Merge branch 'main' into Alpaqua-Engineering-now-supporting-PLR

Author: rickwierenga

docs/img/used_by/logo_bio_techne.jpg

@@ -125,6 +125,12 @@ PyHamilton is a Windows only interface to Hamilton's VENUS.
 :target: https://www.sanofi.com
 ```
 
+```{image} /img/used_by/logo_bio_techne.jpg
+:alt: Bio-Techne
+:class: company
+:target: https://www.bio-techne.com/
+```
+
 ```{raw} html
 <style>
 .company {

docs/index.md

@@ -7,34 +7,9 @@
    "source": [
     "# Inheco Incubator (Shaker)\n",
     "\n",
-    "<table style=\"width:100%; border-collapse:collapse;\">\n",
-    "<tr>\n",
-    "<td style=\"width:60%; font-size:15px; line-height:1.7; vertical-align:top; padding-right:15px;\">\n",
-    "\n",
-    "<ul style=\"margin-top:0;\">\n",
-    "  <li><a href=\"https://www.inheco.com/incubator-shaker.html\" target=\"_blank\"><b>OEM Link</b></a></li>\n",
-    "  <li><b>Communication Protocol / Hardware:</b> Serial (FTDI) / USB-A</li>\n",
-    "  <li><b>Communication Level:</b> Firmware (documentation shared by OEM)</li>\n",
-    "  <li>Same command set for:\n",
-    "    <ul>\n",
-    "      <li>Incubator “MP”</li>\n",
-    "      <li>Incubator “DWP”</li>\n",
-    "      <li>Incubator Shaker “MP”</li>\n",
-    "      <li>Incubator Shaker “DWP”</li>\n",
-    "    </ul>\n",
-    "  </li>\n",
-    "  <li><b>Incubator Shaker “MP”</b> VID:PID <code>0403:6001</code></li>\n",
-    "  <li>Takes in a single plate via a loading tray, heats it to the set temperature, and shakes it to the set RPM.</li>\n",
-    "</ul>\n",
-    "\n",
-    "</td>\n",
-    "\n",
-    "<td style=\"width:40%; text-align:center; vertical-align:middle;\">\n",
-    "  <img src=\"img/inheco_incubator_shaker_mp_dwp.png\" width=\"500\"/><br>\n",
-    "  <i>Figure: Inheco Incubator Shaker MP & DWP models</i>\n",
-    "</td>\n",
-    "</tr>\n",
-    "</table>"
+    "| Summary | Image |\n",
+    "|------------|--------|\n",
+    "| <ul style=\"font-size:15px; line-height:1.6; margin-top:0;\"> <li><a href=\"https://www.inheco.com/incubator-shaker.html\" target=\"_blank\"><b>OEM Link</b></a></li> <li><b>Communication Protocol / Hardware:</b> Serial / USB-A/B</li> <li><b>Communication Level:</b> Firmware (documentation shared by OEM)</li> <li>Same command set for: <ul> <li>Incubator “MP”</li> <li>Incubator “DWP”</li> <li>Incubator Shaker “MP”</li> <li>Incubator Shaker “DWP”</li> </ul></li> <li>VID:PID <code>0403:6001</code></li> <li>Takes in a single plate via a loading tray, heats it to the set temperature, and shakes it to the set RPM.</li> </ul> | <div style=\"width:320px; text-align:center;\"> ![shaker](img/inheco_incubator_shaker_mp_dwp.png) <br><i>Figure: Inheco Incubator Shaker MP & DWP models</i> </div> |\n"
    ]
   },
   {
@@ -76,19 +51,10 @@
   },
   {
    "cell_type": "markdown",
-   "id": "95e39b36-c441-499d-bfaa-327d49d5cc04",
+   "id": "38dcc34a",
    "metadata": {},
    "source": [
-    "<!-- ![quadrants](img/inheco_incubator_shaker_physical_setup_overview.png) -->\n",
-    "<table style=\"width:100%; border-collapse:collapse; margin-top:10px;\">\n",
-    "<tr>\n",
-    "<td style=\"text-align:center; vertical-align:middle;\">\n",
-    "  <img src=\"img/inheco_incubator_shaker_physical_setup_overview.png\" width=\"950\" style=\"border-radius:8px;\"/>\n",
-    "  <br>\n",
-    "  <i>Figure: Physical setup overview of the Inheco Incubator Shaker system</i>\n",
-    "</td>\n",
-    "</tr>\n",
-    "</table>\n"
+    "![copy-me](img/inheco_incubator_shaker_physical_setup_overview.png)"
    ]
   },
   {
@@ -123,43 +89,12 @@
   },
   {
    "cell_type": "markdown",
-   "id": "40f8dcb4-7779-4c51-9bdf-bf8d05f46c46",
+   "id": "69f8951f",
    "metadata": {},
    "source": [
-    "<table>\n",
-    "<tr>\n",
-    "<td style=\"font-size:15px; line-height:1.6; width:60%; vertical-align:top; padding-right:10px;\">\n",
-    "\n",
-    "To connect an <code>InhecoIncubatorShakerStackBackend</code> you have to specify the <b>DIP switch identifier</b>:\n",
-    "<ul style=\"margin-left: 20px;\">\n",
-    "<li>located on the back of the bottom machine,<br>\n",
-    "<li>it defines the DIP switch configuration for the entire stack above it.</li>\n",
-    "\n",
-    "</ul>\n",
-    "\n",
-    "<h3>Setting the DIP switch to generate a machine address</h3>\n",
-    "\n",
-    "The DIP switch at the back of each machine has to be set manually and consists of 4 pins that can be set into an <code>UP</code> / <code>0</code> or a <code>DOWN</code> / <code>1</code> position.\n",
-    "\n",
-    "(<i>Note:</b> There are two more pins to the left of the DIP switch pins. They are not involved in setting the DIP switch address, and should be left in their <code>DOWN</code> position.</i>)</li>\n",
-    "\n",
-    "This represents <i>binary encoding</i>:\n",
-    "<ul>\n",
-    "<li>All pins at <code>0</code> → DIP switch is set to address binary <code>0 0 0 0</code> -> decimal <code>0</code></li>\n",
-    "<li>All pins at <code>1</code> → DIP switch is set to address binary <code>1 1 1 1</code> -> decimal <code>15</code> (2<sup>4</sup>-1)</li>\n",
-    "</ul>\n",
-    "\n",
-    "This information is crucial for creating the correct commands to communicate with the machine stack.\n",
-    "\n",
-    "</td>\n",
-    "\n",
-    "<td style=\"width:40%; text-align:center; vertical-align:middle;\">\n",
-    "<img src=\"img/inheco_incubator_shaker_dip_switch_addressing.png\" width=\"500\"/><br>\n",
-    "<i>Figure: DIP switch layout to generate different identifiers/addresses</i>\n",
-    "</td>\n",
-    "</tr>\n",
-    "\n",
-    "</table>"
+    "| Explanation | Image |\n",
+    "|------------|--------|\n",
+    "| <div style=\"font-size:15px; line-height:1.6; margin-top:0;\"> To connect an <code>InhecoIncubatorShakerStackBackend</code> you must set the <b>DIP switch identifier</b> on the back of the bottom machine: <ul style=\"margin-left:20px;\"> <li>located on the back of the bottom machine,</li> <li>defines the DIP switch configuration for the entire stack.</li> </ul> <h3>Setting the DIP switch to generate a machine address</h3> Each machine has a 4-pin DIP switch. Each pin can be <code>UP</code> (<code>0</code>) or <code>DOWN</code> (<code>1</code>). <br><br> <i>Note:</i> the two pins to the left of the DIP switch are not part of the addressing and should remain in the <code>DOWN</code> position. <br><br> This forms a <i>4-bit binary address</i>: <ul> <li>All pins at <code>0</code> → binary <code>0 0 0 0</code> → decimal <code>0</code></li> <li>All pins at <code>1</code> → binary <code>1 1 1 1</code> → decimal <code>15</code> (<code>2<sup>4</sup>-1</code>)</li> </ul> This address is crucial for generating valid communication commands for your Inheco stack. </div> | <div style=\"width:320px; text-align:center;\"> ![dip switches](img/inheco_incubator_shaker_dip_switch_addressing.png) <br><i>Figure: DIP switch layout to generate different identifiers/addresses</i> </div> |\n"
    ]
   },
   {
@@ -501,38 +436,9 @@
    "id": "438e19d7-714d-46f3-8a9e-f00798ca9893",
    "metadata": {},
    "source": [
-    "<table style=\"width:100%; border-collapse:collapse;\">\n",
-    "  <tr>\n",
-    "  <td style=\"width:60%; font-size:15px; line-height:1.7; vertical-align:top; padding-right:20px;\">\n",
-    "      <p style=\"margin-top:0;\">The Inheco Incubator (Shaker) contains three independent temperature sensors:</p>\n",
-    "      <ol style=\"margin-top:0; margin-bottom:10px; padding-left:20px;\">\n",
-    "        <li>main sensor — close to the door/front, inside the machine</li>\n",
-    "        <li>validation sensor — back, inside the machine</li>\n",
-    "        <li>boost sensor — on heating foil, inside the machine</li>\n",
-    "      </ol>\n",
-    "      <p>\n",
-    "        By default, <code>iis_stack[0].get_temperature()</code>’s argument is set to\n",
-    "        <code>sensor=\"main\"</code>.  \n",
-    "        This can be changed to any of the following:\n",
-    "      </p>\n",
-    "      <ul style=\"margin-top:0; padding-left:20px;\">\n",
-    "        <li><code>\"main\"</code></li>\n",
-    "        <li><code>\"dif\"</code></li>\n",
-    "        <li><code>\"boost\"</code></li>\n",
-    "        <li><code>\"mean\"</code> - takes all three sensors’ measurements and returns their geometric mean</li>\n",
-    "      </ul>\n",
-    "    </td>\n",
-    "    <td style=\"width:40%; text-align:center; vertical-align:middle;\">\n",
-    "      <img src=\"img/inheco_incubator_shaker_t_sensor_positioning.png\"\n",
-    "           alt=\"Inheco Incubator Shaker sensor positions\"\n",
-    "           style=\"width:300px; border-radius:6px; margin-bottom:8px;\"/>\n",
-    "      <br>\n",
-    "      <i style=\"font-size:13px; color:#6c757d;\">\n",
-    "        Figure: Inheco Incubator Shaker Temperature Sensor Positioning\n",
-    "      </i>\n",
-    "    </td>\n",
-    "  </tr>\n",
-    "</table>\n"
+    "| Explanation | Image |\n",
+    "|------------|--------|\n",
+    "| <div style=\"font-size:15px; line-height:1.7; margin-top:0; padding-right:20px;\"> <p>The Inheco Incubator (Shaker) contains three independent temperature sensors:</p> <ol style=\"margin-top:0; margin-bottom:10px; padding-left:20px;\"> <li>main sensor — close to the door/front, inside the machine</li> <li>validation sensor — back, inside the machine</li> <li>boost sensor — on heating foil, inside the machine</li> </ol> <p>By default, <code>iis_stack[0].get_temperature()</code>’s argument is set to <code>sensor=\"main\"</code>.<br> This can be changed to any of the following:</p> <ul style=\"margin-top:0; padding-left:20px;\"> <li><code>\"main\"</code></li> <li><code>\"dif\"</code></li> <li><code>\"boost\"</code></li> <li><code>\"mean\"</code> — takes all three sensors’ measurements and returns their geometric mean</li> </ul> </div> | <div style=\"width:280px; text-align:center;\"> ![sensor positions](img/inheco_incubator_shaker_t_sensor_positioning.png) <br><i style=\"font-size:13px; color:#6c757d;\">Figure: Inheco Incubator Shaker Temperature Sensor Positioning</i> </div> |\n"
    ]
   },
   {
@@ -951,19 +857,19 @@
     {
      "data": {
       "text/plain": [
-        "{\n",
-        "  \"drawer_error\": False,\n",
-        "  \"homogeneity_sensor_3_vs_1_error\": False,\n",
-        "  \"homogeneity_sensor_2_vs_1_error\": False,\n",
-        "  \"sensor_1_target_temp_error\": False,\n",
-        "  \"y_amplitude_shaker_error\": False,\n",
-        "  \"x_amplitude_shaker_error\": False,\n",
-        "  \"phase_shift_shaker_error\": False,\n",
-        "  \"y_frequency_shaker_error\": False,\n",
-        "  \"x_frequency_shaker_error\": False,\n",
-        "  \"line_boost_heater_broken\": False,\n",
-        "  \"line_main_heater_broken\": False,\n",
-        "}\n"
+       "{\n",
+       "  \"drawer_error\": False,\n",
+       "  \"homogeneity_sensor_3_vs_1_error\": False,\n",
+       "  \"homogeneity_sensor_2_vs_1_error\": False,\n",
+       "  \"sensor_1_target_temp_error\": False,\n",
+       "  \"y_amplitude_shaker_error\": False,\n",
+       "  \"x_amplitude_shaker_error\": False,\n",
+       "  \"phase_shift_shaker_error\": False,\n",
+       "  \"y_frequency_shaker_error\": False,\n",
+       "  \"x_frequency_shaker_error\": False,\n",
+       "  \"line_boost_heater_broken\": False,\n",
+       "  \"line_main_heater_broken\": False,\n",
+       "}\n"
       ]
      },
      "execution_count": 19,
@@ -1276,7 +1182,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "plr",
    "language": "python",
    "name": "python3"
   },