peclet-core 1.3.0__tar.gz → 1.3.2__tar.gz

{peclet_core-1.3.0 → peclet_core-1.3.2}/.github/workflows/ci.yml

@@ -110,7 +110,9 @@ jobs:
                                   python3-dev python3-pip
           # nanobind is located through the interpreter (cmake/SuiteNanobind.cmake); mpi4py builds
           # against the apt OpenMPI just installed (same MPI the modules link).
-          python3 -m pip install "nanobind==${NANOBIND_VERSION}" numpy pytest mpi4py
+          # peclet-geom (a wheel) lets python_shell_deprecation_geom run instead of SKIPping: the
+          # compatibility shell re-exports it, so the warning gate needs it importable.
+          python3 -m pip install "nanobind==${NANOBIND_VERSION}" numpy pytest mpi4py "peclet-geom>=1.0,<2"
 
       - name: Cache Kokkos install
         id: kokkos-cache

{peclet_core-1.3.0 → peclet_core-1.3.2}/CITATION.cff

@@ -16,8 +16,8 @@ authors:
     orcid: "https://orcid.org/0000-0001-6099-3583"
     email: e.a.j.f.peters@tue.nl
     affiliation: "Eindhoven University of Technology"
-version: 1.3.0
-date-released: 2026-09-26
+version: 1.3.2
+date-released: 2026-10-03
 license: MIT
 doi: 10.5281/zenodo.21132435
 identifiers:

{peclet_core-1.3.0 → peclet_core-1.3.2}/CLAUDE.md

@@ -37,7 +37,7 @@ ctest --test-dir build --output-on-failure -LE bench   # 76 ctests (77 with `ben
 export PATH=/usr/local/cuda-13.2/bin:$PATH    # if the Kokkos install targets the CUDA backend
 cmake -S . -B build_kokkos -DPECLET_CORE_ENABLE_KOKKOS=ON \
   -DCMAKE_PREFIX_PATH=../extern/install/nvidia-cuda
-cmake --build build_kokkos -j && ctest --test-dir build_kokkos --output-on-failure -LE bench  # 91 ctests (92 with `bench`): + device halo / geometry / solver, np=1,2,4,8
+cmake --build build_kokkos -j && ctest --test-dir build_kokkos --output-on-failure -LE bench  # 92 ctests (93 with `bench`): + device halo / geometry / solver / VoF PV fit, np=1,2,4,8
 mpirun -np 4 ./build/benchmarks/bench_halo 48 1 300
 
 # Python modules + their ctests (test_mpi.py np=1,2,4,8; state_hash; ndarray interop). Release is

{peclet_core-1.3.0 → peclet_core-1.3.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: peclet-core
-Version: 1.3.0
+Version: 1.3.2
 Summary: peclet.core — compatibility shell: peclet.core.geom is now peclet.geom, peclet.core.mpi is now peclet.halo
 Project-URL: Homepage, https://github.com/computational-chemical-engineering/peclet
 Project-URL: Documentation, https://computational-chemical-engineering.github.io/peclet/
@@ -15,7 +15,7 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Topic :: Scientific/Engineering
 Requires-Python: >=3.10
 Requires-Dist: peclet-geom<2,>=1.0
-Requires-Dist: peclet-halo<2,>=1.1
+Requires-Dist: peclet-halo<2,>=1.2
 Description-Content-Type: text/markdown
 
 # core — `peclet-halo` (+ the `peclet-core` compatibility shell)
@@ -127,8 +127,8 @@ after `cmake --install`, or as a sibling checkout in the suite.
   `find_package(MPI REQUIRED)` — so a pure-geometry API could not be installed without an MPI
   toolchain. The C++ headers `include/peclet/core/geom/` **stay here**; peclet-geom vendors them at
   `PECLET_CORE_TAG`. The old spellings keep working through the `peclet-core` compatibility shell
-  until 2.0.0 — `peclet.core.geom` is now `peclet.geom`, `peclet.core.mpi` is now `peclet.halo`,
-  and each pair is the same object. See
+  until 2.0.0, with a `DeprecationWarning` since 1.3.1 — `peclet.core.geom` is now `peclet.geom`,
+  `peclet.core.mpi` is now `peclet.halo`, and each pair is the same object. See
   [docs/CORE_BOUNDARY.md](https://github.com/computational-chemical-engineering/peclet/blob/main/docs/CORE_BOUNDARY.md).
 
 Validated end-to-end by distributed explicit heat-diffusion solvers (plain, and **around an SDF solid

{peclet_core-1.3.0 → peclet_core-1.3.2}/README.md

@@ -107,8 +107,8 @@ after `cmake --install`, or as a sibling checkout in the suite.
   `find_package(MPI REQUIRED)` — so a pure-geometry API could not be installed without an MPI
   toolchain. The C++ headers `include/peclet/core/geom/` **stay here**; peclet-geom vendors them at
   `PECLET_CORE_TAG`. The old spellings keep working through the `peclet-core` compatibility shell
-  until 2.0.0 — `peclet.core.geom` is now `peclet.geom`, `peclet.core.mpi` is now `peclet.halo`,
-  and each pair is the same object. See
+  until 2.0.0, with a `DeprecationWarning` since 1.3.1 — `peclet.core.geom` is now `peclet.geom`,
+  `peclet.core.mpi` is now `peclet.halo`, and each pair is the same object. See
   [docs/CORE_BOUNDARY.md](https://github.com/computational-chemical-engineering/peclet/blob/main/docs/CORE_BOUNDARY.md).
 
 Validated end-to-end by distributed explicit heat-diffusion solvers (plain, and **around an SDF solid

{peclet_core-1.3.0 → peclet_core-1.3.2}/docs/Doxyfile

@@ -5,7 +5,7 @@
 
 DOXYFILE_ENCODING      = UTF-8
 PROJECT_NAME           = "core"
-PROJECT_NUMBER         = 1.3.0
+PROJECT_NUMBER         = 1.3.2
 PROJECT_BRIEF          = "Shared MPI block decomposition, asynchronous ghost-layer exchange, SDF geometry, load balancing (header-only C++20)"
 OUTPUT_DIRECTORY       = docs
 HTML_OUTPUT            = html

{peclet_core-1.3.0 → peclet_core-1.3.2}/include/peclet/core/vof/curvature.hpp

@@ -729,7 +729,7 @@ KOKKOS_INLINE_FUNCTION void pvFitInit(PvFit& f) {
   f.npoly = 0;
 }
 
-/// Fold one stencil cell's PLIC polygon into the fit.
+/// One stencil cell's PLIC polygon in the PV fit: the parameters of `pvFitTerm` and `pvFitAdd`.
 ///
 /// @param mx,my,mz,alpha  the cell's PLIC plane in ITS OWN unit-cell coordinates (`plic.hpp`).
 /// @param off             the cell's integer index offset from the target cell.
@@ -744,11 +744,25 @@ KOKKOS_INLINE_FUNCTION void pvFitInit(PvFit& f) {
 ///                        integrated with the wrong sign of `z'`. Jibben's area projection
 ///                        `A (n.n_p)` decays to zero over the same range; this is the explicit
 ///                        version of the same guard.
-/// @return true if the polygon contributed.
-KOKKOS_INLINE_FUNCTION bool pvFitAdd(PvFit& f, double mx, double my, double mz, double alpha,
-                                     const double off[3], const double org[3], const double t1[3],
-                                     const double t2[3], const double nn[3], double dW,
-                                     double cosMin, const VofMetric& g) {
+///
+/// `pvFitAdd` is the composition of `pvFitTerm` (the per-polygon map) and `pvFitAccum` (the `+=`
+/// into the normal equations), bitwise (`tests/test_vof_pvfit.cpp`). The split lets a device
+/// fallback evaluate the stencil's terms in parallel and still accumulate them in the canonical
+/// order (flow `doc/vof_step_performance_design.md` §4.7, §5.11).
+struct PvTerm {
+  double w, B, s[6];
+  bool ok;
+};
+
+/// One stencil polygon's contribution to the PV fit: everything `pvFitAdd` computes before the
+/// accumulation — the polygon, the frame transform, the moments `s`, the Wendland weight `w` and
+/// `B`. Same parameters as `pvFitAdd`. Sets `t.ok` and returns it: false exactly where `pvFitAdd`
+/// returns false (a rejected polygon), and then `w`, `B`, `s` are unspecified.
+KOKKOS_INLINE_FUNCTION bool pvFitTerm(PvTerm& t, double mx, double my, double mz, double alpha,
+                                      const double off[3], const double org[3], const double t1[3],
+                                      const double t2[3], const double nn[3], double dW,
+                                      double cosMin, const VofMetric& g) {
+  t.ok = false;
   const double n2 = mx * mx + my * my + mz * mz;
   if (!(n2 > 0.0))
     return false;
@@ -804,12 +818,38 @@ KOKKOS_INLINE_FUNCTION bool pvFitAdd(PvFit& f, double mx, double my, double mz,
     return false;
 
   const double B = b0 * s[0] + b1 * s[1] + b2 * s[2];
+  t.w = w;
+  t.B = B;
+  for (int i = 0; i < 6; ++i)
+    t.s[i] = s[i];
+  t.ok = true;
+  return true;
+}
+
+/// Fold one accepted term (`t.ok`) into the fit — the accumulation half of `pvFitAdd`, with its
+/// expressions verbatim. Calling it in the stencil's canonical order reproduces `pvFitAdd`'s sums.
+KOKKOS_INLINE_FUNCTION void pvFitAccum(PvFit& f, const PvTerm& t) {
+  const double w = t.w, B = t.B;
+  const double* s = t.s;
   for (int i = 0; i < 6; ++i) {
     f.b[i] += w * s[i] * B;
     for (int j = 0; j < 6; ++j)
       f.A[i][j] += w * s[i] * s[j];
   }
   ++f.npoly;
+}
+
+/// Fold one stencil cell's PLIC polygon into the fit: `pvFitTerm`, then `pvFitAccum` if the
+/// polygon is accepted. Parameters as documented above `PvTerm`.
+/// @return true if the polygon contributed.
+KOKKOS_INLINE_FUNCTION bool pvFitAdd(PvFit& f, double mx, double my, double mz, double alpha,
+                                     const double off[3], const double org[3], const double t1[3],
+                                     const double t2[3], const double nn[3], double dW,
+                                     double cosMin, const VofMetric& g) {
+  PvTerm t;
+  if (!pvFitTerm(t, mx, my, mz, alpha, off, org, t1, t2, nn, dW, cosMin, g))
+    return false;
+  pvFitAccum(f, t);
   return true;
 }
 

{peclet_core-1.3.0 → peclet_core-1.3.2}/packaging/pyproject-core.toml

@@ -7,7 +7,7 @@
 #     peclet.core.mpi   ->  peclet.halo   (peclet-halo, sdist, needs MPI)
 #
 # This distribution keeps `import peclet.core.{geom,mpi}` working by re-exporting them — the same
-# objects, not wrappers. It warns from 1.3.0 and is removed at 2.0.0, where the `<2` ceiling on its
+# objects, not wrappers. It warns from 1.3.1 and is removed at 2.0.0, where the `<2` ceiling on its
 # pins makes a 2.x install fail LOUDLY at resolution instead of silently importing nothing.
 #
 # The umbrella release workflow copies this over pyproject.toml to build the shell, the same
@@ -19,7 +19,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "peclet-core"
-version = "1.3.0"
+version = "1.3.2"
 description = "peclet.core — compatibility shell: peclet.core.geom is now peclet.geom, peclet.core.mpi is now peclet.halo"
 readme = "README.md"
 requires-python = ">=3.10"
@@ -35,7 +35,7 @@ classifiers = [
 # The `<2` ceiling is load-bearing, not caution: at 2.0.0 this shell is gone, and a 2.x environment
 # that installs peclet-core must fail at RESOLUTION with the constraint named, rather than resolve
 # and then fail at import. A pinned 1.x family keeps working forever.
-dependencies = ["peclet-geom>=1.0,<2", "peclet-halo>=1.1,<2"]
+dependencies = ["peclet-geom>=1.0,<2", "peclet-halo>=1.2,<2"]
 
 [project.urls]
 Homepage = "https://github.com/computational-chemical-engineering/peclet"

peclet_core-1.3.2/packaging/shell/core_geom.py

@@ -0,0 +1,16 @@
+"""peclet.core.geom — the pre-1.2 spelling of peclet.geom; `from peclet import geom` is canonical.
+
+Re-exports peclet.geom unchanged: the objects here ARE the objects there. Works unchanged in
+peclet 1.2.0, warns from peclet-core 1.3.1 (family 1.3.0), removed in 2.0.0
+(suite/docs/CORE_BOUNDARY.md).
+"""
+import warnings
+
+warnings.warn(
+    "peclet.core.geom is peclet.geom since peclet 1.2.0 — use `from peclet import geom`. "
+    "peclet.core is removed in peclet 2.0.0.", DeprecationWarning, stacklevel=2)
+
+from peclet.geom import *  # noqa: F401,F403,E402
+from peclet import geom as _canonical  # noqa: E402
+
+__all__ = [n for n in dir(_canonical) if not n.startswith("_")]

{peclet_core-1.3.0 → peclet_core-1.3.2}/packaging/shell/core_init.py

@@ -13,7 +13,8 @@ Why the split: `peclet.core.geom` is host-only SDF authoring with no MPI in it,
 distribution with the halo bindings whose build requires an MPI toolchain — so a pure-geometry API
 could not be pip-installed without MPI. See suite/docs/CORE_BOUNDARY.md.
 
-These spellings keep working unchanged in peclet 1.2.0, gain a DeprecationWarning in 1.3.0, and are
+These spellings keep working unchanged in peclet 1.2.0, warn (DeprecationWarning, on importing
+``peclet.core.geom`` / ``peclet.core.mpi``) from peclet-core 1.3.1 in family 1.3.0, and are
 removed in 2.0.0. The canonical spellings are ``from peclet import geom`` and
 ``from peclet import halo``.
 """

peclet_core-1.3.2/packaging/shell/core_mpi.py

@@ -0,0 +1,16 @@
+"""peclet.core.mpi — the pre-1.2 spelling of peclet.halo; `from peclet import halo` is canonical.
+
+Re-exports peclet.halo unchanged: the objects here ARE the objects there. Works unchanged in
+peclet 1.2.0, warns from peclet-core 1.3.1 (family 1.3.0), removed in 2.0.0
+(suite/docs/CORE_BOUNDARY.md).
+"""
+import warnings
+
+warnings.warn(
+    "peclet.core.mpi is peclet.halo since peclet 1.2.0 — use `from peclet import halo`. "
+    "peclet.core is removed in peclet 2.0.0.", DeprecationWarning, stacklevel=2)
+
+from peclet.halo import *  # noqa: F401,F403,E402
+from peclet import halo as _canonical  # noqa: E402
+
+__all__ = [n for n in dir(_canonical) if not n.startswith("_")]

{peclet_core-1.3.0 → peclet_core-1.3.2}/pyproject.toml

@@ -7,7 +7,7 @@
 #     peclet.core.mpi   ->  peclet.halo   (peclet-halo, sdist, needs MPI)
 #
 # This distribution keeps `import peclet.core.{geom,mpi}` working by re-exporting them — the same
-# objects, not wrappers. It warns from 1.3.0 and is removed at 2.0.0, where the `<2` ceiling on its
+# objects, not wrappers. It warns from 1.3.1 and is removed at 2.0.0, where the `<2` ceiling on its
 # pins makes a 2.x install fail LOUDLY at resolution instead of silently importing nothing.
 #
 # The umbrella release workflow copies this over pyproject.toml to build the shell, the same
@@ -19,7 +19,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "peclet-core"
-version = "1.3.0"
+version = "1.3.2"
 description = "peclet.core — compatibility shell: peclet.core.geom is now peclet.geom, peclet.core.mpi is now peclet.halo"
 readme = "README.md"
 requires-python = ">=3.10"
@@ -35,7 +35,7 @@ classifiers = [
 # The `<2` ceiling is load-bearing, not caution: at 2.0.0 this shell is gone, and a 2.x environment
 # that installs peclet-core must fail at RESOLUTION with the constraint named, rather than resolve
 # and then fail at import. A pinned 1.x family keeps working forever.
-dependencies = ["peclet-geom>=1.0,<2", "peclet-halo>=1.1,<2"]
+dependencies = ["peclet-geom>=1.0,<2", "peclet-halo>=1.2,<2"]
 
 [project.urls]
 Homepage = "https://github.com/computational-chemical-engineering/peclet"

{peclet_core-1.3.0 → peclet_core-1.3.2}/python/CMakeLists.txt

@@ -105,6 +105,16 @@ if(PECLET_CORE_PYTHON_TESTS)
   # type exits 77 and ctest reports the gate SKIPPED (CI), never passed.
   set_tests_properties(python_state_hash PROPERTIES LABELS "python" SKIP_RETURN_CODE 77
     ENVIRONMENT "${_py_env};OMP_NUM_THREADS=1")
+  # The peclet-core compatibility shell (packaging/shell) warns on `import peclet.core.{geom,mpi}`
+  # and the canonical `peclet.geom` / `peclet.halo` stay silent — CORE_BOUNDARY step 2, gated.
+  # The geom half SKIPs (77) where the separate peclet-geom distribution is not installed.
+  foreach(_old IN ITEMS geom mpi)
+    add_test(NAME python_shell_deprecation_${_old}
+             COMMAND "${Python_EXECUTABLE}" "${CMAKE_CURRENT_SOURCE_DIR}/test_shell_deprecation.py"
+                     ${_old} "${CMAKE_CURRENT_SOURCE_DIR}/../packaging/shell")
+    set_tests_properties(python_shell_deprecation_${_old} PROPERTIES LABELS "python"
+      SKIP_RETURN_CODE 77 ENVIRONMENT "${_py_env}")
+  endforeach()
   if(Kokkos_FOUND)
     add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/../tests/python tests_python)
   else()

{peclet_core-1.3.0 → peclet_core-1.3.2}/python/packaging/halo_init.py

@@ -8,7 +8,7 @@ Needs an MPI toolchain to build and an MPI runtime to use, which is why it ships
 `pip install peclet[mpi]` while its former housemate `peclet.geom` ships wheels.
 
 Until peclet 1.2.0 this was ``peclet.core.mpi`` in the ``peclet-core`` distribution. That spelling
-still works and is the same object; it warns from 1.3.0 and is removed in 2.0.0.
+still works and is the same object; it warns from 1.3.1 and is removed in 2.0.0.
 """
 from importlib.metadata import PackageNotFoundError, version as _version
 

peclet_core-1.3.2/python/test_shell_deprecation.py

@@ -0,0 +1,78 @@
+"""The peclet-core compatibility shell warns on the old spelling; the canonical spelling is silent.
+
+    python test_shell_deprecation.py {geom|mpi} <core>/packaging/shell
+
+The ladder step 2 of suite/docs/CORE_BOUNDARY.md, gated rather than trusted. The three shell files
+are staged as ``peclet/core/`` in a temporary directory -- the layout the peclet-core wheel installs
+(packaging/pyproject-core.toml) -- and each check runs in a fresh interpreter:
+
+1. ``python -W error::DeprecationWarning -c "import peclet.core.<old>"`` must exit NON-ZERO, and
+   its stderr must carry the shell's message (so an ImportError cannot pass for the warning);
+2. ``python -c "import peclet.core.<old>"`` with the default filters must exit 0 and PRINT the
+   warning -- stacklevel=2 attributes it to the importing ``__main__``, which is what makes a
+   user see it rather than only a test runner;
+3. ``python -W error::DeprecationWarning -c "import peclet.<canonical>"`` must exit 0.
+
+Exits 77 (ctest SKIP) when the canonical module is not importable at all: peclet.geom is a separate
+distribution (peclet-geom), and without it check 1 would "fail" by ImportError for the wrong reason.
+"""
+import os
+import shutil
+import subprocess
+import sys
+import tempfile
+
+CANONICAL = {"geom": "geom", "mpi": "halo"}
+
+
+def run(args, env):
+    return subprocess.run([sys.executable, *args], env=env, capture_output=True, text=True)
+
+
+def main():
+    old, shell_dir = sys.argv[1], sys.argv[2]
+    canon = CANONICAL[old]
+    message = f"peclet.core.{old} is peclet.{canon} since peclet 1.2.0"
+
+    with tempfile.TemporaryDirectory() as tmp:
+        pkg = os.path.join(tmp, "peclet", "core")   # `peclet` stays a PEP 420 namespace: no __init__
+        os.makedirs(pkg)
+        for src, dst in (("core_init.py", "__init__.py"), ("core_geom.py", "geom.py"),
+                         ("core_mpi.py", "mpi.py")):
+            shutil.copy(os.path.join(shell_dir, src), os.path.join(pkg, dst))
+        env = dict(os.environ)
+        env["PYTHONPATH"] = os.pathsep.join(p for p in (tmp, env.get("PYTHONPATH", "")) if p)
+        env.pop("PYTHONWARNINGS", None)
+
+        r = run(["-c", f"import peclet.{canon}"], env)
+        if r.returncode != 0:
+            print(f"SKIP: peclet.{canon} is not importable here:\n{r.stderr}")
+            return 77
+
+        failures = []
+        r = run(["-W", "error::DeprecationWarning", "-c", f"import peclet.core.{old}"], env)
+        if r.returncode == 0:
+            failures.append(f"`import peclet.core.{old}` under -W error exited 0: no DeprecationWarning")
+        elif f"DeprecationWarning: {message}" not in r.stderr:
+            failures.append(f"`import peclet.core.{old}` failed, but not with the shell's warning:\n{r.stderr}")
+
+        r = run(["-c", f"import peclet.core.{old}"], env)
+        if r.returncode != 0:
+            failures.append(f"`import peclet.core.{old}` (default filters) failed:\n{r.stderr}")
+        elif message not in r.stderr:
+            failures.append(f"`import peclet.core.{old}` (default filters) did not show the warning; "
+                            f"stderr was:\n{r.stderr!r}")
+
+        r = run(["-W", "error::DeprecationWarning", "-c", f"import peclet.{canon}"], env)
+        if r.returncode != 0:
+            failures.append(f"canonical `import peclet.{canon}` is not silent:\n{r.stderr}")
+
+    for f in failures:
+        print("FAIL:", f)
+    if not failures:
+        print(f"OK: peclet.core.{old} warns ({message}...); peclet.{canon} is silent")
+    return 1 if failures else 0
+
+
+if __name__ == "__main__":
+    sys.exit(main())

{peclet_core-1.3.0 → peclet_core-1.3.2}/tests/CMakeLists.txt

@@ -282,6 +282,14 @@ if(MPI_FOUND)
     target_link_libraries(test_csr_solver PRIVATE Kokkos::kokkos)
     peclet_core_add_test(csr_solver test_csr_solver)
 
+    # VoF PV fit: pvFitAdd == pvFitTerm + pvFitAccum bitwise, device and host spaces (10^5
+    # random cases incl. rejected polygons; flow vof_step_performance_design.md §5.11, WO-7a).
+    add_executable(test_vof_pvfit test_vof_pvfit.cpp)
+    target_include_directories(test_vof_pvfit PRIVATE
+      ${PROJECT_SOURCE_DIR}/include ${CMAKE_CURRENT_SOURCE_DIR})
+    target_link_libraries(test_vof_pvfit PRIVATE Kokkos::kokkos)
+    peclet_core_add_test(vof_pvfit test_vof_pvfit)
+
     # Device GraphAMG apply vs the host oracle (no MPI; serial + device).
     add_executable(test_graph_amg_device test_graph_amg_device.cpp)
     target_include_directories(test_graph_amg_device PRIVATE