[ty] Disallow std::env and io methods in most ty crates (#20046)

## Summary

We use the `System` abstraction in ty to abstract away the host/system
on which ty runs.
This has a few benefits:

* Tests can run in full isolation using a memory system (that uses an
in-memory file system)
* The LSP has a custom implementation where `read_to_string` returns the
content as seen by the editor (e.g. unsaved changes) instead of always
returning the content as it is stored on disk
* We don't require any file system polyfills for wasm in the browser


However, it does require extra care that we don't accidentally use
`std::fs` or `std::env` (etc.) methods in ty's code base (which is very
easy).

This PR sets up Clippy and disallows the most common methods, instead
pointing users towards the corresponding `System` methods.

The setup is a bit awkward because clippy doesn't support inheriting
configurations. That means, a crate can only override the entire
workspace configuration or not at all.
The approach taken in this PR is:

* Configure the disallowed methods at the workspace level
* Allow `disallowed_methods` at the workspace level
* Enable the lint at the crate level using the warn attribute (in code)


The obvious downside is that it won't work if we ever want to disallow
other methods, but we can figure that out once we reach that point.

What about false positives: Just add an `allow` and move on with your
life :) This isn't something that we have to enforce strictly; the goal
is to catch accidental misuse.

## Test Plan

Clippy found a place where we incorrectly used `std::fs::read_to_string`

crates/ty_python_semantic/src/lib.rs

@@ -1,3 +1,7 @@
+#![warn(
+    clippy::disallowed_methods,
+    reason = "Prefer System trait methods over std methods in ty crates"
+)]
 use std::hash::BuildHasherDefault;
 
 use rustc_hash::FxHasher;

crates/ty_python_semantic/src/module_resolver/list.rs

@@ -363,6 +363,11 @@ fn is_python_extension(ext: &str) -> bool {
 
 #[cfg(test)]
 mod tests {
+    #![expect(
+        clippy::disallowed_methods,
+        reason = "These are tests, so it's fine to do I/O by-passing System."
+    )]
+
     use camino::{Utf8Component, Utf8Path};
     use ruff_db::Db as _;
     use ruff_db::files::{File, FilePath, FileRootKind};

crates/ty_python_semantic/src/module_resolver/resolver.rs

@@ -1115,6 +1115,10 @@ impl fmt::Display for RelaxedModuleName {
 
 #[cfg(test)]
 mod tests {
+    #![expect(
+        clippy::disallowed_methods,
+        reason = "These are tests, so it's fine to do I/O by-passing System."
+    )]
     use ruff_db::Db;
     use ruff_db::files::{File, FilePath, system_path_to_file};
     use ruff_db::system::{DbWithTestSystem as _, DbWithWritableSystem as _};

crates/ty_python_semantic/src/module_resolver/typeshed.rs

@@ -304,6 +304,11 @@ impl fmt::Display for PyVersionRange {
 
 #[cfg(test)]
 mod tests {
+    #![expect(
+        clippy::disallowed_methods,
+        reason = "These are tests, so it's fine to do I/O by-passing System."
+    )]
+
     use std::fmt::Write as _;
     use std::num::{IntErrorKind, NonZeroU16};
     use std::path::Path;

crates/ty_python_semantic/src/site_packages.rs

@@ -211,7 +211,7 @@ impl PythonEnvironment {
         match VirtualEnvironment::new(path, system) {
             Ok(venv) => Ok(Self::Virtual(venv)),
             // If there's not a `pyvenv.cfg` marker, attempt to inspect as a system environment
-            Err(SitePackagesDiscoveryError::NoPyvenvCfgFile(path, _))
+            Err(SitePackagesDiscoveryError::NoPyvenvCfgFile(path, _, _))
                 if !path.origin.must_be_virtual_env() =>
             {
                 Ok(Self::System(SystemEnvironment::new(path)))
@@ -378,7 +378,13 @@ impl VirtualEnvironment {
 
         let pyvenv_cfg = match system.read_to_string(&pyvenv_cfg_path) {
             Ok(pyvenv_cfg) => pyvenv_cfg,
-            Err(err) => return Err(SitePackagesDiscoveryError::NoPyvenvCfgFile(path, err)),
+            Err(err) => {
+                return Err(SitePackagesDiscoveryError::NoPyvenvCfgFile(
+                    path,
+                    err,
+                    system.dyn_clone(),
+                ));
+            }
         };
 
         let parsed_pyvenv_cfg =
@@ -833,16 +839,26 @@ impl SystemEnvironment {
 #[derive(Debug)]
 pub enum SitePackagesDiscoveryError {
     /// `site-packages` discovery failed because the provided path couldn't be canonicalized.
-    CanonicalizationError(SystemPathBuf, SysPrefixPathOrigin, io::Error),
+    CanonicalizationError(
+        SystemPathBuf,
+        SysPrefixPathOrigin,
+        io::Error,
+        Box<dyn System>,
+    ),
 
     /// `site-packages` discovery failed because the provided path doesn't appear to point to
     /// a Python executable or a `sys.prefix` directory.
-    PathNotExecutableOrDirectory(SystemPathBuf, SysPrefixPathOrigin, Option<io::Error>),
+    PathNotExecutableOrDirectory(
+        SystemPathBuf,
+        SysPrefixPathOrigin,
+        Option<io::Error>,
+        Box<dyn System>,
+    ),
 
     /// `site-packages` discovery failed because the [`SysPrefixPathOrigin`] indicated that
     /// the provided path should point to the `sys.prefix` of a virtual environment,
     /// but there was no file at `<sys.prefix>/pyvenv.cfg`.
-    NoPyvenvCfgFile(SysPrefixPath, io::Error),
+    NoPyvenvCfgFile(SysPrefixPath, io::Error, Box<dyn System>),
 
     /// `site-packages` discovery failed because the `pyvenv.cfg` file could not be parsed.
     PyvenvCfgParseError(SystemPathBuf, PyvenvCfgParseErrorKind),
@@ -852,11 +868,11 @@ pub enum SitePackagesDiscoveryError {
     /// would be relative to the `sys.prefix` path, and we tried to fallback to iterating
     /// through the `<sys.prefix>/lib` directory looking for a `site-packages` directory,
     /// but we came across some I/O error while trying to do so.
-    CouldNotReadLibDirectory(SysPrefixPath),
+    CouldNotReadLibDirectory(SysPrefixPath, Box<dyn System>),
 
     /// We looked everywhere we could think of for the `site-packages` directory,
     /// but none could be found despite our best endeavours.
-    NoSitePackagesDirFound(SysPrefixPath),
+    NoSitePackagesDirFound(SysPrefixPath, Box<dyn System>),
 }
 
 /// Enumeration of ways in which stdlib discovery can fail.
@@ -864,13 +880,13 @@ pub enum SitePackagesDiscoveryError {
 pub enum StdlibDiscoveryError {
     /// We looked everywhere we could think of for the standard library's directory,
     /// but none could be found despite our best endeavours.
-    NoStdlibFound(SysPrefixPath),
+    NoStdlibFound(SysPrefixPath, Box<dyn System>),
     /// Stdlib discovery failed because we're on a Unix system,
     /// we weren't able to figure out from the `pyvenv.cfg` file exactly where the stdlib
     /// would be relative to the `sys.prefix` path, and we tried to fallback to iterating
     /// through the `<sys.prefix>/lib` directory looking for a stdlib directory,
     /// but we came across some I/O error while trying to do so.
-    CouldNotReadLibDirectory(SysPrefixPath, io::Error),
+    CouldNotReadLibDirectory(SysPrefixPath, io::Error, Box<dyn System>),
     /// We failed to resolve the value of `sys.prefix`.
     NoSysPrefixFound(SystemPathBuf),
 }
@@ -878,14 +894,14 @@ pub enum StdlibDiscoveryError {
 impl std::error::Error for SitePackagesDiscoveryError {
     fn source(&self) -> Option<&(dyn std::error::Error + 'static)> {
         match self {
-            Self::CanonicalizationError(_, _, io_err) => Some(io_err),
-            Self::PathNotExecutableOrDirectory(_, _, io_err) => {
+            Self::CanonicalizationError(_, _, io_err, _) => Some(io_err),
+            Self::PathNotExecutableOrDirectory(_, _, io_err, _) => {
                 io_err.as_ref().map(|e| e as &dyn std::error::Error)
             }
-            Self::NoPyvenvCfgFile(_, io_err) => Some(io_err),
+            Self::NoPyvenvCfgFile(_, io_err, _) => Some(io_err),
             Self::PyvenvCfgParseError(_, _)
-            | Self::CouldNotReadLibDirectory(_)
-            | Self::NoSitePackagesDirFound(_) => None,
+            | Self::CouldNotReadLibDirectory(_, _)
+            | Self::NoSitePackagesDirFound(_, _) => None,
         }
     }
 }
@@ -893,10 +909,15 @@ impl std::error::Error for SitePackagesDiscoveryError {
 impl std::fmt::Display for SitePackagesDiscoveryError {
     fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
         match self {
-            Self::CanonicalizationError(given_path, origin, _) => {
-                display_error(f, origin, given_path, "Failed to canonicalize", None)
-            }
-            Self::PathNotExecutableOrDirectory(path, origin, _) => {
+            Self::CanonicalizationError(given_path, origin, _, system) => display_error(
+                f,
+                origin,
+                given_path,
+                "Failed to canonicalize",
+                None,
+                &**system,
+            ),
+            Self::PathNotExecutableOrDirectory(path, origin, _, system) => {
                 let thing = if origin.must_point_directly_to_sys_prefix() {
                     "directory on disk"
                 } else {
@@ -908,14 +929,16 @@ impl std::fmt::Display for SitePackagesDiscoveryError {
                     path,
                     &format!("Invalid {origin}"),
                     Some(&format!("does not point to a {thing}")),
+                    &**system,
                 )
             }
-            Self::NoPyvenvCfgFile(SysPrefixPath { inner, origin }, _) => display_error(
+            Self::NoPyvenvCfgFile(SysPrefixPath { inner, origin }, _, system) => display_error(
                 f,
                 origin,
                 inner,
                 &format!("Invalid {origin}"),
                 Some("points to a broken venv with no pyvenv.cfg file"),
+                &**system,
             ),
             Self::PyvenvCfgParseError(path, kind) => {
                 write!(
@@ -923,14 +946,17 @@ impl std::fmt::Display for SitePackagesDiscoveryError {
                     "Failed to parse the `pyvenv.cfg` file at `{path}` because {kind}"
                 )
             }
-            Self::CouldNotReadLibDirectory(SysPrefixPath { inner, origin }) => display_error(
-                f,
-                origin,
-                inner,
-                "Failed to iterate over the contents of the `lib`/`lib64` directories of the Python installation",
-                None,
-            ),
-            Self::NoSitePackagesDirFound(SysPrefixPath { inner, origin }) => display_error(
+            Self::CouldNotReadLibDirectory(SysPrefixPath { inner, origin }, system) => {
+                display_error(
+                    f,
+                    origin,
+                    inner,
+                    "Failed to iterate over the contents of the `lib`/`lib64` directories of the Python installation",
+                    None,
+                    &**system,
+                )
+            }
+            Self::NoSitePackagesDirFound(SysPrefixPath { inner, origin }, system) => display_error(
                 f,
                 origin,
                 inner,
@@ -938,6 +964,7 @@ impl std::fmt::Display for SitePackagesDiscoveryError {
                 Some(
                     "Could not find a `site-packages` directory for this Python installation/executable",
                 ),
+                &**system,
             ),
         }
     }
@@ -946,8 +973,8 @@ impl std::fmt::Display for SitePackagesDiscoveryError {
 impl std::error::Error for StdlibDiscoveryError {
     fn source(&self) -> Option<&(dyn std::error::Error + 'static)> {
         match self {
-            Self::CouldNotReadLibDirectory(_, io_err) => Some(io_err),
-            Self::NoStdlibFound(_) => None,
+            Self::CouldNotReadLibDirectory(_, io_err, _) => Some(io_err),
+            Self::NoStdlibFound(_, _) => None,
             Self::NoSysPrefixFound(_) => None,
         }
     }
@@ -962,19 +989,23 @@ impl std::fmt::Display for StdlibDiscoveryError {
                     "Failed to resolve a `sys.prefix` from the `pyvenv.cfg` file at `{path}`"
                 )
             }
-            Self::CouldNotReadLibDirectory(SysPrefixPath { inner, origin }, _) => display_error(
-                f,
-                origin,
-                inner,
-                "Failed to iterate over the contents of the `lib` directory of the Python installation",
-                None,
-            ),
-            Self::NoStdlibFound(SysPrefixPath { inner, origin }) => display_error(
+            Self::CouldNotReadLibDirectory(SysPrefixPath { inner, origin }, _, system) => {
+                display_error(
+                    f,
+                    origin,
+                    inner,
+                    "Failed to iterate over the contents of the `lib` directory of the Python installation",
+                    None,
+                    &**system,
+                )
+            }
+            Self::NoStdlibFound(SysPrefixPath { inner, origin }, system) => display_error(
                 f,
                 origin,
                 inner,
                 &format!("Invalid {origin}"),
                 Some("Could not find a stdlib directory for this Python installation/executable"),
+                &**system,
             ),
         }
     }
@@ -986,6 +1017,7 @@ fn display_error(
     given_path: &SystemPath,
     primary_message: &str,
     secondary_message: Option<&str>,
+    system: &dyn System,
 ) -> std::fmt::Result {
     let fallback: &mut dyn FnMut() -> std::fmt::Result = &mut || {
         f.write_str(primary_message)?;
@@ -1003,7 +1035,7 @@ fn display_error(
         return fallback();
     };
 
-    let Ok(config_file_source) = std::fs::read_to_string((**config_file_path).as_ref()) else {
+    let Ok(config_file_source) = system.read_to_string(config_file_path) else {
         return fallback();
     };
 
@@ -1099,7 +1131,10 @@ fn site_packages_directories_from_sys_prefix(
             .is_directory(&site_packages)
             .then(|| SitePackagesPaths::from([site_packages]))
             .ok_or_else(|| {
-                SitePackagesDiscoveryError::NoSitePackagesDirFound(sys_prefix_path.to_owned())
+                SitePackagesDiscoveryError::NoSitePackagesDirFound(
+                    sys_prefix_path.to_owned(),
+                    system.dyn_clone(),
+                )
             });
     }
 
@@ -1206,10 +1241,12 @@ fn site_packages_directories_from_sys_prefix(
         if found_at_least_one_lib_dir {
             Err(SitePackagesDiscoveryError::NoSitePackagesDirFound(
                 sys_prefix_path.to_owned(),
+                system.dyn_clone(),
             ))
         } else {
             Err(SitePackagesDiscoveryError::CouldNotReadLibDirectory(
                 sys_prefix_path.to_owned(),
+                system.dyn_clone(),
             ))
         }
     } else {
@@ -1238,7 +1275,7 @@ fn real_stdlib_directory_from_sys_prefix(
     if cfg!(target_os = "windows") {
         let stdlib = sys_prefix_path.join("Lib");
         return system.is_directory(&stdlib).then_some(stdlib).ok_or(
-            StdlibDiscoveryError::NoStdlibFound(sys_prefix_path.to_owned()),
+            StdlibDiscoveryError::NoStdlibFound(sys_prefix_path.to_owned(), system.dyn_clone()),
         );
     }
 
@@ -1274,7 +1311,11 @@ fn real_stdlib_directory_from_sys_prefix(
         // must be `lib`, not `lib64`, for the stdlib
         .read_directory(&sys_prefix_path.join(UnixLibDir::Lib))
         .map_err(|io_err| {
-            StdlibDiscoveryError::CouldNotReadLibDirectory(sys_prefix_path.to_owned(), io_err)
+            StdlibDiscoveryError::CouldNotReadLibDirectory(
+                sys_prefix_path.to_owned(),
+                io_err,
+                system.dyn_clone(),
+            )
         })?
     {
         let Ok(entry) = entry_result else {
@@ -1299,6 +1340,7 @@ fn real_stdlib_directory_from_sys_prefix(
     }
     Err(StdlibDiscoveryError::NoStdlibFound(
         sys_prefix_path.to_owned(),
+        system.dyn_clone(),
     ))
 }
 
@@ -1357,6 +1399,7 @@ impl SysPrefixPath {
                     unvalidated_path.to_path_buf(),
                     origin,
                     None,
+                    system.dyn_clone(),
                 ));
             };
             sys_prefix
@@ -1376,12 +1419,14 @@ impl SysPrefixPath {
                         unvalidated_path,
                         origin,
                         Some(io_err),
+                        system.dyn_clone(),
                     )
                 } else {
                     SitePackagesDiscoveryError::CanonicalizationError(
                         unvalidated_path,
                         origin,
                         io_err,
+                        system.dyn_clone(),
                     )
                 };
                 return Err(err);
@@ -1393,6 +1438,7 @@ impl SysPrefixPath {
                 unvalidated_path.to_path_buf(),
                 origin,
                 None,
+                system.dyn_clone(),
             ));
         }