Change dockerfile setup, switch to pybind11 as a dependency, not vendorized

.github/workflows/dockerbuild.yml

@@ -27,8 +27,11 @@ jobs:
         username: ${{ github.actor }}
         password: ${{ secrets.GITHUB_TOKEN }}
 
-    - name: Build and push docker image
-      run: sh ./docker/dockerbuild.sh \
-        "${{github.sha}}" \
-        "dipy"
-
+    - name: Build and push Docker image
+      uses: docker/build-push-action@v5
+      with:
+        context: .
+        push: true
+        tags: |
+          ghcr.io/dipy/gpustreamlines:${{ github.sha }}
+          ghcr.io/dipy/gpustreamlines:latest

CMakeLists.txt

@@ -47,8 +47,14 @@ if(OPENMP_FOUND)
     message(STATUS "OpenMP runtime used: ${OMP_RUNTIME}")
 endif()
 
+# Find pybind11
+execute_process(COMMAND python -c "import pybind11; print(pybind11.get_cmake_dir())"
+                OUTPUT_VARIABLE pybind11_DIR
+                OUTPUT_STRIP_TRAILING_WHITESPACE)
+list(APPEND CMAKE_PREFIX_PATH ${pybind11_DIR})
+find_package(pybind11 REQUIRED)
+
 # Build library and pybind11 module
-add_subdirectory(external/pybind11)
 add_library(cuslines_kernels)
 target_sources(cuslines_kernels
 	       PRIVATE

docker/Dockerfile → Dockerfile

@@ -30,11 +30,9 @@ ENV LD_LIBRARY_PATH /opt/anaconda/lib:${LD_LIBRARY_PATH}
 RUN conda install -c conda-forge git
 RUN pip install numpy>=2.0.0
 RUN pip install scipy>=1.13.0 cython nibabel dipy tqdm
+RUN pip install pybind11
 
-RUN git clone --recurse-submodules \
-	https://github.com/dipy/GPUStreamlines.git \
-	/opt/GPUStreamlines
-RUN cd /opt/GPUStreamlines && git reset --hard ${COMMIT}
+COPY . /opt/GPUStreamlines/
 
 # compile
 RUN cd /opt/GPUStreamlines && mkdir build && cd build \

README.md

@@ -1,8 +1,6 @@
 # GPUStreamlines
 
 ## Installation
-When cloning the repo, please use "git clone --recursive" to pull all the requirements.
-
 To install, simply run `pip install .` in the top-level repository directory.
 
 ## Running the examples

pyproject.toml

@@ -8,6 +8,10 @@ version = "1.0.0"
 description="GPU-accelerated tractography package"
 readme = "README.md"
 requires-python = ">=3.7"
+dependencies = [
+    "numpy",
+    "pybind11"
+]
 
 [tool.scikit-build]
 cmake.build-type = "Release"