Merge regex and globs options from args and config

Options that take lists (regexes and globs) are now merged from the command line and config file, rather than previously overriding the config file.

This is a breaking change, so bump the version.

Fixes #526, #527

Author: sourcefrog

Cargo.lock

@@ -1,6 +1,6 @@
 [package]
 name = "cargo-mutants"
-version = "26.2.0"
+version = "27.0.0-pre"
 edition = "2024"
 authors = ["Martin Pool"]
 license = "MIT"

Cargo.toml

@@ -2,6 +2,8 @@
 
 ## Unreleased
 
+- Changed: Command line values for `--file`, `--exclude`, `--examine-re`, and `--exclude-re` are now combined with, rather than replacing, values given in the configuration file, consistently with every other option that takes a list. (Use `--config=OTHER` or `--no-config` to avoid using values in the configuration.) Thanks to @sandersaares for pointing this out.
+
 - New: `--Zmutate-file` lists the mutants generated from a single Rust source file in text or JSON, without reading or requiring a containing package. This is intended as an aid for developing and debugging mutation patterns.
 
 ## 26.2.0 - 2026-01-31

NEWS.md

@@ -19,7 +19,7 @@ An example config file with detailed comments can be found at
 
 ## Merging config and command-line options
 
-When options are specified in both the config file and the command line, the command line options take precedence.
+When options are specified in both the config file and the command line, for scalar options, the command line options take precedence.
 
 For options that take a list of values, values from the configuration file are appended
 to values from the command line.

book/src/config-file.md

@@ -47,7 +47,7 @@ This can be helpful
 if you want to systematically skip testing implementations of certain traits, or functions
 with certain names.
 
-From cargo-mutants 23.11.2 onwards, if the command line options are given then the corresponding config file option is ignored.
+From cargo-mutants 27.0.0 onwards, the command line options are combined with filters specified in the configuration file.
 
 For example:
 

book/src/filter_mutants.md

@@ -1,4 +1,4 @@
-// Copyright 2022-2025 Martin Pool.
+// Copyright 2022-2026 Martin Pool.
 
 //! `.cargo/mutants.toml` configuration file.
 //!

src/config.rs

@@ -1,6 +1,6 @@
-// Copyright 2024 Martin Pool
+// Copyright 2024-2026 Martin Pool
 
-//! Build globsets.
+//! Build globsets from lists of strings.
 
 use std::borrow::Cow;
 
@@ -9,15 +9,15 @@ use globset::{GlobBuilder, GlobSet, GlobSetBuilder};
 
 use crate::Result;
 
-pub fn build_glob_set<S>(globs: &[S]) -> Result<Option<GlobSet>>
+pub fn build_glob_set<S, I>(globs: I) -> Result<Option<GlobSet>>
 where
     S: AsRef<str>,
+    I: IntoIterator<Item = S>,
 {
-    if globs.is_empty() {
-        return Ok(None);
-    }
+    let mut has_globs = false;
     let mut builder = GlobSetBuilder::new();
     for glob_str in globs {
+        has_globs = true;
         let glob_str = glob_str.as_ref();
         let match_whole_path = if cfg!(windows) {
             glob_str.contains(['/', '\\'])
@@ -41,7 +41,11 @@ where
             );
         }
     }
-    Ok(Some(builder.build().context("Failed to build glob set")?))
+    if has_globs {
+        Ok(Some(builder.build().context("Failed to build glob set")?))
+    } else {
+        Ok(None)
+    }
 }
 
 #[cfg(test)]

src/glob.rs

@@ -1,4 +1,4 @@
-// Copyright 2021-2025 Martin Pool
+// Copyright 2021-2026 Martin Pool
 
 //! Global in-process options for experimenting on mutants.
 //!
@@ -141,10 +141,10 @@ pub struct Options {
     pub exclude_globset: Option<GlobSet>,
 
     /// Mutants to examine, as a regexp matched against the full name.
-    pub examine_names: RegexSet,
+    pub examine_name_re: RegexSet,
 
     /// Mutants to skip, as a regexp matched against the full name.
-    pub exclude_names: RegexSet,
+    pub exclude_name_re: RegexSet,
 
     /// Create `mutants.out` within this directory (by default, the source directory).
     pub output_in_dir: Option<Utf8PathBuf>,
@@ -166,6 +166,8 @@ pub struct Options {
 
 // Options that are implemented only once between clap and serde.
 //
+// (This is not a docstring so that clap doesn't try to render it as part of the help.)
+//
 // All fields should be optional so that we can represent a field being set on the command line but
 // not in the config, or vice versa.
 //
@@ -345,12 +347,14 @@ impl Options {
             emit_json: args.json,
             common: args.common.merge(&config.common),
             error_values: join_slices(&args.error, &config.error_values),
-            examine_names: RegexSet::new(or_slices(&args.examine_re, &config.examine_re))
+            examine_name_re: RegexSet::new(args.examine_re.iter().chain(config.examine_re.iter()))
                 .context("Failed to compile examine_re regex")?,
-            exclude_names: RegexSet::new(or_slices(&args.exclude_re, &config.exclude_re))
+            exclude_name_re: RegexSet::new(args.exclude_re.iter().chain(&config.exclude_re))
                 .context("Failed to compile exclude_re regex")?,
-            examine_globset: build_glob_set(or_slices(&args.file, &config.examine_globs))?,
-            exclude_globset: build_glob_set(or_slices(&args.exclude, &config.exclude_globs))?,
+            examine_globset: build_glob_set(args.file.iter().chain(config.examine_globs.iter()))?,
+            exclude_globset: build_glob_set(
+                args.exclude.iter().chain(config.exclude_globs.iter()),
+            )?,
             features: join_slices(&args.features, &config.features),
             gitignore: args
                 .gitignore
@@ -474,8 +478,8 @@ impl Options {
     /// True if the options allow this mutant to be tested.
     pub fn allows_mutant(&self, mutant: &Mutant) -> bool {
         let name = mutant.name(true);
-        (self.examine_names.is_empty() || self.examine_names.is_match(&name))
-            && (self.exclude_names.is_empty() || !self.exclude_names.is_match(&name))
+        (self.examine_name_re.is_empty() || self.examine_name_re.is_match(&name))
+            && (self.exclude_name_re.is_empty() || !self.exclude_name_re.is_match(&name))
     }
 
     pub fn emit_diffs(&self) -> bool {
@@ -491,11 +495,6 @@ impl Options {
     }
 }
 
-/// If the first slices is non-empty, return that, otherwise the second.
-fn or_slices<'a: 'c, 'b: 'c, 'c, T>(a: &'a [T], b: &'b [T]) -> &'c [T] {
-    if a.is_empty() { b } else { a }
-}
-
 #[cfg(test)]
 mod test {
     use std::io::Write;
@@ -1217,6 +1216,65 @@ mod test {
         let options = Options::new(&args, &config).unwrap();
         assert!(options.shuffle);
     }
+
+    #[test]
+    fn merge_exclude_from_config_and_command_line() {
+        let args = Args::parse_from([
+            "mutants",
+            "--exclude-re=foo",
+            "--exclude-re=bar",
+            "--exclude=foo.rs",
+            "--file=ex1.rs",
+            "--examine-re=exr1",
+        ]);
+        let config = Config::from_str(
+            r#"
+            exclude_re = ["baz"]
+            exclude_globs = ["baz.rs"]
+            examine_globs = ["ex2.rs"]
+            examine_re = ["exr2"]
+        "#,
+        )
+        .unwrap();
+        let options = Options::new(&args, &config).unwrap();
+        for name in ["foo", "bar", "baz"] {
+            assert!(
+                options.exclude_name_re.is_match(name),
+                "Expected {name} to be excluded"
+            );
+        }
+        assert!(
+            !options.exclude_name_re.is_match("qux"),
+            "Expected qux not to be excluded"
+        );
+
+        assert!(
+            options.exclude_globset.as_ref().unwrap().is_match("baz.rs"),
+            "Expected baz.rs to be excluded"
+        );
+        assert!(
+            options.exclude_globset.as_ref().unwrap().is_match("foo.rs"),
+            "Expected foo.rs to be excluded"
+        );
+        assert!(
+            !options.exclude_globset.as_ref().unwrap().is_match("qux.rs"),
+            "Expected qux.rs NOT to be excluded"
+        );
+
+        for path in ["ex1.rs", "ex2.rs"] {
+            assert!(
+                options.examine_globset.as_ref().unwrap().is_match(path),
+                "Expected {path} to be examined"
+            );
+        }
+
+        for name in ["exr1", "exr2"] {
+            assert!(
+                options.examine_name_re.is_match(name),
+                "Expected {name} to be examined"
+            );
+        }
+    }
 }
 
 #[cfg(test)]

src/options.rs

@@ -3484,10 +3484,8 @@ fn list_with_config_file_inclusion() {
 }
 
 #[test]
-fn file_argument_overrides_config_examine_globs_key() {
+fn file_argument_merges_with_config_examine_globs_key() {
     let testdata = copy_of_testdata("well_tested");
-    // This config key has no effect because the command line argument
-    // takes precedence.
     write_config_file(
         &testdata,
         r#"examine_globs = ["src/*_mod.rs"]
@@ -3500,15 +3498,15 @@ fn file_argument_overrides_config_examine_globs_key() {
         .assert()
         .success()
         .stdout(predicates::str::diff(indoc! { "\
+            src/inside_mod.rs
+            src/item_mod.rs
             src/simple_fns.rs
         " }));
 }
 
 #[test]
-fn exclude_file_argument_overrides_config() {
+fn exclude_file_argument_merge_with_config() {
     let testdata = copy_of_testdata("well_tested");
-    // This config key has no effect because the command line argument
-    // takes precedence.
     write_config_file(
         &testdata,
         indoc! { r#"
@@ -3526,7 +3524,8 @@ fn exclude_file_argument_overrides_config() {
         .args(["--exclude", "src/b*.rs"])
         .assert()
         .success()
-        .stdout(predicates::str::diff(indoc! { "\
+        .stderr("")
+        .stdout(predicates::str::diff(indoc! {"\
             src/lib.rs
             src/arc.rs
             src/empty_fns.rs
@@ -3569,7 +3568,7 @@ fn list_with_config_file_regexps() {
 }
 
 #[test]
-fn exclude_re_overrides_config() {
+fn exclude_re_on_command_line_merged_with_config() {
     let testdata = copy_of_testdata("well_tested");
     write_config_file(
         &testdata,
@@ -3591,16 +3590,7 @@ fn exclude_re_overrides_config() {
         .args(["-f", "src/simple_fns.rs"])
         .assert()
         .success();
-    assert_snapshot!(
-        String::from_utf8_lossy(&cmd.get_output().stdout),
-        @r###"
-    src/simple_fns.rs: replace returns_unit with ()
-    src/simple_fns.rs: replace += with -= in returns_unit
-    src/simple_fns.rs: replace += with *= in returns_unit
-    src/simple_fns.rs: replace == with != in divisible_by_three
-    src/simple_fns.rs: replace % with / in divisible_by_three
-    src/simple_fns.rs: replace % with + in divisible_by_three
-    "###);
+    assert_eq!(String::from_utf8_lossy(&cmd.get_output().stdout), "");
 }
 
 #[test]