update: wrap m4ri

.github/workflows/test-build.yml

@@ -23,8 +23,22 @@ jobs:
     - name: Install uv
       run: curl -LsSf https://astral.sh/uv/install.sh | sh
 
+    - name: Install Python dependencies
+      run: |
+        export PATH="$HOME/.cargo/bin:$PATH"
+        uv venv
+        source .venv/bin/activate
+        uv pip install cython setuptools
+
+    - name: Build m4ri library
+      run: |
+        export PATH="$HOME/.cargo/bin:$PATH"
+        source .venv/bin/activate
+        make build-m4ri
+
     - name: Test package build
       run: |
         export PATH="$HOME/.cargo/bin:$PATH"
+        source .venv/bin/activate
         make build
         echo "✓ Build successful"

.github/workflows/test-import.yml

@@ -12,13 +12,30 @@ jobs:
     steps:
     - name: Checkout code
       uses: actions/checkout@v4
+      with:
+        submodules: recursive
+
+    - name: Install build dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y autoconf automake libtool m4 build-essential
 
     - name: Install uv
       run: curl -LsSf https://astral.sh/uv/install.sh | sh
 
-    - name: Create venv and test import
+    - name: Build m4ri library
+      run: |
+        export PATH="$HOME/.cargo/bin:$PATH"
+        make build-m4ri
+
+    - name: Build and install package
       run: |
         export PATH="$HOME/.cargo/bin:$PATH"
+        make build
         make sync
+
+    - name: Test import
+      run: |
+        export PATH="$HOME/.cargo/bin:$PATH"
         source .venv/bin/activate
-        uv run python -c "import scloop; print('✓ Import successful')"
+        python -c "import scloop; print('✓ Import successful')"

MANIFEST.in

@@ -0,0 +1,6 @@
+include src/scloop/utils/linear_algebra_gf2/libm4ri.a
+recursive-include src/scloop/utils/linear_algebra_gf2/include *.h
+include src/scloop/utils/linear_algebra_gf2/*.pyx
+include src/scloop/data/*.pyx
+include src/scloop/data/*.cpp
+include src/scloop/data/*.h

Makefile

@@ -8,19 +8,24 @@ M4RI_PREFIX := $(PROJECT_ROOT)/src/scloop/utils/linear_algebra_gf2
 build-m4ri:
 	cd $(M4RI_SRC) && \
 		autoreconf -i && \
-		./configure --prefix=$(M4RI_PREFIX) --libdir=$(M4RI_PREFIX) --disable-static --enable-shared --enable-openmp && \
+		./configure --prefix=$(M4RI_PREFIX) --libdir=$(M4RI_PREFIX) \
+					--enable-static --disable-shared --enable-openmp \
+					CFLAGS="-fPIC -O3" && \
 		$(MAKE) && \
 		$(MAKE) install
 
 build: build-m4ri
-	CPLUS_INCLUDE_PATH=$(PROJECT_ROOT)/src/scloop/data uv build
+	CFLAGS="-I$(M4RI_PREFIX)/include" \
+	LDFLAGS="-L$(M4RI_PREFIX) -Wl,-rpath,$(M4RI_PREFIX)" \
+	CPLUS_INCLUDE_PATH=$(PROJECT_ROOT)/src/scloop/data \
+		uv build
 
 sync:
 	CPLUS_INCLUDE_PATH=$(PROJECT_ROOT)/src/scloop/data uv sync
 
 clean:
 	rm -rf dist/ *.egg-info
 	cd $(M4RI_SRC) && $(MAKE) clean || true
-	rm -rf $(M4RI_PREFIX)/include $(M4RI_PREFIX)/lib*.so* $(M4RI_PREFIX)/lib*.la $(M4RI_PREFIX)/pkgconfig
+	rm -rf $(M4RI_PREFIX)/include $(M4RI_PREFIX)/lib*.a $(M4RI_PREFIX)/lib*.so* $(M4RI_PREFIX)/lib*.la $(M4RI_PREFIX)/pkgconfig
 
 rebuild: clean build

pyproject.toml

@@ -1,7 +1,3 @@
-[build-system]
-build-backend = "setuptools.build_meta"
-requires = [ "cython", "setuptools>74.1" ]
-
 [project]
 name = "scloop"
 version = "0.1.0"
@@ -35,18 +31,12 @@ dependencies = [
   "umap-learn>=0.5.7",
 ]
 
-[tool.setuptools]
-package-dir = { "" = "src" }
-ext-modules = [
-  { name = "scloop.data.ripser_lib", sources = [
-    "./src/scloop/data/ripser_lib.pyx",
-    "./src/scloop/data/ripser.cpp",
-  ], language = "c++", optional = false },
-]
-
 [tool.uv]
 package = true
 
+[tool.uv.extra-build-dependencies]
+scloop = [ "Cython" ]
+
 [tool.uv.sources]
 torch = [
   { index = "pytorch-cu128", marker = "sys_platform == 'linux'" },
@@ -63,4 +53,24 @@ explicit = true
 
 [tool.ruff]
 format.indent-style = "space"
+# archive
+# [build-system]
+# build-backend = "setuptools.build_meta"
+# requires = [ "cython", "setuptools>74.1" ]
+
+# [tool.setuptools]
+# package-dir = { "" = "src" }
+# ext-modules = [
+#   { name = "scloop.data.ripser_lib", sources = [
+#     "./src/scloop/data/ripser_lib.pyx",
+#     "./src/scloop/data/ripser.cpp",
+#   ], language = "c++", optional = false },
+#   { name = "scloop.utils.linear_algebra_gf2.m4ri_lib", sources = [
+#     "./src/scloop/utils/linear_algebra_gf2/m4ri_lib.pyx",
+#   ], language = "c", optional = false, libraries = ["m4ri"], extra-objects = [
+#     "./src/scloop/utils/linear_algebra_gf2/libm4ri.a",
+#   ], include-dirs = [
+#     "./src/scloop/utils/linear_algebra_gf2/include",
+#   ] },
+# ]
 format.quote-style = "double"

setup.py

@@ -0,0 +1,25 @@
+from setuptools import setup, Extension
+from Cython.Build import cythonize
+import os
+
+project_root = os.path.dirname(os.path.abspath(__file__))
+m4ri_dir = os.path.join(project_root, "src/scloop/utils/linear_algebra_gf2")
+
+extensions = [
+    Extension(
+        "scloop.data.ripser_lib",
+        sources=["./src/scloop/data/ripser_lib.pyx", "./src/scloop/data/ripser.cpp"],
+        language="c++",
+        include_dirs=["./src/scloop/data"],
+    ),
+    Extension(
+        "scloop.utils.linear_algebra_gf2.m4ri_lib",
+        sources=["./src/scloop/utils/linear_algebra_gf2/m4ri_lib.pyx"],
+        include_dirs=[os.path.join(m4ri_dir, "include")],
+        extra_objects=[os.path.join(m4ri_dir, "libm4ri.a")],
+        extra_compile_args=["-fopenmp"],
+        extra_link_args=["-fopenmp"],
+    ),
+]
+
+setup(ext_modules=cythonize(extensions, compiler_directives={"language_level": "3"}))

src/scloop/data/utils.py

@@ -10,6 +10,7 @@
 
 warnings.filterwarnings("ignore", category=RuntimeWarning)
 
+
 def subsample(
     x: np.ndarray,
     n: int,
@@ -35,6 +36,7 @@ def subsample(
         pass
     pw_dist = pdist(x)
 
+
 def edge_idx_encode(i, j, n_vertices, self_edge=True):
     if i > j:
         i, j = j, i
@@ -44,6 +46,7 @@ def edge_idx_encode(i, j, n_vertices, self_edge=True):
     else:
         return i * n_vertices - i * (i + 1) // 2 + (j - i - 1)
 
+
 def trig_idx_encode(i, j, k, n_vertices, self_edge=True):
     i, j, k = sorted([i, j, k])
     # // make sure it returns integer
@@ -299,6 +302,7 @@ def disk_2d_two_holes(r, r1, r2, c1_x, c1_y, c2_x, c2_y, n_points, noise, seed):
     y = y[idx_keep] + np.random.normal(0, noise, n_points)
     return (x, y)
 
+
 # # TODO: grid search, adjust radius based on gaussian prior
 # # TODO: generate a set of representative loops through custom distance function
 # # TODO: pair up loops from two sets though frechet distance and do regression based matching

src/scloop/utils/linear_algebra_gf2/__init__.py

@@ -0,0 +1 @@
+from .m4ri_lib import solve_gf2