@mark1russell7/rigor-mutation 0.0.0-stage → 0.1.1

package/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Mark Russell
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

package/README.md

@@ -1,3 +1,104 @@
-# Temporary Holding Version
+# @mark1russell7/rigor-mutation
 
-This version is a temporary placeholder for this package. An operational version to replace this has been submitted for review and is awaiting a staged release.
+Mutation tests with [Stryker](https://stryker-mutator.io) and Vitest for each package of a repository. A mutation test changes the source a little (a mutant), and starts the tests. A good test fails on the mutant, so it detects the mutant. The score is the percent of the mutants that the tests detect.
+
+This package gives three things:
+
+- The Stryker config of each package, or of each part of a big package, from one lane file.
+- The score of each package, with its own gate. A score under the gate fails, and the message names the package.
+- A check of the disabled mutants: each `Stryker disable` comment is also in a list, with its reason.
+
+```sh
+npm install --save-dev @mark1russell7/rigor-mutation @stryker-mutator/core @stryker-mutator/vitest-runner
+```
+
+Use Stryker 10.1.0 or later with Vitest 5. Stryker 10.0 started no test on each mutant with Vitest 5 ([stryker-js#6210](https://github.com/stryker-mutator/stryker-js/issues/6210)). The score then fails, because the tests detect no mutant.
+
+## The lane file
+
+The lane file `mutation.json` is at the root of the repository:
+
+```json
+{
+  "packages": {
+    "collections": {
+      "dir": "packages/collections",
+      "mutate": ["src/**/*.ts", "!src/**/*.test.ts", "!src/index.ts"],
+      "gate": 80,
+      "parts": { "impl": ["src/impl/**/*.ts"], "core": ["src/core/**/*.ts"] }
+    }
+  }
+}
+```
+
+- `dir` is the folder of the package. Stryker starts in this folder.
+- `mutate` has the globs of the files to mutate, from `dir`. A glob with `!` removes the files of the globs before it.
+- `gate` is the lowest score in percent that passes. Without a gate, the lane only reports the score.
+- `parts` divides a big package. A part has its own globs, and the `!` globs of `mutate` also apply to it. Each file of `mutate` must be in exactly one part.
+- `vitestConfig` names the Vitest config of the package, from `dir`. Without it, Vitest finds its config.
+- `timeoutMS` is the time in milliseconds that the clock adds to the time of the tests for each mutant. The default is 120000. The default of Stryker (5000) is too short on a loaded CI runner.
+- `dryRunTimeoutMinutes` is the time in minutes for the run of the tests without mutants. The default is 15.
+- `stryker` has more options for the Stryker config of each selection of the package, for example `{ "ignoreStatic": true }`. Its keys replace the keys of the config, but `--concurrency` replaces its `concurrency`. The lane owns `mutate`, `thresholds`, `jsonReporter`, `htmlReporter`, `timeoutMS` and `dryRunTimeoutMinutes`, so `stryker` cannot have them.
+- `disables` (at the root of the lane) names the list of the disabled mutants. The default is `mutation-disables.json`.
+
+A selection is one Stryker run: a package (`collections`) or a part (`collections.impl`). `rigor-mutation list --runs` gives the selections of a full run: the parts of each package with parts, else the package.
+
+A full run mutates only the files of the parts. Thus a file in no part has no score, and a file in two parts has two scores. `list --runs`, and `config` and `scores` of a part, examine the source files of the package. They fail and name each file that is in no part, in two parts, or in a part but not in `mutate`. In the example, a file `src/util.ts` is in no part, so the lane fails.
+
+## A run
+
+```sh
+pnpm exec rigor-mutation config collections --out reports/stryker.json
+cd "$(pnpm exec rigor-mutation dir collections)"
+pnpm exec stryker run ../../reports/stryker.json
+cd -
+pnpm exec rigor-mutation scores collections
+```
+
+Each run starts the tests of `dir` only. A test in another folder, for example a test of the repository root, does not detect a mutant of the package.
+
+`rigor-mutation scores` reads `<dir>/reports/mutation/mutation.json` and applies the gate. It exits with 1 when a selection fails. With `--summary "$GITHUB_STEP_SUMMARY"`, it adds a table of the scores to the summary of the job. The shared workflow `reusable-mutation.yml` of the template starts these steps on one runner for each selection.
+
+A run of mutation tests is long and it uses much memory. Start it in CI, and on a local computer start one part with `--concurrency 2`.
+
+Two options make a run shorter:
+
+- `config --dry-run` gives a config that starts only the tests without mutants. Stryker does not stop at the first failed test. Use it to see if the tests pass under Stryker before a long run.
+- `--changed <file>` reads a file with one changed path on each line, from the folder of the lane file. Make the file with `git diff --name-only`. Then `list --runs` gives only the runs with a changed file, and `config` mutates only the changed files of the selection. `config` fails for a selection with no changed file.
+
+## The score
+
+The score counts the detected mutants, out of the mutants that a test covers or that survive. Compile errors, runtime errors and ignored mutants do not count.
+
+A detected mutant has the status `Killed`, or a `Timeout` of the hit limit. Stryker gives the status `Timeout` for two events:
+
+- The hit limit stopped the mutant. The mutant has an endless loop, and its `statusReason` starts with `Hit limit`. The mutant is detected.
+- The clock stopped the mutant. The load of the runner can cause this, so the mutant is not detected for certain. It counts as not detected.
+
+The score line gives the count of each kind of time-out. It also gives the score with the clock time-outs counted as detected, as Stryker counts them. The gate does not use that second score.
+
+A selection fails in these conditions:
+
+- The report has no mutants that count. Stryker found no files, or it did not start.
+- The report has mutants that count, but the tests detect none. The test runner started no test on the mutants.
+- The selection has a gate, and the score is under it.
+
+The gate of a package with parts applies to each part. Each part must have a score at the gate or above it. A part under the gate fails, also when the score of all the parts together is above the gate.
+
+## The disabled mutants
+
+A comment `// Stryker disable next-line <Mutator>: <reason>` disables a mutant that is equivalent. The disable raises the score, so each one is also in the list, with its reason. `rigor-mutation disables` compares the comments of the sources of each package with the list. It fails when they are not the same, or when a comment has no reason. After you add or remove a disable, start `rigor-mutation disables --write` and examine the diff of the list.
+
+## The API
+
+```ts
+import { parseLane, select, strykerConfig, parseReport, scoreReport, formatScore } from "@mark1russell7/rigor-mutation";
+
+const lane = parseLane(JSON.parse(laneText));
+const selection = select(lane, "collections.impl");
+const config = strykerConfig(selection, { concurrency: 2 });
+const score = scoreReport(parseReport(JSON.parse(reportText)), selection);
+console.log(formatScore(score)); // collections.impl: 91.20 % (456 of 500, 44 survived), gate 80 %: pass
+```
+
+The package also exports `selectionNames`, `runSelections`, `summaryMarkdown`, `findDisables`, `compareDisables` and `runCli`.

package/build/cli.d.ts

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+export {}

package/build/cli.js

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+#!/usr/bin/env node
+import { n as runCli } from "./run-CveACYFE.js";
+// src/cli.ts
+try {
+	process.exitCode = runCli(process.argv.slice(2), {
+		cwd: process.cwd(),
+		stdout: (text) => process.stdout.write(text),
+		stderr: (text) => process.stderr.write(text)
+	});
+} catch (error) {
+	process.stderr.write(`rigor-mutation: ${error instanceof Error ? error.message : String(error)}\n`);
+	process.exitCode = 1;
+}
+export {};
+
+//# sourceMappingURL=cli.js.map

package/build/cli.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"cli.js","names":[],"sources":["../src/cli.ts"],"sourcesContent":["#!/usr/bin/env node\n// The bin `rigor-mutation`. The work is in run.ts, so a test can start the same CLI in a fixture folder.\nimport { runCli } from \"./run.ts\";\n\ntry {\n  process.exitCode = runCli(process.argv.slice(2), {\n    cwd: process.cwd(),\n    stdout: (text) => process.stdout.write(text),\n    stderr: (text) => process.stderr.write(text),\n  });\n} catch (error) {\n  process.stderr.write(`rigor-mutation: ${error instanceof Error ? error.message : String(error)}\\n`);\n  process.exitCode = 1;\n}\n"],"mappings":";;;AAIA,IAAI;CACF,QAAQ,WAAW,OAAO,QAAQ,KAAK,MAAM,CAAC,GAAG;EAC/C,KAAK,QAAQ,IAAI;EACjB,SAAS,SAAS,QAAQ,OAAO,MAAM,IAAI;EAC3C,SAAS,SAAS,QAAQ,OAAO,MAAM,IAAI;CAC7C,CAAC;AACH,SAAS,OAAO;CACd,QAAQ,OAAO,MAAM,mBAAmB,iBAAiB,QAAQ,MAAM,UAAU,OAAO,KAAK,EAAE,GAAG;CAClG,QAAQ,WAAW;AACrB"}

package/build/index.d.ts

@@ -0,0 +1,246 @@
+/**
+ * The lane file of a repository (`mutation.json`) names the packages that the mutation tests mutate. A package has
+ * its folder, its globs and an optional gate. A big package has parts, so that each part has its own runner.
+ */
+/** The mutation tests of one package. */
+interface PackageLane {
+  /** This field gives the folder of the package, from the folder of the lane file. Stryker starts in this folder. */
+  readonly dir: string;
+  /** These globs give the files to mutate, from `dir`. A glob with `!` removes the files of the globs before it. */
+  readonly mutate: readonly string[];
+  /**
+   * Each part has its own globs. The `!` globs of `mutate` also apply to each part. Each file of `mutate` must be in
+   * exactly one part, so that a full run mutates each file one time. `partErrors` examines this.
+   */
+  readonly parts?: Readonly<Record<string, readonly string[]>>;
+  /** This field gives the lowest mutation score in percent that passes. Without a gate, the lane only reports the score. */
+  readonly gate?: number;
+  /** This field gives the Vitest config file, from `dir`. Without it, Vitest finds its config in `dir`. */
+  readonly vitestConfig?: string;
+  /**
+   * This field gives the time in milliseconds that the clock adds to the time of the tests for each mutant. The
+   * default is 120000. A short time on a loaded runner stops mutants that the tests detect later.
+   */
+  readonly timeoutMS?: number;
+  /** This field gives the time in minutes for the run of the tests without mutants. The default is 15. */
+  readonly dryRunTimeoutMinutes?: number;
+  /**
+   * These options go into the Stryker config of each selection of the package, for example `ignoreStatic`. The lane
+   * owns the keys of `STRYKER_OWNED`, so the field cannot have them.
+   */
+  readonly stryker?: Readonly<Record<string, unknown>>;
+}
+/** The keys of the Stryker config that the lane owns. The field `stryker` of a package cannot have them. */
+export declare const STRYKER_OWNED: readonly string[];
+/** The lane file: the packages of the mutation tests, and the list of the disabled mutants. */
+interface Lane {
+  readonly packages: Readonly<Record<string, PackageLane>>;
+  /** This field gives the list of the disabled mutants, from the folder of the lane file. The default is `mutation-disables.json`. */
+  readonly disables?: string;
+}
+/** A selection is one Stryker run: a package (`collections`) or a part of a package (`collections.impl`). */
+interface Selection {
+  readonly name: string;
+  readonly pkg: string;
+  readonly dir: string;
+  readonly mutate: readonly string[];
+  readonly gate: number | undefined;
+  readonly vitestConfig: string | undefined;
+  readonly timeoutMS: number | undefined;
+  readonly dryRunTimeoutMinutes: number | undefined;
+  readonly stryker: Readonly<Record<string, unknown>> | undefined;
+}
+/**
+ * This function examines the JSON of a lane file and gives the lane.
+ *
+ * @throws Error with each problem of the file
+ */
+export declare function parseLane(json: unknown): Lane;
+/** This function gives the names of all the selections of a lane: each package, then each part of the package. */
+export declare function selectionNames(lane: Lane): string[];
+/** This function gives the selections of a full run: the parts of each package with parts, else the package. Each file is in one run. */
+export declare function runSelections(lane: Lane): string[];
+/**
+ * This function gives the selection of a name: a package, or a part of a package.
+ *
+ * @throws Error when the lane has no package or part of that name
+ */
+export declare function select(lane: Lane, name: string): Selection;
+/**
+ * This function gives the changed files of a selection, from the folder of its package. The globs of the selection
+ * select the files.
+ *
+ * @param changed - the changed paths, from the folder of the lane file, with `/`
+ */
+export declare function changedFiles(selection: Selection, changed: readonly string[]): string[];
+/**
+ * This function examines the parts of a package against its files. It gives an error for each file of `mutate` in no
+ * part. It also gives an error for each file in two parts, and for each file of a part that is not in `mutate`. A
+ * package with no parts has no errors.
+ *
+ * @param files - the source files of the package, from its folder, with `/`
+ */
+export declare function partErrors(lane: Lane, pkg: string, files: readonly string[]): string[];
+/** The options of `strykerConfig`. */
+interface ConfigOptions {
+  /** This option gives the number of test processes. The default is 2. */
+  readonly concurrency?: number;
+  /** This option gives the folder of the reports, from the folder of the package. The default is `reports/mutation`. */
+  readonly reportDir?: string;
+  /**
+   * When this option is true, Stryker starts only the tests without mutants, and it does not stop at the first failed
+   * test. Use it to see if the tests pass under Stryker before a long run.
+   */
+  readonly dryRun?: boolean;
+}
+/** The Stryker config of one selection, as JSON. Stryker starts in the folder of the package. The field `stryker` of the lane adds keys. */
+interface StrykerConfig {
+  readonly [key: string]: unknown;
+  readonly testRunner: "vitest";
+  readonly plugins: readonly string[];
+  readonly vitest?: {
+    readonly configFile: string;
+  };
+  readonly mutate: readonly string[];
+  readonly coverageAnalysis: "perTest";
+  readonly reporters: readonly string[];
+  readonly htmlReporter: {
+    readonly fileName: string;
+  };
+  readonly jsonReporter: {
+    readonly fileName: string;
+  };
+  readonly thresholds: {
+    readonly high: number;
+    readonly low: number;
+    readonly break: null;
+  };
+  readonly concurrency: number;
+  readonly timeoutMS: number;
+  readonly dryRunTimeoutMinutes: number;
+  readonly dryRunOnly?: true;
+  readonly disableBail?: true;
+}
+/** The default folder of the reports, from the folder of the package. */
+export declare const REPORT_DIR = "reports/mutation";
+/**
+ * The default time in milliseconds that the clock adds to the time of the tests for each mutant. The default of
+ * Stryker is 5000. On a loaded CI runner that time stopped mutants that the tests detected later.
+ */
+export declare const TIMEOUT_MS = 12e4;
+/** The default time in minutes for the run of the tests without mutants. The default of Stryker is 5. */
+export declare const DRY_RUN_TIMEOUT_MINUTES = 15;
+/**
+ * This function gives the Stryker config of a selection. The break of Stryker is off, because the gate of each
+ * package is in `scoreReport`. Stryker 10.1.0 or later is necessary with Vitest 5: version 10.0 started no test on each
+ * mutant (stryker-js issue 6210).
+ */
+export declare function strykerConfig(selection: Selection, options?: ConfigOptions): StrykerConfig;
+/**
+ * The score of a Stryker report, with the gate of the package. The score counts the detected mutants, out of the
+ * mutants that a test covers or that survive. Compile errors, runtime errors and ignored mutants do not count.
+ *
+ * Stryker gives the status `Timeout` for two events. The hit limit stops a mutant with an endless loop: its
+ * `statusReason` starts with `Hit limit`, and the mutant is detected. The clock stops a mutant that took too long. The
+ * load of the runner can cause this. Thus the mutant is not detected for certain, and it counts as not detected.
+ */
+/** A mutant of the JSON report of Stryker (the schema of mutation-testing-elements). */
+interface Mutant {
+  readonly status: string;
+  readonly mutatorName: string;
+  /** Stryker gives the reason of some statuses here. A `Timeout` of the hit limit has a reason that starts with `Hit limit`. */
+  readonly statusReason?: string | undefined;
+  readonly location: {
+    readonly start: {
+      readonly line: number;
+    };
+  };
+}
+/** The JSON report of Stryker: the mutants of each mutated file. */
+interface MutationReport {
+  readonly files: Readonly<Record<string, {
+    readonly mutants: readonly Mutant[];
+  }>>;
+}
+/** The score of one selection. */
+interface Score {
+  readonly name: string;
+  readonly gate: number | undefined;
+  /** The mutants with the status `Killed`, and the mutants that the hit limit stopped. */
+  readonly detected: number;
+  /** The mutants that the hit limit stopped. They are in `detected`. */
+  readonly hitLimit: number;
+  /** The mutants that the clock stopped. They count as not detected, and they are in `survived`. */
+  readonly clockTimeouts: number;
+  /** The mutants that count: detected, survived or with no coverage. */
+  readonly valid: number;
+  /** Each mutant that survived, had no coverage or was stopped by the clock, as `file:line Mutator`. */
+  readonly survived: readonly string[];
+  /** The score in percent. It is 0 when no mutant counts. */
+  readonly percent: number;
+  /** The score in percent with the clock time-outs counted as detected, as Stryker counts them. The gate does not read it. */
+  readonly percentWithClock: number;
+  readonly pass: boolean;
+  /** The reason of a failure. */
+  readonly reason: string | undefined;
+}
+/** This function tells if the hit limit of Stryker stopped a mutant. Then the mutant has an endless loop, and it is detected. */
+export declare const isHitLimit: (m: Mutant) => boolean;
+/**
+ * This function examines the JSON of a Stryker report and gives the report.
+ *
+ * @throws Error when the JSON has no files with mutants
+ */
+export declare function parseReport(json: unknown): MutationReport;
+/**
+ * This function gives the score of a report and applies the gate. A report with no mutants that count fails, also
+ * without a gate: Stryker found no files. A report with mutants that count and none detected also fails: the test
+ * runner started no test on the mutants. Stryker 10.0 with Vitest 5 gave this result.
+ */
+export declare function scoreReport(report: MutationReport, selection: {
+  readonly name: string;
+  readonly gate: number | undefined;
+}): Score;
+/** This function gives one line for a score, with the name of the selection and its result. The time-outs are in it when the report has some. */
+export declare function formatScore(s: Score): string;
+/** This function gives a Markdown table of scores, for the summary of a CI job. */
+export declare function summaryMarkdown(scores: readonly Score[]): string;
+/**
+ * A comment `// Stryker disable next-line <Mutator>: <reason>` disables a mutant that is equivalent. The disable
+ * raises the score, so each one is also in a list with its reason. These functions find the comments in the
+ * sources and compare them with the list.
+ */
+/** One disable comment of a source file. */
+interface Disable {
+  readonly file: string;
+  readonly comment: string;
+}
+/** The result of `compareDisables`. */
+interface DisableCheck {
+  /** The comments of the sources that are not in the list, as `file: comment`. */
+  readonly added: readonly string[];
+  /** The comments of the list that are not in the sources, as `file: comment`. */
+  readonly removed: readonly string[];
+  /** The comments with no reason after a colon. */
+  readonly noReason: readonly Disable[];
+  readonly ok: boolean;
+}
+/** This function finds each `Stryker disable` comment of the files. A file name uses `/`. */
+export declare function findDisables(files: readonly {
+  readonly file: string;
+  readonly text: string;
+}[]): Disable[];
+/** This function compares the comments of the sources with the list. A file with the same comment two times needs it two times in the list. */
+export declare function compareDisables(found: readonly Disable[], listed: readonly Disable[]): DisableCheck;
+/** The input and the output of the CLI. */
+interface CliIo {
+  readonly cwd: string;
+  readonly stdout: (text: string) => void;
+  readonly stderr: (text: string) => void;
+}
+/** The help text of the CLI. */
+export declare const HELP: string;
+/** This function starts the CLI with its arguments and gives the exit code. */
+export declare function runCli(argv: readonly string[], io: CliIo): number;
+export type { CliIo, ConfigOptions, Disable, DisableCheck, Lane, Mutant, MutationReport, PackageLane, Score, Selection, StrykerConfig };
+//# sourceMappingURL=index.d.ts.map

package/build/index.d.ts.map

@@ -0,0 +1 @@
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package/build/index.js

@@ -0,0 +1 @@
+export { u as DRY_RUN_TIMEOUT_MINUTES, t as HELP, d as REPORT_DIR, m as STRYKER_OWNED, f as TIMEOUT_MS, h as changedFiles, r as compareDisables, i as findDisables, a as formatScore, o as isHitLimit, g as parseLane, s as parseReport, _ as partErrors, n as runCli, v as runSelections, c as scoreReport, y as select, b as selectionNames, p as strykerConfig, l as summaryMarkdown } from "./run-CveACYFE.js";

package/build/run-CveACYFE.js

@@ -0,0 +1,521 @@
+import { dirname, matchesGlob, posix, relative, resolve } from "node:path";
+import { appendFileSync, existsSync, mkdirSync, readFileSync, readdirSync, writeFileSync } from "node:fs";
+import { parseArgs } from "node:util";
+// src/lane.ts
+/** The keys of the Stryker config that the lane owns. The field `stryker` of a package cannot have them. */
+const STRYKER_OWNED = [
+	"mutate",
+	"thresholds",
+	"jsonReporter",
+	"htmlReporter",
+	"timeoutMS",
+	"dryRunTimeoutMinutes"
+];
+const NAME = /^[\w-]+$/;
+const isRecord = (x) => typeof x === "object" && x !== null && !Array.isArray(x);
+const isGlobs = (x) => Array.isArray(x) && x.length > 0 && x.every((g) => typeof g === "string" && g !== "");
+/** This function examines a package of the lane file. It gives the errors, with the name of the package. */
+function packageErrors(name, p) {
+	if (!NAME.test(name)) return [`the package name "${name}" has a character that is not a letter, a digit, "_" or "-"`];
+	if (!isRecord(p)) return [`${name}: the package is not an object`];
+	const errors = [];
+	if (typeof p["dir"] !== "string" || p["dir"] === "") errors.push(`${name}: "dir" is not a folder name`);
+	if (!isGlobs(p["mutate"])) errors.push(`${name}: "mutate" is not a list of globs`);
+	else if (p["mutate"].every((g) => g.startsWith("!"))) errors.push(`${name}: "mutate" has only "!" globs`);
+	const gate = p["gate"];
+	if (gate !== void 0 && (typeof gate !== "number" || !(gate >= 0 && gate <= 100))) errors.push(`${name}: "gate" is not a percent from 0 to 100`);
+	if (p["vitestConfig"] !== void 0 && typeof p["vitestConfig"] !== "string") errors.push(`${name}: "vitestConfig" is not a file name`);
+	for (const field of ["timeoutMS", "dryRunTimeoutMinutes"]) {
+		const v = p[field];
+		if (v !== void 0 && !(typeof v === "number" && Number.isInteger(v) && v > 0)) errors.push(`${name}: "${field}" is not a positive integer`);
+	}
+	const stryker = p["stryker"];
+	if (stryker !== void 0) {
+		if (!isRecord(stryker)) errors.push(`${name}: "stryker" is not an object`);
+		else {
+			const owned = Object.keys(stryker).filter((k) => STRYKER_OWNED.includes(k));
+			if (owned.length > 0) errors.push(`${name}: "stryker" has ${owned.map((k) => `"${k}"`).join(", ")}, but the lane owns these keys`);
+		}
+	}
+	const parts = p["parts"];
+	if (parts !== void 0) {
+		if (!isRecord(parts) || Object.keys(parts).length === 0) errors.push(`${name}: "parts" is not an object with parts`);
+		else for (const [part, globs] of Object.entries(parts)) {
+			if (!NAME.test(part)) errors.push(`${name}: the part name "${part}" has a character that is not a letter, a digit, "_" or "-"`);
+			if (!isGlobs(globs) || globs.some((g) => g.startsWith("!"))) errors.push(`${name}.${part}: the part is not a list of globs without "!"`);
+		}
+	}
+	return errors;
+}
+/**
+* This function examines the JSON of a lane file and gives the lane.
+*
+* @throws Error with each problem of the file
+*/
+function parseLane(json) {
+	if (!isRecord(json) || !isRecord(json["packages"])) throw new Error(`the lane has no object "packages"`);
+	const errors = Object.entries(json["packages"]).flatMap(([name, p]) => packageErrors(name, p));
+	if (Object.keys(json["packages"]).length === 0) errors.push(`the lane has no packages`);
+	if (json["disables"] !== void 0 && typeof json["disables"] !== "string") errors.push(`"disables" is not a file name`);
+	if (errors.length > 0) throw new Error(`the lane is not valid:\n  ${errors.join("\n  ")}`);
+	return json;
+}
+/** This function gives the names of all the selections of a lane: each package, then each part of the package. */
+function selectionNames(lane) {
+	return Object.entries(lane.packages).flatMap(([name, p]) => [name, ...Object.keys(p.parts ?? {}).map((part) => `${name}.${part}`)]);
+}
+/** This function gives the selections of a full run: the parts of each package with parts, else the package. Each file is in one run. */
+function runSelections(lane) {
+	return Object.entries(lane.packages).flatMap(([name, p]) => p.parts === void 0 ? [name] : Object.keys(p.parts).map((part) => `${name}.${part}`));
+}
+/**
+* This function gives the selection of a name: a package, or a part of a package.
+*
+* @throws Error when the lane has no package or part of that name
+*/
+function select(lane, name) {
+	const [pkg = "", part, ...rest] = name.split(".");
+	const p = lane.packages[pkg];
+	const globs = part === void 0 ? void 0 : p?.parts?.[part];
+	if (p === void 0 || rest.length > 0 || part !== void 0 && globs === void 0) throw new Error(`the lane has no package or part "${name}". It has: ${selectionNames(lane).join(", ")}`);
+	const mutate = globs === void 0 ? p.mutate : [...globs, ...p.mutate.filter((g) => g.startsWith("!"))];
+	return {
+		name,
+		pkg,
+		dir: p.dir,
+		mutate,
+		gate: p.gate,
+		vitestConfig: p.vitestConfig,
+		timeoutMS: p.timeoutMS,
+		dryRunTimeoutMinutes: p.dryRunTimeoutMinutes,
+		stryker: p.stryker
+	};
+}
+/**
+* This function tells if globs select a file. It reads the globs as Stryker does. A glob adds its files. A glob with
+* `!` removes its files from the files of the globs before it.
+*/
+function globsSelect(globs, file) {
+	let selected = false;
+	for (const g of globs) if (g.startsWith("!")) {
+		if (selected && matchesGlob(file, g.slice(1))) selected = false;
+	} else if (!selected && matchesGlob(file, g)) selected = true;
+	return selected;
+}
+/**
+* This function gives the changed files of a selection, from the folder of its package. The globs of the selection
+* select the files.
+*
+* @param changed - the changed paths, from the folder of the lane file, with `/`
+*/
+function changedFiles(selection, changed) {
+	const dir = posix.normalize(selection.dir.replaceAll("\\", "/"));
+	return changed.map((f) => posix.relative(dir, posix.normalize(f.replaceAll("\\", "/")))).filter((f) => f !== "" && !f.startsWith("../") && !posix.isAbsolute(f) && globsSelect(selection.mutate, f));
+}
+/**
+* This function examines the parts of a package against its files. It gives an error for each file of `mutate` in no
+* part. It also gives an error for each file in two parts, and for each file of a part that is not in `mutate`. A
+* package with no parts has no errors.
+*
+* @param files - the source files of the package, from its folder, with `/`
+*/
+function partErrors(lane, pkg, files) {
+	const p = lane.packages[pkg];
+	if (p?.parts === void 0) return [];
+	const parts = Object.keys(p.parts).map((part) => ({
+		part,
+		mutate: select(lane, `${pkg}.${part}`).mutate
+	}));
+	const errors = [];
+	for (const file of files) {
+		const inMutate = globsSelect(p.mutate, file);
+		const inParts = parts.filter((x) => globsSelect(x.mutate, file)).map((x) => x.part);
+		if (inMutate && inParts.length === 0) errors.push(`${pkg}: the file ${file} is in no part, so a full run does not mutate it`);
+		else if (inParts.length > 1) errors.push(`${pkg}: the file ${file} is in more than one part: ${inParts.join(", ")}`);
+		else if (!inMutate && inParts.length === 1) errors.push(`${pkg}: the file ${file} is in the part ${inParts.join("")}, but not in "mutate"`);
+	}
+	return errors;
+}
+// src/config.ts
+/** The default folder of the reports, from the folder of the package. */
+const REPORT_DIR = "reports/mutation";
+/**
+* The default time in milliseconds that the clock adds to the time of the tests for each mutant. The default of
+* Stryker is 5000. On a loaded CI runner that time stopped mutants that the tests detected later.
+*/
+const TIMEOUT_MS = 12e4;
+/** The default time in minutes for the run of the tests without mutants. The default of Stryker is 5. */
+const DRY_RUN_TIMEOUT_MINUTES = 15;
+/**
+* This function gives the Stryker config of a selection. The break of Stryker is off, because the gate of each
+* package is in `scoreReport`. Stryker 10.1.0 or later is necessary with Vitest 5: version 10.0 started no test on each
+* mutant (stryker-js issue 6210).
+*/
+function strykerConfig(selection, options = {}) {
+	const reportDir = options.reportDir ?? "reports/mutation";
+	const low = selection.gate ?? 60;
+	return {
+		testRunner: "vitest",
+		plugins: ["@stryker-mutator/vitest-runner"],
+		...selection.vitestConfig === void 0 ? {} : { vitest: { configFile: selection.vitestConfig } },
+		mutate: selection.mutate,
+		coverageAnalysis: "perTest",
+		reporters: [
+			"clear-text",
+			"progress",
+			"html",
+			"json"
+		],
+		htmlReporter: { fileName: `${reportDir}/index.html` },
+		jsonReporter: { fileName: `${reportDir}/mutation.json` },
+		thresholds: {
+			high: Math.max(low, 90),
+			low,
+			break: null
+		},
+		concurrency: options.concurrency ?? 2,
+		timeoutMS: selection.timeoutMS ?? 12e4,
+		dryRunTimeoutMinutes: selection.dryRunTimeoutMinutes ?? 15,
+		...selection.stryker,
+		...options.concurrency === void 0 ? {} : { concurrency: options.concurrency },
+		...options.dryRun === true ? {
+			dryRunOnly: true,
+			disableBail: true
+		} : {}
+	};
+}
+// src/score.ts
+const UNDETECTED = /* @__PURE__ */ new Set(["Survived", "NoCoverage"]);
+/** This function tells if the hit limit of Stryker stopped a mutant. Then the mutant has an endless loop, and it is detected. */
+const isHitLimit = (m) => m.status === "Timeout" && (m.statusReason ?? "").startsWith("Hit limit");
+/**
+* This function examines the JSON of a Stryker report and gives the report.
+*
+* @throws Error when the JSON has no files with mutants
+*/
+function parseReport(json) {
+	const files = typeof json === "object" && json !== null ? json.files : void 0;
+	if (typeof files !== "object" || files === null) throw new Error(`the report has no object "files"`);
+	for (const [file, data] of Object.entries(files)) if (!Array.isArray(data?.mutants)) throw new Error(`the report has no list "mutants" for ${file}`);
+	return json;
+}
+/**
+* This function gives the score of a report and applies the gate. A report with no mutants that count fails, also
+* without a gate: Stryker found no files. A report with mutants that count and none detected also fails: the test
+* runner started no test on the mutants. Stryker 10.0 with Vitest 5 gave this result.
+*/
+function scoreReport(report, selection) {
+	let detected = 0;
+	let valid = 0;
+	let hitLimit = 0;
+	let clockTimeouts = 0;
+	const survived = [];
+	for (const [file, data] of Object.entries(report.files)) for (const m of data.mutants) {
+		const at = `${file}:${String(m.location.start.line)} ${m.mutatorName}`;
+		if (m.status === "Killed" || isHitLimit(m)) {
+			detected++;
+			valid++;
+			if (m.status === "Timeout") hitLimit++;
+		} else if (m.status === "Timeout") {
+			clockTimeouts++;
+			valid++;
+			survived.push(`${at} (the clock stopped it)`);
+		} else if (UNDETECTED.has(m.status)) {
+			valid++;
+			survived.push(at);
+		}
+	}
+	const percent = valid === 0 ? 0 : 100 * detected / valid;
+	const percentWithClock = valid === 0 ? 0 : 100 * (detected + clockTimeouts) / valid;
+	const { name, gate } = selection;
+	const reason = valid === 0 ? "the report has no mutants that count: Stryker found no files to mutate, or it did not start" : detected === 0 ? `the tests detected none of the ${String(valid)} mutants: the test runner started no test on the mutants` : gate !== void 0 && percent < gate ? `the score ${percent.toFixed(2)} % is under the gate ${String(gate)} %` : void 0;
+	return {
+		name,
+		gate,
+		detected,
+		hitLimit,
+		clockTimeouts,
+		valid,
+		survived,
+		percent,
+		percentWithClock,
+		pass: reason === void 0,
+		reason
+	};
+}
+/** This function gives the time-outs of a score as text: the count of each kind, and the score that counts the clock time-outs as detected. */
+const timeouts = (s) => `time-outs: ${String(s.hitLimit)} hit limit, ${String(s.clockTimeouts)} clock (${s.percentWithClock.toFixed(2)} % with the clock time-outs as detected)`;
+/** This function gives one line for a score, with the name of the selection and its result. The time-outs are in it when the report has some. */
+function formatScore(s) {
+	const gate = s.gate === void 0 ? "no gate" : `gate ${String(s.gate)} %`;
+	const result = s.pass ? "pass" : `FAIL: ${s.reason ?? ""}`;
+	const time = s.hitLimit + s.clockTimeouts === 0 ? "" : `, ${timeouts(s)}`;
+	return `${s.name}: ${s.percent.toFixed(2)} % (${String(s.detected)} of ${String(s.valid)}, ${String(s.survived.length)} survived${time}), ${gate}: ${result}`;
+}
+/** This function gives a Markdown table of scores, for the summary of a CI job. */
+function summaryMarkdown(scores) {
+	return [
+		"| Selection | Score | Detected | Valid | Survived | Clock time-outs | Score with them | Gate | Result |",
+		"| --- | ---: | ---: | ---: | ---: | ---: | ---: | ---: | --- |",
+		...scores.map((s) => `| ${s.name} | ${s.percent.toFixed(2)} % | ${String(s.detected)} | ${String(s.valid)} | ${String(s.survived.length)} | ${String(s.clockTimeouts)} | ${s.percentWithClock.toFixed(2)} % | ${s.gate === void 0 ? "none" : `${String(s.gate)} %`} | ${s.pass ? "pass" : `fail: ${s.reason ?? ""}`} |`),
+		""
+	].join("\n");
+}
+// src/disables.ts
+/** This function finds each `Stryker disable` comment of the files. A file name uses `/`. */
+function findDisables(files) {
+	return files.flatMap(({ file, text }) => text.split("\n").filter((line) => line.includes("Stryker disable")).map((line) => ({
+		file,
+		comment: line.trim()
+	})));
+}
+const counts = (xs) => {
+	const m = /* @__PURE__ */ new Map();
+	for (const x of xs) {
+		const k = `${x.file}: ${x.comment}`;
+		m.set(k, (m.get(k) ?? 0) + 1);
+	}
+	return m;
+};
+/**
+* This function tells if a comment has a reason: a mutator name, a colon, a space and a text. It reads the text by
+* index, so its time is linear in the length of the comment (a regular expression here was quadratic).
+*/
+function hasReason(comment) {
+	const start = comment.indexOf("Stryker disable ");
+	if (start < 0) return false;
+	const rest = comment.slice(start + 16);
+	const colon = rest.indexOf(":");
+	return colon > 0 && rest[colon + 1] === " " && /\S/.test(rest[colon + 2] ?? "");
+}
+/** This function compares the comments of the sources with the list. A file with the same comment two times needs it two times in the list. */
+function compareDisables(found, listed) {
+	const noReason = found.filter((d) => !hasReason(d.comment));
+	const a = counts(found);
+	const b = counts(listed);
+	const added = [...a].filter(([k, n]) => n > (b.get(k) ?? 0)).map(([k]) => k);
+	const removed = [...b].filter(([k, n]) => n > (a.get(k) ?? 0)).map(([k]) => k);
+	return {
+		added,
+		removed,
+		noReason,
+		ok: added.length === 0 && removed.length === 0 && noReason.length === 0
+	};
+}
+// src/run.ts
+/**
+* The CLI `rigor-mutation`. The work is in `runCli`, so a test can start the CLI in a fixture folder.
+*/
+/** The help text of the CLI. */
+const HELP = `rigor-mutation: the mutation tests of a repository, with Stryker and a gate for each package.
+
+  rigor-mutation list [--runs] [--changed <file>]
+                                               the packages and the parts of the lane. With --runs, the
+                                               selections of a full run: the parts of a package with parts.
+                                               With --changed, only the runs with a changed file.
+  rigor-mutation dir <selection>               the folder of the package of a selection
+  rigor-mutation config <selection> [--out <file>] [--concurrency <n>] [--dry-run] [--changed <file>]
+                                               the Stryker config of a selection, as JSON. With --dry-run,
+                                               Stryker starts only the tests. With --changed, it mutates only
+                                               the changed files of the selection.
+  rigor-mutation scores <selection>... [--report <file>] [--summary <file>]
+                                               the score of each selection, with its gate
+  rigor-mutation disables [--write]            compare the disable comments with their list
+
+  --lane <file>      the lane file. The default is mutation.json.
+  --changed <file>   a file with one changed path on each line, from the folder of the lane file,
+                     for example the output of git diff --name-only.
+
+A selection is a package ("collections") or a part of a package ("collections.impl").
+Each file of a package with parts must be in exactly one part. list --runs, and config and scores
+of a part, fail when it is not.
+The score of a selection reads <dir>/${REPORT_DIR}/mutation.json, or the file of --report.
+`;
+const SOURCE = /\.(?:[cm]?[jt]s|tsx)$/;
+const TEST = /\.(?:test|spec)\.[^.]+$/;
+const SKIP = /* @__PURE__ */ new Set([
+	"node_modules",
+	"build",
+	"dist",
+	"reports",
+	"coverage"
+]);
+/** This function gives each source file of a folder, from `root`, with `/`. It skips the tests, the outputs and the dot folders. */
+function sourcesOf(root, dir) {
+	return readdirSync(dir, { withFileTypes: true }).toSorted((x, y) => x.name.localeCompare(y.name)).flatMap((e) => {
+		const path = resolve(dir, e.name);
+		if (e.isDirectory()) return e.name.startsWith(".") || SKIP.has(e.name) ? [] : sourcesOf(root, path);
+		return e.isFile() && SOURCE.test(e.name) && !TEST.test(e.name) ? [relative(root, path).replaceAll("\\", "/")] : [];
+	});
+}
+const readJson = (file) => JSON.parse(readFileSync(file, "utf8"));
+/**
+* This function examines the parts of the packages against their source files.
+*
+* @throws Error with each file that is in no part, in more than one part, or in a part and not in `mutate`
+*/
+function checkParts(lane, laneDir, pkgs) {
+	const errors = pkgs.flatMap((pkg) => {
+		const p = lane.packages[pkg];
+		if (p?.parts === void 0) return [];
+		const dir = resolve(laneDir, p.dir);
+		if (!existsSync(dir)) return [`${pkg}: the folder ${p.dir} does not exist`];
+		return partErrors(lane, pkg, sourcesOf(dir, dir));
+	});
+	if (errors.length > 0) throw new Error(`the parts do not cover each file exactly one time:\n  ${errors.join("\n  ")}`);
+}
+/** This function examines the parts of the package of each selection that is a part. */
+const checkPartsOf = (lane, laneDir, names) => checkParts(lane, laneDir, [...new Set(names.map((n) => select(lane, n)).filter((s) => s.name !== s.pkg).map((s) => s.pkg))]);
+function disables(lane, laneDir, write, io) {
+	const files = /* @__PURE__ */ new Set();
+	for (const [name, p] of Object.entries(lane.packages)) {
+		const dir = resolve(laneDir, p.dir);
+		if (!existsSync(dir)) throw new Error(`${name}: the folder ${p.dir} does not exist`);
+		for (const f of sourcesOf(laneDir, dir)) files.add(f);
+	}
+	const found = findDisables([...files].map((file) => ({
+		file,
+		text: readFileSync(resolve(laneDir, file), "utf8")
+	})));
+	const listFile = resolve(laneDir, lane.disables ?? "mutation-disables.json");
+	const check = compareDisables(found, existsSync(listFile) ? readJson(listFile) : []);
+	for (const d of check.noReason) io.stderr(`a disable without a reason after a colon: ${d.file}: ${d.comment}\n`);
+	if (write) {
+		if (check.noReason.length > 0) return 1;
+		writeFileSync(listFile, `${JSON.stringify(found, null, 2)}\n`);
+		io.stdout(`disables: wrote ${String(found.length)} comments to ${relative(io.cwd, listFile).replaceAll("\\", "/")}\n`);
+		return 0;
+	}
+	const perFile = /* @__PURE__ */ new Map();
+	for (const d of found) perFile.set(d.file, (perFile.get(d.file) ?? 0) + 1);
+	io.stdout(`disables: ${String(found.length)} in ${String(perFile.size)} files\n`);
+	for (const [file, n] of perFile) io.stdout(`  ${file}: ${String(n)}\n`);
+	for (const k of check.added) io.stderr(`not in the list: ${k}\n`);
+	for (const k of check.removed) io.stderr(`in the list, not in the sources: ${k}\n`);
+	if (check.added.length > 0 || check.removed.length > 0) io.stderr("disables: the sources and the list are not the same. Add each new disable with its reason, or start with --write and examine the diff.\n");
+	return check.ok ? 0 : 1;
+}
+/** This function starts the CLI with its arguments and gives the exit code. */
+function runCli(argv, io) {
+	const { values, positionals } = parseArgs({
+		args: [...argv],
+		allowPositionals: true,
+		options: {
+			lane: {
+				type: "string",
+				default: "mutation.json"
+			},
+			out: { type: "string" },
+			concurrency: { type: "string" },
+			report: { type: "string" },
+			summary: { type: "string" },
+			write: {
+				type: "boolean",
+				default: false
+			},
+			runs: {
+				type: "boolean",
+				default: false
+			},
+			"dry-run": {
+				type: "boolean",
+				default: false
+			},
+			changed: { type: "string" },
+			help: {
+				type: "boolean",
+				default: false
+			}
+		}
+	});
+	const [command, ...names] = positionals;
+	if (values.help || command === void 0) {
+		io.stdout(HELP);
+		return command === void 0 && !values.help ? 1 : 0;
+	}
+	const laneFile = resolve(io.cwd, values.lane);
+	const laneDir = dirname(laneFile);
+	const lane = parseLane(readJson(laneFile));
+	const changed = values.changed === void 0 ? void 0 : readFileSync(resolve(io.cwd, values.changed), "utf8").split("\n").map((line) => line.trim()).filter((line) => line !== "");
+	const one = () => {
+		if (names.length !== 1 || names[0] === void 0) throw new Error(`"${command}" takes one selection`);
+		return names[0];
+	};
+	switch (command) {
+		case "list": {
+			if (values.runs) checkParts(lane, laneDir, Object.keys(lane.packages));
+			if (changed !== void 0 && !values.runs) throw new Error(`--changed of "list" takes --runs`);
+			const runs = values.runs ? runSelections(lane) : selectionNames(lane);
+			const shown = changed === void 0 ? runs : runs.filter((n) => changedFiles(select(lane, n), changed).length > 0);
+			io.stdout(shown.length === 0 ? "" : `${shown.join("\n")}\n`);
+			return 0;
+		}
+		case "dir":
+			io.stdout(`${relative(io.cwd, resolve(laneDir, select(lane, one()).dir)).replaceAll("\\", "/") || "."}\n`);
+			return 0;
+		case "config": {
+			const concurrency = values.concurrency === void 0 ? void 0 : Number(values.concurrency);
+			if (concurrency !== void 0 && !(Number.isInteger(concurrency) && concurrency > 0)) throw new Error(`--concurrency is not a positive integer`);
+			checkPartsOf(lane, laneDir, [one()]);
+			const all = select(lane, one());
+			const files = changed === void 0 ? void 0 : changedFiles(all, changed);
+			if (files?.length === 0) throw new Error(`the selection ${all.name} has no changed file`);
+			const selection = files === void 0 ? all : {
+				...all,
+				mutate: files
+			};
+			const options = {
+				...concurrency === void 0 ? {} : { concurrency },
+				dryRun: values["dry-run"]
+			};
+			const text = `${JSON.stringify(strykerConfig(selection, options), null, 2)}\n`;
+			if (values.out === void 0) io.stdout(text);
+			else {
+				mkdirSync(dirname(resolve(io.cwd, values.out)), { recursive: true });
+				writeFileSync(resolve(io.cwd, values.out), text);
+			}
+			return 0;
+		}
+		case "scores": {
+			if (names.length === 0) throw new Error(`"scores" takes one or more selections`);
+			if (values.report !== void 0 && names.length > 1) throw new Error(`--report takes one selection`);
+			checkPartsOf(lane, laneDir, names);
+			const scores = names.map((name) => {
+				const s = select(lane, name);
+				const file = values.report === void 0 ? resolve(laneDir, s.dir, REPORT_DIR, "mutation.json") : resolve(io.cwd, values.report);
+				if (!existsSync(file)) {
+					const reason = `the report ${relative(io.cwd, file)} does not exist`;
+					return {
+						name,
+						gate: s.gate,
+						detected: 0,
+						hitLimit: 0,
+						clockTimeouts: 0,
+						valid: 0,
+						survived: [],
+						percent: 0,
+						percentWithClock: 0,
+						pass: false,
+						reason
+					};
+				}
+				return scoreReport(parseReport(readJson(file)), s);
+			});
+			for (const s of scores) {
+				io.stdout(`${formatScore(s)}\n`);
+				if (!s.pass) for (const m of s.survived) io.stdout(`  survived: ${m}\n`);
+			}
+			if (values.summary !== void 0) appendFileSync(resolve(io.cwd, values.summary), `### Mutation scores\n\n${summaryMarkdown(scores)}\n`);
+			const failed = scores.filter((s) => !s.pass).map((s) => s.name);
+			if (failed.length > 0) io.stderr(`The gate failed for ${failed.join(", ")}.\n`);
+			return failed.length > 0 ? 1 : 0;
+		}
+		case "disables": return disables(lane, laneDir, values.write, io);
+		default:
+			io.stderr(`unknown command "${command}"\n\n${HELP}`);
+			return 1;
+	}
+}
+export { partErrors as _, formatScore as a, selectionNames as b, scoreReport as c, REPORT_DIR as d, TIMEOUT_MS as f, parseLane as g, changedFiles as h, findDisables as i, summaryMarkdown as l, STRYKER_OWNED as m, runCli as n, isHitLimit as o, strykerConfig as p, compareDisables as r, parseReport as s, HELP as t, DRY_RUN_TIMEOUT_MINUTES as u, runSelections as v, select as y };
+
+//# sourceMappingURL=run-CveACYFE.js.map

package/build/run-CveACYFE.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"run-CveACYFE.js","names":[],"sources":["../src/lane.ts","../src/config.ts","../src/score.ts","../src/disables.ts","../src/run.ts"],"sourcesContent":["import { matchesGlob, posix } from \"node:path\";\n\n/**\n * The lane file of a repository (`mutation.json`) names the packages that the mutation tests mutate. A package has\n * its folder, its globs and an optional gate. A big package has parts, so that each part has its own runner.\n */\n\n/** The mutation tests of one package. */\nexport interface PackageLane {\n  /** This field gives the folder of the package, from the folder of the lane file. Stryker starts in this folder. */\n  readonly dir: string;\n  /** These globs give the files to mutate, from `dir`. A glob with `!` removes the files of the globs before it. */\n  readonly mutate: readonly string[];\n  /**\n   * Each part has its own globs. The `!` globs of `mutate` also apply to each part. Each file of `mutate` must be in\n   * exactly one part, so that a full run mutates each file one time. `partErrors` examines this.\n   */\n  readonly parts?: Readonly<Record<string, readonly string[]>>;\n  /** This field gives the lowest mutation score in percent that passes. Without a gate, the lane only reports the score. */\n  readonly gate?: number;\n  /** This field gives the Vitest config file, from `dir`. Without it, Vitest finds its config in `dir`. */\n  readonly vitestConfig?: string;\n  /**\n   * This field gives the time in milliseconds that the clock adds to the time of the tests for each mutant. The\n   * default is 120000. A short time on a loaded runner stops mutants that the tests detect later.\n   */\n  readonly timeoutMS?: number;\n  /** This field gives the time in minutes for the run of the tests without mutants. The default is 15. */\n  readonly dryRunTimeoutMinutes?: number;\n  /**\n   * These options go into the Stryker config of each selection of the package, for example `ignoreStatic`. The lane\n   * owns the keys of `STRYKER_OWNED`, so the field cannot have them.\n   */\n  readonly stryker?: Readonly<Record<string, unknown>>;\n}\n\n/** The keys of the Stryker config that the lane owns. The field `stryker` of a package cannot have them. */\nexport const STRYKER_OWNED: readonly string[] = [\"mutate\", \"thresholds\", \"jsonReporter\", \"htmlReporter\", \"timeoutMS\", \"dryRunTimeoutMinutes\"];\n\n/** The lane file: the packages of the mutation tests, and the list of the disabled mutants. */\nexport interface Lane {\n  readonly packages: Readonly<Record<string, PackageLane>>;\n  /** This field gives the list of the disabled mutants, from the folder of the lane file. The default is `mutation-disables.json`. */\n  readonly disables?: string;\n}\n\n/** A selection is one Stryker run: a package (`collections`) or a part of a package (`collections.impl`). */\nexport interface Selection {\n  readonly name: string;\n  readonly pkg: string;\n  readonly dir: string;\n  readonly mutate: readonly string[];\n  readonly gate: number | undefined;\n  readonly vitestConfig: string | undefined;\n  readonly timeoutMS: number | undefined;\n  readonly dryRunTimeoutMinutes: number | undefined;\n  readonly stryker: Readonly<Record<string, unknown>> | undefined;\n}\n\nconst NAME = /^[\\w-]+$/;\n\nconst isRecord = (x: unknown): x is Record<string, unknown> => typeof x === \"object\" && x !== null && !Array.isArray(x);\n\nconst isGlobs = (x: unknown): x is string[] => Array.isArray(x) && x.length > 0 && x.every((g) => typeof g === \"string\" && g !== \"\");\n\n/** This function examines a package of the lane file. It gives the errors, with the name of the package. */\nfunction packageErrors(name: string, p: unknown): string[] {\n  if (!NAME.test(name)) return [`the package name \"${name}\" has a character that is not a letter, a digit, \"_\" or \"-\"`];\n  if (!isRecord(p)) return [`${name}: the package is not an object`];\n  const errors: string[] = [];\n  if (typeof p[\"dir\"] !== \"string\" || p[\"dir\"] === \"\") errors.push(`${name}: \"dir\" is not a folder name`);\n  if (!isGlobs(p[\"mutate\"])) errors.push(`${name}: \"mutate\" is not a list of globs`);\n  else if (p[\"mutate\"].every((g) => g.startsWith(\"!\"))) errors.push(`${name}: \"mutate\" has only \"!\" globs`);\n  const gate = p[\"gate\"];\n  if (gate !== undefined && (typeof gate !== \"number\" || !(gate >= 0 && gate <= 100))) errors.push(`${name}: \"gate\" is not a percent from 0 to 100`);\n  if (p[\"vitestConfig\"] !== undefined && typeof p[\"vitestConfig\"] !== \"string\") errors.push(`${name}: \"vitestConfig\" is not a file name`);\n  for (const field of [\"timeoutMS\", \"dryRunTimeoutMinutes\"]) {\n    const v = p[field];\n    if (v !== undefined && !(typeof v === \"number\" && Number.isInteger(v) && v > 0)) errors.push(`${name}: \"${field}\" is not a positive integer`);\n  }\n  const stryker = p[\"stryker\"];\n  if (stryker !== undefined) {\n    if (!isRecord(stryker)) errors.push(`${name}: \"stryker\" is not an object`);\n    else {\n      const owned = Object.keys(stryker).filter((k) => STRYKER_OWNED.includes(k));\n      if (owned.length > 0) errors.push(`${name}: \"stryker\" has ${owned.map((k) => `\"${k}\"`).join(\", \")}, but the lane owns these keys`);\n    }\n  }\n  const parts = p[\"parts\"];\n  if (parts !== undefined) {\n    if (!isRecord(parts) || Object.keys(parts).length === 0) errors.push(`${name}: \"parts\" is not an object with parts`);\n    else {\n      for (const [part, globs] of Object.entries(parts)) {\n        if (!NAME.test(part)) errors.push(`${name}: the part name \"${part}\" has a character that is not a letter, a digit, \"_\" or \"-\"`);\n        if (!isGlobs(globs) || globs.some((g) => g.startsWith(\"!\"))) errors.push(`${name}.${part}: the part is not a list of globs without \"!\"`);\n      }\n    }\n  }\n  return errors;\n}\n\n/**\n * This function examines the JSON of a lane file and gives the lane.\n *\n * @throws Error with each problem of the file\n */\nexport function parseLane(json: unknown): Lane {\n  if (!isRecord(json) || !isRecord(json[\"packages\"])) throw new Error(`the lane has no object \"packages\"`);\n  const errors = Object.entries(json[\"packages\"]).flatMap(([name, p]) => packageErrors(name, p));\n  if (Object.keys(json[\"packages\"]).length === 0) errors.push(`the lane has no packages`);\n  if (json[\"disables\"] !== undefined && typeof json[\"disables\"] !== \"string\") errors.push(`\"disables\" is not a file name`);\n  if (errors.length > 0) throw new Error(`the lane is not valid:\\n  ${errors.join(\"\\n  \")}`);\n  return json as unknown as Lane;\n}\n\n/** This function gives the names of all the selections of a lane: each package, then each part of the package. */\nexport function selectionNames(lane: Lane): string[] {\n  return Object.entries(lane.packages).flatMap(([name, p]) => [name, ...Object.keys(p.parts ?? {}).map((part) => `${name}.${part}`)]);\n}\n\n/** This function gives the selections of a full run: the parts of each package with parts, else the package. Each file is in one run. */\nexport function runSelections(lane: Lane): string[] {\n  return Object.entries(lane.packages).flatMap(([name, p]) => (p.parts === undefined ? [name] : Object.keys(p.parts).map((part) => `${name}.${part}`)));\n}\n\n/**\n * This function gives the selection of a name: a package, or a part of a package.\n *\n * @throws Error when the lane has no package or part of that name\n */\nexport function select(lane: Lane, name: string): Selection {\n  const [pkg = \"\", part, ...rest] = name.split(\".\");\n  const p = lane.packages[pkg];\n  const globs = part === undefined ? undefined : p?.parts?.[part];\n  if (p === undefined || rest.length > 0 || (part !== undefined && globs === undefined)) {\n    throw new Error(`the lane has no package or part \"${name}\". It has: ${selectionNames(lane).join(\", \")}`);\n  }\n  // Stryker applies a \"!\" glob to the globs before it, so the \"!\" globs of the package go after the globs of the part.\n  const mutate = globs === undefined ? p.mutate : [...globs, ...p.mutate.filter((g) => g.startsWith(\"!\"))];\n  return { name, pkg, dir: p.dir, mutate, gate: p.gate, vitestConfig: p.vitestConfig, timeoutMS: p.timeoutMS, dryRunTimeoutMinutes: p.dryRunTimeoutMinutes, stryker: p.stryker };\n}\n\n/**\n * This function tells if globs select a file. It reads the globs as Stryker does. A glob adds its files. A glob with\n * `!` removes its files from the files of the globs before it.\n */\nexport function globsSelect(globs: readonly string[], file: string): boolean {\n  let selected = false;\n  for (const g of globs) {\n    if (g.startsWith(\"!\")) {\n      if (selected && matchesGlob(file, g.slice(1))) selected = false;\n    } else if (!selected && matchesGlob(file, g)) selected = true;\n  }\n  return selected;\n}\n\n/**\n * This function gives the changed files of a selection, from the folder of its package. The globs of the selection\n * select the files.\n *\n * @param changed - the changed paths, from the folder of the lane file, with `/`\n */\nexport function changedFiles(selection: Selection, changed: readonly string[]): string[] {\n  const dir = posix.normalize(selection.dir.replaceAll(\"\\\\\", \"/\"));\n  return changed\n    .map((f) => posix.relative(dir, posix.normalize(f.replaceAll(\"\\\\\", \"/\"))))\n    .filter((f) => f !== \"\" && !f.startsWith(\"../\") && !posix.isAbsolute(f) && globsSelect(selection.mutate, f));\n}\n\n/**\n * This function examines the parts of a package against its files. It gives an error for each file of `mutate` in no\n * part. It also gives an error for each file in two parts, and for each file of a part that is not in `mutate`. A\n * package with no parts has no errors.\n *\n * @param files - the source files of the package, from its folder, with `/`\n */\nexport function partErrors(lane: Lane, pkg: string, files: readonly string[]): string[] {\n  const p = lane.packages[pkg];\n  if (p?.parts === undefined) return [];\n  const parts = Object.keys(p.parts).map((part) => ({ part, mutate: select(lane, `${pkg}.${part}`).mutate }));\n  const errors: string[] = [];\n  for (const file of files) {\n    const inMutate = globsSelect(p.mutate, file);\n    const inParts = parts.filter((x) => globsSelect(x.mutate, file)).map((x) => x.part);\n    if (inMutate && inParts.length === 0) errors.push(`${pkg}: the file ${file} is in no part, so a full run does not mutate it`);\n    else if (inParts.length > 1) errors.push(`${pkg}: the file ${file} is in more than one part: ${inParts.join(\", \")}`);\n    else if (!inMutate && inParts.length === 1) errors.push(`${pkg}: the file ${file} is in the part ${inParts.join(\"\")}, but not in \"mutate\"`);\n  }\n  return errors;\n}\n","import type { Selection } from \"./lane.ts\";\n\n/** The options of `strykerConfig`. */\nexport interface ConfigOptions {\n  /** This option gives the number of test processes. The default is 2. */\n  readonly concurrency?: number;\n  /** This option gives the folder of the reports, from the folder of the package. The default is `reports/mutation`. */\n  readonly reportDir?: string;\n  /**\n   * When this option is true, Stryker starts only the tests without mutants, and it does not stop at the first failed\n   * test. Use it to see if the tests pass under Stryker before a long run.\n   */\n  readonly dryRun?: boolean;\n}\n\n/** The Stryker config of one selection, as JSON. Stryker starts in the folder of the package. The field `stryker` of the lane adds keys. */\nexport interface StrykerConfig {\n  readonly [key: string]: unknown;\n  readonly testRunner: \"vitest\";\n  readonly plugins: readonly string[];\n  readonly vitest?: { readonly configFile: string };\n  readonly mutate: readonly string[];\n  readonly coverageAnalysis: \"perTest\";\n  readonly reporters: readonly string[];\n  readonly htmlReporter: { readonly fileName: string };\n  readonly jsonReporter: { readonly fileName: string };\n  readonly thresholds: { readonly high: number; readonly low: number; readonly break: null };\n  readonly concurrency: number;\n  readonly timeoutMS: number;\n  readonly dryRunTimeoutMinutes: number;\n  readonly dryRunOnly?: true;\n  readonly disableBail?: true;\n}\n\n/** The default folder of the reports, from the folder of the package. */\nexport const REPORT_DIR = \"reports/mutation\";\n\n/**\n * The default time in milliseconds that the clock adds to the time of the tests for each mutant. The default of\n * Stryker is 5000. On a loaded CI runner that time stopped mutants that the tests detected later.\n */\nexport const TIMEOUT_MS = 120_000;\n\n/** The default time in minutes for the run of the tests without mutants. The default of Stryker is 5. */\nexport const DRY_RUN_TIMEOUT_MINUTES = 15;\n\n/**\n * This function gives the Stryker config of a selection. The break of Stryker is off, because the gate of each\n * package is in `scoreReport`. Stryker 10.1.0 or later is necessary with Vitest 5: version 10.0 started no test on each\n * mutant (stryker-js issue 6210).\n */\nexport function strykerConfig(selection: Selection, options: ConfigOptions = {}): StrykerConfig {\n  const reportDir = options.reportDir ?? REPORT_DIR;\n  const low = selection.gate ?? 60;\n  return {\n    testRunner: \"vitest\",\n    plugins: [\"@stryker-mutator/vitest-runner\"],\n    ...(selection.vitestConfig === undefined ? {} : { vitest: { configFile: selection.vitestConfig } }),\n    mutate: selection.mutate,\n    coverageAnalysis: \"perTest\",\n    reporters: [\"clear-text\", \"progress\", \"html\", \"json\"],\n    htmlReporter: { fileName: `${reportDir}/index.html` },\n    jsonReporter: { fileName: `${reportDir}/mutation.json` },\n    thresholds: { high: Math.max(low, 90), low, break: null },\n    concurrency: options.concurrency ?? 2,\n    timeoutMS: selection.timeoutMS ?? TIMEOUT_MS,\n    dryRunTimeoutMinutes: selection.dryRunTimeoutMinutes ?? DRY_RUN_TIMEOUT_MINUTES,\n    // The keys of the lane field \"stryker\" replace the keys above, but \"--concurrency\" replaces its \"concurrency\".\n    ...selection.stryker,\n    ...(options.concurrency === undefined ? {} : { concurrency: options.concurrency }),\n    ...(options.dryRun === true ? { dryRunOnly: true, disableBail: true } : {}),\n  };\n}\n","/**\n * The score of a Stryker report, with the gate of the package. The score counts the detected mutants, out of the\n * mutants that a test covers or that survive. Compile errors, runtime errors and ignored mutants do not count.\n *\n * Stryker gives the status `Timeout` for two events. The hit limit stops a mutant with an endless loop: its\n * `statusReason` starts with `Hit limit`, and the mutant is detected. The clock stops a mutant that took too long. The\n * load of the runner can cause this. Thus the mutant is not detected for certain, and it counts as not detected.\n */\n\n/** A mutant of the JSON report of Stryker (the schema of mutation-testing-elements). */\nexport interface Mutant {\n  readonly status: string;\n  readonly mutatorName: string;\n  /** Stryker gives the reason of some statuses here. A `Timeout` of the hit limit has a reason that starts with `Hit limit`. */\n  readonly statusReason?: string | undefined;\n  readonly location: { readonly start: { readonly line: number } };\n}\n\n/** The JSON report of Stryker: the mutants of each mutated file. */\nexport interface MutationReport {\n  readonly files: Readonly<Record<string, { readonly mutants: readonly Mutant[] }>>;\n}\n\n/** The score of one selection. */\nexport interface Score {\n  readonly name: string;\n  readonly gate: number | undefined;\n  /** The mutants with the status `Killed`, and the mutants that the hit limit stopped. */\n  readonly detected: number;\n  /** The mutants that the hit limit stopped. They are in `detected`. */\n  readonly hitLimit: number;\n  /** The mutants that the clock stopped. They count as not detected, and they are in `survived`. */\n  readonly clockTimeouts: number;\n  /** The mutants that count: detected, survived or with no coverage. */\n  readonly valid: number;\n  /** Each mutant that survived, had no coverage or was stopped by the clock, as `file:line Mutator`. */\n  readonly survived: readonly string[];\n  /** The score in percent. It is 0 when no mutant counts. */\n  readonly percent: number;\n  /** The score in percent with the clock time-outs counted as detected, as Stryker counts them. The gate does not read it. */\n  readonly percentWithClock: number;\n  readonly pass: boolean;\n  /** The reason of a failure. */\n  readonly reason: string | undefined;\n}\n\nconst UNDETECTED = new Set([\"Survived\", \"NoCoverage\"]);\n\n/** This function tells if the hit limit of Stryker stopped a mutant. Then the mutant has an endless loop, and it is detected. */\nexport const isHitLimit = (m: Mutant): boolean => m.status === \"Timeout\" && (m.statusReason ?? \"\").startsWith(\"Hit limit\");\n\n/**\n * This function examines the JSON of a Stryker report and gives the report.\n *\n * @throws Error when the JSON has no files with mutants\n */\nexport function parseReport(json: unknown): MutationReport {\n  const files = typeof json === \"object\" && json !== null ? (json as { files?: unknown }).files : undefined;\n  if (typeof files !== \"object\" || files === null) throw new Error(`the report has no object \"files\"`);\n  for (const [file, data] of Object.entries(files)) {\n    if (!Array.isArray((data as { mutants?: unknown } | null)?.mutants)) throw new Error(`the report has no list \"mutants\" for ${file}`);\n  }\n  return json as MutationReport;\n}\n\n/**\n * This function gives the score of a report and applies the gate. A report with no mutants that count fails, also\n * without a gate: Stryker found no files. A report with mutants that count and none detected also fails: the test\n * runner started no test on the mutants. Stryker 10.0 with Vitest 5 gave this result.\n */\nexport function scoreReport(report: MutationReport, selection: { readonly name: string; readonly gate: number | undefined }): Score {\n  let detected = 0;\n  let valid = 0;\n  let hitLimit = 0;\n  let clockTimeouts = 0;\n  const survived: string[] = [];\n  for (const [file, data] of Object.entries(report.files)) {\n    for (const m of data.mutants) {\n      const at = `${file}:${String(m.location.start.line)} ${m.mutatorName}`;\n      if (m.status === \"Killed\" || isHitLimit(m)) {\n        detected++;\n        valid++;\n        if (m.status === \"Timeout\") hitLimit++;\n      } else if (m.status === \"Timeout\") {\n        clockTimeouts++;\n        valid++;\n        survived.push(`${at} (the clock stopped it)`);\n      } else if (UNDETECTED.has(m.status)) {\n        valid++;\n        survived.push(at);\n      }\n    }\n  }\n  const percent = valid === 0 ? 0 : (100 * detected) / valid;\n  const percentWithClock = valid === 0 ? 0 : (100 * (detected + clockTimeouts)) / valid;\n  const { name, gate } = selection;\n  const reason =\n    valid === 0\n      ? \"the report has no mutants that count: Stryker found no files to mutate, or it did not start\"\n      : detected === 0\n        ? `the tests detected none of the ${String(valid)} mutants: the test runner started no test on the mutants`\n        : gate !== undefined && percent < gate\n          ? `the score ${percent.toFixed(2)} % is under the gate ${String(gate)} %`\n          : undefined;\n  return { name, gate, detected, hitLimit, clockTimeouts, valid, survived, percent, percentWithClock, pass: reason === undefined, reason };\n}\n\n/** This function gives the time-outs of a score as text: the count of each kind, and the score that counts the clock time-outs as detected. */\nconst timeouts = (s: Score): string =>\n  `time-outs: ${String(s.hitLimit)} hit limit, ${String(s.clockTimeouts)} clock (${s.percentWithClock.toFixed(2)} % with the clock time-outs as detected)`;\n\n/** This function gives one line for a score, with the name of the selection and its result. The time-outs are in it when the report has some. */\nexport function formatScore(s: Score): string {\n  const gate = s.gate === undefined ? \"no gate\" : `gate ${String(s.gate)} %`;\n  const result = s.pass ? \"pass\" : `FAIL: ${s.reason ?? \"\"}`;\n  const time = s.hitLimit + s.clockTimeouts === 0 ? \"\" : `, ${timeouts(s)}`;\n  return `${s.name}: ${s.percent.toFixed(2)} % (${String(s.detected)} of ${String(s.valid)}, ${String(s.survived.length)} survived${time}), ${gate}: ${result}`;\n}\n\n/** This function gives a Markdown table of scores, for the summary of a CI job. */\nexport function summaryMarkdown(scores: readonly Score[]): string {\n  const rows = scores.map(\n    (s) =>\n      `| ${s.name} | ${s.percent.toFixed(2)} % | ${String(s.detected)} | ${String(s.valid)} | ${String(s.survived.length)} | ${String(s.clockTimeouts)} | ${s.percentWithClock.toFixed(2)} % | ${s.gate === undefined ? \"none\" : `${String(s.gate)} %`} | ${s.pass ? \"pass\" : `fail: ${s.reason ?? \"\"}`} |`,\n  );\n  return [\n    \"| Selection | Score | Detected | Valid | Survived | Clock time-outs | Score with them | Gate | Result |\",\n    \"| --- | ---: | ---: | ---: | ---: | ---: | ---: | ---: | --- |\",\n    ...rows,\n    \"\",\n  ].join(\"\\n\");\n}\n","/**\n * A comment `// Stryker disable next-line <Mutator>: <reason>` disables a mutant that is equivalent. The disable\n * raises the score, so each one is also in a list with its reason. These functions find the comments in the\n * sources and compare them with the list.\n */\n\n/** One disable comment of a source file. */\nexport interface Disable {\n  readonly file: string;\n  readonly comment: string;\n}\n\n/** The result of `compareDisables`. */\nexport interface DisableCheck {\n  /** The comments of the sources that are not in the list, as `file: comment`. */\n  readonly added: readonly string[];\n  /** The comments of the list that are not in the sources, as `file: comment`. */\n  readonly removed: readonly string[];\n  /** The comments with no reason after a colon. */\n  readonly noReason: readonly Disable[];\n  readonly ok: boolean;\n}\n\n/** This function finds each `Stryker disable` comment of the files. A file name uses `/`. */\nexport function findDisables(files: readonly { readonly file: string; readonly text: string }[]): Disable[] {\n  return files.flatMap(({ file, text }) =>\n    text\n      .split(\"\\n\")\n      .filter((line) => line.includes(\"Stryker disable\"))\n      .map((line) => ({ file, comment: line.trim() })),\n  );\n}\n\nconst counts = (xs: readonly Disable[]): Map<string, number> => {\n  const m = new Map<string, number>();\n  for (const x of xs) {\n    const k = `${x.file}: ${x.comment}`;\n    m.set(k, (m.get(k) ?? 0) + 1);\n  }\n  return m;\n};\n\n/**\n * This function tells if a comment has a reason: a mutator name, a colon, a space and a text. It reads the text by\n * index, so its time is linear in the length of the comment (a regular expression here was quadratic).\n */\nfunction hasReason(comment: string): boolean {\n  const start = comment.indexOf(\"Stryker disable \");\n  if (start < 0) return false;\n  const rest = comment.slice(start + \"Stryker disable \".length);\n  const colon = rest.indexOf(\":\");\n  return colon > 0 && rest[colon + 1] === \" \" && /\\S/.test(rest[colon + 2] ?? \"\");\n}\n\n/** This function compares the comments of the sources with the list. A file with the same comment two times needs it two times in the list. */\nexport function compareDisables(found: readonly Disable[], listed: readonly Disable[]): DisableCheck {\n  const noReason = found.filter((d) => !hasReason(d.comment));\n  const a = counts(found);\n  const b = counts(listed);\n  const added = [...a].filter(([k, n]) => n > (b.get(k) ?? 0)).map(([k]) => k);\n  const removed = [...b].filter(([k, n]) => n > (a.get(k) ?? 0)).map(([k]) => k);\n  return { added, removed, noReason, ok: added.length === 0 && removed.length === 0 && noReason.length === 0 };\n}\n","/**\n * The CLI `rigor-mutation`. The work is in `runCli`, so a test can start the CLI in a fixture folder.\n */\nimport { existsSync, mkdirSync, readdirSync, readFileSync, writeFileSync, appendFileSync } from \"node:fs\";\nimport { dirname, relative, resolve } from \"node:path\";\nimport { parseArgs } from \"node:util\";\nimport { REPORT_DIR, strykerConfig } from \"./config.ts\";\nimport { compareDisables, findDisables, type Disable } from \"./disables.ts\";\nimport { changedFiles, parseLane, partErrors, runSelections, select, selectionNames, type Lane } from \"./lane.ts\";\nimport { formatScore, parseReport, scoreReport, summaryMarkdown, type Score } from \"./score.ts\";\n\n/** The input and the output of the CLI. */\nexport interface CliIo {\n  readonly cwd: string;\n  readonly stdout: (text: string) => void;\n  readonly stderr: (text: string) => void;\n}\n\n/** The help text of the CLI. */\nexport const HELP: string = `rigor-mutation: the mutation tests of a repository, with Stryker and a gate for each package.\n\n  rigor-mutation list [--runs] [--changed <file>]\n                                               the packages and the parts of the lane. With --runs, the\n                                               selections of a full run: the parts of a package with parts.\n                                               With --changed, only the runs with a changed file.\n  rigor-mutation dir <selection>               the folder of the package of a selection\n  rigor-mutation config <selection> [--out <file>] [--concurrency <n>] [--dry-run] [--changed <file>]\n                                               the Stryker config of a selection, as JSON. With --dry-run,\n                                               Stryker starts only the tests. With --changed, it mutates only\n                                               the changed files of the selection.\n  rigor-mutation scores <selection>... [--report <file>] [--summary <file>]\n                                               the score of each selection, with its gate\n  rigor-mutation disables [--write]            compare the disable comments with their list\n\n  --lane <file>      the lane file. The default is mutation.json.\n  --changed <file>   a file with one changed path on each line, from the folder of the lane file,\n                     for example the output of git diff --name-only.\n\nA selection is a package (\"collections\") or a part of a package (\"collections.impl\").\nEach file of a package with parts must be in exactly one part. list --runs, and config and scores\nof a part, fail when it is not.\nThe score of a selection reads <dir>/${REPORT_DIR}/mutation.json, or the file of --report.\n`;\n\nconst SOURCE = /\\.(?:[cm]?[jt]s|tsx)$/;\nconst TEST = /\\.(?:test|spec)\\.[^.]+$/;\nconst SKIP = new Set([\"node_modules\", \"build\", \"dist\", \"reports\", \"coverage\"]);\n\n/** This function gives each source file of a folder, from `root`, with `/`. It skips the tests, the outputs and the dot folders. */\nfunction sourcesOf(root: string, dir: string): string[] {\n  return readdirSync(dir, { withFileTypes: true })\n    .toSorted((x, y) => x.name.localeCompare(y.name))\n    .flatMap((e) => {\n      const path = resolve(dir, e.name);\n      if (e.isDirectory()) return e.name.startsWith(\".\") || SKIP.has(e.name) ? [] : sourcesOf(root, path);\n      return e.isFile() && SOURCE.test(e.name) && !TEST.test(e.name) ? [relative(root, path).replaceAll(\"\\\\\", \"/\")] : [];\n    });\n}\n\nconst readJson = (file: string): unknown => JSON.parse(readFileSync(file, \"utf8\"));\n\n/**\n * This function examines the parts of the packages against their source files.\n *\n * @throws Error with each file that is in no part, in more than one part, or in a part and not in `mutate`\n */\nfunction checkParts(lane: Lane, laneDir: string, pkgs: readonly string[]): void {\n  const errors = pkgs.flatMap((pkg) => {\n    const p = lane.packages[pkg];\n    if (p?.parts === undefined) return [];\n    const dir = resolve(laneDir, p.dir);\n    if (!existsSync(dir)) return [`${pkg}: the folder ${p.dir} does not exist`];\n    return partErrors(lane, pkg, sourcesOf(dir, dir));\n  });\n  if (errors.length > 0) throw new Error(`the parts do not cover each file exactly one time:\\n  ${errors.join(\"\\n  \")}`);\n}\n\n/** This function examines the parts of the package of each selection that is a part. */\nconst checkPartsOf = (lane: Lane, laneDir: string, names: readonly string[]): void =>\n  checkParts(lane, laneDir, [...new Set(names.map((n) => select(lane, n)).filter((s) => s.name !== s.pkg).map((s) => s.pkg))]);\n\nfunction disables(lane: Lane, laneDir: string, write: boolean, io: CliIo): number {\n  const files = new Set<string>();\n  for (const [name, p] of Object.entries(lane.packages)) {\n    const dir = resolve(laneDir, p.dir);\n    if (!existsSync(dir)) throw new Error(`${name}: the folder ${p.dir} does not exist`);\n    for (const f of sourcesOf(laneDir, dir)) files.add(f);\n  }\n  const found = findDisables([...files].map((file) => ({ file, text: readFileSync(resolve(laneDir, file), \"utf8\") })));\n  const listFile = resolve(laneDir, lane.disables ?? \"mutation-disables.json\");\n  const listed = existsSync(listFile) ? (readJson(listFile) as Disable[]) : [];\n  const check = compareDisables(found, listed);\n  for (const d of check.noReason) io.stderr(`a disable without a reason after a colon: ${d.file}: ${d.comment}\\n`);\n  if (write) {\n    if (check.noReason.length > 0) return 1;\n    writeFileSync(listFile, `${JSON.stringify(found, null, 2)}\\n`);\n    io.stdout(`disables: wrote ${String(found.length)} comments to ${relative(io.cwd, listFile).replaceAll(\"\\\\\", \"/\")}\\n`);\n    return 0;\n  }\n  const perFile = new Map<string, number>();\n  for (const d of found) perFile.set(d.file, (perFile.get(d.file) ?? 0) + 1);\n  io.stdout(`disables: ${String(found.length)} in ${String(perFile.size)} files\\n`);\n  for (const [file, n] of perFile) io.stdout(`  ${file}: ${String(n)}\\n`);\n  for (const k of check.added) io.stderr(`not in the list: ${k}\\n`);\n  for (const k of check.removed) io.stderr(`in the list, not in the sources: ${k}\\n`);\n  if (check.added.length > 0 || check.removed.length > 0) {\n    io.stderr(\"disables: the sources and the list are not the same. Add each new disable with its reason, or start with --write and examine the diff.\\n\");\n  }\n  return check.ok ? 0 : 1;\n}\n\n/** This function starts the CLI with its arguments and gives the exit code. */\nexport function runCli(argv: readonly string[], io: CliIo): number {\n  const { values, positionals } = parseArgs({\n    args: [...argv],\n    allowPositionals: true,\n    options: {\n      lane: { type: \"string\", default: \"mutation.json\" },\n      out: { type: \"string\" },\n      concurrency: { type: \"string\" },\n      report: { type: \"string\" },\n      summary: { type: \"string\" },\n      write: { type: \"boolean\", default: false },\n      runs: { type: \"boolean\", default: false },\n      \"dry-run\": { type: \"boolean\", default: false },\n      changed: { type: \"string\" },\n      help: { type: \"boolean\", default: false },\n    },\n  });\n  const [command, ...names] = positionals;\n  if (values.help || command === undefined) {\n    io.stdout(HELP);\n    return command === undefined && !values.help ? 1 : 0;\n  }\n  const laneFile = resolve(io.cwd, values.lane);\n  const laneDir = dirname(laneFile);\n  const lane = parseLane(readJson(laneFile));\n  const changed =\n    values.changed === undefined\n      ? undefined\n      : readFileSync(resolve(io.cwd, values.changed), \"utf8\")\n          .split(\"\\n\")\n          .map((line) => line.trim())\n          .filter((line) => line !== \"\");\n  const one = (): string => {\n    if (names.length !== 1 || names[0] === undefined) throw new Error(`\"${command}\" takes one selection`);\n    return names[0];\n  };\n  switch (command) {\n    case \"list\": {\n      if (values.runs) checkParts(lane, laneDir, Object.keys(lane.packages));\n      if (changed !== undefined && !values.runs) throw new Error(`--changed of \"list\" takes --runs`);\n      const runs = values.runs ? runSelections(lane) : selectionNames(lane);\n      const shown = changed === undefined ? runs : runs.filter((n) => changedFiles(select(lane, n), changed).length > 0);\n      io.stdout(shown.length === 0 ? \"\" : `${shown.join(\"\\n\")}\\n`);\n      return 0;\n    }\n    case \"dir\":\n      io.stdout(`${relative(io.cwd, resolve(laneDir, select(lane, one()).dir)).replaceAll(\"\\\\\", \"/\") || \".\"}\\n`);\n      return 0;\n    case \"config\": {\n      const concurrency = values.concurrency === undefined ? undefined : Number(values.concurrency);\n      if (concurrency !== undefined && !(Number.isInteger(concurrency) && concurrency > 0)) throw new Error(`--concurrency is not a positive integer`);\n      checkPartsOf(lane, laneDir, [one()]);\n      const all = select(lane, one());\n      const files = changed === undefined ? undefined : changedFiles(all, changed);\n      if (files?.length === 0) throw new Error(`the selection ${all.name} has no changed file`);\n      const selection = files === undefined ? all : { ...all, mutate: files };\n      const options = { ...(concurrency === undefined ? {} : { concurrency }), dryRun: values[\"dry-run\"] };\n      const text = `${JSON.stringify(strykerConfig(selection, options), null, 2)}\\n`;\n      if (values.out === undefined) io.stdout(text);\n      else {\n        mkdirSync(dirname(resolve(io.cwd, values.out)), { recursive: true });\n        writeFileSync(resolve(io.cwd, values.out), text);\n      }\n      return 0;\n    }\n    case \"scores\": {\n      if (names.length === 0) throw new Error(`\"scores\" takes one or more selections`);\n      if (values.report !== undefined && names.length > 1) throw new Error(`--report takes one selection`);\n      checkPartsOf(lane, laneDir, names);\n      const scores: Score[] = names.map((name) => {\n        const s = select(lane, name);\n        const file = values.report === undefined ? resolve(laneDir, s.dir, REPORT_DIR, \"mutation.json\") : resolve(io.cwd, values.report);\n        if (!existsSync(file)) {\n          const reason = `the report ${relative(io.cwd, file)} does not exist`;\n          return { name, gate: s.gate, detected: 0, hitLimit: 0, clockTimeouts: 0, valid: 0, survived: [], percent: 0, percentWithClock: 0, pass: false, reason };\n        }\n        return scoreReport(parseReport(readJson(file)), s);\n      });\n      for (const s of scores) {\n        io.stdout(`${formatScore(s)}\\n`);\n        if (!s.pass) for (const m of s.survived) io.stdout(`  survived: ${m}\\n`);\n      }\n      if (values.summary !== undefined) appendFileSync(resolve(io.cwd, values.summary), `### Mutation scores\\n\\n${summaryMarkdown(scores)}\\n`);\n      const failed = scores.filter((s) => !s.pass).map((s) => s.name);\n      if (failed.length > 0) io.stderr(`The gate failed for ${failed.join(\", \")}.\\n`);\n      return failed.length > 0 ? 1 : 0;\n    }\n    case \"disables\":\n      return disables(lane, laneDir, values.write, io);\n    default:\n      io.stderr(`unknown command \"${command}\"\\n\\n${HELP}`);\n      return 1;\n  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package/package.json

@@ -1,6 +1,64 @@
 {
+  "$schema": "https://json.schemastore.org/package",
   "name": "@mark1russell7/rigor-mutation",
-  "version": "0.0.0-stage",
-  "stub": true,
-  "description": "Temporary package placeholder for staged publishing"
+  "version": "0.1.1",
+  "description": "Mutation tests with Stryker and Vitest for each package of a repository: the Stryker config of each package or part, a score with a gate for each package, and a check of the disabled mutants.",
+  "keywords": [
+    "mutation",
+    "mutation-testing",
+    "stryker",
+    "vitest",
+    "gate",
+    "monorepo",
+    "testing",
+    "ci"
+  ],
+  "homepage": "https://github.com/mark1russell7/rigor/tree/main/packages/mutation#readme",
+  "bugs": {
+    "url": "https://github.com/mark1russell7/rigor/issues"
+  },
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/mark1russell7/rigor.git",
+    "directory": "packages/mutation"
+  },
+  "license": "MIT",
+  "author": "Mark Russell (https://github.com/mark1russell7)",
+  "type": "module",
+  "sideEffects": false,
+  "main": "./build/index.js",
+  "bin": {
+    "rigor-mutation": "./build/cli.js"
+  },
+  "files": [
+    "build"
+  ],
+  "publishConfig": {
+    "access": "public"
+  },
+  "engines": {
+    "node": ">=22"
+  },
+  "devDependencies": {
+    "@mark1russell7/cue": "^2.0.0",
+    "@types/node": "^26.6.5",
+    "typescript": "^7.0.2",
+    "vitest": "^5.0.3",
+    "esbuild": "^0.28.2",
+    "tsdown": "^0.23.1"
+  },
+  "scripts": {
+    "build": "tsdown",
+    "test": "vitest run",
+    "test:watch": "vitest",
+    "typecheck": "tsc -p tsconfig.json && tsc -p tsconfig.test.json"
+  },
+  "types": "./build/index.d.ts",
+  "exports": {
+    ".": {
+      "types": "./build/index.d.ts",
+      "import": "./build/index.js"
+    },
+    "./package.json": "./package.json"
+  }
 }