dep-up-surgeon 2.2.0 → 2.2.2

package/dist/cli/lockfileFix.js

@@ -0,0 +1,509 @@
+/**
+ * `--fix-lockfile` implementation.
+ *
+ * This pass improves the lockfile's dependency graph WITHOUT touching `package.json`. The
+ * two complementary effects:
+ *
+ *   1. **Dedupe** — collapse multiple copies of the same package to a single installed
+ *      version when semver ranges permit it. `npm dedupe` / `pnpm dedupe` / `yarn dedupe`
+ *      (berry only) do this natively; we just orchestrate the run and surface the diff.
+ *   2. **Outdated-but-not-vulnerable transitive detection** — a best-effort scan of the
+ *      pre-dedupe lockfile for transitives that have newer published versions available.
+ *      These are the "nobody complains about them but they're 6 months behind" deps that
+ *      no direct bump can reach. We report them; an override step (`--apply-overrides`)
+ *      handles the vulnerable subset.
+ *
+ * Safety model — we never leave the tree in a worse state than we found it:
+ *   - Backup lockfile (+ package.json, which dedupe should never touch but belt-and-braces)
+ *     before running the manager's dedupe command.
+ *   - If dedupe exits non-zero, restore the backup and report the failure.
+ *   - If the validator (same `--validate`/default heuristic as everywhere else) fails on the
+ *     deduped tree, restore the backup, reinstall, and report validation as the reason.
+ *   - On success, emit `report.lockfileFix` with a list of packages whose installed version
+ *     changed (dedup winners + losers) and a list of transitives flagged as stale.
+ *
+ * Non-goals:
+ *   - We do NOT rewrite the lockfile ourselves — only the package manager does. Parsing
+ *     lockfiles across npm v1/v2/v3, pnpm v5/v6/v9, yarn classic, and yarn berry is a
+ *     quagmire; using the tool's own command is both safer and future-proof.
+ *   - We don't attempt to dedupe yarn classic — it has no `dedupe` subcommand. We record
+ *     a `skipped: 'unsupported'` entry and move on.
+ */
+import path from 'node:path';
+import fs from 'fs-extra';
+import semver from 'semver';
+import { execa } from 'execa';
+import { log } from '../utils/logger.js';
+import { fetchLatestVersion } from '../utils/npm.js';
+import { tailLines } from '../utils/output.js';
+import { runWithConcurrency } from '../utils/concurrency.js';
+/**
+ * Returns the lockfile basename for a manager, or `undefined` when the tree has no lockfile
+ * yet (we'd create one as a side-effect of install; there's nothing to "fix" in that case).
+ */
+function lockfileBasenameFor(manager) {
+    switch (manager) {
+        case 'pnpm':
+            return 'pnpm-lock.yaml';
+        case 'yarn':
+            return 'yarn.lock';
+        case 'npm':
+        default:
+            return 'package-lock.json';
+    }
+}
+/**
+ * Build the dedupe command for each manager. Returns `undefined` when the manager has no
+ * dedupe subcommand at all (yarn classic) — caller records a skip.
+ *
+ * Notes:
+ *   - `npm dedupe` returns non-zero when audit issues are found (even without `--audit`).
+ *     We pass `--no-audit` to keep the run about dedupe only; the security loop does audit.
+ *   - `pnpm dedupe` is stable since pnpm 8.1 (Feb 2024). Older pnpm silently ignores the
+ *     subcommand with exit 1 — we treat that the same as "no changes" and move on.
+ *   - `yarn dedupe` is berry-only. Yarn classic: we detect `yarnMajorVersion < 2` externally
+ *     and return `undefined` here so the caller can emit a `skipped: unsupported` result.
+ */
+export function dedupeCommandFor(manager, opts = {}) {
+    switch (manager) {
+        case 'pnpm':
+            return { bin: 'pnpm', args: ['dedupe'] };
+        case 'yarn':
+            if ((opts.yarnMajorVersion ?? 1) >= 2) {
+                return { bin: 'yarn', args: ['dedupe'] };
+            }
+            return undefined;
+        case 'npm':
+        default:
+            return { bin: 'npm', args: ['dedupe', '--no-audit', '--loglevel', 'error'] };
+    }
+}
+/**
+ * Main entry point. Orchestrates dedupe + validation + stale-transitive scan and returns
+ * a structured report suitable for inclusion in `FinalReport.lockfileFix`.
+ */
+export async function runLockfileFix(opts) {
+    const { cwd, manager, yarnMajorVersion, json, dryRun } = opts;
+    const lockfileBasename = lockfileBasenameFor(manager);
+    const lockfilePath = path.join(cwd, lockfileBasename);
+    // No lockfile → nothing to dedupe. Emit a `skipped` report so --json consumers see the
+    // reason explicitly rather than the field being absent.
+    if (!(await fs.pathExists(lockfilePath))) {
+        return {
+            report: {
+                status: 'skipped',
+                skipReason: 'no-lockfile',
+                manager,
+                lockfile: lockfileBasename,
+                dedupeChanges: [],
+                stale: [],
+            },
+        };
+    }
+    const dedupe = dedupeCommandFor(manager, { yarnMajorVersion });
+    if (!dedupe) {
+        return {
+            report: {
+                status: 'skipped',
+                skipReason: 'unsupported',
+                manager,
+                lockfile: lockfileBasename,
+                dedupeChanges: [],
+                stale: [],
+            },
+        };
+    }
+    // Snapshot the pre-dedupe lockfile so we can diff + roll back.
+    const before = await fs.readFile(lockfilePath, 'utf8');
+    const beforeTree = parseLockfileInstalledVersions(before, manager);
+    // Pre-flight stale-transitive scan. Runs BEFORE dedupe because (a) dedupe may remove
+    // some entries entirely, and (b) we want to report what WOULD benefit from a package.json
+    // bump even if dedupe doesn't touch it. Bounded + best-effort — any error drops the scan
+    // silently so we never block on it.
+    const stale = await scanStaleTransitives(beforeTree, opts.registryCache, opts.staleScanLimit ?? 250);
+    if (dryRun) {
+        return {
+            report: {
+                status: 'dry-run',
+                manager,
+                lockfile: lockfileBasename,
+                command: `${dedupe.bin} ${dedupe.args.join(' ')}`,
+                dedupeChanges: [],
+                stale,
+            },
+        };
+    }
+    if (!json) {
+        log.info(`Running \`${dedupe.bin} ${dedupe.args.join(' ')}\` to dedupe the lockfile …`);
+    }
+    const r = await execa(dedupe.bin, dedupe.args, { cwd, reject: false, all: true });
+    const output = [r.stdout, r.stderr].filter(Boolean).join('\n');
+    const lastLines = tailLines(output, 20);
+    if ((r.exitCode ?? 1) !== 0) {
+        // Restore lockfile from snapshot — if the manager partially rewrote it before bailing,
+        // this puts us back exactly where we started.
+        await fs.writeFile(lockfilePath, before, 'utf8');
+        if (opts.runInstallAfterRollback) {
+            try {
+                await opts.runInstallAfterRollback();
+            }
+            catch {
+                /* non-fatal; tree may be briefly out of sync */
+            }
+        }
+        return {
+            report: {
+                status: 'failed',
+                manager,
+                lockfile: lockfileBasename,
+                command: `${dedupe.bin} ${dedupe.args.join(' ')}`,
+                exitCode: r.exitCode ?? 1,
+                failureKind: 'dedupe',
+                lastLines,
+                dedupeChanges: [],
+                stale,
+            },
+        };
+    }
+    // Dedupe succeeded — now validate. If the user turned validation off, skip this step.
+    const after = await fs.readFile(lockfilePath, 'utf8');
+    const afterTree = parseLockfileInstalledVersions(after, manager);
+    const dedupeChanges = diffLockfileTrees(beforeTree, afterTree);
+    if (opts.runValidator) {
+        const vr = await opts.runValidator();
+        if (!vr.ok) {
+            await fs.writeFile(lockfilePath, before, 'utf8');
+            if (opts.runInstallAfterRollback) {
+                try {
+                    await opts.runInstallAfterRollback();
+                }
+                catch {
+                    /* non-fatal */
+                }
+            }
+            return {
+                report: {
+                    status: 'failed',
+                    manager,
+                    lockfile: lockfileBasename,
+                    command: `${dedupe.bin} ${dedupe.args.join(' ')}`,
+                    exitCode: 0,
+                    failureKind: 'validation',
+                    validatorCommand: vr.command,
+                    lastLines: vr.lastLines ?? lastLines,
+                    dedupeChanges,
+                    stale,
+                },
+            };
+        }
+    }
+    return {
+        report: {
+            status: 'ok',
+            manager,
+            lockfile: lockfileBasename,
+            command: `${dedupe.bin} ${dedupe.args.join(' ')}`,
+            exitCode: 0,
+            dedupeChanges,
+            stale,
+        },
+    };
+}
+/**
+ * Parse a lockfile and return a `Map<packageName, Set<installedVersion>>` of every concrete
+ * version that actually made it into `node_modules`. This is the minimum information we need
+ * for a useful before/after diff — we DON'T try to reconstruct the dep graph, only "which
+ * versions of X are installed".
+ *
+ * The parsers are format-tolerant by design: on any unexpected shape we return an empty map
+ * rather than throw. The caller treats that as "no diff was computable" — `dedupeChanges`
+ * stays empty and the `status: 'ok'` is honest (we really did run dedupe, we just can't
+ * quantify the delta).
+ */
+export function parseLockfileInstalledVersions(raw, manager) {
+    const out = new Map();
+    try {
+        if (manager === 'npm') {
+            return parseNpmLockfile(raw);
+        }
+        if (manager === 'pnpm') {
+            return parsePnpmLockfile(raw);
+        }
+        if (manager === 'yarn') {
+            return parseYarnLockfile(raw);
+        }
+    }
+    catch {
+        /* fall through */
+    }
+    return out;
+}
+/**
+ * npm lockfile parsers handle both v1 (top-level `dependencies`) and v2/v3 (`packages` map
+ * keyed by on-disk path). v2 lockfiles carry BOTH fields for backward compatibility with
+ * npm@6; we prefer `packages` because it's flatter and reliable.
+ */
+function parseNpmLockfile(raw) {
+    const out = new Map();
+    const j = JSON.parse(raw);
+    if (j.packages && typeof j.packages === 'object') {
+        for (const [key, entry] of Object.entries(j.packages)) {
+            // `""` is the root workspace entry; skip. For nested paths the package name is the
+            // segment after the LAST `/node_modules/` occurrence. For scoped packages (`@scope/x`)
+            // that segment actually contains a `/`, which our splitter handles.
+            if (!key || typeof entry?.version !== 'string')
+                continue;
+            const name = extractPackageNameFromNodeModulesPath(key);
+            if (!name)
+                continue;
+            addVersion(out, name, entry.version);
+        }
+        return out;
+    }
+    if (j.dependencies && typeof j.dependencies === 'object') {
+        // v1: walk recursively; names are keys, nested `dependencies` follow the same shape.
+        const walk = (deps) => {
+            for (const [name, d] of Object.entries(deps)) {
+                if (typeof d?.version === 'string')
+                    addVersion(out, name, d.version);
+                if (d && typeof d.dependencies === 'object') {
+                    walk(d.dependencies);
+                }
+            }
+        };
+        walk(j.dependencies);
+        return out;
+    }
+    return out;
+}
+/**
+ * pnpm lockfile is YAML. We avoid pulling in a full YAML parser by doing a targeted scrape
+ * of the `packages:` section keys, which look like:
+ *   /axios@1.6.2:
+ *   /@types/node@20.4.5:
+ *   /@babel/core@7.22.5(something):
+ * pnpm v9 switched to `'axios@1.6.2':` (unslashed, quoted). Both shapes are supported; we
+ * strip the prefix, split on the LAST `@`, and that's the version.
+ */
+function parsePnpmLockfile(raw) {
+    const out = new Map();
+    const lines = raw.split(/\r?\n/);
+    let inPackages = false;
+    for (const line of lines) {
+        if (/^packages:\s*$/.test(line)) {
+            inPackages = true;
+            continue;
+        }
+        // Top-level key at column 0 other than `packages:` ends the block.
+        if (inPackages && /^[^\s#]/.test(line) && !/^packages:/.test(line)) {
+            inPackages = false;
+        }
+        if (!inPackages)
+            continue;
+        const m = line.match(/^\s{2}['"]?\/?(@?[^@'"/\s]+(?:\/[^@'"/\s]+)?)@([^(:'"\s]+)/);
+        if (m)
+            addVersion(out, m[1], m[2]);
+    }
+    return out;
+}
+/**
+ * yarn.lock is a bespoke text format (classic) or YAML-ish (berry). We scrape `version
+ * "x.y.z"` lines following a `<spec>:` header — that shape is common across both versions
+ * and gives us everything we need without a real parser.
+ */
+function parseYarnLockfile(raw) {
+    const out = new Map();
+    const lines = raw.split(/\r?\n/);
+    let currentNames = [];
+    for (const line of lines) {
+        // Entry header examples:
+        //   axios@^1.6.0:
+        //   "axios@^1.6.0", "axios@1.7.2":
+        //   "@types/node@^20":
+        const headerMatch = line.match(/^(?:"[^"]+"|\S[^:]*):\s*$/);
+        if (headerMatch && !/^\s/.test(line)) {
+            currentNames = parseYarnEntryHeader(line);
+            continue;
+        }
+        const versionMatch = line.match(/^\s+version\s+"?([^"]+)"?\s*$/);
+        if (versionMatch && currentNames.length > 0) {
+            for (const n of currentNames)
+                addVersion(out, n, versionMatch[1]);
+            currentNames = [];
+        }
+    }
+    return out;
+}
+/** Parse a yarn.lock header line into the list of package names it declares. */
+function parseYarnEntryHeader(header) {
+    const raw = header.replace(/:\s*$/, '').trim();
+    // Split on commas outside quotes.
+    const parts = [];
+    let cur = '';
+    let inQ = false;
+    for (const ch of raw) {
+        if (ch === '"') {
+            inQ = !inQ;
+            continue;
+        }
+        if (ch === ',' && !inQ) {
+            parts.push(cur.trim());
+            cur = '';
+            continue;
+        }
+        cur += ch;
+    }
+    if (cur.trim())
+        parts.push(cur.trim());
+    const names = new Set();
+    for (const spec of parts) {
+        // Scoped: @scope/name@range → we want `@scope/name`.
+        if (spec.startsWith('@')) {
+            const at2 = spec.indexOf('@', 1);
+            if (at2 > 0)
+                names.add(spec.slice(0, at2));
+        }
+        else {
+            const at = spec.indexOf('@');
+            if (at > 0)
+                names.add(spec.slice(0, at));
+        }
+    }
+    return [...names];
+}
+/** Extract the package name from `node_modules/<pkg>` or `<ws>/node_modules/<pkg>` paths. */
+function extractPackageNameFromNodeModulesPath(key) {
+    const marker = '/node_modules/';
+    const idx = key.lastIndexOf(marker);
+    if (idx < 0) {
+        // Top-level workspace entry (`node_modules/<pkg>` with no leading slash) — rare but handled.
+        if (key.startsWith('node_modules/'))
+            return key.slice('node_modules/'.length);
+        return undefined;
+    }
+    return key.slice(idx + marker.length);
+}
+function addVersion(m, name, version) {
+    let s = m.get(name);
+    if (!s) {
+        s = new Set();
+        m.set(name, s);
+    }
+    s.add(version);
+}
+/**
+ * Given pre/post lockfile version maps, emit one `LockfileDedupeChange` per package whose
+ * installed-version set changed. Three change shapes:
+ *   - `merged`:  { before: [v1, v2], after: [v1] }  — classic dedupe win
+ *   - `updated`: { before: [v1], after: [v2] }      — version shifted (resolver picked newer)
+ *   - `added` / `removed`: { before: [], after: [v] } / vice-versa — install-side effects
+ *
+ * Only `merged` and `updated` are "interesting" from a dedupe-report perspective; the
+ * summary filters on those. We still include `added`/`removed` in the raw list so
+ * auditors see the full delta.
+ */
+export function diffLockfileTrees(before, after) {
+    const out = [];
+    const names = new Set([...before.keys(), ...after.keys()]);
+    for (const name of names) {
+        const b = [...(before.get(name) ?? new Set())].sort(semverCompareSafe);
+        const a = [...(after.get(name) ?? new Set())].sort(semverCompareSafe);
+        if (b.length === 0 && a.length > 0) {
+            out.push({ name, change: 'added', before: [], after: a });
+            continue;
+        }
+        if (a.length === 0 && b.length > 0) {
+            out.push({ name, change: 'removed', before: b, after: [] });
+            continue;
+        }
+        if (setsEqual(b, a))
+            continue;
+        if (b.length > 1 && a.length < b.length) {
+            out.push({ name, change: 'merged', before: b, after: a });
+            continue;
+        }
+        out.push({ name, change: 'updated', before: b, after: a });
+    }
+    // Sort by interestingness: merges first, then updates, then adds, then removes; within each
+    // group sort by name so the summary output is deterministic.
+    const rank = { merged: 0, updated: 1, added: 2, removed: 3 };
+    out.sort((x, y) => {
+        const d = rank[x.change] - rank[y.change];
+        return d !== 0 ? d : x.name.localeCompare(y.name);
+    });
+    return out;
+}
+function setsEqual(a, b) {
+    if (a.length !== b.length)
+        return false;
+    for (let i = 0; i < a.length; i++)
+        if (a[i] !== b[i])
+            return false;
+    return true;
+}
+function semverCompareSafe(a, b) {
+    try {
+        return semver.compare(a, b);
+    }
+    catch {
+        return a.localeCompare(b);
+    }
+}
+/**
+ * Best-effort "which transitives are outdated but not vulnerable" scan. For every package
+ * installed at one or more versions in the lockfile, we look up `latest` from the registry
+ * (via the shared cache so the main flow's lookups are reused) and flag it when the HIGHEST
+ * installed version is more than one minor OR one full major behind latest.
+ *
+ * Why "more than one minor"? — the very common case of `some-dep@1.2.0` installed while
+ * latest is `1.2.4` isn't news. The case that matters is `some-dep@1.2.0` while latest is
+ * `1.9.0` (6 months of patches missed) or worse, `2.x`. Those are the ones a reviewer
+ * actually cares to see.
+ *
+ * Bounded at `limit` packages to keep the scan under a few seconds even on giant monorepos.
+ * We pick the `limit` packages with the MOST installed versions first (highest dedupe
+ * potential) and then fill out to `limit` by package name ordering.
+ */
+async function scanStaleTransitives(tree, cache, limit) {
+    if (tree.size === 0)
+        return [];
+    const ranked = [...tree.entries()]
+        .map(([name, versions]) => ({ name, versions: [...versions] }))
+        .sort((a, b) => b.versions.length - a.versions.length || a.name.localeCompare(b.name))
+        .slice(0, limit);
+    const results = await runWithConcurrency(ranked, 8, async (entry) => {
+        try {
+            const latest = await fetchLatestVersion(entry.name, cache);
+            const highestInstalled = entry.versions.sort(semverCompareSafe).pop();
+            if (!semver.valid(latest) || !semver.valid(highestInstalled))
+                return undefined;
+            if (semver.gte(highestInstalled, latest))
+                return undefined;
+            const majorDelta = semver.major(latest) - semver.major(highestInstalled);
+            const minorDelta = semver.minor(latest) - semver.minor(highestInstalled);
+            // Filter out trivial drift — a patch release or a single minor isn't "stale".
+            if (majorDelta === 0 && minorDelta <= 1)
+                return undefined;
+            return {
+                name: entry.name,
+                installed: entry.versions.sort(semverCompareSafe),
+                latest,
+                majorBehind: Math.max(0, majorDelta),
+                minorBehind: Math.max(0, minorDelta),
+            };
+        }
+        catch {
+            return undefined;
+        }
+    });
+    const stale = results.filter((r) => Boolean(r));
+    stale.sort((a, b) => {
+        if (a.majorBehind !== b.majorBehind)
+            return b.majorBehind - a.majorBehind;
+        if (a.minorBehind !== b.minorBehind)
+            return b.minorBehind - a.minorBehind;
+        return a.name.localeCompare(b.name);
+    });
+    return stale;
+}
+//# sourceMappingURL=lockfileFix.js.map

package/dist/cli/lockfileFix.js.map

@@ -0,0 +1 @@
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package/dist/cli/report.d.ts

@@ -34,6 +34,8 @@ export interface StructuredReport {
     installMode?: 'root' | 'filtered';
     /** Effective number of targets traversed in parallel (`1` = serial). */
     concurrency?: number;
+    /** True when installs + validation ran concurrently per-workspace (isolated-lockfile monorepo). */
+    parallelInstalls?: boolean;
     /**
      * Git commits created during the run (only present when `--git-commit` was set). Failed
      * commit attempts are also recorded here with `ok: false` so CI can surface the reason
@@ -48,6 +50,8 @@ export interface StructuredReport {
     overrides?: FinalReport['overrides'];
     /** Result of the `--open-pr` step (only present when the flag was passed). */
     pullRequest?: FinalReport['pullRequest'];
+    /** Result of the `--fix-lockfile` step (only present when the flag was passed). */
+    lockfileFix?: FinalReport['lockfileFix'];
 }
 export declare function buildStructuredReport(report: FinalReport, options?: {
     parsedConflicts?: Conflict[];

package/dist/cli/report.d.ts.map

@@ -1 +1 @@
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package/dist/cli/report.js

@@ -21,11 +21,13 @@ export function buildStructuredReport(report, options = {}) {
         ...(report.ignored?.length ? { ignored: report.ignored } : {}),
         ...(report.installMode ? { installMode: report.installMode } : {}),
         ...(report.concurrency && report.concurrency > 1 ? { concurrency: report.concurrency } : {}),
+        ...(report.parallelInstalls ? { parallelInstalls: true } : {}),
         ...(report.commits && report.commits.length > 0 ? { commits: report.commits } : {}),
         ...(report.gitCommitMode ? { gitCommitMode: report.gitCommitMode } : {}),
         ...(report.policy ? { policy: report.policy } : {}),
         ...(report.overrides ? { overrides: report.overrides } : {}),
         ...(report.pullRequest ? { pullRequest: report.pullRequest } : {}),
+        ...(report.lockfileFix ? { lockfileFix: report.lockfileFix } : {}),
     };
 }
 export function printStructuredCliSummary(structured) {
@@ -40,6 +42,9 @@ export function printStructuredCliSummary(structured) {
     if (structured.targets && structured.targets.length > 1) {
         log.dim(`  targets: ${structured.targets.map((t) => t.label).join(', ')}`);
     }
+    if (structured.parallelInstalls) {
+        log.dim(`  parallel installs: per-workspace (isolated-lockfile monorepo)`);
+    }
     if (structured.groups.length) {
         log.info(chalk.bold('Groups'));
         for (const g of structured.groups) {

package/dist/cli/report.js.map

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package/dist/cli/summary.d.ts.map

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