Merge pull request #250 from brainglobe/mega-fix

Mega fix of brainrender
brainglobe · Dec 1, 2023 · 19350ce · 19350ce
2 parents 5a8418c + 5be13ea
commit 19350ce
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diff --git a/.coveragerc b/.coveragerc
@@ -1,10 +1,10 @@
 [RUN]
-omit = 
+omit =
     brainrender/gui/*
     brainrender/gui
 
 [report]
-omit = 
+omit =
     brainrender/gui/*
     brainrender/gui
 

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml
@@ -0,0 +1,72 @@
+name: tests
+
+on:
+  push:
+    branches:
+      - '*'
+    tags:
+      - '*'
+  pull_request:
+
+jobs:
+  linting:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: neuroinformatics-unit/actions/lint@v2
+
+  test:
+    needs: [linting]
+    name: ${{ matrix.os }} py${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        # Run all supported Python versions on linux
+        python-version: ["3.9", "3.10", "3.11"]
+        os: [ubuntu-latest]
+        # Include one windows and macos run
+        include:
+        - os: macos-latest
+          python-version: "3.11"
+        - os: windows-latest
+          python-version: "3.11"
+
+    steps:
+      - name: Install hdf5 libs for Mac
+        if: runner.os == 'macOS'
+        run: brew install hdf5
+
+      # Helps set up VTK with a headless display
+      - uses: pyvista/setup-headless-display-action@v2
+
+      # Sets up ffmpeg to we can run video tests on CI
+      - uses: FedericoCarboni/setup-ffmpeg@v2
+        id: setup-ffmpeg
+
+      # Run tests
+      - uses: neuroinformatics-unit/actions/test@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+  build_sdist_wheels:
+    name: Build source distribution
+    needs: [test]
+    if: github.event_name == 'push' && github.ref_type == 'tag'
+    runs-on: ubuntu-latest
+    steps:
+    - uses: neuroinformatics-unit/actions/build_sdist_wheels@v2
+
+
+  upload_all:
+    name: Publish build distributions
+    needs: [build_sdist_wheels]
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/download-artifact@v3
+      with:
+        name: artifact
+        path: dist
+    - uses: pypa/gh-action-pypi-publish@v1.5.0
+      with:
+        user: __token__
+        password: ${{ secrets.TWINE_API_KEY }}
diff --git a/.gitignore b/.gitignore
@@ -175,5 +175,3 @@ venv.bak/
 .idea/
 
 *.~lock.*
-
-
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,9 +1,21 @@
 repos:
--   repo: https://github.com/psf/black
-    rev: 23.10.1
-    hooks:
-    - id: black
--   repo: https://github.com/PyCQA/flake8
-    rev: 6.1.0
-    hooks:
-    - id: flake8
+    - repo: https://github.com/pre-commit/pre-commit-hooks
+      rev: v4.4.0
+      hooks:
+          - id: check-docstring-first
+          - id: check-executables-have-shebangs
+          - id: check-merge-conflict
+          - id: check-toml
+          - id: end-of-file-fixer
+          - id: mixed-line-ending
+            args: [--fix=lf]
+          - id: requirements-txt-fixer
+          - id: trailing-whitespace
+    - repo: https://github.com/charliermarsh/ruff-pre-commit
+      rev: v0.0.272
+      hooks:
+        - id: ruff
+    - repo: https://github.com/psf/black
+      rev: 23.3.0
+      hooks:
+          - id: black
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -6,4 +6,4 @@ recursive-exclude tests *
 recursive-exclude examples *
 recursive-exclude imgs *
 recursive-exclude videos *
-recursive-exclude benchmark *
+recursive-exclude benchmark *
diff --git a/README.md b/README.md
@@ -1,7 +1,3 @@
-## Update 2023-10-05:  brainrender is currently unsupported
-### brainrender has a number of critical bugs that we are aiming to address. Until these issues are fixed, we will be able to offer very limited support. 
-### For further details please see [this issue](https://github.com/brainglobe/brainrender/issues/247).
-
 
 # Brainrender
 <p align="center">
@@ -28,10 +24,10 @@ You can [install `brainrender`](https://brainglobe.info/documentation/brainrende
 
 ```
 pip install brainrender
-``` 
+```
 
 ## Contributing
-Contributions to brainrender are more than welcome. Please see the [developers guide](https://brainglobe.info/developers/index.html).
+Contributions to brainrender are more than welcome. Please see the [developers guide](https://brainglobe.info/community/developers/index.html). Note that some tests are only run locally, by specifying `--runslow --runlocal` in `pytest`.
 
 ## Citing brainrender
 If you use `brainrender` in your work, please cite:

diff --git a/benchmark/README.md b/benchmark/README.md
@@ -8,7 +8,7 @@ Note: the duration reported in the results does not include scene creation (`sce
 ## Machines tested
 * **[1]** macOS - Mojave 10.14.6 - MacBook Pro (15-inch, 2019) - 2.3 GHz Intel Core i9 - Radeon Pro 560X 4 GB GPU
 * **[2]** Ubuntu - 18.04.2 LTS x86_64 - Intel i7-8565U (x) @ 4.5GHz - NO GPU
-* **[3]** Windows 10 - Intel(R) Core i7-7700HQ 2.8GHz - NO GPU 
+* **[3]** Windows 10 - Intel(R) Core i7-7700HQ 2.8GHz - NO GPU
 * **[4]** Windows 10 - Intel(R) Xeon(R) CPU E5-2643 v3 3.4GHz - NVIDIA GeForce GTX 1080 Ti
 
 ## Tests
@@ -23,7 +23,7 @@ through the midline, as well as rendering the scene full screen.
 
 ### Brain regions
 Render >1k brain region meshes. Measures how long it takes to fetch and render the meshes
-for almost all brain regions in the mouse brain. 
+for almost all brain regions in the mouse brain.
 
 ### Animation
 Make a short animation
@@ -78,4 +78,3 @@ Note: these tests are designed to push brainrender to the limits, in practice se
 and increase FPS. This includes decimating/smoothing Actors to reduce the number of vertices or creating meshes with lower resolution to
 begin with. For most cases a significant increase in performance can be achieved with no noticeable loss in rendering quality.
 For instance on computer [4] lowering the resolution of the Points actor from 8 to 4 when rendering 1M points tripled the FPS.
-
diff --git a/benchmark/bm_animation.py b/benchmark/bm_animation.py
@@ -1,6 +1,5 @@
-from brainrender import Scene, Animation
 from benchmark.timer import Timer
-
+from brainrender import Animation, Scene
 
 # Create a brainrender scene
 scene = Scene(title="brain regions", inset=False)

diff --git a/benchmark/bm_brain_regions.py b/benchmark/bm_brain_regions.py
@@ -1,7 +1,6 @@
 from benchmark.timer import Timer
 from brainrender import Scene
 
-
 scene = Scene(inset=False)
 regions = scene.atlas.get_structure_descendants("root")
 

diff --git a/benchmark/bm_cells.py b/benchmark/bm_cells.py
@@ -1,7 +1,9 @@
+import random
+
+import numpy as np
+
 from benchmark.timer import Timer
 from brainrender import Scene, actors
-import numpy as np
-import random
 
 # create N random cells coordinates
 
@@ -17,7 +19,7 @@ def get_n_random_points_in_region(region, N):
     Z = np.random.randint(region_bounds[4], region_bounds[5], size=10000)
     pts = [[x, y, z] for x, y, z in zip(X, Y, Z)]
 
-    ipts = region.mesh.insidePoints(pts).points()
+    ipts = region.mesh.inside_points(pts).coordinates
     return np.vstack(random.choices(ipts, k=N))
 
 

diff --git a/benchmark/bm_napari.py b/benchmark/bm_napari.py
@@ -1,13 +1,12 @@
-import numpy as np
+"""
+Compare performance on napari
+"""
 import napari
+import numpy as np
 
 from benchmark.timer import SimpleTimer
 from brainrender import Scene
 
-"""
-    Compare performance on napari
-"""
-
 # get a couple meshes with brainrender
 scene = Scene()
 
@@ -22,7 +21,7 @@
 surfaces = []
 for act in scene.clean_actors:
     surfaces.append(
-        (act.points(), act.faces(), np.ones(len(act.points())) * 0.5)
+        (act.vertices, act.cells, np.ones(len(act.vertices)) * 0.5)
     )
 
 # render stuff in napar

diff --git a/benchmark/bm_napari_volume.py b/benchmark/bm_napari_volume.py
@@ -1,6 +1,7 @@
+import napari
 import numpy as np
+
 from benchmark.timer import SimpleTimer
-import napari
 
 data = np.load("benchmark/volume.npy")
 

diff --git a/benchmark/bm_volume.py b/benchmark/bm_volume.py
@@ -1,7 +1,8 @@
 import numpy as np
+
+from benchmark.timer import Timer
 from brainrender import Scene
 from brainrender.actors import Volume
-from benchmark.timer import Timer
 
 scene = Scene(inset=False)
 data = np.load("benchmark/volume.npy")

diff --git a/benchmark/timer.py b/benchmark/timer.py
@@ -1,19 +1,20 @@
-from rich.layout import Layout
-from rich import print
-from rich.panel import Panel
-import time
+import multiprocessing
+import os
 import sys
+import time
+
 import pyinspect as pi
 from myterial import (
-    salmon,
+    amber,
+    blue_light,
     orange,
     orange_darker,
-    amber,
     pink_light,
-    blue_light,
+    salmon,
 )
-import multiprocessing
-import os
+from rich import print
+from rich.layout import Layout
+from rich.panel import Panel
 
 
 def is_GPU_available():
@@ -36,7 +37,7 @@ def __rich_console__(self, console, dimension):
         )
         for act in self.scene.clean_actors:
             try:
-                points = len(act.points())
+                points = act.npoints
             except AttributeError:
                 points = 0
             actors.add(
@@ -70,7 +71,7 @@ def __rich_console__(self, console, dimension):
         points = []
         for act in self.scene.clean_actors:
             try:
-                points.append(len(act.points()))
+                points.append(act.npoints)
             except AttributeError:
                 pass
         tot_points = sum(points)