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Fix notebook precommit #378

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merged 4 commits into from
Dec 30, 2024
Merged

Fix notebook precommit #378

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d1d68e2
remove nbqa
atmorling Dec 30, 2024
7d3f0f4
notebook update
atmorling Dec 30, 2024
62b404b
fix
atmorling Dec 30, 2024
a78d190
line-length fix
atmorling Dec 30, 2024
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12 changes: 2 additions & 10 deletions .pre-commit-config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -7,9 +7,10 @@ repos:
hooks:
# Run the linter and absolufy-imports.
- id: ruff
args: [--fix]
args: [--fix, --extend-select, E501, --line-length, "120"]
# Run the formatter.
- id: ruff-format
args: [--line-length, "120"]
- repo: https://github.com/kynan/nbstripout
rev: 0.5.0
hooks:
Expand All @@ -21,13 +22,4 @@ repos:
- id: codespell
files: ^.*\.(py|md|rst|ipynb)$
args: ["-w"]
- repo: https://github.com/nbQA-dev/nbQA
rev: 1.3.1
hooks:
- id: nbqa-black
args: ['--line-length=120']
- id: nbqa-flake8
args: ['--ignore=E203,E402,W503', '--max-line-length=120']
#- id: nbqa-isort
#args: ['-m3', '--tc']
exclude: ^ecoscope/contrib/
3 changes: 2 additions & 1 deletion doc/source/notebooks/01. IO/EarthRanger_IO.ipynb
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Expand Up @@ -29,7 +29,8 @@
},
"outputs": [],
"source": [
"%pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected]' &> /dev/null"
"%pip install \\\n",
" 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected]' &> /dev/null"
]
},
{
Expand Down
3 changes: 2 additions & 1 deletion doc/source/notebooks/01. IO/GEE_IO.ipynb
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Expand Up @@ -27,7 +27,8 @@
"metadata": {},
"outputs": [],
"source": [
"!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected]' &> /dev/null"
"%pip install \\\n",
" 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected]' &> /dev/null"
]
},
{
Expand Down
10 changes: 8 additions & 2 deletions doc/source/notebooks/01. IO/Landscape Dynamics Data.ipynb
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Expand Up @@ -29,7 +29,8 @@
"metadata": {},
"outputs": [],
"source": [
"!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected]' &> /dev/null"
"%pip install \\\n",
" 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected]' &> /dev/null"
]
},
{
Expand Down Expand Up @@ -155,7 +156,12 @@
"metadata": {},
"outputs": [],
"source": [
"types = [\"Road_Primary_Murram\", \"Road_Primary_Dirt/Sand\", \"Road_Secondary_Dirt/Sand\", \"Road_Secondary_Murram\"]\n",
"types = [\n",
" \"Road_Primary_Murram\",\n",
" \"Road_Primary_Dirt/Sand\",\n",
" \"Road_Secondary_Dirt/Sand\",\n",
" \"Road_Secondary_Murram\",\n",
"]\n",
"\n",
"roads_gdf = polylines_gdf[polylines_gdf[\"type\"].isin(types)].copy()"
]
Expand Down
16 changes: 13 additions & 3 deletions doc/source/notebooks/02. Relocations & Trajectories/Relocations_and_Trajectories.ipynb
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Expand Up @@ -36,7 +36,8 @@
"metadata": {},
"outputs": [],
"source": [
"%pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected]' &> /dev/null"
"%pip install \\\n",
" 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected]' &> /dev/null"
]
},
{
Expand Down Expand Up @@ -142,7 +143,11 @@
"metadata": {},
"outputs": [],
"source": [
"gdf = gpd.GeoDataFrame(data, geometry=gpd.points_from_xy(x=data[\"location-long\"], y=data[\"location-lat\"]), crs=4326)"
"gdf = gpd.GeoDataFrame(\n",
" data,\n",
" geometry=gpd.points_from_xy(x=data[\"location-long\"], y=data[\"location-lat\"]),\n",
" crs=4326,\n",
")"
]
},
{
Expand Down Expand Up @@ -444,7 +449,12 @@
"metadata": {},
"outputs": [],
"source": [
"relocs.to_csv(os.path.join(output_dir, \"relocs_clean.csv.zip\"), header=True, index=True, compression=\"zip\")"
"relocs.to_csv(\n",
" os.path.join(output_dir, \"relocs_clean.csv.zip\"),\n",
" header=True,\n",
" index=True,\n",
" compression=\"zip\",\n",
")"
]
},
{
Expand Down
8 changes: 6 additions & 2 deletions doc/source/notebooks/03. Home Range & Movescape/EcoGraph.ipynb
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Expand Up @@ -29,7 +29,8 @@
"source": [
"ECOSCOPE_RAW = \"https://raw.githubusercontent.com/wildlife-dynamics/ecoscope/master\"\n",
"\n",
"!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected]' &> /dev/null"
"%pip install \\\n",
" 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected]' &> /dev/null"
]
},
{
Expand Down Expand Up @@ -526,7 +527,10 @@
"# Wrong individual name\n",
"try:\n",
" ecograph.to_geotiff(\n",
" \"collective_influence\", os.path.join(output_dir, \"salif_ci_int.tif\"), individual=\"ofjoodjo\", interpolation=\"max\"\n",
" \"collective_influence\",\n",
" os.path.join(output_dir, \"salif_ci_int.tif\"),\n",
" individual=\"ofjoodjo\",\n",
" interpolation=\"max\",\n",
" )\n",
"except ValueError as e:\n",
" print(e)"
Expand Down
7 changes: 5 additions & 2 deletions doc/source/notebooks/03. Home Range & Movescape/Elliptical Time Density (ETD).ipynb
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Expand Up @@ -29,7 +29,8 @@
"source": [
"ECOSCOPE_RAW = \"https://raw.githubusercontent.com/wildlife-dynamics/ecoscope/master\"\n",
"\n",
"!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected]' &> /dev/null"
"%pip install \\\n",
" 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected]' &> /dev/null"
]
},
{
Expand Down Expand Up @@ -299,7 +300,9 @@
"outputs": [],
"source": [
"salif = get_percentile_area(\n",
" percentile_levels=[50, 60, 70, 80, 90, 99.9], raster_path=etd.at[\"Salif Keita\"], subject_id=\"Salif Keita\"\n",
" percentile_levels=[50, 60, 70, 80, 90, 99.9],\n",
" raster_path=etd.at[\"Salif Keita\"],\n",
" subject_id=\"Salif Keita\",\n",
")"
]
}
Expand Down
3 changes: 2 additions & 1 deletion doc/source/notebooks/03. Home Range & Movescape/Reduce Regions.ipynb
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Expand Up @@ -29,7 +29,8 @@
"source": [
"ECOSCOPE_RAW = \"https://raw.githubusercontent.com/wildlife-dynamics/ecoscope/master\"\n",
"\n",
"!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected]' &> /dev/null"
"%pip install \\\n",
" 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected]' &> /dev/null"
]
},
{
Expand Down
61 changes: 50 additions & 11 deletions doc/source/notebooks/04. EcoMap & EcoPlot/EcoMap.ipynb
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Expand Up @@ -36,7 +36,8 @@
"metadata": {},
"outputs": [],
"source": [
"%pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected]' &> /dev/null"
"%pip install \\\n",
" 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected]' &> /dev/null"
]
},
{
Expand Down Expand Up @@ -210,7 +211,11 @@
")\n",
"\n",
"df = pd.read_csv(os.path.join(output_dir, \"movebank_data.csv\"), index_col=0)\n",
"gdf = gpd.GeoDataFrame(df, geometry=gpd.points_from_xy(x=df[\"location-long\"], y=df[\"location-lat\"]), crs=4326)\n",
"gdf = gpd.GeoDataFrame(\n",
" df,\n",
" geometry=gpd.points_from_xy(x=df[\"location-long\"], y=df[\"location-lat\"]),\n",
" crs=4326,\n",
")\n",
"movebank_relocations_gdf = ecoscope.base.Relocations.from_gdf(\n",
" gdf, groupby_col=\"individual-local-identifier\", time_col=\"timestamp\"\n",
")\n",
Expand Down Expand Up @@ -276,13 +281,23 @@
"m.add_layer(EcoMap.get_named_tile_layer(\"OpenStreetMap\"))\n",
"\n",
"# Set DEM visualization parameters\n",
"vis_params = {\"min\": 0, \"max\": 4000, \"opacity\": 0.5, \"palette\": [\"006633\", \"E5FFCC\", \"662A00\", \"D8D8D8\", \"F5F5F5\"]}\n",
"vis_params = {\n",
" \"min\": 0,\n",
" \"max\": 4000,\n",
" \"opacity\": 0.5,\n",
" \"palette\": [\"006633\", \"E5FFCC\", \"662A00\", \"D8D8D8\", \"F5F5F5\"],\n",
"}\n",
"\n",
"# Add Google Earth Engine elevation layer\n",
"dem = ee.Image(\"USGS/SRTMGL1_003\")\n",
"m.add_layer(m.ee_layer(dem.updateMask(dem.gt(0)), vis_params))\n",
"\n",
"apply_color_map(region_gdf, \"ZoneID\", [\"#7fc97f\", \"#beaed4\", \"#fdc086\", \"#ffff99\"], output_column_name=\"zone_colors\")\n",
"apply_color_map(\n",
" region_gdf,\n",
" \"ZoneID\",\n",
" [\"#7fc97f\", \"#beaed4\", \"#fdc086\", \"#ffff99\"],\n",
" output_column_name=\"zone_colors\",\n",
")\n",
"m.add_layer(m.polygon_layer(region_gdf, opacity=0.5, fill_color_column=\"zone_colors\"), zoom=True)\n",
"\n",
"# Add trajectory\n",
Expand Down Expand Up @@ -324,7 +339,10 @@
"\n",
"m = EcoMap(width=800, height=600)\n",
"m.add_layer(EcoMap.get_named_tile_layer(\"OpenStreetMap\"))\n",
"m.add_layer(m.geotiff_layer(tiff=os.path.join(output_dir, \"mara_dem.tif\"), cmap=\"jet\"), zoom=True)\n",
"m.add_layer(\n",
" m.geotiff_layer(tiff=os.path.join(output_dir, \"mara_dem.tif\"), cmap=\"jet\"),\n",
" zoom=True,\n",
")\n",
"m"
]
},
Expand Down Expand Up @@ -357,8 +375,16 @@
"m.add_layer(EcoMap.get_named_tile_layer(\"OpenStreetMap\"))\n",
"\n",
"# Add day_night\n",
"apply_color_map(movebank_relocations_gdf, \"is_night\", [\"#292965\", \"#e7a553\"], output_column_name=\"colors\")\n",
"m.add_layer(m.point_layer(movebank_relocations_gdf, get_radius=700, fill_color_column=\"colors\"), zoom=True)\n",
"apply_color_map(\n",
" movebank_relocations_gdf,\n",
" \"is_night\",\n",
" [\"#292965\", \"#e7a553\"],\n",
" output_column_name=\"colors\",\n",
")\n",
"m.add_layer(\n",
" m.point_layer(movebank_relocations_gdf, get_radius=700, fill_color_column=\"colors\"),\n",
" zoom=True,\n",
")\n",
"\n",
"m.add_legend(title=\"Is Night\", labels=[\"True\", \"False\"], colors=[\"#292965\", \"#e7a553\"])\n",
"m.add_north_arrow(placement=\"top-left\")\n",
Expand Down Expand Up @@ -403,8 +429,16 @@
"m.add_layer(EcoMap.get_named_tile_layer(\"OpenStreetMap\"))\n",
"\n",
"# Add day_night\n",
"apply_color_map(movebank_trajectory_gdf, \"extra__is_night\", [\"#292965\", \"#e7a553\"], output_column_name=\"colors\")\n",
"m.add_layer(m.polyline_layer(movebank_trajectory_gdf, get_width=200, color_column=\"colors\"), zoom=True)\n",
"apply_color_map(\n",
" movebank_trajectory_gdf,\n",
" \"extra__is_night\",\n",
" [\"#292965\", \"#e7a553\"],\n",
" output_column_name=\"colors\",\n",
")\n",
"m.add_layer(\n",
" m.polyline_layer(movebank_trajectory_gdf, get_width=200, color_column=\"colors\"),\n",
" zoom=True,\n",
")\n",
"\n",
"m.add_legend(title=\"Is Night\", labels=[\"True\", \"False\"], colors=[\"#292965\", \"#e7a553\"])\n",
"m.add_north_arrow(placement=\"top-left\")\n",
Expand Down Expand Up @@ -463,15 +497,20 @@
"outputs": [],
"source": [
"percentile_areas = get_percentile_area(\n",
" percentile_levels=[50, 60, 70, 80, 90, 99.9], raster_path=etd.at[\"Salif Keita\"], subject_id=\"Salif Keita\"\n",
" percentile_levels=[50, 60, 70, 80, 90, 99.9],\n",
" raster_path=etd.at[\"Salif Keita\"],\n",
" subject_id=\"Salif Keita\",\n",
").to_crs(4326)\n",
"\n",
"m = EcoMap(width=800, height=600, static=True)\n",
"m.add_layer(EcoMap.get_named_tile_layer(\"OpenStreetMap\"))\n",
"\n",
"apply_color_map(percentile_areas, \"percentile\", \"RdYlGn\")\n",
"\n",
"m.add_layer(m.polygon_layer(percentile_areas, fill_color_column=\"percentile_colormap\"), zoom=True)\n",
"m.add_layer(\n",
" m.polygon_layer(percentile_areas, fill_color_column=\"percentile_colormap\"),\n",
" zoom=True,\n",
")\n",
"\n",
"m.add_north_arrow(placement=\"top-left\")\n",
"m.add_title(\"Salif ETD Range\")\n",
Expand Down
9 changes: 7 additions & 2 deletions doc/source/notebooks/04. EcoMap & EcoPlot/EcoPlot.ipynb
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Expand Up @@ -36,7 +36,8 @@
"metadata": {},
"outputs": [],
"source": [
"%pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected]' &> /dev/null"
"%pip install \\\n",
" 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected]' &> /dev/null"
]
},
{
Expand Down Expand Up @@ -134,7 +135,11 @@
"epdata2 = plotting.EcoPlotData(grouped2, \"segment_start\", \"speed_kmhr\", line=dict(color=\"blue\"))\n",
"epdata3 = plotting.EcoPlotData(grouped2, \"segment_start\", \"timespan_seconds\", line=dict(color=\"red\"))\n",
"\n",
"plotting.ecoplot([epdata1, epdata2, epdata3], \"My Plot\", os.path.join(output_dir, \"ecoplot_example.png\"))"
"plotting.ecoplot(\n",
" [epdata1, epdata2, epdata3],\n",
" \"My Plot\",\n",
" os.path.join(output_dir, \"ecoplot_example.png\"),\n",
")"
]
}
],
Expand Down
13 changes: 10 additions & 3 deletions doc/source/notebooks/05. Environmental Analyses/Landscape Grid.ipynb
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Expand Up @@ -29,7 +29,8 @@
"source": [
"ECOSCOPE_RAW = \"https://raw.githubusercontent.com/wildlife-dynamics/ecoscope/master\"\n",
"\n",
"!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected]' &> /dev/null"
"%pip install \\\n",
" 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected]' &> /dev/null"
]
},
{
Expand Down Expand Up @@ -183,7 +184,11 @@
"metadata": {},
"outputs": [],
"source": [
"new_grid_5_km.to_file(os.path.join(output_dir, \"out_landscape_grid.gpkg\"), layer=\"new_grid_5_km\", driver=\"GPKG\")"
"new_grid_5_km.to_file(\n",
" os.path.join(output_dir, \"out_landscape_grid.gpkg\"),\n",
" layer=\"new_grid_5_km\",\n",
" driver=\"GPKG\",\n",
")"
]
},
{
Expand Down Expand Up @@ -228,7 +233,9 @@
"outputs": [],
"source": [
"new_grid_1_km_aligned.to_file(\n",
" os.path.join(output_dir, \"out_landscape_grid.gpkg\"), layer=\"new_grid_1_km_aligned\", driver=\"GPKG\"\n",
" os.path.join(output_dir, \"out_landscape_grid.gpkg\"),\n",
" layer=\"new_grid_1_km_aligned\",\n",
" driver=\"GPKG\",\n",
")"
]
}
Expand Down
3 changes: 2 additions & 1 deletion doc/source/notebooks/05. Environmental Analyses/Remote Sensing Time Series Anomaly.ipynb
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Expand Up @@ -29,7 +29,8 @@
"source": [
"ECOSCOPE_RAW = \"https://raw.githubusercontent.com/wildlife-dynamics/ecoscope/master\"\n",
"\n",
"!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected]' &> /dev/null"
"%pip install \\\n",
" 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected]' &> /dev/null"
]
},
{
Expand Down
13 changes: 10 additions & 3 deletions doc/source/notebooks/05. Environmental Analyses/Seasonal Calculation.ipynb
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Expand Up @@ -29,7 +29,8 @@
"source": [
"ECOSCOPE_RAW = \"https://raw.githubusercontent.com/wildlife-dynamics/ecoscope/master\"\n",
"\n",
"!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected]' &> /dev/null"
"%pip install \\\n",
" 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected]' &> /dev/null"
]
},
{
Expand Down Expand Up @@ -207,7 +208,11 @@
"metadata": {},
"outputs": [],
"source": [
"windows.to_csv(os.path.join(output_dir, \"season_time_windows.csv\"), date_format=\"%Y-%m-%d %H:%M:%S\", index=True)"
"windows.to_csv(\n",
" os.path.join(output_dir, \"season_time_windows.csv\"),\n",
" date_format=\"%Y-%m-%d %H:%M:%S\",\n",
" index=True,\n",
")"
]
},
{
Expand Down Expand Up @@ -246,7 +251,9 @@
"source": [
"# Plot the NDVI Distribution and Seasonal Transition\n",
"fig = plotting.plot.plot_seasonal_dist(\n",
" ndvi_vals[\"NDVI\"], cuts, output_file=os.path.join(output_dir, \"seasonal_transition.png\")\n",
" ndvi_vals[\"NDVI\"],\n",
" cuts,\n",
" output_file=os.path.join(output_dir, \"seasonal_transition.png\"),\n",
")\n",
"fig.show()"
]
Expand Down
3 changes: 2 additions & 1 deletion doc/source/notebooks/06. Data Management/Tracking Data Gantt Chart.ipynb
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Expand Up @@ -29,7 +29,8 @@
"source": [
"ECOSCOPE_RAW = \"https://raw.githubusercontent.com/wildlife-dynamics/ecoscope/master\"\n",
"\n",
"!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected]' &> /dev/null"
"%pip install \\\n",
" 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected]' &> /dev/null"
]
},
{
Expand Down
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