Fix rye add and rye remove to create proper tool.rye section on -…

…-dev and --exclude flags (#1256)

Hey!

This is to address issue #1249

Closes #1249

Looks like the `[tool.rye]` section in `pyproject.toml` is not created
properly if it was not already presented in the file.
This was due to the it not being created as a table.

Tested it like that:
- Have `pyproject.toml` without `[tool.rye]` table:
```
[project]
authors = [{ name = "xxx", email = "xxx@xxx.com" }]
name = "rye-test"
version = "0.1.0"
description = "wasm sample use py2wasm, rust, wasmer, gowasm, wasmedge"
readme = "README.md"
requires-python = ">=3.11.7"


[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"
```
- 
```
$ rye add --dev ipython
```
results in 
`pyproject.toml`
```
[project]
authors = [{ name = "xxx", email = "xxx@xxx.com" }]
name = "rye-test"
version = "0.1.0"
description = "wasm sample use py2wasm, rust, wasmer, gowasm, wasmedge"
readme = "README.md"
requires-python = ">=3.11.7"


[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

[tool.rye]
dev-dependencies = [
    "ipython>=8.26.0",
]
```

Before fix it was:
`pyproject.toml`
```
tool = { rye = { dev-dependencies = [
    "ipython>=8.26.0",
] } }
[project]
authors = [{ name = "xxx", email = "xxx@xxx.com" }]
name = "rye-test"
version = "0.1.0"
description = "wasm sample use py2wasm, rust, wasmer, gowasm, wasmedge"
readme = "README.md"
requires-python = ">=3.11.7"


[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

```

rye/src/pyproject.rs

@@ -579,6 +579,13 @@ pub struct PyProject {
     doc: DocumentMut,
 }
 
+/// Returns an implicit table.
+fn implicit() -> Item {
+    let mut table = Table::new();
+    table.set_implicit(true);
+    Item::Table(table)
+}
+
 impl PyProject {
     /// Load a pyproject toml if explicitly given, else discover from current directory
     ///
@@ -912,8 +919,14 @@ impl PyProject {
     ) -> Result<(), Error> {
         let dependencies = match kind {
             DependencyKind::Normal => &mut self.doc["project"]["dependencies"],
-            DependencyKind::Dev => &mut self.doc["tool"]["rye"]["dev-dependencies"],
-            DependencyKind::Excluded => &mut self.doc["tool"]["rye"]["excluded-dependencies"],
+            DependencyKind::Dev => self
+                .obtain_tool_config_table()?
+                .entry("dev-dependencies")
+                .or_insert(Item::Value(Value::Array(Array::new()))),
+            DependencyKind::Excluded => self
+                .obtain_tool_config_table()?
+                .entry("excluded-dependencies")
+                .or_insert(Item::Value(Value::Array(Array::new()))),
             DependencyKind::Optional(ref section) => {
                 // add this as a proper non-inline table if it's missing
                 let table = &mut self.doc["project"]["optional-dependencies"];
@@ -943,8 +956,14 @@ impl PyProject {
     ) -> Result<Option<Requirement>, Error> {
         let dependencies = match kind {
             DependencyKind::Normal => &mut self.doc["project"]["dependencies"],
-            DependencyKind::Dev => &mut self.doc["tool"]["rye"]["dev-dependencies"],
-            DependencyKind::Excluded => &mut self.doc["tool"]["rye"]["excluded-dependencies"],
+            DependencyKind::Dev => self
+                .obtain_tool_config_table()?
+                .entry("dev-dependencies")
+                .or_insert(Item::Value(Value::Array(Array::new()))),
+            DependencyKind::Excluded => self
+                .obtain_tool_config_table()?
+                .entry("excluded-dependencies")
+                .or_insert(Item::Value(Value::Array(Array::new()))),
             DependencyKind::Optional(ref section) => {
                 &mut self.doc["project"]["optional-dependencies"][section as &str]
             }
@@ -1047,6 +1066,19 @@ impl PyProject {
         fs::write(&path, self.doc.to_string()).path_context(&path, "unable to write changes")?;
         Ok(())
     }
+
+    /// Gets or creates the [tool.rye] table in pyproject.toml
+    fn obtain_tool_config_table(&mut self) -> Result<&mut Table, Error> {
+        self.doc
+            .entry("tool")
+            .or_insert(implicit())
+            .as_table_mut()
+            .ok_or(anyhow!("[tool.rye] in pyproject.toml is malformed"))?
+            .entry("rye")
+            .or_insert(implicit())
+            .as_table_mut()
+            .ok_or(anyhow!("[tool.rye] in pyproject.toml is malformed"))
+    }
 }
 
 pub fn normalize_package_name(x: &str) -> String {

rye/tests/test_add.rs

@@ -1,5 +1,5 @@
+use insta::assert_snapshot;
 use std::fs;
-
 use toml_edit::{value, ArrayOfTables, Table};
 
 use crate::common::{rye_cmd_snapshot, Space};
@@ -39,6 +39,14 @@ fn test_add_flask() {
      + my-project==0.1.0 (from file:[TEMP_PATH]/project)
      + werkzeug==3.0.1
     "###);
+
+    assert_snapshot!(space.read_toml("pyproject.toml")["project"]["dependencies"], @r###"
+     [
+        "flask>=3.0.0",
+        "colorama>=0.4.6",
+    ]
+    "###
+    );
 }
 
 #[test]
@@ -76,12 +84,13 @@ fn test_add_flask_dotenv() {
      + werkzeug==3.0.1
     "###);
 
-    space.load_toml("pyproject.toml", |doc| {
-        let deps = doc["project"]["dependencies"].as_array().unwrap();
-        assert!(deps
-            .iter()
-            .any(|x| x.as_str() == Some("flask[dotenv]>=3.0.0")));
-    });
+    assert_snapshot!(space.read_toml("pyproject.toml")["project"]["dependencies"], @r###"
+     [
+        "flask[dotenv]>=3.0.0",
+        "colorama>=0.4.6",
+    ]
+    "###
+    );
 }
 
 #[test]
@@ -120,6 +129,13 @@ fn test_add_from_find_links() {
      + my-project==0.1.0 (from file:[TEMP_PATH]/project)
      + tqdm==4.66.1
     "###);
+
+    assert_snapshot!(space.read_toml("pyproject.toml")["tool"]["rye"], @r###"
+    managed = true
+    dev-dependencies = []
+    sources = [{ name = "extra", type = "find-links", url = "https://download.pytorch.org/whl/torch_stable.html" }]
+    "###
+    );
 }
 
 #[test]
@@ -208,3 +224,47 @@ fn test_add_explicit_version_or_url() {
      + pip==1.3.1 (from https://github.com/pypa/pip/archive/1.3.1.zip#sha1=da9234ee9982d4bbb3c72346a6de940a148ea686)
     "###);
 }
+
+#[test]
+fn test_add_dev() {
+    let space = Space::new();
+    space.init("my-project");
+    // add colorama to ensure we have this as a dependency on all platforms
+    rye_cmd_snapshot!(space.rye_cmd().arg("add").arg("flask").arg("colorama").arg("--dev"), @r###"
+    success: true
+    exit_code: 0
+    ----- stdout -----
+    Initializing new virtualenv in [TEMP_PATH]/project/.venv
+    Python version: cpython@3.12.3
+    Added flask>=3.0.0 as dev dependency
+    Added colorama>=0.4.6 as dev dependency
+    Reusing already existing virtualenv
+    Generating production lockfile: [TEMP_PATH]/project/requirements.lock
+    Generating dev lockfile: [TEMP_PATH]/project/requirements-dev.lock
+    Installing dependencies
+    Done!
+
+    ----- stderr -----
+    Resolved 9 packages in [EXECUTION_TIME]
+    Prepared 9 packages in [EXECUTION_TIME]
+    Installed 9 packages in [EXECUTION_TIME]
+     + blinker==1.7.0
+     + click==8.1.7
+     + colorama==0.4.6
+     + flask==3.0.0
+     + itsdangerous==2.1.2
+     + jinja2==3.1.2
+     + markupsafe==2.1.3
+     + my-project==0.1.0 (from file:[TEMP_PATH]/project)
+     + werkzeug==3.0.1
+    "###);
+
+    assert_snapshot!(space.read_toml("pyproject.toml")["tool"]["rye"], @r###"
+    managed = true
+    dev-dependencies = [
+        "flask>=3.0.0",
+        "colorama>=0.4.6",
+    ]
+    "###
+    );
+}