Merge pull request #1443 from OceanParcels/rerunning_notebooks

Updating all tutorials with latest conda environment and parcels v3 code
OceanParcels · Oct 10, 2023 · 8597833 · 8597833
2 parents 2f721d1 + 4d4b5eb
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diff --git a/docs/examples/documentation_advanced_zarr.ipynb b/docs/examples/documentation_advanced_zarr.ipynb
diff --git a/docs/examples/documentation_geospatial.ipynb b/docs/examples/documentation_geospatial.ipynb
@@ -127,7 +127,13 @@
     "from lxml import etree\n",
     "from shapely.geometry import LineString, Point\n",
     "\n",
-    "from parcels import AdvectionRK4, ErrorCode, FieldSet, JITParticle, ParticleSet\n",
+    "from parcels import (\n",
+    "    AdvectionRK4,\n",
+    "    FieldSet,\n",
+    "    JITParticle,\n",
+    "    ParticleSet,\n",
+    "    download_example_dataset,\n",
+    ")\n",
     "\n",
     "DATA_OUTPUT_FOLDER = Path(\"tutorial_geospatial_output\")\n",
     "DATA_OUTPUT_FOLDER.mkdir(exist_ok=True)\n",
@@ -140,16 +146,18 @@
    "metadata": {},
    "outputs": [
     {
-     "name": "stderr",
+     "name": "stdout",
      "output_type": "stream",
      "text": [
-      "INFO: Compiled ArrayJITParticleAdvectionRK4 ==> /tmp/parcels-1000/libcc2185fa8a93ecc6f43d3f424a40fb67_0.so\n"
+      "INFO: Output files are stored in tutorial_geospatial_output/agulhas_trajectories.zarr.\n",
+      "100%|██████████| 10368000.0/10368000.0 [00:15<00:00, 651613.20it/s]\n"
      ]
     }
    ],
    "source": [
     "# An example parcels simulation\n",
-    "filenames = \"GlobCurrent_example_data/20*.nc\"\n",
+    "data_folder = download_example_dataset(\"GlobCurrent_example_data\")\n",
+    "filenames = filename = str(data_folder / \"20*.nc\")\n",
     "variables = {\n",
     "    \"U\": \"eastward_eulerian_current_velocity\",\n",
     "    \"V\": \"northward_eulerian_current_velocity\",\n",
@@ -175,6 +183,7 @@
     "    if particle.state > 4:\n",
     "        particle.delete()\n",
     "\n",
+    "\n",
     "pset.execute(\n",
     "    [AdvectionRK4, DeleteParticle],\n",
     "    runtime=timedelta(days=120),\n",

diff --git a/docs/examples/documentation_indexing.ipynb b/docs/examples/documentation_indexing.ipynb
diff --git a/docs/examples/documentation_stuck_particles.ipynb b/docs/examples/documentation_stuck_particles.ipynb
diff --git a/docs/examples/documentation_unstuck_Agrid.ipynb b/docs/examples/documentation_unstuck_Agrid.ipynb
diff --git a/docs/examples/parcels_tutorial.ipynb b/docs/examples/parcels_tutorial.ipynb
diff --git a/docs/examples/tutorial_Argofloats.ipynb b/docs/examples/tutorial_Argofloats.ipynb
diff --git a/docs/examples/tutorial_NestedFields.ipynb b/docs/examples/tutorial_NestedFields.ipynb
diff --git a/docs/examples/tutorial_analyticaladvection.ipynb b/docs/examples/tutorial_analyticaladvection.ipynb
diff --git a/docs/examples/tutorial_delaystart.ipynb b/docs/examples/tutorial_delaystart.ipynb
diff --git a/docs/examples/tutorial_diffusion.ipynb b/docs/examples/tutorial_diffusion.ipynb
diff --git a/docs/examples/tutorial_interaction.ipynb b/docs/examples/tutorial_interaction.ipynb
diff --git a/docs/examples/tutorial_interpolation.ipynb b/docs/examples/tutorial_interpolation.ipynb
diff --git a/docs/examples/tutorial_jit_vs_scipy.ipynb b/docs/examples/tutorial_jit_vs_scipy.ipynb
@@ -39,11 +39,12 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "INFO: Compiled ArrayJITParticleAdvectionRK4 ==> /var/folders/1n/500ln6w97859_nqq86vwpl000000gr/T/parcels-504/libe8a271835dbec54c6df79d8b8421813a_0.so\n",
-      "(100%)  Timer root                       : 6.879e+00 s\n",
-      "(  1%)    (  1%) Timer fieldset creation : 7.331e-02 s\n",
-      "( 76%)    ( 76%) Timer scipy             : 5.246e+00 s\n",
-      "( 23%)    ( 23%) Timer jit               : 1.558e+00 s\n"
+      "100%|██████████| 3600.0/3600.0 [00:01<00:00, 1843.14it/s]\n",
+      "100%|██████████| 3600.0/3600.0 [00:00<00:00, 533400.25it/s]\n",
+      "(100%)  Timer root                       : 3.165e+00 s\n",
+      "(  3%)    (  3%) Timer fieldset creation : 9.443e-02 s\n",
+      "( 65%)    ( 65%) Timer scipy             : 2.073e+00 s\n",
+      "( 32%)    ( 32%) Timer jit               : 9.969e-01 s\n"
      ]
     }
    ],
@@ -98,7 +99,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "As you can see above, even in this very small example **Scipy mode took almost 5 times as long** (4.7 seconds versus 1.1 seconds) as the JIT mode. For larger examples, this can grow to hundreds of times slower.\n",
+    "As you can see above, even in this very small example **Scipy mode took more than 2 times as long** (2.1 seconds versus 1.0 seconds) as the JIT mode. For larger examples, this can grow to hundreds of times slower.\n",
     "\n",
     "This is just an illustrative example, depending on the number of calls to `AdvectionRK4`, the size of the `FieldSet`, the size of the `pset`, the ratio between `dt` and `outputdt` in the `.execute` etc, the difference between JIT and Scipy can vary significantly. However, JIT will almost always be faster!\n",
     "\n",
@@ -166,9 +167,18 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "(100%)  Timer root                       : 4.803e+00 s\n",
-      "( 49%)    ( 49%) Timer dllt              : 2.351e+00 s\n",
-      "( 51%)    ( 51%) Timer dllt_p            : 2.445e+00 s\n"
+      "  0%|          | 0/3600.0 [00:00<?, ?it/s]"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "100%|██████████| 3600.0/3600.0 [00:00<00:00, 4426.66it/s]\n",
+      "100%|██████████| 3600.0/3600.0 [00:00<00:00, 4111.05it/s]\n",
+      "(100%)  Timer root                       : 1.705e+00 s\n",
+      "( 48%)    ( 48%) Timer dllt              : 8.206e-01 s\n",
+      "( 52%)    ( 52%) Timer dllt_p            : 8.785e-01 s\n"
      ]
     }
    ],
@@ -241,9 +251,11 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "(100%)  Timer root                       : 8.433e+00 s\n",
-      "( 96%)    ( 96%) Timer dllt              : 8.085e+00 s\n",
-      "(  4%)    (  4%) Timer dllt_p            : 3.461e-01 s\n"
+      "100%|██████████| 864000.0/864000.0 [00:03<00:00, 243133.93it/s]\n",
+      "100%|██████████| 864000.0/864000.0 [00:00<00:00, 5615534.75it/s]\n",
+      "(100%)  Timer root                       : 3.715e+00 s\n",
+      "( 96%)    ( 96%) Timer dllt              : 3.558e+00 s\n",
+      "(  4%)    (  4%) Timer dllt_p            : 1.568e-01 s\n"
      ]
     }
    ],
@@ -298,7 +310,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.13"
+   "version": "3.11.6"
   }
  },
  "nbformat": 4,

diff --git a/docs/examples/tutorial_kernelloop.ipynb b/docs/examples/tutorial_kernelloop.ipynb
diff --git a/docs/examples/tutorial_nemo_3D.ipynb b/docs/examples/tutorial_nemo_3D.ipynb
diff --git a/docs/examples/tutorial_nemo_curvilinear.ipynb b/docs/examples/tutorial_nemo_curvilinear.ipynb
diff --git a/docs/examples/tutorial_output.ipynb b/docs/examples/tutorial_output.ipynb
diff --git a/docs/examples/tutorial_parcels_structure.ipynb b/docs/examples/tutorial_parcels_structure.ipynb
@@ -370,7 +370,8 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "INFO: Compiled ArrayAgeParticleAgeNorthVelAdvectionRK4 ==> /var/folders/1n/500ln6w97859_nqq86vwpl000000gr/T/parcels-504/libaf3202ef8aa79577647d9631e4f42fe7_0.so\n"
+      "INFO: Output files are stored in GCParticles.zarr.\n",
+      "100%|██████████| 2073600.0/2073600.0 [00:04<00:00, 444884.89it/s]\n"
      ]
     }
    ],
@@ -433,7 +434,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.13"
+   "version": "3.11.6"
   }
  },
  "nbformat": 4,

diff --git a/docs/examples/tutorial_particle_field_interaction.ipynb b/docs/examples/tutorial_particle_field_interaction.ipynb
diff --git a/docs/examples/tutorial_periodic_boundaries.ipynb b/docs/examples/tutorial_periodic_boundaries.ipynb
diff --git a/docs/examples/tutorial_sampling.ipynb b/docs/examples/tutorial_sampling.ipynb