Set up testing infrastructure

.github/workflows/ci-workflows.yml

@@ -19,6 +19,35 @@ jobs:
         # Code style
         - linux: codestyle
 
+  tests:
+    needs: initial_checks
+    uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@v1
+    with:
+      display: true
+      coverage: codecov
+      libraries: |
+        apt:
+          - '^libxcb.*-dev'
+          - libxkbcommon-x11-0
+          - libegl1-mesa
+          - libhdf5-dev
+      envs: |
+        - linux: py39-test
+        - linux: py310-test
+        - linux: py311-test
+        - linux: py312-test
+
+        - macos: py39-test
+        - macos: py310-test
+        - macos: py311-test
+        - macos: py312-test
+
+        - windows: py39-test
+        - windows: py310-test
+        - windows: py311-test
+        - windows: py312-test
+
+
   deploy-examples:
     needs: initial_checks
     if: github.event_name != 'pull_request'

codecov.yml

@@ -0,0 +1,10 @@
+comment: off
+coverage:
+  status:
+    project:
+      default:
+        target: auto
+        # adjust accordingly based on how flaky your tests are
+        # this allows a 0.001% drop from the previous base commit coverage
+        # basically just to prevent counting zero changes as negative
+        threshold: 0.001%

glue_ar/__init__.py

@@ -1,5 +1,10 @@
-from glue_ar.common.scatter_export_options import *  # noqa
-from glue_ar.common.volume_export_options import *  # noqa
+from pkg_resources import get_distribution, DistributionNotFound
+import traceback
+
+try:
+    __version__ = get_distribution(__name__).version
+except DistributionNotFound:
+    pass
 
 
 def setup_qt():
@@ -8,7 +13,7 @@
     except ImportError:
         from glue_vispy_viewers.scatter.scatter_viewer import VispyScatterViewer
 
-    from glue_ar.qt.export_tool import QtARExportTool  # noqa
+    from .qt.export_tool import QtARExportTool  # noqa
 
     VispyScatterViewer.subtools = {
         **VispyScatterViewer.subtools,
@@ -26,7 +31,7 @@
     }
 
     try:
-        from glue_ar.qt.qr_tool import ARLocalQRTool  # noqa
+        from .qt.qr_tool import ARLocalQRTool  # noqa
         VispyScatterViewer.tools = [t for t in VispyScatterViewer.tools] + ["ar"]
         VispyVolumeViewer.tools = [t for t in VispyVolumeViewer.tools] + ["ar"]
         VispyScatterViewer.subtools["ar"] = ["ar:qr"]
@@ -36,7 +41,7 @@
 
 
 def setup_jupyter():
-    from glue_ar.jupyter.export_tool import JupyterARExportTool  # noqa
+    from .jupyter.export_tool import JupyterARExportTool  # noqa
     from glue_vispy_viewers.scatter.jupyter import JupyterVispyScatterViewer
     from glue_vispy_viewers.volume.jupyter import JupyterVispyVolumeViewer
     JupyterVispyScatterViewer.tools = [t for t in JupyterVispyScatterViewer.tools] + ["save:ar_jupyter"]
@@ -46,14 +51,14 @@
 def setup():
     try:
         setup_qt()
-    except ImportError as e:
+    except ImportError:
         print("Qt setup error")
-        print(e)
+        print(traceback.format_exc())
         pass
 
     try:
         setup_jupyter()
-    except ImportError as e:
+    except ImportError:
         print("Jupyter setup error")
-        print(e)
+        print(traceback.format_exc())
         pass

glue_ar/common/__init__.py

@@ -1,3 +1,5 @@
 from .marching_cubes import add_isosurface_layer_gltf, add_isosurface_layer_usd  # noqa: F401
 from .scatter import add_scatter_layer_gltf, add_scatter_layer_usd  # noqa: F401
 from .voxels import add_voxel_layers_gltf, add_voxel_layers_usd  # noqa: F401
+from .scatter_export_options import ARScatterExportOptions  # noqa: F401
+from .volume_export_options import ARIsosurfaceExportOptions, ARVoxelExportOptions  # noqa: F401

glue_ar/common/gltf_builder.py

@@ -1,10 +1,11 @@
+from __future__ import annotations
+
 from gltflib import Accessor, AccessorType, AlphaMode, Asset, Attributes, Buffer, \
                     BufferTarget, BufferView, ComponentType, GLTFModel, \
                     Material, Mesh, Node, PBRMetallicRoughness, Primitive, PrimitiveMode, Scene
 from gltflib.gltf import GLTF
 from gltflib.gltf_resource import FileResource
-
-from typing import Iterable, List, Optional, Self, Union
+from typing import Iterable, List, Optional, Union
 
 
 class GLTFBuilder:
@@ -22,7 +23,7 @@ def add_material(self,
                      opacity: float = 1,
                      roughness_factor: float = 1,
                      metallic_factor: float = 0,
-                     alpha_mode: AlphaMode = AlphaMode.BLEND) -> Self:
+                     alpha_mode: AlphaMode = AlphaMode.BLEND) -> GLTFBuilder:
         if any(c > 1 for c in color):
             color = [c / 256 for c in color[:3]]
         self.materials.append(
@@ -41,7 +42,7 @@ def add_mesh(self,
                  position_accessor: int,
                  indices_accessor: Optional[int] = None,
                  material: Optional[int] = None,
-                 mode: PrimitiveMode = PrimitiveMode.TRIANGLES) -> Self:
+                 mode: PrimitiveMode = PrimitiveMode.TRIANGLES) -> GLTFBuilder:
 
         primitive_kwargs = {
                 "attributes": Attributes(POSITION=position_accessor),
@@ -60,7 +61,7 @@ def add_mesh(self,
 
     def add_buffer(self,
                    byte_length: int,
-                   uri: str) -> Self:
+                   uri: str) -> GLTFBuilder:
         self.buffers.append(
             Buffer(
                 byteLength=byte_length,
@@ -73,7 +74,7 @@ def add_buffer_view(self,
                         buffer: int,
                         byte_length: int,
                         byte_offset: int,
-                        target: BufferTarget) -> Self:
+                        target: BufferTarget) -> GLTFBuilder:
         self.buffer_views.append(
             BufferView(
                 buffer=buffer,
@@ -90,7 +91,7 @@ def add_accessor(self,
                      count: int,
                      type: AccessorType,
                      mins: List[Union[int, float]],
-                     maxes: List[Union[int, float]]) -> Self:
+                     maxes: List[Union[int, float]]) -> GLTFBuilder:
         self.accessors.append(
             Accessor(
                 bufferView=buffer_view,
@@ -105,7 +106,7 @@ def add_accessor(self,
 
     def add_file_resource(self,
                           filename: str,
-                          data: bytearray) -> Self:
+                          data: bytearray) -> GLTFBuilder:
         self.file_resources.append(
             FileResource(
                 filename,

glue_ar/common/tests/test_scatter_gltf.py

@@ -0,0 +1,2 @@
+class TestScatterGLTF:
+    pass

glue_ar/common/tests/test_shapes.py

@@ -1,6 +1,10 @@
 from itertools import product
 from math import sqrt
-from ..shapes import cone_points, cylinder_points, rectangular_prism_points, sphere_points
+import pytest
+from glue_ar.common.shapes import cone_points, cone_triangles, \
+                                  cylinder_points, cylinder_triangles, \
+                                  rectangular_prism_points, rectangular_prism_triangulation, \
+                                  sphere_points, sphere_triangles
 
 
 class TestShapes:
@@ -20,6 +24,38 @@ def test_rectangular_prism_points(self):
                 (2.0, 1.5, -0.5),
                 (2.0, 1.5, 2.5)} == points
 
+    def test_rectangular_prism_triangles(self):
+        triangles = set(rectangular_prism_triangulation())
+
+        assert {(0, 2, 1),
+                (0, 4, 2),
+                (1, 2, 3),
+                (4, 0, 1),
+                (4, 7, 6),
+                (5, 1, 7),
+                (5, 4, 1),
+                (6, 2, 4),
+                (7, 1, 3),
+                (7, 2, 6),
+                (7, 3, 2),
+                (7, 4, 5)} == triangles
+
+        start_index = 5
+        triangles = set(rectangular_prism_triangulation(start_index=start_index))
+
+        assert {(5, 7, 6),
+                (5, 9, 7),
+                (6, 7, 8),
+                (9, 5, 6),
+                (9, 12, 11),
+                (10, 6, 12),
+                (10, 9, 6),
+                (11, 7, 9),
+                (12, 6, 8),
+                (12, 7, 11),
+                (12, 8, 7),
+                (12, 9, 10)} == triangles
+
     def test_sphere_points(self):
         center = (1, 2, 3)
         radius = 2
@@ -50,6 +86,19 @@ def test_sphere_points(self):
 
         assert points == expected
 
+    @pytest.mark.parametrize("theta_resolution,phi_resolution", product((5, 8, 10, 12, 15, 20), repeat=2))
+    def test_sphere_points_count(self, theta_resolution, phi_resolution):
+        points = sphere_points(center=(0, 0, 0,), radius=1,
+                               theta_resolution=theta_resolution,
+                               phi_resolution=phi_resolution)
+        assert len(points) == 2 + (theta_resolution - 2) * phi_resolution
+
+    @pytest.mark.parametrize("theta_resolution,phi_resolution", product((5, 8, 10, 12, 15, 20), repeat=2))
+    def test_sphere_triangles_count(self, theta_resolution, phi_resolution):
+        triangles = sphere_triangles(theta_resolution=theta_resolution,
+                                     phi_resolution=phi_resolution)
+        assert len(triangles) == 2 * phi_resolution * (theta_resolution - 2)
+
     def test_cylinder_points(self):
         center = (-1, 2, -5)
         radius = 3
@@ -70,7 +119,20 @@ def test_cylinder_points(self):
 
         assert points == expected
 
-    def test_points(self):
+    @pytest.mark.parametrize("theta_resolution", (3, 5, 8, 10, 12, 15, 20))
+    def test_cylinder_points_count(self, theta_resolution):
+        points = cylinder_points(center=(0, 0, 0,), radius=1,
+                                 length=1, central_axis=(0, 0, 1),
+                                 theta_resolution=theta_resolution)
+        assert len(points) == 2 * theta_resolution
+
+    @pytest.mark.parametrize("theta_resolution,start_index", product((3, 5, 8, 10, 12, 15), (0, 2, 5, 7, 10)))
+    def test_cylinder_triangles_count(self, theta_resolution, start_index):
+        triangles = cylinder_triangles(theta_resolution=theta_resolution,
+                                       start_index=start_index)
+        assert len(triangles) == 2 * (theta_resolution - 2) + 2 * theta_resolution
+
+    def test_cone_points(self):
         center = (2, 0, -1)
         radius = 6
         height = 10
@@ -86,3 +148,16 @@ def test_points(self):
         expected = {tuple(round(t, precision) for t in pt) for pt in expected}
 
         assert points == expected
+
+    @pytest.mark.parametrize("theta_resolution", (3, 5, 8, 10, 12, 15, 20))
+    def test_cone_points_count(self, theta_resolution):
+        points = cone_points(base_center=(0, 0, 0,), radius=1,
+                             height=1, central_axis=(0, 0, 1),
+                             theta_resolution=theta_resolution)
+        assert len(points) == theta_resolution + 1
+
+    @pytest.mark.parametrize("theta_resolution,start_index", product((3, 5, 8, 10, 12, 15), (0, 2, 5, 7, 10)))
+    def test_cone_triangles_count(self, theta_resolution, start_index):
+        triangles = cone_triangles(theta_resolution=theta_resolution,
+                                   start_index=start_index)
+        assert len(triangles) == 2 * theta_resolution - 2

glue_ar/common/voxels.py

@@ -93,7 +93,7 @@
         color_components = hex_to_components(color)
 
         for indices in nonempty_indices:
-            value = data[*indices]
+            value = data[tuple(indices)]
             adjusted_opacity = min(max(layer_state.alpha * opacity_factor * (value - isomin) / isorange, 0), 1)
             indices_tpl = tuple(indices)
             if indices_tpl in occupied_voxels:
@@ -208,7 +208,7 @@
         color_components = hex_to_components(color)
 
         for indices in nonempty_indices:
-            value = data[*indices]
+            value = data[tuple(indices)]
             adjusted_opacity = min(max(layer_state.alpha * opacity_factor * (value - isomin) / isorange, 0), 1)
             indices_tpl = tuple(indices)
             if indices_tpl in occupied_voxels:

glue_ar/conftest.py

@@ -0,0 +1,3 @@
+def pytest_configure(config):
+    from glue_ar import setup
+    setup()

glue_ar/qt/qr.py

@@ -5,7 +5,7 @@
 import segno
 
 
-GLUE_LOGO = os.path.abspath(os.path.join(os.path.dirname(__file__), "logo.png"))
+GLUE_LOGO = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "logo.png"))
 GLUE_RED = "#eb1c24"
 
 
@@ -23,19 +23,20 @@
     return IP
 
 
-def create_qr(url):
+def create_qr(url, with_logo=True, color=GLUE_RED):
     qr = segno.make_qr(url)
     out = BytesIO()
-    qr.save(out, kind="png", scale=7, dark=GLUE_RED, light="white")
+    qr.save(out, kind="png", scale=7, dark=color, light="white")
     out.seek(0)
     img = Image.open(out)
     img = img.convert("RGB")
-    width, height = img.size
-    logo_max_size = height // 3
-    logo_img = Image.open(GLUE_LOGO)
-    # Resize the logo to logo_max_size
-    logo_img.thumbnail((logo_max_size, logo_max_size), Image.Resampling.LANCZOS)
-    # Calculate the center of the QR code
-    box = ((width - logo_img.size[0]) // 2, (height - logo_img.size[1]) // 2)
-    img.paste(logo_img, box)
+    if with_logo:
+        width, height = img.size
+        logo_max_size = height // 3
+        logo_img = Image.open(GLUE_LOGO)
+        # Resize the logo to logo_max_size
+        logo_img.thumbnail((logo_max_size, logo_max_size), Image.Resampling.LANCZOS)
+        # Calculate the center of the QR code
+        box = ((width - logo_img.size[0]) // 2, (height - logo_img.size[1]) // 2)
+        img.paste(logo_img, box)
     return img