Revert "remove duplicated docs inside repo."

This reverts commit fceb3ef.

.gitignore

@@ -5,7 +5,6 @@ egg-info
 *checkpoint*
 *.h5
 *.nc
-*.pickle
 git_push.sh
 build/
 documentation_source/build/

docs/_downloads/126324517196134368a58612b6143418/plot_csv_skytem_to_netcdf.ipynb

@@ -40,7 +40,7 @@
       },
       "outputs": [],
       "source": [
-        "# Path to example files\ndata_path = '..//..//supplemental//region//WI'\n\n# Survey metadata file\nmetadata = join(data_path, \"data//WI_SkyTEM_survey_md.yml\")\n\n# Establish the Survey\nsurvey = Survey(metadata)"
+        "# Path to example files\ndata_path = '..//..//supplemental//region//WI'\n\n# Survey metadata file\nmetadata = join(data_path, \"data//WI_SkyTEM_survey_md.json\")\n\n# Establish the Survey\nsurvey = Survey(metadata)"
       ]
     },
     {

docs/_downloads/f3e493e44e38f967de3a7f8f6377576b/plot_csv_skytem_to_netcdf.py

@@ -32,7 +32,7 @@
 data_path = '..//..//supplemental//region//WI'
 
 # Survey metadata file
-metadata = join(data_path, "data//WI_SkyTEM_survey_md.yml")
+metadata = join(data_path, "data//WI_SkyTEM_survey_md.json")
 
 # Establish the Survey
 survey = Survey(metadata)

docs/_sources/examples/Creating_GS_Files/plot_aseg_tempest_to_netcdf.rst.txt

@@ -95,13 +95,6 @@ Define input data file and associated metadata file
 
 
 
-.. rst-class:: sphx-glr-script-out
-
- .. code-block:: none
-
-    /Users/nfoks/codes/repositories/gspy/gspy_secondary/gspy/src/utilities/aseg_gdf_handler.py:144: SyntaxWarning: invalid escape sequence '\s'
-      self._df = read_csv(self.data_file_name, names=self.columns, dtype=self.numpy_formats, index_col=False, sep='\s+')
-
 
 
 
@@ -237,7 +230,7 @@ Plotting
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 14.141 seconds)
+   **Total running time of the script:** (0 minutes 3.511 seconds)
 
 
 .. _sphx_glr_download_examples_Creating_GS_Files_plot_aseg_tempest_to_netcdf.py:

docs/_sources/examples/Creating_GS_Files/plot_csv_resolve_to_netcdf.rst.txt

@@ -227,7 +227,7 @@ Plotting
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 1.437 seconds)
+   **Total running time of the script:** (0 minutes 1.497 seconds)
 
 
 .. _sphx_glr_download_examples_Creating_GS_Files_plot_csv_resolve_to_netcdf.py:

docs/_sources/examples/Creating_GS_Files/plot_csv_skytem_to_netcdf.rst.txt

@@ -68,7 +68,7 @@ Initialize the Survey
     data_path = '..//..//supplemental//region//WI'
 
     # Survey metadata file
-    metadata = join(data_path, "data//WI_SkyTEM_survey_md.yml")
+    metadata = join(data_path, "data//WI_SkyTEM_survey_md.json")
 
     # Establish the Survey
     survey = Survey(metadata)
@@ -274,7 +274,7 @@ Plotting
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 2.890 seconds)
+   **Total running time of the script:** (0 minutes 2.983 seconds)
 
 
 .. _sphx_glr_download_examples_Creating_GS_Files_plot_csv_skytem_to_netcdf.py:

docs/_sources/examples/Creating_GS_Files/plot_tifs_to_netcdf.rst.txt

@@ -232,7 +232,7 @@ Plotting
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 2.026 seconds)
+   **Total running time of the script:** (0 minutes 1.652 seconds)
 
 
 .. _sphx_glr_download_examples_Creating_GS_Files_plot_tifs_to_netcdf.py:

docs/_sources/examples/Creating_GS_Files/sg_execution_times.rst.txt

@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**00:20.493** total execution time for 5 files **from examples/Creating_GS_Files**:
+**00:09.642** total execution time for 5 files **from examples/Creating_GS_Files**:
 
 .. container::
 
@@ -33,16 +33,16 @@ Computation times
      - Time
      - Mem (MB)
    * - :ref:`sphx_glr_examples_Creating_GS_Files_plot_aseg_tempest_to_netcdf.py` (``plot_aseg_tempest_to_netcdf.py``)
-     - 00:14.141
+     - 00:03.511
      - 0.0
    * - :ref:`sphx_glr_examples_Creating_GS_Files_plot_csv_skytem_to_netcdf.py` (``plot_csv_skytem_to_netcdf.py``)
-     - 00:02.890
+     - 00:02.983
      - 0.0
    * - :ref:`sphx_glr_examples_Creating_GS_Files_plot_tifs_to_netcdf.py` (``plot_tifs_to_netcdf.py``)
-     - 00:02.026
+     - 00:01.652
      - 0.0
    * - :ref:`sphx_glr_examples_Creating_GS_Files_plot_csv_resolve_to_netcdf.py` (``plot_csv_resolve_to_netcdf.py``)
-     - 00:01.437
+     - 00:01.497
      - 0.0
    * - :ref:`sphx_glr_examples_Creating_GS_Files_help_I_have_no_variable_metadata.py` (``help_I_have_no_variable_metadata.py``)
      - 00:00.000

docs/_sources/examples/Interacting_With_GS_Files/plot_coordinate_reference_systems.rst.txt

@@ -294,7 +294,7 @@ changed to longitude and latitude.
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 0.447 seconds)
+   **Total running time of the script:** (0 minutes 0.469 seconds)
 
 
 .. _sphx_glr_download_examples_Interacting_With_GS_Files_plot_coordinate_reference_systems.py:

docs/_sources/examples/Interacting_With_GS_Files/plot_xarray_methods.rst.txt

@@ -709,7 +709,7 @@ of that individual variable. These follow the `Climate and Forecast (CF) metadat
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 1.199 seconds)
+   **Total running time of the script:** (0 minutes 1.320 seconds)
 
 
 .. _sphx_glr_download_examples_Interacting_With_GS_Files_plot_xarray_methods.py:

docs/_sources/examples/Interacting_With_GS_Files/sg_execution_times.rst.txt

@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**00:01.646** total execution time for 2 files **from examples/Interacting_With_GS_Files**:
+**00:01.789** total execution time for 2 files **from examples/Interacting_With_GS_Files**:
 
 .. container::
 
@@ -33,8 +33,8 @@ Computation times
      - Time
      - Mem (MB)
    * - :ref:`sphx_glr_examples_Interacting_With_GS_Files_plot_xarray_methods.py` (``plot_xarray_methods.py``)
-     - 00:01.199
+     - 00:01.320
      - 0.0
    * - :ref:`sphx_glr_examples_Interacting_With_GS_Files_plot_coordinate_reference_systems.py` (``plot_coordinate_reference_systems.py``)
-     - 00:00.447
+     - 00:00.469
      - 0.0

docs/_sources/sg_execution_times.rst.txt

@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**00:22.138** total execution time for 7 files **from all galleries**:
+**00:11.431** total execution time for 7 files **from all galleries**:
 
 .. container::
 
@@ -33,22 +33,22 @@ Computation times
      - Time
      - Mem (MB)
    * - :ref:`sphx_glr_examples_Creating_GS_Files_plot_aseg_tempest_to_netcdf.py` (``examples/Creating_GS_Files/plot_aseg_tempest_to_netcdf.py``)
-     - 00:14.141
+     - 00:03.511
      - 0.0
    * - :ref:`sphx_glr_examples_Creating_GS_Files_plot_csv_skytem_to_netcdf.py` (``examples/Creating_GS_Files/plot_csv_skytem_to_netcdf.py``)
-     - 00:02.890
+     - 00:02.983
      - 0.0
    * - :ref:`sphx_glr_examples_Creating_GS_Files_plot_tifs_to_netcdf.py` (``examples/Creating_GS_Files/plot_tifs_to_netcdf.py``)
-     - 00:02.026
+     - 00:01.652
      - 0.0
    * - :ref:`sphx_glr_examples_Creating_GS_Files_plot_csv_resolve_to_netcdf.py` (``examples/Creating_GS_Files/plot_csv_resolve_to_netcdf.py``)
-     - 00:01.437
+     - 00:01.497
      - 0.0
    * - :ref:`sphx_glr_examples_Interacting_With_GS_Files_plot_xarray_methods.py` (``examples/Interacting_With_GS_Files/plot_xarray_methods.py``)
-     - 00:01.199
+     - 00:01.320
      - 0.0
    * - :ref:`sphx_glr_examples_Interacting_With_GS_Files_plot_coordinate_reference_systems.py` (``examples/Interacting_With_GS_Files/plot_coordinate_reference_systems.py``)
-     - 00:00.447
+     - 00:00.469
      - 0.0
    * - :ref:`sphx_glr_examples_Creating_GS_Files_help_I_have_no_variable_metadata.py` (``examples/Creating_GS_Files/help_I_have_no_variable_metadata.py``)
      - 00:00.000

docs/content/api/classes/data/tabular_aseg.html

@@ -195,6 +195,17 @@ <h1>Tabular_aseg<a class="headerlink" href="#tabular-aseg" title="Link to this h
 </dl>
 </dd></dl>
 
+<dl class="py method">
+<dt class="sig sig-object py" id="gspy.src.classes.data.tabular_aseg.Tabular_aseg.write">
+<span class="sig-name descname"><span class="pre">write</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">default_f32</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'f10.3'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">default_f64</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'g12.6'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#gspy.src.classes.data.tabular_aseg.Tabular_aseg.write" title="Link to this definition"></a></dt>
+<dd><p>Export tabular data to an ASEG formatted data file</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>filename</strong> (<em>str</em>) – Path to output aseg file</p>
+</dd>
+</dl>
+</dd></dl>
+
 <dl class="py method">
 <dt class="sig sig-object py" id="gspy.src.classes.data.tabular_aseg.Tabular_aseg.write_aseg_dfn_file">
 <span class="sig-name descname"><span class="pre">write_aseg_dfn_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">default_f32</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'f10.3'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">default_f64</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'g12.6'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#gspy.src.classes.data.tabular_aseg.Tabular_aseg.write_aseg_dfn_file" title="Link to this definition"></a></dt>

docs/examples/Creating_GS_Files/plot_aseg_tempest_to_netcdf.html

@@ -141,10 +141,6 @@ <h2>Convert the ASEG data to NetCDF<a class="headerlink" href="#convert-the-aseg
 <span class="n">survey</span><span class="o">.</span><span class="n">add_tabular</span><span class="p">(</span><span class="nb">type</span><span class="o">=</span><span class="s1">&#39;aseg&#39;</span><span class="p">,</span> <span class="n">data_filename</span><span class="o">=</span><span class="n">d_data</span><span class="p">,</span> <span class="n">metadata_file</span><span class="o">=</span><span class="n">d_supp</span><span class="p">)</span>
 </pre></div>
 </div>
-<div class="sphx-glr-script-out highlight-none notranslate"><div class="highlight"><pre><span></span>/Users/nfoks/codes/repositories/gspy/gspy_secondary/gspy/src/utilities/aseg_gdf_handler.py:144: SyntaxWarning: invalid escape sequence &#39;\s&#39;
-  self._df = read_csv(self.data_file_name, names=self.columns, dtype=self.numpy_formats, index_col=False, sep=&#39;\s+&#39;)
-</pre></div>
-</div>
 <p>2. Inverted Models -
 Import inverted AEM models from ASEG-format.
 Define input data file and associated metadata file</p>
@@ -206,7 +202,7 @@ <h2>Convert the ASEG data to NetCDF<a class="headerlink" href="#convert-the-aseg
 <li><img src="../../_images/sphx_glr_plot_aseg_tempest_to_netcdf_001.png" srcset="../../_images/sphx_glr_plot_aseg_tempest_to_netcdf_001.png" alt="plot aseg tempest to netcdf" class = "sphx-glr-multi-img"/></li>
 <li><img src="../../_images/sphx_glr_plot_aseg_tempest_to_netcdf_002.png" srcset="../../_images/sphx_glr_plot_aseg_tempest_to_netcdf_002.png" alt="spatial_ref = 0.0" class = "sphx-glr-multi-img"/></li>
 </ul>
-<p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (0 minutes 14.141 seconds)</p>
+<p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (0 minutes 3.511 seconds)</p>
 <div class="sphx-glr-footer sphx-glr-footer-example docutils container" id="sphx-glr-download-examples-creating-gs-files-plot-aseg-tempest-to-netcdf-py">
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 <p><a class="reference download internal" download="" href="../../_downloads/5d748e1ff1eae67bd06af2fe99354ec8/plot_aseg_tempest_to_netcdf.ipynb"><code class="xref download docutils literal notranslate"><span class="pre">Download</span> <span class="pre">Jupyter</span> <span class="pre">notebook:</span> <span class="pre">plot_aseg_tempest_to_netcdf.ipynb</span></code></a></p>

docs/examples/Creating_GS_Files/plot_csv_resolve_to_netcdf.html

@@ -207,7 +207,7 @@ <h2>Convert the resolve csv data to NetCDF<a class="headerlink" href="#convert-t
 <span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
 </pre></div>
 </div>
-<img src="../../_images/sphx_glr_plot_csv_resolve_to_netcdf_001.png" srcset="../../_images/sphx_glr_plot_csv_resolve_to_netcdf_001.png" alt="plot csv resolve to netcdf" class = "sphx-glr-single-img"/><p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (0 minutes 1.437 seconds)</p>
+<img src="../../_images/sphx_glr_plot_csv_resolve_to_netcdf_001.png" srcset="../../_images/sphx_glr_plot_csv_resolve_to_netcdf_001.png" alt="plot csv resolve to netcdf" class = "sphx-glr-single-img"/><p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (0 minutes 1.497 seconds)</p>
 <div class="sphx-glr-footer sphx-glr-footer-example docutils container" id="sphx-glr-download-examples-creating-gs-files-plot-csv-resolve-to-netcdf-py">
 <div class="sphx-glr-download sphx-glr-download-jupyter docutils container">
 <p><a class="reference download internal" download="" href="../../_downloads/8c74c090dc8f02c5545f332bf2007ead/plot_csv_resolve_to_netcdf.ipynb"><code class="xref download docutils literal notranslate"><span class="pre">Download</span> <span class="pre">Jupyter</span> <span class="pre">notebook:</span> <span class="pre">plot_csv_resolve_to_netcdf.ipynb</span></code></a></p>

docs/examples/Creating_GS_Files/plot_csv_skytem_to_netcdf.html

@@ -129,7 +129,7 @@ <h2>Convert the Skytem csv data to NetCDF<a class="headerlink" href="#convert-th
 <span class="n">data_path</span> <span class="o">=</span> <span class="s1">&#39;..//..//supplemental//region//WI&#39;</span>
 
 <span class="c1"># Survey metadata file</span>
-<span class="n">metadata</span> <span class="o">=</span> <span class="n">join</span><span class="p">(</span><span class="n">data_path</span><span class="p">,</span> <span class="s2">&quot;data//WI_SkyTEM_survey_md.yml&quot;</span><span class="p">)</span>
+<span class="n">metadata</span> <span class="o">=</span> <span class="n">join</span><span class="p">(</span><span class="n">data_path</span><span class="p">,</span> <span class="s2">&quot;data//WI_SkyTEM_survey_md.json&quot;</span><span class="p">)</span>
 
 <span class="c1"># Establish the Survey</span>
 <span class="n">survey</span> <span class="o">=</span> <span class="n">Survey</span><span class="p">(</span><span class="n">metadata</span><span class="p">)</span>
@@ -213,7 +213,7 @@ <h2>Convert the Skytem csv data to NetCDF<a class="headerlink" href="#convert-th
 <span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
 </pre></div>
 </div>
-<img src="../../_images/sphx_glr_plot_csv_skytem_to_netcdf_001.png" srcset="../../_images/sphx_glr_plot_csv_skytem_to_netcdf_001.png" alt="spatial_ref = 0.0" class = "sphx-glr-single-img"/><p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (0 minutes 2.890 seconds)</p>
+<img src="../../_images/sphx_glr_plot_csv_skytem_to_netcdf_001.png" srcset="../../_images/sphx_glr_plot_csv_skytem_to_netcdf_001.png" alt="spatial_ref = 0.0" class = "sphx-glr-single-img"/><p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (0 minutes 2.983 seconds)</p>
 <div class="sphx-glr-footer sphx-glr-footer-example docutils container" id="sphx-glr-download-examples-creating-gs-files-plot-csv-skytem-to-netcdf-py">
 <div class="sphx-glr-download sphx-glr-download-jupyter docutils container">
 <p><a class="reference download internal" download="" href="../../_downloads/126324517196134368a58612b6143418/plot_csv_skytem_to_netcdf.ipynb"><code class="xref download docutils literal notranslate"><span class="pre">Download</span> <span class="pre">Jupyter</span> <span class="pre">notebook:</span> <span class="pre">plot_csv_skytem_to_netcdf.ipynb</span></code></a></p>

docs/examples/Creating_GS_Files/plot_tifs_to_netcdf.html

@@ -205,7 +205,7 @@ <h2>Convert data from GeoTIFF to NetCDF<a class="headerlink" href="#convert-data
     long_name:      Total magnetic intensity, diurnally corrected and filtered
 </pre></div>
 </div>
-<p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (0 minutes 2.026 seconds)</p>
+<p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (0 minutes 1.652 seconds)</p>
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 <div class="sphx-glr-download sphx-glr-download-jupyter docutils container">
 <p><a class="reference download internal" download="" href="../../_downloads/837570887e1177f6458167c81aa9af45/plot_tifs_to_netcdf.ipynb"><code class="xref download docutils literal notranslate"><span class="pre">Download</span> <span class="pre">Jupyter</span> <span class="pre">notebook:</span> <span class="pre">plot_tifs_to_netcdf.ipynb</span></code></a></p>

docs/examples/Creating_GS_Files/sg_execution_times.html

@@ -83,7 +83,7 @@
 
   <section id="computation-times">
 <span id="sphx-glr-examples-creating-gs-files-sg-execution-times"></span><h1>Computation times<a class="headerlink" href="#computation-times" title="Link to this heading"></a></h1>
-<p><strong>00:20.493</strong> total execution time for 5 files <strong>from examples/Creating_GS_Files</strong>:</p>
+<p><strong>00:09.642</strong> total execution time for 5 files <strong>from examples/Creating_GS_Files</strong>:</p>
 <div class="docutils container">
 <style scoped>
 <link href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/5.3.0/css/bootstrap.min.css" rel="stylesheet" />
@@ -105,19 +105,19 @@
 </thead>
 <tbody>
 <tr class="row-even"><td><p><a class="reference internal" href="plot_aseg_tempest_to_netcdf.html#sphx-glr-examples-creating-gs-files-plot-aseg-tempest-to-netcdf-py"><span class="std std-ref">ASEG to NetCDF</span></a> (<code class="docutils literal notranslate"><span class="pre">plot_aseg_tempest_to_netcdf.py</span></code>)</p></td>
-<td><p>00:14.141</p></td>
+<td><p>00:03.511</p></td>
 <td><p>0.0</p></td>
 </tr>
 <tr class="row-odd"><td><p><a class="reference internal" href="plot_csv_skytem_to_netcdf.html#sphx-glr-examples-creating-gs-files-plot-csv-skytem-to-netcdf-py"><span class="std std-ref">Multi-dataset Survey</span></a> (<code class="docutils literal notranslate"><span class="pre">plot_csv_skytem_to_netcdf.py</span></code>)</p></td>
-<td><p>00:02.890</p></td>
+<td><p>00:02.983</p></td>
 <td><p>0.0</p></td>
 </tr>
 <tr class="row-even"><td><p><a class="reference internal" href="plot_tifs_to_netcdf.html#sphx-glr-examples-creating-gs-files-plot-tifs-to-netcdf-py"><span class="std std-ref">GeoTIFFs to NetCDF</span></a> (<code class="docutils literal notranslate"><span class="pre">plot_tifs_to_netcdf.py</span></code>)</p></td>
-<td><p>00:02.026</p></td>
+<td><p>00:01.652</p></td>
 <td><p>0.0</p></td>
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-<td><p>00:01.437</p></td>
+<td><p>00:01.497</p></td>
 <td><p>0.0</p></td>
 </tr>
 <tr class="row-even"><td><p><a class="reference internal" href="help_I_have_no_variable_metadata.html#sphx-glr-examples-creating-gs-files-help-i-have-no-variable-metadata-py"><span class="std std-ref">Help! I have no variable metadata</span></a> (<code class="docutils literal notranslate"><span class="pre">help_I_have_no_variable_metadata.py</span></code>)</p></td>

docs/examples/Interacting_With_GS_Files/plot_coordinate_reference_systems.html

@@ -245,7 +245,7 @@ <h2>Making a new Spatial Ref<a class="headerlink" href="#making-a-new-spatial-re
 projected coordinate system with easting and northing coordinates to a geographic
 coordinate system, then the <code class="docutils literal notranslate"><span class="pre">x</span></code> and <code class="docutils literal notranslate"><span class="pre">y</span></code> coordinate variables need to be
 changed to longitude and latitude.</p>
-<p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (0 minutes 0.447 seconds)</p>
+<p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (0 minutes 0.469 seconds)</p>
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