Changed swash to use provided path in conf

swash/config.ini

@@ -12,8 +12,8 @@ out=out_data
 
 [swash]
 input=sws/INPUT.sws
-swashrun=/opt/swash/swash/swashrun
-out=out
+path=/opt/swash
+out=out_sws
 mpi=4
 
 [post]

swash/processing/swash.py

@@ -30,9 +30,7 @@ with tempfile.TemporaryDirectory(prefix="swash_", dir=".") as tmp_raw:
 
     log.info(f"Copying files to '{tmpdir}'")
     shutil.copy2(inp, tmpdir)
-    shutil.copytree(
-        pathlib.Path(config.get("data", "out")), tmpdir, dirs_exist_ok=True
-    )
+    shutil.copytree(pathlib.Path(config.get("data", "out")), tmpdir, dirs_exist_ok=True)
 
     if config.has_option("swash", "mpi"):
         mpi = ("-mpi", config.get("swash", "mpi"))
@@ -42,15 +40,13 @@ with tempfile.TemporaryDirectory(prefix="swash_", dir=".") as tmp_raw:
 
     with open(tmpdir.joinpath("sws.log"), "w") as logfile:
         log.info(f"Runing swash in '{tmpdir}'")
+        path = pathlib.Path(config.get("swash", "swashrun"))
 
-        cmd = (config.get("swash", "swashrun"), *mpi, "-input", inp.name)
+        cmd = (path.joinpath("swashrun"), *mpi, "-input", inp.name)
         log.info(f"Running {cmd}")
 
         swash_run = subprocess.Popen(
-            cmd,
-            cwd=tmpdir,
-            stdout=logfile,
-            stderr=logfile,
+            cmd, cwd=tmpdir, stdout=logfile, stderr=logfile, env={"PATH": path}
         )
 
         code = swash_run.wait()