feat: Add ONTOENV_LOG support and refactor logging initialization

Co-authored-by: aider (gemini/gemini-2.5-pro) <[email protected]>

Author: gtfierro

cli/src/main.rs

@@ -352,11 +352,19 @@ fn handle_config_command(config_cmd: ConfigCommands, temporary: bool) -> Result<
 }
 
 fn main() -> Result<()> {
+    ontoenv::api::init_logging();
     let cmd = Cli::parse();
 
-    let log_level = if cmd.verbose { "info" } else { "warn" };
-    let log_level = if cmd.debug { "debug" } else { log_level };
-    std::env::set_var("RUST_LOG", log_level);
+    // The RUST_LOG env var is set by `init_logging` if ONTOENV_LOG is present.
+    // CLI flags for verbosity take precedence. If nothing is set, we default to "warn".
+    if cmd.debug {
+        std::env::set_var("RUST_LOG", "debug");
+    } else if cmd.verbose {
+        std::env::set_var("RUST_LOG", "info");
+    } else if std::env::var("RUST_LOG").is_err() {
+        // If no CLI flags and no env var is set, default to "warn".
+        std::env::set_var("RUST_LOG", "warn");
+    }
     env_logger::init();
 
     let policy = cmd.policy.unwrap_or_else(|| "default".to_string());

lib/src/api.rs

@@ -23,6 +23,18 @@ use petgraph::graph::{Graph as DiGraph, NodeIndex};
 use std::collections::{HashMap, HashSet, VecDeque};
 use std::fs;
 
+/// Initializes logging for the ontoenv library.
+///
+/// This function checks for the `ONTOENV_LOG` environment variable. If it is set,
+/// `RUST_LOG` is set to its value. `ONTOENV_LOG` takes precedence over `RUST_LOG`.
+/// The logger initialization (e.g., `env_logger::init()`) must be called after
+/// this function for the log level to take effect.
+pub fn init_logging() {
+    if let Ok(log_level) = std::env::var("ONTOENV_LOG") {
+        std::env::set_var("RUST_LOG", log_level);
+    }
+}
+
 /// Searches for the .ontoenv directory in the given directory and then recursively up its parent directories.
 /// Returns the path to the directory containing the .ontoenv directory if found.
 pub fn find_ontoenv_root_from(start_dir: &Path) -> Option<PathBuf> {

python/src/lib.rs

@@ -13,14 +13,12 @@ use pyo3::{
 use std::borrow::Borrow;
 use std::collections::{HashMap, HashSet};
 use std::path::PathBuf;
-use std::sync::{Arc, Mutex, Once};
+use std::sync::{Arc, Mutex};
 
 fn anyhow_to_pyerr(e: Error) -> PyErr {
     PyErr::new::<pyo3::exceptions::PyValueError, _>(e.to_string())
 }
 
-static INIT: Once = Once::new();
-
 #[allow(dead_code)]
 struct MyTerm(Term);
 impl From<Result<Bound<'_, PyAny>, pyo3::PyErr>> for MyTerm {
@@ -248,12 +246,6 @@ impl OntoEnv {
         recreate: bool,
         read_only: bool,
     ) -> PyResult<Self> {
-        // wrap env_logger::init() in a Once to ensure it's only called once. This can
-        // happen if a user script creates multiple OntoEnv instances
-        INIT.call_once(|| {
-            env_logger::init();
-        });
-
         let env = if let Some(c) = config {
             let config_path = path.unwrap_or_else(|| PathBuf::from("."));
             // if temporary is true, create a new OntoEnv
@@ -952,6 +944,11 @@ impl OntoEnv {
 
 #[pymodule]
 fn ontoenv(_py: Python, m: &Bound<'_, PyModule>) -> PyResult<()> {
+    // Initialize logging when the python module is loaded.
+    ::ontoenv::api::init_logging();
+    // Use try_init to avoid panic if logging is already initialized.
+    let _ = env_logger::try_init();
+
     m.add_class::<Config>()?;
     m.add_class::<OntoEnv>()?;
     m.add_class::<PyOntology>()?;