diff --git a/Tests/Data/Parabolic/ComponentTransport/MultiLayerDiffusion/MultiLayerDiffusion.ipynb b/Tests/Data/Parabolic/ComponentTransport/MultiLayerDiffusion/MultiLayerDiffusion.ipynb
index 958fa35f8d668787541cfaa9286f74653d4fbfc0..d1cfcbec8cbb7517cf4ee763cebdc0f9f5a061df 100644
--- a/Tests/Data/Parabolic/ComponentTransport/MultiLayerDiffusion/MultiLayerDiffusion.ipynb
+++ b/Tests/Data/Parabolic/ComponentTransport/MultiLayerDiffusion/MultiLayerDiffusion.ipynb
@@ -265,7 +265,7 @@
" color_map = iter(cm.rainbow(np.linspace(0, 1, len(time))))\n",
"\n",
" # Plot semi-analytical solutions\n",
- " for col_name, t, color in zip(soln[[\"1e3\", \"1e4\", \"1e5\", \"1e6\"]], time, color_map):\n",
+ " for col_name, _t, color in zip(soln[[\"1e3\", \"1e4\", \"1e5\", \"1e6\"]], time, color_map):\n",
" ax.plot(\n",
" soln[\"x\"],\n",
" soln[col_name],\n",
@@ -352,7 +352,7 @@
}
],
"source": [
- "from IPython.display import Image, display\n",
+ "from IPython.display import display\n",
"\n",
"display(Image(filename=\"./sketch_molar_flux_calculation.jpg\", width=400))"
]
diff --git a/Tests/Data/Parabolic/ComponentTransport/ReactiveTransport/CO2Injection/CO2Injection.md b/Tests/Data/Parabolic/ComponentTransport/ReactiveTransport/CO2Injection/CO2Injection.md
index 511c263dced93a64a15d26b06e05d30f49e25d77..b32bf2f1fdbc79cd4916e4c84694b7d5c1a9e88b 100644
--- a/Tests/Data/Parabolic/ComponentTransport/ReactiveTransport/CO2Injection/CO2Injection.md
+++ b/Tests/Data/Parabolic/ComponentTransport/ReactiveTransport/CO2Injection/CO2Injection.md
@@ -88,7 +88,8 @@ check_file = os.path.isfile(f"{out_dir}/calcite_simple_ts_43_t_30000.000000.vtu"
if check_file:
print("OGS simulation for the scenario simple case runs successfully")
else:
- raise Exception("OGS simulation failed.")
+ msg = "OGS simulation failed."
+ raise Exception(msg)
# pwp
prj_name = "calcite_pwp.prj"
@@ -106,7 +107,8 @@ check_file = os.path.isfile(f"{out_dir}/calcite_pwp_ts_43_t_30000.000000.vtu")
if check_file:
print("OGS simulation for the scenario PWP case runs successfully")
else:
- raise Exception("OGS simulation failed.")
+ msg = "OGS simulation failed."
+ raise Exception(msg)
```
```python
diff --git a/Tests/Data/Parabolic/ComponentTransport/ReactiveTransport/DecayChain/DecayChain.ipynb b/Tests/Data/Parabolic/ComponentTransport/ReactiveTransport/DecayChain/DecayChain.ipynb
index a13cf21781f6060f0a313dd7abadcbf67f774530..750e5fe934edbc8d2ee451280d9eff50c11d4455 100644
--- a/Tests/Data/Parabolic/ComponentTransport/ReactiveTransport/DecayChain/DecayChain.ipynb
+++ b/Tests/Data/Parabolic/ComponentTransport/ReactiveTransport/DecayChain/DecayChain.ipynb
@@ -191,7 +191,7 @@
"source": [
"def computeProduct(j, i, k, c_inlet):\n",
" value = 1\n",
- " for l in range(j, i):\n",
+ " for l in range(j, i): # noqa: E741\n",
" value *= k[l] / (k[l] - k[i]) * c_inlet[j]\n",
"\n",
" return value\n",
diff --git a/Tests/Data/Parabolic/ComponentTransport/ReactiveTransport/DecayChain/GlobalImplicitApproach/performance_measurements.ipynb b/Tests/Data/Parabolic/ComponentTransport/ReactiveTransport/DecayChain/GlobalImplicitApproach/performance_measurements.ipynb
index e7280929cf45b8e6450f2ee84f206ed20e942f4d..f122f03a36d0f4720b016180c0058c4ff2279cac 100644
--- a/Tests/Data/Parabolic/ComponentTransport/ReactiveTransport/DecayChain/GlobalImplicitApproach/performance_measurements.ipynb
+++ b/Tests/Data/Parabolic/ComponentTransport/ReactiveTransport/DecayChain/GlobalImplicitApproach/performance_measurements.ipynb
@@ -78,7 +78,12 @@
}
],
"source": [
- "out_dir_base = os.environ.get(\"OGS_TESTRUNNER_OUT_DIR\", \"_out\")\n",
+ "from pathlib import Path\n",
+ "\n",
+ "out_dir_base = Path(os.environ.get(\"OGS_TESTRUNNER_OUT_DIR\", \"_out\"))\n",
+ "if not out_dir_base.exists():\n",
+ " out_dir_base.mkdir(parents=True)\n",
+ "\n",
"print(\"base output directory is\", out_dir_base)"
]
},
@@ -90,7 +95,7 @@
"outputs": [],
"source": [
"def get_out_dir(case):\n",
- " return os.path.join(out_dir_base, os.path.dirname(case))"
+ " return out_dir_base / Path(case).parent"
]
},
{
@@ -179,15 +184,15 @@
}
],
"source": [
- "for name, case in cases:\n",
+ "for _name, case in cases:\n",
" outdir = get_out_dir(case)\n",
- " if not os.path.exists(outdir):\n",
- " os.makedirs(outdir)\n",
- " with open(os.path.join(outdir, \".gitignore\"), \"w\") as fh:\n",
+ " if not outdir.exists():\n",
+ " outdir.mkdir(parents=True)\n",
+ " with (outdir / \".gitignore\").open(mode=\"w\") as fh:\n",
" fh.write(\"*\\n\")\n",
"\n",
" print(f\"running case {case}\")\n",
- " with open(os.path.join(outdir, \"ogs-out.txt\"), \"w\") as fh:\n",
+ " with (outdir / \"ogs-out.txt\").open(mode=\"w\") as fh:\n",
" subprocess.run(\n",
" [\"ogs\", \"-o\", outdir, case], check=True, stdout=fh, stderr=subprocess.STDOUT\n",
" )"
@@ -349,9 +354,9 @@
"stats = []\n",
"exec_times = []\n",
"\n",
- "for name, case in cases:\n",
+ "for _name, case in cases:\n",
" outdir = get_out_dir(case)\n",
- " logfile = os.path.join(outdir, \"ogs-out.txt\")\n",
+ " logfile = outdir / \"ogs-out.txt\"\n",
"\n",
" records = parse_file(logfile)\n",
"\n",
@@ -385,7 +390,7 @@
"# df_stats = stats[0].copy()\n",
"# df_stats[\"case_name\"] = cases[0][0]\n",
"\n",
- "for (name, case), stat in zip(cases, stats):\n",
+ "for (name, _case), stat in zip(cases, stats):\n",
" tmp = stat.copy()\n",
" tmp[\"case_name\"] = name\n",
" df_stats = pd.concat([df_stats, tmp])\n",
@@ -523,7 +528,7 @@
"source": [
"assert np.all(df_it_num[\"min\"] == df_it_num[\"max\"])\n",
"# attention: depends on the order of cases!\n",
- "assert np.all(df_it_num[\"max\"].values == [2, 1, 1, 2, 1, 1, 2, 1, 1])"
+ "assert np.all(df_it_num[\"max\"].values == [2, 1, 1, 2, 1, 1, 2, 1, 1]) # noqa: PD011"
]
},
{
@@ -779,7 +784,7 @@
"df_time_step_speedups[\"dirichlet_time\"] /= df_time_step_speedups[\"iteration_number\"]\n",
"\n",
"for col in df_time_step_speedups.columns:\n",
- " c = df_time_step_speedups[col].values\n",
+ " c = df_time_step_speedups[col].to_numpy()\n",
" # c[:3] = np.max(c[:3]) / c[:3]\n",
" # c[3:] = np.max(c[3:]) / c[3:]\n",
" c[:3] = c[0] / c[:3]\n",
@@ -854,7 +859,7 @@
"assert np.all(df_time_step_speedups.index == [name for name, case in cases])\n",
"\n",
"for col in df_time_step_speedups.columns:\n",
- " c = df_time_step_speedups[col].values\n",
+ " c = df_time_step_speedups[col].to_numpy()\n",
" # c[:3] = np.max(c[:3]) / c[:3]\n",
" # c[3:] = np.max(c[3:]) / c[3:]\n",
" c[:3] = c[0] / c[:3]\n",
@@ -928,9 +933,9 @@
"computes = []\n",
"solves = []\n",
"\n",
- "for name, case in cases:\n",
+ "for _name, case in cases:\n",
" outdir = get_out_dir(case)\n",
- " logfile = os.path.join(outdir, \"ogs-out.txt\")\n",
+ " logfile = outdir / \"ogs-out.txt\"\n",
"\n",
" res = subprocess.run(\n",
" f'grep \"compute with Eigen .* linear solver\" {logfile} | wc -l',\n",
@@ -1129,7 +1134,7 @@
"simulation_results = {}\n",
"\n",
"for name, case in cases:\n",
- " pvdfile = os.path.join(get_out_dir(case), \"1d_decay_chain_GIA.pvd\")\n",
+ " pvdfile = get_out_dir(case) / \"1d_decay_chain_GIA.pvd\"\n",
" print(\"reading\", pvdfile)\n",
" reader = pv.get_reader(pvdfile)\n",
" # print(reader.time_values)\n",
diff --git a/Tests/Data/Parabolic/ComponentTransport/elder/elder-python-bcs.py b/Tests/Data/Parabolic/ComponentTransport/elder/elder-python-bcs.py
index 487aa5419938d1e4ee3317e8cf92ea4f767a752a..9946f3130a773282b772423d885f8836bb97f48a 100644
--- a/Tests/Data/Parabolic/ComponentTransport/elder/elder-python-bcs.py
+++ b/Tests/Data/Parabolic/ComponentTransport/elder/elder-python-bcs.py
@@ -5,7 +5,7 @@ except ModuleNotFoundError:
class BCPressure(OpenGeoSys.BoundaryCondition):
- def getDirichletBCValue(self, t, coords, node_id, primary_vars):
+ def getDirichletBCValue(self, _t, coords, _node_id, _primary_vars):
x, y, z = coords
if x == -150 and z == 75:
@@ -17,7 +17,7 @@ class BCPressure(OpenGeoSys.BoundaryCondition):
class BCConcentration(OpenGeoSys.BoundaryCondition):
- def getDirichletBCValue(self, t, coords, node_id, primary_vars):
+ def getDirichletBCValue(self, _t, coords, _node_id, _primary_vars):
x, y, z = coords
if z == -75:
diff --git a/Tests/Data/Parabolic/LiquidFlow/BlockingConductingFracture/BlockingConductingFracture.ipynb b/Tests/Data/Parabolic/LiquidFlow/BlockingConductingFracture/BlockingConductingFracture.ipynb
index d5446562b9b3778a0875da6d764500268dde3ade..cfac425871e4d917d2454bd372635116dc762304 100644
--- a/Tests/Data/Parabolic/LiquidFlow/BlockingConductingFracture/BlockingConductingFracture.ipynb
+++ b/Tests/Data/Parabolic/LiquidFlow/BlockingConductingFracture/BlockingConductingFracture.ipynb
@@ -117,9 +117,7 @@
],
"source": [
"# Run the analysis\n",
- "model_lf.run_model(\n",
- " logfile=os.path.join(out_dir, \"block_conduct_frac.txt\"), args=f\"-o {out_dir}\"\n",
- ")"
+ "model_lf.run_model(logfile=(out_dir / \"block_conduct_frac.txt\"), args=f\"-o {out_dir}\")"
]
},
{
@@ -232,9 +230,6 @@
],
"source": [
"# Post-Processing\n",
- "import matplotlib.pyplot as plt\n",
- "import numpy as np\n",
- "\n",
"levels = np.linspace(np.min(field), np.max(field), 60)\n",
"levelsf = np.linspace(np.min(field), np.max(field), 60)\n",
"\n",