Merge branch 'fury-gl:master' into cube_viz

.github/workflows/check_format.yml

@@ -0,0 +1,29 @@
+name: code format
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+jobs:
+  pre-commit:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ['3.10']
+        requires: ['latest']
+
+    steps:
+    - name: Check out repository
+      uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install and run pre-commit hooks
+      uses: pre-commit/[email protected]

.github/workflows/test.yml

@@ -18,6 +18,7 @@ defaults:
 jobs:
   build:
     runs-on: ${{ matrix.os }}
+    timeout-minutes: 60
     defaults:
       run:
         shell: bash

.pre-commit-config.yaml

@@ -14,15 +14,12 @@ repos:
       - id: check-merge-conflict
       - id: check-vcs-permalinks
       - id: detect-aws-credentials
+        args: [--allow-missing-credentials]
       - id: detect-private-key
   # - repo: https://github.com/grantjenks/blue
   #   rev: v0.9.1
   #   hooks:
   #     - id: blue
-  - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
-    hooks:
-      - id: isort
   - repo: https://github.com/pycqa/flake8
     rev: 6.0.0
     hooks:
@@ -49,3 +46,9 @@ repos:
           - importlib_resources
         args: ["fury"]
         pass_filenames: false
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.7
+    hooks:
+      # Run the linter
+      - id: ruff
+        args: [ --fix ]

docs/examples/viz_advanced.py

@@ -11,7 +11,6 @@
 the main functions using the following modules.
 """
 
-import numpy as np
 from dipy.data.fetcher import fetch_bundles_2_subjects, read_bundles_2_subjects
 
 ###############################################################################
@@ -36,6 +35,7 @@
 #
 # First we need to fetch and load some datasets.
 from dipy.tracking.streamline import Streamlines
+import numpy as np
 
 from fury import actor, ui, window
 

docs/examples/viz_bundles.py

@@ -7,9 +7,9 @@
 which provides metrics and bundles.
 """
 
-import numpy as np
 from dipy.data import fetch_bundles_2_subjects, read_bundles_2_subjects
 from dipy.tracking.streamline import length, transform_streamlines
+import numpy as np
 
 from fury import actor, window
 

docs/examples/viz_dt_ellipsoids.py

@@ -12,12 +12,11 @@
 """
 import itertools
 
-import numpy as np
-
 from dipy.io.image import load_nifti
+import numpy as np
 
-from fury import window, actor, ui
-from fury.actor import _fa, _color_fa
+from fury import actor, ui, window
+from fury.actor import _color_fa, _fa
 from fury.data import fetch_viz_dmri, read_viz_dmri
 from fury.primitive import prim_sphere
 

docs/examples/viz_fiber_odf.py

@@ -7,12 +7,12 @@
 orientation distribution functions (ODF) using fury's odf_slicer.
 """
 
+from dipy.data import get_sphere
+from dipy.reconst.shm import sh_to_sf_matrix
 import nibabel as nib
 
 # First, we import some useful modules and methods.
 import numpy as np
-from dipy.data import get_sphere
-from dipy.reconst.shm import sh_to_sf_matrix
 
 from fury import actor, ui, window
 from fury.data import fetch_viz_dmri, fetch_viz_icons, read_viz_dmri

docs/examples/viz_multithread.py

@@ -10,8 +10,8 @@
 adds and removes elements from the scene.
 """
 
-import time
 from threading import Thread
+import time
 
 import numpy as np
 

docs/examples/viz_network.py

@@ -15,9 +15,7 @@
 
 import numpy as np
 
-from fury import actor
-from fury import colormap as cmap
-from fury import window
+from fury import actor, colormap as cmap, window
 from fury.data import fetch_viz_wiki_nw
 
 ###############################################################################

docs/examples/viz_network_animated.py

@@ -18,9 +18,7 @@
 
 import numpy as np
 
-from fury import actor
-from fury import colormap as cmap
-from fury import window
+from fury import actor, colormap as cmap, window
 from fury.utils import compute_bounds, update_actor, vertices_from_actor
 
 ###############################################################################

docs/examples/viz_no_interaction.py

@@ -12,9 +12,7 @@
 # multiprocessing.set_start_method('spawn')
 import numpy as np
 
-from fury import actor
-from fury import colormap as cmap
-from fury import window
+from fury import actor, colormap as cmap, window
 from fury.data.fetcher import fetch_viz_wiki_nw
 from fury.stream.client import FuryStreamClient
 from fury.stream.server.main import web_server_raw_array

docs/examples/viz_roi_contour.py

@@ -13,13 +13,13 @@
 from dipy.reconst.shm import CsaOdfModel
 
 try:
-    from dipy.tracking.local import LocalTracking
     from dipy.tracking.local import (
+        LocalTracking,
         ThresholdTissueClassifier as ThresholdStoppingCriterion,
     )
 except ImportError:
-    from dipy.tracking.stopping_criterion import ThresholdStoppingCriterion
     from dipy.tracking.local_tracking import LocalTracking
+    from dipy.tracking.stopping_criterion import ThresholdStoppingCriterion
 
 from dipy.tracking import utils
 from dipy.tracking.streamline import Streamlines

docs/examples/viz_slice.py

@@ -8,8 +8,8 @@
 
 import os
 
-import nibabel as nib
 from dipy.data import fetch_bundles_2_subjects
+import nibabel as nib
 
 from fury import actor, ui, window
 

docs/examples/viz_spinbox.py

@@ -9,9 +9,10 @@
 
 First, some imports.
 """
+import numpy as np
+
 from fury import actor, ui, utils, window
 from fury.data import fetch_viz_icons
-import numpy as np
 
 ##############################################################################
 # First we need to fetch some icons that are included in FURY.

docs/examples/viz_tab.py

@@ -27,6 +27,12 @@
 
 tab_ui = ui.TabUI(position=(49, 94), size=(300, 300), nb_tabs=3, draggable=True)
 
+###############################################################################
+# We can also define the position of the Tab Bar.
+# By default the Tab Bar is positioned at top
+
+tab_ui.tab_bar_pos = 'bottom'
+
 ###############################################################################
 # Slider Controls for a Cube for Tab Index 0
 # ==========================================

docs/experimental/viz_canvas.py

@@ -2,8 +2,8 @@
 import vtk
 from vtk.util import numpy_support
 
-import fury.primitive as fp
 from fury import actor, window
+import fury.primitive as fp
 from fury.utils import (
     get_actor_from_polydata,
     numpy_to_vtk_colors,

docs/experimental/viz_molecular_demo.py

@@ -33,9 +33,7 @@
 
 import numpy as np
 
-from fury import actor
-from fury import molecular as mol
-from fury import ui, window
+from fury import actor, molecular as mol, ui, window
 
 ###############################################################################
 # Downloading the PDB file of the protein to be rendered (the user can change

docs/experimental/viz_multisdf.py

@@ -2,9 +2,9 @@
 import vtk
 from vtk.util import numpy_support
 
+from fury import actor, window
 import fury.primitive as fp
 import fury.shaders as fs
-from fury import actor, window
 from fury.utils import get_actor_from_primitive
 
 verts, faces = fp.prim_box()

docs/experimental/viz_shader_canvas.py

@@ -1,6 +1,6 @@
 import numpy as np
-import vtk
 from scipy.spatial import Delaunay
+import vtk
 from vtk.util import numpy_support
 
 from fury.utils import (

docs/experimental/viz_shader_canvas_sk.py

@@ -1,6 +1,6 @@
 import numpy as np
-import vtk
 from viz_shader_canvas import cube, disk, rectangle, rectangle2, square
+import vtk
 
 from fury import actor, window
 

docs/experimental/viz_shader_faces.py

@@ -1,6 +1,6 @@
 import numpy as np
-import vtk
 from viz_shader_canvas import glyph_dot
+import vtk
 
 from fury import actor, window
 

docs/experimental/viz_shader_parallax_truchet.py

@@ -1,5 +1,5 @@
-import vtk
 from viz_shader_canvas import cube
+import vtk
 
 from fury import window
 

docs/experimental/viz_shader_perlin_noise.py

@@ -1,7 +1,7 @@
 import numpy as np
-import vtk
 from scipy.spatial import Delaunay
 from viz_shader_canvas import surface
+import vtk
 
 from fury import window
 

docs/experimental/viz_shader_sines_1.py

@@ -1,5 +1,5 @@
-import vtk
 from viz_shader_canvas import cube
+import vtk
 
 from fury import window
 

docs/experimental/viz_shader_square.py

@@ -1,6 +1,6 @@
 import numpy as np
-import vtk
 from viz_shader_canvas import cube, square
+import vtk
 
 from fury import actor, window
 

docs/experimental/viz_shader_texture.py

@@ -1,6 +1,6 @@
 import numpy as np
-import vtk
 from viz_shader_canvas import cube
+import vtk
 
 from fury import window
 from fury.utils import rgb_to_vtk

docs/experimental/viz_shader_wave.py

@@ -1,5 +1,5 @@
-import vtk
 from viz_shader_canvas import cube, disk, rectangle, square
+import vtk
 
 from fury import actor, window
 

docs/source/_static/css/comp-soft.css

@@ -51,7 +51,7 @@
   width: var(--s);
   min-width: var(--s);
   margin: var(--m) var(--m) 0;
-  height: var(--s); 
+  height: var(--s);
   font-size:initial;
   border-radius: 50%;
   background: white;
@@ -73,4 +73,4 @@
 
 .comp-soft-image-holder img {
   max-width: 80%;
-}
+}

docs/source/_static/css/custom.css

@@ -161,7 +161,7 @@ html[data-theme="light"] {
   --pst-color-navbar-link-hover: rgb(77, 171, 207);
 
 }
-/* Log:3/3/24 
+/* Log:3/3/24
 With updating the pydata-theme, there was issue with the <a> elements (They were underlined and colored by default, unlike previously), adding this code snippet helped fix the issue.
 You wouldn't want the links to be colored as there is a dark mode now, which will conflict with the color that pydata is assigning*/
 
@@ -171,4 +171,4 @@ a, a:visited {
 }
 a:hover, a:active {
   text-decoration: underline;
-}
+}

docs/source/_static/css/sponsors.css

@@ -55,4 +55,4 @@
   .cite-wrapper {
     margin: 20px 20px 0;
   }
-}
+}

docs/source/_static/css/util.css

@@ -2961,4 +2961,4 @@ iframe {border: none;}
 	.g-m-rows-3 {
 		grid-template-rows: repeat(3, 1fr);
 	}
-}
+}

docs/source/_static/vendor/display-card.css

@@ -120,7 +120,7 @@
 
 .h-card__divider {
   margin-top: -10px;
-  
+
 }
 
 .h-card__data-background {