Actual implementation changes

Author: GeigerJ2

pyproject.toml

@@ -35,7 +35,8 @@ dependencies = [
   "termcolor",
   "pygraphviz",
   "lxml",
-  "f90nml"
+  "f90nml",
+  "aiida-shell @ git+https://github.com/sphuber/aiida-shell.git@fix/105/handle-remote-data-argument-placeholders",
 ]
 license = {file = "LICENSE"}
 
@@ -76,6 +77,9 @@ ignore = [
 
 ## Hatch configurations
 
+[tool.hatch.metadata]
+allow-direct-references = true
+
 [tool.hatch.build.targets.sdist]
 include = [
   "src/sirocco/",
@@ -148,3 +152,7 @@ ignore_missing_imports = true
 [[tool.mypy.overrides]]
 module = ["aiida_workgraph.sockets.builtins"]
 ignore_missing_imports = true
+
+[[tool.mypy.overrides]]
+module = ["termcolor._types"]
+ignore_missing_imports = true

src/sirocco/core/graph_items.py

@@ -51,6 +51,7 @@ def from_config(cls, config: ConfigBaseData, coordinates: dict) -> AvailableData
         data_class = AvailableData if isinstance(config, ConfigAvailableData) else GeneratedData
         return data_class(
             name=config.name,
+            computer=config.computer,
             type=config.type,
             src=config.src,
             coordinates=coordinates,

src/sirocco/parsing/yaml_data_models.py

@@ -279,7 +279,14 @@ class ConfigShellTaskSpecs:
     plugin: ClassVar[Literal["shell"]] = "shell"
     port_pattern: ClassVar[re.Pattern] = field(default=re.compile(r"{PORT(\[sep=.+\])?::(.+?)}"), repr=False)
     sep_pattern: ClassVar[re.Pattern] = field(default=re.compile(r"\[sep=(.+)\]"), repr=False)
-    src: str | None = None
+    src: str | None = Field(
+        default=None,
+        description=(
+            "If `src` not absolute, this ends up to be relative to the root directory of the config file."
+            "This should also be solved by registering `Code`s in AiiDA for the required scripts."
+            "See issue #127 and #60"
+        ),
+    )
     command: str
     env_source_files: list[str] = field(default_factory=list)
 

src/sirocco/workgraph.py

@@ -56,7 +56,15 @@ def _prepare_for_shell_task(task: dict, inputs: dict) -> dict:
     # Workaround starts here
     # This part is part of the workaround. We need to manually add the outputs from the task.
     # Because kwargs are not populated with outputs
-    default_outputs = {"remote_folder", "remote_stash", "retrieved", "_outputs", "_wait", "stdout", "stderr"}
+    default_outputs = {
+        "remote_folder",
+        "remote_stash",
+        "retrieved",
+        "_outputs",
+        "_wait",
+        "stdout",
+        "stderr",
+    }
     task_outputs = set(task["outputs"].keys())
     task_outputs = task_outputs.union(set(inputs.pop("outputs", [])))
     missing_outputs = task_outputs.difference(default_outputs)
@@ -105,6 +113,7 @@ def __init__(self, core_workflow: core.Workflow):
         for task in self._core_workflow.tasks:
             if isinstance(task, core.ShellTask):
                 self._set_shelljob_arguments(task)
+                self._set_shelljob_filenames(task)
 
         # link wait on to workgraph tasks
         for task in self._core_workflow.tasks:
@@ -238,6 +247,8 @@ def _create_shell_task_node(self, task: core.ShellTask):
         ]
         prepend_text = "\n".join([f"source {env_source_path}" for env_source_path in env_source_paths])
         metadata["options"] = {"prepend_text": prepend_text}
+        # NOTE: Hardcoded for now, possibly make user-facing option
+        metadata["options"]["use_symlinks"] = True
 
         ## computer
         if task.computer is not None:
@@ -292,7 +303,10 @@ def _link_input_node_to_shelltask(self, task: core.ShellTask, input_: core.Data)
             socket = getattr(workgraph_task.inputs.nodes, f"{input_label}")
             socket.value = self.data_from_core(input_)
         elif isinstance(input_, core.GeneratedData):
-            self._workgraph.add_link(self.socket_from_core(input_), workgraph_task.inputs[f"nodes.{input_label}"])
+            self._workgraph.add_link(
+                self.socket_from_core(input_),
+                workgraph_task.inputs[f"nodes.{input_label}"],
+            )
         else:
             raise TypeError
 
@@ -317,6 +331,23 @@ def _set_shelljob_arguments(self, task: core.ShellTask):
         _, arguments = self.split_cmd_arg(task.resolve_ports(input_labels))
         workgraph_task_arguments.value = arguments
 
+    def _set_shelljob_filenames(self, task: core.ShellTask):
+        """set AiiDA ShellJob filenames for AvailableData entities"""
+
+        filenames = {}
+
+        for input_ in task.input_data_nodes():
+            # Some empty lists appear here?
+            if not input_:
+                continue
+
+            core_input = input_[0]
+            if isinstance(core_input, core.AvailableData):
+                filenames[core_input.name] = Path(core_input.src).name
+
+        workgraph_task = self.task_from_core(task)
+        workgraph_task.inputs.filenames.value = filenames
+
     def run(
         self,
         inputs: None | dict[str, Any] = None,