Implemented property based testing via PyCall.jl and hypothesis.py

.gitignore

@@ -72,6 +72,167 @@ Manifest.toml
 *.out
 *.app
 
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
 # Project specific gitignores
 # Original notes from when developing
 notes/*

Project.toml

@@ -1,15 +1,17 @@
 name = "nanoconc"
 uuid = "9a947172-b1ea-4b16-84a6-f3d50752424d"
 authors = ["Cian Hughes <chughes000@gmail.com>"]
-version = "0.1.0"
+version = "0.1.1"
 
 [deps]
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Debugger = "31a5f54b-26ea-5ae9-a837-f05ce5417438"
+Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
 Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
 Memoize = "c03570c3-d221-55d1-a50c-7939bbd78826"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
+PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
 QuadGK = "1fd47b50-473d-5c70-9696-f719f8f3bcdc"
 XLSX = "fdbf4ff8-1666-58a4-91e7-1b58723a45e0"

requirements.txt

@@ -0,0 +1,4 @@
+attrs==23.2.0
+hypothesis==6.98.4
+numpy==1.26.4
+sortedcontainers==2.4.0

setup_venv.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+python -m venv .venv
+source .venv/bin/activate
+pip install -r requirements.txt

src/nanoconc.jl

@@ -49,6 +49,7 @@ columns entitled "w","n" and "k" for wavelength in nm, n and k respectively)
 function addmaterial(z::Float64, am::Float64, rho::Float64, res::Float64,
     filepath::String, material::String, description::String;
     disp::Bool=true)
+    flag = false
     try
         flag = h5open(matfile, "r") do file
             has(file, material)
@@ -96,6 +97,7 @@ An alternative version of the addmaterial function for materials with known mie
 function addmaterial(omp::Float64, om0::Float64, fv::Float64,
     filepath::String, material::String, description::String;
     disp::Bool=true)
+    flag = false
     try
         flag = h5open(matfile, "r") do file
             has(file, material)

test/Project.toml

@@ -1,5 +1,4 @@
 [deps]
 AirspeedVelocity = "1c8270ee-6884-45cc-9545-60fa71ec23e4"
 BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
-PropCheck = "ca382230-33be-11e9-0059-d981d03070e4"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

test/benchmarks.jl

@@ -67,10 +67,10 @@ if abspath(PROGRAM_FILE) == @__FILE__
     current_package_version = Pkg.TOML.parsefile("$ROOT_DIR/Project.toml")["version"]
 
     function display_to_file(io, x)
-        show(IOContext(io, :limit => false), "text/plain", x)
+        show(IOContext(io, :limit => false, :color => true), "text/plain", x)
     end
 
-    open("$ROOT_DIR/benchmarks/$current_package_version.txt", "w") do io
+    open("$ROOT_DIR/benchmarks/$current_package_version.ansi", "w") do io
         println(io, "C Implementation")
         display_to_file(io, result[1])
         println(io, "\n\nFortran Implementation")

test/build_ffi.sh

@@ -53,6 +53,6 @@ done
 
 # And, finally, we can compile the C, and Fortran implementations
 cd $bhmie_dir
-gcc -shared -fPIC -o bhmie-c/bhmie.so bhmie-c/bhmie.c bhmie-c/complex.c bhmie-c/nrutil.c -lm -Wno-builtin-declaration-mismatch -Wno-implicit-function-declaration
+gcc -g -shared -fPIC -o bhmie-c/bhmie.so bhmie-c/bhmie.c bhmie-c/complex.c bhmie-c/nrutil.c -lm -Wno-builtin-declaration-mismatch -Wno-implicit-function-declaration
-gfortran -shared -fPIC -o bhmie-f/bhmie.so bhmie-f/bhmie.f
+gfortran -g -shared -fPIC -o bhmie-f/bhmie.so bhmie-f/bhmie.f
-gfortran -shared -fPIC -o bhmie-f/bhmie_f77.so bhmie-f/bhmie_f77.f
+gfortran -g -shared -fPIC -o bhmie-f/bhmie_f77.so bhmie-f/bhmie_f77.f

test/miemfp_tests.jl

@@ -1,9 +1,13 @@
 using Test
+using Random
 using PropCheck
+using Debugger
+using PyCall
+
 
 include("../anchors.jl")
 
-import .Anchors: TEST_DIR, SRC_DIR
+import .Anchors: TEST_DIR, SRC_DIR, ROOT_DIR
 
 if !@isdefined TestUtils
     include(joinpath(TEST_DIR, "testutils.jl"))
@@ -15,85 +19,129 @@ if !@isdefined FFIWraps
     include(joinpath(TEST_DIR, "ffi_wraps.jl"))
 end
 
-# function julia_vs_c(args::Tuple{Float64, Float64, Float64, UInt32, Vector{Float64}, Vector{Float64}, Vector{Float64}, Vector{Float64}})
+
-#     x, cxref_re, cxref_im, nang, cxs1_re, cxs1_im, cxs2_re, cxs2_im = args
+# Set up the Python environment
-function julia_vs_c(x, cxref_re, cxref_im, nang, cxs1_re, cxs1_im, cxs2_re, cxs2_im)
+run(`$ROOT_DIR/setup_venv.sh`)
-    cxref, cxs1, cxs2 = ComplexF64(cxref_re, cxref_im), ComplexF64.(cxs1_re, cxs1_im), ComplexF64.(cxs2_re, cxs2_im)
+ENV["PYTHON"] = joinpath(ROOT_DIR, ".venv/bin/python")
-    x_c, cxref_c, nang_c, cxs1_c, cxs2_c = Float32(x), ComplexF32(cxref), UInt32(nang), ComplexF32.(cxs1), ComplexF32.(cxs2)
+
-    return isapprox(
+@pyinclude(joinpath(TEST_DIR, "miemfp_tests.py"))
-        miemfp.bhmie(x, cxref, nang),
+
-        FFIWraps.bhmie_c(x_c, cxref_c, nang_c, cxs1_c, cxs2_c),
+
-        rtol=0.1,
+miemfp.bhmie(
-    )
+    x::Float64,
+    cxref::ComplexF64,
+    nang::Int64,
+    s1::Vector{ComplexF64},
+    s2::Vector{ComplexF64},
+) = miemfp.bhmie(x, cxref, UInt32(nang))
+
+function miemfp.bhmie(
+    x::Float64,
+    cxref::ComplexF64,
+    nang::Int64,
+    s1::Vector{ComplexF64},
+    s2::Vector{ComplexF64},
+    event::PyObject,
+)
+    event.clear()
+    result = miemfp.bhmie(x, cxref, nang, s1, s2)
+    event.set()
+    return result
 end
 
-# function julia_vs_fortran(args::Tuple{Float64, Float64, Float64, UInt32, Vector{Float64}, Vector{Float64}, Vector{Float64}, Vector{Float64}})
+FFIWraps.bhmie_fortran(
-#     x, cxref_re, cxref_im, nang, cxs1_re, cxs1_im, cxs2_re, cxs2_im = args
+    x::Float64,
-function julia_vs_fortran(x, cxref_re, cxref_im, nang, cxs1_re, cxs1_im, cxs2_re, cxs2_im)
+    refrel::ComplexF64,
-    cxref, cxs1, cxs2 = ComplexF64(cxref_re, cxref_im), ComplexF64.(cxs1_re, cxs1_im), ComplexF64.(cxs2_re, cxs2_im)
+    nang::Int64,
-    x_f, cxref_f, nang_f, cxs1_f, cxs2_f = Float32(x), ComplexF32(cxref), Int32(nang), ComplexF32.(cxs1), ComplexF32.(cxs2)
+    s1::Vector{ComplexF64},
-    b = miemfp.bhmie(x, cxref, nang)
+    s2::Vector{ComplexF64},
-    f = FFIWraps.bhmie_fortran(x_f, cxref_f, nang_f, cxs1_f, cxs2_f)
+) = FFIWraps.bhmie_fortran(
-    # open("bhmie_julia_vs_fortran.txt", "a") do io
+    Float32(x),
-    #     println(io, "julia: ", b)
+    ComplexF32(refrel),
-    #     println(io, "fortran: ", f)
+    Int32(nang),
-    # end
+    ComplexF32.(s1),
-    # return is_approx(b, f)
+    ComplexF32.(s2),
-    return isapprox(
-        miemfp.bhmie(x, cxref, nang),
-        FFIWraps.bhmie_fortran(x_f, cxref_f, nang_f, cxs1_f, cxs2_f),
-        rtol=0.1,
-    )
-end
-
-# function julia_vs_fortran77(args::Tuple{Float64, Float64, Float64, UInt32, Vector{Float64}, Vector{Float64}, Vector{Float64}, Vector{Float64}})
-#     x, cxref_re, cxref_im, nang, cxs1_re, cxs1_im, cxs2_re, cxs2_im = args
-function julia_vs_fortran77(x, cxref_re, cxref_im, nang, cxs1_re, cxs1_im, cxs2_re, cxs2_im)
-    cxref, cxs1, cxs2 = ComplexF64(cxref_re, cxref_im), ComplexF64.(cxs1_re, cxs1_im), ComplexF64.(cxs2_re, cxs2_im)
-    x_f, cxref_f, nang_f, cxs1_f, cxs2_f = Float32(x), ComplexF32(cxref), Int32(nang), ComplexF32.(cxs1), ComplexF32.(cxs2)
-    return isapprox(
-        miemfp.bhmie(x, cxref, nang),
-        FFIWraps.bhmie_fortran77(x_f, cxref_f, nang_f, cxs1_f, cxs2_f),
-        rtol=0.1,
-    )
-end
-
-f64_gen = PropCheck.itype(Float64)
-UInt32_gen = PropCheck.itype(UInt32)
-f64_vec_gen = PropCheck.vector(isample(1:100), f64_gen)
-bhmie_gen = PropCheck.interleave(
-    f64_gen,
-    f64_gen,
-    f64_gen,
-    UInt32_gen,
-    f64_vec_gen,
-    f64_vec_gen,
-    f64_vec_gen,
-    f64_vec_gen,
 )
 
-@testset "bhmie" begin
+function FFIWraps.bhmie_fortran(
+    x::Float64,
+    refrel::ComplexF64,
+    nang::Int64,
+    s1::Vector{ComplexF64},
+    s2::Vector{ComplexF64},
+    event::PyObject,
+)
+    event.clear()
+    result = FFIWraps.bhmie_fortran(x, refrel, nang, s1, s2)
+    event.set()
+    return result
+end
+
+FFIWraps.bhmie_fortran77(
+    x::Float64,
+    refrel::ComplexF64,
+    nang::Int64,
+    s1::Vector{ComplexF64},
+    s2::Vector{ComplexF64},
+) = FFIWraps.bhmie_fortran77(
+    Float32(x),
+    ComplexF32(refrel),
+    Int32(nang),
+    ComplexF32.(s1),
+    ComplexF32.(s2),
+)
+
+function FFIWraps.bhmie_fortran77(
+    x::Float64,
+    refrel::ComplexF64,
+    nang::Int64,
+    s1::Vector{ComplexF64},
+    s2::Vector{ComplexF64},
+    event::PyObject,
+)
+    event.clear()
+    result = FFIWraps.bhmie_fortran77(x, refrel, nang, s1, s2)
+    event.set()
+    return result
+end
+
+FFIWraps.bhmie_c(
+    x::Float64,
+    refrel::ComplexF64,
+    nang::Int64,
+    s1::Vector{ComplexF64},
+    s2::Vector{ComplexF64},
+) = FFIWraps.bhmie_c(
+    Float32(x),
+    ComplexF32(refrel),
+    UInt32(nang),
+    ComplexF32.(s1),
+    ComplexF32.(s2),
+)
+
+function FFIWraps.bhmie_c(
+    x::Float64,
+    refrel::ComplexF64,
+    nang::Int64,
+    s1::Vector{ComplexF64},
+    s2::Vector{ComplexF64},
+    event::PyObject,
+)
+    event.clear()
+    result = FFIWraps.bhmie_c(x, refrel, nang, s1, s2)
+    event.set()
+    return result
+end
+
+@testset "miemfp" begin
     @testset "miemfp.bhmie" begin
-        c_check = PropCheck.check(julia_vs_c, bhmie_gen)
+        event1, event2 = py"asyncio.Event"(), py"asyncio.Event"()
-        c_result = c_check == true
+        event1.set(), event2.set()
-        if !c_result
+        result, output = py"compare_bhmie_functions"(miemfp.bhmie, FFIWraps.bhmie_fortran, event1, event2)
-            println("Fail vs C, PropCheck:")
+        @test result
-            display(c_check)
+        result, output = py"compare_bhmie_functions"(miemfp.bhmie, FFIWraps.bhmie_fortran77, event1, event2)
-        end
+        @test result
-        @test c_result
+        result, output = py"compare_bhmie_functions"(miemfp.bhmie, FFIWraps.bhmie_c, event1, event2)
-        f_check = PropCheck.check(julia_vs_fortran, bhmie_gen)
+        @test result
-        f_result = f_check == true
-        if !f_result
-            println("Fail vs Fortran, PropCheck:")
-            display(f_check)
-        end
-        @test f_result
-        f77_check = PropCheck.check(julia_vs_fortran77, bhmie_gen)
-        f77_result = f77_check == true
-        if !f77_result
-            println("Fail vs Fortran77, PropCheck:")
-            display(f77_check)
-        end
-        @test f77_result
     end
 end

test/miemfp_tests.py

@@ -0,0 +1,49 @@
+from typing import List, Tuple
+import asyncio
+import numpy as np
+from hypothesis import errors, given, settings, strategies as st # type: ignore
+
+def compare_bhmie_functions(f1, f2, event1: asyncio.Event, event2: asyncio.Event) -> Tuple[bool, str]:
+    async def async_closure(
+        x: float,
+        cxref: Tuple[float, float],
+        cxs1: List[Tuple[float, float]],
+        cxs2: List[Tuple[float, float]],
+    ) -> bool:
+        cxref = complex(*cxref)
+        cxs1 = [complex(*c) for c in cxs1]
+        cxs2 = [complex(*c) for c in cxs2]
+        
+        # This is to ensure that only one instance of each function is running at a time
+        # to avoid memory issues in the FFI code
+        await event1.wait()
+        f1_result = f1(x, cxref, 2, cxs1, cxs2)[:2]
+        await event2.wait()
+        f2_result = f2(x, cxref, 2, cxs1, cxs2)[:2]
+        
+        return np.all(np.isclose(f1_result, f2_result))
+    
+    @settings(deadline=None)
+    @given(
+        # Must be bigger than an atom but still nanoscale
+        x=st.floats(min_value=0.1, max_value=100),
+        # Refractive indeces must be within a physically reasonable range
+        cxref=st.tuples(st.floats(min_value=0.1, max_value=4.0), st.floats(min_value=0.1, max_value=4.0)),
+        cxs1=st.lists(st.tuples(st.floats(min_value=0.1, allow_infinity=False), st.floats(min_value=0.1, allow_infinity=False)), min_size=10, max_size=100),
+        cxs2=st.lists(st.tuples(st.floats(min_value=0.1, allow_infinity=False), st.floats(min_value=0.1, allow_infinity=False)), min_size=10, max_size=100),
+    )
+    def sync_closure(
+        x: float,
+        cxref: Tuple[float, float],
+        cxs1: List[Tuple[float, float]],
+        cxs2: List[Tuple[float, float]],
+    ) -> bool:
+        assert asyncio.run(async_closure(x, cxref, cxs1, cxs2))
+    
+    try:
+        sync_closure()
+        return True, "Test passed"
+    except AssertionError as e:
+        return False, f"AssertionError: {str(e)}"
+    except errors.HypothesisException as e:
+        return False, f"HypothesisException: {str(e)}"

test/testutils.jl

@@ -22,4 +22,9 @@ function test_from_serialized(fn::Function, filename::String)
     @test deep_compare([fn(a...; kw...) for (a, kw) in argskwargs], out)
 end
 
-end # module TestUtils
+function asymmetric_floatvec_to_complexvec(vec_a::Vector{Float32}, vec_b::Vector{Float32})
+    shortest = min(length(vec_a), length(vec_b))
+    ComplexF32.(vec_a[1:shortest], vec_b[1:shortest])
+end
+
+end