Homing & GUI (#14)

* Uniformize the usage of "Vector" for "position" property in Tic and M3FS * Fix issue #12 * Autodetect CNCRouter dev device * Black Format * Initialisation of files for GUI * Usage of Enum (python 3.9) instead of StrEnum (python 3.10) * Position label and regular updates (100ms) * Move buttons * Fix Readthedocs configuration * Add home() function for stages * Code formating * Put home button at the center of gui * Implement Home function for CNC and make Home button on gui effective * Formatting files and little updates to remove warnings * raise exception in case of device not found for tic * Find devices per serial number * Add comport selection in gui * Remove magic numbers in M3FS code * GUI update: enable/disable controls while connection is not done, add absolute position move, usage of validators * Find devices per serial number, usage for Corvus * Adding Qt Event processing as wait routine in GUI + typing * Make home function not abstract with default implementation * Add the possibility to perform wait-routine while homing * Remove several linter warnings * Update comments * Update to PyQt6 in documentation and requirements * Enforce Exception raise when ALARM is reported by the CNC Sometimes the CNC does not answer to '?'. Returns after 10 tries to get a byte considering the 1 second timeout. In get_status, retries if there has been no answer from the CNC * Bumping version and correcting typo * Update docs * Update pyproject.toml Put 'beta' in version * Add M3FS in GUI * Bump version * Update pyproject.toml * Update conf.py * Removing "(object)" in "Vector" class definition
Ledger-Donjon · Jul 22, 2024 · f2fd098 · f2fd098
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diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -1,9 +1,23 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
 version: 2
+
+# Set the OS, Python version and other tools you might need
 build:
   os: "ubuntu-22.04"
   tools:
-    python: "3.8"
-
+    python: "3.9"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# Declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
 python:
   install:
-    - requirements: requirements.txt
+    - requirements: docs/requirements.txt
diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
-[![Documentation Status](https://readthedocs.org/projects/pystages/badge/?version=latest)](https://pystages.readthedocs.io/en/latest/?badge=latest)
-
 # PyStages
 
+[![Documentation Status](https://readthedocs.org/projects/pystages/badge/?version=latest)](https://pystages.readthedocs.io/en/latest/?badge=latest)
+
 PyStages is a Python 3 library for controlling motorized stages which have a
 motion controller. It has been designed for microscopy test benches automation.
 
@@ -14,16 +14,28 @@ are implemented):
 - Tic Stepper Motor controller (USB only)
 - CNC Router with GRBL/GCode instructions (CNC 3018-PRO)
 
-The library also provides helper classes for basic vector manipulation and 
-autofocus calculation
+The library also provides helper classes for basic vector manipulation and
+autofocus computation.
 
 ## Documentation
 
 Documentation is available on [Read the Docs](https://pystages.readthedocs.io).
 
+## PyStages GUI
+
+A user interface has been implemented to control the stages.
+
+You can run it with the following command:
+
+```bash
+python -m pystages.gui
+```
+
 ## Requirements
 
 This library requires the following packages:
+
 - [pyserial](https://pypi.org/project/pyserial/)
 - [numpy](https://pypi.org/project/numpy/)
-- [pyusb](https://pypi.org/project/pyusb/)
+- [pyusb](https://pypi.org/project/pyusb/)
+- [PyQt6](https://pypi.org/project/PyQt6/)
diff --git a/docs/api.rst b/docs/api.rst
@@ -17,10 +17,10 @@ Classes
 .. automodule:: pystages
     :members:
 
-.. autoclass:: Autofocus
-    :members:
+.. .. autoclass:: Autofocus
+..     :members:
 
-.. autoclass:: Vector
-    :special-members: __init__
-    :members:
+.. .. autoclass:: Vector
+..     :special-members: __init__
+..     :members:
 
diff --git a/docs/conf.py b/docs/conf.py
@@ -10,27 +10,30 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
-# import os
-# import sys
-# sys.path.insert(0, os.path.abspath('.'))
+
+import sys
+import os
+
+# Add path for autodoc
+sys.path.insert(0, os.path.abspath(".."))
 
 
 # -- Project information -----------------------------------------------------
 
 project = "pystages"
-copyright = "2022, Olivier Hériveaux, Manuel San Pedro, Michaël Mouchous"
+copyright = "2024, Olivier Hériveaux, Manuel San Pedro, Michaël Mouchous"
 author = "Olivier Hériveaux, Manuel San Pedro, Michaël Mouchous"
 
 # The full version, including alpha/beta/rc tags
-release = "1.1"
+release = "1.2"
 
 
 # -- General configuration ---------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = ["sphinx.ext.autodoc"]
+extensions = ["sphinx.ext.autodoc", "myst_parser"]
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
@@ -54,3 +57,8 @@
 html_static_path = []
 
 html_logo = "logo.png"
+
+source_suffix = {
+    ".rst": "restructuredtext",
+    ".md": "markdown",
+}
diff --git a/docs/gui.md b/docs/gui.md
@@ -0,0 +1,41 @@
+# PyStages GUI
+
+A user interface has been implemented to control the stages.
+
+You can run it with the following command:
+
+```bash
+python -m pystages.gui
+```
+
+This tool presents basic controls. After connection to the stage, it polls the position and prints out
+at the bottom of the window.
+
+## Stage selection and connection
+
+Select the type of stage that you want to control and chose either a serial port to connect to, or select `Auto detect`
+to make pystage to select the correct one according to the device description.
+
+Then click to `Connect`. If the connection success, the control buttons are activated.
+
+## Relative move
+
+You can click on buttons to move for a positive of negative relative distance. 
+The direction correspond to the axis number of the stage (`X` for first axe, `Y` for the second one,
+`Z` for the third one). The moving distance is selected throug the `Step` dropdown menu.
+
+## Absolute move
+
+You can enter absolute coordinates in the 3 entry boxes and trigger the move by clicking the `Go To Position` button.
+
+## Z offset
+
+The `Z offset` checkbox and dropdown menu permit for each horizontal move (X or Y)
+to make first a vertical-up displacement (Z+) followed by the
+actual move, and then a final vertical-down displacement (Z-).
+
+## Homing
+
+The `Home` button permits to trigger the calibration process of the stage. 
+Be careful that your setup is clear before using it.
+
diff --git a/docs/index.rst b/docs/index.rst
@@ -1,8 +1,3 @@
-.. pystages documentation master file, created by
-   sphinx-quickstart on Tue Jul  7 15:03:18 2020.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
 Welcome to pystages's documentation!
 ====================================
 
@@ -24,13 +19,14 @@ The library also provides helper classes for basic vector manipulation
 (:class:`pystages.Autofocus`).
 
 .. toctree::
-   :maxdepth: 2
-   :caption: Contents:
-
-   Vectors <vectors.rst>
-   Autofocus <autofocus.rst>
-   Python API <api.rst>
-   Troubleshooting <troubleshooting.rst>
+  :maxdepth: 2
+  :caption: Contents:
+
+  Vectors <vectors.rst>
+  Autofocus <autofocus.rst>
+  Python API <api.rst>
+  GUI <gui.md>
+  Troubleshooting <troubleshooting.rst>
 
 
 Indices and tables

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -0,0 +1,6 @@
+pyserial
+pyusb
+numpy
+sphinx
+sphinx-rtd-theme
+myst-parser
diff --git a/pyproject.toml b/pyproject.toml
@@ -4,26 +4,22 @@ build-backend = "hatchling.build"
 
 [project]
 name = "pystages"
-version = "1.1.0"
+version = "1.2"
 authors = [
-  { name="Olivier Hérivaux", email="olivier.heriveaux@ledger.fr" },
-  { name="Michaël Mouchous", email="michael.mouchous@ledger.fr" },
+  { name = "Olivier Hérivaux", email = "olivier.heriveaux@ledger.fr" },
+  { name = "Michaël Mouchous", email = "michael.mouchous@ledger.fr" },
 ]
 description = "Motorized stage control library for scientific applications"
 readme = "README.md"
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 classifiers = [
-    "Programming Language :: Python :: 3",
-    "License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)",
-    "Operating System :: OS Independent",
-]
-dependencies = [
-    "pyserial",
-    "pyusb",
-    "numpy"
+  "Programming Language :: Python :: 3",
+  "License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)",
+  "Operating System :: OS Independent",
 ]
+dependencies = ["pyserial", "pyusb", "numpy", "pyqt6"]
 
 [project.urls]
 "Homepage" = "https://github.com/Ledger-Donjon/pystages"
 "Bug Tracker" = "https://github.com/Ledger-Donjon/pystages/issues"
-"Documentation" = "https://pystages.readthedocs.io/en/latest"
+"Documentation" = "https://pystages.readthedocs.io/en/latest"
diff --git a/pystages/__init__.py b/pystages/__init__.py
@@ -24,3 +24,16 @@
 from .vector import Vector
 from .tic import Tic, TicDirection
 from .cncrouter import CNCRouter, CNCStatus
+
+__all__ = [
+    "Stage",
+    "Corvus",
+    "M3FS",
+    "SMC100",
+    "Autofocus",
+    "Vector",
+    "Tic",
+    "TicDirection",
+    "CNCRouter",
+    "CNCStatus",
+]