Update documentation

_sources/docfiles/markdown/QUICKSTART.md.txt

@@ -22,9 +22,6 @@ In order to run FarmVibes.AI cluster, you need the following:
     the repository. If you already have access to the source code, then Git is
     not required.
 
-  * [Git LFS](https://git-lfs.com/) to restore some of the large files in the
-    repository (e.g., model weights).
-
   * [Docker](https://docs.docker.com/engine/install/ubuntu/). Make sure you can
     run the docker client without running `sudo` by adding your user account to
     the `docker` group (which might require a logout/login when adding oneself
@@ -63,20 +60,6 @@ bash ./resources/vm/setup_farmvibes_ai_vm.sh
 
 You might needed to restart your shell session once the script finishes.
 
-## Restore files with Git LFS
-
-In case you did not have Git LFS installed when cloning the repository, you will need to do so
-to restore the large files in the repository. Note that the last step
-["Installing software dependencies](#optional-installing-software-dependencies) already installs
-Git LFS.
-
-To restore the missing files, you can run the following command in the root of the repository:
-
-```shell
-git lfs install
-git lfs pull
-```
-
 ## Install the FarmVibes.AI cluster
 
 With python3.8+ and pip installed on your machine, please install

_sources/docfiles/markdown/TROUBLESHOOTING.md.txt

@@ -122,15 +122,6 @@ that are currently being addressed by the development team.
 
     </details>
 
-    <details>
-    <summary> Updating cluster in the `dev` branch after pulling files with Git LFS </summary>
-
-    If you did not have Git LFS installed when cloning the repository and checking out to `dev`,
-    you will be missing some of the large files in the repository (e.g., ONNX models). Make sure
-    to install and setup Git LFS as described in the [Quickstart guide](QUICKSTART.md#restore-files-with-git-lfs).
-    You will also need to update your cluster with `make local`.
-    </details>
-
 <br>
 
 - **Composing and running workflows:**

docfiles/code/vibe_core_client/additional_modules/logconfig.html

@@ -208,7 +208,7 @@
 
 <dl class="py function">
 <dt class="sig sig-object py" id="vibe_core.logconfig.configure_logging">
-<span class="sig-prename descclassname"><span class="pre">vibe_core.logconfig.</span></span><span class="sig-name descname"><span class="pre">configure_logging</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">default_level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">logdir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_log_file_bytes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">log_backup_count</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">logfile</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'8e72b7ebc1a2.log'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">json</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">appname</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">''</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#vibe_core.logconfig.configure_logging" title="Permalink to this definition"></a></dt>
+<span class="sig-prename descclassname"><span class="pre">vibe_core.logconfig.</span></span><span class="sig-name descname"><span class="pre">configure_logging</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">default_level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">logdir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_log_file_bytes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">log_backup_count</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">logfile</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'2b1f2ea3e47e.log'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">json</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">appname</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">''</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#vibe_core.logconfig.configure_logging" title="Permalink to this definition"></a></dt>
 <dd><p>Configure logging for the calling process.</p>
 <p>This method will create a logger and set its level to the given default_level argument.
 It will also create a StreamHandler and FileHandler if the logdir argument is provided,

docfiles/code/vibe_core_data/core_types.html

@@ -69,6 +69,7 @@
 <li class="toctree-l4"><a class="reference internal" href="#vibe_core.data.core_types.AssetVibe"><code class="docutils literal notranslate"><span class="pre">AssetVibe</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="#vibe_core.data.core_types.BaseVibe"><code class="docutils literal notranslate"><span class="pre">BaseVibe</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="#vibe_core.data.core_types.CarbonOffsetInfo"><code class="docutils literal notranslate"><span class="pre">CarbonOffsetInfo</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="#vibe_core.data.core_types.ChipWindow"><code class="docutils literal notranslate"><span class="pre">ChipWindow</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="#vibe_core.data.core_types.DataSequence"><code class="docutils literal notranslate"><span class="pre">DataSequence</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="#vibe_core.data.core_types.DataSummaryStatistics"><code class="docutils literal notranslate"><span class="pre">DataSummaryStatistics</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="#vibe_core.data.core_types.DataVibe"><code class="docutils literal notranslate"><span class="pre">DataVibe</span></code></a></li>
@@ -92,7 +93,6 @@
 <li class="toctree-l4"><a class="reference internal" href="#vibe_core.data.core_types.get_filtered_init_fields"><code class="docutils literal notranslate"><span class="pre">get_filtered_init_fields()</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="#vibe_core.data.core_types.get_init_field_names"><code class="docutils literal notranslate"><span class="pre">get_init_field_names()</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="#vibe_core.data.core_types.BBox"><code class="docutils literal notranslate"><span class="pre">BBox</span></code></a></li>
-<li class="toctree-l4"><a class="reference internal" href="#vibe_core.data.core_types.ChipWindow"><code class="docutils literal notranslate"><span class="pre">ChipWindow</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="#vibe_core.data.core_types.Point"><code class="docutils literal notranslate"><span class="pre">Point</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="#vibe_core.data.core_types.TimeRange"><code class="docutils literal notranslate"><span class="pre">TimeRange</span></code></a></li>
 </ul>
@@ -352,6 +352,63 @@ <h2>Hierarchy<a class="headerlink" href="#hierarchy" title="Permalink to this he
 
 </dd></dl>
 
+<dl class="py class">
+<dt class="sig sig-object py" id="vibe_core.data.core_types.ChipWindow">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">vibe_core.data.core_types.</span></span><span class="sig-name descname"><span class="pre">ChipWindow</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">col_offset</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">row_offset</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">width</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">height</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#vibe_core.data.core_types.ChipWindow" title="Permalink to this definition"></a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></p>
+<p>Represent a window of a raster chip.</p>
+<dl class="field-list simple">
+</dl>
+<dl class="py attribute">
+<dt class="sig sig-object py" id="vibe_core.data.core_types.ChipWindow.col_offset">
+<span class="sig-name descname"><span class="pre">col_offset</span></span><a class="headerlink" href="#vibe_core.data.core_types.ChipWindow.col_offset" title="Permalink to this definition"></a></dt>
+<dd><p>The column offset of the window with relation to the raster chip.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="vibe_core.data.core_types.ChipWindow.row_offset">
+<span class="sig-name descname"><span class="pre">row_offset</span></span><a class="headerlink" href="#vibe_core.data.core_types.ChipWindow.row_offset" title="Permalink to this definition"></a></dt>
+<dd><p>The row offset of the window with relation to the raster chip.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="vibe_core.data.core_types.ChipWindow.width">
+<span class="sig-name descname"><span class="pre">width</span></span><a class="headerlink" href="#vibe_core.data.core_types.ChipWindow.width" title="Permalink to this definition"></a></dt>
+<dd><p>The width of the window.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="vibe_core.data.core_types.ChipWindow.height">
+<span class="sig-name descname"><span class="pre">height</span></span><a class="headerlink" href="#vibe_core.data.core_types.ChipWindow.height" title="Permalink to this definition"></a></dt>
+<dd><p>The height of the window.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="id0">
+<span class="sig-name descname"><span class="pre">col_offset</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></em><a class="headerlink" href="#id0" title="Permalink to this definition"></a></dt>
+<dd><p>Alias for field number 0</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="id1">
+<span class="sig-name descname"><span class="pre">height</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></em><a class="headerlink" href="#id1" title="Permalink to this definition"></a></dt>
+<dd><p>Alias for field number 3</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="id2">
+<span class="sig-name descname"><span class="pre">row_offset</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></em><a class="headerlink" href="#id2" title="Permalink to this definition"></a></dt>
+<dd><p>Alias for field number 1</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="id3">
+<span class="sig-name descname"><span class="pre">width</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></em><a class="headerlink" href="#id3" title="Permalink to this definition"></a></dt>
+<dd><p>Alias for field number 2</p>
+</dd></dl>
+
+</dd></dl>
+
 <dl class="py class">
 <dt class="sig sig-object py" id="vibe_core.data.core_types.DataSequence">
 <em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">vibe_core.data.core_types.</span></span><span class="sig-name descname"><span class="pre">DataSequence</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">id</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">time_range</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">geometry</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">assets</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">asset_order=&lt;factory&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">asset_time_range=&lt;factory&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">asset_geometry=&lt;factory&gt;</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#vibe_core.data.core_types.DataSequence" title="Permalink to this definition"></a></dt>
@@ -1223,13 +1280,6 @@ <h2>Hierarchy<a class="headerlink" href="#hierarchy" title="Permalink to this he
 <p>alias of <code class="xref py py-class docutils literal notranslate"><span class="pre">Tuple</span></code>[<code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code>, <code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code>, <code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code>, <code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code>]</p>
 </dd></dl>
 
-<dl class="py data">
-<dt class="sig sig-object py" id="vibe_core.data.core_types.ChipWindow">
-<span class="sig-prename descclassname"><span class="pre">vibe_core.data.core_types.</span></span><span class="sig-name descname"><span class="pre">ChipWindow</span></span><a class="headerlink" href="#vibe_core.data.core_types.ChipWindow" title="Permalink to this definition"></a></dt>
-<dd><p>Type alias representing a raster chip window, as (col_offset, row_offset, width, height).</p>
-<p>alias of <code class="xref py py-class docutils literal notranslate"><span class="pre">Tuple</span></code>[<code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code>, <code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code>, <code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code>, <code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code>]</p>
-</dd></dl>
-
 <dl class="py data">
 <dt class="sig sig-object py" id="vibe_core.data.core_types.Point">
 <span class="sig-prename descclassname"><span class="pre">vibe_core.data.core_types.</span></span><span class="sig-name descname"><span class="pre">Point</span></span><a class="headerlink" href="#vibe_core.data.core_types.Point" title="Permalink to this definition"></a></dt>

docfiles/code/vibe_core_data/rasters.html

@@ -416,7 +416,7 @@ <h2>Hierarchy<a class="headerlink" href="#hierarchy" title="Permalink to this he
 </dl>
 <dl class="py attribute">
 <dt class="sig sig-object py" id="vibe_core.data.rasters.SamMaskRaster.chip_window">
-<span class="sig-name descname"><span class="pre">chip_window</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><code class="xref py py-data docutils literal notranslate"><span class="pre">Tuple</span></code><span class="pre">[</span><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code><span class="pre">,</span> <code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code><span class="pre">,</span> <code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code><span class="pre">,</span> <code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code><span class="pre">]</span></em><a class="headerlink" href="#vibe_core.data.rasters.SamMaskRaster.chip_window" title="Permalink to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">chip_window</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><a class="reference internal" href="core_types.html#vibe_core.data.core_types.ChipWindow" title="vibe_core.data.core_types.ChipWindow"><code class="xref py py-class docutils literal notranslate"><span class="pre">ChipWindow</span></code></a></em><a class="headerlink" href="#vibe_core.data.rasters.SamMaskRaster.chip_window" title="Permalink to this definition"></a></dt>
 <dd><p>The chip window (col_offset, row_offset, width, height) covered by this raster.</p>
 </dd></dl>