe.directory /__w/spack/spack
           git fetch --unshallow
           . .github/workflows/bin/setup_git.sh
           useradd spack-test
@@ -187,7 +175,7 @@ jobs:
         spack bootstrap status
         spack solve zlib
         spack unit-test --verbose --cov --cov-config=pyproject.toml --cov-report=xml:coverage.xml lib/spack/spack/test/concretization/core.py
-    - uses: actions/upload-artifact@6f51ac03b9356f520e9adb1b1b7802705f340c2b
+    - uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882
       with:
         name: coverage-clingo-cffi
         path: coverage
@@ -225,7 +213,7 @@ jobs:
         $(which spack) solve zlib
         common_args=(--dist loadfile --tx '4*popen//python=./bin/spack-tmpconfig python -u ./bin/spack python' -x)
         $(which spack) unit-test --verbose --cov --cov-config=pyproject.toml --cov-report=xml:coverage.xml "${common_args[@]}"
-    - uses: actions/upload-artifact@6f51ac03b9356f520e9adb1b1b7802705f340c2b
+    - uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882
       with:
         name: coverage-${{ matrix.os }}-python${{ matrix.python-version }}
         path: coverage
@@ -256,7 +244,7 @@ jobs:
       run: |
         spack unit-test -x --verbose --cov --cov-config=pyproject.toml
         ./share/spack/qa/validate_last_exit.ps1
-    - uses: actions/upload-artifact@6f51ac03b9356f520e9adb1b1b7802705f340c2b
+    - uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882
       with:
         name: coverage-windows
         path: coverage

.github/workflows/valid-style.yml

@@ -13,14 +13,15 @@ concurrency:
 
 
 jobs:
-  # Validate that the code can be run on all the Python versions supported by Spack
+  # Validate that the code can be run on all the Python versions
+  # supported by Spack
   validate:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
     - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b
       with:
-        python-version: '3.13'
+        python-version: '3.11'
         cache: 'pip'
     - name: Install Python Packages
       run: |
@@ -39,7 +40,7 @@ jobs:
         fetch-depth: 0
     - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b
       with:
-        python-version: '3.13'
+        python-version: '3.11'
         cache: 'pip'
     - name: Install Python packages
       run: |
@@ -58,7 +59,7 @@ jobs:
     secrets: inherit
     with:
       with_coverage: ${{ inputs.with_coverage }}
-      python_version: '3.13'
+      python_version: '3.11'
   # Check that spack can bootstrap the development environment on Python 3.6 - RHEL8
   bootstrap-dev-rhel8:
     runs-on: ubuntu-latest
@@ -73,7 +74,7 @@ jobs:
       - name: Setup repo and non-root user
         run: |
           git --version
-          git config --global --add safe.directory '*'
+          git config --global --add safe.directory /__w/spack/spack
           git fetch --unshallow
           . .github/workflows/bin/setup_git.sh
           useradd spack-test
@@ -86,7 +87,6 @@ jobs:
           spack -d bootstrap now --dev
           spack -d style -t black
           spack unit-test -V
-  # Check we don't make the situation with circular imports worse
   import-check:
     runs-on: ubuntu-latest
     steps:
@@ -121,46 +121,28 @@ jobs:
       uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
       with:
         repository: haampie/circular-import-fighter
-        ref: b5d6ce9be35f602cca7d5a6aa0259fca10639cca
+        ref: 9f60f51bc7134e0be73f27623f1b0357d1718427
         path: circular-import-fighter
     - name: Install dependencies
       working-directory: circular-import-fighter
       run: make -j dependencies
-    - name: Problematic imports before
+    - name: Import cycles before
       working-directory: circular-import-fighter
-      run: make SPACK_ROOT=../old SUFFIX=.old
-    - name: Problematic imports after
+      run: make SPACK_ROOT=../old && cp solution solution.old
+    - name: Import cycles after
       working-directory: circular-import-fighter
-      run: make SPACK_ROOT=../new SUFFIX=.new
+      run: make clean-graph && make SPACK_ROOT=../new && cp solution solution.new
     - name: Compare import cycles
       working-directory: circular-import-fighter
       run: |
-        edges_before="$(head -n1 solution.old)"
-        edges_after="$(head -n1 solution.new)"
+        edges_before="$(grep -oP 'edges to delete: \K\d+' solution.old)"
+        edges_after="$(grep -oP 'edges to delete: \K\d+' solution.new)"
         if [ "$edges_after" -gt "$edges_before" ]; then
           printf '\033[1;31mImport check failed: %s imports need to be deleted, ' "$edges_after"
           printf 'previously this was %s\033[0m\n'  "$edges_before"
-          printf 'Compare \033[1;97m"Problematic imports before"\033[0m and '
-          printf '\033[1;97m"Problematic imports after"\033[0m.\n'
+          printf 'Compare \033[1;97m"Import cycles before"\033[0m and '
+          printf '\033[1;97m"Import cycles after"\033[0m to see problematic imports.\n'
           exit 1
         else
           printf '\033[1;32mImport check passed: %s <= %s\033[0m\n' "$edges_after" "$edges_before"
         fi
-
-  # Further style checks from pylint
-  pylint:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
-        with:
-          fetch-depth: 0
-      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b
-        with:
-          python-version: '3.13'
-          cache: 'pip'
-      - name: Install Python packages
-        run: |
-          pip install --upgrade pip setuptools pylint
-      - name: Pylint (Spack Core)
-        run: |
-          pylint -j 4 --disable=all --enable=unspecified-encoding --ignore-paths=lib/spack/external lib

COPYRIGHT

@@ -8,9 +8,8 @@ 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 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
+Spack 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.
 
 
@@ -103,6 +102,6 @@ PackageName: sbang
 PackageHomePage: https://github.com/spack/sbang
 PackageLicenseDeclared: Apache-2.0 OR MIT
 
-PackageName: typing_extensions
-PackageHomePage: https://pypi.org/project/typing-extensions/
-PackageLicenseDeclared: Python-2.0
+PackageName: six
+PackageHomePage: https://pypi.python.org/pypi/six
+PackageLicenseDeclared: MIT

LICENSE-MIT

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) Spack Project Developers.
+Copyright (c) 2013-2024 LLNS, LLC and other 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

bin/haspywin.py

@@ -1,4 +1,5 @@
-# Copyright Spack Project Developers. See COPYRIGHT file for details.
+# Copyright 2013-2024 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)
 import subprocess

bin/sbang

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

bin/spack

@@ -1,7 +1,8 @@
 #!/bin/sh
 # -*- python -*-
 #
-# Copyright Spack Project Developers. See COPYRIGHT file for details.
+# Copyright 2013-2024 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)
 

bin/spack-python

@@ -1,6 +1,7 @@
 #!/bin/sh
 #
-# Copyright Spack Project Developers. See COPYRIGHT file for details.
+# Copyright 2013-2024 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)
 

bin/spack.bat

@@ -1,4 +1,5 @@
-:: Copyright Spack Project Developers. See COPYRIGHT file for details.
+:: Copyright 2013-2024 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)
 ::#######################################################################

bin/spack.ps1

@@ -1,4 +1,5 @@
-#  Copyright Spack Project Developers. See COPYRIGHT file for details.
+#  Copyright 2013-2024 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)
 # #######################################################################

bin/spack_pwsh.ps1

@@ -1,4 +1,5 @@
-# Copyright Spack Project Developers. See COPYRIGHT file for details.
+# Copyright 2013-2024 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)
 

etc/spack/defaults/config.yaml

@@ -194,12 +194,6 @@ config:
     # executables with many dependencies, in particular on slow filesystems.
     bind: false
 
-    # Controls the handling of missing dynamic libraries after installation.
-    # Options are ignore (default), warn, or error. If set to error, the
-    # installation fails if installed binaries reference dynamic libraries that
-    # are not found in their specified rpaths.
-    missing_library_policy: ignore
-
 
   # Set to 'false' to allow installation on filesystems that doesn't allow setgid bit
   # manipulation by unprivileged user (e.g. AFS)

etc/spack/defaults/packages.yaml

@@ -65,7 +65,6 @@ 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]
@@ -77,8 +76,6 @@ packages:
     buildable: false
   cray-mvapich2:
     buildable: false
-  egl:
-    buildable: false
   fujitsu-mpi:
     buildable: false
   hpcx-mpi:

lib/spack/docs/_pygments/style.py

@@ -1,4 +1,5 @@
-# Copyright Spack Project Developers. See COPYRIGHT file for details.
+# Copyright 2013-2024 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)
 

lib/spack/docs/basic_usage.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/binary_caches.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 
@@ -264,30 +265,25 @@ infrastructure, or to cache Spack built binaries in Github Actions and
 GitLab CI.
 
 To get started, configure an OCI mirror using ``oci://`` as the scheme,
-and optionally specify variables that hold the username and password (or
-personal access token) for the registry:
+and optionally specify a username and password (or personal access token):
 
 .. code-block:: console
 
-    $ spack mirror add --oci-username-variable REGISTRY_USER \
-                       --oci-password-variable REGISTRY_TOKEN \
-                       my_registry oci://example.com/my_image
+    $ spack mirror add --oci-username username --oci-password password my_registry oci://example.com/my_image
 
 Spack follows the naming conventions of Docker, with Dockerhub as the default
 registry. To use Dockerhub, you can omit the registry domain:
 
 .. code-block:: console
 
-    $ spack mirror add ... my_registry oci://username/my_image
+    $ spack mirror add --oci-username username --oci-password password my_registry oci://username/my_image
 
 From here, you can use the mirror as any other build cache:
 
 .. code-block:: console
 
-    $ export REGISTRY_USER=...
-    $ export REGISTRY_TOKEN=...
     $ spack buildcache push my_registry <specs...>  # push to the registry
-    $ spack install <specs...>  # or install from the registry
+    $ spack install <specs...> # install from the registry
 
 A unique feature of buildcaches on top of OCI registries is that it's incredibly
 easy to generate get a runnable container image with the binaries installed. This

lib/spack/docs/bootstrapping.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/build_settings.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/build_systems.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/build_systems/autotoolspackage.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/build_systems/bundlepackage.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/build_systems/cachedcmakepackage.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/build_systems/cmakepackage.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/build_systems/cudapackage.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/build_systems/custompackage.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/build_systems/inteloneapipackage.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/build_systems/intelpackage.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/build_systems/luapackage.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/build_systems/makefilepackage.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/build_systems/mavenpackage.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/build_systems/mesonpackage.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/build_systems/octavepackage.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/build_systems/perlpackage.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/build_systems/pythonpackage.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/build_systems/qmakepackage.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 
@@ -24,14 +25,6 @@ QMake does not appear to have a standardized way of specifying
 the installation directory, so you may have to set environment
 variables or edit ``*.pro`` files to get things working properly.
 
-QMake packages will depend on the virtual ``qmake`` package which
-is provided by multiple versions of Qt: ``qt`` provides Qt up to
-Qt5, and ``qt-base`` provides Qt from version Qt6 onwards. This
-split was motivated by the desire to split the single Qt package
-into its components to allow for more fine-grained installation.
-To depend on a specific version, refer to the documentation on
-:ref:`virtual-dependencies`.
-
 ^^^^^^
 Phases
 ^^^^^^

lib/spack/docs/build_systems/racketpackage.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/build_systems/rocmpackage.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/build_systems/rpackage.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/build_systems/rubypackage.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/build_systems/sconspackage.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/build_systems/sippackage.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/build_systems/sourceforgepackage.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/build_systems/wafpackage.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/chain.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/conf.py

@@ -1,4 +1,5 @@
-# Copyright Spack Project Developers. See COPYRIGHT file for details.
+# Copyright 2013-2024 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)
 

lib/spack/docs/config_yaml.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 
@@ -25,23 +26,14 @@ 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``.
 
----------------
-``projections``
----------------
+---------------------------------------------------
+``install_hash_length`` and ``install_path_scheme``
+---------------------------------------------------
 
-.. 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:
+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:
 
      .. code-block:: console
 
@@ -49,25 +41,36 @@ very old versions of the Intel compiler are known to segfault when input paths a
        ** Segmentation violation signal raised. **
        Access violation or stack overflow. Please contact Intel Support for assistance.
 
-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.
+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.
 
-For this reason, Spack allows users to modify the installation layout through custom
-projections. For example
+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
 
      .. code-block:: yaml
 
        config:
-         install_tree:
-           root: $spack/opt/spack
-           projections:
-             all: "{name}/{version}/{hash:16}"
+         install_path_scheme: '{name}/{version}/{hash:7}'
 
-would install packages into sub-directories using only the package name, version and a
-hash length of 16 characters.
+would install packages into sub-directories using only the package
+name, version and a hash length of 7 characters.
 
-Notice that reducing the hash length increases the likelihood of hash collisions.
+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.
 
 --------------------
 ``build_stage``

lib/spack/docs/configuration.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/containers.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 
@@ -37,11 +38,9 @@ just have to configure and OCI registry and run ``spack buildcache push``.
    spack -e . install
 
    # Configure the registry
-   spack -e . mirror add --oci-username-variable REGISTRY_USER \
-                         --oci-password-variable REGISTRY_TOKEN \
-                        container-registry oci://example.com/name/image
+   spack -e . mirror add --oci-username ... --oci-password ... container-registry oci://example.com/name/image
 
-   # Push the image (do set REGISTRY_USER and REGISTRY_TOKEN)
+   # Push the image
    spack -e . buildcache push --update-index --base-image ubuntu:22.04 --tag my_env container-registry
 
 The resulting container image can then be run as follows:

lib/spack/docs/contribution_guide.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/developer_guide.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 
@@ -177,8 +178,8 @@ Spec-related modules
   Contains :class:`~spack.spec.Spec`. Also implements most of the logic for concretization
   of specs.
 
-:mod:`spack.spec_parser`
-  Contains :class:`~spack.spec_parser.SpecParser` and functions related to parsing specs.
+:mod:`spack.parser`
+  Contains :class:`~spack.parser.SpecParser` and functions related to parsing specs.
 
 :mod:`spack.version`
   Implements a simple :class:`~spack.version.Version` class with simple

lib/spack/docs/environments.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/extensions.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/features.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/frequently_asked_questions.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/getting_started.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 
@@ -34,7 +35,7 @@ A build matrix showing which packages are working on which systems is shown belo
       .. code-block:: console
 
          apt update
-         apt install bzip2 ca-certificates g++ gcc gfortran git gzip lsb-release patch python3 tar unzip xz-utils zstd
+         apt install bzip2 ca-certificates file g++ gcc gfortran git gzip lsb-release patch python3 tar unzip xz-utils zstd
 
    .. tab-item:: RHEL
 
@@ -147,22 +148,20 @@ The first time you concretize a spec, Spack will bootstrap automatically:
    --------------------------------
    zlib@1.2.13%gcc@9.4.0+optimize+pic+shared build_system=makefile arch=linux-ubuntu20.04-icelake
 
-The default bootstrap behavior is to use pre-built binaries. You can verify the
-active bootstrap repositories with:
-
-.. command-output:: spack bootstrap list
-
 If for security concerns you cannot bootstrap ``clingo`` from pre-built
 binaries, you have to disable fetching the binaries we generated with Github Actions.
 
 .. code-block:: console
 
-   $ spack bootstrap disable github-actions-v0.6
-   ==> "github-actions-v0.6" is now disabled and will not be used for bootstrapping
-   $ spack bootstrap disable github-actions-v0.5
-   ==> "github-actions-v0.5" is now disabled and will not be used for bootstrapping
+   $ spack bootstrap disable github-actions-v0.4
+   ==> "github-actions-v0.4" is now disabled and will not be used for bootstrapping
+   $ spack bootstrap disable github-actions-v0.3
+   ==> "github-actions-v0.3" is now disabled and will not be used for bootstrapping
+
+You can verify that the new settings are effective with:
+
+.. command-output:: spack bootstrap list
 
-You can verify that the new settings are effective with ``spack bootstrap list``.
 
 .. note::
 
@@ -1327,7 +1326,6 @@ Required:
 * Microsoft Visual Studio
 * Python
 * Git
-* 7z
 
 Optional:
 * Intel Fortran (needed for some packages)
@@ -1393,13 +1391,6 @@ as the project providing Git support on Windows. This is additionally the recomm
 for installing Git on Windows, a link to which can be found above. Spack requires the
 utilities vendored by this project.
 
-"""
-7zip
-"""
-
-A tool for extracting ``.xz`` files is required for extracting source tarballs. The latest 7zip
-can be located at https://sourceforge.net/projects/sevenzip/.
-
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 Step 2: Install and setup Spack
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

lib/spack/docs/gpu_configuration.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/index.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/mirrors.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/module_file_support.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/packages_yaml.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/packaging_guide.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 
@@ -236,7 +237,8 @@ for details):
 .. code-block:: python
    :linenos:
 
-   # Copyright Spack Project Developers. See COPYRIGHT file for details.
+   # Copyright 2013-2024 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)
 
@@ -4898,15 +4900,15 @@ 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 openmpi, you'll
+additional properties on it to help you out.  E.g., in mvapich2, you'll
 find this:
 
-.. literalinclude:: _spack_root/var/spack/repos/builtin/packages/openmpi/package.py
-   :pyobject: Openmpi.setup_dependent_package
+.. literalinclude:: _spack_root/var/spack/repos/builtin/packages/mvapich2/package.py
+   :pyobject: Mvapich2.setup_dependent_package
 
-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
+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
 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.
@@ -5135,7 +5137,7 @@ other checks.
      - Not applicable
    * - :ref:`PythonPackage <pythonpackage>`
      - Not applicable
-     - ``test_imports`` (module imports)
+     - ``test`` (module imports)
    * - :ref:`QMakePackage <qmakepackage>`
      - ``check`` (``make check``)
      - Not applicable
@@ -5144,7 +5146,7 @@ other checks.
      - Not applicable
    * - :ref:`SIPPackage <sippackage>`
      - Not applicable
-     - ``test_imports`` (module imports)
+     - ``test`` (module imports)
    * - :ref:`WafPackage <wafpackage>`
      - ``build_test`` (must be overridden)
      - ``install_test`` (must be overridden)

lib/spack/docs/pipelines.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/replace_conda_homebrew.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/repositories.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/requirements.txt

@@ -1,12 +1,12 @@
 sphinx==8.1.3
-sphinxcontrib-programoutput==0.18
+sphinxcontrib-programoutput==0.17
 sphinx_design==0.6.1
 sphinx-rtd-theme==3.0.2
 python-levenshtein==0.26.1
 docutils==0.21.2
-pygments==2.19.1
-urllib3==2.3.0
-pytest==8.3.4
+pygments==2.18.0
+urllib3==2.2.3
+pytest==8.3.3
 isort==5.13.2
 black==24.10.0
 flake8==7.1.1

lib/spack/docs/signing.rst

@@ -1,4 +1,5 @@
-.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+.. Copyright 2013-2024 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)
 

lib/spack/docs/spack.yaml

@@ -1,4 +1,5 @@
-# Copyright Spack Project Developers. See COPYRIGHT file for details.
+# Copyright 2013-2024 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)
 

lib/spack/docs/tables/system_prerequisites.csv

@@ -8,6 +8,7 @@ unzip, , , Compress/Decompress archives
 bzip2, , , Compress/Decompress archives
 xz, , , Compress/Decompress archives
 zstd, , Optional, Compress/Decompress archives
+file, , , Create/Use Buildcaches
 lsb-release, , , Linux: identify operating system version
 gnupg2, , , Sign/Verify Buildcaches
 git, , , Manage Software Repositories

lib/spack/env/cc

@@ -1,7 +1,8 @@
 #!/bin/sh -f
 # shellcheck disable=SC2034  # evals in this script fool shellcheck
 #
-# Copyright Spack Project Developers. See COPYRIGHT file for details.
+# Copyright 2013-2024 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)
 

lib/spack/external/__init__.py

@@ -1,4 +1,5 @@
-# Copyright Spack Project Developers. See COPYRIGHT file for details.
+# Copyright 2013-2024 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)
 

lib/spack/external/_vendoring/typing_extensions.LICENSE

@@ -1,254 +0,0 @@
-A. HISTORY OF THE SOFTWARE
-==========================
-
-Python was created in the early 1990s by Guido van Rossum at Stichting
-Mathematisch Centrum (CWI, see http://www.cwi.nl) in the Netherlands
-as a successor of a language called ABC.  Guido remains Python's
-principal author, although it includes many contributions from others.
-
-In 1995, Guido continued his work on Python at the Corporation for
-National Research Initiatives (CNRI, see http://www.cnri.reston.va.us)
-in Reston, Virginia where he released several versions of the
-software.
-
-In May 2000, Guido and the Python core development team moved to
-BeOpen.com to form the BeOpen PythonLabs team.  In October of the same
-year, the PythonLabs team moved to Digital Creations (now Zope
-Corporation, see http://www.zope.com).  In 2001, the Python Software
-Foundation (PSF, see http://www.python.org/psf/) was formed, a
-non-profit organization created specifically to own Python-related
-Intellectual Property.  Zope Corporation is a sponsoring member of
-the PSF.
-
-All Python releases are Open Source (see http://www.opensource.org for
-the Open Source Definition).  Historically, most, but not all, Python
-releases have also been GPL-compatible; the table below summarizes
-the various releases.
-
-    Release         Derived     Year        Owner       GPL-
-                    from                                compatible? (1)
-
-    0.9.0 thru 1.2              1991-1995   CWI         yes
-    1.3 thru 1.5.2  1.2         1995-1999   CNRI        yes
-    1.6             1.5.2       2000        CNRI        no
-    2.0             1.6         2000        BeOpen.com  no
-    1.6.1           1.6         2001        CNRI        yes (2)
-    2.1             2.0+1.6.1   2001        PSF         no
-    2.0.1           2.0+1.6.1   2001        PSF         yes
-    2.1.1           2.1+2.0.1   2001        PSF         yes
-    2.1.2           2.1.1       2002        PSF         yes
-    2.1.3           2.1.2       2002        PSF         yes
-    2.2 and above   2.1.1       2001-now    PSF         yes
-
-Footnotes:
-
-(1) GPL-compatible doesn't mean that we're distributing Python under
-    the GPL.  All Python licenses, unlike the GPL, let you distribute
-    a modified version without making your changes open source.  The
-    GPL-compatible licenses make it possible to combine Python with
-    other software that is released under the GPL; the others don't.
-
-(2) According to Richard Stallman, 1.6.1 is not GPL-compatible,
-    because its license has a choice of law clause.  According to
-    CNRI, however, Stallman's lawyer has told CNRI's lawyer that 1.6.1
-    is "not incompatible" with the GPL.
-
-Thanks to the many outside volunteers who have worked under Guido's
-direction to make these releases possible.
-
-
-B. TERMS AND CONDITIONS FOR ACCESSING OR OTHERWISE USING PYTHON
-===============================================================
-
-PYTHON SOFTWARE FOUNDATION LICENSE VERSION 2
---------------------------------------------
-
-1. This LICENSE AGREEMENT is between the Python Software Foundation
-("PSF"), and the Individual or Organization ("Licensee") accessing and
-otherwise using this software ("Python") in source or binary form and
-its associated documentation.
-
-2. Subject to the terms and conditions of this License Agreement, PSF hereby
-grants Licensee a nonexclusive, royalty-free, world-wide license to reproduce,
-analyze, test, perform and/or display publicly, prepare derivative works,
-distribute, and otherwise use Python alone or in any derivative version,
-provided, however, that PSF's License Agreement and PSF's notice of copyright,
-i.e., "Copyright (c) 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010,
-2011, 2012, 2013, 2014 Python Software Foundation; All Rights Reserved" are
-retained in Python alone or in any derivative version prepared by Licensee.
-
-3. In the event Licensee prepares a derivative work that is based on
-or incorporates Python or any part thereof, and wants to make
-the derivative work available to others as provided herein, then
-Licensee hereby agrees to include in any such work a brief summary of
-the changes made to Python.
-
-4. PSF is making Python available to Licensee on an "AS IS"
-basis.  PSF MAKES NO REPRESENTATIONS OR WARRANTIES, EXPRESS OR
-IMPLIED.  BY WAY OF EXAMPLE, BUT NOT LIMITATION, PSF MAKES NO AND
-DISCLAIMS ANY REPRESENTATION OR WARRANTY OF MERCHANTABILITY OR FITNESS
-FOR ANY PARTICULAR PURPOSE OR THAT THE USE OF PYTHON WILL NOT
-INFRINGE ANY THIRD PARTY RIGHTS.
-
-5. PSF SHALL NOT BE LIABLE TO LICENSEE OR ANY OTHER USERS OF PYTHON
-FOR ANY INCIDENTAL, SPECIAL, OR CONSEQUENTIAL DAMAGES OR LOSS AS
-A RESULT OF MODIFYING, DISTRIBUTING, OR OTHERWISE USING PYTHON,
-OR ANY DERIVATIVE THEREOF, EVEN IF ADVISED OF THE POSSIBILITY THEREOF.
-
-6. This License Agreement will automatically terminate upon a material
-breach of its terms and conditions.
-
-7. Nothing in this License Agreement shall be deemed to create any
-relationship of agency, partnership, or joint venture between PSF and
-Licensee.  This License Agreement does not grant permission to use PSF
-trademarks or trade name in a trademark sense to endorse or promote
-products or services of Licensee, or any third party.
-
-8. By copying, installing or otherwise using Python, Licensee
-agrees to be bound by the terms and conditions of this License
-Agreement.
-
-
-BEOPEN.COM LICENSE AGREEMENT FOR PYTHON 2.0
--------------------------------------------
-
-BEOPEN PYTHON OPEN SOURCE LICENSE AGREEMENT VERSION 1
-
-1. This LICENSE AGREEMENT is between BeOpen.com ("BeOpen"), having an
-office at 160 Saratoga Avenue, Santa Clara, CA 95051, and the
-Individual or Organization ("Licensee") accessing and otherwise using
-this software in source or binary form and its associated
-documentation ("the Software").
-
-2. Subject to the terms and conditions of this BeOpen Python License
-Agreement, BeOpen hereby grants Licensee a non-exclusive,
-royalty-free, world-wide license to reproduce, analyze, test, perform
-and/or display publicly, prepare derivative works, distribute, and
-otherwise use the Software alone or in any derivative version,
-provided, however, that the BeOpen Python License is retained in the
-Software, alone or in any derivative version prepared by Licensee.
-
-3. BeOpen is making the Software available to Licensee on an "AS IS"
-basis.  BEOPEN MAKES NO REPRESENTATIONS OR WARRANTIES, EXPRESS OR
-IMPLIED.  BY WAY OF EXAMPLE, BUT NOT LIMITATION, BEOPEN MAKES NO AND
-DISCLAIMS ANY REPRESENTATION OR WARRANTY OF MERCHANTABILITY OR FITNESS
-FOR ANY PARTICULAR PURPOSE OR THAT THE USE OF THE SOFTWARE WILL NOT
-INFRINGE ANY THIRD PARTY RIGHTS.
-
-4. BEOPEN SHALL NOT BE LIABLE TO LICENSEE OR ANY OTHER USERS OF THE
-SOFTWARE FOR ANY INCIDENTAL, SPECIAL, OR CONSEQUENTIAL DAMAGES OR LOSS
-AS A RESULT OF USING, MODIFYING OR DISTRIBUTING THE SOFTWARE, OR ANY
-DERIVATIVE THEREOF, EVEN IF ADVISED OF THE POSSIBILITY THEREOF.
-
-5. This License Agreement will automatically terminate upon a material
-breach of its terms and conditions.
-
-6. This License Agreement shall be governed by and interpreted in all
-respects by the law of the State of California, excluding conflict of
-law provisions.  Nothing in this License Agreement shall be deemed to
-create any relationship of agency, partnership, or joint venture
-between BeOpen and Licensee.  This License Agreement does not grant
-permission to use BeOpen trademarks or trade names in a trademark
-sense to endorse or promote products or services of Licensee, or any
-third party.  As an exception, the "BeOpen Python" logos available at
-http://www.pythonlabs.com/logos.html may be used according to the
-permissions granted on that web page.
-
-7. By copying, installing or otherwise using the software, Licensee
-agrees to be bound by the terms and conditions of this License
-Agreement.
-
-
-CNRI LICENSE AGREEMENT FOR PYTHON 1.6.1
----------------------------------------
-
-1. This LICENSE AGREEMENT is between the Corporation for National
-Research Initiatives, having an office at 1895 Preston White Drive,
-Reston, VA 20191 ("CNRI"), and the Individual or Organization
-("Licensee") accessing and otherwise using Python 1.6.1 software in
-source or binary form and its associated documentation.
-
-2. Subject to the terms and conditions of this License Agreement, CNRI
-hereby grants Licensee a nonexclusive, royalty-free, world-wide
-license to reproduce, analyze, test, perform and/or display publicly,
-prepare derivative works, distribute, and otherwise use Python 1.6.1
-alone or in any derivative version, provided, however, that CNRI's
-License Agreement and CNRI's notice of copyright, i.e., "Copyright (c)
-1995-2001 Corporation for National Research Initiatives; All Rights
-Reserved" are retained in Python 1.6.1 alone or in any derivative
-version prepared by Licensee.  Alternately, in lieu of CNRI's License
-Agreement, Licensee may substitute the following text (omitting the
-quotes): "Python 1.6.1 is made available subject to the terms and
-conditions in CNRI's License Agreement.  This Agreement together with
-Python 1.6.1 may be located on the Internet using the following
-unique, persistent identifier (known as a handle): 1895.22/1013.  This
-Agreement may also be obtained from a proxy server on the Internet
-using the following URL: http://hdl.handle.net/1895.22/1013".
-
-3. In the event Licensee prepares a derivative work that is based on
-or incorporates Python 1.6.1 or any part thereof, and wants to make
-the derivative work available to others as provided herein, then
-Licensee hereby agrees to include in any such work a brief summary of
-the changes made to Python 1.6.1.
-
-4. CNRI is making Python 1.6.1 available to Licensee on an "AS IS"
-basis.  CNRI MAKES NO REPRESENTATIONS OR WARRANTIES, EXPRESS OR
-IMPLIED.  BY WAY OF EXAMPLE, BUT NOT LIMITATION, CNRI MAKES NO AND
-DISCLAIMS ANY REPRESENTATION OR WARRANTY OF MERCHANTABILITY OR FITNESS
-FOR ANY PARTICULAR PURPOSE OR THAT THE USE OF PYTHON 1.6.1 WILL NOT
-INFRINGE ANY THIRD PARTY RIGHTS.
-
-5. CNRI SHALL NOT BE LIABLE TO LICENSEE OR ANY OTHER USERS OF PYTHON
-1.6.1 FOR ANY INCIDENTAL, SPECIAL, OR CONSEQUENTIAL DAMAGES OR LOSS AS
-A RESULT OF MODIFYING, DISTRIBUTING, OR OTHERWISE USING PYTHON 1.6.1,
-OR ANY DERIVATIVE THEREOF, EVEN IF ADVISED OF THE POSSIBILITY THEREOF.
-
-6. This License Agreement will automatically terminate upon a material
-breach of its terms and conditions.
-
-7. This License Agreement shall be governed by the federal
-intellectual property law of the United States, including without
-limitation the federal copyright law, and, to the extent such
-U.S. federal law does not apply, by the law of the Commonwealth of
-Virginia, excluding Virginia's conflict of law provisions.
-Notwithstanding the foregoing, with regard to derivative works based
-on Python 1.6.1 that incorporate non-separable material that was
-previously distributed under the GNU General Public License (GPL), the
-law of the Commonwealth of Virginia shall govern this License
-Agreement only as to issues arising under or with respect to
-Paragraphs 4, 5, and 7 of this License Agreement.  Nothing in this
-License Agreement shall be deemed to create any relationship of
-agency, partnership, or joint venture between CNRI and Licensee.  This
-License Agreement does not grant permission to use CNRI trademarks or
-trade name in a trademark sense to endorse or promote products or
-services of Licensee, or any third party.
-
-8. By clicking on the "ACCEPT" button where indicated, or by copying,
-installing or otherwise using Python 1.6.1, Licensee agrees to be
-bound by the terms and conditions of this License Agreement.
-
-        ACCEPT
-
-
-CWI LICENSE AGREEMENT FOR PYTHON 0.9.0 THROUGH 1.2
---------------------------------------------------
-
-Copyright (c) 1991 - 1995, Stichting Mathematisch Centrum Amsterdam,
-The Netherlands.  All rights reserved.
-
-Permission to use, copy, modify, and distribute this software and its
-documentation for any purpose and without fee is hereby granted,
-provided that the above copyright notice appear in all copies and that
-both that copyright notice and this permission notice appear in
-supporting documentation, and that the name of Stichting Mathematisch
-Centrum or CWI not be used in advertising or publicity pertaining to
-distribution of the software without specific, written prior
-permission.
-
-STICHTING MATHEMATISCH CENTRUM DISCLAIMS ALL WARRANTIES WITH REGARD TO
-THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND
-FITNESS, IN NO EVENT SHALL STICHTING MATHEMATISCH CENTRUM BE LIABLE
-FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
-WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
-ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT
-OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.

lib/spack/external/_vendoring/typing_extensions.pyi

@@ -1 +0,0 @@
-from typing_extensions import *

lib/spack/external/vendor.txt

@@ -8,4 +8,3 @@ six==1.16.0
 macholib==1.16.2
   altgraph==0.17.3
 ruamel.yaml==0.17.21
-typing_extensions==4.1.1

lib/spack/llnl/__init__.py

@@ -1,3 +1,4 @@
-# Copyright Spack Project Developers. See COPYRIGHT file for details.
+# Copyright 2013-2024 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)

lib/spack/llnl/path.py

@@ -1,4 +1,5 @@
-# Copyright Spack Project Developers. See COPYRIGHT file for details.
+# Copyright 2013-2024 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)
 """Path primitives that just require Python standard library."""
@@ -65,7 +66,7 @@ def _is_url(path_or_url: str) -> bool:
     return result
 
 
-def _system_path_filter(_func=None, arg_slice: Optional[slice] = None):
+def system_path_filter(_func=None, arg_slice: Optional[slice] = None):
     """Filters function arguments to account for platform path separators.
     Optional slicing range can be specified to select specific arguments
 
@@ -99,16 +100,6 @@ def path_filter_caller(*args, **kwargs):
     return holder_func
 
 
-def _noop_decorator(_func=None, arg_slice: Optional[slice] = None):
-    return _func if _func else lambda x: x
-
-
-if sys.platform == "win32":
-    system_path_filter = _system_path_filter
-else:
-    system_path_filter = _noop_decorator
-
-
 def sanitize_win_longpath(path: str) -> str:
     """Strip Windows extended path prefix from strings
     Returns sanitized string.

lib/spack/llnl/string.py

@@ -1,4 +1,5 @@
-# Copyright Spack Project Developers. See COPYRIGHT file for details.
+# Copyright 2013-2024 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)
 """String manipulation functions that do not have other dependencies than Python

lib/spack/llnl/url.py

@@ -1,4 +1,5 @@
-# Copyright Spack Project Developers. See COPYRIGHT file for details.
+# Copyright 2013-2024 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)
 """URL primitives that just require Python standard library."""

lib/spack/llnl/util/__init__.py

@@ -1,3 +1,4 @@
-# Copyright Spack Project Developers. See COPYRIGHT file for details.
+# Copyright 2013-2024 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)

lib/spack/llnl/util/argparsewriter.py

@@ -1,4 +1,5 @@
-# Copyright Spack Project Developers. See COPYRIGHT file for details.
+# Copyright 2013-2024 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)
 

lib/spack/llnl/util/filesystem.py

@@ -1,4 +1,5 @@
-# Copyright Spack Project Developers. See COPYRIGHT file for details.
+# Copyright 2013-2024 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)
 import collections
@@ -23,7 +24,6 @@
     Callable,
     Deque,
     Dict,
-    Generator,
     Iterable,
     List,
     Match,
@@ -300,32 +300,35 @@ def filter_file(
     ignore_absent: bool = False,
     start_at: Optional[str] = None,
     stop_at: Optional[str] = None,
-    encoding: Optional[str] = "utf-8",
 ) -> None:
     r"""Like sed, but uses python regular expressions.
 
-    Filters every line of each file through regex and replaces the file with a filtered version.
-    Preserves mode of filtered files.
+    Filters every line of each file through regex and replaces the file
+    with a filtered version.  Preserves mode of filtered files.
 
-    As with re.sub, ``repl`` can be either a string or a callable. If it is a callable, it is
-    passed the match object and should return a suitable replacement string.  If it is a string, it
-    can contain ``\1``, ``\2``, etc. to represent back-substitution as sed would allow.
+    As with re.sub, ``repl`` can be either a string or a callable.
+    If it is a callable, it is passed the match object and should
+    return a suitable replacement string.  If it is a string, it
+    can contain ``\1``, ``\2``, etc. to represent back-substitution
+    as sed would allow.
 
     Args:
-        regex: The regular expression to search for
-        repl: The string to replace matches with
-        *filenames: One or more files to search and replace string: Treat regex as a plain string.
-            Default it False backup: Make backup file(s) suffixed with ``~``. Default is False
-        ignore_absent: Ignore any files that don't exist. Default is False
-        start_at: Marker used to start applying the replacements. If a text line matches this
-            marker filtering is started at the next line. All contents before the marker and the
-            marker itself are copied verbatim. Default is to start filtering from the first line of
-            the file.
-        stop_at: Marker used to stop scanning the file further. If a text line matches this marker
-            filtering is stopped and the rest of the file is copied verbatim. Default is to filter
-            until the end of the file.
-        encoding: The encoding to use when reading and writing the files. Default is None, which
-            uses the system's default encoding.
+        regex (str): The regular expression to search for
+        repl (str): The string to replace matches with
+        *filenames: One or more files to search and replace
+        string (bool): Treat regex as a plain string. Default it False
+        backup (bool): Make backup file(s) suffixed with ``~``. Default is False
+        ignore_absent (bool): Ignore any files that don't exist.
+            Default is False
+        start_at (str): Marker used to start applying the replacements. If a
+            text line matches this marker filtering is started at the next line.
+            All contents before the marker and the marker itself are copied
+            verbatim. Default is to start filtering from the first line of the
+            file.
+        stop_at (str): Marker used to stop scanning the file further. If a text
+            line matches this marker filtering is stopped and the rest of the
+            file is copied verbatim. Default is to filter until the end of the
+            file.
     """
     # Allow strings to use \1, \2, etc. for replacement, like sed
     if not callable(repl):
@@ -341,56 +344,72 @@ def groupid_to_group(x):
 
     if string:
         regex = re.escape(regex)
-    regex_compiled = re.compile(regex)
-    for path in path_to_os_path(*filenames):
-        if ignore_absent and not os.path.exists(path):
-            tty.debug(f'FILTER FILE: file "{path}" not found. Skipping to next file.')
+    for filename in path_to_os_path(*filenames):
+        msg = 'FILTER FILE: {0} [replacing "{1}"]'
+        tty.debug(msg.format(filename, regex))
+
+        backup_filename = filename + "~"
+        tmp_filename = filename + ".spack~"
+
+        if ignore_absent and not os.path.exists(filename):
+            msg = 'FILTER FILE: file "{0}" not found. Skipping to next file.'
+            tty.debug(msg.format(filename))
             continue
-        else:
-            tty.debug(f'FILTER FILE: {path} [replacing "{regex}"]')
 
-        fd, temp_path = tempfile.mkstemp(
-            prefix=f"{os.path.basename(path)}.", dir=os.path.dirname(path)
-        )
-        os.close(fd)
+        # Create backup file. Don't overwrite an existing backup
+        # file in case this file is being filtered multiple times.
+        if not os.path.exists(backup_filename):
+            shutil.copy(filename, backup_filename)
 
-        shutil.copy(path, temp_path)
-        errored = False
+        # Create a temporary file to read from. We cannot use backup_filename
+        # in case filter_file is invoked multiple times on the same file.
+        shutil.copy(filename, tmp_filename)
 
         try:
-            # Open as a text file and filter until the end of the file is reached, or we found a
-            # marker in the line if it was specified. To avoid translating line endings (\n to
-            # \r\n and vice-versa) use newline="".
-            with open(
-                temp_path, mode="r", errors="surrogateescape", newline="", encoding=encoding
-            ) as input_file, open(
-                path, mode="w", errors="surrogateescape", newline="", encoding=encoding
-            ) as output_file:
-                if start_at is None and stop_at is None:  # common case, avoids branching in loop
-                    for line in input_file:
-                        output_file.write(re.sub(regex_compiled, repl, line))
-                else:
-                    # state is -1 before start_at; 0 between; 1 after stop_at
-                    state = 0 if start_at is None else -1
-                    for line in input_file:
-                        if state == 0:
+            # Open as a text file and filter until the end of the file is
+            # reached, or we found a marker in the line if it was specified
+            #
+            # To avoid translating line endings (\n to \r\n and vice-versa)
+            # we force os.open to ignore translations and use the line endings
+            # the file comes with
+            with open(tmp_filename, mode="r", errors="surrogateescape", newline="") as input_file:
+                with open(filename, mode="w", errors="surrogateescape", newline="") as output_file:
+                    do_filtering = start_at is None
+                    # Using iter and readline is a workaround needed not to
+                    # disable input_file.tell(), which will happen if we call
+                    # input_file.next() implicitly via the for loop
+                    for line in iter(input_file.readline, ""):
+                        if stop_at is not None:
+                            current_position = input_file.tell()
                             if stop_at == line.strip():
-                                state = 1
-                            else:
-                                line = re.sub(regex_compiled, repl, line)
-                        elif state == -1 and start_at == line.strip():
-                            state = 0
-                        output_file.write(line)
+                                output_file.write(line)
+                                break
+                        if do_filtering:
+                            filtered_line = re.sub(regex, repl, line)
+                            output_file.write(filtered_line)
+                        else:
+                            do_filtering = start_at == line.strip()
+                            output_file.write(line)
+                    else:
+                        current_position = None
+
+            # If we stopped filtering at some point, reopen the file in
+            # binary mode and copy verbatim the remaining part
+            if current_position and stop_at:
+                with open(tmp_filename, mode="rb") as input_binary_buffer:
+                    input_binary_buffer.seek(current_position)
+                    with open(filename, mode="ab") as output_binary_buffer:
+                        output_binary_buffer.writelines(input_binary_buffer.readlines())
 
         except BaseException:
-            # restore the original file
-            os.rename(temp_path, path)
-            errored = True
+            # clean up the original file on failure.
+            shutil.move(backup_filename, filename)
             raise
 
         finally:
-            if not errored and not backup:
-                os.unlink(temp_path)
+            os.remove(tmp_filename)
+            if not backup and os.path.exists(backup_filename):
+                os.remove(backup_filename)
 
 
 class FileFilter:
@@ -1095,12 +1114,12 @@ def hash_directory(directory, ignore=[]):
 
 @contextmanager
 @system_path_filter
-def write_tmp_and_move(filename: str, *, encoding: Optional[str] = None):
+def write_tmp_and_move(filename):
     """Write to a temporary file, then move into place."""
     dirname = os.path.dirname(filename)
     basename = os.path.basename(filename)
     tmp = os.path.join(dirname, ".%s.tmp" % basename)
-    with open(tmp, "w", encoding=encoding) as f:
+    with open(tmp, "w") as f:
         yield f
     shutil.move(tmp, filename)
 
@@ -2753,6 +2772,22 @@ def prefixes(path):
     return paths
 
 
+@system_path_filter
+def md5sum(file):
+    """Compute the MD5 sum of a file.
+
+    Args:
+        file (str): file to be checksummed
+
+    Returns:
+        MD5 sum of the file's content
+    """
+    md5 = hashlib.md5()
+    with open(file, "rb") as f:
+        md5.update(f.read())
+    return md5.digest()
+
+
 @system_path_filter
 def remove_directory_contents(dir):
     """Remove all contents of a directory."""
@@ -2803,25 +2838,6 @@ def temporary_dir(
         remove_directory_contents(tmp_dir)
 
 
-@contextmanager
-def edit_in_place_through_temporary_file(file_path: str) -> Generator[str, None, None]:
-    """Context manager for modifying ``file_path`` in place, preserving its inode and hardlinks,
-    for functions or external tools that do not support in-place editing. Notice that this function
-    is unsafe in that it works with paths instead of a file descriptors, but this is by design,
-    since we assume the call site will create a new inode at the same path."""
-    tmp_fd, tmp_path = tempfile.mkstemp(
-        dir=os.path.dirname(file_path), prefix=f"{os.path.basename(file_path)}."
-    )
-    # windows cannot replace a file with open fds, so close since the call site needs to replace.
-    os.close(tmp_fd)
-    try:
-        shutil.copyfile(file_path, tmp_path, follow_symlinks=True)
-        yield tmp_path
-        shutil.copyfile(tmp_path, file_path, follow_symlinks=True)
-    finally:
-        os.unlink(tmp_path)
-
-
 def filesummary(path, print_bytes=16) -> Tuple[int, bytes]:
     """Create a small summary of the given file. Does not error
     when file does not exist.

lib/spack/llnl/util/lang.py

@@ -1,4 +1,5 @@
-# Copyright Spack Project Developers. See COPYRIGHT file for details.
+# Copyright 2013-2024 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)
 
@@ -862,10 +863,8 @@ def elide_list(line_list: List[str], max_num: int = 10) -> List[str]:
 
 if sys.version_info >= (3, 9):
     PatternStr = re.Pattern[str]
-    PatternBytes = re.Pattern[bytes]
 else:
     PatternStr = typing.Pattern[str]
-    PatternBytes = typing.Pattern[bytes]
 
 
 def fnmatch_translate_multiple(named_patterns: Dict[str, str]) -> str:

lib/spack/llnl/util/link_tree.py

@@ -1,4 +1,5 @@
-# Copyright Spack Project Developers. See COPYRIGHT file for details.
+# Copyright 2013-2024 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)
 

lib/spack/llnl/util/lock.py

@@ -1,4 +1,5 @@
-# Copyright Spack Project Developers. See COPYRIGHT file for details.
+# Copyright 2013-2024 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)
 
@@ -95,8 +96,8 @@ def get_fh(self, path: str) -> IO:
         Arguments:
           path: path to lock file we want a filehandle for
         """
-        # Open writable files as rb+ so we can upgrade to write later
-        os_mode, fh_mode = (os.O_RDWR | os.O_CREAT), "rb+"
+        # Open writable files as 'r+' so we can upgrade to write later
+        os_mode, fh_mode = (os.O_RDWR | os.O_CREAT), "r+"
 
         pid = os.getpid()
         open_file = None  # OpenFile object, if there is one
@@ -123,7 +124,7 @@ def get_fh(self, path: str) -> IO:
                 # we know path exists but not if it's writable. If it's read-only,
                 # only open the file for reading (and fail if we're trying to get
                 # an exclusive (write) lock on it)
-                os_mode, fh_mode = os.O_RDONLY, "rb"
+                os_mode, fh_mode = os.O_RDONLY, "r"
 
             fd = os.open(path, os_mode)
             fh = os.fdopen(fd, fh_mode)
@@ -242,7 +243,7 @@ def __init__(
                 helpful for distinguishing between different Spack locks.
         """
         self.path = path
-        self._file: Optional[IO[bytes]] = None
+        self._file: Optional[IO] = None
         self._reads = 0
         self._writes = 0
 
@@ -328,9 +329,9 @@ def _lock(self, op: int, timeout: Optional[float] = None) -> Tuple[float, int]:
             self._ensure_parent_directory()
             self._file = FILE_TRACKER.get_fh(self.path)
 
-        if LockType.to_module(op) == fcntl.LOCK_EX and self._file.mode == "rb":
+        if LockType.to_module(op) == fcntl.LOCK_EX and self._file.mode == "r":
             # Attempt to upgrade to write lock w/a read-only file.
-            # If the file were writable, we'd have opened it rb+
+            # If the file were writable, we'd have opened it 'r+'
             raise LockROFileError(self.path)
 
         self._log_debug(
@@ -425,7 +426,7 @@ def _read_log_debug_data(self) -> None:
 
         line = self._file.read()
         if line:
-            pid, host = line.decode("utf-8").strip().split(",")
+            pid, host = line.strip().split(",")
             _, _, pid = pid.rpartition("=")
             _, _, self.host = host.rpartition("=")
             self.pid = int(pid)
@@ -441,7 +442,7 @@ def _write_log_debug_data(self) -> None:
 
         # write pid, host to disk to sync over FS
         self._file.seek(0)
-        self._file.write(f"pid={self.pid},host={self.host}".encode("utf-8"))
+        self._file.write("pid=%s,host=%s" % (self.pid, self.host))
         self._file.truncate()
         self._file.flush()
         os.fsync(self._file.fileno())

lib/spack/llnl/util/multiproc.py

@@ -1,4 +1,5 @@
-# Copyright Spack Project Developers. See COPYRIGHT file for details.
+# Copyright 2013-2024 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)
 

lib/spack/llnl/util/symlink.py

@@ -1,4 +1,5 @@
-# Copyright Spack Project Developers. See COPYRIGHT file for details.
+# Copyright 2013-2024 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)
 import os

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

@@ -1,4 +1,5 @@
-# Copyright Spack Project Developers. See COPYRIGHT file for details.
+# Copyright 2013-2024 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)
 

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

@@ -1,4 +1,5 @@
-# Copyright Spack Project Developers. See COPYRIGHT file for details.
+# Copyright 2013-2024 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)
 

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

@@ -1,4 +1,5 @@
-# Copyright Spack Project Developers. See COPYRIGHT file for details.
+# Copyright 2013-2024 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)
 
@@ -160,7 +161,7 @@ def _err_check(result, func, args):
             )
             # Use conout$ here to handle a redirectired stdout/get active console associated
             # with spack
-            with open(r"\\.\CONOUT$", "w", encoding="utf-8") as conout:
+            with open(r"\\.\CONOUT$", "w") as conout:
                 # Link above would use kernel32.GetStdHandle(-11) however this would not handle
                 # a redirected stdout appropriately, so we always refer to the current CONSOLE out
                 # which is defined as conout$ on Windows.

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

@@ -1,4 +1,5 @@
-# Copyright Spack Project Developers. See COPYRIGHT file for details.
+# Copyright 2013-2024 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)
 
@@ -761,7 +762,7 @@ def __enter__(self):
             self.reader = open(self.logfile, mode="rb+")
 
             # Dup stdout so we can still write to it after redirection
-            self.echo_writer = open(os.dup(sys.stdout.fileno()), "w", encoding=sys.stdout.encoding)
+            self.echo_writer = open(os.dup(sys.stdout.fileno()), "w")
             # Redirect stdout and stderr to write to logfile
             self.stderr.redirect_stream(self.writer.fileno())
             self.stdout.redirect_stream(self.writer.fileno())
@@ -878,13 +879,10 @@ def _writer_daemon(
     write_fd.close()
 
     # 1. Use line buffering (3rd param = 1) since Python 3 has a bug
-    #    that prevents unbuffered text I/O. [needs citation]
-    # 2. Enforce a UTF-8 interpretation of build process output with errors replaced by '?'.
-    #    The downside is that the log file will not contain the exact output of the build process.
+    # that prevents unbuffered text I/O.
+    # 2. Python 3.x before 3.7 does not open with UTF-8 encoding by default
     # 3. closefd=False because Connection has "ownership"
-    read_file = os.fdopen(
-        read_fd.fileno(), "r", 1, encoding="utf-8", errors="replace", closefd=False
-    )
+    read_file = os.fdopen(read_fd.fileno(), "r", 1, encoding="utf-8", closefd=False)
 
     if stdin_fd:
         stdin_file = os.fdopen(stdin_fd.fileno(), closefd=False)
@@ -930,7 +928,11 @@ def _writer_daemon(
                     try:
                         while line_count < 100:
                             # Handle output from the calling process.
-                            line = _retry(read_file.readline)()
+                            try:
+                                line = _retry(read_file.readline)()
+                            except UnicodeDecodeError:
+                                # installs like --test=root gpgme produce non-UTF8 logs
+                                line = "<line lost: output was not encoded as UTF-8>\n"
 
                             if not line:
                                 return
@@ -944,13 +946,6 @@ def _writer_daemon(
                                 output_line = clean_line
                                 if filter_fn:
                                     output_line = filter_fn(clean_line)
-                                enc = sys.stdout.encoding
-                                if enc != "utf-8":
-                                    # On Python 3.6 and 3.7-3.14 with non-{utf-8,C} locale stdout
-                                    # may not be able to handle utf-8 output. We do an inefficient
-                                    # dance of re-encoding with errors replaced, so stdout.write
-                                    # does not raise.
-                                    output_line = output_line.encode(enc, "replace").decode(enc)
                                 sys.stdout.write(output_line)
 
                             # Stripped output to log file.

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

@@ -1,4 +1,5 @@
-# Copyright Spack Project Developers. See COPYRIGHT file for details.
+# Copyright 2013-2024 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)
 

lib/spack/spack/__init__.py

@@ -1,4 +1,5 @@
-# Copyright Spack Project Developers. See COPYRIGHT file for details.
+# Copyright 2013-2024 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)
 

lib/spack/spack/audit.py

@@ -1,4 +1,5 @@
-# Copyright Spack Project Developers. See COPYRIGHT file for details.
+# Copyright 2013-2024 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)
 """Classes and functions to register audit checks for various parts of
@@ -655,7 +656,7 @@ def _ensure_docstring_and_no_fixme(pkgs, error_cls):
     for pkg_name in pkgs:
         details = []
         filename = spack.repo.PATH.filename_for_package_name(pkg_name)
-        with open(filename, "r", encoding="utf-8") as package_file:
+        with open(filename, "r") as package_file:
             for i, line in enumerate(package_file):
                 pattern = next((r for r in fixme_regexes if r.search(line)), None)
                 if pattern:
@@ -692,19 +693,19 @@ def invalid_sha256_digest(fetcher):
                     return h, True
             return None, False
 
-        error_msg = f"Package '{pkg_name}' does not use sha256 checksum"
+        error_msg = "Package '{}' does not use sha256 checksum".format(pkg_name)
         details = []
         for v, args in pkg.versions.items():
             fetcher = spack.fetch_strategy.for_package_version(pkg, v)
             digest, is_bad = invalid_sha256_digest(fetcher)
             if is_bad:
-                details.append(f"{pkg_name}@{v} uses {digest}")
+                details.append("{}@{} uses {}".format(pkg_name, v, digest))
 
         for _, resources in pkg.resources.items():
             for resource in resources:
                 digest, is_bad = invalid_sha256_digest(resource.fetcher)
                 if is_bad:
-                    details.append(f"Resource in '{pkg_name}' uses {digest}")
+                    details.append("Resource in '{}' uses {}".format(pkg_name, digest))
         if details:
             errors.append(error_cls(error_msg, details))
 
@@ -808,7 +809,7 @@ def _uses_deprecated_globals(pkgs, error_cls):
             continue
 
         file = spack.repo.PATH.filename_for_package_name(pkg_name)
-        tree = ast.parse(open(file, "rb").read())
+        tree = ast.parse(open(file).read())
         visitor = DeprecatedMagicGlobals(("std_cmake_args", "std_meson_args", "std_pip_args"))
         visitor.visit(tree)
         if visitor.references_to_globals:
@@ -1008,6 +1009,20 @@ def _issues_in_depends_on_directive(pkgs, error_cls):
 
         for when, deps_by_name in pkg_cls.dependencies.items():
             for dep_name, dep in deps_by_name.items():
+                # Check if there are nested dependencies declared. We don't want directives like:
+                #
+                #     depends_on('foo+bar ^fee+baz')
+                #
+                # but we'd like to have two dependencies listed instead.
+                nested_dependencies = dep.spec.dependencies()
+                if nested_dependencies:
+                    summary = f"{pkg_name}: nested dependency declaration '{dep.spec}'"
+                    ndir = len(nested_dependencies) + 1
+                    details = [
+                        f"split depends_on('{dep.spec}', when='{when}') into {ndir} directives",
+                        f"in {filename}",
+                    ]
+                    errors.append(error_cls(summary=summary, details=details))
 
                 def check_virtual_with_variants(spec, msg):
                     if not spec.virtual or not spec.variants:

lib/spack/spack/binary_distribution.py

@@ -1,4 +1,5 @@
-# Copyright Spack Project Developers. See COPYRIGHT file for details.
+# Copyright 2013-2024 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)
 
@@ -23,12 +24,13 @@
 import urllib.request
 import warnings
 from contextlib import closing
-from typing import IO, Dict, Iterable, List, NamedTuple, Optional, Set, Tuple, Union
+from typing import Dict, Iterable, List, NamedTuple, Optional, Set, Tuple, Union
 
 import llnl.util.filesystem as fsys
 import llnl.util.lang
 import llnl.util.tty as tty
-from llnl.util.filesystem import mkdirp
+from llnl.util.filesystem import BaseDirectoryVisitor, mkdirp, visit_directory_tree
+from llnl.util.symlink import readlink
 
 import spack.caches
 import spack.config as config
@@ -38,7 +40,7 @@
 import spack.hash_types as ht
 import spack.hooks
 import spack.hooks.sbang
-import spack.mirrors.mirror
+import spack.mirror
 import spack.oci.image
 import spack.oci.oci
 import spack.oci.opener
@@ -52,6 +54,7 @@
 import spack.util.archive
 import spack.util.crypto
 import spack.util.file_cache as file_cache
+import spack.util.filesystem as ssys
 import spack.util.gpg
 import spack.util.parallel
 import spack.util.path
@@ -66,8 +69,10 @@
     Digest,
     ImageReference,
     default_config,
+    default_index_tag,
     default_manifest,
-    ensure_valid_tag,
+    default_tag,
+    tag_is_spec,
 )
 from spack.oci.oci import (
     copy_missing_layers_with_retry,
@@ -78,6 +83,7 @@
 )
 from spack.package_prefs import get_package_dir_permissions, get_package_group
 from spack.relocate_text import utf8_paths_to_single_binary_regex
+from spack.spec import Spec
 from spack.stage import Stage
 from spack.util.executable import which
 
@@ -363,7 +369,7 @@ def update(self, with_cooldown=False):
         on disk under ``_index_cache_root``)."""
         self._init_local_index_cache()
         configured_mirror_urls = [
-            m.fetch_url for m in spack.mirrors.mirror.MirrorCollection(binary=True).values()
+            m.fetch_url for m in spack.mirror.MirrorCollection(binary=True).values()
         ]
         items_to_remove = []
         spec_cache_clear_needed = False
@@ -580,43 +586,177 @@ def buildinfo_file_name(prefix):
 
 def read_buildinfo_file(prefix):
     """Read buildinfo file"""
-    with open(buildinfo_file_name(prefix), "r", encoding="utf-8") as f:
+    with open(buildinfo_file_name(prefix), "r") as f:
         return syaml.load(f)
 
 
-def file_matches(f: IO[bytes], regex: llnl.util.lang.PatternBytes) -> bool:
-    try:
-        return bool(regex.search(f.read()))
-    finally:
-        f.seek(0)
+class BuildManifestVisitor(BaseDirectoryVisitor):
+    """Visitor that collects a list of files and symlinks
+    that can be checked for need of relocation. It knows how
+    to dedupe hardlinks and deal with symlinks to files and
+    directories."""
+
+    def __init__(self):
+        # Save unique identifiers of hardlinks to avoid relocating them multiple times
+        self.visited = set()
+
+        # Lists of files we will check
+        self.files = []
+        self.symlinks = []
+
+    def seen_before(self, root, rel_path):
+        stat_result = os.lstat(os.path.join(root, rel_path))
+        if stat_result.st_nlink == 1:
+            return False
+        identifier = (stat_result.st_dev, stat_result.st_ino)
+        if identifier in self.visited:
+            return True
+        else:
+            self.visited.add(identifier)
+            return False
+
+    def visit_file(self, root, rel_path, depth):
+        if self.seen_before(root, rel_path):
+            return
+        self.files.append(rel_path)
+
+    def visit_symlinked_file(self, root, rel_path, depth):
+        # Note: symlinks *can* be hardlinked, but it is unclear if
+        # symlinks can be relinked in-place (preserving inode).
+        # Therefore, we do *not* de-dupe hardlinked symlinks.
+        self.symlinks.append(rel_path)
+
+    def before_visit_dir(self, root, rel_path, depth):
+        return os.path.basename(rel_path) not in (".spack", "man")
+
+    def before_visit_symlinked_dir(self, root, rel_path, depth):
+        # Treat symlinked directories simply as symlinks.
+        self.visit_symlinked_file(root, rel_path, depth)
+        # Never recurse into symlinked directories.
+        return False
 
 
-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 = [
+def file_matches(path, regex):
+    with open(path, "rb") as f:
+        contents = f.read()
+    return bool(regex.search(contents))
+
+
+def get_buildfile_manifest(spec):
+    """
+    Return a data structure with information about a build, including
+    text_to_relocate, binary_to_relocate, binary_to_relocate_fullpath
+    link_to_relocate, and other, which means it doesn't fit any of previous
+    checks (and should not be relocated). We exclude docs (man) and
+    metadata (.spack). This can be used to find a particular kind of file
+    in spack, or to generate the build metadata.
+    """
+    data = {
+        "text_to_relocate": [],
+        "binary_to_relocate": [],
+        "link_to_relocate": [],
+        "other": [],
+        "binary_to_relocate_fullpath": [],
+        "hardlinks_deduped": True,
+    }
+
+    # Guard against filesystem footguns of hardlinks and symlinks by using
+    # a visitor to retrieve a list of files and symlinks, so we don't have
+    # to worry about hardlinks of symlinked dirs and what not.
+    visitor = BuildManifestVisitor()
+    root = spec.prefix
+    visit_directory_tree(root, visitor)
+
+    # Collect a list of prefixes for this package and it's dependencies, Spack will
+    # look for them to decide if text file needs to be relocated or not
+    prefixes = [d.prefix for d in spec.traverse(root=True, deptype="all") if not d.external]
+    prefixes.append(spack.hooks.sbang.sbang_install_path())
+    prefixes.append(str(spack.store.STORE.layout.root))
+
+    # Create a giant regex that matches all prefixes
+    regex = utf8_paths_to_single_binary_regex(prefixes)
+
+    # Symlinks.
+
+    # Obvious bugs:
+    #   1. relative links are not relocated.
+    #   2. paths are used as strings.
+    for rel_path in visitor.symlinks:
+        abs_path = os.path.join(root, rel_path)
+        link = readlink(abs_path)
+        if os.path.isabs(link) and link.startswith(spack.store.STORE.layout.root):
+            data["link_to_relocate"].append(rel_path)
+
+    # Non-symlinks.
+    for rel_path in visitor.files:
+        abs_path = os.path.join(root, rel_path)
+        m_type, m_subtype = ssys.mime_type(abs_path)
+
+        if relocate.needs_binary_relocation(m_type, m_subtype):
+            # Why is this branch not part of needs_binary_relocation? :(
+            if (
+                (
+                    m_subtype in ("x-executable", "x-sharedlib", "x-pie-executable")
+                    and sys.platform != "darwin"
+                )
+                or (m_subtype in ("x-mach-binary") and sys.platform == "darwin")
+                or (not rel_path.endswith(".o"))
+            ):
+                data["binary_to_relocate"].append(rel_path)
+                data["binary_to_relocate_fullpath"].append(abs_path)
+                continue
+
+        elif relocate.needs_text_relocation(m_type, m_subtype) and file_matches(abs_path, regex):
+            data["text_to_relocate"].append(rel_path)
+            continue
+
+        data["other"].append(abs_path)
+
+    return data
+
+
+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 = [
         s
         for s in itertools.chain(
-            spec.traverse(root=True, deptype="link", order="breadth", key=traverse.by_dag_hash),
-            spec.dependencies(deptype="run"),
+            spec.traverse(root=True, deptype="link"), spec.dependencies(deptype="run")
         )
         if not s.external
     ]
-    return list(llnl.util.lang.dedupe(specs, key=lambda s: s.dag_hash()))
+    return llnl.util.lang.dedupe(deps, key=lambda s: s.dag_hash())
 
 
 def get_buildinfo_dict(spec):
     """Create metadata for a tarball"""
+    manifest = get_buildfile_manifest(spec)
+
     return {
         "sbang_install_path": spack.hooks.sbang.sbang_install_path(),
         "buildpath": spack.store.STORE.layout.root,
         "spackprefix": spack.paths.prefix,
         "relative_prefix": os.path.relpath(spec.prefix, spack.store.STORE.layout.root),
-        # "relocate_textfiles": [],
-        # "relocate_binaries": [],
-        # "relocate_links": [],
-        "hardlinks_deduped": True,
-        "hash_to_prefix": {d.dag_hash(): str(d.prefix) for d in specs_to_relocate(spec)},
+        "relocate_textfiles": manifest["text_to_relocate"],
+        "relocate_binaries": manifest["binary_to_relocate"],
+        "relocate_links": manifest["link_to_relocate"],
+        "hardlinks_deduped": manifest["hardlinks_deduped"],
+        "hash_to_prefix": {d.dag_hash(): str(d.prefix) for d in deps_to_relocate(spec)},
     }
 
 
@@ -687,10 +827,10 @@ def _read_specs_and_push_index(
         contents = read_method(file)
         # Need full spec.json name or this gets confused with index.json.
         if file.endswith(".json.sig"):
-            specfile_json = spack.spec.Spec.extract_json_from_clearsig(contents)
-            fetched_spec = spack.spec.Spec.from_dict(specfile_json)
+            specfile_json = Spec.extract_json_from_clearsig(contents)
+            fetched_spec = Spec.from_dict(specfile_json)
         elif file.endswith(".json"):
-            fetched_spec = spack.spec.Spec.from_json(contents)
+            fetched_spec = Spec.from_json(contents)
         else:
             continue
 
@@ -700,17 +840,17 @@ def _read_specs_and_push_index(
     # Now generate the index, compute its hash, and push the two files to
     # the mirror.
     index_json_path = os.path.join(temp_dir, "index.json")
-    with open(index_json_path, "w", encoding="utf-8") as f:
+    with open(index_json_path, "w") as f:
         db._write_to_file(f)
 
     # Read the index back in and compute its hash
-    with open(index_json_path, encoding="utf-8") as f:
+    with open(index_json_path) as f:
         index_string = f.read()
         index_hash = compute_hash(index_string)
 
     # Write the hash out to a local file
     index_hash_path = os.path.join(temp_dir, "index.json.hash")
-    with open(index_hash_path, "w", encoding="utf-8") as f:
+    with open(index_hash_path, "w") as f:
         f.write(index_hash)
 
     # Push the index itself
@@ -744,7 +884,7 @@ def _specs_from_cache_aws_cli(cache_prefix):
     aws = which("aws")
 
     def file_read_method(file_path):
-        with open(file_path, encoding="utf-8") as fd:
+        with open(file_path) as fd:
             return fd.read()
 
     tmpspecsdir = tempfile.mkdtemp()
@@ -889,7 +1029,7 @@ def generate_key_index(key_prefix: str, tmpdir: str) -> None:
     target = os.path.join(tmpdir, "index.json")
 
     index = {"keys": dict((fingerprint, {}) for fingerprint in sorted(set(fingerprints)))}
-    with open(target, "w", encoding="utf-8") as f:
+    with open(target, "w") as f:
         sjson.dump(index, f)
 
     try:
@@ -905,55 +1045,7 @@ def generate_key_index(key_prefix: str, tmpdir: str) -> None:
         ) from e
 
 
-class FileTypes:
-    BINARY = 0
-    TEXT = 1
-    UNKNOWN = 2
-
-
-NOT_ISO8859_1_TEXT = re.compile(b"[\x00\x7F-\x9F]")
-
-
-def file_type(f: IO[bytes]) -> int:
-    try:
-        # first check if this is an ELF or mach-o binary.
-        magic = f.read(8)
-        if len(magic) < 8:
-            return FileTypes.UNKNOWN
-        elif relocate.is_elf_magic(magic) or relocate.is_macho_magic(magic):
-            return FileTypes.BINARY
-
-        f.seek(0)
-
-        # Then try utf-8, which has a fast exponential decay in false positive rate with file size.
-        # Use chunked reads for fast early exit.
-        f_txt = io.TextIOWrapper(f, encoding="utf-8", errors="strict")
-        try:
-            while f_txt.read(1024):
-                pass
-            return FileTypes.TEXT
-        except UnicodeError:
-            f_txt.seek(0)
-            pass
-        finally:
-            f_txt.detach()
-        # Finally try iso-8859-1 heuristically. In Python, all possible 256 byte values are valid.
-        # We classify it as text if it does not contain any control characters / null bytes.
-        data = f.read(1024)
-        while data:
-            if NOT_ISO8859_1_TEXT.search(data):
-                break
-            data = f.read(1024)
-        else:
-            return FileTypes.TEXT
-        return FileTypes.UNKNOWN
-    finally:
-        f.seek(0)
-
-
-def tarfile_of_spec_prefix(
-    tar: tarfile.TarFile, prefix: str, prefixes_to_relocate: List[str]
-) -> dict:
+def tarfile_of_spec_prefix(tar: tarfile.TarFile, prefix: str) -> None:
     """Create a tarfile of an install prefix of a spec. Skips existing buildinfo file.
 
     Args:
@@ -969,33 +1061,6 @@ def tarfile_of_spec_prefix(
     except OSError:
         skip = lambda entry: False
 
-    binary_regex = utf8_paths_to_single_binary_regex(prefixes_to_relocate)
-
-    relocate_binaries = []
-    relocate_links = []
-    relocate_textfiles = []
-
-    # use callbacks to add files and symlinks, so we can register which files need relocation upon
-    # extraction.
-    def add_file(tar: tarfile.TarFile, info: tarfile.TarInfo, path: str):
-        with open(path, "rb") as f:
-            relpath = os.path.relpath(path, prefix)
-            # no need to relocate anything in the .spack directory
-            if relpath.split(os.sep, 1)[0] == ".spack":
-                tar.addfile(info, f)
-                return
-            f_type = file_type(f)
-            if f_type == FileTypes.BINARY:
-                relocate_binaries.append(os.path.relpath(path, prefix))
-            elif f_type == FileTypes.TEXT and file_matches(f, binary_regex):
-                relocate_textfiles.append(os.path.relpath(path, prefix))
-            tar.addfile(info, f)
-
-    def add_symlink(tar: tarfile.TarFile, info: tarfile.TarInfo, path: str):
-        if os.path.isabs(info.linkname) and binary_regex.match(info.linkname.encode("utf-8")):
-            relocate_links.append(os.path.relpath(path, prefix))
-        tar.addfile(info)
-
     spack.util.archive.reproducible_tarfile_from_prefix(
         tar,
         prefix,
@@ -1003,51 +1068,29 @@ def add_symlink(tar: tarfile.TarFile, info: tarfile.TarInfo, path: str):
         # used in runtimes like AWS lambda.
         include_parent_directories=True,
         skip=skip,
-        add_file=add_file,
-        add_symlink=add_symlink,
-    )
-
-    return {
-        "relocate_binaries": relocate_binaries,
-        "relocate_links": relocate_links,
-        "relocate_textfiles": relocate_textfiles,
-    }
-
-
-def create_tarball(spec: spack.spec.Spec, tarfile_path: str) -> Tuple[str, str]:
-    """Create a tarball of a spec and return the checksums of the compressed tarfile and the
-    uncompressed tarfile."""
-    return _do_create_tarball(
-        tarfile_path,
-        spec.prefix,
-        buildinfo=get_buildinfo_dict(spec),
-        prefixes_to_relocate=prefixes_to_relocate(spec),
     )
 
 
-def _do_create_tarball(
-    tarfile_path: str, prefix: str, buildinfo: dict, prefixes_to_relocate: List[str]
-) -> Tuple[str, str]:
+def _do_create_tarball(tarfile_path: str, binaries_dir: str, buildinfo: dict):
     with spack.util.archive.gzip_compressed_tarfile(tarfile_path) as (
         tar,
-        tar_gz_checksum,
-        tar_checksum,
+        inner_checksum,
+        outer_checksum,
     ):
         # Tarball the install prefix
-        files_to_relocate = tarfile_of_spec_prefix(tar, prefix, prefixes_to_relocate)
-        buildinfo.update(files_to_relocate)
+        tarfile_of_spec_prefix(tar, binaries_dir)
 
         # Serialize buildinfo for the tarball
         bstring = syaml.dump(buildinfo, default_flow_style=True).encode("utf-8")
         tarinfo = tarfile.TarInfo(
-            name=spack.util.archive.default_path_to_name(buildinfo_file_name(prefix))
+            name=spack.util.archive.default_path_to_name(buildinfo_file_name(binaries_dir))
         )
         tarinfo.type = tarfile.REGTYPE
         tarinfo.size = len(bstring)
         tarinfo.mode = 0o644
         tar.addfile(tarinfo, io.BytesIO(bstring))
 
-    return tar_gz_checksum.hexdigest(), tar_checksum.hexdigest()
+    return inner_checksum.hexdigest(), outer_checksum.hexdigest()
 
 
 class ExistsInBuildcache(NamedTuple):
@@ -1057,7 +1100,7 @@ class ExistsInBuildcache(NamedTuple):
 
 
 class BuildcacheFiles:
-    def __init__(self, spec: spack.spec.Spec, local: str, remote: str):
+    def __init__(self, spec: Spec, local: str, remote: str):
         """
         Args:
             spec: The spec whose tarball and specfile are being managed.
@@ -1087,7 +1130,7 @@ def local_tarball(self) -> str:
         return os.path.join(self.local, f"{self.spec.dag_hash()}.tar.gz")
 
 
-def _exists_in_buildcache(spec: spack.spec.Spec, tmpdir: str, out_url: str) -> ExistsInBuildcache:
+def _exists_in_buildcache(spec: Spec, tmpdir: str, out_url: str) -> ExistsInBuildcache:
     """returns a tuple of bools (signed, unsigned, tarball) indicating whether specfiles/tarballs
     exist in the buildcache"""
     files = BuildcacheFiles(spec, tmpdir, out_url)
@@ -1097,23 +1140,12 @@ def _exists_in_buildcache(spec: spack.spec.Spec, tmpdir: str, out_url: str) -> E
     return ExistsInBuildcache(signed, unsigned, tarball)
 
 
-def prefixes_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
-
-
 def _url_upload_tarball_and_specfile(
-    spec: spack.spec.Spec,
-    tmpdir: str,
-    out_url: str,
-    exists: ExistsInBuildcache,
-    signing_key: Optional[str],
+    spec: Spec, tmpdir: str, out_url: str, exists: ExistsInBuildcache, signing_key: Optional[str]
 ):
     files = BuildcacheFiles(spec, tmpdir, out_url)
     tarball = files.local_tarball()
-    checksum, _ = create_tarball(spec, tarball)
+    checksum, _ = _do_create_tarball(tarball, spec.prefix, get_buildinfo_dict(spec))
     spec_dict = spec.to_dict(hash=ht.dag_hash)
     spec_dict["buildcache_layout_version"] = CURRENT_BUILD_CACHE_LAYOUT_VERSION
     spec_dict["binary_cache_checksum"] = {"hash_algorithm": "sha256", "hash": checksum}
@@ -1127,7 +1159,7 @@ def _url_upload_tarball_and_specfile(
     web_util.push_to_url(tarball, files.remote_tarball(), keep_original=False)
 
     specfile = files.local_specfile()
-    with open(specfile, "w", encoding="utf-8") as f:
+    with open(specfile, "w") as f:
         # Note: when using gpg clear sign, we need to avoid long lines (19995 chars).
         # If lines are longer, they are truncated without error. Thanks GPG!
         # So, here we still add newlines, but no indent, so save on file size and
@@ -1144,7 +1176,7 @@ def _url_upload_tarball_and_specfile(
 
 
 class Uploader:
-    def __init__(self, mirror: spack.mirrors.mirror.Mirror, force: bool, update_index: bool):
+    def __init__(self, mirror: spack.mirror.Mirror, force: bool, update_index: bool):
         self.mirror = mirror
         self.force = force
         self.update_index = update_index
@@ -1192,7 +1224,7 @@ def tag(self, tag: str, roots: List[spack.spec.Spec]):
 class OCIUploader(Uploader):
     def __init__(
         self,
-        mirror: spack.mirrors.mirror.Mirror,
+        mirror: spack.mirror.Mirror,
         force: bool,
         update_index: bool,
         base_image: Optional[str],
@@ -1241,7 +1273,7 @@ def tag(self, tag: str, roots: List[spack.spec.Spec]):
 class URLUploader(Uploader):
     def __init__(
         self,
-        mirror: spack.mirrors.mirror.Mirror,
+        mirror: spack.mirror.Mirror,
         force: bool,
         update_index: bool,
         signing_key: Optional[str],
@@ -1265,7 +1297,7 @@ def push(
 
 
 def make_uploader(
-    mirror: spack.mirrors.mirror.Mirror,
+    mirror: spack.mirror.Mirror,
     force: bool = False,
     update_index: bool = False,
     signing_key: Optional[str] = None,
@@ -1282,7 +1314,7 @@ def make_uploader(
         )
 
 
-def _format_spec(spec: spack.spec.Spec) -> str:
+def _format_spec(spec: Spec) -> str:
     return spec.cformat("{name}{@version}{/hash:7}")
 
 
@@ -1305,7 +1337,7 @@ def _progress(self):
             return f"[{self.n:{digits}}/{self.total}] "
         return ""
 
-    def start(self, spec: spack.spec.Spec, running: bool) -> None:
+    def start(self, spec: Spec, running: bool) -> None:
         self.n += 1
         self.running = running
         self.pre = self._progress()
@@ -1324,18 +1356,18 @@ def fail(self) -> None:
 
 
 def _url_push(
-    specs: List[spack.spec.Spec],
+    specs: List[Spec],
     out_url: str,
     signing_key: Optional[str],
     force: bool,
     update_index: bool,
     tmpdir: str,
     executor: concurrent.futures.Executor,
-) -> Tuple[List[spack.spec.Spec], List[Tuple[spack.spec.Spec, BaseException]]]:
+) -> Tuple[List[Spec], List[Tuple[Spec, BaseException]]]:
     """Pushes to the provided build cache, and returns a list of skipped specs that were already
     present (when force=False), and a list of errors. Does not raise on error."""
-    skipped: List[spack.spec.Spec] = []
-    errors: List[Tuple[spack.spec.Spec, BaseException]] = []
+    skipped: List[Spec] = []
+    errors: List[Tuple[Spec, BaseException]] = []
 
     exists_futures = [
         executor.submit(_exists_in_buildcache, spec, tmpdir, out_url) for spec in specs
@@ -1408,7 +1440,7 @@ def _url_push(
     return skipped, errors
 
 
-def _oci_upload_success_msg(spec: spack.spec.Spec, digest: Digest, size: int, elapsed: float):
+def _oci_upload_success_msg(spec: Spec, digest: Digest, size: int, elapsed: float):
     elapsed = max(elapsed, 0.001)  # guard against division by zero
     return (
         f"Pushed {_format_spec(spec)}: {digest} ({elapsed:.2f}s, "
@@ -1437,11 +1469,13 @@ def _oci_push_pkg_blob(
     filename = os.path.join(tmpdir, f"{spec.dag_hash()}.tar.gz")
 
     # Create an oci.image.layer aka tarball of the package
-    tar_gz_checksum, tar_checksum = create_tarball(spec, filename)
+    compressed_tarfile_checksum, tarfile_checksum = _do_create_tarball(
+        filename, spec.prefix, get_buildinfo_dict(spec)
+    )
 
     blob = spack.oci.oci.Blob(
-        Digest.from_sha256(tar_gz_checksum),
-        Digest.from_sha256(tar_checksum),
+        Digest.from_sha256(compressed_tarfile_checksum),
+        Digest.from_sha256(tarfile_checksum),
         os.path.getsize(filename),
     )
 
@@ -1492,7 +1526,7 @@ def _oci_put_manifest(
 ):
     architecture = _oci_archspec_to_gooarch(specs[0])
 
-    expected_blobs: List[spack.spec.Spec] = [
+    expected_blobs: List[Spec] = [
         s
         for s in traverse.traverse_nodes(specs, order="topo", deptype=("link", "run"), root=True)
         if not s.external
@@ -1536,7 +1570,7 @@ def _oci_put_manifest(
 
     config_file = os.path.join(tmpdir, f"{specs[0].dag_hash()}.config.json")
 
-    with open(config_file, "w", encoding="utf-8") as f:
+    with open(config_file, "w") as f:
         json.dump(config, f, separators=(",", ":"))
 
     config_file_checksum = Digest.from_sha256(
@@ -1606,33 +1640,19 @@ def _oci_update_base_images(
         )
 
 
-def _oci_default_tag(spec: spack.spec.Spec) -> str:
-    """Return a valid, default image tag for a spec."""
-    return ensure_valid_tag(f"{spec.name}-{spec.version}-{spec.dag_hash()}.spack")
-
-
-#: Default OCI index tag
-default_index_tag = "index.spack"
-
-
-def tag_is_spec(tag: str) -> bool:
-    """Check if a tag is likely a Spec"""
-    return tag.endswith(".spack") and tag != default_index_tag
-
-
 def _oci_push(
     *,
     target_image: ImageReference,
     base_image: Optional[ImageReference],
-    installed_specs_with_deps: List[spack.spec.Spec],
+    installed_specs_with_deps: List[Spec],
     tmpdir: str,
     executor: concurrent.futures.Executor,
     force: bool = False,
 ) -> Tuple[
-    List[spack.spec.Spec],
+    List[Spec],
     Dict[str, Tuple[dict, dict]],
     Dict[str, spack.oci.oci.Blob],
-    List[Tuple[spack.spec.Spec, BaseException]],
+    List[Tuple[Spec, BaseException]],
 ]:
     # Spec dag hash -> blob
     checksums: Dict[str, spack.oci.oci.Blob] = {}
@@ -1641,15 +1661,13 @@ def _oci_push(
     base_images: Dict[str, Tuple[dict, dict]] = {}
 
     # Specs not uploaded because they already exist
-    skipped: List[spack.spec.Spec] = []
+    skipped: List[Spec] = []
 
     if not force:
         tty.info("Checking for existing specs in the buildcache")
         blobs_to_upload = []
 
-        tags_to_check = (
-            target_image.with_tag(_oci_default_tag(s)) for s in installed_specs_with_deps
-        )
+        tags_to_check = (target_image.with_tag(default_tag(s)) for s in installed_specs_with_deps)
         available_blobs = executor.map(_oci_get_blob_info, tags_to_check)
 
         for spec, maybe_blob in zip(installed_specs_with_deps, available_blobs):
@@ -1677,8 +1695,8 @@ def _oci_push(
         executor.submit(_oci_push_pkg_blob, target_image, spec, tmpdir) for spec in blobs_to_upload
     ]
 
-    manifests_to_upload: List[spack.spec.Spec] = []
-    errors: List[Tuple[spack.spec.Spec, BaseException]] = []
+    manifests_to_upload: List[Spec] = []
+    errors: List[Tuple[Spec, BaseException]] = []
 
     # And update the spec to blob mapping for successful uploads
     for spec, blob_future in zip(blobs_to_upload, blob_futures):
@@ -1704,7 +1722,7 @@ def _oci_push(
             base_image_cache=base_images,
         )
 
-    def extra_config(spec: spack.spec.Spec):
+    def extra_config(spec: Spec):
         spec_dict = spec.to_dict(hash=ht.dag_hash)
         spec_dict["buildcache_layout_version"] = CURRENT_BUILD_CACHE_LAYOUT_VERSION
         spec_dict["binary_cache_checksum"] = {
@@ -1720,7 +1738,7 @@ def extra_config(spec: spack.spec.Spec):
             _oci_put_manifest,
             base_images,
             checksums,
-            target_image.with_tag(_oci_default_tag(spec)),
+            target_image.with_tag(default_tag(spec)),
             tmpdir,
             extra_config(spec),
             {"org.opencontainers.image.description": spec.format()},
@@ -1737,7 +1755,7 @@ def extra_config(spec: spack.spec.Spec):
         manifest_progress.start(spec, manifest_future.running())
         if error is None:
             manifest_progress.ok(
-                f"Tagged {_format_spec(spec)} as {target_image.with_tag(_oci_default_tag(spec))}"
+                f"Tagged {_format_spec(spec)} as {target_image.with_tag(default_tag(spec))}"
             )
         else:
             manifest_progress.fail()
@@ -1772,13 +1790,13 @@ def _oci_update_index(
     db = BuildCacheDatabase(db_root_dir)
 
     for spec_dict in spec_dicts:
-        spec = spack.spec.Spec.from_dict(spec_dict)
+        spec = Spec.from_dict(spec_dict)
         db.add(spec)
         db.mark(spec, "in_buildcache", True)
 
     # Create the index.json file
     index_json_path = os.path.join(tmpdir, "index.json")
-    with open(index_json_path, "w", encoding="utf-8") as f:
+    with open(index_json_path, "w") as f:
         db._write_to_file(f)
 
     # Create an empty config.json file
@@ -1887,7 +1905,7 @@ def _get_valid_spec_file(path: str, max_supported_layout: int) -> Tuple[Dict, in
     try:
         as_string = binary_content.decode("utf-8")
         if path.endswith(".json.sig"):
-            spec_dict = spack.spec.Spec.extract_json_from_clearsig(as_string)
+            spec_dict = Spec.extract_json_from_clearsig(as_string)
         else:
             spec_dict = json.loads(as_string)
     except Exception as e:
@@ -1935,9 +1953,9 @@ def download_tarball(spec, unsigned: Optional[bool] = False, mirrors_for_spec=No
            "signature_verified": "true-if-binary-pkg-was-already-verified"
        }
     """
-    configured_mirrors: Iterable[spack.mirrors.mirror.Mirror] = (
-        spack.mirrors.mirror.MirrorCollection(binary=True).values()
-    )
+    configured_mirrors: Iterable[spack.mirror.Mirror] = spack.mirror.MirrorCollection(
+        binary=True
+    ).values()
     if not configured_mirrors:
         tty.die("Please add a spack mirror to allow download of pre-compiled packages.")
 
@@ -1962,7 +1980,7 @@ def fetch_url_to_mirror(url):
         for mirror in configured_mirrors:
             if mirror.fetch_url == url:
                 return mirror
-        return spack.mirrors.mirror.Mirror(url)
+        return spack.mirror.Mirror(url)
 
     mirrors = [fetch_url_to_mirror(url) for url in mirror_urls]
 
@@ -1983,7 +2001,7 @@ def fetch_url_to_mirror(url):
             if fetch_url.startswith("oci://"):
                 ref = spack.oci.image.ImageReference.from_string(
                     fetch_url[len("oci://") :]
-                ).with_tag(_oci_default_tag(spec))
+                ).with_tag(spack.oci.image.default_tag(spec))
 
                 # Fetch the manifest
                 try:
@@ -2175,12 +2193,7 @@ 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)
-
-    # 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."
-        )
+    rel = buildinfo.get("relative_rpaths", False)
 
     # In the past prefix_to_hash was the default and externals were not dropped, so prefixes
     # were not unique.
@@ -2220,7 +2233,7 @@ 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 = specs_to_relocate(spec)
+    relocation_specs = deps_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
@@ -2232,8 +2245,7 @@ def relocate_package(spec):
             ]
             if analogs:
                 # Prefer same-name analogs and prefer higher versions
-                # This matches the preferences in spack.spec.Spec.splice, so we
-                # will find same node
+                # This matches the preferences in Spec.splice, so we will find same node
                 analog = max(analogs, key=lambda a: (a.name == s.name, a.version))
 
         lookup_dag_hash = analog.dag_hash()
@@ -2258,11 +2270,19 @@ def relocate_package(spec):
 
     tty.debug("Relocating package from", "%s to %s." % (old_layout_root, new_layout_root))
 
-    # Old archives may have hardlinks repeated.
+    # Old archives maybe 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 = [os.path.join(workdir, f) for f in buildinfo["relocate_textfiles"]]
+    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)
 
     # If we are not installing back to the same install tree do the relocation
     if old_prefix != new_prefix:
@@ -2273,11 +2293,29 @@ def relocate_package(spec):
         # 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, prefix_to_prefix_bin)
-        elif "elf" 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:
             # The new ELF dynamic section relocation logic only handles absolute to
             # absolute relocation.
-            relocate.relocate_elf_binaries(files_to_relocate, prefix_to_prefix_bin)
+            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 links to the new install prefix
         links = [os.path.join(workdir, f) for f in buildinfo.get("relocate_links", [])]
@@ -2296,9 +2334,7 @@ def relocate_package(spec):
             if not codesign:
                 return
             for binary in changed_files:
-                # preserve the original inode by running codesign on a copy
-                with fsys.edit_in_place_through_temporary_file(binary) as tmp_binary:
-                    codesign("-fs-", tmp_binary)
+                codesign("-fs-", binary)
 
     # If we are installing back to the same location
     # relocate the sbang location if the spack directory changed
@@ -2379,14 +2415,6 @@ def _tar_strip_component(tar: tarfile.TarFile, prefix: str):
         yield m
 
 
-def extract_buildcache_tarball(tarfile_path: str, destination: str) -> None:
-    with closing(tarfile.open(tarfile_path, "r")) as tar:
-        # Remove common prefix from tarball entries and directly extract them to the install dir.
-        tar.extractall(
-            path=destination, members=_tar_strip_component(tar, prefix=_ensure_common_prefix(tar))
-        )
-
-
 def extract_tarball(spec, download_result, force=False, timer=timer.NULL_TIMER):
     """
     extract binary tarball for given package into install area
@@ -2456,7 +2484,12 @@ def extract_tarball(spec, download_result, force=False, timer=timer.NULL_TIMER):
                 tarfile_path, size, contents, "sha256", expected, local_checksum
             )
     try:
-        extract_buildcache_tarball(tarfile_path, destination=spec.prefix)
+        with closing(tarfile.open(tarfile_path, "r")) as tar:
+            # Remove install prefix from tarfil to extract directly into spec.prefix
+            tar.extractall(
+                path=spec.prefix,
+                members=_tar_strip_component(tar, prefix=_ensure_common_prefix(tar)),
+            )
     except Exception:
         shutil.rmtree(spec.prefix, ignore_errors=True)
         _delete_staged_downloads(download_result)
@@ -2615,7 +2648,7 @@ def try_direct_fetch(spec, mirrors=None):
     specfile_is_signed = False
     found_specs = []
 
-    binary_mirrors = spack.mirrors.mirror.MirrorCollection(mirrors=mirrors, binary=True).values()
+    binary_mirrors = spack.mirror.MirrorCollection(mirrors=mirrors, binary=True).values()
 
     for mirror in binary_mirrors:
         buildcache_fetch_url_json = url_util.join(
@@ -2646,10 +2679,10 @@ def try_direct_fetch(spec, mirrors=None):
         # are concrete (as they are built) so we need to mark this spec
         # concrete on read-in.
         if specfile_is_signed:
-            specfile_json = spack.spec.Spec.extract_json_from_clearsig(specfile_contents)
-            fetched_spec = spack.spec.Spec.from_dict(specfile_json)
+            specfile_json = Spec.extract_json_from_clearsig(specfile_contents)
+            fetched_spec = Spec.from_dict(specfile_json)
         else:
-            fetched_spec = spack.spec.Spec.from_json(specfile_contents)
+            fetched_spec = Spec.from_json(specfile_contents)
         fetched_spec._mark_concrete()
 
         found_specs.append({"mirror_url": mirror.fetch_url, "spec": fetched_spec})
@@ -2676,7 +2709,7 @@ def get_mirrors_for_spec(spec=None, mirrors_to_check=None, index_only=False):
     if spec is None:
         return []
 
-    if not spack.mirrors.mirror.MirrorCollection(mirrors=mirrors_to_check, binary=True):
+    if not spack.mirror.MirrorCollection(mirrors=mirrors_to_check, binary=True):
         tty.debug("No Spack mirrors are currently configured")
         return {}
 
@@ -2715,7 +2748,7 @@ def clear_spec_cache():
 
 def get_keys(install=False, trust=False, force=False, mirrors=None):
     """Get pgp public keys available on mirror with suffix .pub"""
-    mirror_collection = mirrors or spack.mirrors.mirror.MirrorCollection(binary=True)
+    mirror_collection = mirrors or spack.mirror.MirrorCollection(binary=True)
 
     if not mirror_collection:
         tty.die("Please add a spack mirror to allow " + "download of build caches.")
@@ -2770,7 +2803,7 @@ def get_keys(install=False, trust=False, force=False, mirrors=None):
 
 
 def _url_push_keys(
-    *mirrors: Union[spack.mirrors.mirror.Mirror, str],
+    *mirrors: Union[spack.mirror.Mirror, str],
     keys: List[str],
     tmpdir: str,
     update_index: bool = False,
@@ -2837,7 +2870,7 @@ def check_specs_against_mirrors(mirrors, specs, output_file=None):
 
     """
     rebuilds = {}
-    for mirror in spack.mirrors.mirror.MirrorCollection(mirrors, binary=True).values():
+    for mirror in spack.mirror.MirrorCollection(mirrors, binary=True).values():
         tty.debug("Checking for built specs at {0}".format(mirror.fetch_url))
 
         rebuild_list = []
@@ -2854,7 +2887,7 @@ def check_specs_against_mirrors(mirrors, specs, output_file=None):
             }
 
     if output_file:
-        with open(output_file, "w", encoding="utf-8") as outf:
+        with open(output_file, "w") as outf:
             outf.write(json.dumps(rebuilds))
 
     return 1 if rebuilds else 0
@@ -2881,7 +2914,7 @@ def _download_buildcache_entry(mirror_root, descriptions):
 
 
 def download_buildcache_entry(file_descriptions, mirror_url=None):
-    if not mirror_url and not spack.mirrors.mirror.MirrorCollection(binary=True):
+    if not mirror_url and not spack.mirror.MirrorCollection(binary=True):
         tty.die(
             "Please provide or add a spack mirror to allow " + "download of buildcache entries."
         )
@@ -2890,7 +2923,7 @@ def download_buildcache_entry(file_descriptions, mirror_url=None):
         mirror_root = os.path.join(mirror_url, BUILD_CACHE_RELATIVE_PATH)
         return _download_buildcache_entry(mirror_root, file_descriptions)
 
-    for mirror in spack.mirrors.mirror.MirrorCollection(binary=True).values():
+    for mirror in spack.mirror.MirrorCollection(binary=True).values():
         mirror_root = os.path.join(mirror.fetch_url, BUILD_CACHE_RELATIVE_PATH)
 
         if _download_buildcache_entry(mirror_root, file_descriptions):
@@ -2948,7 +2981,7 @@ def __init__(self, all_architectures):
 
         self.possible_specs = specs
 
-    def __call__(self, spec: spack.spec.Spec, **kwargs):
+    def __call__(self, spec: Spec, **kwargs):
         """
         Args:
             spec: The spec being searched for
@@ -3086,7 +3119,7 @@ def __init__(self, url: str, local_hash, urlopen=None) -> None:
 
     def conditional_fetch(self) -> FetchIndexResult:
         """Download an index from an OCI registry type mirror."""
-        url_manifest = self.ref.with_tag(default_index_tag).manifest_url()
+        url_manifest = self.ref.with_tag(spack.oci.image.default_index_tag).manifest_url()
         try:
             response = self.urlopen(
                 urllib.request.Request(