Merge pull request #1397 from pyiron/file_obj_str

File: no longer derive from string

pyiron_base/jobs/job/extension/files.py

@@ -1,4 +1,5 @@
 import os
+import posixpath
 from typing import List
 from pyiron_base.jobs.job.util import (
     _working_directory_list_files,
@@ -96,12 +97,12 @@ def __getitem__(self, item):
             working_directory=self._working_directory,
             include_archive=False,
         ):
-            return File(os.path.join(self._working_directory, item))
+            return File(posixpath.join(self._working_directory, item))
         elif item in _working_directory_list_files(
             working_directory=self._working_directory,
             include_archive=True,
         ):
-            return File(os.path.join(self._working_directory, item))
+            return File(posixpath.join(self._working_directory, item))
         else:
             raise FileNotFoundError(item)
 
@@ -115,13 +116,24 @@ def __getattr__(self, item):
                 raise FileNotFoundError(item) from None
 
 
-class File(str):
+class File:
+    __slots__ = ("_path",)
+
+    def __init__(self, path):
+        self._path = path
+
+    def __str__(self):
+        return self._path
+
     def tail(self, lines: int = 100):
         print(
             *_working_directory_read_file(
-                working_directory=os.path.dirname(self),
-                file_name=os.path.basename(self),
+                working_directory=os.path.dirname(self._path),
+                file_name=os.path.basename(self._path),
                 tail=lines,
             ),
             sep="",
         )
+
+    def __eq__(self, other):
+        return self.__str__().__eq__(other)

pyiron_base/jobs/job/generic.py

@@ -23,6 +23,7 @@
     _doc_str_job_core_attr,
 )
 from pyiron_base.jobs.job.extension.executable import Executable
+from pyiron_base.jobs.job.extension.files import File
 from pyiron_base.jobs.job.extension.jobstatus import JobStatus
 from pyiron_base.jobs.job.runfunction import (
     run_job_with_parameter_repair,
@@ -275,7 +276,7 @@ def restart_file_list(self):
         Returns:
             list: list of files
         """
-        return self._restart_file_list
+        return [str(f) if isinstance(f, File) else f for f in self._restart_file_list]
 
     @restart_file_list.setter
     def restart_file_list(self, filenames):
@@ -286,6 +287,8 @@ def restart_file_list(self, filenames):
             filenames (list):
         """
         for f in filenames:
+            if isinstance(f, File):
+                f = str(f)
             if not (os.path.isfile(f)):
                 raise IOError("File: {} does not exist".format(f))
             self.restart_file_list.append(f)
@@ -295,7 +298,7 @@ def restart_file_dict(self):
         """
         A dictionary of the new name of the copied restart files
         """
-        for actual_name in [os.path.basename(f) for f in self._restart_file_list]:
+        for actual_name in [os.path.basename(f) for f in self.restart_file_list]:
             if actual_name not in self._restart_file_dict.keys():
                 self._restart_file_dict[actual_name] = actual_name
         return self._restart_file_dict
@@ -305,7 +308,13 @@ def restart_file_dict(self, val):
         if not isinstance(val, dict):
             raise ValueError("restart_file_dict should be a dictionary!")
         else:
-            self._restart_file_dict = val
+            self._restart_file_dict = {}
+            for k, v in val.items():
+                if isinstance(k, File):
+                    k = str(k)
+                if isinstance(v, File):
+                    v = str(v)
+                self._restart_file_dict[k] = v
 
     @property
     def exclude_nodes_hdf(self):
@@ -1043,7 +1052,7 @@ def to_dict(self):
         data_dict = self._type_to_dict()
         data_dict["status"] = self.status.string
         data_dict["input/generic_dict"] = {
-            "restart_file_list": self._restart_file_list,
+            "restart_file_list": self.restart_file_list,
             "restart_file_dict": self._restart_file_dict,
             "exclude_nodes_hdf": self._exclude_nodes_hdf,
             "exclude_groups_hdf": self._exclude_groups_hdf,

tests/flex/test_executablecontainer.py

@@ -102,7 +102,7 @@ def test_job_files(self):
         if os.name != "nt":
             self.assertEqual(job.files.error_out, output_file_path)
         else:
-            self.assertEqual(job.files.error_out.replace("/", "\\"), output_file_path)
+            self.assertEqual(job.files.error_out, output_file_path.replace("\\", "/"))
 
     def test_create_job_factory_typeerror(self):
         create_catjob = create_job_factory(

tests/flex/test_wrap_executable.py

@@ -1,4 +1,5 @@
 import os
+import posixpath
 from pyiron_base._tests import TestWithProject
 
 
@@ -28,7 +29,7 @@ def test_python_version(self):
         self.assertTrue(python_version_step.status.finished)
         self.assertEqual(
             python_version_step.files.error_out,
-            os.path.join(python_version_step.working_directory, "error.out")
+            posixpath.join(python_version_step.working_directory, "error.out")
         )
 
     def test_cat(self):