feat: when patch package does not specify a version, use locally installed version by default. (#6197)

close #6192
2026-02-15 01:24:07 -05:00 · 2023-03-13 22:40:21 +08:00
parent 787c43dcc1
commit 185ab01adf
13 changed files with 404 additions and 61 deletions
--- a/.changeset/khaki-icons-rest.md
+++ b/.changeset/khaki-icons-rest.md
@@ -0,0 +1,8 @@
+---
+"@pnpm/plugin-commands-patching": patch
+"@pnpm/audit": patch
+"@pnpm/list": patch
+"pnpm": patch
+---
+
+When patch package does not specify a version, use locally installed version by default [#6192](https://github.com/pnpm/pnpm/issues/6192).
--- a/.gitignore
+++ b/.gitignore
@@ -47,3 +47,5 @@ RELEASE.md

 ## custom modules-dir fixture
 __fixtures__/custom-modules-dir/**/fake_modules/
+__fixtures__/custom-modules-dir/cache/
+__fixtures__/custom-modules-dir/patches/
--- a/lockfile/audit/src/index.ts
+++ b/lockfile/audit/src/index.ts
@@ -6,7 +6,7 @@ import { Lockfile } from '@pnpm/lockfile-types'
 import { DependenciesField } from '@pnpm/types'
 import { lockfileToAuditTree } from './lockfileToAuditTree'
 import { AuditReport } from './types'
-import { searchForPackages, PackageNode } from '@pnpm/list'
+import { searchForPackages, flattenSearchedPackages } from '@pnpm/list'

 export * from './types'

@@ -95,28 +95,7 @@ async function searchPackagePaths (
  pkg: string
 ) {
  const pkgs = await searchForPackages([pkg], projectDirs, searchOpts)
-  const paths: string[] = []
-
-  for (const pkg of pkgs) {
-    _walker([
-      ...(pkg.optionalDependencies ?? []),
-      ...(pkg.dependencies ?? []),
-      ...(pkg.devDependencies ?? []),
-      ...(pkg.unsavedDependencies ?? []),
-    ], path.relative(searchOpts.lockfileDir, pkg.path) || '.')
-  }
-  return paths
-
-  function _walker (packages: PackageNode[], depPath: string) {
-    for (const pkg of packages) {
-      const nextDepPath = `${depPath} > ${pkg.name}@${pkg.version}`
-      if (pkg.dependencies?.length) {
-        _walker(pkg.dependencies, nextDepPath)
-      } else {
-        paths.push(nextDepPath)
-      }
-    }
-  }
+  return flattenSearchedPackages(pkgs, { lockfileDir: searchOpts.lockfileDir }).map(({ depPath }) => depPath)
 }

 export class AuditEndpointNotExistsError extends PnpmError {
--- a/patching/plugin-commands-patching/package.json
+++ b/patching/plugin-commands-patching/package.json
@@ -37,13 +37,17 @@
    "@pnpm/plugin-commands-patching": "workspace:*",
    "@pnpm/prepare": "workspace:*",
    "@pnpm/registry-mock": "3.5.0",
+    "@pnpm/test-fixtures": "workspace:*",
    "@types/ramda": "0.28.20",
+    "@types/semver": "7.3.13",
    "write-yaml-file": "^4.2.0"
  },
  "dependencies": {
    "@pnpm/cli-utils": "workspace:*",
    "@pnpm/config": "workspace:*",
+    "@pnpm/constants": "workspace:*",
    "@pnpm/error": "workspace:*",
+    "@pnpm/modules-yaml": "workspace:*",
    "@pnpm/parse-wanted-dependency": "workspace:*",
    "@pnpm/patching.apply-patch": "workspace:*",
    "@pnpm/pick-registry-for-package": "workspace:*",
@@ -51,10 +55,15 @@
    "@pnpm/read-package-json": "workspace:*",
    "@pnpm/read-project-manifest": "workspace:*",
    "@pnpm/store-connection-manager": "workspace:*",
+    "@pnpm/lockfile-file": "workspace:*",
+    "@pnpm/lockfile-utils": "workspace:*",
+    "enquirer": "^2.3.6",
    "escape-string-regexp": "^4.0.0",
    "ramda": "npm:@pnpm/ramda@0.28.1",
+    "realpath-missing": "^1.1.0",
    "render-help": "^1.0.3",
    "safe-execa": "^0.1.3",
+    "semver": "^7.3.8",
    "tempy": "^1.0.1"
  },
  "peerDependencies": {
--- a/patching/plugin-commands-patching/src/getPatchedDependency.ts
+++ b/patching/plugin-commands-patching/src/getPatchedDependency.ts
@@ -0,0 +1,72 @@
+import path from 'path'
+import { parseWantedDependency, ParseWantedDependencyResult } from '@pnpm/parse-wanted-dependency'
+import { prompt } from 'enquirer'
+import { readCurrentLockfile } from '@pnpm/lockfile-file'
+import { nameVerFromPkgSnapshot } from '@pnpm/lockfile-utils'
+import { PnpmError } from '@pnpm/error'
+import { WANTED_LOCKFILE } from '@pnpm/constants'
+import { readModulesManifest } from '@pnpm/modules-yaml'
+import realpathMissing from 'realpath-missing'
+import semver from 'semver'
+import { Config } from '@pnpm/config'
+
+type GetPatchedDependencyOptions = {
+  lockfileDir: string
+} & Pick<Config, 'virtualStoreDir' | 'modulesDir'>
+
+export async function getPatchedDependency (rawDependency: string, opts: GetPatchedDependencyOptions): Promise<ParseWantedDependencyResult> {
+  const dep = parseWantedDependency(rawDependency)
+
+  const { versions, preferredVersions } = await getVersionsFromLockfile(dep, opts)
+
+  if (!preferredVersions.length) {
+    throw new PnpmError(
+      'PATCH_VERSION_NOT_FOUND',
+      `Can not find ${rawDependency} in project ${opts.lockfileDir}, ${versions.length ? `you can specify currently installed version: ${versions.join(', ')}.` : `did you forget to install ${rawDependency}?`}`
+    )
+  }
+
+  dep.alias = dep.alias ?? rawDependency
+  if (preferredVersions.length > 1) {
+    const { version } = await prompt<{
+      version: string
+    }>({
+      type: 'select',
+      name: 'version',
+      message: 'Choose which version to patch',
+      choices: versions,
+    })
+    dep.pref = version
+  } else {
+    dep.pref = preferredVersions[0]
+  }
+
+  return dep
+}
+
+async function getVersionsFromLockfile (dep: ParseWantedDependencyResult, opts: GetPatchedDependencyOptions) {
+  const modulesDir = await realpathMissing(path.join(opts.lockfileDir, opts.modulesDir ?? 'node_modules'))
+  const modules = await readModulesManifest(modulesDir)
+  const lockfile = (modules?.virtualStoreDir && await readCurrentLockfile(modules.virtualStoreDir, {
+    ignoreIncompatible: true,
+  })) ?? null
+
+  if (!lockfile) {
+    throw new PnpmError(
+      'PATCH_NO_LOCKFILE',
+      `No ${WANTED_LOCKFILE} found: Cannot patch without a lockfile`
+    )
+  }
+
+  const pkgName = dep.alias && dep.pref ? dep.alias : (dep.pref ?? dep.alias)
+
+  const versions = Object.entries(lockfile.packages ?? {})
+    .map(([depPath, pkgSnapshot]) => nameVerFromPkgSnapshot(depPath, pkgSnapshot))
+    .filter(({ name }) => name === pkgName)
+    .map(({ version }) => version)
+
+  return {
+    versions,
+    preferredVersions: versions.filter(version => dep.alias && dep.pref ? semver.satisfies(version, dep.pref) : true),
+  }
+}
--- a/patching/plugin-commands-patching/src/patch.ts
+++ b/patching/plugin-commands-patching/src/patch.ts
@@ -11,7 +11,9 @@ import pick from 'ramda/src/pick'
 import renderHelp from 'render-help'
 import tempy from 'tempy'
 import { PnpmError } from '@pnpm/error'
-import { writePackage, ParseWantedDependencyResult } from './writePackage'
+import { ParseWantedDependencyResult } from '@pnpm/parse-wanted-dependency'
+import { writePackage } from './writePackage'
+import { getPatchedDependency } from './getPatchedDependency'

 export function rcOptionsTypes () {
  return pick([], allTypes)
@@ -48,7 +50,16 @@ export function help () {
  })
 }

-export type PatchCommandOptions = Pick<Config, 'dir' | 'registries' | 'tag' | 'storeDir' | 'rootProjectManifest' | 'lockfileDir'> & CreateStoreControllerOptions & {
+export type PatchCommandOptions = Pick<Config,
+| 'dir'
+| 'registries'
+| 'tag'
+| 'storeDir'
+| 'rootProjectManifest'
+| 'lockfileDir'
+| 'modulesDir'
+| 'virtualStoreDir'
+> & CreateStoreControllerOptions & {
  editDir?: string
  reporter?: (logObj: LogBase) => void
  ignoreExisting?: boolean
@@ -58,14 +69,24 @@ export async function handler (opts: PatchCommandOptions, params: string[]) {
  if (opts.editDir && fs.existsSync(opts.editDir) && fs.readdirSync(opts.editDir).length > 0) {
    throw new PnpmError('PATCH_EDIT_DIR_EXISTS', `The target directory already exists: '${opts.editDir}'`)
  }
+  if (!params[0]) {
+    throw new PnpmError('MISSING_PACKAGE_NAME', '`pnpm patch` requires the package name')
+  }
  const editDir = opts.editDir ?? tempy.directory()
-  const patchedDep = await writePackage(params[0], editDir, opts)
+  const lockfileDir = opts.lockfileDir ?? opts.dir ?? process.cwd()
+  const patchedDep = await getPatchedDependency(params[0], {
+    lockfileDir,
+    modulesDir: opts.modulesDir,
+    virtualStoreDir: opts.virtualStoreDir,
+  })
+
+  await writePackage(patchedDep, editDir, opts)
  if (!opts.ignoreExisting && opts.rootProjectManifest?.pnpm?.patchedDependencies) {
    tryPatchWithExistingPatchFile({
      patchedDep,
      patchedDir: editDir,
      patchedDependencies: opts.rootProjectManifest.pnpm.patchedDependencies,
-      lockfileDir: opts.lockfileDir ?? opts.dir ?? process.cwd(),
+      lockfileDir,
    })
  }
  return `You can now edit the following folder: ${editDir}
--- a/patching/plugin-commands-patching/src/patchCommit.ts
+++ b/patching/plugin-commands-patching/src/patchCommit.ts
@@ -11,6 +11,7 @@ import escapeStringRegexp from 'escape-string-regexp'
 import renderHelp from 'render-help'
 import tempy from 'tempy'
 import { writePackage } from './writePackage'
+import { parseWantedDependency } from '@pnpm/parse-wanted-dependency'

 export const rcOptionsTypes = cliOptionsTypes

@@ -37,7 +38,7 @@ export async function handler (opts: install.InstallCommandOptions & Pick<Config
  const patchedPkgManifest = await readPackageJsonFromDir(userDir)
  const pkgNameAndVersion = `${patchedPkgManifest.name}@${patchedPkgManifest.version}`
  const srcDir = tempy.directory()
-  await writePackage(pkgNameAndVersion, srcDir, opts)
+  await writePackage(parseWantedDependency(pkgNameAndVersion), srcDir, opts)
  const patchContent = await diffFolders(srcDir, userDir)
  const patchFileName = pkgNameAndVersion.replace('/', '__')
  await fs.promises.writeFile(path.join(patchesDir, `${patchFileName}.patch`), patchContent, 'utf8')
--- a/patching/plugin-commands-patching/src/writePackage.ts
+++ b/patching/plugin-commands-patching/src/writePackage.ts
@@ -4,14 +4,11 @@ import {
  CreateStoreControllerOptions,
 } from '@pnpm/store-connection-manager'
 import { pickRegistryForPackage } from '@pnpm/pick-registry-for-package'
-import { parseWantedDependency, ParseWantedDependencyResult } from '@pnpm/parse-wanted-dependency'
-
-export { ParseWantedDependencyResult }
+import type { ParseWantedDependencyResult } from '@pnpm/parse-wanted-dependency'

 export type WritePackageOptions = CreateStoreControllerOptions & Pick<Config, 'registries'>

-export async function writePackage (pkg: string, dest: string, opts: WritePackageOptions): Promise<ParseWantedDependencyResult> {
-  const dep = parseWantedDependency(pkg)
+export async function writePackage (dep: ParseWantedDependencyResult, dest: string, opts: WritePackageOptions) {
  const store = await createOrConnectStoreController({
    ...opts,
    packageImportMethod: 'clone-or-copy',
@@ -28,5 +25,4 @@ export async function writePackage (pkg: string, dest: string, opts: WritePackag
    filesResponse,
    force: true,
  })
-  return dep
 }
--- a/patching/plugin-commands-patching/test/patch.test.ts
+++ b/patching/plugin-commands-patching/test/patch.test.ts
@@ -10,31 +10,51 @@ import { patch, patchCommit } from '@pnpm/plugin-commands-patching'
 import { readProjectManifest } from '@pnpm/read-project-manifest'
 import { REGISTRY_MOCK_PORT } from '@pnpm/registry-mock'
 import { DEFAULT_OPTS } from './utils/index'
+import { fixtures } from '@pnpm/test-fixtures'
+import * as enquirer from 'enquirer'
+
+jest.mock('enquirer', () => ({ prompt: jest.fn() }))
+
+// eslint-disable-next-line
+const prompt = enquirer.prompt as any
+const f = fixtures(__dirname)
+const customModulesDirFixture = f.find('custom-modules-dir')
+
+const basePatchOption = {
+  pnpmHomeDir: '',
+  rawConfig: {
+    registry: `http://localhost:${REGISTRY_MOCK_PORT}/`,
+  },
+  registries: { default: `http://localhost:${REGISTRY_MOCK_PORT}/` },
+  userConfig: {},
+  virtualStoreDir: 'node_modules/.pnpm',
+}

 describe('patch and commit', () => {
  let defaultPatchOption: patch.PatchCommandOptions

-  beforeEach(() => {
+  beforeEach(async () => {
    prepare({
      dependencies: {
        'is-positive': '1.0.0',
      },
    })
-
    const cacheDir = path.resolve('cache')
    const storeDir = path.resolve('store')
-
    defaultPatchOption = {
+      ...basePatchOption,
      cacheDir,
      dir: process.cwd(),
-      pnpmHomeDir: '',
-      rawConfig: {
-        registry: `http://localhost:${REGISTRY_MOCK_PORT}/`,
-      },
-      registries: { default: `http://localhost:${REGISTRY_MOCK_PORT}/` },
      storeDir,
-      userConfig: {},
    }
+
+    await install.handler({
+      ...DEFAULT_OPTS,
+      cacheDir,
+      storeDir,
+      dir: process.cwd(),
+      saveLockfile: true,
+    })
  })

  test('patch and commit', async () => {
@@ -55,6 +75,8 @@ describe('patch and commit', () => {
    await patchCommit.handler({
      ...DEFAULT_OPTS,
      dir: process.cwd(),
+      frozenLockfile: false,
+      fixLockfile: true,
    }, [patchDir])

    const { manifest } = await readProjectManifest(process.cwd())
@@ -84,6 +106,8 @@ describe('patch and commit', () => {
    await patchCommit.handler({
      ...DEFAULT_OPTS,
      dir: process.cwd(),
+      frozenLockfile: false,
+      fixLockfile: true,
    }, [patchDir])

    expect(fs.readFileSync('node_modules/is-positive/index.js', 'utf8')).toContain('// test patching')
@@ -111,6 +135,8 @@ describe('patch and commit', () => {
    await patchCommit.handler({
      ...DEFAULT_OPTS,
      dir: process.cwd(),
+      frozenLockfile: false,
+      fixLockfile: true,
    }, [patchDir])

    expect(fs.readFileSync('node_modules/is-positive/index.js', 'utf8')).toContain('// test patching')
@@ -126,6 +152,8 @@ describe('patch and commit', () => {
    await patchCommit.handler({
      ...DEFAULT_OPTS,
      dir: process.cwd(),
+      frozenLockfile: false,
+      fixLockfile: true,
    }, [patchDir])

    const { manifest } = await readProjectManifest(process.cwd())
@@ -171,6 +199,8 @@ describe('patch and commit', () => {
    await patchCommit.handler({
      ...DEFAULT_OPTS,
      dir: process.cwd(),
+      frozenLockfile: false,
+      fixLockfile: true,
    }, [patchDir])

    const { manifest } = await readProjectManifest(process.cwd())
@@ -187,12 +217,101 @@ describe('patch and commit', () => {
    expect(fs.existsSync(path.join(patchDir, 'license'))).toBe(true)
    expect(fs.readFileSync(path.join(patchDir, 'index.js'), 'utf8')).not.toContain('// test patching')
  })
+
+  test('patch throw an error if no package specified', async () => {
+    await expect(() => patch.handler({ ...defaultPatchOption }, []))
+      .rejects.toThrow('`pnpm patch` requires the package name')
+  })
+
+  test('should throw an error if no installed versions found for patched package', async () => {
+    await expect(() => patch.handler(defaultPatchOption, ['chalk']))
+      .rejects.toThrow(`Can not find chalk in project ${process.cwd()}, did you forget to install chalk?`)
+  })
+
+  test('should throw an error if no preferred versions found for patched package', async () => {
+    await expect(() => patch.handler(defaultPatchOption, ['is-positive@2.0.0']))
+      .rejects.toThrow(`Can not find is-positive@2.0.0 in project ${process.cwd()}, you can specify currently installed version: 1.0.0.`)
+  })
+
+  test('patch package with installed version', async () => {
+    const output = await patch.handler(defaultPatchOption, ['is-positive@1'])
+    const patchDir = getPatchDirFromPatchOutput(output)
+    const tempDir = os.tmpdir()
+    expect(patchDir).toContain(tempDir)
+    expect(fs.existsSync(patchDir)).toBe(true)
+    expect(JSON.parse(fs.readFileSync(path.join(patchDir, 'package.json'), 'utf8')).version).toBe('1.0.0')
+  })
+})
+
+describe('prompt to choose version', () => {
+  let defaultPatchOption: patch.PatchCommandOptions
+  let cacheDir: string
+  let storeDir: string
+  beforeEach(() => {
+    prepare({
+      dependencies: {
+        ava: '5.2.0',
+        chalk: '4.1.2',
+      },
+    })
+    cacheDir = path.resolve('cache')
+    storeDir = path.resolve('store')
+    defaultPatchOption = {
+      ...basePatchOption,
+      cacheDir,
+      dir: process.cwd(),
+      storeDir,
+    }
+  })
+
+  test('prompt to choose version if multiple version founded for patched package', async () => {
+    await install.handler({
+      ...DEFAULT_OPTS,
+      cacheDir,
+      storeDir,
+      dir: process.cwd(),
+      saveLockfile: true,
+    })
+    prompt.mockResolvedValue({
+      version: '5.2.0',
+    })
+
+    const output = await patch.handler(defaultPatchOption, ['chalk'])
+
+    expect(prompt.mock.calls[0][0].choices).toEqual(expect.arrayContaining(['5.2.0', '4.1.2']))
+    prompt.mockClear()
+
+    const patchDir = getPatchDirFromPatchOutput(output)
+    const tempDir = os.tmpdir()
+
+    expect(patchDir).toContain(tempDir)
+    expect(fs.existsSync(patchDir)).toBe(true)
+    expect(JSON.parse(fs.readFileSync(path.join(patchDir, 'package.json'), 'utf8')).version).toBe('5.2.0')
+    expect(fs.existsSync(path.join(patchDir, 'source/index.js'))).toBe(true)
+
+    fs.appendFileSync(path.join(patchDir, 'source/index.js'), '// test patching', 'utf8')
+    await patchCommit.handler({
+      ...DEFAULT_OPTS,
+      dir: process.cwd(),
+      frozenLockfile: false,
+      fixLockfile: true,
+    }, [patchDir])
+
+    const { manifest } = await readProjectManifest(process.cwd())
+    expect(manifest.pnpm?.patchedDependencies).toStrictEqual({
+      'chalk@5.2.0': 'patches/chalk@5.2.0.patch',
+    })
+    const patchContent = fs.readFileSync('patches/chalk@5.2.0.patch', 'utf8')
+    expect(patchContent).toContain('diff --git')
+    expect(patchContent).toContain('// test patching')
+    expect(fs.readFileSync('node_modules/.pnpm/ava@5.2.0/node_modules/chalk/source/index.js', 'utf8')).toContain('// test patching')
+  })
 })

 describe('patching should work when there is a no EOL in the patched file', () => {
  let defaultPatchOption: patch.PatchCommandOptions

-  beforeEach(() => {
+  beforeEach(async () => {
    prepare({
      dependencies: {
        'safe-execa': '0.1.2',
@@ -203,16 +322,19 @@ describe('patching should work when there is a no EOL in the patched file', () =
    const storeDir = path.resolve('store')

    defaultPatchOption = {
+      ...basePatchOption,
      cacheDir,
      dir: process.cwd(),
-      pnpmHomeDir: '',
-      rawConfig: {
-        registry: `http://localhost:${REGISTRY_MOCK_PORT}/`,
-      },
-      registries: { default: `http://localhost:${REGISTRY_MOCK_PORT}/` },
      storeDir,
-      userConfig: {},
    }
+
+    await install.handler({
+      ...DEFAULT_OPTS,
+      cacheDir,
+      storeDir,
+      dir: process.cwd(),
+      saveLockfile: true,
+    })
  })
  it('should work when adding content on a newline', async () => {
    const output = await patch.handler(defaultPatchOption, ['safe-execa@0.1.2'])
@@ -228,6 +350,8 @@ describe('patching should work when there is a no EOL in the patched file', () =
    await patchCommit.handler({
      ...DEFAULT_OPTS,
      dir: process.cwd(),
+      frozenLockfile: false,
+      fixLockfile: true,
    }, [userPatchDir])

    const { manifest } = await readProjectManifest(process.cwd())
@@ -254,6 +378,8 @@ describe('patching should work when there is a no EOL in the patched file', () =
    await patchCommit.handler({
      ...DEFAULT_OPTS,
      dir: process.cwd(),
+      frozenLockfile: false,
+      fixLockfile: true,
    }, [userPatchDir])

    const { manifest } = await readProjectManifest(process.cwd())
@@ -300,15 +426,10 @@ describe('patch and commit in workspaces', () => {
    storeDir = path.resolve('store')

    defaultPatchOption = {
+      ...basePatchOption,
      cacheDir,
      dir: process.cwd(),
-      pnpmHomeDir: '',
-      rawConfig: {
-        registry: `http://localhost:${REGISTRY_MOCK_PORT}/`,
-      },
-      registries: { default: `http://localhost:${REGISTRY_MOCK_PORT}/` },
      storeDir,
-      userConfig: {},
    }
  })

@@ -322,11 +443,11 @@ describe('patch and commit in workspaces', () => {
      allProjects,
      allProjectsGraph,
      dir: process.cwd(),
+      lockfileDir: process.cwd(),
      selectedProjectsGraph,
      workspaceDir: process.cwd(),
      saveLockfile: true,
    })
-
    const output = await patch.handler(defaultPatchOption, ['is-positive@1.0.0'])
    const patchDir = getPatchDirFromPatchOutput(output)
    const tempDir = os.tmpdir()
@@ -350,6 +471,8 @@ describe('patch and commit in workspaces', () => {
      lockfileDir: process.cwd(),
      workspaceDir: process.cwd(),
      saveLockfile: true,
+      frozenLockfile: false,
+      fixLockfile: true,
    }, [patchDir])

    const { manifest } = await readProjectManifest(process.cwd())
@@ -366,6 +489,66 @@ describe('patch and commit in workspaces', () => {
  })
 })

+describe('patch with custom modules-dir and virtual-store-dir', () => {
+  const cacheDir = path.resolve(customModulesDirFixture, 'cache')
+  const storeDir = path.resolve(customModulesDirFixture, 'store')
+  const defaultPatchOption = {
+    ...basePatchOption,
+    cacheDir,
+    dir: customModulesDirFixture,
+    storeDir,
+    modulesDir: 'fake_modules',
+    virtualStoreDir: 'fake_modules/.fake_store',
+  }
+
+  test('should work with custom modules-dir and virtual-store-dir', async () => {
+    const manifest = fs.readFileSync(path.join(customModulesDirFixture, 'package.json'), 'utf8')
+    const lockfileYaml = fs.readFileSync(path.join(customModulesDirFixture, 'pnpm-lock.yaml'), 'utf8')
+    const { allProjects, allProjectsGraph, selectedProjectsGraph } = await readProjects(customModulesDirFixture, [])
+    await install.handler({
+      ...DEFAULT_OPTS,
+      cacheDir,
+      storeDir,
+      dir: customModulesDirFixture,
+      lockfileDir: customModulesDirFixture,
+      allProjects,
+      allProjectsGraph,
+      selectedProjectsGraph,
+      workspaceDir: customModulesDirFixture,
+      saveLockfile: true,
+      modulesDir: 'fake_modules',
+      virtualStoreDir: 'fake_modules/.fake_store',
+    })
+    const output = await patch.handler(defaultPatchOption, ['is-positive@1'])
+    const patchDir = getPatchDirFromPatchOutput(output)
+    const tempDir = os.tmpdir()
+    expect(patchDir).toContain(tempDir)
+    expect(fs.existsSync(patchDir)).toBe(true)
+    expect(JSON.parse(fs.readFileSync(path.join(patchDir, 'package.json'), 'utf8')).version).toBe('1.0.0')
+
+    fs.appendFileSync(path.join(patchDir, 'index.js'), '// test patching', 'utf8')
+
+    await patchCommit.handler({
+      ...DEFAULT_OPTS,
+      dir: customModulesDirFixture,
+      saveLockfile: true,
+      frozenLockfile: false,
+      fixLockfile: true,
+      allProjects,
+      allProjectsGraph,
+      selectedProjectsGraph,
+      modulesDir: 'fake_modules',
+      virtualStoreDir: 'fake_modules/.fake_store',
+      lockfileDir: customModulesDirFixture,
+      workspaceDir: customModulesDirFixture,
+    }, [patchDir])
+    expect(fs.readFileSync(path.join(customModulesDirFixture, 'packages/bar/fake_modules/is-positive/index.js'), 'utf8')).toContain('// test patching')
+    // restore package.json and package-lock.yaml
+    fs.writeFileSync(path.join(customModulesDirFixture, 'package.json'), manifest, 'utf8')
+    fs.writeFileSync(path.join(customModulesDirFixture, 'pnpm-lock.yaml'), lockfileYaml, 'utf8')
+  })
+})
+
 function getPatchDirFromPatchOutput (output: string) {
  const [firstLine] = output.split('\n')
  return firstLine.substring(firstLine.indexOf(':') + 1).trim()
--- a/patching/plugin-commands-patching/tsconfig.json
+++ b/patching/plugin-commands-patching/tsconfig.json
@@ -12,6 +12,9 @@
    {
      "path": "../../__utils__/prepare"
    },
+    {
+      "path": "../../__utils__/test-fixtures"
+    },
    {
      "path": "../../cli/cli-utils"
    },
@@ -21,12 +24,24 @@
    {
      "path": "../../config/pick-registry-for-package"
    },
+    {
+      "path": "../../lockfile/lockfile-file"
+    },
+    {
+      "path": "../../lockfile/lockfile-utils"
+    },
+    {
+      "path": "../../packages/constants"
+    },
    {
      "path": "../../packages/error"
    },
    {
      "path": "../../packages/parse-wanted-dependency"
    },
+    {
+      "path": "../../pkg-manager/modules-yaml"
+    },
    {
      "path": "../../pkg-manager/plugin-commands-installation"
    },
--- a/pnpm-lock.yaml
+++ b/pnpm-lock.yaml
@@ -2486,12 +2486,24 @@ importers:
      '@pnpm/config':
        specifier: workspace:*
        version: link:../../config/config
+      '@pnpm/constants':
+        specifier: workspace:*
+        version: link:../../packages/constants
      '@pnpm/error':
        specifier: workspace:*
        version: link:../../packages/error
+      '@pnpm/lockfile-file':
+        specifier: workspace:*
+        version: link:../../lockfile/lockfile-file
+      '@pnpm/lockfile-utils':
+        specifier: workspace:*
+        version: link:../../lockfile/lockfile-utils
      '@pnpm/logger':
        specifier: ^5.0.0
        version: 5.0.0
+      '@pnpm/modules-yaml':
+        specifier: workspace:*
+        version: link:../../pkg-manager/modules-yaml
      '@pnpm/parse-wanted-dependency':
        specifier: workspace:*
        version: link:../../packages/parse-wanted-dependency
@@ -2513,18 +2525,27 @@ importers:
      '@pnpm/store-connection-manager':
        specifier: workspace:*
        version: link:../../store/store-connection-manager
+      enquirer:
+        specifier: ^2.3.6
+        version: 2.3.6
      escape-string-regexp:
        specifier: ^4.0.0
        version: 4.0.0
      ramda:
        specifier: npm:@pnpm/ramda@0.28.1
        version: /@pnpm/ramda@0.28.1
+      realpath-missing:
+        specifier: ^1.1.0
+        version: 1.1.0
      render-help:
        specifier: ^1.0.3
        version: 1.0.3
      safe-execa:
        specifier: ^0.1.3
        version: 0.1.3
+      semver:
+        specifier: ^7.3.8
+        version: 7.3.8
      tempy:
        specifier: ^1.0.1
        version: 1.0.1
@@ -2541,9 +2562,15 @@ importers:
      '@pnpm/registry-mock':
        specifier: 3.5.0
        version: 3.5.0(typanion@3.12.1)
+      '@pnpm/test-fixtures':
+        specifier: workspace:*
+        version: link:../../__utils__/test-fixtures
      '@types/ramda':
        specifier: 0.28.20
        version: 0.28.20
+      '@types/semver':
+        specifier: 7.3.13
+        version: 7.3.13
      write-yaml-file:
        specifier: ^4.2.0
        version: 4.2.0
@@ -8006,7 +8033,7 @@ packages:
      '@pnpm/find-workspace-dir': 5.0.1
      '@pnpm/find-workspace-packages': 5.0.36(@pnpm/logger@5.0.0)(@yarnpkg/core@4.0.0-rc.14)(typanion@3.12.1)
      '@pnpm/logger': 5.0.0
-      '@pnpm/types': 8.10.0
+      '@pnpm/types': 8.9.0
      '@yarnpkg/core': 4.0.0-rc.14(typanion@3.12.1)
      load-json-file: 7.0.1
      meow: 10.1.5
@@ -8555,7 +8582,6 @@ packages:
  /@pnpm/types@8.9.0:
    resolution: {integrity: sha512-3MYHYm8epnciApn6w5Fzx6sepawmsNU7l6lvIq+ER22/DPSrr83YMhU/EQWnf4lORn2YyiXFj0FJSyJzEtIGmw==}
    engines: {node: '>=14.6'}
-    dev: false

  /@pnpm/util.lex-comparator@1.0.0:
    resolution: {integrity: sha512-3aBQPHntVgk5AweBWZn+1I/fqZ9krK/w01197aYVkAJQGftb+BVWgEepxY5GChjSW12j52XX+CmfynYZ/p0DFQ==}
--- a/pnpm/src/main.ts
+++ b/pnpm/src/main.ts
@@ -168,7 +168,7 @@ export async function main (inputArgv: string[]) {
  }

  if (
-    (cmd === 'install' || cmd === 'import' || cmd === 'dedupe' || cmd === 'patch-commit') &&
+    (cmd === 'install' || cmd === 'import' || cmd === 'dedupe' || cmd === 'patch-commit' || cmd === 'patch') &&
    typeof workspaceDir === 'string'
  ) {
    cliOptions['recursive'] = true
--- a/reviewing/list/src/index.ts
+++ b/reviewing/list/src/index.ts
@@ -1,6 +1,7 @@
+import path from 'path'
 import { readProjectManifestOnly } from '@pnpm/read-project-manifest'
 import { DependenciesField, Registries } from '@pnpm/types'
-import { buildDependenciesHierarchy } from '@pnpm/reviewing.dependencies-hierarchy'
+import { PackageNode, buildDependenciesHierarchy } from '@pnpm/reviewing.dependencies-hierarchy'
 import { createPackagesSearcher } from './createPackagesSearcher'
 import { renderJson } from './renderJson'
 import { renderParseable } from './renderParseable'
@@ -18,6 +19,36 @@ const DEFAULTS = {
  showExtraneous: true,
 }

+export function flattenSearchedPackages (pkgs: PackageDependencyHierarchy[], opts: {
+  lockfileDir: string
+}) {
+  const flattedPkgs: Array<PackageDependencyHierarchy & { depPath: string }> = []
+  for (const pkg of pkgs) {
+    _walker([
+      ...(pkg.optionalDependencies ?? []),
+      ...(pkg.dependencies ?? []),
+      ...(pkg.devDependencies ?? []),
+      ...(pkg.unsavedDependencies ?? []),
+    ], path.relative(opts.lockfileDir, pkg.path) || '.')
+  }
+
+  return flattedPkgs
+
+  function _walker (packages: PackageNode[], depPath: string) {
+    for (const pkg of packages) {
+      const nextDepPath = `${depPath} > ${pkg.name}@${pkg.version}`
+      if (pkg.dependencies?.length) {
+        _walker(pkg.dependencies, nextDepPath)
+      } else {
+        flattedPkgs.push({
+          depPath: nextDepPath,
+          ...pkg,
+        })
+      }
+    }
+  }
+}
+
 export async function searchForPackages (
  packages: string[],
  projectPaths: string[],