fix singlefiledata and some names (stfc#116)

* fix singlefiledata and some names

* Revert changes not to singlefiledata filenames

This reverts commit 87444c1.

---------

Co-authored-by: ElliottKasoar <[email protected]>

aiida_mlip/parsers/base_parser.py

@@ -80,7 +80,9 @@ def parse(self, **kwargs) -> int:
             self.retrieved.open(log_output, "rb") as log,
             self.retrieved.open(output_filename, "rb") as output,
         ):
-            self.out("log_output", SinglefileData(file=log))
-            self.out("std_output", SinglefileData(file=output))
+            self.out("log_output", SinglefileData(file=log, filename=log_output))
+            self.out(
+                "std_output", SinglefileData(file=output, filename=output_filename)
+            )
 
         return ExitCode(0)

aiida_mlip/parsers/md_parser.py

@@ -85,7 +85,7 @@ def parse(self, **kwargs) -> ExitCode:
         # Process trajectory file saving both the file and trajectory as aiida data
         traj_filepath = md_dictionary.get("traj-file", MD.DEFAULT_TRAJ_FILE)
         with self.retrieved.open(traj_filepath, "rb") as handle:
-            self.out("traj_file", SinglefileData(file=handle))
+            self.out("traj_file", SinglefileData(file=handle, filename=traj_filepath))
         final_str, traj_output = xyz_to_aiida_traj(
             Path(self.node.get_remote_workdir(), traj_filepath)
         )
@@ -95,13 +95,13 @@ def parse(self, **kwargs) -> ExitCode:
         # Process stats file as singlefiledata
         stats_filepath = md_dictionary.get("stats-file", MD.DEFAULT_STATS_FILE)
         with self.retrieved.open(stats_filepath, "rb") as handle:
-            self.out("stats_file", SinglefileData(file=handle))
+            self.out("stats_file", SinglefileData(file=handle, filename=stats_filepath))
 
         # Process summary as both singlefiledata and results dictionary
         summary_filepath = md_dictionary.get("summary", MD.DEFAULT_SUMMARY_FILE)
         print(self.node.get_remote_workdir(), summary_filepath)
         with self.retrieved.open(summary_filepath, "rb") as handle:
-            self.out("summary", SinglefileData(file=handle))
+            self.out("summary", SinglefileData(file=handle, filename=summary_filepath))
 
         with self.retrieved.open(summary_filepath, "r") as handle:
             try:

aiida_mlip/parsers/opt_parser.py

@@ -79,7 +79,7 @@ def parse(self, **kwargs) -> ExitCode:
 
             # Parse the trajectory file and save it as `SingleFileData`
             with self.retrieved.open(traj_file, "rb") as handle:
-                self.out("traj_file", SinglefileData(file=handle))
+                self.out("traj_file", SinglefileData(file=handle, filename=traj_file))
             # Parse trajectory and save it as `TrajectoryData`
             opt, traj_output = xyz_to_aiida_traj(
                 Path(self.node.get_remote_workdir(), traj_file)

aiida_mlip/parsers/sp_parser.py

@@ -96,7 +96,7 @@ def parse(self, **kwargs) -> int:
         self.logger.info(f"Parsing '{xyz_output}'")
 
         with self.retrieved.open(xyz_output, "rb") as handle:
-            self.out("xyz_output", SinglefileData(file=handle))
+            self.out("xyz_output", SinglefileData(file=handle, filename=xyz_output))
 
         content = read(Path(self.node.get_remote_workdir(), xyz_output))
         results = convert_numpy(content.todict())

tests/calculations/test_geomopt.py

@@ -92,6 +92,7 @@ def test_run_opt(model_folder, janus_code):
     assert "traj_file" in result
     assert result["traj_output"].numsteps == 3
     assert result["final_structure"].cell[0][1] == pytest.approx(2.8442048309822)
+    assert result["xyz_output"].filename == "aiida-results.xyz"
 
 
 def test_example_opt(example_path):