add test files

tests/files/configs/test_config_parameters.yml

@@ -64,10 +64,10 @@ data:
   available:
     - initial_conditions:
         type: file
-        src: .
+        src: initial_conditions
     - forcing:
         type: file
-        src: .
+        src: forcing
   generated:
     - icon_output:
         type: file

tests/files/scripts/cleanup.py

@@ -0,0 +1,9 @@
+#!/usr/bin/env python
+
+def main():
+    # Main script execution continues here
+    print("Cleaning")
+
+
+if __name__ == '__main__':
+    main()

tests/files/scripts/cleanup.sh

@@ -0,0 +1 @@
+echo "cleanup" > output

tests/files/scripts/extpar

@@ -0,0 +1 @@
+echo "extpar" > output

tests/files/scripts/icon

@@ -0,0 +1,4 @@
+echo "icon" > restart
+echo "icon" > output
+echo "icon" > output_1
+echo "icon" > output_2

tests/files/scripts/icon.py

@@ -0,0 +1,41 @@
+#!/usr/bin/env python
+
+import argparse
+from pathlib import Path
+
+def main():
+    parser = argparse.ArgumentParser(description='A simple script with an optional restart argument.')
+    parser.add_argument('icon_input', type=str, help='The icon input.')
+    parser.add_argument('--restart', nargs='?', type=str, help='The icon restart file.')
+    #parser.add_argument('--restart', nargs='?', const='default', type=str, help='Initiate a restart operation with an optional string argument.')
+
+
+    args = parser.parse_args()
+
+    output = Path('output')
+    output.write_text("")
+
+    if args.restart:
+        restart = Path(args.restart)
+        restart.read_text()
+        text = "Restart operation initiated..."
+        print(text)
+        with output.open("a") as f:
+            f.write(text)
+    else:
+        text = "No restart option provided. Continuing without restart."
+        print(text)
+        with output.open("a") as f:
+            f.write(text)
+
+    # Main script execution continues here
+    text = "Script execution continues..."
+    print(text)
+    with output.open("a") as f:
+        f.write(text)
+
+    restart = Path('restart')
+    restart.write_text("")
+
+if __name__ == '__main__':
+    main()

tests/files/scripts/icon.sh

@@ -0,0 +1,48 @@
+#!/bin/bash
+
+# Function to write text to the output file
+write_to_output() {
+  local text="$1"
+  echo "$text"
+  echo "$text" >> output
+}
+
+# Check if at least one argument is provided
+if [ "$#" -lt 1 ]; then
+  echo "Usage: $0 icon_input [--restart [restart_file]]"
+  exit 1
+fi
+
+# Positional argument
+icon_input="$1"
+
+# Optional restart argument
+restart_file=""
+
+if [ "$2" == "--restart" ]; then
+  if [ -n "$3" ]; then
+    restart_file="$3"
+  fi
+fi
+
+# Create/empty the output file
+> output
+
+# Handling restart if the argument is provided
+if [ -n "$restart_file" ]; then
+  if [ -f "$restart_file" ]; then
+    cat "$restart_file" > /dev/null
+    write_to_output "Restart operation initiated..."
+  else
+    echo "Restart file $restart_file does not exist."
+    exit 1
+  fi
+else
+  write_to_output "No restart option provided. Continuing without restart."
+fi
+
+# Main script execution continues here
+write_to_output "Script execution continues..."
+
+# Create/empty the restart file
+> restart

tests/files/scripts/main_script_atm.sh

@@ -0,0 +1 @@
+echo "main_script_atm.sh" > postout

tests/files/scripts/main_script_ocn.sh

@@ -0,0 +1 @@
+echo "python main_script_ocn.sh" > postout

tests/files/scripts/post_clean.sh

@@ -0,0 +1 @@
+echo "store_and_clean" > stored_data

tests/test_wc_workflow.py

@@ -12,17 +12,47 @@ def pprinter():
     return PrettyPrinter()
 
 
+# configs that are tested only tested parsing
 config_test_files = [
     "tests/files/configs/test_config_small.yml",
-    #"tests/files/configs/test_config_large.yml",
+    "tests/files/configs/test_config_large.yml",
     "tests/files/configs/test_config_parameters.yml",
 ]
 
-def test_run_workgraph(config_case, aiida_profile):  # noqa: ARG001
-    config_path, _ = config_case
+
+@pytest.mark.parametrize("config_path", [
+    "tests/files/configs/test_config_small.yml",
+    #"tests/files/configs/test_config_parameters.yml",
+])
+def test_run_workgraph(config_path):
     core_workflow = Workflow.from_yaml(config_path)
     aiida_workflow = AiidaWorkGraph(core_workflow)
-    aiida_workflow.run()
+    # ERROR that is not shown if not run manually:
+    #
+    # Continue workgraph.
+    # ------------------------------------------------------------
+    # ------------------------------------------------------------
+    # task:  icon_date_2026_01_01_00_00_00 RUNNING
+    # task:  icon_date_2026_03_01_00_00_00 PLANNED
+    # task:  icon_date_2026_05_01_00_00_00 PLANNED
+    # task:  cleanup RUNNING
+    # is workgraph finished:  False
+    # on awaitable finished:  icon_date_2026_01_01_00_00_00
+    # update task state:  icon_date_2026_01_01_00_00_00
+    # on awaitable finished:  cleanup
+    # update task state:  cleanup
+    # Continue workgraph.
+    # task:  icon_date_2026_01_01_00_00_00 FAILED
+    # task:  icon_date_2026_03_01_00_00_00 SKIPPED
+    # task:  icon_date_2026_05_01_00_00_00 SKIPPED
+    # task:  cleanup FAILED
+    # is workgraph finished:  True
+    # {}
+    #
+    # Figure out why output is not generated 
+    breakpoint()
+    out = aiida_workflow.run()
+    assert out != {} # should contain node id
 
 @pytest.fixture(params=config_test_files)
 def config_case(request):