patchpkg: don't error on missing store refs

internal/patchpkg/builder.go

@@ -96,32 +96,11 @@ func (d *DerivationBuilder) Build(ctx context.Context, pkgStorePath string) erro
 
 func (d *DerivationBuilder) build(ctx context.Context, pkg, out *packageFS) error {
 	if d.RestoreRefs {
-		// Find store path references to build inputs that were removed
-		// from Python.
-		refs, err := d.findRemovedRefs(ctx, pkg)
-		if err != nil {
-			return err
-		}
-
-		// Group the references we want to restore by file path.
-		d.bytePatches = make(map[string][]fileSlice, len(refs))
-		for _, ref := range refs {
-			d.bytePatches[ref.path] = append(d.bytePatches[ref.path], ref)
-		}
-
-		// If any of those references have shared libraries, add them
-		// back to Python's RPATH.
-		if d.glibcPatcher != nil {
-			nixStore := cmp.Or(os.Getenv("NIX_STORE"), "/nix/store")
-			seen := make(map[string]bool)
-			for _, ref := range refs {
-				storePath := filepath.Join(nixStore, string(ref.data))
-				if seen[storePath] {
-					continue
-				}
-				seen[storePath] = true
-				d.glibcPatcher.prependRPATH(newPackageFS(storePath))
-			}
+		if err := d.restoreMissingRefs(ctx, pkg); err != nil {
+			// Don't break the flake build if we're unable to
+			// restore some of the refs. Having some is still an
+			// improvement.
+			slog.ErrorContext(ctx, "unable to restore all removed refs", "err", err)
 		}
 	}
 
@@ -152,6 +131,37 @@ func (d *DerivationBuilder) build(ctx context.Context, pkg, out *packageFS) erro
 	return cmd.Run()
 }
 
+func (d *DerivationBuilder) restoreMissingRefs(ctx context.Context, pkg *packageFS) error {
+	// Find store path references to build inputs that were removed
+	// from Python.
+	refs, err := d.findRemovedRefs(ctx, pkg)
+	if err != nil {
+		return err
+	}
+
+	// Group the references we want to restore by file path.
+	d.bytePatches = make(map[string][]fileSlice, len(refs))
+	for _, ref := range refs {
+		d.bytePatches[ref.path] = append(d.bytePatches[ref.path], ref)
+	}
+
+	// If any of those references have shared libraries, add them
+	// back to Python's RPATH.
+	if d.glibcPatcher != nil {
+		nixStore := cmp.Or(os.Getenv("NIX_STORE"), "/nix/store")
+		seen := make(map[string]bool)
+		for _, ref := range refs {
+			storePath := filepath.Join(nixStore, string(ref.data))
+			if seen[storePath] {
+				continue
+			}
+			seen[storePath] = true
+			d.glibcPatcher.prependRPATH(newPackageFS(storePath))
+		}
+	}
+	return nil
+}
+
 func (d *DerivationBuilder) copyDir(out *packageFS, path string) error {
 	path, err := out.OSPath(path)
 	if err != nil {

testscripts/languages/python_patch_missing_ref.test.txt

@@ -0,0 +1,96 @@
+# Python Auto-Patch Handles Missing Ref
+#
+# Check that `devbox patch --restore-refs` doesn't break the flake build when a
+# a store path cannot be restored.
+#
+# The nixpkgs commit hash and version of Python chosen in this test is very
+# specific. Most versions don't encounter this error, so be careful that the
+# test still fails with Devbox v0.13.0 if changing the devbox.lock.
+#
+# https://github.com/jetify-com/devbox/issues/2289
+
+exec devbox install
+
+-- devbox.json --
+{
+  "packages": {
+    "python": "latest"
+  },
+  "env": {
+    "PIP_DISABLE_PIP_VERSION_CHECK": "1",
+    "PIP_NO_INPUT":                  "1",
+    "PIP_NO_PYTHON_VERSION_WARNING": "1",
+    "PIP_PROGRESS_BAR":              "off",
+    "PIP_REQUIRE_VIRTUALENV":        "1",
+    "PIP_ROOT_USER_ACTION":          "ignore"
+  },
+  "shell": {
+    "scripts": {
+      "venv": ". $VENV_DIR/bin/activate && \"$@\""
+    }
+  }
+}
+
+-- devbox.lock --
+{
+  "lockfile_version": "1",
+  "packages": {
+    "python@latest": {
+      "last_modified": "2024-09-10T15:01:03Z",
+      "plugin_version": "0.0.4",
+      "resolved": "github:NixOS/nixpkgs/5ed627539ac84809c78b2dd6d26a5cebeb5ae269#python3",
+      "source": "devbox-search",
+      "version": "3.12.5",
+      "systems": {
+        "aarch64-darwin": {
+          "outputs": [
+            {
+              "name": "out",
+              "path": "/nix/store/9pj4rzx5pbynkkxq1srzwjhywmcfxws3-python3-3.12.5",
+              "default": true
+            }
+          ],
+          "store_path": "/nix/store/9pj4rzx5pbynkkxq1srzwjhywmcfxws3-python3-3.12.5"
+        },
+        "aarch64-linux": {
+          "outputs": [
+            {
+              "name": "out",
+              "path": "/nix/store/6iq3nhgdyp8a5wzwf097zf2mn4zyqxr6-python3-3.12.5",
+              "default": true
+            },
+            {
+              "name": "debug",
+              "path": "/nix/store/xc4hygp28y7g1rvjf0vi7fj0d83a75pj-python3-3.12.5-debug"
+            }
+          ],
+          "store_path": "/nix/store/6iq3nhgdyp8a5wzwf097zf2mn4zyqxr6-python3-3.12.5"
+        },
+        "x86_64-darwin": {
+          "outputs": [
+            {
+              "name": "out",
+              "path": "/nix/store/ks8acr22s4iggnmvxydm5czl30racy32-python3-3.12.5",
+              "default": true
+            }
+          ],
+          "store_path": "/nix/store/ks8acr22s4iggnmvxydm5czl30racy32-python3-3.12.5"
+        },
+        "x86_64-linux": {
+          "outputs": [
+            {
+              "name": "out",
+              "path": "/nix/store/h3i0acpmr8mrjx07519xxmidv8mpax4y-python3-3.12.5",
+              "default": true
+            },
+            {
+              "name": "debug",
+              "path": "/nix/store/0a39pi2s6kxqc3kjjz2y9yzibd62zhhb-python3-3.12.5-debug"
+            }
+          ],
+          "store_path": "/nix/store/h3i0acpmr8mrjx07519xxmidv8mpax4y-python3-3.12.5"
+        }
+      }
+    }
+  }
+}

testscripts/languages/python_missing_so.test.txt → testscripts/languages/python_patch_missing_so.test.txt

@@ -7,8 +7,6 @@
 # libstdc++.so. The nixpkgs Python interpreter doesn't search standard system
 # paths, so Devbox must patch it or provide the location of native dependencies.
 
-[!env:DEVBOX_RUN_FAILING_TESTS] skip 'this test doesn''t pass on Linux yet'
-
 exec devbox install
 
 # pip install numpy

testscripts/languages/python_old_glibc.test.txt → testscripts/languages/python_patch_old_glibc.test.txt

@@ -3,8 +3,6 @@
 # Check that an older version of the Python interpreter (3.7) can import and run
 # pip packages that are built from source.
 
-[!env:DEVBOX_RUN_FAILING_TESTS] skip 'this test doesn''t pass on Linux yet'
-
 exec devbox install
 
 # pip install psycopg2