[skip ci] Updates

OpenDrift · Apr 24, 2024 · a481fab · a481fab
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diff --git a/.buildinfo b/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 2e1beade1efde30bca4cb3ffbdde04d8
+config: 5e1b922fdd7bed5cbb07478d2a34103e
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/_downloads/46b4cb42d5bb56cc39e2b5b2b520b38d/gallery_python.zip b/_downloads/46b4cb42d5bb56cc39e2b5b2b520b38d/gallery_python.zip
diff --git a/_downloads/fcaddee3a42ae2e2c41e00ae08d70347/gallery_jupyter.zip b/_downloads/fcaddee3a42ae2e2c41e00ae08d70347/gallery_jupyter.zip
diff --git a/_images/example_2d_0.gif b/_images/example_2d_0.gif
diff --git a/_images/example_biodegradation_0.gif b/_images/example_biodegradation_0.gif
diff --git a/_images/example_chemicaldrift_0.gif b/_images/example_chemicaldrift_0.gif
diff --git a/_images/example_chemicaldrift_1.gif b/_images/example_chemicaldrift_1.gif
diff --git a/_images/example_coastline_options_0.gif b/_images/example_coastline_options_0.gif
diff --git a/_images/example_codegg_0.gif b/_images/example_codegg_0.gif
diff --git a/_images/example_codegg_1.gif b/_images/example_codegg_1.gif
diff --git a/_images/example_compare_0.gif b/_images/example_compare_0.gif
diff --git a/_images/example_cone_0.gif b/_images/example_cone_0.gif
diff --git a/_images/example_depth_0.gif b/_images/example_depth_0.gif
diff --git a/_images/example_dominating_0.gif b/_images/example_dominating_0.gif
diff --git a/_images/example_double_gyre_LCS_particles_0.gif b/_images/example_double_gyre_LCS_particles_0.gif
diff --git a/_images/example_ensemble_0.gif b/_images/example_ensemble_0.gif
diff --git a/_images/example_entrainment_rate_oil_types_0.gif b/_images/example_entrainment_rate_oil_types_0.gif
diff --git a/_images/example_entrainment_rate_oil_types_1.gif b/_images/example_entrainment_rate_oil_types_1.gif
diff --git a/_images/example_huge_output_0.gif b/_images/example_huge_output_0.gif
diff --git a/_images/example_huge_output_1.gif b/_images/example_huge_output_1.gif
diff --git a/_images/example_macondo_0.gif b/_images/example_macondo_0.gif
diff --git a/_images/example_mixed_layer_depth_0.gif b/_images/example_mixed_layer_depth_0.gif
diff --git a/_images/example_mixed_layer_depth_1.gif b/_images/example_mixed_layer_depth_1.gif
diff --git a/_images/example_mixed_layer_depth_2.gif b/_images/example_mixed_layer_depth_2.gif
diff --git a/_images/example_multi_seed_0.gif b/_images/example_multi_seed_0.gif
diff --git a/_images/example_oil_budget_0.gif b/_images/example_oil_budget_0.gif
diff --git a/_images/example_oil_budget_noaa_0.gif b/_images/example_oil_budget_noaa_0.gif
diff --git a/_images/example_oil_ice_0.gif b/_images/example_oil_ice_0.gif
diff --git a/_images/example_oil_thickness_0.gif b/_images/example_oil_thickness_0.gif
diff --git a/_images/example_oil_thickness_1.gif b/_images/example_oil_thickness_1.gif
diff --git a/_images/example_oil_verticalmixing_0.gif b/_images/example_oil_verticalmixing_0.gif
diff --git a/_images/example_oil_verticalmixing_1.gif b/_images/example_oil_verticalmixing_1.gif
diff --git a/_images/example_oilspill_seafloor_biodegradation_0.gif b/_images/example_oilspill_seafloor_biodegradation_0.gif
diff --git a/_images/example_oilspill_seafloor_biodegradation_1.gif b/_images/example_oilspill_seafloor_biodegradation_1.gif
diff --git a/_images/example_openoil_0.gif b/_images/example_openoil_0.gif
diff --git a/_images/example_plast_0.gif b/_images/example_plast_0.gif
diff --git a/_images/example_plot_0.gif b/_images/example_plot_0.gif
diff --git a/_images/example_radionuclides_0.gif b/_images/example_radionuclides_0.gif
diff --git a/_images/example_radionuclides_1.gif b/_images/example_radionuclides_1.gif
diff --git a/_images/example_river_runoff_0.gif b/_images/example_river_runoff_0.gif
diff --git a/_images/example_sediments_0.gif b/_images/example_sediments_0.gif
diff --git a/_images/example_sediments_resuspension_0.gif b/_images/example_sediments_resuspension_0.gif
diff --git a/_images/example_seed_from_shapefile_0.gif b/_images/example_seed_from_shapefile_0.gif
diff --git a/_images/example_shipdrift_0.gif b/_images/example_shipdrift_0.gif
diff --git a/_images/example_shipdrift_leeway_0.gif b/_images/example_shipdrift_leeway_0.gif
diff --git a/_images/example_static_2d_current_0.gif b/_images/example_static_2d_current_0.gif
diff --git a/_images/sphx_glr_example_2d_001.png b/_images/sphx_glr_example_2d_001.png
diff --git a/_images/sphx_glr_example_2d_thumb.png b/_images/sphx_glr_example_2d_thumb.png
diff --git a/_images/sphx_glr_example_LCS_norkyst_001.png b/_images/sphx_glr_example_LCS_norkyst_001.png
diff --git a/_images/sphx_glr_example_LCS_norkyst_thumb.png b/_images/sphx_glr_example_LCS_norkyst_thumb.png
diff --git a/_images/sphx_glr_example_advection_schemes_eddy_001.png b/_images/sphx_glr_example_advection_schemes_eddy_001.png
diff --git a/_images/sphx_glr_example_advection_schemes_eddy_thumb.png b/_images/sphx_glr_example_advection_schemes_eddy_thumb.png
diff --git a/_images/sphx_glr_example_biodegradation_001.png b/_images/sphx_glr_example_biodegradation_001.png
diff --git a/_images/sphx_glr_example_biodegradation_thumb.png b/_images/sphx_glr_example_biodegradation_thumb.png
diff --git a/_images/sphx_glr_example_chemicaldrift_001.png b/_images/sphx_glr_example_chemicaldrift_001.png
diff --git a/_images/sphx_glr_example_chemicaldrift_thumb.png b/_images/sphx_glr_example_chemicaldrift_thumb.png
diff --git a/_images/sphx_glr_example_coastline_options_001.png b/_images/sphx_glr_example_coastline_options_001.png
diff --git a/_images/sphx_glr_example_coastline_options_thumb.png b/_images/sphx_glr_example_coastline_options_thumb.png
diff --git a/_images/sphx_glr_example_codegg_001.png b/_images/sphx_glr_example_codegg_001.png
diff --git a/_images/sphx_glr_example_codegg_thumb.png b/_images/sphx_glr_example_codegg_thumb.png
diff --git a/_images/sphx_glr_example_cone_001.png b/_images/sphx_glr_example_cone_001.png
diff --git a/_images/sphx_glr_example_cone_thumb.png b/_images/sphx_glr_example_cone_thumb.png
diff --git a/_images/sphx_glr_example_depth_001.png b/_images/sphx_glr_example_depth_001.png
diff --git a/_images/sphx_glr_example_depth_thumb.png b/_images/sphx_glr_example_depth_thumb.png
diff --git a/_images/sphx_glr_example_double_gyre_LCS_001.png b/_images/sphx_glr_example_double_gyre_LCS_001.png
diff --git a/_images/sphx_glr_example_double_gyre_LCS_thumb.png b/_images/sphx_glr_example_double_gyre_LCS_thumb.png
diff --git a/_images/sphx_glr_example_ensemble_001.png b/_images/sphx_glr_example_ensemble_001.png
diff --git a/_images/sphx_glr_example_ensemble_thumb.png b/_images/sphx_glr_example_ensemble_thumb.png
diff --git a/_images/sphx_glr_example_entrainment_rate_oil_types_001.png b/_images/sphx_glr_example_entrainment_rate_oil_types_001.png
diff --git a/_images/sphx_glr_example_entrainment_rate_oil_types_002.png b/_images/sphx_glr_example_entrainment_rate_oil_types_002.png
diff --git a/_images/sphx_glr_example_entrainment_rate_oil_types_thumb.png b/_images/sphx_glr_example_entrainment_rate_oil_types_thumb.png
diff --git a/_images/sphx_glr_example_huge_output_001.png b/_images/sphx_glr_example_huge_output_001.png
diff --git a/_images/sphx_glr_example_huge_output_thumb.png b/_images/sphx_glr_example_huge_output_thumb.png
diff --git a/_images/sphx_glr_example_macondo_002.png b/_images/sphx_glr_example_macondo_002.png
diff --git a/_images/sphx_glr_example_multi_seed_001.png b/_images/sphx_glr_example_multi_seed_001.png
diff --git a/_images/sphx_glr_example_multi_seed_thumb.png b/_images/sphx_glr_example_multi_seed_thumb.png
diff --git a/_images/sphx_glr_example_oil_budget_001.png b/_images/sphx_glr_example_oil_budget_001.png
diff --git a/_images/sphx_glr_example_oil_budget_noaa_001.png b/_images/sphx_glr_example_oil_budget_noaa_001.png
diff --git a/_images/sphx_glr_example_oil_budget_noaa_002.png b/_images/sphx_glr_example_oil_budget_noaa_002.png
diff --git a/_images/sphx_glr_example_oil_budget_noaa_003.png b/_images/sphx_glr_example_oil_budget_noaa_003.png
diff --git a/_images/sphx_glr_example_oil_budget_noaa_005.png b/_images/sphx_glr_example_oil_budget_noaa_005.png
diff --git a/_images/sphx_glr_example_oil_budget_noaa_006.png b/_images/sphx_glr_example_oil_budget_noaa_006.png
diff --git a/_images/sphx_glr_example_oil_budget_noaa_007.png b/_images/sphx_glr_example_oil_budget_noaa_007.png
diff --git a/_images/sphx_glr_example_oil_budget_noaa_008.png b/_images/sphx_glr_example_oil_budget_noaa_008.png
diff --git a/_images/sphx_glr_example_oil_budget_noaa_thumb.png b/_images/sphx_glr_example_oil_budget_noaa_thumb.png
diff --git a/_images/sphx_glr_example_oil_budget_thumb.png b/_images/sphx_glr_example_oil_budget_thumb.png
diff --git a/_images/sphx_glr_example_oil_ice_001.png b/_images/sphx_glr_example_oil_ice_001.png
diff --git a/_images/sphx_glr_example_oil_ice_thumb.png b/_images/sphx_glr_example_oil_ice_thumb.png
diff --git a/_images/sphx_glr_example_oil_thickness_001.png b/_images/sphx_glr_example_oil_thickness_001.png
diff --git a/_images/sphx_glr_example_oil_thickness_002.png b/_images/sphx_glr_example_oil_thickness_002.png
diff --git a/_images/sphx_glr_example_oil_thickness_thumb.png b/_images/sphx_glr_example_oil_thickness_thumb.png
diff --git a/_images/sphx_glr_example_oil_verticalmixing_001.png b/_images/sphx_glr_example_oil_verticalmixing_001.png
diff --git a/_images/sphx_glr_example_oil_verticalmixing_002.png b/_images/sphx_glr_example_oil_verticalmixing_002.png
diff --git a/_images/sphx_glr_example_oil_verticalmixing_003.png b/_images/sphx_glr_example_oil_verticalmixing_003.png
diff --git a/_images/sphx_glr_example_oil_verticalmixing_thumb.png b/_images/sphx_glr_example_oil_verticalmixing_thumb.png
diff --git a/_images/sphx_glr_example_oilspill_seafloor_biodegradation_001.png b/_images/sphx_glr_example_oilspill_seafloor_biodegradation_001.png
diff --git a/_images/sphx_glr_example_oilspill_seafloor_biodegradation_002.png b/_images/sphx_glr_example_oilspill_seafloor_biodegradation_002.png
diff --git a/_images/sphx_glr_example_oilspill_seafloor_biodegradation_thumb.png b/_images/sphx_glr_example_oilspill_seafloor_biodegradation_thumb.png
diff --git a/_images/sphx_glr_example_openberg_new_001.png b/_images/sphx_glr_example_openberg_new_001.png
diff --git a/_images/sphx_glr_example_openberg_new_thumb.png b/_images/sphx_glr_example_openberg_new_thumb.png
diff --git a/_images/sphx_glr_example_openoil_001.png b/_images/sphx_glr_example_openoil_001.png
diff --git a/_images/sphx_glr_example_openoil_002.png b/_images/sphx_glr_example_openoil_002.png
diff --git a/_images/sphx_glr_example_openoil_003.png b/_images/sphx_glr_example_openoil_003.png
diff --git a/_images/sphx_glr_example_openoil_005.png b/_images/sphx_glr_example_openoil_005.png
diff --git a/_images/sphx_glr_example_openoil_thumb.png b/_images/sphx_glr_example_openoil_thumb.png
diff --git a/_images/sphx_glr_example_radionuclides_001.png b/_images/sphx_glr_example_radionuclides_001.png
diff --git a/_images/sphx_glr_example_radionuclides_002.png b/_images/sphx_glr_example_radionuclides_002.png
diff --git a/_images/sphx_glr_example_radionuclides_thumb.png b/_images/sphx_glr_example_radionuclides_thumb.png
diff --git a/_images/sphx_glr_example_river_runoff_001.png b/_images/sphx_glr_example_river_runoff_001.png
diff --git a/_images/sphx_glr_example_river_runoff_002.png b/_images/sphx_glr_example_river_runoff_002.png
diff --git a/_images/sphx_glr_example_river_runoff_thumb.png b/_images/sphx_glr_example_river_runoff_thumb.png
diff --git a/_images/sphx_glr_example_satellite_001.png b/_images/sphx_glr_example_satellite_001.png
diff --git a/_images/sphx_glr_example_satellite_thumb.png b/_images/sphx_glr_example_satellite_thumb.png
diff --git a/_images/sphx_glr_example_sediments_001.png b/_images/sphx_glr_example_sediments_001.png
diff --git a/_images/sphx_glr_example_sediments_resuspension_001.png b/_images/sphx_glr_example_sediments_resuspension_001.png
diff --git a/_images/sphx_glr_example_sediments_resuspension_thumb.png b/_images/sphx_glr_example_sediments_resuspension_thumb.png
diff --git a/_images/sphx_glr_example_sediments_thumb.png b/_images/sphx_glr_example_sediments_thumb.png
diff --git a/_images/sphx_glr_example_seed_from_shapefile_001.png b/_images/sphx_glr_example_seed_from_shapefile_001.png
diff --git a/_images/sphx_glr_example_seed_from_shapefile_thumb.png b/_images/sphx_glr_example_seed_from_shapefile_thumb.png
diff --git a/_images/sphx_glr_example_shipdrift_001.png b/_images/sphx_glr_example_shipdrift_001.png
diff --git a/_images/sphx_glr_example_shipdrift_leeway_001.png b/_images/sphx_glr_example_shipdrift_leeway_001.png
diff --git a/_images/sphx_glr_example_shipdrift_leeway_thumb.png b/_images/sphx_glr_example_shipdrift_leeway_thumb.png
diff --git a/_images/sphx_glr_example_shipdrift_thumb.png b/_images/sphx_glr_example_shipdrift_thumb.png
diff --git a/_modules/opendrift/export/io_netcdf.html b/_modules/opendrift/export/io_netcdf.html
@@ -175,7 +175,11 @@ <h1>Source code for opendrift.export.io_netcdf</h1><div class="highlight"><pre>
             <span class="n">dtype</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">history</span><span class="o">.</span><span class="n">dtype</span><span class="p">[</span><span class="n">prop</span><span class="p">]</span>
         <span class="k">except</span><span class="p">:</span>
             <span class="n">dtype</span> <span class="o">=</span> <span class="s1">&#39;f4&#39;</span>
-        <span class="n">var</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">outfile</span><span class="o">.</span><span class="n">createVariable</span><span class="p">(</span><span class="n">prop</span><span class="p">,</span> <span class="n">dtype</span><span class="p">,</span> <span class="p">(</span><span class="s1">&#39;trajectory&#39;</span><span class="p">,</span> <span class="s1">&#39;time&#39;</span><span class="p">))</span>
+        <span class="k">if</span> <span class="n">np</span><span class="o">.</span><span class="n">issubdtype</span><span class="p">(</span><span class="n">dtype</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">integer</span><span class="p">):</span>
+            <span class="n">fill</span><span class="o">=-</span><span class="mi">999</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="n">fill</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">nan</span>
+        <span class="n">var</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">outfile</span><span class="o">.</span><span class="n">createVariable</span><span class="p">(</span><span class="n">prop</span><span class="p">,</span> <span class="n">dtype</span><span class="p">,</span> <span class="p">(</span><span class="s1">&#39;trajectory&#39;</span><span class="p">,</span> <span class="s1">&#39;time&#39;</span><span class="p">),</span> <span class="n">fill_value</span><span class="o">=</span><span class="n">fill</span><span class="p">)</span>
         <span class="k">for</span> <span class="n">subprop</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">history_metadata</span><span class="p">[</span><span class="n">prop</span><span class="p">]</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
             <span class="k">if</span> <span class="n">subprop</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">[</span><span class="s1">&#39;dtype&#39;</span><span class="p">,</span> <span class="s1">&#39;constant&#39;</span><span class="p">,</span> <span class="s1">&#39;default&#39;</span><span class="p">,</span> <span class="s1">&#39;seed&#39;</span><span class="p">]:</span>
                 <span class="c1"># Apparently axis attribute shall not be given for lon and lat:</span>
@@ -291,8 +295,12 @@ <h1>Source code for opendrift.export.io_netcdf</h1><div class="highlight"><pre>
                     <span class="n">dst</span><span class="o">.</span><span class="n">createDimension</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">dimension</span><span class="p">))</span>
 
             <span class="k">for</span> <span class="n">name</span><span class="p">,</span> <span class="n">variable</span> <span class="ow">in</span> <span class="n">src</span><span class="o">.</span><span class="n">variables</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
+                <span class="k">if</span> <span class="s1">&#39;_FillValue&#39;</span> <span class="ow">in</span> <span class="n">variable</span><span class="o">.</span><span class="n">ncattrs</span><span class="p">():</span>
+                    <span class="n">fill</span> <span class="o">=</span> <span class="n">variable</span><span class="o">.</span><span class="n">getncattr</span><span class="p">(</span><span class="s1">&#39;_FillValue&#39;</span><span class="p">)</span>
+                <span class="k">else</span><span class="p">:</span>
+                    <span class="n">fill</span> <span class="o">=</span> <span class="kc">None</span>
                 <span class="n">dstVar</span> <span class="o">=</span> <span class="n">dst</span><span class="o">.</span><span class="n">createVariable</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">variable</span><span class="o">.</span><span class="n">datatype</span><span class="p">,</span>
-                                             <span class="n">variable</span><span class="o">.</span><span class="n">dimensions</span><span class="p">)</span>
+                                             <span class="n">variable</span><span class="o">.</span><span class="n">dimensions</span><span class="p">,</span> <span class="n">fill_value</span><span class="o">=</span><span class="n">fill</span><span class="p">)</span>
                 <span class="n">srcVar</span> <span class="o">=</span> <span class="n">src</span><span class="o">.</span><span class="n">variables</span><span class="p">[</span><span class="n">name</span><span class="p">]</span>
                 <span class="c1"># Truncate data to number actually seeded</span>
                 <span class="k">if</span> <span class="s1">&#39;trajectory&#39;</span> <span class="ow">in</span> <span class="n">variable</span><span class="o">.</span><span class="n">dimensions</span><span class="p">:</span>
@@ -307,6 +315,8 @@ <h1>Source code for opendrift.export.io_netcdf</h1><div class="highlight"><pre>
                     <span class="n">dstVar</span><span class="p">[:]</span> <span class="o">=</span> <span class="n">srcVar</span><span class="p">[:]</span>
                 <span class="k">for</span> <span class="n">att</span> <span class="ow">in</span> <span class="n">src</span><span class="o">.</span><span class="n">variables</span><span class="p">[</span><span class="n">name</span><span class="p">]</span><span class="o">.</span><span class="n">ncattrs</span><span class="p">():</span>
                     <span class="c1"># Copy variable attributes</span>
+                    <span class="k">if</span> <span class="n">att</span> <span class="ow">in</span> <span class="p">[</span><span class="s1">&#39;_FillValue&#39;</span><span class="p">]:</span>
+                        <span class="k">continue</span>
                     <span class="n">dstVar</span><span class="o">.</span><span class="n">setncattr</span><span class="p">(</span><span class="n">att</span><span class="p">,</span> <span class="n">srcVar</span><span class="o">.</span><span class="n">getncattr</span><span class="p">(</span><span class="n">att</span><span class="p">))</span>
 
             <span class="k">for</span> <span class="n">att</span> <span class="ow">in</span> <span class="n">src</span><span class="o">.</span><span class="n">ncattrs</span><span class="p">():</span>  <span class="c1"># Copy global attributes</span>