docs: minor update

Technoculture · Jul 5, 2023 · 67fc66d · 67fc66d
1 parent 602f251
commit 67fc66d
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Showing 5 changed files with 37 additions and 20 deletions.
diff --git a/docs/api/models.html b/docs/api/models.html
@@ -2263,7 +2263,7 @@ <h3>Methods</h3>
 
   <div class="item">
     <div class="name def" id="openoligo.api.models.SynthesisQueue.clone">
-    <p>def <span class="ident">clone</span>(</p><p>self: ~MODEL, pk: Any = &lt;object object at 0x1036d3c60&gt;)</p>
+    <p>def <span class="ident">clone</span>(</p><p>self: ~MODEL, pk: Any = &lt;object object at 0x1056d3c60&gt;)</p>
     </div>
 
 

diff --git a/docs/hal/board.html b/docs/hal/board.html
@@ -1064,6 +1064,7 @@ <h1>Index</h1>
 
   <ul>
     <li class="mono"><a href="#openoligo.hal.board.fixed_pinout">fixed_pinout</a></li>
+    <li class="mono"><a href="#openoligo.hal.board.reactants">reactants</a></li>
   </ul>
 
     </li>
@@ -1155,6 +1156,8 @@ <h1 class="title"><span class="name">openoligo.hal.board</span> module</h1>
     <span class="n">air_pressure</span><span class="p">:</span> <span class="n">Switch</span>
     <span class="n">liquid_regulator_err</span><span class="p">:</span> <span class="n">DigitalSensor</span>
     <span class="n">air_regulator_err</span><span class="p">:</span> <span class="n">DigitalSensor</span>
+    <span class="n">server_led</span><span class="p">:</span> <span class="n">Switch</span>
+    <span class="n">runner_led</span><span class="p">:</span> <span class="n">Switch</span>
 
 
 <span class="n">fixed_pinout</span><span class="p">:</span> <span class="n">FixedPinoutDict</span> <span class="o">=</span> <span class="p">{</span>
@@ -1169,6 +1172,17 @@ <h1 class="title"><span class="name">openoligo.hal.board</span> module</h1>
     <span class="s2">&quot;air_pressure&quot;</span><span class="p">:</span> <span class="n">Switch</span><span class="p">(</span><span class="n">gpio_pin</span><span class="o">=</span><span class="n">board</span><span class="o">.</span><span class="n">P29</span><span class="p">),</span>
     <span class="s2">&quot;liquid_regulator_err&quot;</span><span class="p">:</span> <span class="n">DigitalSensor</span><span class="p">(</span><span class="n">gpio_pin</span><span class="o">=</span><span class="n">board</span><span class="o">.</span><span class="n">P31</span><span class="p">),</span>
     <span class="s2">&quot;air_regulator_err&quot;</span><span class="p">:</span> <span class="n">DigitalSensor</span><span class="p">(</span><span class="n">gpio_pin</span><span class="o">=</span><span class="n">board</span><span class="o">.</span><span class="n">P33</span><span class="p">),</span>
+    <span class="s2">&quot;server_led&quot;</span><span class="p">:</span> <span class="n">Switch</span><span class="p">(</span><span class="n">gpio_pin</span><span class="o">=</span><span class="n">board</span><span class="o">.</span><span class="n">P36</span><span class="p">),</span>
+    <span class="s2">&quot;runner_led&quot;</span><span class="p">:</span> <span class="n">Switch</span><span class="p">(</span><span class="n">gpio_pin</span><span class="o">=</span><span class="n">board</span><span class="o">.</span><span class="n">P38</span><span class="p">),</span>
+<span class="p">}</span>
+
+<span class="n">reactants</span> <span class="o">=</span> <span class="p">{</span>
+    <span class="s2">&quot;ACT&quot;</span><span class="p">:</span> <span class="n">Valve</span><span class="p">(</span><span class="n">gpio_pin</span><span class="o">=</span><span class="n">board</span><span class="o">.</span><span class="n">P18</span><span class="p">),</span>
+    <span class="s2">&quot;OXI&quot;</span><span class="p">:</span> <span class="n">Valve</span><span class="p">(</span><span class="n">gpio_pin</span><span class="o">=</span><span class="n">board</span><span class="o">.</span><span class="n">P19</span><span class="p">),</span>
+    <span class="s2">&quot;CAP1&quot;</span><span class="p">:</span> <span class="n">Valve</span><span class="p">(</span><span class="n">gpio_pin</span><span class="o">=</span><span class="n">board</span><span class="o">.</span><span class="n">P21</span><span class="p">),</span>
+    <span class="s2">&quot;CAP2&quot;</span><span class="p">:</span> <span class="n">Valve</span><span class="p">(</span><span class="n">gpio_pin</span><span class="o">=</span><span class="n">board</span><span class="o">.</span><span class="n">P22</span><span class="p">),</span>
+    <span class="s2">&quot;DEB&quot;</span><span class="p">:</span> <span class="n">Valve</span><span class="p">(</span><span class="n">gpio_pin</span><span class="o">=</span><span class="n">board</span><span class="o">.</span><span class="n">P23</span><span class="p">),</span>
+    <span class="s2">&quot;CLDE&quot;</span><span class="p">:</span> <span class="n">Valve</span><span class="p">(</span><span class="n">gpio_pin</span><span class="o">=</span><span class="n">board</span><span class="o">.</span><span class="n">P24</span><span class="p">),</span>
 <span class="p">}</span>
 
 
@@ -1189,15 +1203,15 @@ <h1 class="title"><span class="name">openoligo.hal.board</span> module</h1>
     <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
         <span class="bp">self</span><span class="p">,</span>
         <span class="n">phosphoramidites</span><span class="p">:</span> <span class="n">Dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Valve</span><span class="p">],</span>
-        <span class="n">reactants</span><span class="p">:</span> <span class="n">Dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Valve</span><span class="p">],</span>
     <span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Initialize the pinout.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">fixed</span> <span class="o">=</span> <span class="n">fixed_pinout</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">phosphoramidites</span> <span class="o">=</span> <span class="n">phosphoramidites</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">reactants</span> <span class="o">=</span> <span class="n">reactants</span>
 
+        <span class="bp">self</span><span class="o">.</span><span class="n">phosphoramidites</span> <span class="o">=</span> <span class="n">phosphoramidites</span>
+
         <span class="bp">self</span><span class="o">.</span><span class="n">__pinout</span><span class="p">:</span> <span class="n">Dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Switchable</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">init_pinout</span><span class="p">()</span>
 
@@ -1285,6 +1299,14 @@ <h2 class="section-title" id="header-variables">Module variables</h2>
       <p id="openoligo.hal.board.fixed_pinout" class="name">var <span class="ident">fixed_pinout</span></p>
 
 
+  <div class="source_cont">
+</div>
+
+      </div>
+      <div class="item">
+      <p id="openoligo.hal.board.reactants" class="name">var <span class="ident">reactants</span></p>
+
+
   <div class="source_cont">
 </div>
 
@@ -1346,6 +1368,8 @@ <h2 class="section-title" id="header-classes">Classes</h2>
     <span class="n">air_pressure</span><span class="p">:</span> <span class="n">Switch</span>
     <span class="n">liquid_regulator_err</span><span class="p">:</span> <span class="n">DigitalSensor</span>
     <span class="n">air_regulator_err</span><span class="p">:</span> <span class="n">DigitalSensor</span>
+    <span class="n">server_led</span><span class="p">:</span> <span class="n">Switch</span>
+    <span class="n">runner_led</span><span class="p">:</span> <span class="n">Switch</span>
 </pre></div>
 
   </div>
@@ -1550,15 +1574,15 @@ <h3>Methods</h3>
     <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
         <span class="bp">self</span><span class="p">,</span>
         <span class="n">phosphoramidites</span><span class="p">:</span> <span class="n">Dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Valve</span><span class="p">],</span>
-        <span class="n">reactants</span><span class="p">:</span> <span class="n">Dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Valve</span><span class="p">],</span>
     <span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Initialize the pinout.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">fixed</span> <span class="o">=</span> <span class="n">fixed_pinout</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">phosphoramidites</span> <span class="o">=</span> <span class="n">phosphoramidites</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">reactants</span> <span class="o">=</span> <span class="n">reactants</span>
 
+        <span class="bp">self</span><span class="o">.</span><span class="n">phosphoramidites</span> <span class="o">=</span> <span class="n">phosphoramidites</span>
+
         <span class="bp">self</span><span class="o">.</span><span class="n">__pinout</span><span class="p">:</span> <span class="n">Dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Switchable</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">init_pinout</span><span class="p">()</span>
 

diff --git a/docs/hal/index.html b/docs/hal/index.html
@@ -1635,15 +1635,15 @@ <h3>Methods</h3>
     <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
         <span class="bp">self</span><span class="p">,</span>
         <span class="n">phosphoramidites</span><span class="p">:</span> <span class="n">Dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Valve</span><span class="p">],</span>
-        <span class="n">reactants</span><span class="p">:</span> <span class="n">Dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Valve</span><span class="p">],</span>
     <span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Initialize the pinout.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">fixed</span> <span class="o">=</span> <span class="n">fixed_pinout</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">phosphoramidites</span> <span class="o">=</span> <span class="n">phosphoramidites</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">reactants</span> <span class="o">=</span> <span class="n">reactants</span>
 
+        <span class="bp">self</span><span class="o">.</span><span class="n">phosphoramidites</span> <span class="o">=</span> <span class="n">phosphoramidites</span>
+
         <span class="bp">self</span><span class="o">.</span><span class="n">__pinout</span><span class="p">:</span> <span class="n">Dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Switchable</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">init_pinout</span><span class="p">()</span>
 

diff --git a/docs/hal/instrument.html b/docs/hal/instrument.html
@@ -1108,29 +1108,22 @@ <h1 class="title"><span class="name">openoligo.hal.instrument</span> module</h1>
 <span class="kn">import</span> <span class="nn">logging</span>
 <span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Callable</span>
 
-<span class="kn">import</span> <span class="nn">anyio</span>
-
 <span class="kn">from</span> <span class="nn">openoligo.hal.board</span> <span class="kn">import</span> <span class="n">Pinout</span>
 <span class="kn">from</span> <span class="nn">openoligo.hal.devices</span> <span class="kn">import</span> <span class="n">DigitalSensor</span><span class="p">,</span> <span class="n">Valve</span>
 <span class="kn">from</span> <span class="nn">openoligo.hal.gpio</span> <span class="kn">import</span> <span class="n">get_gpio</span>
 <span class="kn">from</span> <span class="nn">openoligo.hal.types</span> <span class="kn">import</span> <span class="n">OneDestinationException</span><span class="p">,</span> <span class="n">OneSourceException</span><span class="p">,</span> <span class="n">ValveRole</span><span class="p">,</span> <span class="n">board</span>
 <span class="kn">from</span> <span class="nn">openoligo.utils.singleton</span> <span class="kn">import</span> <span class="n">Singleton</span>
 
+<span class="c1"># import anyio</span>
+
+
 <span class="n">default_pinout</span> <span class="o">=</span> <span class="n">Pinout</span><span class="p">(</span>
     <span class="n">phosphoramidites</span><span class="o">=</span><span class="p">{</span>
         <span class="s2">&quot;A&quot;</span><span class="p">:</span> <span class="n">Valve</span><span class="p">(</span><span class="n">gpio_pin</span><span class="o">=</span><span class="n">board</span><span class="o">.</span><span class="n">P26</span><span class="p">),</span>
         <span class="s2">&quot;C&quot;</span><span class="p">:</span> <span class="n">Valve</span><span class="p">(</span><span class="n">gpio_pin</span><span class="o">=</span><span class="n">board</span><span class="o">.</span><span class="n">P28</span><span class="p">),</span>
         <span class="s2">&quot;G&quot;</span><span class="p">:</span> <span class="n">Valve</span><span class="p">(</span><span class="n">gpio_pin</span><span class="o">=</span><span class="n">board</span><span class="o">.</span><span class="n">P15</span><span class="p">),</span>
         <span class="s2">&quot;T&quot;</span><span class="p">:</span> <span class="n">Valve</span><span class="p">(</span><span class="n">gpio_pin</span><span class="o">=</span><span class="n">board</span><span class="o">.</span><span class="n">P16</span><span class="p">),</span>
     <span class="p">},</span>
-    <span class="n">reactants</span><span class="o">=</span><span class="p">{</span>
-        <span class="s2">&quot;ACT&quot;</span><span class="p">:</span> <span class="n">Valve</span><span class="p">(</span><span class="n">gpio_pin</span><span class="o">=</span><span class="n">board</span><span class="o">.</span><span class="n">P18</span><span class="p">),</span>
-        <span class="s2">&quot;OXI&quot;</span><span class="p">:</span> <span class="n">Valve</span><span class="p">(</span><span class="n">gpio_pin</span><span class="o">=</span><span class="n">board</span><span class="o">.</span><span class="n">P19</span><span class="p">),</span>
-        <span class="s2">&quot;CAP1&quot;</span><span class="p">:</span> <span class="n">Valve</span><span class="p">(</span><span class="n">gpio_pin</span><span class="o">=</span><span class="n">board</span><span class="o">.</span><span class="n">P21</span><span class="p">),</span>
-        <span class="s2">&quot;CAP2&quot;</span><span class="p">:</span> <span class="n">Valve</span><span class="p">(</span><span class="n">gpio_pin</span><span class="o">=</span><span class="n">board</span><span class="o">.</span><span class="n">P22</span><span class="p">),</span>
-        <span class="s2">&quot;DEB&quot;</span><span class="p">:</span> <span class="n">Valve</span><span class="p">(</span><span class="n">gpio_pin</span><span class="o">=</span><span class="n">board</span><span class="o">.</span><span class="n">P23</span><span class="p">),</span>
-        <span class="s2">&quot;CLDE&quot;</span><span class="p">:</span> <span class="n">Valve</span><span class="p">(</span><span class="n">gpio_pin</span><span class="o">=</span><span class="n">board</span><span class="o">.</span><span class="n">P24</span><span class="p">),</span>
-    <span class="p">},</span>
 <span class="p">)</span>
 
 
@@ -1250,7 +1243,7 @@ <h1 class="title"><span class="name">openoligo.hal.instrument</span> module</h1>
         <span class="bp">self</span><span class="o">.</span><span class="n">pinout</span><span class="o">.</span><span class="n">fixed</span><span class="p">[</span><span class="s2">&quot;liquid_pressure&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="kc">False</span><span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">pinout</span><span class="o">.</span><span class="n">fixed</span><span class="p">[</span><span class="s2">&quot;air_pressure&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="kc">False</span><span class="p">)</span>
 
-    <span class="c1">#async def monitor_pressure(self) -&gt; None:</span>
+    <span class="c1"># async def monitor_pressure(self) -&gt; None:</span>
     <span class="c1">#    &quot;&quot;&quot;</span>
     <span class="c1">#    Monitor the pressure sensors.</span>
     <span class="c1">#    &quot;&quot;&quot;</span>
@@ -1415,7 +1408,7 @@ <h2 class="section-title" id="header-classes">Classes</h2>
         <span class="bp">self</span><span class="o">.</span><span class="n">pinout</span><span class="o">.</span><span class="n">fixed</span><span class="p">[</span><span class="s2">&quot;liquid_pressure&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="kc">False</span><span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">pinout</span><span class="o">.</span><span class="n">fixed</span><span class="p">[</span><span class="s2">&quot;air_pressure&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="kc">False</span><span class="p">)</span>
 
-    <span class="c1">#async def monitor_pressure(self) -&gt; None:</span>
+    <span class="c1"># async def monitor_pressure(self) -&gt; None:</span>
     <span class="c1">#    &quot;&quot;&quot;</span>
     <span class="c1">#    Monitor the pressure sensors.</span>
     <span class="c1">#    &quot;&quot;&quot;</span>

diff --git a/docs/scripts/runner.html b/docs/scripts/runner.html
@@ -1109,8 +1109,8 @@ <h1 class="title"><span class="name">openoligo.scripts.runner</span> module</h1>
 <span class="kn">from</span> <span class="nn">anyio</span> <span class="kn">import</span> <span class="n">run</span><span class="p">,</span> <span class="n">sleep</span>
 
 <span class="kn">from</span> <span class="nn">openoligo.api.db</span> <span class="kn">import</span> <span class="n">db_init</span><span class="p">,</span> <span class="n">get_db_url</span>
+<span class="kn">from</span> <span class="nn">openoligo.api.helpers</span> <span class="kn">import</span> <span class="n">get_next_task</span>  <span class="c1"># set_failed_now,</span>
 <span class="kn">from</span> <span class="nn">openoligo.api.helpers</span> <span class="kn">import</span> <span class="p">(</span>
-    <span class="n">get_next_task</span><span class="p">,</span>  <span class="c1"># set_failed_now,</span>
     <span class="n">set_completed_now</span><span class="p">,</span>
     <span class="n">set_log_file</span><span class="p">,</span>
     <span class="n">set_started_now</span><span class="p">,</span>