Create Stub Files: Scripts & CI (#184)

* Create Stub Files: Scripts & CI
* Fixes to Unbound C++ Types
* Update Stub Files
* CI: Stub-Update Last

Since bot pushes to not trigger CI reruns for GH Actions.

* Fix using in headers
* Update Stub Files

.github/update_stub.sh

@@ -0,0 +1,18 @@
+#!/usr/bin/env bash
+#
+# Copyright 2021-2023 The AMReX Community
+#
+# This script updates the .pyi stub files for documentation and interactive use.
+# To run this script, pyAMReX needs to be installed (all dimensions) and importable.
+#
+# Authors: Axel Huebl
+# License: BSD-3-Clause-LBNL
+#
+set -eu -o pipefail
+
+# we are in the source directory, .github/
+this_dir=$(cd $(dirname $0) && pwd)
+
+pybind11-stubgen --exit-code -o ${this_dir}/../src/amrex/ amrex.space1d
+pybind11-stubgen --exit-code -o ${this_dir}/../src/amrex/ amrex.space2d
+pybind11-stubgen --exit-code -o ${this_dir}/../src/amrex/ amrex.space3d

.github/workflows/ci.yml

@@ -0,0 +1,35 @@
+name: 👑 CI
+
+# This workflow updates the .pyi stub files for documentation and interactive use.
+
+on: [push, pull_request]
+
+concurrency:
+ group: ${{ github.ref }}-${{ github.head_ref }}-ci
+ cancel-in-progress: true
+
+jobs:
+ ubuntu:
+ name: 🐧 Ubuntu
+ uses: ./.github/workflows/ubuntu.yml
+
+ intel:
+ name: 🐧 Intel
+ uses: ./.github/workflows/intel.yml
+
+ hip:
+ name: 🐧 HIP
+ uses: ./.github/workflows/hip.yml
+
+ macos:
+ name: 🍏 macOS
+ uses: ./.github/workflows/macos.yml
+
+ windows:
+ name: 🪟 Windows
+ uses: ./.github/workflows/windows.yml
+
+ stubs:
+ name: 🔄 Update Stub Files
+ needs: [ubuntu, intel, hip, macos, windows]
+ uses: ./.github/workflows/stubs.yml

.github/workflows/codeql.yml

@@ -1,4 +1,4 @@
-name: "CodeQL"
+name: 🔎 CodeQL
 
 on:
  push:

.github/workflows/hip.yml

@@ -1,6 +1,6 @@
 name: 🐧 HIP
 
-on: [push, pull_request]
+on: [workflow_call]
 
 concurrency:
  group: ${{ github.ref }}-${{ github.head_ref }}-hip

.github/workflows/intel.yml

@@ -1,6 +1,6 @@
 name: 🐧 Intel
 
-on: [push, pull_request]
+on: [workflow_call]
 
 concurrency:
  group: ${{ github.ref }}-${{ github.head_ref }}-intel

.github/workflows/macos.yml

@@ -1,6 +1,6 @@
 name: 🍏 macOS
 
-on: [push, pull_request]
+on: [workflow_call]
 
 concurrency:
  group: ${{ github.ref }}-${{ github.head_ref }}-macos

.github/workflows/stubs.yml

@@ -0,0 +1,73 @@
+name: 🔄 Update Stub Files
+
+# This workflow updates the .pyi stub files for documentation and interactive use.
+
+on: [workflow_call]
+
+concurrency:
+ group: ${{ github.ref }}-${{ github.head_ref }}-stubs
+ cancel-in-progress: true
+
+jobs:
+ # Build and install libamrex as AMReX CMake project
+ stubs:
+ name: Stubs
+ runs-on: ubuntu-22.04
+ env:
+ CC: gcc
+ CXX: g++
+ CXXFLAGS: "-O1"
+ OMP_NUM_THREAD: 2
+
+ if: github.event.pull_request.draft == false
+ permissions:
+ # Give the default GITHUB_TOKEN write permission to commit and push the
+ # changed files back to the repository.
+ contents: write
+
+ steps:
+ - uses: actions/checkout@v3
+ with:
+ repository: ${{ github.event.pull_request.head.repo.full_name }}
+ ref: ${{ github.head_ref }}
+
+ - name: Pull Remote Changes
+ run: git pull
+
+ - uses: actions/setup-python@v4
+ name: Install Python
+ with:
+ python-version: '3.9'
+
+ - name: Dependencies
+ run: .github/workflows/dependencies/dependencies_gcc10.sh
+
+ - name: Build & Install
+ run: |
+ python3 -m pip install -U pip setuptools wheel
+ python3 -m pip install -U pip mpi4py pytest pybind11-stubgen pre-commit
+ cmake -S . -B build -DAMReX_SPACEDIM="1;2;3" -DpyAMReX_IPO=OFF
+ cmake --build build -j 2 --target pip_install
+
+ - name: Update Stubs
+ run: |
+ .github/update_stub.sh
+
+ - name: Run pre-commit cleanup
+ run: |
+ git add .
+ pre-commit run -a || true
+ git add .
+
+ - name: Update Install
+ run: |
+ cmake --build build -j 2 --target pip_install
+
+ - name: Unit tests
+ run: |
+ mpiexec -np 1 python3 -m pytest tests/
+
+ - uses: stefanzweifel/git-auto-commit-action@v4
+ name: Commit Updated Stub Files
+ with:
+ commit_message: Update Stub Files

.github/workflows/ubuntu.yml

@@ -1,6 +1,6 @@
 name: 🐧 Ubuntu
 
-on: [push, pull_request]
+on: [workflow_call]
 
 concurrency:
  group: ${{ github.ref }}-${{ github.head_ref }}-linux

.github/workflows/windows.yml

@@ -1,6 +1,6 @@
 name: 🪟 Windows
 
-on: [push, pull_request]
+on: [workflow_call]
 
 concurrency:
  group: ${{ github.ref }}-${{ github.head_ref }}-windows

.pre-commit-config.yaml

@@ -30,6 +30,7 @@ repos:
  args: [--allow-multiple-documents]
  - id: check-added-large-files
  args: ['--maxkb=40']
+ exclude: ^.*\.pyi$
  - id: requirements-txt-fixer
 # - id: fix-encoding-pragma
 # exclude: ^noxfile.py$

src/Base/Array4.cpp

@@ -76,9 +76,12 @@ void make_Array4(py::module &m, std::string typestr)
 {
  using namespace amrex;
 
+ constexpr bool is_not_const = std::is_same_v<std::remove_cv_t<T>, T>;
+
  // dispatch simpler via: py::format_descriptor<T>::format() naming
  auto const array_name = std::string("Array4_").append(typestr);
- py::class_< Array4<T> >(m, array_name.c_str())
+ py::class_< Array4<T> > py_array4(m, array_name.c_str());
+ py_array4
  .def("__repr__",
  [typestr](Array4<T> const & a4) {
  std::stringstream s;
@@ -193,15 +196,7 @@ void make_Array4(py::module &m, std::string typestr)
  .def("contains", &Array4<T>::contains)
  //.def("__contains__", &Array4<T>::contains)
 
- // setter & getter
- .def("__setitem__", [](Array4<T> & a4, IntVect const & v, T const value){ a4(v) = value; })
- .def("__setitem__", [](Array4<T> & a4, std::array<int, 4> const key, T const value){
- a4(key[0], key[1], key[2], key[3]) = value;
- })
- .def("__setitem__", [](Array4<T> & a4, std::array<int, 3> const key, T const value){
- a4(key[0], key[1], key[2]) = value;
- })
-
+ // getter
  .def("__getitem__", [](Array4<T> & a4, IntVect const & v){ return a4(v); })
  .def("__getitem__", [](Array4<T> & a4, std::array<int, 4> const key){
  return a4(key[0], key[1], key[2], key[3]);
@@ -211,11 +206,25 @@ void make_Array4(py::module &m, std::string typestr)
  })
  ;
 
+ // setter
+ if constexpr (is_not_const)
+ {
+ py_array4
+ .def("__setitem__", [](Array4<T> & a4, IntVect const & v, T const value){ a4(v) = value; })
+ .def("__setitem__", [](Array4<T> & a4, std::array<int, 4> const key, T const value){
+ a4(key[0], key[1], key[2], key[3]) = value;
+ })
+ .def("__setitem__", [](Array4<T> & a4, std::array<int, 3> const key, T const value){
+ a4(key[0], key[1], key[2]) = value;
+ })
+ ;
+ }
+
  // free standing C++ functions:
- m.def("lbound", &lbound< Array4<T> >);
- m.def("ubound", &ubound< Array4<T> >);
- m.def("length", &length< Array4<T> >);
- m.def("makePolymorphic", &makePolymorphic< Array4<T> >);
+ m.def("lbound", &lbound< T >);
+ m.def("ubound", &ubound< T >);
+ m.def("length", &length< T >);
+ //m.def("makePolymorphic", &makePolymorphic< T >);
 }
 
 void init_Array4(py::module &m) {
@@ -233,6 +242,20 @@ void init_Array4(py::module &m) {
  make_Array4< unsigned long >(m, "ulong");
  make_Array4< unsigned long long >(m, "ulonglong");
 
+ make_Array4< float const >(m, "float_const");
+ make_Array4< double const >(m, "double_const");
+ make_Array4< long double const >(m, "longdouble_const");
+
+ make_Array4< short const >(m, "short_const");
+ make_Array4< int const >(m, "int_const");
+ make_Array4< long const >(m, "long_const");
+ make_Array4< long long const >(m, "longlong_const");
+
+ make_Array4< unsigned short const >(m, "ushort_const");
+ make_Array4< unsigned int const >(m, "uint_const");
+ make_Array4< unsigned long const >(m, "ulong_const");
+ make_Array4< unsigned long long const >(m, "ulonglong_const");
+
  // std::complex< float|double|long double> ?
 
  /*

src/Base/BoxArray.cpp

@@ -5,6 +5,8 @@
  */
 #include "pyAMReX.H"
 
+#include "Base/Vector.H"
+
 #include <AMReX_BoxArray.H>
 #include <AMReX_IntVect.H>
 
@@ -281,4 +283,6 @@ void init_BoxArray(py::module &m) {
 */
 
  ;
+
+ make_Vector<BoxArray> (m, "BoxArray");
 }

src/Base/CoordSys.cpp

@@ -1,3 +1,8 @@
+/* Copyright 2021-2023 The AMReX Community
+ *
+ * Authors: Axel Huebl, Ryan Sandberg
+ * License: BSD-3-Clause-LBNL
+ */
 #include "pyAMReX.H"
 
 #include <AMReX_CoordSys.H>
@@ -8,6 +13,14 @@ void init_CoordSys(py::module& m)
  using namespace amrex;
 
  py::class_<CoordSys> coord_sys(m, "CoordSys");
+
+ py::enum_<CoordSys::CoordType>(coord_sys, "CoordType")
+ .value("undef", CoordSys::CoordType::undef)
+ .value("cartesian", CoordSys::CoordType::cartesian)
+ .value("RZ", CoordSys::CoordType::RZ)
+ .value("SPHERICAL", CoordSys::CoordType::SPHERICAL)
+ .export_values();
+
  coord_sys.def("__repr__",
  [](const CoordSys&) {
  return "<amrex.CoordSys>";
@@ -27,10 +40,4 @@ void init_CoordSys(py::module& m)
  // ...
  ;
 
- py::enum_<CoordSys::CoordType>(coord_sys, "CoordType")
- .value("undef", CoordSys::CoordType::undef)
- .value("cartesian", CoordSys::CoordType::cartesian)
- .value("RZ", CoordSys::CoordType::RZ)
- .value("SPHERICAL", CoordSys::CoordType::SPHERICAL)
- .export_values();
 }

src/Base/DistributionMapping.cpp

@@ -5,6 +5,8 @@
  */
 #include "pyAMReX.H"
 
+#include "Base/Vector.H"
+
 #include <AMReX_BoxArray.H>
 #include <AMReX_DistributionMapping.H>
 #include <AMReX_Vector.H>
@@ -73,4 +75,6 @@ void init_DistributionMapping(py::module &m) {
  return dm[index];
  })
  ;
+
+ make_Vector<DistributionMapping> (m, "DistributionMapping");
 }

src/Base/FArrayBox.cpp

@@ -27,14 +27,15 @@ void init_FArrayBox(py::module &m) {
  .def(py::init< Arena* >())
  .def(py::init< Box const &, int, Arena* >())
  .def(py::init< Box const &, int, bool, bool, Arena* >())
- .def(py::init< FArrayBox const &, MakeType, int, int >())
+ //.def(py::init< FArrayBox const &, MakeType, int, int >())
  .def(py::init< Box const &, int, Real const* >())
  .def(py::init< Box const &, int, Real* >())
  .def(py::init< Array4<Real> const& >())
  .def(py::init< Array4<Real> const&, IndexType >())
  .def(py::init< Array4<Real const> const& >())
  .def(py::init< Array4<Real const> const&, IndexType >())
 
+ /*
  .def("read_from",
  py::overload_cast<std::istream&>(&FArrayBox::readFrom),
  py::arg("is")
@@ -51,5 +52,6 @@ void init_FArrayBox(py::module &m) {
  py::overload_cast<std::ostream&, int, int>(&FArrayBox::writeOn, py::const_),
  py::arg("of"), py::arg("comp"), py::arg("num_comp")
  )
+ */
  ;
 }

src/Base/Geometry.cpp

@@ -1,5 +1,7 @@
 #include "pyAMReX.H"
 
+#include "Base/Vector.H"
+
 #include <AMReX_Geometry.H>
 #include <AMReX_CoordSys.H>
 #include <AMReX_MultiFab.H>
@@ -205,4 +207,6 @@ void init_Geometry(py::module& m)
  // .def("computeRoundoffDomain")
  ;
 
+
+ make_Vector<Geometry> (m, "Geometry");
 }