Compatibility with IconBaseRestartWorkChain

.gitignore

@@ -165,3 +165,8 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
+html/
+
+tests/cases/APE_R02B04/config/AQUAPLANET.svg
+examples/DYAMOND_aiida/CHANGES_90s_TEST.md
+**/*.svg

aiida-icon-link-dir-contents-race-condition.md

@@ -0,0 +1,131 @@
+# aiida-icon `link_dir_contents` Race Condition with SLURM Pre-submission
+
+## Issue Summary
+
+The `link_dir_contents` feature in aiida-icon is incompatible with SLURM pre-submission when using job dependencies. The IconCalculation fails during `prepare_for_submission` because it tries to list remote directory contents that don't exist yet (upstream jobs are still creating them).
+
+## Root Cause
+
+### How SLURM Pre-submission Works
+
+1. Upstream job (e.g., `prepare_input`) is submitted to SLURM and returns `job_id` + `remote_folder` PK immediately
+2. Downstream job (e.g., `icon`) gets this information via `get_job_data`
+3. Downstream job's `prepare_for_submission` runs **locally** to prepare submission files
+4. Job is submitted to SLURM with `--dependency=afterok:<upstream_job_id>`
+5. SLURM holds the job until upstream finishes
+
+### The Problem
+
+aiida-icon's `prepare_for_submission` method (line 190 in `calculations.py`) calls `remotedata.listdir()` to enumerate files in `link_dir_contents`:
+
+```python
+if "link_dir_contents" in self.inputs:
+    for remotedata in self.inputs.link_dir_contents.values():
+        for subpath in remotedata.listdir():  # <-- FAILS HERE
+            calcinfo.remote_symlink_list.append(...)
+```
+
+This happens **locally before SLURM submission**, but the remote directory doesn't exist yet because the upstream job is still running.
+
+**SLURM dependencies prevent jobs from starting on compute nodes, but they don't prevent AiiDA from running local preparation steps.**
+
+## Timeline Example (from DYAMOND workflow)
+
+| Time | Event | Status |
+|------|-------|--------|
+| 06:36:54 | `prepare_input` job submitted to SLURM (job 545483) | Running on SLURM |
+| 06:37:40 | `remote_folder` node created (PK 43155) | - |
+| 06:37:50 | `get_job_data` returns job_id + remote_folder PK | Correct behavior |
+| 06:37:52 | `icon` job's `prepare_for_submission` starts **locally** | - |
+| 06:37:52-06:38:18 | `icon` calls `listdir()` on `icon_input/` directory | **FAILS** - directory doesn't exist |
+| 06:38:18 | IconCalculation excepted with OSError | ❌ Failure |
+| 06:39:43 | `prepare_input` finishes, creates `icon_input/` | Too late |
+
+## Error Message
+
+```
+OSError: The required remote path /capstor/scratch/cscs/jgeiger/aiida/6a/5c/345a-8d48-44ca-a10d-6e1c0fb44d27/icon_input/.
+on santis-async-ssh does not exist, is not a directory or has been deleted.
+```
+
+## Proposed Solutions
+
+### Option 1: Skip Non-existing Directories (Simple)
+
+Modify `aiida-icon/src/aiida_icon/calculations.py` line 188-197:
+
+```python
+if "link_dir_contents" in self.inputs:
+    for remotedata in self.inputs.link_dir_contents.values():
+        try:
+            subpaths = remotedata.listdir()
+        except OSError as e:
+            # Directory doesn't exist yet - skip for now
+            # It will be created by upstream job before this job starts (SLURM dependency)
+            self.logger.warning(
+                f"Directory {remotedata.get_remote_path()} does not exist yet, "
+                f"skipping link_dir_contents enumeration. Will be created by upstream job."
+            )
+            continue
+
+        for subpath in subpaths:
+            calcinfo.remote_symlink_list.append(
+                (
+                    remotedata.computer.uuid,
+                    str(pathlib.Path(remotedata.get_remote_path()) / subpath),
+                    subpath,
+                )
+            )
+```
+
+**Pros:**
+- Simple fix
+- Maintains SLURM dependency semantics
+- Job will still fail if directory truly doesn't exist when it starts running
+
+**Cons:**
+- Can't validate directory contents during submission
+- Symlinks won't be enumerated in advance (but they'll be created via different mechanism?)
+
+### Option 2: Defer Symlink Creation to Compute Node
+
+Instead of enumerating files during `prepare_for_submission`, create a wrapper script that:
+1. Waits for upstream jobs (handled by SLURM)
+2. Creates symlinks from the remote directory contents on the compute node
+3. Runs ICON
+
+This would require more extensive changes to the workflow.
+
+### Option 3: Wait for Directory in prepare_for_submission (Not Recommended)
+
+Poll until the directory exists before calling `listdir()`.
+
+**Problems:**
+- Defeats the purpose of SLURM pre-submission
+- Introduces arbitrary delays in workflow submission
+- Could cause deadlocks if upstream job fails
+
+## Recommendation
+
+**Option 1** is the best approach:
+- Skip non-existing directories with a warning
+- Trust SLURM dependencies to ensure directory exists when job starts
+- Simple, minimal change to aiida-icon
+- Preserves the benefits of SLURM pre-submission
+
+## Context
+
+This issue was discovered in the DYAMOND workflow where:
+- `prepare_input` task creates an `icon_input/` directory with symlinks
+- `icon` task uses `link_dir_contents` to reference this directory
+- With SLURM pre-submission enabled, the race condition manifests
+
+The workflow configuration:
+```yaml
+- icon:
+    inputs:
+      - icon_link_input:
+          port: link_dir_contents
+```
+
+Where `icon_link_input` is a GeneratedData output from `prepare_input`.

pyproject.toml

@@ -33,16 +33,29 @@ dependencies = [
   "isoduration",
   "pydantic",
   "ruamel.yaml",
-  "aiida-core>=2.5",
-  "aiida-icon>=0.4.0",
-  "aiida-workgraph==0.5.2",
+  # "aiida-core==2.7.1",
+  # "aiida-core@git+https://github.com/aiidateam/aiida-core.git@f21bcd49d60b2e35b8b4df417f46ac15bd5bc861",
+  "aiida-core@git+https://github.com/aiidateam/aiida-core.git",
+  # "aiida-firecrest@git+https://github.com/aiidateam/aiida-firecrest.git@edab99ac6808c0ccfc63329d365654f54deacf5e",
+  "aiida-firecrest@git+https://github.com/aiidateam/aiida-firecrest.git@c4e287ffe40ae57db7032fe1c80d2c4def0dc7fa",
+  # "pyfirecrest",
+  # "aiida-icon @ git+https://github.com/aiida-icon/aiida-icon.git@add-arbitrary-inputs",
+  "aiida-icon @ git+https://github.com/aiida-icon/aiida-icon.git@dyamond-changes",
+  # "aiida-workgraph==1.0.0b4",  # need latest for presubmission
+  # "aiida-workgraph @ git+https://github.com/GeigerJ2/aiida-workgraph.git@task-window-dynamic",  # <-- now in `patches/` in Sirocco
+  "aiida-workgraph @git+https://github.com/aiidateam/aiida-workgraph.git",
+  "aiida-gui",
+  "aiida-gui-workgraph",
+  "ipdb",
   "termcolor",
   "pygraphviz",
   "lxml",
   "f90nml",
   "aiida-shell>=0.8.1",
   "rich~=14.0",
   "typer~=0.16.0",
+  "aiida-gui-workgraph>=0.1.3",
+  "jinja2>=3.0",
 ]
 license = {file = "LICENSE"}
 
@@ -99,6 +112,9 @@ include = [
 [tool.hatch.version]
 path = "src/sirocco/__init__.py"
 
+[tool.hatch.metadata]
+allow-direct-references = true
+
 [tool.hatch.envs.default]
 installer = "uv"
 python = "3.12"
@@ -145,12 +161,17 @@ extra-dependencies = [
   "types-colorama",
   "types-Pygments",
   "types-termcolor",
-  "types-requests"
+  "types-requests",
+  "types-PyYAML"
+
 ]
 
 [tool.hatch.envs.types.scripts]
 check = "mypy --exclude 'tests/cases/*' --no-incremental {args:.}"
 
+[tool.mypy]
+disable_error_code = ["import-untyped"]
+
 [[tool.mypy.overrides]]
 module = ["isoduration", "isoduration.*"]
 follow_untyped_imports = true