refactors RUN_PY as a file

Makes RUN_PY a part of linting and testing,
as suggested by Sebastian Björkqvist

runner/runner.py

@@ -13,7 +13,7 @@
 from abc import ABC, abstractmethod
 from ase import db
 from ase import Atoms
-from runner.utils import Cd, RUN_PY
+from runner.utils import Cd, run
 from runner.utils.runnerdata import RunnerData
 
 logger = logging.getLogger(__name__)
@@ -27,9 +27,6 @@
 logger.addHandler(stream_handler)
 
 
-default_files = ["run.sh", "batch.slrm", "atoms.pkl"]
-
-
 class BaseRunner(ABC):
     """
     Runner runs tasks
@@ -494,6 +491,9 @@ def _write_run_data(self, atoms, tasks, files, status, log_msg):
         with open("atoms.pkl", "wb") as file_o:
             pickle.dump(atoms, file_o)
 
+        # copy run file
+        shutil.copyfile(run.__file__, "run.py")
+
         # write run scripts
         run_scripts = []
         py_run = 0
@@ -509,29 +509,29 @@ def _write_run_data(self, atoms, tasks, files, status, log_msg):
                 shell_run = "python"
                 if len(task) > 3:
                     shell_run = task[3]
-                shell_run += " run{}.py".format(py_run)
-                shell_run += " > run{}.out".format(py_run)
-                run_scripts.append(shell_run)
 
                 if len(task) > 2:
                     params = task[2]
                 else:
                     params = {}
+
                 # write params
                 try:
                     with open("params{}.json".format(py_run), "w") as file_o:
                         json.dump(params, file_o)
                 except TypeError as err:
                     status = "failed"
-                    log_msg = "{}\n Error writing params: " "{}\n".format(
+                    log_msg = "{}\n Error writing params: {}\n".format(
                         datetime.now(), err.args[0]
                     )
                     break
                 # making python executable
                 func_name = task[1]
                 func_name = func_name[:-3] if func_name.endswith(".py") else func_name
-                with open("run{}.py".format(py_run), "w") as file_o:
-                    file_o.write(RUN_PY.format(func=func_name, ind=py_run))
+
+                # add to run_scripts
+                shell_run += f" run.py {func_name} {py_run} > run{py_run}.out"
+                run_scripts.append(shell_run)
                 py_run += 1
 
         return run_scripts, status, log_msg

runner/utils/__init__.py

@@ -2,7 +2,6 @@
 from runner.utils.utils import (
     Cd,
     json_keys2int,
-    RUN_PY,
     get_status,
     submit,
     cancel,
@@ -14,7 +13,6 @@
 
 
 __all__ = [
-    "RUN_PY",
     "Cd",
     "json_keys2int",
     "get_status",

runner/utils/run.py

@@ -0,0 +1,35 @@
+"""
+python file to run python tasks
+"""
+
+import json
+import pickle
+import argparse
+
+
+def main():
+    # parse args
+    parser = argparse.ArgumentParser(description="Run function with params.")
+    parser.add_argument("func", type=str)
+    parser.add_argument("indx", type=int)
+    args = parser.parse_args()
+
+    # import module
+    func = __import__(args.func)
+
+    # open params and atoms
+    with open(f"params{args.indx}.json") as fio:
+        params = json.load(fio)
+    with open("atoms.pkl", "rb") as fio:
+        atoms = pickle.load(fio)
+
+    # run func
+    atoms = func.main(atoms, **params)
+
+    # write atoms
+    with open("atoms.pkl", "wb") as fio:
+        pickle.dump(atoms, fio)
+
+
+if __name__ == "__main__":
+    main()

runner/utils/runnerdata.py

@@ -7,6 +7,9 @@
 from runner.utils.utils import json_keys2int, get_db_connect
 
 
+default_files = ["run.sh", "batch.slrm", "atoms.pkl", "run.py", "status.txt", "job.id"]
+
+
 class RunnerData:
     """Class to handle runner data using helper function
 
@@ -372,6 +375,8 @@ def _test_files(files, log_msg=""):
         err = log_msg + "Runner: files should be a dictionary\n"
         raise RuntimeError(err)
     for filename, content in files.items():
+        if filename in default_files:
+            raise RuntimeError(log_msg + f"Runner: {filename=} in {default_files=}")
         if not isinstance(filename, str):
             err = log_msg + "Runner: filenames should be str\n"
             raise RuntimeError(err)

runner/utils/utils.py

@@ -5,32 +5,6 @@
 import ase.db as db
 
 
-RUN_PY = """
-import json
-import pickle
-from ase.atoms import Atoms
-from {func} import main
-
-def json_keys2int(x):
-    # if dict key can be converted to int
-    # then convert to int
-    if isinstance(x, dict):
-        try:
-            return {{int(k):v for k,v in x.items()}}
-        except ValueError:
-            pass
-    return x
-
-with open("params{ind}.json") as f:
-    params = json.load(f, object_hook=json_keys2int)
-with open("atoms.pkl", "rb") as f:
-    atoms = pickle.load(f)
-atoms = main(atoms, **params)
-with open("atoms.pkl", "wb") as f:
-    pickle.dump(atoms, f)
-"""
-
-
 class Cd:
     """Context manager for changing the current working directory