diff --git a/Cargo.lock b/Cargo.lock
index 7a55a053..364a78a6 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -1318,8 +1318,8 @@ dependencies = [
 
 [[package]]
 name = "tree-sitter-bash"
-version = "0.20.4"
-source = "git+https://github.com/tree-sitter/tree-sitter-bash#1479a4030f1a399c253aee02097576d4af46f23a"
+version = "0.19.0"
+source = "git+https://github.com/tree-sitter/tree-sitter-bash#1b0321ee85701d5036c334a6f04761cdc672e64c"
 dependencies = [
  "cc",
  "tree-sitter",
diff --git a/topiary-cli/src/configuration/serde.rs b/topiary-cli/src/configuration/serde.rs
index 9886a48d..054e6779 100644
--- a/topiary-cli/src/configuration/serde.rs
+++ b/topiary-cli/src/configuration/serde.rs
@@ -181,6 +181,12 @@ impl Serialisation {
     }
 }
 
+impl Default for Serialisation {
+    fn default() -> Self {
+        Self::new()
+    }
+}
+
 /// Convert deserialised TOML values into `Serialisation` values
 // TODO Is this necessary, any more?
 impl TryFrom<toml::Value> for Serialisation {
diff --git a/topiary-cli/src/io.rs b/topiary-cli/src/io.rs
index 22b50060..a207a17b 100644
--- a/topiary-cli/src/io.rs
+++ b/topiary-cli/src/io.rs
@@ -129,8 +129,8 @@ impl<'cfg> InputFile<'cfg> {
         Ok(LanguageDefinition {
             language: Language {
                 name: self.language.name.clone(),
-                query: query,
-                grammar: grammar,
+                query,
+                grammar,
                 indent: self.language().indent.clone(),
             },
         })
diff --git a/topiary-cli/tests/sample-tester.rs b/topiary-cli/tests/sample-tester.rs
new file mode 100644
index 00000000..2ac51470
--- /dev/null
+++ b/topiary-cli/tests/sample-tester.rs
@@ -0,0 +1,76 @@
+use assert_cmd::Command;
+use std::fs;
+use std::path::Path;
+use topiary::test_utils::pretty_assert_eq;
+
+use tempfile::TempDir;
+
+#[test]
+fn input_output_tester() {
+    let input_dir = fs::read_dir("tests/samples/input").unwrap();
+    let expected_dir = Path::new("tests/samples/expected");
+
+    for file in input_dir {
+        let file = file.unwrap();
+
+        // Load the known good formated files
+        let expected_path = expected_dir.join(file.file_name());
+        let expected = fs::read_to_string(expected_path).unwrap();
+
+        let tmp_dir = TempDir::new().unwrap();
+
+        // Copy the file to a temp dir
+        let mut input_file = tmp_dir.path().to_path_buf();
+        input_file.push(file.path().file_name().unwrap());
+        fs::copy(file.path(), &input_file).unwrap();
+
+        // Run topiary on the input file in the temp dir
+        let mut topiary = Command::cargo_bin("topiary").unwrap();
+        topiary
+            // .env("TOPIARY_LANGUAGE_DIR", "../queries/")
+            .arg("fmt")
+            .arg(&input_file)
+            .assert()
+            .success();
+
+        // Read the file after formatting
+        let formatted = fs::read_to_string(input_file).unwrap();
+
+        // Assert the formatted file is as expected
+        pretty_assert_eq(&expected, &formatted);
+    }
+}
+
+// Test that our query files are properly formatted
+#[test]
+fn formatted_query_tester() {
+    let language_dir = fs::read_dir("../queries").unwrap();
+
+    for file in language_dir {
+        let file = file.unwrap();
+
+        // Load the query file (we assume is formatted correctly)
+        let expected = fs::read_to_string(file.path()).unwrap();
+
+        let tmp_dir = TempDir::new().unwrap();
+
+        // Copy the file to a temp dir
+        let mut input_file = tmp_dir.path().to_path_buf();
+        input_file.push(file.path().file_name().unwrap());
+        fs::copy(file.path(), &input_file).unwrap();
+
+        // Run topiary on the input file in the temp dir
+        let mut topiary = Command::cargo_bin("topiary").unwrap();
+        topiary
+            // .env("TOPIARY_LANGUAGE_DIR", "../queries/")
+            .arg("fmt")
+            .arg(&input_file)
+            .assert()
+            .success();
+
+        // Read the file after formatting
+        let formatted = fs::read_to_string(input_file).unwrap();
+
+        pretty_assert_eq(&expected, &formatted);
+    }
+}
diff --git a/topiary/tests/samples/expected/bash.sh b/topiary-cli/tests/samples/expected/bash.sh
similarity index 100%
rename from topiary/tests/samples/expected/bash.sh
rename to topiary-cli/tests/samples/expected/bash.sh
diff --git a/topiary/tests/samples/expected/json.json b/topiary-cli/tests/samples/expected/json.json
similarity index 100%
rename from topiary/tests/samples/expected/json.json
rename to topiary-cli/tests/samples/expected/json.json
diff --git a/topiary/tests/samples/expected/nickel.ncl b/topiary-cli/tests/samples/expected/nickel.ncl
similarity index 100%
rename from topiary/tests/samples/expected/nickel.ncl
rename to topiary-cli/tests/samples/expected/nickel.ncl
diff --git a/topiary/tests/samples/expected/ocaml-interface.mli b/topiary-cli/tests/samples/expected/ocaml-interface.mli
similarity index 100%
rename from topiary/tests/samples/expected/ocaml-interface.mli
rename to topiary-cli/tests/samples/expected/ocaml-interface.mli
diff --git a/topiary/tests/samples/expected/ocaml.ml b/topiary-cli/tests/samples/expected/ocaml.ml
similarity index 100%
rename from topiary/tests/samples/expected/ocaml.ml
rename to topiary-cli/tests/samples/expected/ocaml.ml
diff --git a/topiary/tests/samples/expected/ocamllex.mll b/topiary-cli/tests/samples/expected/ocamllex.mll
similarity index 100%
rename from topiary/tests/samples/expected/ocamllex.mll
rename to topiary-cli/tests/samples/expected/ocamllex.mll
diff --git a/topiary/tests/samples/expected/rust.rs b/topiary-cli/tests/samples/expected/rust.rs
similarity index 100%
rename from topiary/tests/samples/expected/rust.rs
rename to topiary-cli/tests/samples/expected/rust.rs
diff --git a/topiary/tests/samples/expected/toml.toml b/topiary-cli/tests/samples/expected/toml.toml
similarity index 100%
rename from topiary/tests/samples/expected/toml.toml
rename to topiary-cli/tests/samples/expected/toml.toml
diff --git a/topiary/tests/samples/expected/tree-sitter-query.scm b/topiary-cli/tests/samples/expected/tree-sitter-query.scm
similarity index 100%
rename from topiary/tests/samples/expected/tree-sitter-query.scm
rename to topiary-cli/tests/samples/expected/tree-sitter-query.scm
diff --git a/topiary/tests/samples/input/bash.sh b/topiary-cli/tests/samples/input/bash.sh
similarity index 100%
rename from topiary/tests/samples/input/bash.sh
rename to topiary-cli/tests/samples/input/bash.sh
diff --git a/topiary/tests/samples/input/json.json b/topiary-cli/tests/samples/input/json.json
similarity index 100%
rename from topiary/tests/samples/input/json.json
rename to topiary-cli/tests/samples/input/json.json
diff --git a/topiary/tests/samples/input/nickel.ncl b/topiary-cli/tests/samples/input/nickel.ncl
similarity index 100%
rename from topiary/tests/samples/input/nickel.ncl
rename to topiary-cli/tests/samples/input/nickel.ncl
diff --git a/topiary/tests/samples/input/ocaml-interface.mli b/topiary-cli/tests/samples/input/ocaml-interface.mli
similarity index 100%
rename from topiary/tests/samples/input/ocaml-interface.mli
rename to topiary-cli/tests/samples/input/ocaml-interface.mli
diff --git a/topiary/tests/samples/input/ocaml.ml b/topiary-cli/tests/samples/input/ocaml.ml
similarity index 100%
rename from topiary/tests/samples/input/ocaml.ml
rename to topiary-cli/tests/samples/input/ocaml.ml
diff --git a/topiary/tests/samples/input/ocamllex.mll b/topiary-cli/tests/samples/input/ocamllex.mll
similarity index 100%
rename from topiary/tests/samples/input/ocamllex.mll
rename to topiary-cli/tests/samples/input/ocamllex.mll
diff --git a/topiary/tests/samples/input/rust.rs b/topiary-cli/tests/samples/input/rust.rs
similarity index 100%
rename from topiary/tests/samples/input/rust.rs
rename to topiary-cli/tests/samples/input/rust.rs
diff --git a/topiary/tests/samples/input/toml.toml b/topiary-cli/tests/samples/input/toml.toml
similarity index 100%
rename from topiary/tests/samples/input/toml.toml
rename to topiary-cli/tests/samples/input/toml.toml
diff --git a/topiary/tests/samples/input/tree-sitter-query.scm b/topiary-cli/tests/samples/input/tree-sitter-query.scm
similarity index 100%
rename from topiary/tests/samples/input/tree-sitter-query.scm
rename to topiary-cli/tests/samples/input/tree-sitter-query.scm
diff --git a/topiary/benches/benchmark.rs b/topiary/benches/benchmark.rs
index f7777dfd..ac2eff73 100644
--- a/topiary/benches/benchmark.rs
+++ b/topiary/benches/benchmark.rs
@@ -7,7 +7,7 @@ use topiary::{formatter, Language, Operation, TopiaryQuery};
 // FIXME Configuration is no longer part of the library
 
 async fn format() {
-    let input = fs::read_to_string("tests/samples/input/ocaml.ml").unwrap();
+    let input = fs::read_to_string("../topiary-cli/tests/samples/input/ocaml.ml").unwrap();
     let query_content = fs::read_to_string("../queries/ocaml.scm").unwrap();
     let ocaml = tree_sitter_ocaml::language_ocaml();
 
diff --git a/topiary/src/lib.rs b/topiary/src/lib.rs
index f863b413..8489d010 100644
--- a/topiary/src/lib.rs
+++ b/topiary/src/lib.rs
@@ -159,20 +159,25 @@ pub enum Operation {
 /// # tokio_test::block_on(async {
 /// use std::fs::File;
 /// use std::io::{BufReader, Read};
-/// use topiary::{formatter, FormatterError, TopiaryQuery, Operation};
+/// use topiary::{formatter, Language, FormatterError, TopiaryQuery, Operation};
 ///
 /// let input = "[1,2]".to_string();
 /// let mut input = input.as_bytes();
 /// let mut output = Vec::new();
+/// let json = tree_sitter_json::language();
+///
 /// let mut query_file = BufReader::new(File::open("../queries/json.scm").expect("query file"));
 /// let mut query_content = String::new();
 /// query_file.read_to_string(&mut query_content).expect("read query file");
 ///
-/// let grammar = tree_sitter_json::language();
-/// let query = TopiaryQuery::new(&grammar, &query_content).unwrap();
+/// let language: Language = Language {
+///     name: "json".to_owned(),
+///     query: TopiaryQuery::new(&json.into(), &query_content).unwrap(),
+///     grammar: json.into(),
+///     indent: None,
+/// };
 ///
-/// // FIXME The signature of `formatter` has changed
-/// match formatter(&mut input, &mut output, &query, &language, &grammar, Operation::Format{ skip_idempotence: false, tolerate_parsing_errors: false }) {
+/// match formatter(&mut input, &mut output, &language, Operation::Format{ skip_idempotence: false, tolerate_parsing_errors: false }) {
 ///   Ok(()) => {
 ///     let formatted = String::from_utf8(output).expect("valid utf-8");
 ///   }
@@ -359,7 +364,7 @@ mod tests {
         let expected = "{ \"one\": {\"bar\"   \"baz\"}, \"two\": \"bar\" }\n";
 
         let mut output = Vec::new();
-        let query_content = fs::read_to_string("../languages/json.scm").unwrap();
+        let query_content = fs::read_to_string("../topiary-queries/queries/json.scm").unwrap();
         let grammar = tree_sitter_json::language().into();
         let language = Language {
             name: "json".to_owned(),
diff --git a/topiary/tests/sample-tester.rs b/topiary/tests/sample-tester.rs
deleted file mode 100644
index e4a3dd30..00000000
--- a/topiary/tests/sample-tester.rs
+++ /dev/null
@@ -1,141 +0,0 @@
-use std::fs;
-use std::io::BufReader;
-use std::path::Path;
-
-use log::info;
-use test_log::test;
-
-use topiary::{
-    apply_query, formatter, test_utils::pretty_assert_eq, Configuration, FormatterError, Language,
-    Operation, TopiaryQuery,
-};
-
-// FIXME Configuration is no longer part of the library
-
-#[test(tokio::test)]
-async fn input_output_tester() {
-    let input_dir = fs::read_dir("tests/samples/input").unwrap();
-    let expected_dir = Path::new("tests/samples/expected");
-    let config = Configuration::parse_default_configuration().unwrap();
-    let extensions = config.known_extensions();
-
-    for file in input_dir {
-        let file = file.unwrap();
-        if let Some(ext) = file.path().extension().map(|ext| ext.to_string_lossy()) {
-            if !extensions.contains(ext.as_ref()) {
-                continue;
-            }
-
-            let language = Language::detect(file.path(), &config).unwrap();
-
-            let expected_path = expected_dir.join(file.file_name());
-            let expected = fs::read_to_string(expected_path).unwrap();
-
-            let mut input = BufReader::new(fs::File::open(file.path()).unwrap());
-            let mut output = Vec::new();
-            let query_content = fs::read_to_string(language.query_file().unwrap()).unwrap();
-
-            let grammar = language.grammar().await.unwrap();
-
-            let query = TopiaryQuery::new(&grammar, &query_content).unwrap();
-
-            info!(
-                "Formatting file {} as {}.",
-                file.path().display(),
-                language.name,
-            );
-
-            info!("Formatting {}", file.path().display());
-
-            formatter(
-                &mut input,
-                &mut output,
-                &query,
-                language,
-                &grammar,
-                Operation::Format {
-                    skip_idempotence: false,
-                    tolerate_parsing_errors: true,
-                },
-            )
-            .unwrap();
-
-            let formatted = String::from_utf8(output).unwrap();
-            log::debug!("{}", formatted);
-
-            pretty_assert_eq(&expected, &formatted);
-        }
-    }
-}
-
-// Test that our query files are properly formatted
-#[test(tokio::test)]
-async fn formatted_query_tester() {
-    let config = Configuration::parse_default_configuration().unwrap();
-    let language_dir = fs::read_dir("../queries").unwrap();
-
-    for file in language_dir {
-        let file = file.unwrap();
-        let language = Language::detect(file.path(), &config).unwrap();
-
-        let expected = fs::read_to_string(file.path()).unwrap();
-
-        let mut input = BufReader::new(fs::File::open(file.path()).unwrap());
-        let mut output = Vec::new();
-        let query_content = fs::read_to_string(language.query_file().unwrap()).unwrap();
-
-        let grammar = language.grammar().await.unwrap();
-
-        let query = TopiaryQuery::new(&grammar, &query_content).unwrap();
-
-        formatter(
-            &mut input,
-            &mut output,
-            &query,
-            language,
-            &grammar,
-            Operation::Format {
-                skip_idempotence: false,
-                tolerate_parsing_errors: false,
-            },
-        )
-        .unwrap();
-
-        let formatted = String::from_utf8(output).unwrap();
-        log::debug!("{}", formatted);
-
-        pretty_assert_eq(&expected, &formatted);
-    }
-}
-
-// Test that all queries are used on sample files
-#[test(tokio::test)]
-async fn exhaustive_query_tester() {
-    let config = Configuration::parse_default_configuration().unwrap();
-    let input_dir = fs::read_dir("tests/samples/input").unwrap();
-
-    for file in input_dir {
-        let file = file.unwrap();
-        // We skip "ocaml-interface.mli", as its query file is already tested by "ocaml.ml"
-        if file.file_name().to_string_lossy() == "ocaml-interface.mli" {
-            continue;
-        }
-        let language = Language::detect(file.path(), &config).unwrap();
-        let query_file = language.query_file().unwrap();
-
-        let input_content = fs::read_to_string(&file.path()).unwrap();
-        let query_content = fs::read_to_string(&query_file).unwrap();
-
-        let grammar = language.grammar().await.unwrap();
-
-        let query = TopiaryQuery::new(&grammar, &query_content).unwrap();
-
-        apply_query(&input_content, &query, &grammar, false, true).unwrap_or_else(|e| {
-            if let FormatterError::PatternDoesNotMatch(_) = e {
-                panic!("Found untested query in file {query_file:?}:\n{e}");
-            } else {
-                panic!("{e}");
-            }
-        });
-    }
-}