fix patched dependencies across repositories (#42463)

Currently, if a package has a dependency from another repository and patches it,
generation of the patch cache will fail. Concretization succeeds if a fixed patch
cache is in place.

- [x] don't assume that patched dependencies are in the same repo when indexing
- [x] add some test fixtures to support multi-repo tests.

---------

Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>

11 files changed, 80 insertions, 12 deletions

diff --git a/lib/spack/spack/main.py b/lib/spack/spack/main.py
index 7cab47d77f..28567f26e8 100644
--- a/lib/spack/spack/main.py
+++ b/lib/spack/spack/main.py
@@ -547,7 +547,7 @@ def setup_main_options(args):
         key = syaml.syaml_str("repos")
         key.override = True
         spack.config.CONFIG.scopes["command_line"].sections["repos"] = syaml.syaml_dict(
-            [(key, [spack.paths.mock_packages_path])]
+            [(key, [spack.paths.mock_packages_path, spack.paths.mock_packages_path2])]
         )
         spack.repo.PATH = spack.repo.create(spack.config.CONFIG)
 
diff --git a/lib/spack/spack/patch.py b/lib/spack/spack/patch.py
index a0f4152317..d4bc9fb4f4 100644
--- a/lib/spack/spack/patch.py
+++ b/lib/spack/spack/patch.py
@@ -530,7 +530,7 @@ class PatchCache:
 
         # update the index with per-package patch indexes
         pkg_cls = self.repository.get_pkg_class(pkg_fullname)
-        partial_index = self._index_patches(pkg_cls, self.repository)
+        partial_index = self._index_patches(pkg_cls)
         for sha256, package_to_patch in partial_index.items():
             p2p = self.index.setdefault(sha256, {})
             p2p.update(package_to_patch)
@@ -546,14 +546,11 @@ class PatchCache:
             p2p.update(package_to_patch)
 
     @staticmethod
-    def _index_patches(
-        pkg_class: Type["spack.package_base.PackageBase"], repository: "spack.repo.RepoPath"
-    ) -> Dict[Any, Any]:
+    def _index_patches(pkg_class: Type["spack.package_base.PackageBase"]) -> Dict[Any, Any]:
         """Patch index for a specific patch.
 
         Args:
             pkg_class: package object to get patches for
-            repository: repository containing the package
 
         Returns:
             The patch index for that package.
@@ -571,7 +568,7 @@ class PatchCache:
             for dependency in deps_by_name.values():
                 for patch_list in dependency.patches.values():
                     for patch in patch_list:
-                        dspec_cls = repository.get_pkg_class(dependency.spec.name)
+                        dspec_cls = spack.repo.PATH.get_pkg_class(dependency.spec.fullname)
                         patch_dict = patch.to_dict()
                         patch_dict.pop("sha256")  # save some space
                         index[patch.sha256] = {dspec_cls.fullname: patch_dict}
diff --git a/lib/spack/spack/paths.py b/lib/spack/spack/paths.py
index 84583cd552..aeca3a9899 100644
--- a/lib/spack/spack/paths.py
+++ b/lib/spack/spack/paths.py
@@ -60,6 +60,7 @@ var_path = os.path.join(prefix, "var", "spack")
 repos_path = os.path.join(var_path, "repos")
 packages_path = os.path.join(repos_path, "builtin")
 mock_packages_path = os.path.join(repos_path, "builtin.mock")
+mock_packages_path2 = os.path.join(repos_path, "builtin.mock2")
 
 #
 # Writable things in $spack/var/spack
diff --git a/lib/spack/spack/test/conftest.py b/lib/spack/spack/test/conftest.py
index f6670157ed..b66e1edb35 100644
--- a/lib/spack/spack/test/conftest.py
+++ b/lib/spack/spack/test/conftest.py
@@ -575,6 +575,11 @@ def mock_repo_path():
     yield spack.repo.from_path(spack.paths.mock_packages_path)
 
 
+@pytest.fixture(scope="session")
+def mock_repo_path2():
+    yield spack.repo.from_path(spack.paths.mock_packages_path2)
+
+
 def _pkg_install_fn(pkg, spec, prefix):
     # sanity_check_prefix requires something in the install directory
     mkdirp(prefix.bin)
@@ -588,19 +593,20 @@ def mock_pkg_install(monkeypatch):
 
 
 @pytest.fixture(scope="function")
-def mock_packages(mock_repo_path, mock_pkg_install, request):
-    """Use the 'builtin.mock' repository instead of 'builtin'"""
+def mock_packages(mock_repo_path, mock_repo_path2, mock_pkg_install, request):
+    """Use the 'builtin.mock' and 'builtin.mock2' repositories instead of 'builtin'"""
     ensure_configuration_fixture_run_before(request)
-    with spack.repo.use_repositories(mock_repo_path) as mock_repo:
+    with spack.repo.use_repositories(mock_repo_path, mock_repo_path2) as mock_repo:
         yield mock_repo
 
 
 @pytest.fixture(scope="function")
-def mutable_mock_repo(mock_repo_path, request):
+def mutable_mock_repo(request):
     """Function-scoped mock packages, for tests that need to modify them."""
     ensure_configuration_fixture_run_before(request)
     mock_repo = spack.repo.from_path(spack.paths.mock_packages_path)
-    with spack.repo.use_repositories(mock_repo) as mock_repo_path:
+    mock_repo2 = spack.repo.from_path(spack.paths.mock_packages_path2)
+    with spack.repo.use_repositories(mock_repo, mock_repo2) as mock_repo_path:
         yield mock_repo_path
 
 
diff --git a/lib/spack/spack/test/patch.py b/lib/spack/spack/test/patch.py
index 4b5f31b904..1088b1f24b 100644
--- a/lib/spack/spack/test/patch.py
+++ b/lib/spack/spack/test/patch.py
@@ -499,3 +499,9 @@ def test_invalid_from_dict(mock_packages, config):
     }
     with pytest.raises(spack.fetch_strategy.ChecksumError, match="sha256 checksum failed for"):
         spack.patch.from_dict(dictionary)
+
+
+@pytest.mark.regression("43097")
+def test_cross_repo_patch(mock_packages, config):
+    cross_repo_patch = Spec("patch-a-foreign-dependency")
+    cross_repo_patch.concretize()
diff --git a/var/spack/repos/builtin.mock/README.md b/var/spack/repos/builtin.mock/README.md
new file mode 100644
index 0000000000..5a5f6e747f
--- /dev/null
+++ b/var/spack/repos/builtin.mock/README.md
@@ -0,0 +1,7 @@
+# `builtin.mock`
+
+This repository and the secondary mock repo `builtin.mock2` contain mock packages used
+by Spack tests.
+
+Most tests are in `builtin.mock`, but `builtin.mock2` is used for scenarios where we
+need multiple repos for testing.
diff --git a/var/spack/repos/builtin.mock/packages/patch-a-foreign-dependency/mock2-package.patch b/var/spack/repos/builtin.mock/packages/patch-a-foreign-dependency/mock2-package.patch
new file mode 100644
index 0000000000..02bfad9103
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/patch-a-foreign-dependency/mock2-package.patch
@@ -0,0 +1,11 @@
+--- patch-a-dependency/configure	2018-08-13 23:13:51.000000000 -0700
++++ patch-a-dependency/configure.patched	2018-08-13 23:14:15.000000000 -0700
+@@ -2,7 +2,7 @@
+ prefix=$(echo $1 | sed 's/--prefix=//')
+ cat > Makefile <<EOF
+ all:
+-	echo Building...
++	echo Patched!
+ 
+ install:
+ 	mkdir -p $prefix
diff --git a/var/spack/repos/builtin.mock/packages/patch-a-foreign-dependency/package.py b/var/spack/repos/builtin.mock/packages/patch-a-foreign-dependency/package.py
new file mode 100644
index 0000000000..6e52029a1d
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/patch-a-foreign-dependency/package.py
@@ -0,0 +1,17 @@
+# 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)
+
+from spack.package import *
+
+
+class PatchAForeignDependency(Package):
+    """Package that requries a patched version of a dependency."""
+
+    homepage = "http://www.example.com"
+    url = "http://www.example.com/patch-a-dependency-1.0.tar.gz"
+
+    version("1.0", md5="0123456789abcdef0123456789abcdef")
+
+    depends_on("mock2-patched-dependency", patches=patch("mock2-package.patch"))
diff --git a/var/spack/repos/builtin.mock2/README.md b/var/spack/repos/builtin.mock2/README.md
new file mode 100644
index 0000000000..8a079b1a6b
--- /dev/null
+++ b/var/spack/repos/builtin.mock2/README.md
@@ -0,0 +1,6 @@
+# `builtin.mock2`
+
+This is the secondary mock repo for testing Spack, along with `builtin.mock`.
+
+Most tests are in `builtin.mock`, but this repository is used for scenarios where we
+need multiple repos for testing.
diff --git a/var/spack/repos/builtin.mock2/packages/mock2-patched-dependency/package.py b/var/spack/repos/builtin.mock2/packages/mock2-patched-dependency/package.py
new file mode 100644
index 0000000000..ed34ff025a
--- /dev/null
+++ b/var/spack/repos/builtin.mock2/packages/mock2-patched-dependency/package.py
@@ -0,0 +1,15 @@
+# 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)
+
+from spack.package import *
+
+
+class Mock2PatchedDependency(Package):
+    """Package patched by patch-a-foreign-dependency in builtin.mock."""
+
+    homepage = "http://www.example.com"
+    url = "http://www.example.com/mock2-patch-dependency-1.0.tar.gz"
+
+    version("1.0", md5="0123456789abcdef0123456789abcdef")
diff --git a/var/spack/repos/builtin.mock2/repo.yaml b/var/spack/repos/builtin.mock2/repo.yaml
new file mode 100644
index 0000000000..84923d8367
--- /dev/null
+++ b/var/spack/repos/builtin.mock2/repo.yaml
@@ -0,0 +1,2 @@
+repo:
+  namespace: 'builtin.mock2'