Merge branch 'main' into screenshot

.github/workflows/test_and_deploy.yml

@@ -48,6 +48,14 @@ jobs:
           python-version: "3.11"
 
     steps:
+      - name: Cache brainglobe directory
+        uses: actions/cache@v3
+        with:
+          path: | # ensure we don't cache any interrupted atlas download and extraction, if e.g. we cancel the workflow manually
+            ~/.brainglobe
+            !~/.brainglobe/atlas.tar.gz
+          key: brainglobe
+
       - name: Install hdf5 libs for Mac
         if: runner.os == 'macOS'
         run: brew install hdf5

.gitignore

@@ -16,6 +16,8 @@ brainrender/atlas_specific/gene_expression/__pycache__
 brainrender/atlas_specific/gene_expression/__pycache__/*
 brainrender/atlas_specific/__pycache__
 
+example_brainrender_shot*
+
 workspace.py
 workspace.ipynb
 brexport.html

MANIFEST.in

@@ -7,6 +7,7 @@ prune tests
 prune examples
 prune imgs
 prune videos
+prune resources
 
 graft brainrender
 

README.md

@@ -108,4 +108,4 @@ year = {2021}
 
 ## Contributing
 
-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`.
+Contributions to brainrender are more than welcome. Please see the [developers guide](https://brainglobe.info/community/developers/index.html).

examples/__init__.py

@@ -1,20 +1,24 @@
 from examples import (
     add_cells,
+    add_cylinder,
     add_labels,
     add_mesh_from_file,
-    add_cylinder,
     animation,
     brain_regions,
     brainglobe_atlases,
     cell_density,
     custom_camera,
     gene_expression,
+    line,
     neurons,
+    probe_tracks,
     ruler,
+    screenshot,
     settings,
     slice,
     # streamlines,
     user_volumetric_data,
     video,
     volumetric_data,
+    web_export,
 )

examples/add_mesh_from_file.py

@@ -1,11 +1,12 @@
 from pathlib import Path
-from importlib.resources import files
 
 from myterial import orange
 from rich import print
 
 from brainrender import Scene
 
+obj_file = Path(__file__).parent.parent / "resources" / "CC_134_1_ch1inj.obj"
+
 print(f"[{orange}]Running example: {Path(__file__).name}")
 
 # Create a brainrender scene
@@ -15,10 +16,7 @@
 scene.add_brain_region("SCm", alpha=0.2)
 
 # Add from file
-scene.add(
-    files("brainrender").joinpath("resources/CC_134_1_ch1inj.obj"),
-    color="tomato",
-)
+scene.add(obj_file, color="tomato")
 
 # Render!
 scene.render()

examples/brainglobe_atlases.py

@@ -9,6 +9,5 @@
 
 # Create a brainrender scene using the zebrafish atlas
 scene = Scene(atlas_name="mpin_zfish_1um", title="zebrafish")
-
 # Render!
 scene.render()

examples/neurons.py

@@ -8,13 +8,15 @@
 from brainrender import Scene
 from brainrender.actors import Neuron, make_neurons
 
+neuron_file = Path(__file__).parent.parent / "resources" / "neuron1.swc"
+
 print(f"[{orange}]Running example: {Path(__file__).name}")
 
 # Create a brainrender scene
 scene = Scene(title="neurons")
 
 # Add a neuron from file
-scene.add(Neuron(files("brainrender").joinpath("resources/neuron1.swc")))
+scene.add(Neuron(neuron_file))
 
 # Download neurons data with morphapi
 mlapi = MouseLightAPI()

examples/notebook_workflow.ipynb

@@ -35,7 +35,6 @@
    "cell_type": "code",
    "execution_count": 1,
    "metadata": {},
-   "outputs": [],
    "source": [
     "import vedo\n",
     "vedo.settings.default_backend= 'vtk'\n",
@@ -46,7 +45,8 @@
     "popup_scene.add_brain_region('VISp')\n",
     "\n",
     "popup_scene.render()  # press 'Esc' to close"
-   ]
+   ],
+   "outputs": []
   },
   {
    "cell_type": "markdown",
@@ -73,7 +73,6 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
-   "outputs": [],
    "source": [
     "# Set the backend\n",
     "import vedo\n",
@@ -94,7 +93,8 @@
     "from vedo import Plotter  # <- this will be used to render an embedded scene \n",
     "plt = Plotter()\n",
     "plt.show(*scene.renderables)  # same as vedo.show(*scene.renderables)"
-   ]
+   ],
+   "outputs": []
   }
  ],
  "metadata": {

examples/probe_tracks.py

@@ -8,7 +8,7 @@
 from brainrender import Scene
 from brainrender.actors import Points
 
-data_path = Path(__file__).parent.parent / "brainrender" / "resources"
+resource_path = Path(__file__).parent.parent / "resources"
 
 scene = Scene(title="Silicon Probe Visualization")
 
@@ -21,15 +21,15 @@
 # part of the probe.
 scene.add(
     Points(
-        np.load(data_path / "probe_1_striatum.npy"),
+        np.load(resource_path / "probe_1_striatum.npy"),
         name="probe_1",
         colors="darkred",
         radius=50,
     )
 )
 scene.add(
     Points(
-        np.load(data_path / "probe_2_RSP.npy"),
+        np.load(resource_path / "probe_2_RSP.npy"),
         name="probe_2",
         colors="darkred",
         radius=50,

examples/user_volumetric_data.py

@@ -28,23 +28,21 @@
 
 print(f"[{orange}]Running example: {Path(__file__).name}")
 
+download_path = Path.home() / ".brainglobe" / "brainrender" / "example-data"
+filename = "T_AVG_s356tTg.tif"
+scene = Scene(atlas_name="mpin_zfish_1um")
 
-retrieved_paths = pooch.retrieve(
+# for some reason the list of returned by pooch does not seem to be
+# in the same order every time
+_ = pooch.retrieve(
     url="https://api.mapzebrain.org/media/Lines/brn3cGFP/average_data/T_AVG_s356tTg.zip",
     known_hash="54b59146ba08b4d7eea64456bcd67741db4b5395235290044545263f61453a61",
-    path=Path.home()
-    / ".brainglobe"
-    / "brainrender"
-    / "example-data",  # zip will be downloaded here
+    path=download_path,
     progressbar=True,
-    processor=pooch.Unzip(
-        extract_dir=""
-        # path to unzipped dir,
-        # *relative* to the path set in 'path'
-    ),
+    processor=pooch.Unzip(extract_dir="."),
 )
 
-datafile = Path(retrieved_paths[0])  # [0] is zip file
+datafile = download_path / filename
 
 
 # 1. load the data

examples/volumetric_data.py

@@ -11,18 +11,19 @@
 from brainrender.actors import Volume
 
 from pathlib import Path
-from importlib.resources import files
 
 from myterial import orange
 from rich import print
 
 settings.SHOW_AXES = False
+volume_file = Path(__file__).parent.parent / "resources" / "volume.npy"
+
 
 print(f"[{orange}]Running example: {Path(__file__).name}")
 
 scene = Scene(inset=False)
 
-data = np.load(files("brainrender").joinpath("resources/volume.npy"))
+data = np.load(volume_file)
 print(data.shape)
 
 # make a volume actor and add

tests/test_aba_gene.py

@@ -12,7 +12,6 @@
 
 #     return geapi
 
-
 # @pytest.mark.xfail
 # def test_gene_expression_api(geapi):
 

tests/test_examples.py

@@ -1,28 +1,5 @@
-import pytest
-
-from brainrender import settings
-
-settings.INTERACTIVE = False
-
-
-@pytest.mark.slow
-@pytest.mark.local
 def test_examples():
-    import examples
-
-    examples.add_cells
-    examples.add_mesh_from_file
-    examples.animation
-    examples.brain_regions
-    examples.brainglobe_atlases
-    examples.cell_density
-    examples.custom_camera
-    examples.gene_expression
-    examples.neurons
-    examples.ruler
-    examples.settings
-    examples.slice
-    # examples.streamlines
-    examples.user_volumetric_data
-    examples.video
-    examples.volumetric_data
+    """
+    Run every script in the examples directory
+    """
+    import examples  # noqa

tests/test_integration.py

@@ -1,4 +1,3 @@
-from importlib.resources import files
 from pathlib import Path
 
 import numpy as np
@@ -19,6 +18,8 @@
 )
 from brainrender.atlas_specific import GeneExpressionAPI
 
+resources_dir = Path(__file__).parent.parent / "resources"
+
 
 def get_n_points_in_region(region, N):
     """
@@ -109,7 +110,7 @@ def test_add_labels(scene):
 
 
 def test_add_mesh_from_file(scene):
-    data_path = files("brainrender").joinpath("resources/CC_134_1_ch1inj.obj")
+    data_path = resources_dir / "CC_134_1_ch1inj.obj"
     scene.add_brain_region("SCm", alpha=0.2)
     file_mesh = scene.add(data_path, color="tomato")
 
@@ -236,7 +237,7 @@ def test_gene_expression(scene):
 
 
 def test_neurons(scene, pytestconfig):
-    data_path = files("brainrender").joinpath("resources/neuron1.swc")
+    data_path = resources_dir / "neuron1.swc"
 
     neuron = Neuron(data_path)
     scene.add(neuron)
@@ -300,26 +301,24 @@ def test_slice(scene):
     assert np.all(ca1_clone.bounds() != ca1.bounds())
 
 
-@pytest.mark.slow
-@pytest.mark.local
 def test_user_volumetric_data():
+    download_path = (
+        Path.home() / ".brainglobe" / "brainrender" / "example-data"
+    )
+    filename = "T_AVG_s356tTg.tif"
     scene = Scene(atlas_name="mpin_zfish_1um")
-    retrieved_paths = pooch.retrieve(
+
+    # for some reason the list of returned by pooch does not seem to be
+    # in the same order every time
+    _ = pooch.retrieve(
         url="https://api.mapzebrain.org/media/Lines/brn3cGFP/average_data/T_AVG_s356tTg.zip",
         known_hash="54b59146ba08b4d7eea64456bcd67741db4b5395235290044545263f61453a61",
-        path=Path.home()
-        / ".brainglobe"
-        / "brainrender"
-        / "example-data",  # zip will be downloaded here
+        path=download_path,
         progressbar=True,
-        processor=pooch.Unzip(
-            extract_dir=""
-            # path to unzipped dir,
-            # *relative* to the path set in 'path'
-        ),
+        processor=pooch.Unzip(extract_dir="."),
     )
 
-    datafile = Path(retrieved_paths[0])
+    datafile = download_path / filename
     data = load_any(datafile)
     source_space = AnatomicalSpace("ira")
     target_space = scene.atlas.space
@@ -368,7 +367,7 @@ def test_video(scene, pytestconfig):
 
 
 def test_volumetric_data(scene):
-    data_path = files("brainrender").joinpath("resources/volume.npy")
+    data_path = resources_dir / "volume.npy"
     data = np.load(data_path)
     actor = Volume(
         data,