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https://github.com/astral-sh/ruff-pre-commit - rev: v0.2.0 + rev: v0.2.2 hooks: - id: ruff @@ -47,10 +47,7 @@ repos: - id: nbqa-check-ast - id: nbqa-black - id: nbqa-ruff - args: [--fix, --extend-ignore=E402] - # Skipping b/c These notebooks mix R and Python and - # will return false positive for "F821 Undefined name."" - exclude: 2017-11-30-rerddap\.ipynb$|2018-02-20-obis.ipynb$ + args: [--fix] - repo: https://github.com/bdice/nb-strip-paths rev: 'v0.1.0' diff --git a/jupyterbook/content/code_gallery/data_analysis_and_visualization_notebooks/2016-11-16-CF-UGRID-SGRID-conventions.ipynb b/jupyterbook/content/code_gallery/data_analysis_and_visualization_notebooks/2016-11-16-CF-UGRID-SGRID-conventions.ipynb index 3f9eb4e7..3ece688b 100644 --- a/jupyterbook/content/code_gallery/data_analysis_and_visualization_notebooks/2016-11-16-CF-UGRID-SGRID-conventions.ipynb +++ b/jupyterbook/content/code_gallery/data_analysis_and_visualization_notebooks/2016-11-16-CF-UGRID-SGRID-conventions.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "code", - "execution_count": null, + "execution_count": 1, "metadata": { "tags": [ "remove-cell" @@ -48,7 +48,7 @@ "\n", "Created: 2019-11-16\n", "\n", - "Updated: 2022-05-25\n", + "Updated: 2023-02-19\n", "\n", "Metadata conventions, like the Climate and Forecast (CF) conventions,\n", "can be cumbersome to adhere to but it will be very handy when you or other users manipulate the data later in time.\n", @@ -67,50 +67,65 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": 2, "metadata": { "scrolled": false }, "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "0.8.9\n" + ] + }, { "data": { "text/plain": [ + "SGRID:\n", + " CF role: grid_topology: ['grid']\n", "\n", - "- CF Roles: grid_topology: ['grid']\n", + " Axes: * X: ['xi_psi', 'xi_rho', 'xi_u', 'xi_v']\n", + " * Y: ['eta_psi', 'eta_rho', 'eta_u', 'eta_v']\n", + " * Z: ['s_rho', 's_w']\n", "\n", "Coordinates:\n", - "- CF Axes: * Z: ['s_rho', 's_w']\n", - " * T: ['ocean_time']\n", - " X, Y: n/a\n", + " CF Axes: * Z: ['s_rho', 's_w']\n", + " * T: ['ocean_time']\n", + " X, Y: n/a\n", "\n", - "- CF Coordinates: longitude: ['lon_psi', 'lon_rho', 'lon_u', 'lon_v']\n", - " latitude: ['lat_psi', 'lat_rho', 'lat_u', 'lat_v']\n", - " * vertical: ['s_rho', 's_w']\n", - " * time: ['ocean_time']\n", + " CF Coordinates: longitude: ['lon_psi', 'lon_rho', 'lon_u', 'lon_v']\n", + " latitude: ['lat_psi', 'lat_rho', 'lat_u', 'lat_v']\n", + " * vertical: ['s_rho', 's_w']\n", + " * time: ['ocean_time']\n", "\n", - "- Cell Measures: area, volume: n/a\n", + " Cell Measures: area, volume: n/a\n", "\n", - "- Standard Names: * forecast_reference_time: ['run']\n", - " latitude: ['lat_psi', 'lat_rho', 'lat_u', 'lat_v']\n", - " longitude: ['lon_psi', 'lon_rho', 'lon_u', 'lon_v']\n", - " * ocean_s_coordinate_g1: ['s_rho', 's_w']\n", + " Standard Names: * forecast_reference_time: ['run']\n", + " latitude: ['lat_psi', 'lat_rho', 'lat_u', 'lat_v']\n", + " longitude: ['lon_psi', 'lon_rho', 'lon_u', 'lon_v']\n", + " * ocean_s_coordinate_g1: ['s_rho', 's_w']\n", "\n", - "- Bounds: n/a\n", + " Bounds: n/a\n", + "\n", + " Grid Mappings: n/a\n", "\n", "Data Variables:\n", - "- Cell Measures: area, volume: n/a\n", + " Cell Measures: area, volume: n/a\n", + "\n", + " Standard Names: sea_floor_depth_below_sea_surface: ['h']\n", + " sea_surface_elevation_anomaly: ['zeta']\n", + " sea_water_potential_temperature: ['temp']\n", + " sea_water_practical_salinity: ['salt']\n", + " sea_water_x_velocity: ['u']\n", + " sea_water_y_velocity: ['v']\n", "\n", - "- Standard Names: sea_floor_depth_below_sea_surface: ['h']\n", - " sea_surface_elevation_anomaly: ['zeta']\n", - " sea_water_potential_temperature: ['temp']\n", - " sea_water_practical_salinity: ['salt']\n", - " sea_water_x_velocity: ['u']\n", - " sea_water_y_velocity: ['v']\n", + " Bounds: n/a\n", "\n", - "- Bounds: n/a" + " Grid Mappings: n/a" ] }, - "execution_count": 1, + "execution_count": 2, "metadata": {}, "output_type": "execute_result" } @@ -137,17 +152,17 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": 3, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ - "/home/filipe/micromamba/envs/IOOS/lib/python3.11/site-packages/cf_xarray/accessor.py:1638: UserWarning: Variables {'', 'time'} not found in object but are referred to in the CF attributes.\n", - " warnings.warn(\n", - "/home/filipe/micromamba/envs/IOOS/lib/python3.11/site-packages/cf_xarray/accessor.py:1638: UserWarning: Variables {''} not found in object but are referred to in the CF attributes.\n", - " warnings.warn(\n" + "/tmp/ipykernel_26057/1323880464.py:8: UserWarning: Variables {'', 'time'} not found in object but are referred to in the CF attributes.\n", + " eta = ds.cf[\"zeta\"][run, ocean_time, x, y]\n", + "/tmp/ipykernel_26057/1323880464.py:9: UserWarning: Variables {''} not found in object but are referred to in the CF attributes.\n", + " depth = ds.cf[\"h\"][x, y]\n" ] } ], @@ -186,7 +201,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 4, "metadata": { "scrolled": false }, @@ -195,8 +210,8 @@ "name": "stderr", "output_type": "stream", "text": [ - "/home/filipe/micromamba/envs/IOOS/lib/python3.11/site-packages/cf_xarray/accessor.py:1638: UserWarning: Variables {'', 'time'} not found in object but are referred to in the CF attributes.\n", - " warnings.warn(\n" + "/tmp/ipykernel_26057/4185694592.py:1: UserWarning: Variables {'', 'time'} not found in object but are referred to in the CF attributes.\n", + " temp = ds.cf[\"sea_water_potential_temperature\"]\n" ] }, { @@ -566,13 +581,13 @@ " fill: currentColor;\n", "}\n", "
<xarray.DataArray 'temp' (run: 1929, time: 157, s_rho: 36, eta_rho: 82,\n", - " xi_rho: 130)>\n", + " xi_rho: 130)> Size: 465GB\n", "[116222867280 values with dtype=float32]\n", "Coordinates:\n", - " * s_rho (s_rho) float64 -0.9861 -0.9583 -0.9306 ... -0.04167 -0.01389\n", - " * run (run) datetime64[ns] 2013-05-18 2013-05-19 ... 2018-09-14\n", - " lat_rho (eta_rho, xi_rho) float64 33.74 33.79 33.84 ... 42.78 42.82 42.87\n", - " lon_rho (eta_rho, xi_rho) float64 -75.84 -75.78 -75.71 ... -71.49 -71.43\n", + " * run (run) datetime64[ns] 15kB 2013-05-18 2013-05-19 ... 2018-09-14\n", + " * s_rho (s_rho) float64 288B -0.9861 -0.9583 -0.9306 ... -0.04167 -0.01389\n", + " lat_rho (eta_rho, xi_rho) float64 85kB 33.74 33.79 33.84 ... 42.82 42.87\n", + " lon_rho (eta_rho, xi_rho) float64 85kB -75.84 -75.78 ... -71.49 -71.43\n", "Dimensions without coordinates: time, eta_rho, xi_rho\n", "Attributes:\n", " units: Celsius\n", @@ -580,21 +595,21 @@ " time: ocean_time\n", " field: temperature, scalar, series\n", " _ChunkSizes: [ 1 36 82 130]\n", - " standard_name: sea_water_potential_temperature