Merge remote-tracking branch 'upstream/master' into Fixing-PBR-for-gl…

…TF-loader

.codespellrc

@@ -2,4 +2,4 @@
 skip = .git,*.pdf,*.svg,*.bib,*.html
 # ue,lod,ans,lastr,numer,lamda,PrIs -- variable names
 # Hart,Flagg -- name
-ignore-words-list = IST,nd,te,ue,lod,hart,ans,lastr,numer,lamda,flagg,pris,lod,IST
+ignore-words-list = IST,nd,te,ue,lod,hart,ans,lastr,numer,lamda,flagg,pris,lod,IST,tese

.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/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/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

@@ -18,6 +18,7 @@ defaults:
 jobs:
   build:
     runs-on: ${{ matrix.os }}
+    timeout-minutes: 60
     defaults:
       run:
         shell: bash
@@ -54,10 +55,10 @@ 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 +67,22 @@ 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 +91,7 @@ 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 +114,7 @@ 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]>

.pre-commit-config.yaml

@@ -14,20 +14,8 @@ 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:
-      - id: flake8
-        exclude: "^(docs/experimental|tools)/"
   - repo: https://github.com/codespell-project/codespell
     rev: v2.2.2
     hooks:
@@ -49,3 +37,11 @@ repos:
           - importlib_resources
         args: ["fury"]
         pass_filenames: false
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.3
+    hooks:
+      # Run the linter
+      - id: ruff
+        args: [ --fix]
+      # Run the formatter
+      - id: ruff-format

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/collision-particles.py

@@ -24,7 +24,6 @@
 
 
 def box_edges(box_lx, box_ly, box_lz):
-
     edge1 = 0.5 * np.array(
         [
             [box_lx, box_ly, box_lz],
@@ -54,7 +53,6 @@ def collision():
     sec = int(num_vertices / num_particles)
 
     for i, j in np.ndindex(num_particles, num_particles):
-
         if i == j:
             continue
         distance = np.linalg.norm(xyz[i] - xyz[j])
@@ -148,7 +146,7 @@ def collision():
 counter = itertools.count()
 
 vertices = utils.vertices_from_actor(sphere_actor)
-vcolors = utils.colors_from_actor(sphere_actor, 'colors')
+vcolors = utils.colors_from_actor(sphere_actor, "colors")
 no_vertices_per_sphere = len(vertices) / num_particles
 initial_vertices = vertices.copy() - np.repeat(xyz, no_vertices_per_sphere, axis=0)
 
@@ -177,4 +175,4 @@ def timer_callback(_obj, _event):
 if interactive:
     showm.start()
 
-window.record(showm.scene, size=(900, 768), out_path='simple_collisions.png')
+window.record(showm.scene, size=(900, 768), out_path="simple_collisions.png")

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
 
@@ -46,19 +46,19 @@
 # ``af left`` (left arcuate fasciculus) and maps, e.g. FA for a specific
 # subject.
 
-res = read_bundles_2_subjects('subj_1', ['t1', 'fa'], ['af.left', 'cst.right', 'cc_1'])
+res = read_bundles_2_subjects("subj_1", ["t1", "fa"], ["af.left", "cst.right", "cc_1"])
 
 ###############################################################################
 # We will use 3 bundles, FA and the affine transformation that brings the voxel
 # coordinates to world coordinates (RAS 1mm).
 
-streamlines = Streamlines(res['af.left'])
-streamlines.extend(res['cst.right'])
-streamlines.extend(res['cc_1'])
+streamlines = Streamlines(res["af.left"])
+streamlines.extend(res["cst.right"])
+streamlines.extend(res["cc_1"])
 
-data = res['fa']
+data = res["fa"]
 shape = data.shape
-affine = res['affine']
+affine = res["affine"]
 
 ###############################################################################
 # With our current design it is easy to decide in which space you want the
@@ -134,23 +134,23 @@
     min_value=0,
     max_value=shape[2] - 1,
     initial_value=shape[2] / 2,
-    text_template='{value:.0f}',
+    text_template="{value:.0f}",
     length=140,
 )
 
 line_slider_x = ui.LineSlider2D(
     min_value=0,
     max_value=shape[0] - 1,
     initial_value=shape[0] / 2,
-    text_template='{value:.0f}',
+    text_template="{value:.0f}",
     length=140,
 )
 
 line_slider_y = ui.LineSlider2D(
     min_value=0,
     max_value=shape[1] - 1,
     initial_value=shape[1] / 2,
-    text_template='{value:.0f}',
+    text_template="{value:.0f}",
     length=140,
 )
 
@@ -197,8 +197,8 @@ def build_label(text):
     label = ui.TextBlock2D()
     label.message = text
     label.font_size = 18
-    label.font_family = 'Arial'
-    label.justification = 'left'
+    label.font_family = "Arial"
+    label.justification = "left"
     label.bold = False
     label.italic = False
     label.shadow = False
@@ -208,15 +208,15 @@ def build_label(text):
     return label
 
 
-line_slider_label_z = build_label(text='Z Slice')
-line_slider_label_x = build_label(text='X Slice')
-line_slider_label_y = build_label(text='Y Slice')
-opacity_slider_label = build_label(text='Opacity')
+line_slider_label_z = build_label(text="Z Slice")
+line_slider_label_x = build_label(text="X Slice")
+line_slider_label_y = build_label(text="Y Slice")
+opacity_slider_label = build_label(text="Opacity")
 
 ###############################################################################
 # Now we will create a ``panel`` to contain the sliders and labels.
 
-panel = ui.Panel2D(size=(300, 200), color=(1, 1, 1), opacity=0.1, align='right')
+panel = ui.Panel2D(size=(300, 200), color=(1, 1, 1), opacity=0.1, align="right")
 panel.center = (1030, 120)
 
 panel.add_element(line_slider_label_x, (0.1, 0.75))
@@ -262,15 +262,13 @@ def win_callback(obj, _event):
 scene.reset_clipping_range()
 
 if interactive:
-
     show_m.add_window_callback(win_callback)
     show_m.render()
     show_m.start()
 
 else:
-
     window.record(
-        scene, out_path='bundles_and_3_slices.png', size=(1200, 900), reset_camera=False
+        scene, out_path="bundles_and_3_slices.png", size=(1200, 900), reset_camera=False
     )
 
 del show_m