Merge pull request #218 from SciKit-Surgery/216-final-release-200

216 - final release 2.0.0

.github/workflows/ci.yml

@@ -78,6 +78,7 @@ jobs:
           sudo apt-get update
           sudo apt-get install xvfb
           sudo apt-get install libegl-dev
+          sudo apt-get install libxcb-cursor-dev
           ## Qt for X11 Requirements> https://doc.qt.io/qt-6/linux-requirements.html
           sudo apt-get install libfontconfig1-dev libfreetype6-dev
           sudo apt-get install libx11-dev libx11-xcb-dev
@@ -91,6 +92,7 @@ jobs:
           export DISPLAY=:1
           sudo Xvfb $DISPLAY -screen 0 1024x768x24 </dev/null &
           export QT_DEBUG_PLUGINS=0
+          export QT_QPA_PLATFORM=xcb
           export LD_LIBRARY_PATH=$pythonLocation"/lib/python${{ matrix.python-version }}/site-packages/PySide6/Qt/plugins/platforms"
           coverage erase
           coverage run -a --source ./sksurgeryvtk -m pytest -v -s

.gitignore

@@ -14,3 +14,9 @@ dist/
 
 # For unit tests to write to.
 tests/output
+
+# docs/
+docs/sksurgeryvtk.rst
+docs/sksurgeryvtk.*.rst
+docs/modules.rst
+docs/build

.readthedocs.yaml

@@ -0,0 +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 version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.8"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  builder: html
+  configuration: docs/conf.py
+  fail_on_warning: false
+
+# Optionally declare the Python requirements required to build your docs
+python:
+  install:
+    - requirements: requirements-docs.txt

README.rst

@@ -1,7 +1,7 @@
 scikit-surgeryvtk
 ===============================
 
-.. image:: sksvtk_logo.png
+.. image:: https://raw.githubusercontent.com/SciKit-Surgery/scikit-surgeryvtk/master/sksvtk_logo.png
    :height: 128px
    :width: 128px
    :target: https://github.com/SciKit-Surgery/scikit-surgeryvtk 
@@ -29,8 +29,8 @@ scikit-surgeryvtk
    :target: https://twitter.com/scikit_surgery?ref_src=twsrc%5Etfw
    :alt: Follow scikit_surgery on twitter
 
-Author(s): Stephen Thompson and Matt Clarkson;
-Contributor(s): Miguel Xochicale, Thomas Dowrick, and Mian Ahmad.
+Author(s): Stephen Thompson, Matt Clarkson, Thomas Dowrick and Miguel Xochicale;
+Contributor(s): Mian Ahmad.
 
 scikit-surgeryvtk implements VTK for Image Guided Surgery applications.
 
@@ -74,12 +74,14 @@ You can clone the repository using the following command:
 Running the tests
 ^^^^^^^^^^^^^^^^^
 
-You can run the unit tests by installing and running tox:
+You can run the unit tests, build documentation, and other options by installing and running tox:
 
 ::
 
     pip install tox
     tox
+    tox -e docs
+    tox -e lint
 
 
 Encountering Problems?

docs/conf.py

@@ -13,24 +13,19 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import subprocess
-import os
-import sys
-
 # If extensions (or modules to document with autodoc) are in another directory,
 # 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
+import os
+import sys
 # sys.path.insert(0, os.path.abspath('.'))
 
 working_dir = os.path.abspath(os.path.dirname(__file__))
 root_dir_rel = os.path.join('..')
 root_dir_abs = os.path.abspath(root_dir_rel)
 module_path = root_dir_abs
 sys.path.insert(0, module_path)
-logo_file = 'weiss_logo.png'
+logo_file = 'sksvtk_logo.png'
 logo_path = os.path.join('..', logo_file)
 
 # List of patterns, relative to source directory, that match files and
@@ -45,7 +40,6 @@
     '.DS_Store',
     '_verion.py',
     'versioneer.py'
-
 ]
 
 # Add any paths that contain custom static files (such as style sheets) here,
@@ -55,27 +49,6 @@
 html_static_path = [static_folder]
 
 
-def generate_apidocs(*args):
-    """Generate API docs automatically by trawling the available modules"""
-
-    global working_dir, module_path
-    output_path = working_dir
-    apidoc_command_path = 'sphinx-apidoc'
-    if hasattr(sys, 'real_prefix'):  # called from a virtualenv
-        apidoc_command_path = os.path.join(sys.prefix, 'bin', 'sphinx-apidoc')
-        apidoc_command_path = os.path.abspath(apidoc_command_path)
-    subprocess.check_call(
-        [apidoc_command_path, '--force', '--separate'] +
-        ['-o', output_path, module_path] +
-        [os.path.join(root_dir_abs, pattern) for pattern in exclude_patterns])
-
-
-def setup(app):
-    # Hook to allow for automatic generation of API docs
-    # before doc deployment begins.
-    app.connect('builder-inited', generate_apidocs)
-
-
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
@@ -85,7 +58,7 @@ def setup(app):
 # 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', 'sphinx.ext.viewcode', 'sphinx.ext.imgmath', 'nbsphinx']
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.viewcode', 'sphinx.ext.imgmath']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -99,25 +72,25 @@ def setup(app):
 # The master toctree document.
 master_doc = 'index'
 
-
 # This allows modules to be indexed under the submodule name rather than all appearing under sksurgeryvtk
 modindex_common_prefix = [
     'sksurgeryvtk.'
 ]
 
 # General information about the project.
 project = u'scikit-surgeryvtk'
-copyright = u"2018, University College London"
+copyright = u"2023, University College London"
+# Authors: Stephen Thompson, Matt Clarkson, Thomas Dowrick and Miguel Xochicale
 author = u'Thomas Dowrick'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = u''
+version = u'2.0.0'
 # The full version, including alpha/beta/rc tags.
-release = u''
+release = u'2.0.0'
 
 # The short X.Y version.
 # version = sksurgeryvtk.__version__
@@ -129,15 +102,14 @@ def setup(app):
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+# language = en
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'
 
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
 
-
 # -- Options for HTML output ----------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
@@ -196,7 +168,6 @@ def setup(app):
     ]
 }
 
-
 # -- Options for HTMLHelp output ------------------------------------------
 
 # Output file base name for HTML help builder.
@@ -241,7 +212,6 @@ def setup(app):
      [u'Thomas Dowrick'], 1)
 ]
 
-
 # -- Options for Texinfo output -------------------------------------------
 
 # Grouping the document tree into Texinfo files. List of tuples

docs/index.rst

@@ -5,7 +5,7 @@ scikit-surgeryvtk documentation
    :start-after: .. features-start
    :end-before: .. features-end
 
-`Source code <https://github.com/SciKit-Surgery/scikit-surgeryvtk/>`_ is avaialble on GitHub.
+`Source code <https://github.com/SciKit-Surgery/scikit-surgeryvtk/>`_ is available on GitHub.
 
 .. toctree::
   :maxdepth: 2

docs/module_ref.rst

@@ -3,7 +3,7 @@ Custom QtVTK Widgets
 --------------------
 
 Overlay Widget
-^^^^^^^^^^^^^
+^^^^^^^^^^^^^^
 .. automodule:: sksurgeryvtk.widgets.vtk_overlay_window
    :members:
    :undoc-members:
@@ -16,7 +16,6 @@ Stereo interlaced Widget
    :undoc-members:
    :show-inheritance:
 
-
 Rendering Generator
 ^^^^^^^^^^^^^^^^^^^
 .. automodule:: sksurgeryvtk.widgets.vtk_rendering_generator
@@ -53,7 +52,7 @@ Surface Models
    :undoc-members:
    :show-inheritance:
 
-.. automodule:: sksurgeryvtk.models.surface_model_directory_loader
+.. automodule:: sksurgeryvtk.models.vtk_surface_model_directory_loader
    :members:
    :undoc-members:
    :show-inheritance:
@@ -64,6 +63,7 @@ Unstructured Grid Model
    :members:
    :undoc-members:
    :show-inheritance:
+
 Image Model
 ^^^^^^^^^^^
 .. automodule:: sksurgeryvtk.models.vtk_image_model
@@ -90,7 +90,6 @@ Geometric Primitives
    :undoc-members:
    :show-inheritance:
 
-
 Camera Utilities
 ----------------
 

docs/tutorials/text_overlay.rst

@@ -13,18 +13,29 @@ First, we need to import relevant modules, setup a Qt Application, and create a
 
 .. code-block:: python
 
-    import sys
     import cv2
-    from PySide2 import QtWidgets
+    from PySide6.QtWidgets import QApplication, QWidget, QVBoxLayout
     from sksurgeryvtk.widgets import vtk_overlay_window
     from sksurgeryvtk.text import text_overlay
 
-    app = QtWidgets.QApplication([])
+    # Check if already an instance of QApplication is present or not
+    if not QApplication.instance():
+	    app = QApplication([])
+    else:
+	    app = QApplication.instance()
+
+    window_qwidget = QWidget()
+    window_qwidget.show()
+    layout = QVBoxLayout()
+    window_qwidget.setLayout(layout)
 
     background = cv2.imread('tests/data/rendering/background-960-x-540.png')
-    overlay_window = vtk_overlay_window.VTKOverlayWindow()
+    overlay_window = vtk_overlay_window.VTKOverlayWindow(offscreen=False, init_widget=False)
     overlay_window.set_video_image(background)
 
+    layout.addWidget(overlay_window)
+    overlay_window.AddObserver("ExitEvent", lambda o, e, a=app: a.quit())
+
 
 We can now create a corner annotations:
 
@@ -57,5 +68,8 @@ Finally, we execute the Qt app to show the window:
 .. code-block:: python
 
    overlay_window.show()
-   sys.exit(app.exec_())
+   overlay_window.Initialize()
+   overlay_window.Start()
 
+   app.exec()
+   overlay_window.close()

requirements-dev.txt

@@ -1,22 +1,13 @@
-# This file lists the python packages that your software depends on
-# for development.
-# It is used by pip to manage software dependencies. It is not to be
-# confused with the software requirements, which are listed in
-# doc/requirements.rst
 -r requirements.txt
 coverage<=6.5.0
 mock<=5.0.1
 pyfakefs<=5.1.0
 parameterized<=0.8.1
 pylint<=2.16.1
-sphinx<=5.3.0
-sphinx_rtd_theme<=1.2.0
-nbsphinx<=0.8.12
 pyinstaller<=5.7.0
 pytest<=7.2.1
 pytest-qt-app<=1.0.1
 pytest-qt<=4.2.0
 tox<=4.4.5
 coveralls<=3.3.1
-pyyaml<=6.0
-six<=1.16.0
+pyyaml

requirements-docs.txt

@@ -0,0 +1,5 @@
+-r requirements.txt
+six
+docutils
+sphinx
+sphinx_rtd_theme

requirements.txt

@@ -1,10 +1,10 @@
 # This file lists the python packages that your software depends on.
-# It is used by pip to manage software dependencies. It is not to be
-# confused with the software requirements, which are listed in
-# doc/requirements.rst
+# It is used by pip to manage software dependencies.
+# It is not to be confused with the software requirements,
+# which are listed in requirements-dev.rst and requirements-docs.rst
 numpy>=1.11
-vtk>=9.2.5
-PySide6>=6.4.2
-opencv-contrib-python-headless>=4.2.0.32
+vtk>=9.2.6
+PySide6>=6.5.0
+opencv-contrib-python-headless>=4.7.0.72
 scikit-surgerycore>=0.1.7
-scikit-surgeryimage>=0.10.1
+scikit-surgeryimage>=0.10.1