Update documentation with details about EVO/Fluent differences

docs/requirements.txt

@@ -3,3 +3,4 @@ myst-nb
 numpydoc
 nbsphinx
 sphinx-book-theme
+sphinxcontrib.mermaid

docs/source/conf.py

@@ -37,6 +37,7 @@
     "numpydoc",
     "myst_nb",
     "sphinx_book_theme",
+    "sphinxcontrib.mermaid",
 ]
 nb_execution_mode = "off"
 

docs/source/index.rst

@@ -1,23 +1,37 @@
 Welcome to the ``robotools`` documentation!
 ===========================================
 
+.. image:: https://img.shields.io/pypi/v/robotools
+   :target: https://pypi.org/project/robotools
+
 .. image:: https://img.shields.io/badge/code%20on-Github-lightgrey
-    :target: https://github.com/JuBiotech/robotools
+   :target: https://github.com/JuBiotech/robotools
 
 .. image:: https://zenodo.org/badge/358629210.svg
    :target: https://zenodo.org/badge/latestdoi/358629210
 
+
 ``robotools`` is a Python package for planning *in silico* liquid handling operations.
-It can create Tecan Freedom EVO worklist files on the fly, making it possible to program complicated liquid handling operations
+
+It can create Tecan Freedom EVO or Tecan Fluent worklist files on the fly, making it possible to program complicated liquid handling operations
 from Python scripts or Jupyter notebooks.
 
-You can download the latest version from `GitHub <https://github.com/JuBiotech/robotools>`_ or install it via ``pip install robotools``.
+Installation
+============
+
+.. code-block:: bash
+
+   pip install robotools
+
+You can also download the latest version from `GitHub <https://github.com/JuBiotech/robotools>`_.
+
+Tutorials
+=========
 
 In the following chapters, we introduce the data structures, worklist-creation and extra features.
 
 .. toctree::
-   :maxdepth: 2
-   :caption: Examples
+   :maxdepth: 1
 
    notebooks/01_Labware_Basics
    notebooks/02_Worklist_Basics
@@ -28,12 +42,11 @@ In the following chapters, we introduce the data structures, worklist-creation a
    notebooks/07_TipMasks
 
 
-
-You can find autogenerated API documentation below:
+API Reference
+=============
 
 .. toctree::
    :maxdepth: 2
-   :caption: API Reference
 
    robotools_liquidhandling
    robotools_evotools

docs/source/notebooks/01_Labware_Basics.ipynb

@@ -5,11 +5,13 @@
    "metadata": {},
    "source": [
     "# `Labware` Basics\n",
-    "In `robotools` there are two important types of objects: `Labware` and `Worklist`.\n",
+    "In `robotools` there are two important types of objects: `Labware` and worklists.\n",
+    "\n",
     "A `Labware` represents an array of wells, such as a microtiter plate (MTP), one or more troughs or even an arrangement of eppis or falcon tubes.\n",
     "\n",
-    "The `Worklist` helps you to perform liquid handling operations on `Labware` objects while automatically creating an EVOware Worklist file (`*.gwl`) with the corresponding pipetting instructions.\n",
-    "These files contain things like source/destination, volume and can be executed by a Tecan EVOware script.\n",
+    "The worklists help you to perform liquid handling operations on `Labware` objects while automatically creating a Gemini worklist file (`*.gwl`) with the corresponding pipetting instructions.\n",
+    "These files contain things like source/destination, volume and can be executed by a Tecan EVO or Fluent liquid handlers.\n",
+    "\n",
     "But before we'll get creating worklists, this example introduces how `robotools` generally deals with liquid handling."
    ]
   },
@@ -37,8 +39,9 @@
     "Each `Labware` object describes a $R\\times C$ grid (array) of wells.\n",
     "It has a `name` and `min_volume`/`max_volume` to prevent you from pipetting impossible volumes.\n",
     "\n",
-    "The following cell creates a `Labware` with the name \"24-well plate\".\n",
-    "When creating worklists, this name should match the labware defined on the EVOware worktable."
+    "The following cell creates a `Labware` with the name `\"24-well plate\"`.\n",
+    "\n",
+    "When creating worklists, this name should match the labware defined on the liquid handler worktable."
    ]
   },
   {
@@ -67,7 +70,8 @@
    ],
    "source": [
     "plate = robotools.Labware(\n",
-    "    \"24-well plate\", rows=4, columns=6, \n",
+    "    \"24-well plate\",\n",
+    "    rows=4, columns=6, \n",
     "    min_volume=100, max_volume=1_000,\n",
     "    initial_volumes=300\n",
     ")\n",
@@ -149,6 +153,7 @@
    "metadata": {},
    "source": [
     "If you are familiar with Python already, you probably know how [NumPy slicing](https://www.w3schools.com/python/numpy_array_slicing.asp) works.\n",
+    "\n",
     "Because `.wells` and `.volumes` are NumPy `ndarray`s, you can use NumPy slicing to select particular ranges:"
    ]
   },
@@ -186,7 +191,8 @@
    "metadata": {},
    "source": [
     "`Labware`s have methods such as `.add()`, `.remove()` for performing virtual liquid handling operations.\n",
-    "You won't typically work with `.add()` or `.remove()` directly, because most things you do with a `Worklist` will call these methods under the hood.\n",
+    "\n",
+    "You won't typically work with `.add()` or `.remove()` directly, because most things you do with a worklist will call these methods under the hood.\n",
     "\n",
     "One job of the `.add()` and `.remove()` methods is to raise `VolumeOverflowError` or `VolumeUnderflowError` when the minimum/maximum working volumes are violated:"
    ]
@@ -213,11 +219,8 @@
    ],
    "source": [
     "try:\n",
-    "    \n",
     "    plate.add(['A01', 'B01', 'C01'], [200, 200, 2000])\n",
-    "    \n",
-    "# The try/except is just to make the example look nice.\n",
-    "except Exception as ex:\n",
+    "except robotools.VolumeViolationException as ex:\n",
     "    print(ex)"
    ]
   },
@@ -271,9 +274,10 @@
    "metadata": {},
    "source": [
     "### Troughs\n",
-    "Troughs are a little weird, because for the EVOware, they have multiple rows, even though it's actually just one big well.\n",
     "\n",
+    "Troughs are a little weird, because for the EVOware, they have multiple rows, even though it's actually just one big well.\n",
     "Nevertheless, a `Trough` is just a special type of `Labware` that has `virtual_rows`.\n",
+    "For the Tecan Fluent, the `virtual_rows` setting is irrelevant.\n",
     "\n",
     "The following example emulates an arrangement of 4 troughs next to each other.\n",
     "They have `virtual_rows=8`, so there's enough space for 8 tips (`A01` through `H01`), but in reality it's just one well per column:"
@@ -349,7 +353,7 @@
    "source": [
     "vwells = robotools.get_trough_wells(\n",
     "    n=11,\n",
-    "    trough_wells=quadruple_trough.wells[:, 0]   # select the wells from the first trough\n",
+    "    trough_wells=quadruple_trough.wells[:, 0]  # select the wells from the first trough\n",
     ")\n",
     "\n",
     "quadruple_trough.remove(vwells, 100)\n",
@@ -365,10 +369,22 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 10,
    "metadata": {},
-   "outputs": [],
-   "source": []
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Last updated: 2024-04-23T13:11:50.287028+02:00\n",
+      "\n"
+     ]
+    }
+   ],
+   "source": [
+    "%load_ext watermark\n",
+    "%watermark -idu"
+   ]
   }
  ],
  "metadata": {
@@ -387,7 +403,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.16"
+   "version": "3.10.8"
   }
  },
  "nbformat": 4,