feat: patch package (#4885)

ref #3077
ref #2675

.changeset/bright-lemons-arrive.md

@@ -0,0 +1,23 @@
+---
+"@pnpm/core": minor
+"@pnpm/headless": minor
+"@pnpm/types": minor
+"pnpm": minor
+"@pnpm/resolve-dependencies": minor
+"@pnpm/lockfile-types": minor
+"@pnpm/lifecycle": minor
+"@pnpm/plugin-commands-installation": minor
+---
+
+Dependencies patching is possible via the `pnpm.patchedDependencies` field of the `package.json`.
+To patch a package, the package name, exact version, and the relative path to the patch file should be specified. For instance:
+
+```json
+{
+  "pnpm": {
+    "patchedDependencies": {
+      "eslint@1.0.0": "./patches/eslint@1.0.0.patch"
+    }
+  }
+}
+```

.changeset/four-poems-leave.md

@@ -0,0 +1,5 @@
+---
+"@pnpm/calc-dep-state": major
+---
+
+Changed the order of arguments in calcDepState and added an optional last argument for patchFileHash.

.changeset/shiny-countries-behave.md

@@ -0,0 +1,9 @@
+---
+"@pnpm/create-cafs-store": major
+"@pnpm/fetcher-base": major
+"@pnpm/package-store": major
+"@pnpm/server": major
+"@pnpm/store-controller-types": major
+---
+
+Rename engine and targetEngine fields to sideEffectsCacheKey.

.changeset/tasty-cobras-reflect.md

@@ -0,0 +1,5 @@
+---
+"@pnpm/build-modules": minor
+---
+
+Support packages patching.

packages/build-modules/src/buildSequence.ts

@@ -16,6 +16,10 @@ export interface DependenciesGraphNode {
   optionalDependencies: Set<string>
   // eslint-disable-next-line @typescript-eslint/no-explicit-any
   requiresBuild?: boolean | any // this is a durty workaround added in https://github.com/pnpm/pnpm/pull/4898
+  patchFile?: {
+    hash: string
+    path: string
+  }
 }
 
 export interface DependenciesGraph {

packages/build-modules/src/index.ts

@@ -83,6 +83,7 @@ async function buildDependency (
       extraEnv: opts.extraEnv,
       initCwd: opts.lockfileDir,
       optional: depNode.optional,
+      patchPath: depNode.patchFile?.path,
       pkgRoot: depNode.dir,
       rawConfig: opts.rawConfig,
       rootModulesDir: opts.rootModulesDir,
@@ -93,8 +94,9 @@ async function buildDependency (
     })
     if (hasSideEffects && opts.sideEffectsCacheWrite) {
       try {
+        const sideEffectsCacheKey = calcDepState(depGraph, opts.depsStateCache, depPath, depNode.patchFile?.hash)
         await opts.storeController.upload(depNode.dir, {
-          engine: calcDepState(depPath, depGraph, opts.depsStateCache),
+          sideEffectsCacheKey,
           filesIndexFile: depNode.filesIndexFile,
         })
       } catch (err: any) { // eslint-disable-line

packages/calc-dep-state/src/index.ts

@@ -11,7 +11,7 @@ export interface DepsGraphNode {
 }
 
 export interface DepsStateCache {
-  [nodeId: string]: DepStateObj
+  [depPath: string]: DepStateObj
 }
 
 export interface DepStateObj {
@@ -19,22 +19,27 @@ export interface DepStateObj {
 }
 
 export function calcDepState (
-  nodeId: string,
   depsGraph: DepsGraph,
-  cache: DepsStateCache
+  cache: DepsStateCache,
+  depPath: string,
+  patchFileHash?: string
 ): string {
-  const depStateObj = calcDepStateObj(nodeId, depsGraph, cache, new Set())
+  const depStateObj = calcDepStateObj(depPath, depsGraph, cache, new Set())
-  return `${ENGINE_NAME}-${JSON.stringify(depStateObj)}`
+  let result = `${ENGINE_NAME}-${JSON.stringify(depStateObj)}`
+  if (patchFileHash) {
+    result += `-${patchFileHash}`
+  }
+  return result
 }
 
 function calcDepStateObj (
-  nodeId: string,
+  depPath: string,
   depsGraph: DepsGraph,
   cache: DepsStateCache,
   parents: Set<string>
 ): DepStateObj {
-  if (cache[nodeId]) return cache[nodeId]
+  if (cache[depPath]) return cache[depPath]
-  const node = depsGraph[nodeId]
+  const node = depsGraph[depPath]
   if (!node) return {}
   const nextParents = new Set([...Array.from(parents), node.depPath])
   const state: DepStateObj = {}
@@ -47,6 +52,6 @@ function calcDepStateObj (
     }
     state[child.depPath] = calcDepStateObj(childId, depsGraph, cache, nextParents)
   }
-  cache[nodeId] = sortKeys(state)
+  cache[depPath] = sortKeys(state)
-  return cache[nodeId]
+  return cache[depPath]
 }

packages/calc-dep-state/test/index.ts

@@ -2,7 +2,7 @@ import { calcDepState } from '@pnpm/calc-dep-state'
 import { ENGINE_NAME } from '@pnpm/constants'
 
 test('calcDepState()', () => {
-  expect(calcDepState('/registry/foo/1.0.0', {
+  expect(calcDepState({
     'registry/foo/1.0.0': {
       depPath: '/foo/1.0.0',
       children: {
@@ -15,5 +15,5 @@ test('calcDepState()', () => {
         foo: 'registry/foo/1.0.0',
       },
     },
-  }, {})).toBe(`${ENGINE_NAME}-{}`)
+  }, {}, '/registry/foo/1.0.0')).toBe(`${ENGINE_NAME}-{}`)
 })

packages/core/src/install/extendInstallOptions.ts

@@ -100,6 +100,7 @@ export interface StrictInstallOptions {
 
   global: boolean
   globalBin?: string
+  patchedDependencies?: Record<string, string>
 }
 
 export type InstallOptions =

packages/core/src/install/index.ts

@@ -240,6 +240,7 @@ export async function mutateModules (
         neverBuiltDependencies: opts.neverBuiltDependencies,
         onlyBuiltDependencies: opts.onlyBuiltDependencies,
         packageExtensionsChecksum,
+        patchedDependencies: opts.patchedDependencies,
       }) ||
       opts.fixLockfile
     if (needsFullResolution) {
@@ -247,6 +248,7 @@ export async function mutateModules (
       ctx.wantedLockfile.neverBuiltDependencies = opts.neverBuiltDependencies
       ctx.wantedLockfile.onlyBuiltDependencies = opts.onlyBuiltDependencies
       ctx.wantedLockfile.packageExtensionsChecksum = packageExtensionsChecksum
+      ctx.wantedLockfile.patchedDependencies = opts.patchedDependencies
     }
     const frozenLockfile = opts.frozenLockfile ||
       opts.frozenLockfileIfExists && ctx.existsWantedLockfile
@@ -490,16 +492,19 @@ function lockfileIsUpToDate (
     onlyBuiltDependencies,
     overrides,
     packageExtensionsChecksum,
+    patchedDependencies,
   }: {
     neverBuiltDependencies?: string[]
     onlyBuiltDependencies?: string[]
     overrides?: Record<string, string>
     packageExtensionsChecksum?: string
+    patchedDependencies?: Record<string, string>
   }) {
   return !equals(lockfile.overrides ?? {}, overrides ?? {}) ||
     !equals((lockfile.neverBuiltDependencies ?? []).sort(), (neverBuiltDependencies ?? []).sort()) ||
     !equals(onlyBuiltDependencies?.sort(), lockfile.onlyBuiltDependencies) ||
-    lockfile.packageExtensionsChecksum !== packageExtensionsChecksum
+    lockfile.packageExtensionsChecksum !== packageExtensionsChecksum ||
+    !equals(lockfile.patchedDependencies ?? {}, patchedDependencies ?? {})
 }
 
 export function createObjectChecksum (obj: Object) {
@@ -773,6 +778,7 @@ const _installInContext: InstallFunction = async (projects, ctx, opts) => {
       virtualStoreDir: ctx.virtualStoreDir,
       wantedLockfile: ctx.wantedLockfile,
       workspacePackages: opts.workspacePackages,
+      patchedDependencies: opts.patchedDependencies,
     }
   )
 

packages/core/src/install/link.ts

@@ -404,9 +404,9 @@ async function linkAllPkgs (
     depNodes.map(async (depNode) => {
       const filesResponse = await depNode.fetchingFiles()
 
-      let targetEngine: string | undefined
+      let sideEffectsCacheKey: string | undefined
       if (opts.sideEffectsCacheRead && filesResponse.sideEffects && !isEmpty(filesResponse.sideEffects)) {
-        targetEngine = calcDepState(depNode.depPath, opts.depGraph, opts.depsStateCache)
+        sideEffectsCacheKey = calcDepState(opts.depGraph, opts.depsStateCache, depNode.depPath, depNode.patchFile?.hash)
       }
       if (typeof depNode.requiresBuild === 'function') {
         depNode.requiresBuild = await depNode.requiresBuild()
@@ -414,7 +414,7 @@ async function linkAllPkgs (
       const { importMethod, isBuilt } = await storeController.importPackage(depNode.dir, {
         filesResponse,
         force: opts.force,
-        targetEngine,
+        sideEffectsCacheKey,
         requiresBuild: depNode.requiresBuild,
       })
       if (importMethod) {

packages/core/test/fixtures/patch-pkg/is-positive@1.0.0.patch

@@ -0,0 +1,12 @@
+diff --git a/index.js b/index.js
+index 8e020ca..ff3aee4 100644
+--- a/index.js
++++ b/index.js
+@@ -5,5 +5,6 @@ module.exports = function (n) {
+ 		throw new TypeError('Expected a number');
+ 	}
+ 
++  // patched
+ 	return n >= 0;
+ };
+

packages/core/test/install/patch.ts

@@ -0,0 +1,90 @@
+import fs from 'fs'
+import path from 'path'
+import { PackageFilesIndex } from '@pnpm/cafs'
+import { ENGINE_NAME } from '@pnpm/constants'
+import { install } from '@pnpm/core'
+import { prepareEmpty } from '@pnpm/prepare'
+import fixtures from '@pnpm/test-fixtures'
+import rimraf from '@zkochan/rimraf'
+import loadJsonFile from 'load-json-file'
+import { testDefaults } from '../utils'
+
+const f = fixtures(__dirname)
+
+test('patch package', async () => {
+  const project = prepareEmpty()
+  const patchPath = path.join(f.find('patch-pkg'), 'is-positive@1.0.0.patch')
+
+  const patchedDependencies = {
+    'is-positive@1.0.0': path.relative(process.cwd(), patchPath),
+  }
+  const opts = await testDefaults({
+    fastUnpack: false,
+    sideEffectsCacheRead: true,
+    sideEffectsCacheWrite: true,
+    patchedDependencies,
+  }, {}, {}, { packageImportMethod: 'hardlink' })
+  await install({
+    dependencies: {
+      'is-positive': '1.0.0',
+    },
+  }, opts)
+
+  expect(fs.readFileSync('node_modules/is-positive/index.js', 'utf8')).toContain('// patched')
+
+  const lockfile = await project.readLockfile()
+  expect(lockfile.patchedDependencies).toStrictEqual(patchedDependencies)
+
+  const filesIndexFile = path.join(opts.storeDir, 'files/c7/1ccf199e0fdae37aad13946b937d67bcd35fa111b84d21b3a19439cfdc2812c5d8da8a735e94c2a1ccb77b4583808ee8405313951e7146ac83ede3671dc292-index.json')
+  const filesIndex = await loadJsonFile<PackageFilesIndex>(filesIndexFile)
+  const sideEffectsKey = `${ENGINE_NAME}-{}-meyqmf5tej4bwn3gxydpfig6pe`
+  const patchedFileIntegrity = filesIndex.sideEffects?.[sideEffectsKey]['index.js']?.integrity
+  expect(patchedFileIntegrity).toBeTruthy()
+  const originalFileIntegrity = filesIndex.files['index.js'].integrity
+  expect(originalFileIntegrity).toBeTruthy()
+  // The integrity of the original file differs from the integrity of the patched file
+  expect(originalFileIntegrity).not.toEqual(patchedFileIntegrity)
+
+  // The same with frozen lockfile
+  await rimraf('node_modules')
+  await install({
+    dependencies: {
+      'is-positive': '1.0.0',
+    },
+  }, {
+    ...opts,
+    frozenLockfile: true,
+  })
+  expect(fs.readFileSync('node_modules/is-positive/index.js', 'utf8')).toContain('// patched')
+
+  // The same with frozen lockfile and hoisted node_modules
+  await rimraf('node_modules')
+  await install({
+    dependencies: {
+      'is-positive': '1.0.0',
+    },
+  }, {
+    ...opts,
+    frozenLockfile: true,
+    nodeLinker: 'hoisted',
+  })
+  expect(fs.readFileSync('node_modules/is-positive/index.js', 'utf8')).toContain('// patched')
+
+  process.chdir('..')
+  fs.mkdirSync('project2')
+  process.chdir('project2')
+
+  await install({
+    dependencies: {
+      'is-positive': '1.0.0',
+    },
+  }, await testDefaults({
+    fastUnpack: false,
+    sideEffectsCacheRead: true,
+    sideEffectsCacheWrite: true,
+    offline: true,
+  }, {}, {}, { packageImportMethod: 'hardlink' }))
+
+  // The original file did not break, when a patched version was created
+  expect(fs.readFileSync('node_modules/is-positive/index.js', 'utf8')).not.toContain('// patched')
+})

packages/create-cafs-store/src/index.ts

@@ -22,7 +22,7 @@ function createPackageImporter (
   const packageImportMethod = opts.packageImportMethod
   const gfm = getFlatMap.bind(null, opts.cafsDir)
   return async (to, opts) => {
-    const { filesMap, isBuilt } = gfm(opts.filesResponse, opts.targetEngine)
+    const { filesMap, isBuilt } = gfm(opts.filesResponse, opts.sideEffectsCacheKey)
     const pkgImportMethod = (opts.requiresBuild && !isBuilt)
       ? 'clone-or-copy'
       : (opts.filesResponse.packageImportMethod ?? packageImportMethod)

packages/fetcher-base/src/index.ts

@@ -23,7 +23,7 @@ export type PackageFilesResponse = {
 
 export interface ImportPackageOpts {
   requiresBuild?: boolean
-  targetEngine?: string
+  sideEffectsCacheKey?: string
   filesResponse: PackageFilesResponse
   force: boolean
 }

packages/headless/package.json

@@ -71,6 +71,7 @@
     "@pnpm/calc-dep-state": "workspace:2.0.1",
     "@pnpm/constants": "workspace:6.1.0",
     "@pnpm/core-loggers": "workspace:7.0.3",
+    "@pnpm/crypto.base32-hash": "workspace:1.0.0",
     "@pnpm/error": "workspace:3.0.1",
     "@pnpm/filter-lockfile": "workspace:6.0.6",
     "@pnpm/hoist": "workspace:6.1.4",

packages/headless/src/index.ts

@@ -679,15 +679,15 @@ async function linkAllPkgs (
         throw err
       }
 
-      let targetEngine: string | undefined
+      let sideEffectsCacheKey: string | undefined
       if (opts.sideEffectsCacheRead && filesResponse.sideEffects && !isEmpty(filesResponse.sideEffects)) {
-        targetEngine = calcDepState(depNode.dir, opts.depGraph, opts.depsStateCache)
+        sideEffectsCacheKey = calcDepState(opts.depGraph, opts.depsStateCache, depNode.dir, depNode.patchFile?.hash)
       }
       const { importMethod, isBuilt } = await storeController.importPackage(depNode.dir, {
         filesResponse,
         force: opts.force,
         requiresBuild: depNode.requiresBuild,
-        targetEngine,
+        sideEffectsCacheKey,
       })
       if (importMethod) {
         progressLogger.debug({

packages/headless/src/linkHoistedModules.ts

@@ -87,6 +87,7 @@ async function linkAllPkgsInOrder (
     warn: (message: string) => void
   }
 ) {
+  const _calcDepState = calcDepState.bind(null, graph, opts.depsStateCache)
   await Promise.all(
     Object.entries(hierarchy).map(async ([dir, deps]) => {
       const depNode = graph[dir]
@@ -98,15 +99,15 @@ async function linkAllPkgsInOrder (
         throw err
       }
 
-      let targetEngine: string | undefined
+      let sideEffectsCacheKey: string | undefined
       if (opts.sideEffectsCacheRead && filesResponse.sideEffects && !isEmpty(filesResponse.sideEffects)) {
-        targetEngine = calcDepState(dir, graph, opts.depsStateCache)
+        sideEffectsCacheKey = _calcDepState(dir, depNode.patchFile?.hash)
       }
       const { importMethod, isBuilt } = await storeController.importPackage(depNode.dir, {
         filesResponse,
         force: opts.force || depNode.depPath !== prevGraph[dir]?.depPath,
         requiresBuild: depNode.requiresBuild,
-        targetEngine,
+        sideEffectsCacheKey,
       })
       if (importMethod) {
         progressLogger.debug({

packages/headless/src/lockfileToDepGraph.ts

@@ -3,6 +3,7 @@ import { WANTED_LOCKFILE } from '@pnpm/constants'
 import {
   progressLogger,
 } from '@pnpm/core-loggers'
+import { createBase32HashFromFile } from '@pnpm/crypto.base32-hash'
 import {
   Lockfile,
   PackageSnapshot,
@@ -44,6 +45,10 @@ export interface DependenciesGraphNode {
   prepare: boolean
   hasBin: boolean
   filesIndexFile: string
+  patchFile?: {
+    path: string
+    hash: string
+  }
 }
 
 export interface DependenciesGraph {
@@ -175,6 +180,7 @@ export default async function lockfileToDepGraph (
           optionalDependencies: new Set(Object.keys(pkgSnapshot.optionalDependencies ?? {})),
           prepare: pkgSnapshot.prepare === true,
           requiresBuild: pkgSnapshot.requiresBuild === true,
+          patchFile: await tryReadPatchFile(opts.lockfileDir, lockfile, pkgName, pkgVersion),
         }
         pkgSnapshotByLocation[dir] = pkgSnapshot
       })
@@ -214,6 +220,18 @@ export default async function lockfileToDepGraph (
   return { graph, directDependenciesByImporterId }
 }
 
+export async function tryReadPatchFile (lockfileDir: string, lockfile: Lockfile, pkgName: string, pkgVersion: string) {
+  const patchFileRelativePath = lockfile.patchedDependencies?.[`${pkgName}@${pkgVersion}`]
+  if (!patchFileRelativePath) {
+    return undefined
+  }
+  const patchFilePath = path.join(lockfileDir, patchFileRelativePath)
+  return {
+    path: patchFilePath,
+    hash: await createBase32HashFromFile(patchFilePath),
+  }
+}
+
 async function getChildrenPaths (
   ctx: {
     graph: DependenciesGraph

packages/headless/src/lockfileToHoistedDepGraph.ts

@@ -23,6 +23,7 @@ import {
   DepHierarchy,
   DirectDependenciesByImporterId,
   LockfileToDepGraphResult,
+  tryReadPatchFile,
 } from './lockfileToDepGraph'
 
 export interface LockfileToHoistedDepGraphOptions {
@@ -208,6 +209,7 @@ async function fetchDeps (
       optionalDependencies: new Set(Object.keys(pkgSnapshot.optionalDependencies ?? {})),
       prepare: pkgSnapshot.prepare === true,
       requiresBuild: pkgSnapshot.requiresBuild === true,
+      patchFile: await tryReadPatchFile(opts.lockfileDir, opts.lockfile, pkgName, pkgVersion),
     }
     opts.pkgLocationByDepPath[depPath] = dir
     depHierarchy[dir] = await fetchDeps(opts, path.join(dir, 'node_modules'), dep.dependencies)

packages/headless/tsconfig.json

@@ -33,6 +33,9 @@
     {
       "path": "../core-loggers"
     },
+    {
+      "path": "../crypto.base32-hash"
+    },
     {
       "path": "../dependency-path"
     },

packages/lifecycle/src/index.ts

@@ -25,6 +25,10 @@ export async function runPostinstallHooks (
   if (pkg.scripts == null) {
     pkg.scripts = {}
   }
+  if (opts.patchPath) {
+    pkg.scripts['pnpm:patch'] = `git apply ${opts.patchPath}`
+    await runLifecycleHook('pnpm:patch', pkg, opts)
+  }
 
   if (!pkg.scripts.install) {
     await checkBindingGyp(opts.pkgRoot, pkg.scripts)
@@ -42,7 +46,8 @@ export async function runPostinstallHooks (
 
   return pkg.scripts.preinstall != null ||
     pkg.scripts.install != null ||
-    pkg.scripts.postinstall != null
+    pkg.scripts.postinstall != null ||
+    Boolean(opts.patchPath)
 }
 
 /**

packages/lifecycle/src/runLifecycleHook.ts

@@ -12,6 +12,7 @@ export interface RunLifecycleHookOptions {
   extraEnv?: Record<string, string>
   initCwd?: string
   optional?: boolean
+  patchPath?: string
   pkgRoot: string
   rawConfig: object
   rootModulesDir: string

packages/lockfile-types/src/index.ts

@@ -8,6 +8,7 @@ export interface Lockfile {
   onlyBuiltDependencies?: string[]
   overrides?: Record<string, string>
   packageExtensionsChecksum?: string
+  patchedDependencies?: Record<string, string>
 }
 
 export interface ProjectSnapshot {

packages/package-store/src/storeController/index.ts

@@ -53,23 +53,23 @@ export default async function (
     upload,
   }
 
-  async function upload (builtPkgLocation: string, opts: {filesIndexFile: string, engine: string}) {
+  async function upload (builtPkgLocation: string, opts: {filesIndexFile: string, sideEffectsCacheKey: string}) {
     const sideEffectsIndex = await cafs.addFilesFromDir(builtPkgLocation)
     // TODO: move this to a function
     // This is duplicated in @pnpm/package-requester
     const integrity: Record<string, PackageFileInfo> = {}
     await Promise.all(
-      Object.keys(sideEffectsIndex)
+      Object.entries(sideEffectsIndex)
-        .map(async (filename) => {
+        .map(async ([filename, { writeResult, mode, size }]) => {
           const {
             checkedAt,
             integrity: fileIntegrity,
-          } = await sideEffectsIndex[filename].writeResult
+          } = await writeResult
           integrity[filename] = {
             checkedAt,
             integrity: fileIntegrity.toString(), // TODO: use the raw Integrity object
-            mode: sideEffectsIndex[filename].mode,
+            mode,
-            size: sideEffectsIndex[filename].size,
+            size,
           }
         })
     )
@@ -80,7 +80,7 @@ export default async function (
       filesIndex = { files: integrity }
     }
     filesIndex.sideEffects = filesIndex.sideEffects ?? {}
-    filesIndex.sideEffects[opts.engine] = integrity
+    filesIndex.sideEffects[opts.sideEffectsCacheKey] = integrity
     await writeJsonFile(opts.filesIndexFile, filesIndex, { indent: undefined })
   }
 }

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

@@ -11,6 +11,7 @@ export default function getOptionsFromRootManifest (manifest: ProjectManifest):
   neverBuiltDependencies?: string[]
   onlyBuiltDependencies?: string[]
   packageExtensions?: Record<string, PackageExtension>
+  patchedDependencies?: Record<string, string>
   peerDependencyRules?: PeerDependencyRules
 } {
   // We read Yarn's resolutions field for compatibility
@@ -22,6 +23,7 @@ export default function getOptionsFromRootManifest (manifest: ProjectManifest):
   const packageExtensions = manifest.pnpm?.packageExtensions
   const peerDependencyRules = manifest.pnpm?.peerDependencyRules
   const allowedDeprecatedVersions = manifest.pnpm?.allowedDeprecatedVersions
+  const patchedDependencies = manifest.pnpm?.patchedDependencies
   return {
     allowedDeprecatedVersions,
     overrides,
@@ -29,5 +31,6 @@ export default function getOptionsFromRootManifest (manifest: ProjectManifest):
     onlyBuiltDependencies,
     packageExtensions,
     peerDependencyRules,
+    patchedDependencies,
   }
 }

packages/resolve-dependencies/package.json

@@ -31,6 +31,7 @@
   "dependencies": {
     "@pnpm/constants": "workspace:6.1.0",
     "@pnpm/core-loggers": "workspace:7.0.3",
+    "@pnpm/crypto.base32-hash": "workspace:1.0.0",
     "@pnpm/error": "workspace:3.0.1",
     "@pnpm/lockfile-types": "workspace:4.0.3",
     "@pnpm/lockfile-utils": "workspace:4.0.5",

packages/resolve-dependencies/src/index.ts

@@ -256,7 +256,8 @@ async function finishLockfileUpdates (
           Boolean(pkgJson.scripts.postinstall)
         ) ||
         filesResponse.filesIndex['binding.gyp'] ||
-          Object.keys(filesResponse.filesIndex).some((filename) => !(filename.match(/^[.]hooks[\\/]/) == null)) // TODO: optimize this
+          Object.keys(filesResponse.filesIndex).some((filename) => !(filename.match(/^[.]hooks[\\/]/) == null)) || // TODO: optimize this
+        depNode.patchFile != null
       )
     } else {
       // This should never ever happen

packages/resolve-dependencies/src/resolveDependencies.ts

@@ -4,6 +4,7 @@ import {
   progressLogger,
   skippedOptionalDependencyLogger,
 } from '@pnpm/core-loggers'
+import { createBase32HashFromFile } from '@pnpm/crypto.base32-hash'
 import PnpmError from '@pnpm/error'
 import {
   Lockfile,
@@ -129,6 +130,7 @@ export interface ResolutionContext {
   resolvedPackagesByDepPath: ResolvedPackagesByDepPath
   outdatedDependencies: {[pkgId: string]: string}
   childrenByParentDepPath: ChildrenByParentDepPath
+  patchedDependencies?: Record<string, string>
   pendingNodes: PendingNode[]
   wantedLockfile: Lockfile
   currentLockfile: Lockfile
@@ -195,6 +197,10 @@ export interface ResolvedPackage {
   optionalDependencies: Set<string>
   hasBin: boolean
   hasBundledDependencies: boolean
+  patchFile?: {
+    path: string
+    hash: string
+  }
   prepare: boolean
   depPath: string
   requiresBuild: boolean | SafePromiseDefer<boolean>
@@ -915,12 +921,18 @@ async function resolveDependency (
       status: 'resolved',
     })
 
-    ctx.resolvedPackagesByDepPath[depPath] = getResolvedPackage({
+    let patchPath = ctx.patchedDependencies?.[`${pkg.name}@${pkg.version}`]
+    if (patchPath) {
+      patchPath = path.join(ctx.lockfileDir, patchPath)
+    }
+
+    ctx.resolvedPackagesByDepPath[depPath] = await getResolvedPackage({
       allowBuild: ctx.allowBuild,
       dependencyLockfile: currentPkg.dependencyLockfile,
       depPath,
       force: ctx.force,
       hasBin,
+      patchPath,
       pkg,
       pkgResponse,
       prepare,
@@ -1005,19 +1017,20 @@ function pkgIsLeaf (pkg: PackageManifest) {
     isEmpty(pkg.peerDependencies ?? {})
 }
 
-function getResolvedPackage (
+async function getResolvedPackage (
   options: {
     allowBuild?: (pkgName: string) => boolean
     dependencyLockfile?: PackageSnapshot
     depPath: string
     force: boolean
     hasBin: boolean
+    patchPath?: string
     pkg: PackageManifest
     pkgResponse: PackageResponse
     prepare: boolean
     wantedDependency: WantedDependency
   }
-) {
+): Promise<ResolvedPackage> {
   const peerDependencies = peerDependenciesWithoutOwn(options.pkg)
 
   const requiresBuild = (options.allowBuild == null || options.allowBuild(options.pkg.name))
@@ -1046,6 +1059,9 @@ function getResolvedPackage (
     name: options.pkg.name,
     optional: options.wantedDependency.optional,
     optionalDependencies: new Set(Object.keys(options.pkg.optionalDependencies ?? {})),
+    patchFile: options.patchPath
+      ? { path: options.patchPath, hash: await createBase32HashFromFile(options.patchPath) }
+      : undefined,
     peerDependencies: peerDependencies ?? {},
     peerDependenciesMeta: options.pkg.peerDependenciesMeta,
     prepare: options.prepare,

packages/resolve-dependencies/src/resolveDependencyTree.ts

@@ -67,6 +67,7 @@ export interface ResolveDependenciesOptions {
   }
   nodeVersion: string
   registries: Registries
+  patchedDependencies?: Record<string, string>
   pnpmVersion: string
   preferredVersions?: PreferredVersions
   preferWorkspacePackages?: boolean
@@ -103,6 +104,7 @@ export default async function<T> (
     lockfileDir: opts.lockfileDir,
     nodeVersion: opts.nodeVersion,
     outdatedDependencies: {} as {[pkgId: string]: string},
+    patchedDependencies: opts.patchedDependencies,
     pendingNodes: [] as PendingNode[],
     pnpmVersion: opts.pnpmVersion,
     preferWorkspacePackages: opts.preferWorkspacePackages,

packages/resolve-dependencies/tsconfig.json

@@ -15,6 +15,9 @@
     {
       "path": "../core-loggers"
     },
+    {
+      "path": "../crypto.base32-hash"
+    },
     {
       "path": "../dependency-path"
     },

packages/server/src/connectStoreController.ts

@@ -46,7 +46,7 @@ export default async function (
       stop: async () => {
         await limitedFetch(`${remotePrefix}/stop`, {})
       },
-      upload: async (builtPkgLocation: string, opts: {filesIndexFile: string, engine: string}) => {
+      upload: async (builtPkgLocation: string, opts: {filesIndexFile: string, sideEffectsCacheKey: string}) => {
         await limitedFetch(`${remotePrefix}/upload`, {
           builtPkgLocation,
           opts,

packages/server/test/index.ts

@@ -167,7 +167,7 @@ test('server upload', async () => {
   const filesIndexFile = path.join(storeDir, 'test.example.com/fake-pkg/1.0.0.json')
 
   await storeCtrl.upload(path.join(__dirname, 'side-effect-fake-dir'), {
-    engine: fakeEngine,
+    sideEffectsCacheKey: fakeEngine,
     filesIndexFile,
   })
 
@@ -199,7 +199,7 @@ test('disable server upload', async () => {
   let thrown = false
   try {
     await storeCtrl.upload(path.join(__dirname, 'side-effect-fake-dir'), {
-      engine: fakeEngine,
+      sideEffectsCacheKey: fakeEngine,
       filesIndexFile,
     })
   } catch (e) {

packages/store-controller-types/src/index.ts

@@ -35,13 +35,20 @@ DependencyManifest,
 | 'version'
 >
 
+export interface UploadPkgToStoreOpts {
+  filesIndexFile: string
+  sideEffectsCacheKey: string
+}
+
+export type UploadPkgToStore = (builtPkgLocation: string, opts: UploadPkgToStoreOpts) => Promise<void>
+
 export interface StoreController {
   requestPackage: RequestPackageFunction
   fetchPackage: FetchPackageToStoreFunction
   importPackage: ImportPackageFunction
   close: () => Promise<void>
   prune: () => Promise<void>
-  upload: (builtPkgLocation: string, opts: {filesIndexFile: string, engine: string}) => Promise<void>
+  upload: UploadPkgToStore
 }
 
 export type FetchPackageToStoreFunction = (

packages/types/src/package.ts

@@ -50,6 +50,7 @@ export interface DependenciesMeta {
   [dependencyName: string]: {
     injected?: boolean
     node?: string
+    patch?: string
   }
 }
 
@@ -126,6 +127,7 @@ export type ProjectManifest = BaseManifest & {
     packageExtensions?: Record<string, PackageExtension>
     peerDependencyRules?: PeerDependencyRules
     allowedDeprecatedVersions?: AllowedDeprecatedVersions
+    patchedDependencies?: Record<string, string>
   }
   private?: boolean
   resolutions?: Record<string, string>

pnpm-lock.yaml

@@ -1125,6 +1125,7 @@ importers:
       '@pnpm/client': workspace:7.1.5
       '@pnpm/constants': workspace:6.1.0
       '@pnpm/core-loggers': workspace:7.0.3
+      '@pnpm/crypto.base32-hash': workspace:1.0.0
       '@pnpm/error': workspace:3.0.1
       '@pnpm/filter-lockfile': workspace:6.0.6
       '@pnpm/headless': workspace:18.2.0
@@ -1173,6 +1174,7 @@ importers:
       '@pnpm/calc-dep-state': link:../calc-dep-state
       '@pnpm/constants': link:../constants
       '@pnpm/core-loggers': link:../core-loggers
+      '@pnpm/crypto.base32-hash': link:../crypto.base32-hash
       '@pnpm/error': link:../error
       '@pnpm/filter-lockfile': link:../filter-lockfile
       '@pnpm/hoist': link:../hoist
@@ -3211,6 +3213,7 @@ importers:
     specifiers:
       '@pnpm/constants': workspace:6.1.0
       '@pnpm/core-loggers': workspace:7.0.3
+      '@pnpm/crypto.base32-hash': workspace:1.0.0
       '@pnpm/error': workspace:3.0.1
       '@pnpm/lockfile-types': workspace:4.0.3
       '@pnpm/lockfile-utils': workspace:4.0.5
@@ -3246,6 +3249,7 @@ importers:
     dependencies:
       '@pnpm/constants': link:../constants
       '@pnpm/core-loggers': link:../core-loggers
+      '@pnpm/crypto.base32-hash': link:../crypto.base32-hash
       '@pnpm/error': link:../error
       '@pnpm/lockfile-types': link:../lockfile-types
       '@pnpm/lockfile-utils': link:../lockfile-utils