review applied

src/aiida/engine/daemon/execmanager.py

@@ -182,7 +182,7 @@ def upload_calculation(
                 # Since the content of the node could potentially be binary, we read the raw bytes and pass them on
                 for filename in filenames:
                     with NamedTemporaryFile(mode='wb+') as handle:
-                        content = code.base.repository.get_object_content((Path(root) / filename), mode='rb')
+                        content = code.base.repository.get_object_content(Path(root) / filename, mode='rb')
                         handle.write(content)
                         handle.flush()
                         transport.put(handle.name, str(workdir.joinpath(root, filename)))

src/aiida/transports/plugins/ssh.py

@@ -1226,17 +1226,18 @@ def listdir(self, path='.', pattern=None):
         :param pattern: returns the list of files matching pattern.
                              Unix only. (Use to emulate ``ls *`` for example)
         """
-        if not pattern:
-            return self.sftp.listdir(path)
         if path.startswith('/'):
-            base_dir = path
+            abs_dir = path
         else:
-            base_dir = os.path.join(self.getcwd(), path)
+            abs_dir = os.path.join(self.getcwd(), path)
 
-        filtered_list = self.glob(os.path.join(base_dir, pattern))
-        if not base_dir.endswith('/'):
-            base_dir += '/'
-        return [re.sub(base_dir, '', i) for i in filtered_list]
+        if not pattern:
+            return self.sftp.listdir(abs_dir)
+
+        filtered_list = self.glob(os.path.join(abs_dir, pattern))
+        if not abs_dir.endswith('/'):
+            abs_dir += '/'
+        return [re.sub(abs_dir, '', i) for i in filtered_list]
 
     def remove(self, path):
         """Remove a single file at 'path'"""

src/aiida/transports/transport.py

@@ -393,7 +393,7 @@ def exec_command_wait_bytes(self, command, stdin=None, workdir=None, **kwargs):
         """Execute the command on the shell, waits for it to finish,
         and return the retcode, the stdout and the stderr as bytes.
 
-        Enforce the execution to be run from the pwd (as given by self.getcwd), if this is not None.
+        Enforce the execution to be run from workdir, if this is not None.
 
         The command implementation can have some additional plugin-specific kwargs.
 

tests/conftest.py

@@ -211,9 +211,6 @@ def _generate_calcjob_node(
         process_state: ProcessState = ProcessState.FINISHED,
         exit_status: int | None = None,
         entry_point: str | None = None,
-        inputs: dict | None = None,
-        outputs: dict | None = None,
-        repository: pathlib.Path | None = None,
         workdir: pathlib.Path | None = None,
     ):
         """Generate an instance of a `CalcJobNode`..
@@ -228,36 +225,8 @@ def _generate_calcjob_node(
             exit_status = 0
 
         calcjob_node = CalcJobNode(process_type=entry_point)
-        calcjob_node.set_process_state(process_state)
-
-        if exit_status is not None:
-            calcjob_node.set_exit_status(exit_status)
-
-        if repository is not None:
-            calcjob_node.base.repository.put_object_from_tree(repository)
-
         calcjob_node.set_remote_workdir(workdir)
 
-        # For storing, need to first store the input nodes, then the CalcJobNode, then the output nodes
-        if inputs is not None:
-            for input_label, input_node in inputs.items():
-                calcjob_node.base.links.add_incoming(
-                    input_node,
-                    link_type=LinkType.INPUT_CALC,
-                    link_label=input_label,
-                )
-
-                input_node.store()
-
-        if outputs is not None:
-            # Need to first store CalcJobNode before I can attach `created` outputs
-            calcjob_node.store()
-            for output_label, output_node in outputs.items():
-                output_node.base.links.add_incoming(calcjob_node, link_type=LinkType.CREATE, link_label=output_label)
-
-                output_node.store()
-
-        # Return unstored by default
         return calcjob_node
 
     return _generate_calcjob_node