Merge branch 'main' into migrating-web-to-vue

.github/workflows/test.yml

@@ -79,13 +79,28 @@ jobs:
         uses: codecov/codecov-action@v3
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.9'
 
-      - name: Install gcc-11
+      - name: Install dependencies for macOS
         if: matrix.os == 'macos-latest'
         run: |
-          brew install gcc@11
+          brew install libomp llvm
+
+      - name: Set environment variables for macOS
+        if: matrix.os == 'macos-latest'
+        run: |
+          echo "PATH=$(brew --prefix llvm)/bin:$PATH" >> $GITHUB_ENV
+          echo "LDFLAGS=-L$(brew --prefix llvm)/lib" >> $GITHUB_ENV
+          echo "CPPFLAGS=-I$(brew --prefix llvm)/include" >> $GITHUB_ENV
+          echo "CPATH=$(brew --prefix libomp)/include" >> $GITHUB_ENV
+          echo "DEVITO_ARCH=clang" >> $GITHUB_ENV
+
+      - name: Run integration test on macOS
+        if: matrix.os == 'macos-latest'
+        run: |
+          make test-integration
 
       - name: Run integration test
+        if: matrix.os == 'ubuntu-latest'
         env:
-          DEVITO_ARCH: gcc-11
+          DEVITO_ARCH: gcc
         run: |
-          make test-integration
+          make test-integration

docs/examples/plot_ultrasound_imaging_multiplane.py

@@ -29,7 +29,7 @@
 """
 
 # %%
-from typing import List
+from typing import List, cast
 
 import matplotlib.pyplot as plt
 import numpy as np
@@ -129,6 +129,7 @@ def create_scenario(tilt_angle: float = 0.0) -> Scenario3:
 # - rho - density
 # - alpha - attenuation
 fig, axs = plt.subplots(1, 3, figsize=(15, 5))
+axs = cast(np.ndarray, axs)
 
 for idx, attribute in enumerate(["vp", "rho", "alpha"]):
     im = axs[idx].imshow(getattr(scenario.problem.medium, attribute).data)

docs/examples/plot_ultrasound_imaging_scanline.py

@@ -30,7 +30,7 @@
 """
 
 # %%
-from typing import List
+from typing import List, cast
 
 import matplotlib.pyplot as plt
 import numpy as np
@@ -129,6 +129,7 @@ def create_scenario(tilt_angle: float = 0.0) -> Scenario3:
 # - rho - density
 # - alpha - attenuation
 fig, axs = plt.subplots(1, 3, figsize=(15, 5))
+axs = cast(np.ndarray, axs)
 
 for idx, attribute in enumerate(["vp", "rho", "alpha"]):
     im = axs[idx].imshow(getattr(scenario.problem.medium, attribute).data)

docs/installation.md

@@ -45,11 +45,19 @@ As a last step **before running NDK**, follow the instructions below depending o
 
 ??? "Before running on MacOS"
 
+<<<<<<< HEAD
     The two main compiler options for MacOS are **clang** and **gcc**.
 
     ### clang
 
     If you prefer to use **clang** you will have to install `libomp` and `llvm`, you will also have to export a few environment variables needed by the compiler.
+=======
+    The single compiler option for MacOS is **clang**.
+
+    ### clang
+
+    To setup your environment you will have to install `libomp` and `llvm`, you will also have to export a few environment variables needed by the compiler.
+>>>>>>> main
 
     1. Install libomp
 
@@ -89,6 +97,7 @@ As a last step **before running NDK**, follow the instructions below depending o
         source ~/.zshrc
         ```
 
+<<<<<<< HEAD
     ### gcc
 
     On MacOS the `gcc` executable is a symbolic link to `clang`, so by defining ~~DEVITO_ARCH=gcc~~ devito will try to add `gcc` flags to the `clang` compiler, and the compilation will most probably fail.
@@ -114,6 +123,8 @@ As a last step **before running NDK**, follow the instructions below depending o
         ```
 
 
+=======
+>>>>>>> main
 ??? "Before running on Linux"
 
     1. Export the `DEVITO_ARCH` environment variable, or add it to your shell profile:

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "neurotechdevkit"
-version = "v0.6.1"
+version = "v0.6.2"
 description = "Neurotech Development Kit: an open-source software library designed to enhance accessibility to cutting-edge neurotechnology"
 authors = ["AE Studio <[email protected]>"]
 maintainers = ["AE Studio <[email protected]>"]
@@ -47,12 +47,13 @@ pyrevolve = ">=2.2.3"
 pydicom = "^2.4.3"
 nibabel = "^5.1.0"
 flask-cors = "^4.0.0"
+mypy = "1.11"
 
 [tool.poetry.group.dev.dependencies]
 black = {extras = ["jupyter"], version = "^23.9.1"}
 flake8 = "^5.0.4"
 isort = "^5.10.1"
-mypy = "^0.990"
+mypy = "^1.11"
 pytest = "^7.2.0"
 pytest-cov = "^4.0.0"
 pytest-asyncio = "^0.20.2"
@@ -105,5 +106,6 @@ markers = [
 include = ["src"]
 reportGeneralTypeIssues = "none"
 exclude = ["src/web/app"]
+
 # [tool.flake8]
 # flake8 does not support config in pyproject.toml, see .flake8

src/neurotechdevkit/sources.py

@@ -36,8 +36,8 @@ class Source(abc.ABC):
     def __init__(
         self,
         *,
-        position: npt.ArrayLike,
-        direction: npt.ArrayLike,
+        position: list[float],
+        direction: list[float],
         aperture: float,
         focal_length: float,
         num_points: int,
@@ -162,7 +162,7 @@ class PointSource(Source):
     def __init__(
         self,
         *,
-        position: npt.ArrayLike,
+        position: list[float],
         num_dim: int = 2,
         delay: float = 0.0,
     ) -> None:
@@ -209,7 +209,7 @@ class PointSource2D(PointSource):
     def __init__(
         self,
         *,
-        position: npt.ArrayLike,
+        position: list[float],
         delay: float = 0.0,
     ) -> None:
         """Initialize a new 2-D point source."""
@@ -226,7 +226,7 @@ class PointSource3D(PointSource):
     def __init__(
         self,
         *,
-        position: npt.ArrayLike,
+        position: list[float],
         delay: float = 0.0,
     ) -> None:
         """Initialize a new 3-D point source."""
@@ -486,8 +486,8 @@ class UnfocusedSource(Source, abc.ABC):
     def __init__(
         self,
         *,
-        position: npt.ArrayLike,
-        direction: npt.ArrayLike,
+        position: list[float],
+        direction: list[float],
         aperture: float,
         num_points: int,
         delay: float = 0.0,
@@ -624,8 +624,8 @@ class PhasedArraySource(Source):
     def __init__(
         self,
         *,
-        position: npt.ArrayLike,
-        direction: npt.ArrayLike,
+        position: list[float],
+        direction: list[float],
         num_points: int,
         num_elements: int,
         pitch: float,
@@ -1173,9 +1173,9 @@ class PhasedArraySource3D(PhasedArraySource):
     def __init__(
         self,
         *,
-        position: npt.ArrayLike,
-        direction: npt.ArrayLike,
-        center_line: npt.ArrayLike,
+        position: list[float],
+        direction: list[float],
+        center_line: list[float],
         num_points: int,
         num_elements: int,
         pitch: float,

src/web/messages/transducers.py

@@ -169,6 +169,8 @@ def from_source(
             focalLength=focal_length,
             delay=source._delay,
             elementDelays=element_delays,
+            centerLine=None,
+            height=None,
         )
 
     def to_ndk_source(self) -> Union[PhasedArraySource2D, PhasedArraySource3D]: