Add PyRosetta support in executor and CLI

Author: lyskov

src/executor.rs

@@ -115,6 +115,15 @@ pub fn run(
             None,
         ),
 
+        App::PyRosetta => (
+            Image("rosettacommons/rosetta:serial".into()),
+            {
+                app_args.insert(0, "python".into());
+                app_args
+            },
+            None,
+        ),
+
         App::Rfdiffusion => (
             Image("rosettacommons/rfdiffusion".into()),
             {

src/main.rs

@@ -25,7 +25,7 @@ struct Args {
 }
 
 #[derive(ValueEnum, Clone, Copy, Debug, strum::Display)]
-#[strum(serialize_all = "kebab-case")] // "lowercase"
+#[strum(serialize_all = "lowercase")] //  "kebab-case"
 enum ContainerEngine {
     Docker,
     Singularity,
@@ -69,14 +69,18 @@ enum Commands {
 }
 
 #[derive(ValueEnum, Clone, Copy, Debug, strum::Display)]
-#[strum(serialize_all = "kebab-case")] // "lowercase"
+#[clap(rename_all = "lowercase")]
+#[strum(serialize_all = "lowercase")] //  "kebab-case"
 enum App {
     /// Run the Rosetta score command
     Score,
 
     /// Run the Rosetta protocol
     Rosetta,
 
+    /// Start python in env where PyRosetta is installed and execute script
+    PyRosetta,
+
     /// Run the RFdiffusion command https://github.com/RosettaCommons/RFdiffusion
     Rfdiffusion,
 }

tests/pyrosetta.rs

@@ -0,0 +1,61 @@
+mod common;
+
+use assert_cmd::{assert::OutputAssertExt, cargo::cargo_bin_cmd};
+use assert_fs::TempDir;
+use predicates::prelude::*;
+
+common::engine_tests!(pyrosetta);
+
+fn pyrosetta(engine: &str) {
+    use assert_fs::assert::PathAssert;
+    use std::fs;
+
+    let root = std::path::PathBuf::from("target/score").join(engine);
+    std::fs::create_dir_all(&root).expect("create engine testing dir");
+    let work_dir = TempDir::new_in(root).expect("create temp dir");
+
+    let pdb_id = "1brs";
+    let pdb_file = pdb_id.to_string() + ".pdb";
+
+    let pdb_path = work_dir.path().join(&pdb_file);
+    std::fs::write(
+        pdb_path,
+        reqwest::blocking::get(format!("https://files.rcsb.org/download/{pdb_file}"))
+            .unwrap()
+            .bytes()
+            .unwrap(),
+    )
+    .unwrap();
+
+    let cmd = cargo_bin_cmd!()
+        .args([
+            "run",
+            "--container-engine",
+            engine,
+            "-w",
+            work_dir.path().to_str().unwrap(),
+            "pyrosetta", "-c",
+            "import pyrosetta; pyrosetta.init(); pose=pyrosetta.pose_from_pdb('1brs.pdb'); print('1brs.pdb structure SCORE:', pyrosetta.get_score_function()(pose) )",
+        ])
+        .unwrap();
+    cmd.assert().success();
+
+    use assert_fs::prelude::PathChild;
+
+    let log_file_name = work_dir.child(".0000.rc.log");
+
+    log_file_name.assert(predicates::path::exists());
+
+    let log = fs::read_to_string(&log_file_name).unwrap();
+
+    for s in [
+        "PyRosetta-4",
+        "Created in JHU by Sergey Lyskov and PyRosetta Team",
+        "core.init: Checking for fconfig files in pwd and ./rosetta/flags",
+        "1brs.pdb structure SCORE: 255",
+    ] {
+        assert!(predicates::str::contains(s).eval(&log));
+    }
+
+    // std::thread::sleep(std::time::Duration::from_secs(60));
+}