Merge branch 'shodfimpl' of https://github.com/tvcastillod/fury into …

…shodfimpl

.github/workflows/doc.yml

@@ -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: v0.10.x
+        target-folder: v0.11.x
         clean: false

.github/workflows/test.yml

@@ -25,7 +25,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.8, 3.9, '3.10', 3.11]
+        python-version: [3.9, '3.10', 3.11, 3.12]
         os: [ubuntu-latest, macos-latest, windows-latest]
         platform: [x64]
         install-type: [pip, ]  # conda]
@@ -34,13 +34,13 @@ jobs:
         use-pre: [false]
         include:
           - os: macos-latest # ubuntu-latest
-            python-version: '3.10'
+            python-version: 3.11
             install-type: pip
             depends: OPTIONAL_DEPS
             coverage: true
             use-pre: false
           - os: ubuntu-latest
-            python-version: '3.10'
+            python-version: 3.12
             install-type: pip
             depends: OPTIONAL_DEPS
             coverage: false
@@ -53,6 +53,8 @@ jobs:
       USE_PRE: ${{ matrix.use-pre }}
       COVERAGE: ${{ matrix.coverage }}
       PRE_WHEELS: "https://pypi.anaconda.org/scipy-wheels-nightly/simple"
+      # EAGER_IMPORT: 1  # to explore what is the issue.
+
 
     steps:
     - uses: actions/checkout@v4

.mailmap

@@ -63,3 +63,8 @@ Francois Rheault <[email protected]> frheault <francois.m.rheaul
 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]>
+Wachiou BOURAÏMA <[email protected]> Wachiou BOURAÏMA <[email protected]>
+Ishan Kamboj <[email protected]> Ishan Kamboj <[email protected]>
+Robin Roy <[email protected]> Robin Roy <[email protected]>
+Robin Roy <[email protected]> Robin <[email protected]>
+Kaustav Deka <[email protected]> Kaustav Deka <[email protected]>

.pep8speaks.yml

@@ -10,3 +10,26 @@ message:  # Customize the comment made by the bot
         header: "Hello @{name}, Thank you for updating!"
         footer: "To test for issues locally, `pip install flake8` and then run `flake8 fury`."
     no_errors: "Cheers! There are no style issues detected in this Pull Request. :beers: "
+
+pycodestyle:
+    max-line-length: 88  # Default is 79 in PEP8
+    # ignore:  # Errors and warnings to ignore
+    #    - W391
+    #    - E203
+    # exclude:
+    #     - doc/examples
+    #     - dipy/info.py
+    #     - doc/conf.py
+flake8:  # Valid if scanner.linter is flake8
+    max-line-length: 88  # Default is 79 in PEP8
+    ignore: []
+    exclude: []
+    count: False
+    show-source: False
+    statistics: False
+    hang-closing: False
+    filename: []
+    select: []
+
+only_mention_files_with_errors: True  # If False, a separate status comment for each file is made.
+descending_issues_order: False # If True, PEP8 issues in message will be displayed in descending order of line numbers in the file

AUTHORS.rst

@@ -17,71 +17,91 @@ Contributors
 
 * Serge Koudoro
 * Eleftherios Garyfallidis
-* Soham Biswas
+* Mohamed Agour
+* Praneeth Shetty
 * Javier Guaje
-* Sajag Swami
+* Anand Shivam
 * Bruno Messias
+* Soham Biswas
+* Sajag Swami
+* Antriksh Misri
+* Tania Castillo
 * Ranveer Aggarwal
 * Lenix Lobo
+* Joao Victor Dell Agli
 * Marc-Alexandre Côté
 * Melina Raglin
-* Antriksh Misri
-* Karan
 * Ariel Rokem
+* Karan
+* maharshigor
+* Filipi Nascimento Silva
 * David Reagan
-* Vivek Choudhary
+* Nasim Anousheh
 * Prashil
+* Vivek Choudhary
 * Saransh Jain
-* Nasim Anousheh
 * Shreyas Bhujbal
 * Tushar
-* Matthew Brett
+* Wachiou BOURAÏMA
+* Zhiwen Shi
 * Charles Poirier
+* Ishan Kamboj
+* Matthew Brett
+* Frank Cerasoli
+* Sreekar Chigurupati
+* Francois Rheault
 * Naman Bansal
+* Robin Roy
 * Etienne St-Onge
 * Kesshi Jordan
-* Praneeth Shetty
-* ibrahimAnis
+* Amit Chaudhari
 * Bago Amirbekian
+* Jon Haitz Legarreta Gorroño
 * Omar Ocegueda
-* Amit Chaudhari
-* Meha Bhalodiya
+* ibrahimAnis
 * Kevin Sitek
+* Meha Bhalodiya
 * Sanjay Marreddi
+* sparshg
 * ChenCheng0630
-* Jon Haitz Legarreta Gorroño
 * Gregory R. Lee
-* Filipi Nascimento Silva
+* Enes Albay
 * Liam Donohue
-* Anand Shivam
+* Rohit Kharsan
 * Shahnawaz Ahmed
-* Tingyi Wanyan
-* Enes Albay
 * Stefan van der Walt
-* PrayasJ
+* Tingyi Wanyan
+* Dwij Raj Hari
 * Guillaume Favelier
+* Johny Daras
+* PrayasJ
 * Samuel St-Jean
+* Bishakh Ghosh
 * Gottipati Gautam
-* theaverageguy
 * Hariharan Ayappane
-* Bishakh Ghosh
-* Jhalak Gupta
+* Maharshi Gor
+* theaverageguy
 * Aju100
-* Christopher Nguyen
 * Alexandre Gauvin
-* Scott Trinkle
+* Christopher Nguyen
+* Jhalak Gupta
 * Jiri Borovec
 * Marssis
+* Sara Hamza
+* Scott Trinkle
+* Siddharth Gautam
+* dependabot[bot]
 * Adam Rybinski
-* LoopThrough-i-j
-* Ian Nimmo-Smith
 * Aman Soni
+* Daniel S. Katz
+* Devanshu Modi
 * Gauvin Alexandre
-* Pietro Astolfi
 * Gurdit Siyan
-* Devanshu Modi
-* Daniel S. Katz
+* Ian Nimmo-Smith
 * Jacob Wasserth
-* Yaroslav Halchenko
+* Kaustav Deka
+* LoopThrough-i-j
 * MIHIR
-* Shivam Anand
+* Pietro Astolfi
+* Yaroslav Halchenko
+* sailesh

CONTRIBUTING.rst

@@ -125,15 +125,15 @@ Checklist before Releasing
   outstanding issues that can be closed, and whether there are any issues that
   should delay the release.  Label them !
 
-* Check whether there are no build failing on `Travis`.
+* Check whether there are no build failing on `GitHub Actions`.
 
 * Review and update the release notes. Get a partial list of contributors with something like::
 
-      git shortlog -nse v0.1.0..
+      git shortlog -nse v0.10.0..
 
-  where ``v0.1.0`` was the last release tag name.
+  where ``v0.10.0`` was the last release tag name.
 
-  Then manually go over ``git shortlog v0.1.0..`` to make sure the release notes
+  Then manually go over ``git shortlog v0.10.0..`` to make sure the release notes
   are as complete as possible and that every contributor was recognized.
 
 * Use the opportunity to update the ``.mailmap`` file if there are any duplicate
@@ -145,16 +145,18 @@ Checklist before Releasing
 
 * Generate release notes. Go to ``docs/source/ext`` and run ``github_tools.py`` script the following way::
 
-    $ python github_tools.py --tag=v0.1.0 --save --version=0.2.0
+    $ python github_tools.py --tag=v0.10.0 --save --version=0.11.0
 
-  This command will generate a new file named ``release0.2.0.rst`` in ``release_notes`` folder.
+  This command will generate a new file named ``release0.11.0.rst`` in ``release_notes`` folder.
+
+* Add in ``release-history.rst`` the newly created file ``release0.11.0.rst``.
 
 * Check the examples and tutorial - we really need an automated check here.
 
 * Make sure all tests pass on your local machine (from the ``<fury root>`` directory)::
 
     cd ..
-    pytest -s --verbose --doctest-modules fury
+    pytest -svv --doctest-modules fury
     cd fury # back to the root directory
 
 * Check the documentation doctests::
@@ -213,8 +215,7 @@ Doing the release
 
 * Publish a release on PyPI::
 
-    python setup.py sdist
-    python setup.py bdist_wheel
+    python -m build
     twine upload dist/*
 
 

docs/examples/viz_advanced.py

@@ -11,6 +11,7 @@
 the main functions using the following modules.
 """
 
+import fury
 from dipy.data.fetcher import fetch_bundles_2_subjects, read_bundles_2_subjects
 
 ###############################################################################
@@ -37,7 +38,6 @@
 from dipy.tracking.streamline import Streamlines
 import numpy as np
 
-from fury import actor, ui, window
 
 fetch_bundles_2_subjects()
 
@@ -82,13 +82,13 @@
 # Now we create, a ``Scene`` object and add the streamlines using the
 # ``line`` function and an image plane using the ``slice`` function.
 
-scene = window.Scene()
-stream_actor = actor.line(streamlines)
+scene = fury.window.Scene()
+stream_actor = fury.actor.line(streamlines)
 
 if not world_coords:
-    image_actor_z = actor.slicer(data, affine=np.eye(4))
+    image_actor_z = fury.actor.slicer(data, affine=np.eye(4))
 else:
-    image_actor_z = actor.slicer(data, affine)
+    image_actor_z = fury.actor.slicer(data, affine)
 
 ###############################################################################
 # We can also change also the opacity of the slicer.
@@ -123,38 +123,38 @@
 # ``show``. The more appropriate way is to use them with the ``ShowManager``
 # object which allows accessing the pipeline in different areas. Here is how:
 
-show_m = window.ShowManager(scene, size=(1200, 900))
+show_m = fury.window.ShowManager(scene, size=(1200, 900))
 
 
 ###############################################################################
 # After we have initialized the ``ShowManager`` we can go ahead and create
 # sliders to move the slices and change their opacity.
 
-line_slider_z = ui.LineSlider2D(
+line_slider_z = fury.ui.LineSlider2D(
     min_value=0,
     max_value=shape[2] - 1,
     initial_value=shape[2] / 2,
     text_template="{value:.0f}",
     length=140,
 )
 
-line_slider_x = ui.LineSlider2D(
+line_slider_x = fury.ui.LineSlider2D(
     min_value=0,
     max_value=shape[0] - 1,
     initial_value=shape[0] / 2,
     text_template="{value:.0f}",
     length=140,
 )
 
-line_slider_y = ui.LineSlider2D(
+line_slider_y = fury.ui.LineSlider2D(
     min_value=0,
     max_value=shape[1] - 1,
     initial_value=shape[1] / 2,
     text_template="{value:.0f}",
     length=140,
 )
 
-opacity_slider = ui.LineSlider2D(
+opacity_slider = fury.ui.LineSlider2D(
     min_value=0.0, max_value=1.0, initial_value=slicer_opacity, length=140
 )
 
@@ -194,7 +194,7 @@ def change_opacity(slider):
 
 
 def build_label(text):
-    label = ui.TextBlock2D()
+    label = fury.ui.TextBlock2D()
     label.message = text
     label.font_size = 18
     label.font_family = "Arial"
@@ -216,7 +216,7 @@ def build_label(text):
 ###############################################################################
 # 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 = fury.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))
@@ -267,7 +267,7 @@ def win_callback(obj, _event):
     show_m.start()
 
 else:
-    window.record(
+    fury.window.record(
         scene, out_path="bundles_and_3_slices.png", size=(1200, 900), reset_camera=False
     )