fix formatting

Author: kks32

dapi/client.py

@@ -287,9 +287,7 @@ def queues(self, system_id: str, verbose: bool = True) -> List[Any]:
             self._tapis, system_id, verbose=verbose
         )
 
-    def check_credentials(
-        self, system_id: str, username: str = None
-    ) -> bool:
+    def check_credentials(self, system_id: str, username: str = None) -> bool:
         """Check whether TMS credentials exist for a user on a system.
 
         Args:
@@ -407,8 +405,12 @@ def generate(
             *preview* is ``True``.
         """
         return launcher_module.generate_sweep(
-            command, sweep, directory,
-            placeholder_style=placeholder_style, debug=debug, preview=preview,
+            command,
+            sweep,
+            directory,
+            placeholder_style=placeholder_style,
+            debug=debug,
+            preview=preview,
         )
 
     def submit(

dapi/jobs.py

@@ -1412,8 +1412,7 @@ def list_jobs(
             results = [j for j in results if getattr(j, "appId", None) == app_id]
         if status:
             results = [
-                j for j in results
-                if getattr(j, "status", "").upper() == status.upper()
+                j for j in results if getattr(j, "status", "").upper() == status.upper()
             ]
         if verbose:
             print(f"Found {len(results)} jobs.")
@@ -1451,8 +1450,13 @@ def list_jobs(
 
     # Reorder: priority columns first
     priority = [
-        "name", "uuid", "status", "appId", "appVersion",
-        "created_dt", "ended_dt",
+        "name",
+        "uuid",
+        "status",
+        "appId",
+        "appVersion",
+        "created_dt",
+        "ended_dt",
     ]
     priority_present = [c for c in priority if c in df.columns]
     remaining = [c for c in df.columns if c not in priority_present]

dapi/launcher.py

@@ -119,9 +119,7 @@ def generate_sweep(
     dirpath.mkdir(parents=True, exist_ok=True)
 
     # Write runsList.txt
-    (dirpath / "runsList.txt").write_text(
-        "\n".join(commands) + "\n", encoding="utf-8"
-    )
+    (dirpath / "runsList.txt").write_text("\n".join(commands) + "\n", encoding="utf-8")
 
     # Write call_pylauncher.py
     if debug is not None:
@@ -130,10 +128,7 @@ def generate_sweep(
             f'pylauncher.ClassicLauncher("runsList.txt", debug="{debug}")\n'
         )
     else:
-        script = (
-            "import pylauncher\n"
-            'pylauncher.ClassicLauncher("runsList.txt")\n'
-        )
+        script = "import pylauncher\n" 'pylauncher.ClassicLauncher("runsList.txt")\n'
     (dirpath / "call_pylauncher.py").write_text(script, encoding="utf-8")
 
     return commands

dapi/systems.py

@@ -118,9 +118,7 @@ def _resolve_username(t: Tapis, username: Optional[str] = None) -> str:
     return effective
 
 
-def check_credentials(
-    t: Tapis, system_id: str, username: Optional[str] = None
-) -> bool:
+def check_credentials(t: Tapis, system_id: str, username: Optional[str] = None) -> bool:
     """Check whether TMS credentials exist for a user on a Tapis system.
 
     Args:
@@ -141,9 +139,7 @@ def check_credentials(
     effective_username = _resolve_username(t, username)
 
     try:
-        t.systems.checkUserCredential(
-            systemId=system_id, userName=effective_username
-        )
+        t.systems.checkUserCredential(systemId=system_id, userName=effective_username)
         return True
     except (UnauthorizedError, NotFoundError):
         return False
@@ -194,12 +190,8 @@ def establish_credentials(
         authn_method = getattr(system_details, "defaultAuthnMethod", None)
     except BaseTapyException as e:
         if hasattr(e, "response") and e.response and e.response.status_code == 404:
-            raise CredentialError(
-                f"System '{system_id}' not found."
-            ) from e
-        raise CredentialError(
-            f"Failed to retrieve system '{system_id}': {e}"
-        ) from e
+            raise CredentialError(f"System '{system_id}' not found.") from e
+        raise CredentialError(f"Failed to retrieve system '{system_id}': {e}") from e
 
     if authn_method != "TMS_KEYS":
         raise CredentialError(
@@ -268,9 +260,7 @@ def revoke_credentials(
     effective_username = _resolve_username(t, username)
 
     try:
-        t.systems.removeUserCredential(
-            systemId=system_id, userName=effective_username
-        )
+        t.systems.removeUserCredential(systemId=system_id, userName=effective_username)
         if verbose:
             print(
                 f"Credentials revoked for user '{effective_username}' "

examples/mpm/mpm.ipynb

@@ -825,7 +825,31 @@
    "id": "e074a3c3",
    "metadata": {},
    "outputs": [],
-   "source": "# --- Translate Path with Verification ---\nds_path: str = \"/MyData/mpm-benchmarks/2d/uniaxial_stress/\"\nds_path_nonexistent: str = \"/MyData/this/path/does/not/exist/\"\n\ntry:\n    # Translate and verify the existing path\n    print(f\"\\nTranslating and verifying path: {ds_path}\")\n    input_uri = ds.files.to_uri(ds_path, verify_exists=True)\n    print(f\"Input Directory Tapis URI (verified): {input_uri}\")\n\n    # Example: Try translating a non-existent path with verification (will raise error)\n    print(f\"\\nTranslating and verifying non-existent path: {ds_path_nonexistent}\")\n    input_uri_bad = ds.files.to_uri(\n        ds_path_nonexistent, verify_exists=True\n    )\n    print(f\"This line should not be reached.\")\n\nexcept FileOperationError as e:\n    print(f\"Error during path translation/verification: {e}\")\n    # Decide how to handle the error (e.g., stop notebook, use default, etc.)\n    # For this example, we'll stop if verification fails.\n    raise SystemExit(\"Stopping notebook due to path verification error.\")\nexcept Exception as e:\n    print(f\"An unexpected error occurred during path translation: {e}\")\n    raise SystemExit(\"Stopping notebook due to unexpected path translation error.\")"
+   "source": [
+    "# --- Translate Path with Verification ---\n",
+    "ds_path: str = \"/MyData/mpm-benchmarks/2d/uniaxial_stress/\"\n",
+    "ds_path_nonexistent: str = \"/MyData/this/path/does/not/exist/\"\n",
+    "\n",
+    "try:\n",
+    "    # Translate and verify the existing path\n",
+    "    print(f\"\\nTranslating and verifying path: {ds_path}\")\n",
+    "    input_uri = ds.files.to_uri(ds_path, verify_exists=True)\n",
+    "    print(f\"Input Directory Tapis URI (verified): {input_uri}\")\n",
+    "\n",
+    "    # Example: Try translating a non-existent path with verification (will raise error)\n",
+    "    print(f\"\\nTranslating and verifying non-existent path: {ds_path_nonexistent}\")\n",
+    "    input_uri_bad = ds.files.to_uri(ds_path_nonexistent, verify_exists=True)\n",
+    "    print(f\"This line should not be reached.\")\n",
+    "\n",
+    "except FileOperationError as e:\n",
+    "    print(f\"Error during path translation/verification: {e}\")\n",
+    "    # Decide how to handle the error (e.g., stop notebook, use default, etc.)\n",
+    "    # For this example, we'll stop if verification fails.\n",
+    "    raise SystemExit(\"Stopping notebook due to path verification error.\")\n",
+    "except Exception as e:\n",
+    "    print(f\"An unexpected error occurred during path translation: {e}\")\n",
+    "    raise SystemExit(\"Stopping notebook due to unexpected path translation error.\")"
+   ]
   }
  ],
  "metadata": {

examples/pylauncher_sweep.ipynb

@@ -112,7 +112,7 @@
    "source": [
     "sweep = {\n",
     "    \"ALPHA\": [0.3, 0.5, 3.7],\n",
-    "    \"BETA\":  [1.1, 2.0, 3.0],\n",
+    "    \"BETA\": [1.1, 2.0, 3.0],\n",
     "}"
    ]
   },
@@ -130,7 +130,7 @@
    "outputs": [],
    "source": [
     "ds.jobs.parametric_sweep.generate(\n",
-    "    'python3 simulate.py --alpha ALPHA --beta BETA --output out_ALPHA_BETA',\n",
+    "    \"python3 simulate.py --alpha ALPHA --beta BETA --output out_ALPHA_BETA\",\n",
     "    sweep,\n",
     "    preview=True,\n",
     ")"
@@ -150,7 +150,7 @@
    "outputs": [],
    "source": [
     "commands = ds.jobs.parametric_sweep.generate(\n",
-    "    'python3 simulate.py --alpha ALPHA --beta BETA --output out_ALPHA_BETA',\n",
+    "    \"python3 simulate.py --alpha ALPHA --beta BETA --output out_ALPHA_BETA\",\n",
     "    sweep,\n",
     "    input_dir_generic,\n",
     "    debug=\"host+job\",\n",
@@ -245,7 +245,7 @@
     "input_dir_opensees = os.path.expanduser(\"~/MyData/opensees_sweep/\")\n",
     "os.makedirs(input_dir_opensees, exist_ok=True)\n",
     "\n",
-    "cantilever_script = '''\\\n",
+    "cantilever_script = \"\"\"\\\n",
     "# Ex1a.Canti2D.Push — OpenSeesPy cantilever pushover\n",
     "# Adapted from Silvia Mazzoni & Frank McKenna, 2006/2020\n",
     "# Units: kip, inch, second\n",
@@ -317,7 +317,7 @@
     "ops.analyze(1000)\n",
     "\n",
     "print(f\"Done: NodalMass={NodalMass}, LCol={LCol}\")\n",
-    "'''\n",
+    "\"\"\"\n",
     "\n",
     "with open(os.path.join(input_dir_opensees, \"cantilever.py\"), \"w\") as f:\n",
     "    f.write(cantilever_script)\n",

tests/jobs/test_list_jobs.py

@@ -8,11 +8,17 @@
 from dapi.exceptions import JobMonitorError
 
 
-def _make_job(uuid, name, status, app_id, app_version="1.0",
-              created="2025-06-15T10:00:00.000Z",
-              ended="2025-06-15T11:00:00.000Z",
-              remote_started="2025-06-15T10:05:00.000Z",
-              last_updated="2025-06-15T11:00:00.000Z"):
+def _make_job(
+    uuid,
+    name,
+    status,
+    app_id,
+    app_version="1.0",
+    created="2025-06-15T10:00:00.000Z",
+    ended="2025-06-15T11:00:00.000Z",
+    remote_started="2025-06-15T10:05:00.000Z",
+    last_updated="2025-06-15T11:00:00.000Z",
+):
     """Create a mock TapisResult job object."""
     job = Mock()
     job.__dict__ = {
@@ -37,8 +43,14 @@ def _make_job(uuid, name, status, app_id, app_version="1.0",
     _make_job("uuid-001", "matlab-run-1", "FINISHED", "matlab-r2023a"),
     _make_job("uuid-002", "opensees-run-1", "FINISHED", "opensees-mp-s3"),
     _make_job("uuid-003", "matlab-run-2", "FAILED", "matlab-r2023a"),
-    _make_job("uuid-004", "mpm-run-1", "RUNNING", "mpm-s3",
-              ended=None, remote_started="2025-06-15T10:10:00.000Z"),
+    _make_job(
+        "uuid-004",
+        "mpm-run-1",
+        "RUNNING",
+        "mpm-s3",
+        ended=None,
+        remote_started="2025-06-15T10:10:00.000Z",
+    ),
 ]
 
 
@@ -79,8 +91,14 @@ def test_combined_filters(self):
 
     def test_datetime_columns_exist(self):
         df = list_jobs(self.t)
-        for col in ["created_dt", "created_date", "ended_dt", "ended_date",
-                     "remoteStarted_dt", "lastUpdated_dt"]:
+        for col in [
+            "created_dt",
+            "created_date",
+            "ended_dt",
+            "ended_date",
+            "remoteStarted_dt",
+            "lastUpdated_dt",
+        ]:
             self.assertIn(col, df.columns)
 
     def test_datetime_nat_for_missing(self):
@@ -91,9 +109,16 @@ def test_datetime_nat_for_missing(self):
 
     def test_priority_column_order(self):
         df = list_jobs(self.t)
-        expected_first = ["name", "uuid", "status", "appId", "appVersion",
-                          "created_dt", "ended_dt"]
-        actual_first = list(df.columns[:len(expected_first)])
+        expected_first = [
+            "name",
+            "uuid",
+            "status",
+            "appId",
+            "appVersion",
+            "created_dt",
+            "ended_dt",
+        ]
+        actual_first = list(df.columns[: len(expected_first)])
         self.assertEqual(actual_first, expected_first)
 
     def test_passes_limit_to_api(self):

tests/jobs/test_parametric_sweep.py

@@ -17,14 +17,18 @@ def test_empty_sweep_returns_base_command(self):
 
     def test_single_param(self):
         with tempfile.TemporaryDirectory() as d:
-            cmds = generate_sweep("python run.py --alpha ALPHA", {"ALPHA": [1, 2, 3]}, d)
+            cmds = generate_sweep(
+                "python run.py --alpha ALPHA", {"ALPHA": [1, 2, 3]}, d
+            )
             self.assertEqual(len(cmds), 3)
             self.assertEqual(cmds[0], "python run.py --alpha 1")
             self.assertEqual(cmds[2], "python run.py --alpha 3")
 
     def test_multi_param_cartesian_product(self):
         with tempfile.TemporaryDirectory() as d:
-            cmds = generate_sweep("python run.py --a A --b B", {"A": [1, 2], "B": [10, 20]}, d)
+            cmds = generate_sweep(
+                "python run.py --a A --b B", {"A": [1, 2], "B": [10, 20]}, d
+            )
             self.assertEqual(len(cmds), 4)
             self.assertIn("python run.py --a 1 --b 10", cmds)
             self.assertIn("python run.py --a 2 --b 20", cmds)
@@ -36,17 +40,23 @@ def test_deterministic_order(self):
 
     def test_token_placeholder(self):
         with tempfile.TemporaryDirectory() as d:
-            cmds = generate_sweep("echo ALPHA", {"ALPHA": [1]}, d, placeholder_style="token")
+            cmds = generate_sweep(
+                "echo ALPHA", {"ALPHA": [1]}, d, placeholder_style="token"
+            )
             self.assertEqual(cmds, ["echo 1"])
 
     def test_braces_placeholder(self):
         with tempfile.TemporaryDirectory() as d:
-            cmds = generate_sweep("echo {ALPHA}", {"ALPHA": [1]}, d, placeholder_style="braces")
+            cmds = generate_sweep(
+                "echo {ALPHA}", {"ALPHA": [1]}, d, placeholder_style="braces"
+            )
             self.assertEqual(cmds, ["echo 1"])
 
     def test_env_vars_preserved(self):
         with tempfile.TemporaryDirectory() as d:
-            cmds = generate_sweep('run --out "$WORK/$SLURM_JOB_ID" --a A', {"A": [1]}, d)
+            cmds = generate_sweep(
+                'run --out "$WORK/$SLURM_JOB_ID" --a A', {"A": [1]}, d
+            )
             self.assertIn("$WORK", cmds[0])
             self.assertIn("$SLURM_JOB_ID", cmds[0])
 

tests/systems/test_credentials.py

@@ -144,9 +144,7 @@ def test_raises_value_error_for_empty_system_id(self):
 
     def test_uses_explicit_username(self):
         self.t.systems.checkUserCredential.side_effect = UnauthorizedError()
-        establish_credentials(
-            self.t, "frontera", username="otheruser", verbose=False
-        )
+        establish_credentials(self.t, "frontera", username="otheruser", verbose=False)
         self.t.systems.createUserCredential.assert_called_once_with(
             systemId="frontera", userName="otheruser", createTmsKeys=True
         )
@@ -159,7 +157,9 @@ def test_raises_credential_error_on_create_failure(self):
         with self.assertRaises(CredentialError):
             establish_credentials(self.t, "frontera", verbose=False)
 
-    def test_verbose_prints_skip_message(self, ):
+    def test_verbose_prints_skip_message(
+        self,
+    ):
         self.t.systems.checkUserCredential.return_value = Mock()
         # Should not raise; just prints a message
         establish_credentials(self.t, "frontera", verbose=True)