bin_grid news incl. tests (kudos @jcurtis2); tests/pypi workflow cleanup (DLL loading); fix dll path in __init__.py

jcurtis2 · web-flow · commit f23beec5618d · 2022-06-22T23:57:06.000-05:00
diff --git a/.github/workflows/tests+artifacts+pypi.yml b/.github/workflows/tests+artifacts+pypi.yml
@@ -54,15 +54,7 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - run: pip install pytest build
-
-      - run: DEBUG=1 VERBOSE=1 pip install --verbose -e .
-
-      - run: pytest -v -s -We -p no:unraisableexception tests
-
-      - run: DEBUG=0 VERBOSE=1 pip install --verbose -e .
-
-      - run: pytest -v -s -We -p no:unraisableexception tests
+      - run: pip install pytest build wheel
 
       - run: |
           python -m build 2>&1 | tee build.log
@@ -71,12 +63,6 @@ jobs:
       - if: matrix.platform == 'ubuntu-latest'
         run: rm dist/*
 
-      - if: matrix.platform != 'ubuntu-latest'
-        uses: actions/upload-artifact@v2
-        with:
-          name: dist
-          path: dist
-
       - if: matrix.platform == 'ubuntu-latest'
         run: python -c "import sys; vi=sys.version_info; abitag='m' if vi.minor<8 else ''; print(f'PV=cp{vi.major}{vi.minor}-cp{vi.major}{vi.minor}{abitag}')" >> $GITHUB_ENV
 
@@ -88,11 +74,39 @@ jobs:
             pre-build-command: 'git config --global --add safe.directory "*"'
 
       - if: matrix.platform == 'ubuntu-latest'
-        uses: actions/upload-artifact@v2
+        run: rm dist/*-linux_*
+
+      - uses: actions/upload-artifact@v2
         with:
           name: dist
-          path: dist/*-manylinux*.whl
+          path: dist
+
+      # TODO: should be doable on any OS
+      - if: matrix.platform == 'windows-latest' || matrix.platform == 'ubuntu-latest'
+        run: |
+          pip install dist/*.whl
+          pip show --verbose PyPartMC
 
+      - if: startsWith(matrix.platform, 'macos-')
+        run: |
+          DEBUG=0 VERBOSE=1 pip install --verbose -e .
+
+      ### make sure PyPartMC is not picked up from a local folder
+      - run: |
+          cd tests
+          python -v -c "import PyPartMC"
+          pytest -v -s -We -p no:unraisableexception .
+
+# TODO: worth checking but perhaps in a separater workflow? (here conflicts with build dir created for manylinux by other user)
+#      - run: DEBUG=1 VERBOSE=1 pip install --verbose -e .
+#
+#      - run: pytest -v -s -We -p no:unraisableexception tests
+#
+#      - run: DEBUG=0 VERBOSE=1 pip install --verbose -e .
+#
+#      - run: pytest -v -s -We -p no:unraisableexception tests
+
+### uncomment to gain ssh access in case of failure
 #      - if: ${{ failure() }}
 #        uses: mxschmitt/action-tmate@v3
 #        with:
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -35,7 +35,7 @@ endmacro(add_prefix)
 set(PyPartMC_sources 
   pypartmc.cpp gimmicks.cpp fake_netcdf.cpp fake_mpi.cpp fake_spec_file.cpp
   run_part.F90 run_part_opt.F90 util.F90 aero_data.F90 aero_state.F90 env_state.F90 gas_data.F90 
-  gas_state.F90 scenario.F90 condense.F90
+  gas_state.F90 scenario.F90 condense.F90 bin_grid.F90
 )
 add_prefix(src/ PyPartMC_sources)
 
diff --git a/PyPartMC/__init__.py b/PyPartMC/__init__.py
@@ -10,6 +10,9 @@ def __build_extension_env():
     cookies = []
     # https://docs.python.org/3/whatsnew/3.8.html#bpo-36085-whatsnew
     if hasattr(os, "add_dll_directory"):
+        basepath = os.path.dirname(os.path.abspath(__file__))
+        dllspath = os.path.join(basepath, '..')
+        os.environ['PATH'] = dllspath + os.pathsep + os.environ['PATH']
         for path in os.environ.get("PATH", "").split(os.pathsep):
             if path and Path(path).is_absolute() and Path(path).is_dir():
                 cookies.append(os.add_dll_directory(path))
@@ -39,5 +42,5 @@ def __build_extension_env():
 
 with __build_extension_env():
     from _PyPartMC import *
-    from _PyPartMC import __all__
+    from _PyPartMC import __all__, __version__
     import _PyPartMC
diff --git a/src/bin_grid.F90 b/src/bin_grid.F90
@@ -0,0 +1,73 @@
+!###################################################################################################
+! This file is a part of PyPartMC licensed under the GNU General Public License v3 (LICENSE file)  #
+! Copyright (C) 2022 University of Illinois Urbana-Champaign                                       #
+! Authors: https://github.com/open-atmos/PyPartMC/graphs/contributors                              #
+!###################################################################################################
+
+module PyPartMC_bin_grid
+  use iso_c_binding
+  use pmc_bin_grid
+  implicit none
+
+  contains
+
+  subroutine f_bin_grid_ctor(ptr_c) bind(C)
+    type(bin_grid_t), pointer :: ptr_f => null()
+    type(c_ptr), intent(out) :: ptr_c
+
+    allocate(ptr_f)
+    ptr_c = c_loc(ptr_f)
+  end subroutine
+
+  subroutine f_bin_grid_dtor(ptr_c) bind(C)
+    type(bin_grid_t), pointer :: ptr_f => null()
+    type(c_ptr), intent(in) :: ptr_c
+
+    call c_f_pointer(ptr_c, ptr_f)
+    deallocate(ptr_f)
+  end subroutine
+
+  subroutine f_bin_grid_init(ptr_c, n_bin, bin_grid_type, min, max) bind(C)
+    type(c_ptr), intent(in) :: ptr_c
+    type(bin_grid_t), pointer :: bin_grid => null()
+    integer(c_int), intent(in) :: n_bin
+    integer(c_int), intent(in) :: bin_grid_type
+    real(c_double), intent(in) :: min
+    real(c_double), intent(in) :: max
+  
+    call c_f_pointer(ptr_c, bin_grid) 
+    call bin_grid_make(bin_grid, bin_grid_type, n_bin, min, max)
+ 
+  end subroutine
+
+  subroutine f_bin_grid_size(ptr_c, val) bind(C)
+    type(c_ptr), intent(in) :: ptr_c
+    type(bin_grid_t), pointer :: bin_grid => null()
+    integer(c_int), intent(out) :: val
+
+    call c_f_pointer(ptr_c, bin_grid)
+    val = bin_grid_size(bin_grid)
+
+  end subroutine
+
+  subroutine f_bin_grid_edges(ptr_c, arr_data, arr_size) bind(C)
+    type(c_ptr), intent(in) :: ptr_c
+    type(bin_grid_t), pointer :: bin_grid => null()
+    integer(c_int), intent(in) :: arr_size
+    real(c_double), dimension(arr_size), intent(out) :: arr_data
+
+    call c_f_pointer(ptr_c, bin_grid)
+    arr_data = bin_grid%edges
+  end subroutine
+
+  subroutine f_bin_grid_centers(ptr_c, arr_data, arr_size) bind(C)
+    type(c_ptr), intent(in) :: ptr_c
+    type(bin_grid_t), pointer :: bin_grid => null()
+    integer(c_int), intent(in) :: arr_size
+    real(c_double), dimension(arr_size), intent(out) :: arr_data
+
+    call c_f_pointer(ptr_c, bin_grid)
+    arr_data = bin_grid%centers
+  end subroutine
+
+end module
diff --git a/src/bin_grid.hpp b/src/bin_grid.hpp
@@ -0,0 +1,63 @@
+/*##################################################################################################
+# This file is a part of PyPartMC licensed under the GNU General Public License v3 (LICENSE file)  #
+# Copyright (C) 2022 University of Illinois Urbana-Champaign                                       #
+# Authors: https://github.com/open-atmos/PyPartMC/graphs/contributors                              #
+##################################################################################################*/
+
+#pragma once
+
+#include "pmc_resource.hpp"
+#include "pybind11/stl.h"
+
+extern "C" void f_bin_grid_ctor(void *ptr) noexcept;
+extern "C" void f_bin_grid_dtor(void *ptr) noexcept;
+extern "C" void f_bin_grid_init(
+    const void *ptr,
+    const int *n_bin,
+    const int *type,
+    const double *min,
+    const double *max
+) noexcept;
+extern "C" void f_bin_grid_size(const void *ptr, int *val) noexcept;
+extern "C" void f_bin_grid_edges(const void *ptr, void *arr_data, const int *arr_size) noexcept;
+extern "C" void f_bin_grid_centers(const void *ptr, void *arr_data, const int *arr_size) noexcept;
+
+struct BinGrid {
+    PMCResource ptr;
+
+    BinGrid(const int &n_bin, const std::string &grid_type, const double &min, const double &max) :
+        ptr(f_bin_grid_ctor, f_bin_grid_dtor)
+    {
+        int type;
+        type = 0;
+        if (grid_type == "log") type = 1;
+        if (grid_type == "linear") type = 2;
+        if (type == 0) throw std::invalid_argument( "Invalid grid spacing." );
+        f_bin_grid_init(ptr.f_arg(), &n_bin, &type, &min, &max);
+    }
+
+    static std::size_t __len__(const BinGrid &self) {
+        int len;
+        f_bin_grid_size(&self.ptr, &len);
+        return len;
+    }
+
+    static std::valarray<double> edges(const BinGrid &self)
+    {
+        int len;
+        f_bin_grid_size(&self.ptr, &len);
+        len++;
+        std::valarray<double> data(len);
+        f_bin_grid_edges(&self.ptr, begin(data), &len);
+        return data;
+    }
+
+    static std::valarray<double> centers(const BinGrid &self) 
+    {
+        int len;
+        f_bin_grid_size(&self.ptr, &len);
+        std::valarray<double> data(len);
+        f_bin_grid_centers(&self.ptr, begin(data), &len);
+        return data;
+    }
+};
diff --git a/src/pypartmc.cpp b/src/pypartmc.cpp
@@ -7,7 +7,6 @@
 #include "pybind11/pybind11.h"
 #include "nlohmann/json.hpp"
 #include "pybind11_json/pybind11_json.hpp"
-#include "pybind11/numpy.h"
 
 #include "util.hpp"
 #include "run_part.hpp"
@@ -18,6 +17,7 @@
 #include "gas_data.hpp"
 #include "gas_state.hpp"
 #include "condense.hpp"
+#include "bin_grid.hpp"
 
 #define STRINGIFY(x) #x
 #define MACRO_STRINGIFY(x) STRINGIFY(x)
@@ -173,6 +173,12 @@ PYBIND11_MODULE(_PyPartMC, m) {
         .def(py::init<const nlohmann::json&>())
     ;
 
+    py::class_<BinGrid>(m,"BinGrid")
+        .def(py::init<const double, const py::str, const double, const double>())
+        .def("__len__", BinGrid::__len__)
+        .def_property_readonly("edges", BinGrid::edges)
+        .def_property_readonly("centers", BinGrid::centers)
+    ;
     //  TODO: auto util = m.def_submodule("util", "TODO");
     m.def(
         "pow2_above", &pow2_above, py::return_value_policy::copy,
@@ -185,6 +191,7 @@ PYBIND11_MODULE(_PyPartMC, m) {
         "__version__",
         "AeroData",
         "AeroState",
+        "BinGrid",
         "EnvState",
         "GasData",
         "GasState",
diff --git a/tests/test_bin_grid.py b/tests/test_bin_grid.py
@@ -0,0 +1,99 @@
+####################################################################################################
+# This file is a part of PyPartMC licensed under the GNU General Public License v3 (LICENSE file)  #
+# Copyright (C) 2022 University of Illinois Urbana-Champaign                                       #
+# Authors: https://github.com/open-atmos/PyPartMC/graphs/contributors                              #
+####################################################################################################
+
+import numpy as np
+import PyPartMC as ppmc
+
+
+class TestBinGrid:
+    @staticmethod
+    def test_ctor():
+        # arrange
+        pass
+
+        # act
+        sut = ppmc.BinGrid(123, "log", 1, 100)
+
+        # assert
+        assert sut is not None
+
+    @staticmethod
+    def test_len():
+        # arrange
+        grid_size = 666
+        sut = ppmc.BinGrid(grid_size, "log", 1, 100)
+
+        # act
+        size = len(sut)
+
+        # assert
+        assert size == grid_size
+
+    @staticmethod
+    def test_bin_edges_len():
+        # arrange
+        grid_size = 100
+        sut = ppmc.BinGrid(grid_size, "log", 1, 100)
+
+        # act
+        edges = sut.edges
+
+        # assert
+        assert grid_size + 1 == len(edges)
+
+    @staticmethod
+    def test_bin_edges_values():
+        # arrange
+        n_bins = 10
+        left_edge = 1
+        right_edge = 100
+        sut = ppmc.BinGrid(n_bins, "log", left_edge, right_edge)
+
+        # act
+        edges = sut.edges
+
+        # assert
+        np.testing.assert_array_almost_equal(
+            np.logspace(np.log10(left_edge), np.log10(right_edge), n_bins+1),
+            edges
+        )
+
+    @staticmethod
+    def test_bin_centers_len():
+        # arrange
+        grid_size = 44
+        sut = ppmc.BinGrid(grid_size, "log", 1, 100)
+
+        # act
+        centers = sut.centers
+
+        # assert
+        assert grid_size == len(centers)
+
+    @staticmethod
+    def test_bin_centers_values():
+        # arrange
+        n_bins = 10
+        left_edge = 1
+        right_edge = 100
+        sut = ppmc.BinGrid(n_bins, "log", left_edge, right_edge)
+
+        # act
+        centers = sut.centers
+
+        # assert
+        np.testing.assert_array_almost_equal(
+            np.logspace(np.log10(left_edge), np.log10(right_edge), 2*n_bins+1)[1:-1:2],
+            centers
+        )
+
+    @staticmethod
+    def test_invalid_grid():
+        grid_size = 100
+        try:
+            _ = ppmc.BinGrid(grid_size, "X", 1, 100)
+        except ValueError as error:
+            assert str(error) == "Invalid grid spacing."

Original file line number	Diff line number	Diff line change
`@@ -35,7 +35,7 @@ endmacro(add_prefix)`
`35`	`35`	`set(PyPartMC_sources`
`36`	`36`	`pypartmc.cpp gimmicks.cpp fake_netcdf.cpp fake_mpi.cpp fake_spec_file.cpp`
`37`	`37`	`run_part.F90 run_part_opt.F90 util.F90 aero_data.F90 aero_state.F90 env_state.F90 gas_data.F90`
`38`		`- gas_state.F90 scenario.F90 condense.F90`
	`38`	`+ gas_state.F90 scenario.F90 condense.F90 bin_grid.F90`
`39`	`39`	`)`
`40`	`40`	`add_prefix(src/ PyPartMC_sources)`
`41`	`41`