API: reduce size of wheels:

- merge cython source files (reduce disk overhead from generated boilerplate code)
- exclude unused Python implementation of core algorithm from distributions

.github/workflows/ci.yml

@@ -36,6 +36,7 @@ jobs:
         python -m build
 
   unit-tests:
+    name: ${{matrix.os}} x py${{matrix.python-version}} ${{matrix.marker}}
     strategy:
       matrix:
         os:
@@ -44,17 +45,24 @@ jobs:
         - '3.10'
         - '3.11'
         - '3.12'
+
         include:
         - os: macos-latest
           python-version: '3.12'
         - os: windows-latest
           python-version: '3.12'
 
         # test with minimal requirements
-        - os: ubuntu-20.04
+        - marker: minimal
+          os: ubuntu-20.04
           python-version: '3.10'
           deps: minimal
 
+        # test GPGI_PY_LIB
+        #- marker: PY_LIB
+        #  os: ubuntu-latest
+        #  python-version: '3.12'
+
     runs-on: ${{ matrix.os }}
     steps:
     - name: Checkout Source
@@ -73,8 +81,12 @@ jobs:
         python -m pip install --requirement mindeps.txt
 
     - name: Build library
+      env:
+        GPGI_PY_LIB: ${{ matrix.marker == 'PY_LIB' }}
       # install in editable mode to allow coverage measurement
-      run: python -m pip install --editable .
+      run: |
+        echo GPGI_PY_LIB=$GPGI_PY_LIB
+        python -m pip install --editable .
 
     - run: python -m pip install --requirement requirements/tests.txt
 
@@ -91,7 +103,7 @@ jobs:
       if: matrix.os == 'ubuntu-latest'
       uses: actions/upload-artifact@v4
       with:
-        name: gpgi_coverage_data-${{ matrix.os }}-${{ matrix.python-version }}
+        name: gpgi_coverage_data-${{matrix.os}}-${{matrix.python-version}}-${{matrix.marker}}
         path: .coverage.*
         if-no-files-found: ignore
 

.gitignore

@@ -10,6 +10,6 @@ __pycache__
 MANIFEST
 build
 dist
-src/gpgi/clib/*.html
-src/gpgi/clib/*.so
-src/gpgi/clib/*.c
+src/gpgi/_lib.html
+src/gpgi/_lib.*.so
+src/gpgi/_lib.c

MANIFEST.in

@@ -1,7 +1,9 @@
 include LICENCE
 include src/gpgi/py.typed
-include src/gpgi/clib/*.pyx
-exclude src/gpgi/clib/*.c
+include src/gpgi/_lib.pyi
+include src/gpgi/_lib.pyx
+exclude src/gpgi/_lib.c
+exclude src/gpgi/_lib.py
 
 recursive-exclude tests *
 exclude .pre-commit-config.yaml

pyproject.toml

@@ -8,7 +8,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "gpgi"
-version = "1.0.0"
+version = "2.0.dev0"
 description = "A Generic Particle+Grid Interface"
 authors = [
     { name = "C.M.T. Robert" },
@@ -56,7 +56,7 @@ include = [
 omit = [
     "src/gpgi/_backports.py",
     "src/gpgi/_typing.py",
-    "src/gpgi/lib/*.py",
+    "src/gpgi/_lib.py",
 ]
 
 [tool.coverage.report]

setup.py

@@ -1,33 +1,37 @@
 import os
 from distutils.extension import Extension
+from pathlib import Path
 
-import numpy
+import numpy as np
 from Cython.Build import cythonize
 from setuptools import setup
 
+SRC_DIR = Path(__file__).parent / "src" / "gpgi"
 
-def make_ext(path: str) -> Extension:
-    name, _ = os.path.splitext(path)
-    name = name.replace("/", ".")
-
-    return Extension(
-        name,
-        sources=[f"src/{path}"],
-        include_dirs=[numpy.get_include()],
-        define_macros=[
-            # keep in sync with runtime requirements (pyproject.toml)
-            ("NPY_TARGET_VERSION", "NPY_1_23_API_VERSION"),
-            ("NPY_NO_DEPRECATED_API", "NPY_1_7_API_VERSION"),
-        ],
-    )
-
-
-setup(
-    ext_modules=cythonize(
+if os.getenv("GPGI_PY_LIB", "0").lower() in ("1", "true"):
+    if not SRC_DIR.joinpath("_lib.py").exists():
+        raise RuntimeError(
+            "GPGI's pure Python implementation can only be built "
+            "from the development version in editable mode."
+        )
+    ext_modules = []
+    for sofile in SRC_DIR.glob("*.so"):
+        os.remove(sofile)
+else:
+    ext_modules = cythonize(
         [
-            make_ext("gpgi/clib/_indexing.pyx"),
-            make_ext("gpgi/clib/_deposition_methods.pyx"),
+            Extension(
+                "gpgi._lib",
+                sources=["src/gpgi/_lib.pyx"],
+                include_dirs=[np.get_include()],
+                define_macros=[
+                    # keep in sync with runtime requirements (pyproject.toml)
+                    ("NPY_TARGET_VERSION", "NPY_1_23_API_VERSION"),
+                    ("NPY_NO_DEPRECATED_API", "NPY_1_7_API_VERSION"),
+                ],
+            )
         ],
         compiler_directives={"language_level": 3},
-    ),
-)
+    )
+
+setup(ext_modules=ext_modules)

src/gpgi/__init__.py

@@ -4,8 +4,6 @@
 
 from .types import Dataset, FieldMap, Geometry, Grid, ParticleSet
 
-__version__ = "1.0.0"
-
 
 def load(
     *,

src/gpgi/lib/_deposition_methods.py → src/gpgi/_lib.py

@@ -1,7 +1,81 @@
+"""Python implementations of deposition algorithms (dev only)."""
+
 import numpy as np
 
 
-def _deposit_ngp(
+def _index_particles(
+    cell_edges_x1,
+    cell_edges_x2,
+    cell_edges_x3,
+    particles_x1,
+    particles_x2,
+    particles_x3,
+    dx,
+    out,
+):
+    if cell_edges_x3.shape[0] > 1:
+        ndim = 3
+    elif cell_edges_x2.shape[0] > 1:
+        ndim = 2
+    else:
+        ndim = 1
+
+    particle_count = particles_x1.shape[0]
+
+    for ipart in range(particle_count):
+        x = particles_x1[ipart]
+        if dx[0] > 0:
+            out[ipart, 0] = int((x - cell_edges_x1[0]) // dx[0])
+        else:
+            iL = 1
+            iR = cell_edges_x1.shape[0] - 2
+            idx = (iL + iR) // 2
+            while idx != iL:
+                if cell_edges_x1[idx] > x:
+                    iR = idx
+                else:
+                    iL = idx
+                idx = (iL + iR) // 2
+            out[ipart, 0] = idx
+
+        if ndim < 2:
+            continue
+
+        x = particles_x2[ipart]
+        if dx[1] > 0:
+            out[ipart, 1] = int((x - cell_edges_x2[0]) // dx[1])
+        else:
+            iL = 1
+            iR = cell_edges_x2.shape[00] - 2
+            idx = (iL + iR) // 2
+            while idx != iL:
+                if cell_edges_x2[idx] > x:
+                    iR = idx
+                else:
+                    iL = idx
+                idx = (iL + iR) // 2
+            out[ipart, 1] = idx
+
+        if ndim < 3:
+            continue
+
+        x = particles_x3[ipart]
+        if dx[2] > 0:
+            out[ipart, 2] = int((x - cell_edges_x3[0]) // dx[2])
+        else:
+            iL = 1
+            iR = cell_edges_x3.shape[0] - 2
+            idx = (iL + iR) // 2
+            while idx != iL:
+                if cell_edges_x3[idx] > x:
+                    iR = idx
+                else:
+                    iL = idx
+                idx = (iL + iR) // 2
+            out[ipart, 2] = idx
+
+
+def _deposit_ngp_impl(
     cell_edges_x1,
     cell_edges_x2,
     cell_edges_x3,
@@ -23,6 +97,9 @@ def _deposit_ngp(
             out[md_idx] += field[ipart] * weight_field[ipart]
 
 
+_deposit_ngp_1D = _deposit_ngp_2D = _deposit_ngp_3D = _deposit_ngp_impl
+
+
 def _deposit_cic_1D(
     cell_edges_x1,
     cell_edges_x2,

src/gpgi/_lib.pyi

@@ -0,0 +1,124 @@
+import numpy as np
+from numpy.typing import NDArray
+
+NDArrayReal = NDArray[np.float64 | np.float32]
+NDArrayUInt = NDArray[np.uint16]
+
+def _index_particles(
+    cell_edges_x1: NDArrayReal,
+    cell_edges_x2: NDArrayReal,
+    cell_edges_x3: NDArrayReal,
+    particles_x1: NDArrayReal,
+    particles_x2: NDArrayReal,
+    particles_x3: NDArrayReal,
+    dx: NDArrayReal,
+    out: NDArrayUInt,
+) -> None: ...
+def _deposit_ngp_1D(
+    cell_edges_x1: NDArrayReal,
+    cell_edges_x2: NDArrayReal,
+    cell_edges_x3: NDArrayReal,
+    particles_x1: NDArrayReal,
+    particles_x2: NDArrayReal,
+    particles_x3: NDArrayReal,
+    field: NDArrayReal,
+    weight_field: NDArrayReal,
+    hci: NDArrayUInt,  # dim: 2
+    out: NDArrayReal,
+) -> None: ...
+def _deposit_ngp_2D(
+    cell_edges_x1: NDArrayReal,
+    cell_edges_x2: NDArrayReal,
+    cell_edges_x3: NDArrayReal,
+    particles_x1: NDArrayReal,
+    particles_x2: NDArrayReal,
+    particles_x3: NDArrayReal,
+    field: NDArrayReal,
+    weight_field: NDArrayReal,
+    hci: NDArrayUInt,  # dim: 2
+    out: NDArrayReal,
+) -> None: ...
+def _deposit_ngp_3D(
+    cell_edges_x1: NDArrayReal,
+    cell_edges_x2: NDArrayReal,
+    cell_edges_x3: NDArrayReal,
+    particles_x1: NDArrayReal,
+    particles_x2: NDArrayReal,
+    particles_x3: NDArrayReal,
+    field: NDArrayReal,
+    weight_field: NDArrayReal,
+    hci: NDArrayUInt,  # dim: 2
+    out: NDArrayReal,
+) -> None: ...
+def _deposit_cic_1D(
+    cell_edges_x1: NDArrayReal,
+    cell_edges_x2: NDArrayReal,
+    cell_edges_x3: NDArrayReal,
+    particles_x1: NDArrayReal,
+    particles_x2: NDArrayReal,
+    particles_x3: NDArrayReal,
+    field: NDArrayReal,
+    weight_field: NDArrayReal,
+    hci: NDArrayUInt,  # dim: 2
+    out: NDArrayReal,
+) -> None: ...
+def _deposit_cic_2D(
+    cell_edges_x1: NDArrayReal,
+    cell_edges_x2: NDArrayReal,
+    cell_edges_x3: NDArrayReal,
+    particles_x1: NDArrayReal,
+    particles_x2: NDArrayReal,
+    particles_x3: NDArrayReal,
+    field: NDArrayReal,
+    weight_field: NDArrayReal,
+    hci: NDArrayUInt,  # dim: 2
+    out: NDArrayReal,
+) -> None: ...
+def _deposit_cic_3D(
+    cell_edges_x1: NDArrayReal,
+    cell_edges_x2: NDArrayReal,
+    cell_edges_x3: NDArrayReal,
+    particles_x1: NDArrayReal,
+    particles_x2: NDArrayReal,
+    particles_x3: NDArrayReal,
+    field: NDArrayReal,
+    weight_field: NDArrayReal,
+    hci: NDArrayUInt,  # dim: 2
+    out: NDArrayReal,
+) -> None: ...
+def _deposit_tsc_1D(
+    cell_edges_x1: NDArrayReal,
+    cell_edges_x2: NDArrayReal,
+    cell_edges_x3: NDArrayReal,
+    particles_x1: NDArrayReal,
+    particles_x2: NDArrayReal,
+    particles_x3: NDArrayReal,
+    field: NDArrayReal,
+    weight_field: NDArrayReal,
+    hci: NDArrayUInt,  # dim: 2
+    out: NDArrayReal,
+) -> None: ...
+def _deposit_tsc_2D(
+    cell_edges_x1: NDArrayReal,
+    cell_edges_x2: NDArrayReal,
+    cell_edges_x3: NDArrayReal,
+    particles_x1: NDArrayReal,
+    particles_x2: NDArrayReal,
+    particles_x3: NDArrayReal,
+    field: NDArrayReal,
+    weight_field: NDArrayReal,
+    hci: NDArrayUInt,  # dim: 2
+    out: NDArrayReal,
+) -> None: ...
+def _deposit_tsc_3D(
+    cell_edges_x1: NDArrayReal,
+    cell_edges_x2: NDArrayReal,
+    cell_edges_x3: NDArrayReal,
+    particles_x1: NDArrayReal,
+    particles_x2: NDArrayReal,
+    particles_x3: NDArrayReal,
+    field: NDArrayReal,
+    weight_field: NDArrayReal,
+    hci: NDArrayUInt,  # dim: 2
+    out: NDArrayReal,
+) -> None: ...