Merge pull request #348 from brainglobe/slow-tests

Remove the markers to disable specific slowly running tests

.github/workflows/test_and_deploy.yml

@@ -48,6 +48,12 @@ jobs:
           python-version: "3.11"
 
     steps:
+      - name: Cache atlases
+        uses: actions/cache@v3
+        with:
+          path: ~/.brainglobe
+          key: brainglobe
+
       - name: Install hdf5 libs for Mac
         if: runner.os == 'macOS'
         run: brew install hdf5

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/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/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

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

@@ -301,26 +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

tests/test_streamlines.py

@@ -1,38 +1,33 @@
-import pandas as pd
-import pytest
-
-from brainrender import Scene
-from brainrender.actors.streamlines import (
-    Streamlines,
-    make_streamlines,
-)
-from brainrender.atlas_specific import get_streamlines_for_region
-
-
-@pytest.mark.local
-def test_download():
-    streams = get_streamlines_for_region("TH", force_download=False)
-    assert len(streams) == 54
-    assert isinstance(streams[0], pd.DataFrame)
-
-
-@pytest.mark.local
-@pytest.mark.slow
-def test_download_slow():
-    streams = get_streamlines_for_region("TH", force_download=True)
-    assert len(streams) == 54
-    assert isinstance(streams[0], pd.DataFrame)
-
-
-@pytest.mark.local
-def test_streamlines():
-    s = Scene(title="BR")
-    streams = get_streamlines_for_region("TH", force_download=False)
-    s.add(Streamlines(streams[0]))
-    s.add(*make_streamlines(*streams[1:3]))
-
-    with pytest.raises(TypeError):
-        Streamlines([1, 2, 3])
-
-    # s.render(interactive=False)
-    del s
+# import pandas as pd
+# import pytest
+#
+# from brainrender import Scene
+# from brainrender.actors.streamlines import (
+#     Streamlines,
+#     make_streamlines,
+# )
+# from brainrender.atlas_specific import get_streamlines_for_region
+#
+#
+# def test_download():
+#     streams = get_streamlines_for_region("TH", force_download=False)
+#     assert len(streams) == 54
+#     assert isinstance(streams[0], pd.DataFrame)
+#
+#
+# def test_download_slow():
+#     streams = get_streamlines_for_region("TH", force_download=True)
+#     assert len(streams) == 54
+#     assert isinstance(streams[0], pd.DataFrame)
+#
+#
+# def test_streamlines():
+#     s = Scene(title="BR")
+#     streams = get_streamlines_for_region("TH", force_download=False)
+#     s.add(Streamlines(streams[0]))
+#     s.add(*make_streamlines(*streams[1:3]))
+#
+#     with pytest.raises(TypeError):
+#         Streamlines([1, 2, 3])
+#
+#     del s