---
title: "Configuration"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Configuration}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

This vignette documents the options that control how `mutate_package()` runs:
which test strategy is used, how mutant timeouts are calibrated, which tests are
selected, how parallel workers are isolated, how to exclude code from mutation,
and how the optional coverage-guided, precise-location, and
equivalent-mutant-detection features behave. See `?mutate_package` for the full
argument and return-value documentation.

## Mutation testing modes (`strategy`)

mutator selects a package test strategy automatically:

- If `tests/testthat/` exists, mutator loads the mutant in-process with
  `pkgload::load_all()` and mirrors the package's own `tests/testthat.R` harness
  by forwarding extractable arguments (notably any `filter`) from
  `testthat::test_check()` to `testthat::test_dir()`, without paying for an
  install per mutant.
- Otherwise, if `inst/tinytest/` exists, mutator loads the mutant in-process with
  `pkgload::load_all()` and runs `tinytest::run_test_dir("inst/tinytest")`, also
  without an install per mutant.
- Otherwise, if `tests/` exists, mutator falls back to
  `tools::testInstalledPackage(..., types = "tests")` after installing each
  mutant with `--install-tests`.

Both in-process strategies use `pkgload::load_all()`, which in some cases does
not load a package the way an installed copy would (see [pkgload issue
#340](https://github.com/r-lib/pkgload/issues/340)). A tinytest package affected
by this can be run against an installed copy with `strategy =
"tinytest-installed"` (`R CMD INSTALL` plus `tinytest::test_package()`), which is
slower but matches an installed package and still supports coverage-guided
selection. Pass `strategy` to `mutate_package()` to override auto-detection:

```r
mutate_package("path/to/pkg", strategy = "tinytest-installed")
```

## Timeouts and contention in parallel mode

Each mutant is run with a wall-clock timeout; exceeding it is reported as
`HANG`. The timeout is derived from how long the package's own test suite takes,
unless you pass `timeout_seconds` explicitly.

Because mutants run in parallel (`cores` at a time), the timeout must account
for **contention**: with many workers, each test run is slower than it would be
alone for packages that load many dependencies, or do heavy per-mutant install
work. A timeout based on a single, _uncontended_ baseline run
would then fire on nearly every mutant (leading to numerous false `HANG`s).

To avoid this, `mutate_package()` first runs the baseline suite once on its own
(to confirm it passes and fail fast otherwise), then runs it `cores` times
**concurrently** and takes the slowest of those as the _contended baseline_. The
timeout is `max(contended_baseline * 1.5, 5s)`. This self-calibrates to the
machine, the chosen parallelism, and the package's real load/compile cost, avoiding
manual tuning. Pass `timeout_seconds` to override it entirely. 

When `cores = 1`, or when forking is unavailable, the timing for the baseline suite 
is used.

## CRAN mode (test selection)

By default `mutate_package()` runs each mutant's tests in **CRAN mode**
(`cran = TRUE`): the `NOT_CRAN` environment variable is set to `"false"` in the
test subprocess, so `testthat::skip_on_cran()` and `skip_if_offline()` guards
take effect and mutator runs the same tests CRAN would. This skips the slow,
flaky, or network-dependent tests that packages mark as CRAN-skippable, which
keeps mutation runs fast and avoids spurious timeouts/kills from, e.g., tests
that hit the network.

Set `cran = FALSE` to run the **full** suite instead (`NOT_CRAN = "true"`, 
which is what happens by default when running `devtools::test()`):

```r
mutate_package("path/to/pkg", cran = FALSE)
```

This applies to every test strategy (`testthat`, `tinytest`,
`tinytest-installed`, and the installed-tests fallback; the tinytest strategies
map it to `run_test_dir(at_home = )`). Note that it only affects tests the package
_explicitly_ guards with `skip_on_cran()` / `skip_if_offline()` (or `at_home()`
for tinytest); a package whose network test has no such guard will still run that
test in either mode.

## Fail-fast (stop at the first failing test)

A mutant is `KILLED` the instant any of the tests detects it, so running the rest of
its suite is wasted work. By default (`fail_fast = TRUE`), each mutant's test run
**stops at the first failing test** instead of finishing the suite, which speeds
up the test-running phase (often substantially for packages with large suites)
without changing any mutant's verdict.

Set `fail_fast = FALSE` to run the full suite for every mutant:

```r
mutate_package("path/to/pkg", fail_fast = FALSE)
```

This applies to the `testthat` strategy: it sets `TESTTHAT_MAX_FAILS = 1` in the
test subprocess and uses the progress reporter, which aborts the run at the first
failing `test_that()` block. `SURVIVED` mutants are unaffected, as they have no
failure to short-circuit on, so baseline timing and timeout calibration are
unchanged. The `tinytest` strategies run the full set of selected test files (a
mutant is still `KILLED` on the first failing file), and the installed-tests
fallback already stops at the first failing test _file_ regardless of this flag.

## Parallel execution and isolation (`isolate`)

By default, each mutant package copy _symlinks_ the unchanged directories of the
original package and only the mutated `R/` file is materialised, so all parallel
workers point at the same physical `src/`, `tests/`, etc. This is fast, and two
design choices keep it correct:

- **Compiled code is built once, not per mutant.** For the in-process strategies
   (`testthat` and `tinytest`), `pkgload::load_all()` reuses the baseline's
   compiled `src/` since C code is never mutated. The `installed` and
   `tinytest-installed` strategies compile once into a _template_ library and
  install each mutant with `--no-libs`, which never writes into `src/`. This prevents
  parallel workers from fighting over the same compiled objects.
- **Snapshot references are not shared.** For `testthat` packages with `_snaps`
  directories, mutator gives each mutant its own snapshot copy while symlinking
  the rest of `tests/`, so filtered or parallel runs cannot rewrite shared
  snapshot references.

The one remaining hazard is **non-hermetic tests that write files** into a shared
directory (most often `tests/`). When parallel workers' tests fight over the same
files you can still see spurious `KILLED`/`HANG`. Two ways to attenuate it:

1. **Run without parallelism:** `cores = 1`. No contention, no extra disk, but
   the slowest option.
2. **Isolate file state:** `isolate = TRUE`. Each mutant gets its own deep copy
   of `src/` and `tests/` instead of a symlink, so file-writing tests can't
   collide:

   ```r
   mutate_package("path/to/pkg", isolate = TRUE)
   ```

The default (`isolate = FALSE`) is fast and correct for hermetic test suites;
reach for `isolate = TRUE` (or `cores = 1`) only when a package's tests are not
hermetic and you see parallel-only `KILLED`/`HANG` results.

### Progress bar

When the optional [`pbmcapply`](https://cran.r-project.org/package=pbmcapply)
package is installed, the multi-core test run shows a live progress bar.

```r
install.packages("pbmcapply")
```

## Excluding code from mutation

Not all code should be mutation-tested. Vendored/standalone files, generated
code, or deprecated paths a suite is not meant to cover will mostly produce
`SURVIVED` mutants and depress the score without telling you anything useful.
There are a few ways to exclude code.

**1. By file, at the call site, with `exclude_files`.** A character vector of
shell-style glob patterns matched against the base names of the `.R` files in
`R/`. Matching files are skipped entirely before any mutants are generated:

```r
mutate_package("path/to/scales", exclude_files = c("import-standalone-*"))
```

**2. In the source, with `# mutator:ignore` directives.** Place markers in the
`.R` file itself:

- `# mutator:ignore-file` anywhere in a file excludes the **whole file**.
- `# mutator:ignore-start` / `# mutator:ignore-end` exclude the **line region**
  between them (wrap a function to exclude it):

  ```r
  # mutator:ignore-start
  legacy_helper <- function(x) {
    # not worth mutation-testing
    x * 2
  }
  # mutator:ignore-end
  ```

  An unmatched `-start` excludes through the end of the file.

**3. With covr's `# nocov` annotations.** mutator also honours
[covr](https://covr.r-lib.org/)'s coverage-exclusion comments, so code you have
already marked as untested-by-design needs no separate mutator directive:

- `# nocov start` / `# nocov end` exclude the **line region** between them.
- A bare `# nocov` excludes its **own line**, and may trail code:

  ```r
  if (impossible_state) {
    stop("unreachable") # nocov
  }
  ```

**4. With a covr `.covrignore` file.** If the package root has a `.covrignore`
(covr's file-level coverage-exclusion list), mutator reads it too: each line is a
glob expanded relative to the package root (a matched directory expands to the
files under it), and matching `R/` files are skipped before generation, using the
same mechanism covr uses. So files you already exclude from coverage need no
extra mutator configuration.

**Granularity.** Excluding whole _files_ and whole _functions_ is
reliable. More fine-grained than that is not, for operator mutations: R 
mostly only attaches source references to blocks `{}`, so the engine resolves an operator
mutant's position only to its enclosing block. A region directive
inside a function therefore excludes that function's operator mutants as a group:
you cannot single out one operator mid-function. Line-deletion mutants _are_
excluded line-precisely. In practice, wrap whole functions, not fragments.
This only affects the surviving mutant output, which shows a larger context than necessary, 
and prevents the coverage-guided test selection from being as precise as it could be. 
The granularity can be improved with the optional [`imputesrcref`](#imputesrcref) package.

## Coverage-guided test selection (`coverage_guided`)

Most mutants are settled by a small subset of the suite, and a mutant on a line
that **no test exercises** can never be killed. With `coverage_guided = TRUE`
(the default) mutator measures coverage once with
[covr](https://covr.r-lib.org/) and then, for each mutant, runs only the test
files that cover its mutated line, and skips running tests altogether for mutants
on uncovered lines (reported `SURVIVED` immediately).

Coverage guidance applies to the `testthat`, `tinytest`, and `tinytest-installed`
strategies. covr builds the coverage-to-tests map against an instrumented,
installed copy of the package; per test file, it maps each covered source line to
the test files that reach it (for tinytest, by running each `inst/tinytest` file
individually). When the resolved strategy is the generic installed-tests fallback,
mutator cannot attribute coverage to test files, so it emits a warning and runs
the full suite for every mutant. Pass `coverage_guided = FALSE` to disable the
optimisation (and that warning).

```r
# On by default; pass FALSE to run the full suite for every mutant.
mutate_package("path/to/pkg", coverage_guided = FALSE)
```

The single coverage run also serves as the baseline check (it runs the package's
own `tests/testthat.R` harness, which fails if any test fails), so the suite is
not run twice. Selection is at the **test-file** level, as testthat filters tests by
file, and assumes the suite deterministically exercises the code, so it changes
_which_ tests run without changing a mutant's verdict.

Requires the `covr` package. Coverage attribution (and therefore speed-up) depends
on the backend (`coverage_backend`):

- **`"record_tests"`** (default) uses covr's `record_tests` in a single run and
  relies only on covr's public output. Its limitation: covr credits a covered line
  to the _deepest test-directory frame_ on the call stack, so when a test reaches
  package code through a function defined in a `helper-*.R` / `setup-*.R` file
  (a common pattern), covr attributes it to the helper, not the originating
  `test-*.R`. The true triggering test is then unknown, so mutator conservatively
  runs the **full suite** for that mutant. Packages that wrap their API in shared
  test helpers therefore see less speed-up.

- **`"per_file"`** instruments the package once and runs the suite a single time
  through a reporter that snapshots coverage per test file, giving **exact
  file-level attribution** with no helper fallback, at roughly the same cost as
  the single `record_tests` run (often faster overall, since more mutants get a
  narrowed test set). It reaches into covr internals, so it is opt-in:

  ```r
  mutate_package("path/to/pkg", coverage_guided = TRUE, coverage_backend = "per_file")
  ```

Either way the pay-off is largest when the suite is big, many lines are uncovered,
and tests exercise the code directly.

## Precise mutant locations (optional `imputesrcref`) {#imputesrcref}

Each reported mutant carries a source `Range:` (`start:col-end:col`). For
statement- and line-deletion mutants this is precise, but **operator mutants**
(`+`, `<`, `&&`, …) are different: R attaches no `srcref` to nested call
objects, so the engine can only report the bounds of the _enclosing block_ (`{}`), 
effectively a loop body or even the whole function. A surviving `==`-to-`!=` mutant in
a 40-line function therefore points at all 40 lines.

If the optional [`imputesrcref`](https://github.com/PRL-PRG/imputesrcref) package
is installed, `mutator` uses it to recover precise spans for many operator
mutants, typically narrowing a whole-function range down to the exact
sub-expression on a single line. It is a GitHub-only optional package listed in `Enhances`;
install it yourself to opt in:

```r
# install.packages("remotes")
remotes::install_github("PRL-PRG/imputesrcref")
```

When it is **not** installed, `mutator` behaves exactly as before (coarser
operator ranges); nothing else changes. The refinement is used only as a
read-only source-location oracle: mutant files are deparsed from the original
code and are **byte-for-byte identical** whether or not `imputesrcref` is
present, and `# mutator:ignore-*` directives keep their function-granular
semantics regardless. For best results, install the package under test from
source with parse data retained, since `imputesrcref` reads it:

```r
install.packages("<pkg>", INSTALL_opts = c("--with-keep.source", "--with-keep.parse.data"))
```

## Equivalent Mutant Detection

Equivalent-mutant detection calls an OpenAI-compatible Chat Completions API.
Configure it in any of these ways (listed highest precedence first; each
setting is resolved independently, so they can be mixed):

1. **Programmatically**, in your R session:

   ```r
   set_openai_config(
     api_key  = "api-key...",
     model    = "gpt-4",
     base_url = "https://api.openai.com/v1" # any OpenAI-compatible endpoint
   )
   ```

2. **A `.openai_config` file** in the working directory (or in a directory you
   pass via `get_openai_config(dir = ...)`). It is a plain, human-readable file
   of `field: value` lines and is _parsed, never executed_:

   ```
   api_key: api-key...
   model: gpt-4
   base_url: https://api.openai.com/v1
   ```

   Only the given directory is consulted. Parent directories are not searched.

3. **Environment variables** `OPENAI_API_KEY`, `OPENAI_MODEL` and
   `OPENAI_BASE_URL`.

If nothing is configured, the model defaults to `gpt-4` and the base URL to the
public OpenAI API. Set `base_url` to target a self-hosted or alternative
OpenAI-compatible service (for example `http://localhost:11434/v1`).

Enable the analysis when running package mutation tests:

```r
mutate_package("path/to/pkg", detectEqMutants = TRUE)
```

Equivalence detection runs **before** the test suites. Because an equivalent
mutant is behaviorally identical to the original, no test can kill it, so running
its test suite is wasted work. `mutate_package()` therefore analyzes every
generated mutant up front and **skips the test run** for those judged
equivalent: they are recorded as survived directly. Mutants judged
`NOT_EQUIVALENT` or `DONT_KNOW` are tested as usual. The trade-off is that the
equivalence pass now covers all mutants, not only survivors, so it makes more API
calls; in exchange it avoids the far more expensive test runs on equivalent
mutants.

Mutants are analyzed in **bounded batches** (default 25 per request),
and each mutant is shown to the model as a small **unified diff** of its edit
(plus a short change label) rather than its full mutated source. This is compact,
unambiguous, and in a format LLMs read natively. When `mutate_package()` runs
with `cores > 1` the batches are sent **concurrently**, which (with the bounded
size) keeps the equivalence pass fast and avoids the truncated responses that
otherwise drop verdicts.

For mutants the model flags as **EQUIVALENT** (they
are excluded from the adjusted mutation score), it also returns a one-sentence
**reason**, stored as `equivalence_reason` on the mutant so the call can be
audited. No reason is requested for `NOT_EQUIVALENT`/`DONT_KNOW`, keeping
responses small.

Progress and the results summary are emitted via `message()` (so they can be
silenced with `suppressMessages()`). The full prompts and model responses are
not printed by default; set `options(mutator.verbose = TRUE)` to log them.
