Remove file linting exclusions and Fix lint issues

This stops excluding the Jumper notebook and restart files (now removed
from repo) from linting and fixes linting issues. Adds jupyter files
types to pre-commit ruff hook so that notebooks are formatted.

Author: isaacaka

.pre-commit-config.yaml

@@ -11,4 +11,4 @@ repos:
     rev: v0.9.6
     hooks:
     - id: ruff-format
-      types_or: [ python ]
+      types_or: [ python, jupyter ]

Notebooks/Jumper.ipynb

@@ -15,13 +15,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import os\n",
     "import pickle\n",
     "import random\n",
     "from importlib.resources import files\n",
     "from pathlib import Path\n",
     "\n",
-    "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
     "import pandas as pd\n",
     "\n",
@@ -30,13 +28,6 @@
     ")\n",
     "from nemo_spinup_forecast.forecast import Predictions, Simulation, load_ts\n",
     "from nemo_spinup_forecast.forecast_method import forecast_techniques\n",
-    "from nemo_spinup_forecast.utils import (\n",
-    "    create_run_dir,\n",
-    "    get_dr_technique,\n",
-    "    get_forecast_technique,\n",
-    "    get_ocean_term,\n",
-    ")\n",
-    "\n",
     "from nemo_spinup_forecast.plotting_utils import (\n",
     "    plot_bar_with_errors,\n",
     "    plot_component_timeseries,\n",
@@ -48,6 +39,12 @@
     "    plot_rmse_depth_profile,\n",
     "    plot_rmse_maps,\n",
     "    plot_simulation_snapshots,\n",
+    ")\n",
+    "from nemo_spinup_forecast.utils import (\n",
+    "    create_run_dir,\n",
+    "    get_dr_technique,\n",
+    "    get_forecast_technique,\n",
+    "    get_ocean_term,\n",
     ")"
    ]
   },
@@ -198,7 +195,7 @@
     "simus = [simu_zos, simu_so, simu_thetao]\n",
     "# names = [\"zos\",\"so\",\"thetao\"]\n",
     "names = [ssh_term, so_term, thetao_term]\n",
-    "\n",
+    "print(simu_so.simulation[0, 0], simu_so.simulation.shape, simu_so.simulation[0, 0].shape)\n",
     "plot_simulation_snapshots(simus, names)"
    ]
   },
@@ -300,7 +297,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "rmseV_zos\n",
     "values = [rmseV_zos, rmseV_so.T, rmseV_thetao.T]\n",
     "maps = [rmseM_zos, rmseM_so, rmseM_thetao]\n",
     "names = [ssh_term, so_term, thetao_term]\n",
@@ -435,15 +431,15 @@
     "import random\n",
     "\n",
     "random.seed(100)\n",
-    "comp, train_len, steps = 1, len(ts_zos), steps\n",
-    "print(len(ts_zos))\n",
+    "# steps unchanged\n",
+    "comp, train_len = 1, len(ts_zos)\n",
     "\n",
     "hat_zos, std_zos, metrics_zos = ts_zos.forecast_single_series(comp, train_len, steps)\n",
     "hat_so, std_so, metrics_so = ts_so.forecast_single_series(comp, train_len, steps)\n",
     "hat_thetao, std_thetao, metrics_thetao = ts_thetao.forecast_single_series(\n",
     "    comp, train_len, steps\n",
     ")\n",
-    "\n",
+    "print(\"hat_zos shape:\", hat_zos.shape)\n",
     "ts_zos.show(comp, hat_zos, std_zos, train_len)\n",
     "ts_so.show(comp, hat_so, std_so, train_len, color=\"darkgreen\")\n",
     "ts_thetao.show(comp, hat_thetao, std_thetao, train_len, color=\"darkred\")"
@@ -479,7 +475,8 @@
    "outputs": [],
    "source": [
     "n = np.shape(ts_zos.info[\"ts\"])[1]\n",
-    "predictions, n, info = hat_zos, n, ts_zos.info\n",
+    "# n unchanged\n",
+    "predictions, info = hat_zos, ts_zos.info\n",
     "\n",
     "predictions_zos = simu_zos.reconstruct(hat_zos, n, ts_zos.info)\n",
     "\n",
@@ -550,7 +547,6 @@
    },
    "outputs": [],
    "source": [
-    "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
     "import xarray as xr\n",
     "\n",
@@ -581,7 +577,7 @@
     "id_, start2, end2 = \"106\", start, end + steps  # start, end + steps\n",
     "\n",
     "\n",
-    "ye = False\n",
+    "ye = True\n",
     "\n",
     "ref_zos = Simulation(\n",
     "    path=data_path,\n",
@@ -656,6 +652,11 @@
    "source": [
     "print(ref_so.simulation[end:].shape)\n",
     "\n",
+    "print(\"pred_so shape:\")\n",
+    "print(pred_so.shape)\n",
+    "print(\"ref_so shape:\")\n",
+    "print(ref_so.simulation.shape)\n",
+    "\n",
     "err_so = np.abs((ref_so.simulation - pred_so))\n",
     "err_thetao = np.abs((ref_thetao.simulation - pred_thetao))\n",
     "err_zos = np.abs((ref_zos.simulation - pred_zos))\n",

ruff.toml

@@ -24,7 +24,7 @@ extend-select = ["D417"]
 # Ignore D105 (Missing docstring in magic method)
 ignore = ["SIM108", "RUF002", "PLR0913", "PLR2004", "D100", "D104", "D105"]
 
-exclude = ["standalone/**", "src/nemo_spinup_forecast/optimization.py", "main_restart.py", "Notebooks/Restart.ipynb", "Notebooks/Jumper.ipynb"]
+exclude = ["src/nemo_spinup_forecast/density.py"]
 
 [lint.per-file-ignores]
 "tests/**/*.py" = ["S101"]