glasagent · ltalirz · Feb 18, 2026 · Feb 8, 2026 · Feb 8, 2026 · Feb 8, 2026
diff --git a/.github/workflows/amorphouspy_api.yml b/.github/workflows/amorphouspy_api.yml
@@ -36,8 +36,21 @@ jobs:
         shell: bash -l {0}
         working-directory: amorphouspy_api
         run: |
-          amorphouspy_INTEGRATION=1 uvicorn amorphouspy_api.app:app --port 8002 &
-          pytest -m integration -s --durations=0 --cov=src/amorphouspy_api --cov-report=xml --cov-report=term --cov-append
+          cat > test.sh << 'EOF'
+          #!/bin/bash
+          uvicorn amorphouspy_api.app:app --port 8002 &
+          pytest -m integration -s \
+            --durations=0 \
+            --cov=src/amorphouspy_api \
+            --cov-report=xml \
+            --cov-report=term \
+            --cov-append
+          EOF
+          chmod +x test.sh
+          flux start ./test.sh
+        env:
+          AMORPHOUSPY_INTEGRATION: "1"
+          EXECUTOR_TYPE: "flux"
 
       - name: Pytest coverage comment
         uses: MishaKav/pytest-coverage-comment@main

diff --git a/amorphouspy/src/amorphouspy/analysis/bond_angle_distribution.py b/amorphouspy/src/amorphouspy/analysis/bond_angle_distribution.py
@@ -49,7 +49,7 @@ def compute_angles(
         >>> bins, hist = compute_angles(structure, center_type=1, neighbor_type=2, cutoff=3.0)
 
     """
-    ids, types, coords, box_size = get_properties_for_structure_analysis(structure)
+    _ids, types, coords, box_size = get_properties_for_structure_analysis(structure)
 
     neighbors = get_neighbors(
         coords,

diff --git a/amorphouspy/src/amorphouspy/analysis/cavities.py b/amorphouspy/src/amorphouspy/analysis/cavities.py
@@ -56,7 +56,7 @@ def compute_cavities(
 
     """
     # Extract properties using the provided helper
-    ids, types, coords, box_size = get_properties_for_structure_analysis(structure)
+    _ids, types, coords, box_size = get_properties_for_structure_analysis(structure)
     type_dict = type_to_dict(types)
 
     # Use a context manager to ensure the temporary file is cleaned up

diff --git a/amorphouspy/src/amorphouspy/analysis/cte.py b/amorphouspy/src/amorphouspy/analysis/cte.py
@@ -126,7 +126,7 @@ def cte_from_volume_temperature_data(
     volume = np.array(volume)[sorted_indices]
 
     # fit and calculate CTE
-    slope, intercept = np.polyfit(temperature, volume, 1)
+    slope, _intercept = np.polyfit(temperature, volume, 1)
     CTE = slope / volume[0]
 
     return float(CTE)
diff --git a/amorphouspy/src/amorphouspy/analysis/radial_distribution_functions.py b/amorphouspy/src/amorphouspy/analysis/radial_distribution_functions.py
@@ -116,7 +116,7 @@ def compute_rdf(
         >>> r, rdfs, cn = compute_rdf(structure, r_max=10.0, n_bins=500)
 
     """
-    ids, types, coords, box_size = get_properties_for_structure_analysis(structure)
+    _ids, types, coords, box_size = get_properties_for_structure_analysis(structure)
     # Input validation and type conversion
     coords = np.asarray(coords, dtype=np.float64)
     types = np.asarray(types, dtype=np.int64)

diff --git a/amorphouspy/src/amorphouspy/analysis/rings.py b/amorphouspy/src/amorphouspy/analysis/rings.py
@@ -68,7 +68,7 @@ def compute_guttmann_rings(
         ... )
 
     """
-    ids, types, coords, box_size = get_properties_for_structure_analysis(structure)
+    _ids, types, coords, box_size = get_properties_for_structure_analysis(structure)
     type_dict = type_to_dict(types)
     with tempfile.NamedTemporaryFile("w+", suffix=".xyz", delete=True) as tmp:
         write_xyz(filename=tmp.name, coords=coords, types=types, box_size=box_size, type_dict=type_dict)

diff --git a/amorphouspy/src/amorphouspy/structure.py b/amorphouspy/src/amorphouspy/structure.py
@@ -172,7 +172,7 @@ def _integer_fu_from_total(Nfu_target: int, mol_frac: dict[str, float]) -> dict[
     n = {ox: int(np.floor(w[ox])) for ox in x}
     rem = Nfu_target - sum(n.values())
     if rem > 0:
-        order = sorted(x.keys(), key=lambda k: (w[k] - n[k]), reverse=True)
+        order = sorted(x.keys(), key=lambda k: w[k] - n[k], reverse=True)
         for i in range(rem):
             n[order[i % len(order)]] += 1
     return n

diff --git a/amorphouspy/src/amorphouspy/workflows/structural_analysis.py b/amorphouspy/src/amorphouspy/workflows/structural_analysis.py
@@ -203,7 +203,7 @@ def analyze_structure(atoms: Atoms) -> StructureData:  # noqa: C901, PLR0912, PL
     total_mass_g = atoms.get_masses().sum() / avogadro_number  # Convert amu to g
     density = total_mass_g / volume_cm3
 
-    type_map, network_formers, modifiers, oxygen_present = _classify_elements(unique_z)
+    type_map, network_formers, modifiers, _oxygen_present = _classify_elements(unique_z)
     former_types = [z for z, sym in type_map.items() if sym in network_formers]
     modifier_types = [z for z, sym in type_map.items() if sym in modifiers]
     O_type = [z for z, sym in type_map.items() if sym == "O"]

diff --git a/amorphouspy/src/amorphouspy/workflows/viscosity.py b/amorphouspy/src/amorphouspy/workflows/viscosity.py
@@ -209,7 +209,7 @@ def viscosity_simulation(
     )
 
     # Stage 2: Production simulation for viscosity at T
-    structure_final, parsed_output = _run_lammps_md(
+    _structure_final, parsed_output = _run_lammps_md(
         structure=structure1,
         potential=potential,
         tmp_working_directory=tmp_working_directory,

diff --git a/amorphouspy/src/tests/test_structure.py b/amorphouspy/src/tests/test_structure.py
@@ -66,7 +66,7 @@ def test_structure_atom_counts_molar() -> None:
         assert atom_counts[elem] == expected, f"{elem} atoms should be {expected} for {n_molecules} mode."
 
     # Test with target_atoms
-    atoms, atom_counts = ps.create_random_atoms(
+    _atoms, atom_counts = ps.create_random_atoms(
         composition=composition,
         n_molecules=None,
         target_atoms=target_atoms,
@@ -110,7 +110,7 @@ def test_structure_atom_counts_weight() -> None:
         assert atom_counts[elem] == expected, f"{elem} atoms should be {expected} for {n_molecules} mode."
 
     # Test with target_atoms
-    atoms, atom_counts = ps.create_random_atoms(
+    _atoms, atom_counts = ps.create_random_atoms(
         composition=weight_composition,
         n_molecules=None,
         target_atoms=target_atoms,

diff --git a/amorphouspy_api/README.md b/amorphouspy_api/README.md
@@ -10,11 +10,11 @@ This FastAPI-based service provides a Model Context Protocol (MCP) interface for
 
 ```
 ┌─────────────────┐    ┌─────────────────┐    ┌─────────────────┐
-│   FastAPI App   │ ── │  SQLite Cache   │ ── │  Worker Process │
+│   FastAPI App   │ ── │  SQLite Cache   │ ── │   executorlib   │
 │                 │    │                 │    │                 │
-│ • Request hash  │    │ • Task metadata │    │ • amorphouspy   │
-│ • Cache lookup  │    │ • Results       │    │ • LAMMPS sims   │
-│ • Task creation │    │ • Hash index    │    │ • File cleanup  │
+│ • Request hash  │    │ • Task metadata │    │ • Local exec    │
+│ • Cache lookup  │    │ • Results       │    │ • SLURM cluster │
+│ • Task creation │    │ • Hash index    │    │ • Job caching   │
 └─────────────────┘    └─────────────────┘    └─────────────────┘
 ```
 
@@ -32,17 +32,28 @@ This FastAPI-based service provides a Model Context Protocol (MCP) interface for
 - Tracks task states: `processing` → `complete`/`error`
 - Survives server restarts and process crashes
 
-#### 3. **Async Processing with Process Isolation**
-- Uses `ProcessPoolExecutor` to run simulations in separate processes
-- Avoids blocking the FastAPI event loop
-- Proper signal handling for subprocess management
-- Automatic temporary file cleanup using `tempfile.TemporaryDirectory()`
+#### 3. **Job Execution with executorlib**
+- Supports local execution (`SingleNodeExecutor`) or SLURM cluster (`SlurmClusterExecutor`)
+- Executor type configured via environment variables
+- Built-in job caching at the executor level
+- Re-submitting same job returns cached result or running future
 
 #### 4. **Model Context Protocol (MCP) Integration**
 - Exposes simulation capabilities as MCP tools
 - Compatible with Claude, VS Code, and other MCP clients
 - Server-Sent Events (SSE) endpoint at `/mcp`
 
+## Environment Variables
+
+| Variable | Description | Default |
+|----------|-------------|---------|
+| `EXECUTOR_TYPE` | Executor backend: `local` or `slurm` | `local` |
+| `EXECUTOR_CORES` | Number of CPU cores per worker | `4` |
+| `SLURM_PARTITION` | SLURM partition name (slurm only) | - |
+| `SLURM_TIME` | SLURM job time limit (slurm only) | - |
+| `AMORPHOUSPY_PROJECTS` | Directory for project/cache files | `./projects` |
+| `API_BASE_URL` | Base URL for visualization links | - |
+
 
 ## Installation
 

diff --git a/amorphouspy_api/conftest.py b/amorphouspy_api/conftest.py
@@ -0,0 +1,22 @@
+"""Shared test fixtures for amorphouspy_api tests."""
+
+from pathlib import Path
+
+import pytest
+
+from amorphouspy_api.database import close_task_store, init_task_store
+
+
+@pytest.fixture(autouse=True)
+def _fresh_task_store(tmp_path: Path) -> None:
+    """Provide a fresh temporary task store for every test.
+
+    This ensures tests are isolated from each other and from any
+    persistent database left over from previous runs.
+    """
+    # Re-initialise the singleton so every call to get_task_store()
+    # (in routers, visualization, tests, …) returns the fresh instance.
+    db_path = tmp_path / "test_tasks.db"
+    init_task_store(db_path)
+    yield
+    close_task_store()
diff --git a/amorphouspy_api/pyproject.toml b/amorphouspy_api/pyproject.toml
@@ -32,7 +32,7 @@ markers = [
 addopts = ["-m", "not integration"]
 filterwarnings = [
     "ignore::DeprecationWarning:defusedxml.*",
-    "ignore:.*__get_pydantic_core_schema__.*",
+    "ignore::pydantic.PydanticDeprecatedSince211",
     "ignore:.*multi-threaded.*fork.*",
 ]