fix(prune): should work in a workspace (#4691)

close #4647

.changeset/khaki-carrots-smile.md

@@ -0,0 +1,6 @@
+---
+"@pnpm/plugin-commands-installation": patch
+"pnpm": patch
+---
+
+`pnpm prune` works in a workspace [#4647](https://github.com/pnpm/pnpm/pull/4691).

.changeset/shiny-buses-breathe.md

@@ -0,0 +1,6 @@
+---
+"@pnpm/plugin-commands-installation": patch
+"pnpm": patch
+---
+
+`pnpm prune` does not remove hoisted dependencies.

.changeset/silver-falcons-care.md

@@ -0,0 +1,5 @@
+---
+"@pnpm/modules-cleaner": patch
+---
+
+Do not remove hoisted dependencies, when pruneDirectDependencies is set to `true`.

.changeset/thirty-pumpkins-rule.md

@@ -0,0 +1,5 @@
+---
+"@pnpm/core": minor
+---
+
+The `install()` function accepts the `pruneDirectDependencies` option.

packages/core/src/install/index.ts

@@ -119,6 +119,7 @@ export async function install (
   manifest: ProjectManifest,
   opts: InstallOptions & {
     preferredVersions?: PreferredVersions
+    pruneDirectDependencies?: boolean
   }
 ) {
   const projects = await mutateModules(
@@ -127,6 +128,7 @@ export async function install (
         buildIndex: 0,
         manifest,
         mutation: 'install',
+        pruneDirectDependencies: opts.pruneDirectDependencies,
         rootDir: opts.dir ?? process.cwd(),
       },
     ],

packages/modules-cleaner/src/prune.ts

@@ -74,10 +74,11 @@ export default async function prune (
       ...difference(currentPkgs, wantedPkgs).map(([depName]) => depName),
     ])
     if (pruneDirectDependencies) {
+      const publiclyHoistedDeps = getPubliclyHoistedDependencies(opts.hoistedDependencies)
       if (allCurrentPackages.size > 0) {
         const newPkgsSet = new Set<string>(wantedPkgs.map(([depName]) => depName))
         for (const currentPackage of Array.from(allCurrentPackages)) {
-          if (!newPkgsSet.has(currentPackage)) {
+          if (!newPkgsSet.has(currentPackage) && !publiclyHoistedDeps.has(currentPackage)) {
             depsToRemove.add(currentPackage)
           }
         }
@@ -245,3 +246,15 @@ function getPkgsDepPathsOwnedOnlyByImporters (
   const packagesOfSelectedOnly = pickAll(difference(Object.keys(selected.packages!), Object.keys(other.packages!)), selected.packages!) as PackageSnapshots
   return getPkgsDepPaths(registries, packagesOfSelectedOnly, skipped)
 }
+
+function getPubliclyHoistedDependencies (hoistedDependencies: HoistedDependencies): Set<string> {
+  const publiclyHoistedDeps = new Set<string>()
+  for (const hoistedAliases of Object.values(hoistedDependencies)) {
+    for (const [alias, hoistType] of Object.entries(hoistedAliases)) {
+      if (hoistType === 'public') {
+        publiclyHoistedDeps.add(alias)
+      }
+    }
+  }
+  return publiclyHoistedDeps
+}

packages/plugin-commands-installation/src/install.ts

@@ -274,9 +274,11 @@ export type InstallCommandOptions = Pick<Config,
   }
   fixLockfile?: boolean
   useBetaCli?: boolean
+  pruneDirectDependencies?: boolean
+  pruneStore?: boolean
   recursive?: boolean
   workspace?: boolean
-} & Partial<Pick<Config, 'pnpmHomeDir' | 'preferWorkspacePackages'>>
+} & Partial<Pick<Config, 'modulesCacheMaxAge' | 'pnpmHomeDir' | 'preferWorkspacePackages'>>
 
 export async function handler (
   opts: InstallCommandOptions

packages/plugin-commands-installation/src/prune.ts

@@ -1,11 +1,9 @@
-import { docsUrl, readProjectManifestOnly } from '@pnpm/cli-utils'
+import { docsUrl } from '@pnpm/cli-utils'
 import { UNIVERSAL_OPTIONS } from '@pnpm/common-cli-options-help'
-import { Config, types as allTypes } from '@pnpm/config'
-import { createOrConnectStoreController, CreateStoreControllerOptions } from '@pnpm/store-connection-manager'
-import { InstallOptions, mutateModules } from '@pnpm/core'
+import { types as allTypes } from '@pnpm/config'
 import pick from 'ramda/src/pick'
 import renderHelp from 'render-help'
-import getOptionsFromRootManifest from './getOptionsFromRootManifest'
+import * as install from './install'
 
 export const rcOptionsTypes = cliOptionsTypes
 
@@ -45,29 +43,12 @@ export function help () {
 }
 
 export async function handler (
-  opts: Pick<Config, 'dev' | 'engineStrict' | 'optional' | 'production' | 'rootProjectManifest'> & CreateStoreControllerOptions
+  opts: install.InstallCommandOptions
 ) {
-  const store = await createOrConnectStoreController(opts)
-  const manifest = await readProjectManifestOnly(process.cwd(), opts)
-  return mutateModules([
-    {
-      buildIndex: 0,
-      manifest,
-      mutation: 'install',
-      pruneDirectDependencies: true,
-      rootDir: process.cwd(),
-    },
-  ], {
+  return install.handler({
     ...opts,
-    ...getOptionsFromRootManifest(opts.rootProjectManifest ?? {}),
-    include: {
-      dependencies: opts.production !== false,
-      devDependencies: opts.dev !== false,
-      optionalDependencies: opts.optional !== false,
-    },
     modulesCacheMaxAge: 0,
+    pruneDirectDependencies: true,
     pruneStore: true,
-    storeController: store.ctrl,
-    storeDir: store.dir,
-  } as InstallOptions)
+  })
 }

packages/plugin-commands-installation/src/recursive.ts

@@ -80,6 +80,7 @@ type RecursiveOptions = CreateStoreControllerOptions & Pick<Config,
   useBetaCli?: boolean
   selectedProjectsGraph: ProjectsGraph
   preferredVersions?: PreferredVersions
+  pruneDirectDependencies?: boolean
 } & Partial<
 Pick<Config,
 | 'sort'
@@ -258,6 +259,7 @@ export default async function recursive (
           manifest,
           modulesDir,
           mutation,
+          pruneDirectDependencies: opts.pruneDirectDependencies,
           rootDir,
         } as MutatedProject)
       }

packages/plugin-commands-installation/test/prune.ts

@@ -1,5 +1,5 @@
 import path from 'path'
-import { install, link, prune } from '@pnpm/plugin-commands-installation'
+import { add, install, link, prune } from '@pnpm/plugin-commands-installation'
 import prepare from '@pnpm/prepare'
 import { REGISTRY_MOCK_PORT } from '@pnpm/registry-mock'
 import fixtures from '@pnpm/test-fixtures'
@@ -20,6 +20,7 @@ const DEFAULT_OPTIONS = {
     optionalDependencies: true,
   },
   lock: true,
+  linkWorkspacePackages: true,
   pnpmfile: '.pnpmfile.cjs',
   pnpmHomeDir: '',
   rawConfig: { registry: REGISTRY_URL },
@@ -56,6 +57,28 @@ test('prune removes external link that is not in package.json', async () => {
   await project.hasNot('local-pkg')
 })
 
+test('prune keeps hoisted dependencies', async () => {
+  const project = prepare(undefined)
+  const storeDir = path.resolve('store')
+  const cacheDir = path.resolve('cache')
+
+  await add.handler({
+    ...DEFAULT_OPTIONS,
+    cacheDir,
+    dir: process.cwd(),
+    storeDir,
+  }, ['pkg-with-1-dep@100.0.0'])
+
+  await prune.handler({
+    ...DEFAULT_OPTIONS,
+    cacheDir,
+    dir: process.cwd(),
+    storeDir,
+  })
+
+  await project.hasNot('dep-of-pkg-with-1-dep')
+})
+
 test('prune removes dev dependencies', async () => {
   const project = prepare({
     dependencies: { 'is-positive': '1.0.0' },