fix: catalog snapshots removed on filtered install with dedupe-peer-dependents=false (#9175)

* test: add catalog test for --filter and dedupe-peer-dependents=false

* fix: disable dedupe-injected-deps when deploying

* fix: catalog snapshots removed with dedupe-peer-dependents=false

.changeset/strange-tigers-dress.md

@@ -0,0 +1,8 @@
+---
+"@pnpm/plugin-commands-deploy": patch
+"@pnpm/plugin-commands-installation": patch
+"@pnpm/core": patch
+pnpm: patch
+---
+
+Fix a bug causing entries in the `catalogs` section of the `pnpm-lock.yaml` file to be removed when `dedupe-peer-dependents=false` on a filtered install. [#9112](https://github.com/pnpm/pnpm/issues/9112)

pkg-manager/core/test/catalogs.ts

@@ -380,6 +380,74 @@ test('lockfile catalog snapshots do not contain stale references on --filter', a
   expect(loadJsonFile<ProjectManifest>(pathToIsPositivePkgJson)?.version).toBe('3.1.0')
 })
 
+// Regression test for https://github.com/pnpm/pnpm/issues/9112
+test('dedupe-peer-dependents=false with --filter does not erase catalog snapshots', async () => {
+  const { options, projects, readLockfile } = preparePackagesAndReturnObjects([
+    {
+      name: 'project1',
+      dependencies: {},
+    },
+    {
+      name: 'project2',
+      dependencies: {
+        'is-positive': 'catalog:',
+      },
+    },
+  ])
+
+  await mutateModules(installProjects(projects), {
+    ...options,
+    lockfileOnly: true,
+    dedupePeerDependents: false,
+    catalogs: {
+      default: {
+        'is-positive': '1.0.0',
+      },
+    },
+  })
+
+  expect(readLockfile().catalogs).toStrictEqual({
+    default: {
+      'is-positive': { specifier: '1.0.0', version: '1.0.0' },
+    },
+  })
+
+  // Perform a filtered install with only project 1. The catalog protocol usage
+  // in project 2 should be retained.
+  const onlyProject1 = installProjects(projects).slice(0, 1)
+  expect(onlyProject1).toMatchObject([{ id: 'project1' }])
+  await mutateModules(onlyProject1, {
+    ...options,
+    lockfileOnly: true,
+    dedupePeerDependents: false,
+    catalogs: {
+      default: {
+        // Modify the original specifier above from "1.0.0" to "^1.0.0" in order
+        // to force a resolution instead of a frozen install.
+        'is-positive': '^1.0.0',
+      },
+    },
+  })
+
+  // The catalogs snapshot section was erased in the bug report from
+  // https://github.com/pnpm/pnpm/issues/9112 when dedupe-peer-dependents=false.
+  expect(readLockfile()).toEqual(expect.objectContaining({
+    catalogs: {
+      default: {
+        'is-positive': { specifier: '^1.0.0', version: '1.0.0' },
+      },
+    },
+    importers: expect.objectContaining({
+      project1: {},
+      project2: expect.objectContaining({
+        dependencies: {
+          'is-positive': { specifier: 'catalog:', version: '1.0.0' },
+        },
+      }),
+    }),
+  }))
+})
+
 // Regression test for https://github.com/pnpm/pnpm/issues/8639
 test('--fix-lockfile with --filter does not erase catalog snapshots', async () => {
   const { options, projects, readLockfile } = preparePackagesAndReturnObjects([

pkg-manager/plugin-commands-installation/src/installDeps.ts

@@ -219,8 +219,19 @@ when running add/update with the --workspace option')
         })
       }
 
+      const didUserConfigureCatalogs = Object.values(opts.catalogs ?? {})
+        .some(catalog => Object.keys(catalog ?? {}).length > 0)
+
+      // pnpm catalogs and dedupe-peer-dependents are features that require the
+      // allProjectsGraph to contain all projects to correctly update the wanted
+      // lockfile. Otherwise the wanted lockfile would be partially updated for
+      // only the selected projects specified for the filtered install.
+      //
+      // This should still be performance since only dependencies for the
+      // selectedProjectsGraph are installed. The allProjectsGraph is only used
+      // to compute the wanted lockfile.
       let allProjectsGraph!: ProjectsGraph
-      if (opts.dedupePeerDependents) {
+      if (didUserConfigureCatalogs || opts.dedupePeerDependents) {
         allProjectsGraph = opts.allProjectsGraph ?? createPkgGraph(allProjects, {
           linkWorkspacePackages: Boolean(opts.linkWorkspacePackages),
         }).graph

releasing/plugin-commands-deploy/src/deploy.ts

@@ -135,6 +135,13 @@ export async function handler (opts: DeployOptions, params: string[]): Promise<v
     // doesn't work with filters right now.
     // Related issue: https://github.com/pnpm/pnpm/issues/6858
     dedupePeerDependents: false,
+    // If enabled, dedupe-injected-deps will symlink workspace packages in the
+    // deployed dir to their original (non-deployed) directory in an attempt to
+    // dedupe workspace packages that don't need to be injected. The deployed
+    // dir shouldn't have symlinks to the original workspace. Disable
+    // dedupe-injected-deps to always inject workspace packages since copying is
+    // desirable.
+    dedupeInjectedDeps: false,
     depth: Infinity,
     hooks: {
       ...opts.hooks,