Merge branch 'fury-gl:master' into cube_viz

.github/dependabot.yml

@@ -0,0 +1,14 @@
+# Set update schedule for GitHub Actions
+
+version: 2
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions every week
+      interval: "weekly"
+    groups:
+      actions:
+        patterns:
+          - "*"

.github/workflows/codespell.yml

@@ -14,6 +14,6 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Codespell
-        uses: codespell-project/actions-codespell@v1
+        uses: codespell-project/actions-codespell@v2

.github/workflows/doc.yml

@@ -24,11 +24,11 @@ jobs:
       matrix:
         python-version: [3.9]
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install Dependencies
@@ -62,5 +62,5 @@ jobs:
         ssh-key: ${{ secrets.ACTIONS_DEPLOY_KEY }}
         repository-name: fury-gl/fury-website
         folder: ./docs/build/html-web-only
-        target-folder: v0.9.x
+        target-folder: v0.10.x
         clean: false

.github/workflows/test.yml

@@ -54,10 +54,10 @@ jobs:
       PRE_WHEELS: "https://pypi.anaconda.org/scipy-wheels-nightly/simple"
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0
-    - uses: actions/cache@v2
+    - uses: actions/cache@v4
       if: startsWith(runner.os, 'Linux')
       with:
         path: |
@@ -66,22 +66,22 @@ jobs:
         key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
         restore-keys: |
           ${{ runner.os }}-pip-
-    - uses: actions/cache@v2
+    - uses: actions/cache@v4
       if: startsWith(runner.os, 'macOS')
       with:
         path: ~/Library/Caches/pip
         key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
         restore-keys: |
           ${{ runner.os }}-pip-
-    - uses: actions/cache@v2
+    - uses: actions/cache@v4
       if: startsWith(runner.os, 'Windows')
       with:
         path: ~/.pip
         key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
         restore-keys: |
           ${{ runner.os }}-pip-
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Set up Virtualenv
@@ -90,7 +90,7 @@ jobs:
         python -m pip install --upgrade pip virtualenv
         virtualenv $VENV_ARGS venv
     - name: Setup Miniconda
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       if: ${{ matrix.install-type == 'conda' }}
       with:
         auto-update-conda: true
@@ -113,7 +113,7 @@ jobs:
           ci/run_tests.sh
         fi
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       if: ${{ matrix.coverage }}
       with:
         token: ${{ secrets.CODECOV_TOKEN }}

.mailmap

@@ -61,3 +61,5 @@ Sreekar Chigurupati <[email protected]> sreekar chigurupati <chigurup
 Johny Daras <[email protected]> lej0hn <[email protected]>
 Francois Rheault <[email protected]> frheault <[email protected]>
 Dwij Raj Hari <[email protected]> Dwij Raj Hari <[email protected]>
+Tania Castillo <[email protected]> tvcastillod <[email protected]>
+Tania Castillo <[email protected]> Tania Castillo <[email protected]>

LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2023, FURY - Free Unified Rendering in Python. All rights reserved.
+Copyright (c) 2024, FURY - Free Unified Rendering in Python. All rights reserved.
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:

docs/examples/_valid_examples.toml

@@ -88,7 +88,7 @@ readme = "file: _animation.rst"
 position = 10
 enable = true
 files = [
-    "viz_interpolators.py",
+    # "viz_interpolators.py",
     "viz_bezier_interpolator.py",
     "viz_introduction.py",
     "viz_camera.py",

docs/examples/viz_card_sprite_sheet.py

@@ -10,10 +10,11 @@
 First, some imports.
 """
 import os
+from tempfile import TemporaryDirectory as InTemporaryDirectory
+
 from fury import ui, window
 from fury.data import fetch_viz_icons
 from fury.io import load_image, load_sprite_sheet, save_image
-from tempfile import TemporaryDirectory as InTemporaryDirectory
 
 ##############################################################################
 # First we need to fetch some icons that are included in FURY.
@@ -23,7 +24,9 @@
 
 fetch_viz_icons()
 
-sprite_sheet = load_sprite_sheet('https://i.imgur.com/0yKFTBQ.png', 5, 5)
+sprite_sheet = load_sprite_sheet('https://raw.githubusercontent.com/fury-gl/'
+                                 'fury-data/master/unittests/fury_sprite.png',
+                                 5, 5)
 CURRENT_SPRITE_IDX = 0
 
 vtk_sprites = []

docs/examples/viz_chain.py

@@ -92,15 +92,15 @@
     basePosition,
     baseOrientation,
     linkMasses=link_Masses,
-    linkCollisionShapeIndices=linkCollisionShapeIndices,
-    linkVisualShapeIndices=linkVisualShapeIndices,
+    linkCollisionShapeIndices=linkCollisionShapeIndices.astype(int),
+    linkVisualShapeIndices=linkVisualShapeIndices.astype(int),
     linkPositions=linkPositions,
     linkOrientations=linkOrientations,
     linkInertialFramePositions=linkInertialFramePositions,
     linkInertialFrameOrientations=linkInertialFrameOrns,
-    linkParentIndices=indices,
-    linkJointTypes=jointTypes,
-    linkJointAxis=axis,
+    linkParentIndices=indices.astype(int),
+    linkJointTypes=jointTypes.astype(int),
+    linkJointAxis=axis.astype(int),
 )
 
 ###############################################################################

docs/examples/viz_interaction.py

@@ -18,7 +18,6 @@
 
 Notes
 -----
-
 If you don't have ffmpeg installed, you need to install it to use WebRTC
 
 Linux
@@ -29,6 +28,7 @@
 OS X
 
 `brew install ffmpeg opus libvpx pkg-config`
+
 """
 
 import multiprocessing

docs/examples/viz_skinning.py

@@ -32,7 +32,7 @@
 
 # After we get the timeline object, We want to initialise the skinning process.
 # You can set `bones=true` to visualize each bone transformation. Additionally,
-# you can set `lenght` of bones in the `initialise_skin` method.
+# you can set `length` of bones in the `initialise_skin` method.
 # Note: Make sure to call this method before you initialize ShowManager, else
 # bones won't be added to the scene.
 

docs/examples/viz_widget.py

@@ -31,8 +31,9 @@
 `brew install ffmpeg opus libvpx pkg-config`
 
 Notes
-------
+-----
 For this example your python version should be 3.8 or greater
+
 """
 
 import asyncio

docs/examples/viz_wrecking_ball.py

@@ -177,15 +177,15 @@
     basePosition,
     baseOrientation,
     linkMasses=link_Masses,
-    linkCollisionShapeIndices=linkCollisionShapeIndices,
-    linkVisualShapeIndices=linkVisualShapeIndices,
-    linkPositions=linkPositions,
-    linkOrientations=linkOrientations,
-    linkInertialFramePositions=linkInertialFramePositions,
-    linkInertialFrameOrientations=linkInertialFrameOrns,
-    linkParentIndices=indices,
-    linkJointTypes=jointTypes,
-    linkJointAxis=axis,
+    linkCollisionShapeIndices=linkCollisionShapeIndices.astype(int),
+    linkVisualShapeIndices=linkVisualShapeIndices.astype(int),
+    linkPositions=linkPositions.astype(int),
+    linkOrientations=linkOrientations.astype(int),
+    linkInertialFramePositions=linkInertialFramePositions.astype(int),
+    linkInertialFrameOrientations=linkInertialFrameOrns.astype(int),
+    linkParentIndices=indices.astype(int),
+    linkJointTypes=jointTypes.astype(int),
+    linkJointAxis=axis.astype(int),
 )
 
 ###############################################################################

docs/experimental/viz_canvas.py

@@ -194,7 +194,7 @@ def test_sh():
             vec3 lin  = 2.5*occ*vec3(1.0,1.00,1.00)*(0.6+0.4*nor.y);
                  lin += 1.0*sss*vec3(1.0,0.95,0.70)*occ;
 
-            // surface-light interacion
+            // surface-light interaction
             col = mate.xyz * lin;
         }
 

docs/experimental/viz_molecular_demo.py

@@ -25,6 +25,7 @@
 
 
 Importing necessary modules
+
 """
 
 import os

docs/experimental/viz_shader_canvas.py

@@ -160,6 +160,7 @@ def rectangle2(centers, colors, use_vertices=False, size=(2, 2)):
     centers : ndarray, shape (N, 3)
     colors : ndarray (N,3) or (N, 4) or tuple (3,) or tuple (4,)
         RGB or RGBA (for opacity) R, G, B and A should be at the range [0, 1]
+
     """
     if np.array(colors).ndim == 1:
         colors = np.tile(colors, (len(centers), 1))

docs/experimental/viz_shader_frag_fract.py

@@ -1,5 +1,4 @@
-"""
-This simple example demonstrates how to use shaders to modify the fragments in
+"""This simple example demonstrates how to use shaders to modify the fragments in
 your scene. We will use the AddShaderReplacement() function to modify the
 fragment shader with VTK's shader template system.
 

docs/source/_static/versions_switcher.json

@@ -5,8 +5,13 @@
     "url": "https://fury.gl/dev/index.html"
   },
   {
-    "name": "v0.9.x (stable)",
+    "name": "v0.10.x (stable)",
     "version": "stable",
+    "url": "https://fury.gl/v0.10.x/index.html"
+  },
+  {
+    "name": "v0.9.x",
+    "version": "v0.9.x",
     "url": "https://fury.gl/v0.9.x/index.html"
   },
   {

docs/source/conf.py

@@ -341,9 +341,6 @@
     'scipy': ('https://docs.scipy.org/doc/scipy/', None),
     'pandas': ('https://pandas.pydata.org/docs/', None),
     'matplotlib': ('https://matplotlib.org/stable/', None),
-    'dipy': (
-        'https://dipy.org/documentation/latest',
-        'https://dipy.org/documentation/latest/objects.inv/',
-    ),
+    'dipy': ('https://docs.dipy.org/stable', None),
     'scikit-learn': ('https://scikit-learn.org/stable/', None),
 }

docs/source/ext/apigen.py

@@ -1,5 +1,4 @@
-"""
-Attempt to generate templates for module reference with Sphinx.
+"""Attempt to generate templates for module reference with Sphinx.
 
 To include extension modules, first identify them as valid in the
 ``_uri2path`` method, then handle them in the ``_parse_module_with_import``
@@ -15,6 +14,7 @@
 This is a modified version of a script originally shipped with the PyMVPA
 project, then adapted for use first in NIPY and then in skimage. PyMVPA
 is an MIT-licensed project.
+
 """
 
 # Stdlib imports
@@ -29,7 +29,8 @@
 
 class ApiDocWriter:
     """Class for automatic detection and parsing of API docs
-    to Sphinx-parsable reST format."""
+    to Sphinx-parsable reST format.
+    """
 
     # only separating first two levels
     rst_section_levels = ['*', '=', '-', '~', '^']

docs/source/ext/build_modref_templates.py

@@ -54,7 +54,6 @@ def generate_api_reference_rst(
 
 def setup(app):
     """Setup sphinx extension for API reference generation."""
-
     app.connect('builder-inited', generate_api_reference_rst)
     # app.connect('build-finished', summarize_failing_examples)
 

docs/source/ext/github.py

@@ -30,7 +30,6 @@ def make_link_node(rawtext, app, type, slug, options):
     :param slug: ID of the thing to link to
     :param options: Options dictionary passed to role func.
     """
-
     try:
         base = app.config.github_project_url
         if not base:
@@ -68,7 +67,6 @@ def ghissue_role(name, rawtext, text, lineno, inliner, options={}, content=[]):
     :param options: Directive options for customization.
     :param content: The directive content for customization.
     """
-
     try:
         issue_num = int(text)
         if issue_num <= 0:

docs/source/posts/2021/2021-06-28-gsoc-devmessias-4.rst

@@ -156,7 +156,7 @@ must have a way to lock the write/read if the memory resource is busy.
 Meanwhile the
 `multiprocessing.Arrays <https://docs.python.org/3/library/multiprocessing.html#multiprocessing.Array>`__
 already has a context which allows lock (.get_lock()) SharedMemory
-dosen’t[2]. The use of abstract class allowed me to deal with those
+doesn’t[2]. The use of abstract class allowed me to deal with those
 peculiarities. `commit
 358402e <https://github.com/fury-gl/fury/pull/437/commits/358402ea2f06833f66f45f3818ccc3448b2da9cd>`__
 

docs/source/posts/2021/2021-07-05-gsoc-devmessias-5.rst

@@ -35,7 +35,7 @@ tasks related with this PR:
    `#424`_ now is possible to control all the visual characteristics at
    runtime.
 -  2D Layout: Meanwhile 3d network representations are very usefully
-   for exploring a dataset is hard to convice a group of network
+   for exploring a dataset is hard to convince a group of network
    scientists to use a visualization system which doesn't allow 2d
    representations. Because of that I started to coding the 2d behavior
    in the network visualization system.

docs/source/posts/2021/2021-08-23-final-work-antriksh.rst

@@ -83,7 +83,7 @@ Objectives Completed
 
 - **Add Accordion2D UI element to the UI sub-module**
 
-  Added Accordion2D to the UI sub-module. This Ui element allows users to visulize data in a tree with depth of one. Each node has a title and a content panel. The children for each node can be N if and only if the children are not nodes themselves. The child UIs can be placed inside the content panel by passing some coordinates, which can be absolute or normalized w.r.t the node content panel size. Tests and two demos were added for this UI element. Below is a screenshot for reference
+  Added Accordion2D to the UI sub-module. This Ui element allows users to visualize data in a tree with depth of one. Each node has a title and a content panel. The children for each node can be N if and only if the children are not nodes themselves. The child UIs can be placed inside the content panel by passing some coordinates, which can be absolute or normalized w.r.t the node content panel size. Tests and two demos were added for this UI element. Below is a screenshot for reference
 
   .. image:: https://camo.githubusercontent.com/9395d0ea572d7f253a051823f02496450c9f79d19ff0baf32841ec648b6f2860/68747470733a2f2f692e696d6775722e636f6d2f7854754f645a742e706e67
         :width: 200

docs/source/posts/2023/2023-01-24-final-report-praneeth.rst

@@ -133,7 +133,7 @@ Other Objectives
 
 -  **Grouping Shapes**
 
-   Many times we need to perform some actions on a group of shapes so here we are with the grouping feature using which you can group shapes together, reposition them, rotate them and delete them together. To activate grouping of shapes you have to be on selection mode then by holding **Ctrl** key select the required shapes and they will get highlighted. To remove shape from the group just hold the **Ctrl** and click the shape again it will get deselected. Then once eveything is grouped you can use the normal transformation as normal i.e. for translation just drag the shapes around and for rotation the rotation slider appears at usual lower left corner which can be used.
+   Many times we need to perform some actions on a group of shapes so here we are with the grouping feature using which you can group shapes together, reposition them, rotate them and delete them together. To activate grouping of shapes you have to be on selection mode then by holding **Ctrl** key select the required shapes and they will get highlighted. To remove shape from the group just hold the **Ctrl** and click the shape again it will get deselected. Then once everything is grouped you can use the normal transformation as normal i.e. for translation just drag the shapes around and for rotation the rotation slider appears at usual lower left corner which can be used.
 
    *Pull Requests:*