Update to PoPS Core 1.0.0

.clang-format

@@ -0,0 +1,107 @@
+---
+# BasedOnStyle: LLVM  # but heavily modified
+# Modified to resemble Black format for Python
+# The if statements are sub-optimal, it needs dangling parenthesis (D33029).
+# https://reviews.llvm.org/D33029
+Language: Cpp
+AccessModifierOffset: -4
+AlignAfterOpenBracket: AlwaysBreak
+AlignConsecutiveMacros: false
+AlignConsecutiveAssignments: false
+AlignConsecutiveDeclarations: false
+AlignEscapedNewlines: Right
+AlignOperands: true
+AlignTrailingComments: false
+AllowAllArgumentsOnNextLine: true
+AllowAllConstructorInitializersOnNextLine: true
+AllowAllParametersOfDeclarationOnNextLine: true
+AllowShortBlocksOnASingleLine: Never
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: Empty
+AllowShortLambdasOnASingleLine: All
+AllowShortIfStatementsOnASingleLine: Never
+AllowShortLoopsOnASingleLine: false
+AlwaysBreakAfterDefinitionReturnType: None
+AlwaysBreakAfterReturnType: None
+AlwaysBreakBeforeMultilineStrings: true
+AlwaysBreakTemplateDeclarations: Yes
+BinPackArguments: false
+BinPackParameters: false
+BraceWrapping:
+  AfterCaseLabel: false
+  AfterClass: true
+  AfterControlStatement: false
+  AfterEnum: true
+  AfterFunction: true
+  AfterNamespace: false
+  AfterObjCDeclaration: false
+  AfterStruct: true
+  AfterUnion: true
+  AfterExternBlock: false
+  BeforeCatch: true
+  BeforeElse: true
+  IndentBraces: false
+  SplitEmptyFunction: false
+  SplitEmptyRecord: true
+  SplitEmptyNamespace: true
+BreakBeforeBinaryOperators: NonAssignment
+BreakBeforeBraces: Custom
+BreakBeforeInheritanceComma: false
+BreakInheritanceList: BeforeColon
+BreakBeforeTernaryOperators: true
+BreakConstructorInitializersBeforeComma: false
+BreakConstructorInitializers: BeforeColon
+BreakStringLiterals: false
+ColumnLimit: 88
+CompactNamespaces: false
+ConstructorInitializerAllOnOneLineOrOnePerLine: true
+ConstructorInitializerIndentWidth: 4
+ContinuationIndentWidth: 4
+Cpp11BracedListStyle: true
+DeriveLineEnding: true
+DerivePointerAlignment: false
+ExperimentalAutoDetectBinPacking: false
+FixNamespaceComments: true
+IndentCaseLabels: false
+IndentGotoLabels: true
+IndentPPDirectives: None
+IndentWidth: 4
+IndentWrappedFunctionNames: false
+KeepEmptyLinesAtTheStartOfBlocks: true
+MaxEmptyLinesToKeep: 1
+NamespaceIndentation: None
+PenaltyBreakAssignment: 2
+PenaltyBreakBeforeFirstCallParameter: 19
+PenaltyBreakComment: 300
+PenaltyBreakFirstLessLess: 120
+PenaltyBreakString: 1000
+PenaltyBreakTemplateDeclaration: 10
+PenaltyExcessCharacter: 1000000
+PenaltyReturnTypeOnItsOwnLine: 60
+PointerAlignment: Left
+SortIncludes: false
+SortUsingDeclarations: false
+SpaceAfterCStyleCast: false
+SpaceAfterLogicalNot: false
+SpaceAfterTemplateKeyword: false
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeCpp11BracedList: false
+SpaceBeforeCtorInitializerColon: true
+SpaceBeforeInheritanceColon: true
+SpaceBeforeParens: ControlStatements
+SpaceBeforeRangeBasedForLoopColon: true
+SpaceInEmptyBlock: false
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 2
+SpacesInAngles: false
+SpacesInConditionalStatement: false
+SpacesInContainerLiterals: true
+SpacesInCStyleCastParentheses: false
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+SpaceBeforeSquareBrackets: false
+Standard: c++11
+TabWidth: 4
+UseCRLF: false
+UseTab: Never
+...

.github/workflows/clang-format.yml

@@ -0,0 +1,18 @@
+name: Lint clang-format
+
+on:
+- push
+- pull_request
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Get clang-format-lint-action as image
+      run: |
+        docker build -t doozyx/clang-format-lint-action "github.com/DoozyX/clang-format-lint-action"
+    - name: Run clang-format lint
+      run: |
+        docker run --rm --workdir /src -v $(pwd):/src doozyx/clang-format-lint-action --clang-format-executable /clang-format/clang-format10 -r --exclude .git include/*.hpp src/*.cpp

.gitmodules

@@ -1,6 +1,6 @@
 [submodule "pybind11"]
 	path = pybind11
 	url = https://github.com/pybind/pybind11.git
-[submodule "PoPS"]
-	path = PoPS
-	url = https://github.com/ncsu-landscape-dynamics/PoPS.git
+[submodule "pops-core"]
+	path = pops-core
+	url = https://github.com/ncsu-landscape-dynamics/pops-core.git

CMakeLists.txt

@@ -10,7 +10,7 @@ project(PyPoPS
 #include_directories("${PROJECT_SOURCE_DIR}/")
 
 add_subdirectory(pybind11)
-add_subdirectory(PoPS)
+add_subdirectory(pops-core)
 
 pybind11_add_module(_pypops src/pypops.cpp include/raster.hpp include/helpers.hpp)
 

include/helpers.hpp

@@ -7,22 +7,27 @@
 #include <string>
 #include <sstream>
 
-template <typename T>
-std::string to_string(const T& value) {
+template<typename T>
+std::string to_string(const T& value)
+{
     std::stringstream stream;
     stream << value;
     return stream.str();
 }
 
-std::string to_string(const pybind11::buffer_info& info) {
+std::string to_string(const pybind11::buffer_info& info)
+{
     std::stringstream stream;
     stream << "itemsize: " << info.itemsize << "\n"
            << "format: " << info.format << "\n"
-           << "ndim: " << info.ndim << "\n"
+           << "ndim: " << info.ndim
+           << "\n"
            // TODO: generalize
            << "shape[0], shape[1]: " << info.shape[0] << ", " << info.shape[1] << "\n"
-           << "strides[0], strides[1]: " << info.strides[0] << ", " << info.strides[1] << "\n"
-           << "strides / itemsize: " << info.strides[0] / info.itemsize << ", " << info.strides[1] / info.itemsize << "\n";
+           << "strides[0], strides[1]: " << info.strides[0] << ", " << info.strides[1]
+           << "\n"
+           << "strides / itemsize: " << info.strides[0] / info.itemsize << ", "
+           << info.strides[1] / info.itemsize << "\n";
     // TODO: tell if it is C or F order (silent otherwise)
     return stream.str();
 }
@@ -48,13 +53,20 @@ void compatible_scalar_type_or_throw(const pybind11::buffer_info& info)
 
     if (diff_format && !diff_size)
         throw std::runtime_error(
-                "Incompatible scalar format in array: expected " + expected_format + ", got " + provided_format + " (both have " + expected_size + " bytes, using C++ type with id: "+ expected_cpp_typeid + ")");
+            "Incompatible scalar format in array: expected " + expected_format
+            + ", got " + provided_format + " (both have " + expected_size
+            + " bytes, using C++ type with id: " + expected_cpp_typeid + ")");
     else if (!diff_format && diff_size)
         throw std::runtime_error(
-                "Incompatible scalar size in array: expected " + expected_size + ", got " + provided_size + " (both have " + expected_format + " format, using C++ type with id: "+ expected_cpp_typeid + ")");
+            "Incompatible scalar size in array: expected " + expected_size + ", got "
+            + provided_size + " (both have " + expected_format
+            + " format, using C++ type with id: " + expected_cpp_typeid + ")");
     else
         throw std::runtime_error(
-                "Incompatible scalar in array: expected " + expected_format + " format with " + expected_size + " bytes, got " + provided_format + " format with " + provided_size + " bytes (using C++ type with id: "+ expected_cpp_typeid + ")");
+            "Incompatible scalar in array: expected " + expected_format
+            + " format with " + expected_size + " bytes, got " + provided_format
+            + " format with " + provided_size
+            + " bytes (using C++ type with id: " + expected_cpp_typeid + ")");
 }
 
 template<typename Number>
@@ -64,8 +76,10 @@ void raster_compatible_or_throw(const pybind11::buffer_info& info)
     if (info.ndim != 2)
         throw std::runtime_error("Incompatible buffer dimension: expected a 2D array!");
     if (info.strides[0] != info.itemsize * info.shape[1]
-            && info.strides[1] != info.itemsize)
-        throw std::runtime_error("Incompatible order: expected row-major (C-style) order. Got " + to_string(info)); // TODO: tell if it is the F order
+        && info.strides[1] != info.itemsize)
+        throw std::runtime_error(
+            "Incompatible order: expected row-major (C-style) order. Got "
+            + to_string(info));  // TODO: tell if it is the F order
 }
 
-#endif // HELPERS_HPP
+#endif  // HELPERS_HPP

include/raster.hpp

@@ -67,7 +67,8 @@ RasterType py_buffer_info_to_raster(pybind11::buffer b)
 // TODO: The return from function does not work, so unused for now.
 // Perhaps a 3D array will be needed for interface anyway.
 template<typename RasterType>
-std::vector<RasterType> py_buffers_info_to_rasters(std::vector<pybind11::buffer>& buffers)
+std::vector<RasterType>
+py_buffers_info_to_rasters(std::vector<pybind11::buffer>& buffers)
 {
     std::vector<RasterType> rasters;
     rasters.reserve(buffers.size());
@@ -93,33 +94,29 @@ pybind11::buffer_info raster_to_py_buffer_info(RasterType& raster)
         // Buffer dimensions
         {raster.rows(), raster.cols()},
         // Strides (in bytes) for each index, row-major order
-        {sizeof(NumberType) * raster.cols(),
-         sizeof(NumberType) * 1}
-    );
+        {sizeof(NumberType) * raster.cols(), sizeof(NumberType) * 1});
 }
 
 // We use template parameter instead of py::module to avoid this
 // implementation detail by duck typing.
 template<typename RasterType, typename PythonModule>
-void raster_class(PythonModule& m, const std::string& name) {
+void raster_class(PythonModule& m, const std::string& name)
+{
     pybind11::class_<RasterType>(m, name.c_str(), pybind11::buffer_protocol())
-            .def(pybind11::init([](pybind11::buffer b) {
-                     return py_buffer_info_to_raster<RasterType>(b);
-                     // return by raw pointer
-                     // or: return std::make_unique<Foo>(...); // return by holder
-                     // or: return Foo(...); // return by value (move constructor)
-                 }))
+        .def(pybind11::init([](pybind11::buffer b) {
+            return py_buffer_info_to_raster<RasterType>(b);
+            // return by raw pointer
+            // or: return std::make_unique<Foo>(...); // return by holder
+            // or: return Foo(...); // return by value (move constructor)
+        }))
 
-            .def_buffer(
-                raster_to_py_buffer_info<RasterType>
-                );
+        .def_buffer(raster_to_py_buffer_info<RasterType>);
 }
 
 template<typename NumberType, typename PythonModule>
 void test_compatibility(PythonModule m, std::string name)
 {
-    m.def(name.c_str(),
-          [](pybind11::buffer b) {
+    m.def(name.c_str(), [](pybind11::buffer b) {
         pybind11::buffer_info info = b.request();
         raster_compatible_or_throw<NumberType>(info);
     });
@@ -131,17 +128,16 @@ pybind11::object get_float_raster_scalar_type()
     // https://docs.scipy.org/doc/numpy/user/basics.types.html
     pybind11::object dtype = np.attr("dtype");
     std::vector<pybind11::object> candidates = {
-//        numpy.attr("double").attr("itemsize"),
-//        numpy.attr("single"),
-//        numpy.attr("longdouble"),
-//        numpy.attr("float16"),
-//        numpy.attr("half")
+        //        numpy.attr("double").attr("itemsize"),
+        //        numpy.attr("single"),
+        //        numpy.attr("longdouble"),
+        //        numpy.attr("float16"),
+        //        numpy.attr("half")
         dtype("float64"),
         dtype("float32"),
         dtype("double"),
         dtype("single"),
-        dtype("longdouble")
-    };
+        dtype("longdouble")};
     for (const auto candidate : candidates) {
         if (sizeof(Float) == pybind11::int_(candidate.attr("itemsize")))
             return candidate;
@@ -166,4 +162,4 @@ pybind11::object get_integer_raster_scalar_type()
     throw std::logic_error("Cannot find a compatible scalar type");
 }
 
-#endif // RASTER_HPP
+#endif  // RASTER_HPP

pypops/simulation.py

@@ -12,22 +12,36 @@
 """PyPoPS - Main simulation interface
 """
 
+import json
+
 import _pypops
+from _pypops import Config
 
 
 int_type = _pypops.get_integer_raster_scalar_type()
 float_type = _pypops.get_float_raster_scalar_type()
 
 
+def json_to_config(config):
+    """Run one PoPS simulation"""
+    with open(config) as config_file:
+        config_values = json.load(config_file)
+    result = Config()
+    for key, value in config_values.items():
+        setattr(result, key, value)
+    return result
+
+
 def pops(
     random_seed,
-    steps,
     use_lethal_temperature=False,
     lethal_temperature=None,
     infected=None,
     susceptible=None,
+    exposed=None,
     total_plants=None,
     mortality_tracker=None,
+    died=None,
     # dispersers=dispersers,
     weather=False,
     temperature=None,
@@ -50,13 +64,14 @@ def pops(
     """Run one PoPS simulation"""
     result = _pypops.test_simulation(
         random_seed=random_seed,
-        steps=steps,
         use_lethal_temperature=use_lethal_temperature,
         lethal_temperature=lethal_temperature,
         infected=infected,
         susceptible=susceptible,
+        exposed=exposed,
         total_plants=total_plants,
         mortality_tracker=mortality_tracker,
+        died=died,
         weather=weather,
         temperature=temperature,
         weather_coefficient=weather_coefficient,