Add Makefile setup

kdtree/Makefile

+SHELL = /bin/bash
+PROJECT = cython+
+
+VENV_PATH=`conda info --base`/envs/${PROJECT}
+PIP_EXECUTABLE=${VENV_PATH}/bin/pip
+PYTHON_EXECUTABLE=${VENV_PATH}/bin/python
+PYTEST_EXECUTABLE=${VENV_PATH}/bin/pytest
+COMMIT=`git rev-parse --short HEAD`
+
+# Used when not using the python runtime
 INCLUDE_DIRS = -I/usr/include/python3.9
 EXE = kdtree
 CXX = g++
 CPPFLAGS = -O2 -g -Wno-unused-result -Wsign-compare -pthread $(INCLUDE_DIRS) -fopenmp
 LDFLAGS += -Wl,--unresolved-symbols=ignore-all
 MACROS = -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION
-EXT_SUFFIX := $(shell python3 -c "import sysconfig; print(sysconfig.get_config_var('EXT_SUFFIX'))")
+EXT_SUFFIX := $(shell python -c "import sysconfig; print(sysconfig.get_config_var('EXT_SUFFIX'))")
 EXT = $(EXE)$(EXT_SUFFIX)
 
-# Build with Python runtime
-all: clean $(EXT)
+.DEFAULT_GOAL := all
 
-$(EXT): setup.py
-	@echo "[Cython Compiling $^ -> $@]"
-	python3 setup.py build_ext --inplace
-	pip3 install -e . -v
+## help: Display list of commands
+.PHONY: help
+help: Makefile
+	@sed -n 's|^##||p' $< | column -t -s ':' | sed -e 's|^| |'
+
+## all: Run the main targets
+.PHONY: all
+all: install benchmark-sequential benchmark-parallel
 
-# Build without Python runtime
+## install: Install conda env.
+.PHONY: install
+install: clean
+	conda env create --force -f environment.yml
+	${PIP_EXECUTABLE} install -e . -v
+
+# nopython: Build without the Python runtime
+.PHONY: nopython
 nopython: $(EXE)
 
 %.cpp: %.pyx
 	@echo "[Cython Compiling $^ -> $@]"
-	python3 -c "from Cython.Compiler.Main import main; main(command_line=1)" $^ --cplus -3
+	${PYTEST_EXECUTABLE} -c "from Cython.Compiler.Main import main; main(command_line=1)" $^ --cplus -3
 	@rm -f $(subst .cpp,.h,$@)
 
 %: %.cpp
 	@echo "[C++ Compiling $^ -> $@]"
 	$(LINK.cpp) $^ $(MACROS) -o $@
 
-# Run without Python runtime
+## runnopython: Run without Python runtime
+.PHONY: runnopython
 runnopython: $(EXE)
 	# Information of the runtime are currently redirected to stderr.
 	# This is just a simple way to mute them.
 	./$(EXE) 2>/dev/null
 
+## clean: Remove generated files from Cython and C/C++ compilation
+.PHONY: clean
 clean:
 	-rm -f *.c *.cpp *.html
 	-rm -f *.h
@@ -42,5 +65,22 @@ clean:
 	-rm -f -r build
 	-rm -f *.json
 
-.PHONY: all run nopython runnopython clean
 .PRECIOUS: %.cpp
+
+## benchmark-sequential: Run benchmarks for sequential execution, 'NAME' variable can be provided
+# Uses taskset to cap to a cpu solely
+.PHONY: benchmark-sequential
+benchmark-sequential:
+	@[ "${NAME}" ] || export NAME=${COMMIT}
+	taskset -c 0 ${PYTHON_EXECUTABLE} benchmarks/benchmark.py ${NAME}seq
+
+## benchmark-parallel: Run benchmarks for parallel execution, 'NAME' variable can be provided
+.PHONY: benchmark-parallel
+benchmark-parallel:
+	@[ "${NAME}" ] || export NAME=${COMMIT}
+	${PYTHON_EXECUTABLE} benchmarks/benchmark.py ${NAME}par
+
+## test: Launch all the test.
+.PHONY: test
+test:
+	${PYTEST_EXECUTABLE} tests

kdtree/environment.yml

+name: cython+
+channels:
+  - conda-forge
+dependencies:
+  - python=3.9
+  - compilers
+  - jupyter
+  - numpy
+  - matplotlib
+  - seaborn
+  - pandas
+  - pyaml
+  - pip
+  - threadpoolctl
+  - pytest
+  - scikit-learn
+  - memory_profiler
+  - pip:
+      # Install cython+ from upstream directly
+      - -e git+https://lab.nexedi.com/nexedi/cython.git@fd3a224472d75f7c6107828c1e4b9587f3990a46#egg=Cython
+      # The installation of the 'kdtree' module is made then

kdtree/setup.py

@@ -10,6 +10,8 @@ extensions = [
         language="c++",
         define_macros=[("NPY_NO_DEPRECATED_API", "NPY_1_7_API_VERSION")],
         include_dirs=[numpy.get_include()],
+        extra_compile_args=["-fopenmp"],
+        extra_link_args=["-fopenmp"],
         sources=["kdtree.pyx"],
     ),
 ]

kdtree/tests/test_conf.py

@@ -19,6 +19,4 @@ def test_against_sklearn(n, d, k, leaf_size):
     tree.query(query_points, closests)
     skl_closests = skl_tree.query(query_points, k=k, return_distance=False).astype(np.int32)
     
-    # The back tracking part of the algorithm is not yet implemented
-    # hence, we test for a almost equality
     np.testing.assert_equal(closests, skl_closests)
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requirements.txt

-ipython==7.22.0
-jupyter==1.0.0
-line-profiler==3.1.0
-matplotlib==3.4.1
-numpy==1.20.2
-pytest==6.2.3
-pandas==1.2.4
-PyYAML==5.4.1
-memory_profiler==0.58.0
-seaborn==0.11.1
--e git+https://lab.nexedi.com/nexedi/cython.git@fd3a224472d75f7c6107828c1e4b9587f3990a46#egg=Cython
\ No newline at end of file