Merge branch 'develop' into reintroduce-initialize

.github/workflows/pythonpublish.yml

@@ -20,8 +20,8 @@ jobs:
         pip install setuptools wheel twine
     - name: Build and publish
       env:
-        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+        TWINE_USERNAME: __token__
+        TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
       run: |
         python setup.py sdist
         twine upload dist/*

docs/micro-simulation-convert-to-library.md

@@ -14,9 +14,14 @@ Restructure your micro simulation code into a Python class with the structure gi
 
 ```python
 class MicroSimulation: # Name is fixed
-    def __init__(self):
+    def __init__(self, sim_id):
         """
         Constructor of class MicroSimulation.
+
+        Parameters
+        ----------
+        sim_id : int
+            ID of the simulation instance, that the Micro Manager has set for it.
         """
 
     def solve(self, macro_data: dict, dt: float) -> dict:

docs/running.md

@@ -18,8 +18,6 @@ from micro_manager import MicroManager
 
 manager = MicroManager("micro-manager-config.json")
 
-manager.initialize()
-
 manager.solve()
 ```
 

examples/cpp-dummy/micro_cpp_dummy.cpp

@@ -13,7 +13,7 @@
 #include "micro_cpp_dummy.hpp"
 
 // Constructor
-MicroSimulation::MicroSimulation() : _micro_scalar_data(0), _state(0) {}
+MicroSimulation::MicroSimulation(int sim_id) : _sim_id(sim_id), _micro_scalar_data(0), _state(0) {}
 
 // Solve
 py::dict MicroSimulation::solve(py::dict macro_data, double dt)
@@ -64,7 +64,7 @@ PYBIND11_MODULE(micro_dummy, m) {
     m.doc() = "pybind11 micro dummy plugin";
 
     py::class_<MicroSimulation>(m, "MicroSimulation")
-        .def(py::init())
+        .def(py::init<int>())
         .def("solve", &MicroSimulation::solve)
         .def("get_state", &MicroSimulation::get_state)
         .def("set_state", &MicroSimulation::set_state)
@@ -77,7 +77,7 @@ PYBIND11_MODULE(micro_dummy, m) {
                     throw std::runtime_error("Invalid state!");
 
                 /* Create a new C++ instance */
-                MicroSimulation ms;
+                MicroSimulation ms(0);
 
                 ms.set_state(t);
 

examples/cpp-dummy/micro_cpp_dummy.hpp

@@ -14,14 +14,15 @@ namespace py = pybind11;
 class MicroSimulation
 {
 public:
-    MicroSimulation();
+    MicroSimulation(int sim_id);
     // solve takes a python dict data, and the timestep dt as inputs, and returns a python dict
     py::dict solve(py::dict macro_write_data, double dt);
 
     void set_state(py::list state);
     py::list get_state() const;
 
 private:
+    int _sim_id;
     double _micro_scalar_data;
     std::vector<double> _micro_vector_data;
     double _state;

examples/python-dummy/micro_dummy.py

@@ -6,10 +6,11 @@
 
 class MicroSimulation:
 
-    def __init__(self):
+    def __init__(self, sim_id):
         """
         Constructor of MicroSimulation class.
         """
+        self._sim_id = sim_id
         self._dims = 3
         self._micro_scalar_data = None
         self._micro_vector_data = None

micro_manager/micro_simulation.py

@@ -21,13 +21,10 @@ def create_simulation_class(micro_simulation_class):
     """
     class Simulation(micro_simulation_class):
         def __init__(self, global_id):
-            micro_simulation_class.__init__(self)
+            micro_simulation_class.__init__(self, global_id)
             self._global_id = global_id
 
         def get_global_id(self) -> int:
             return self._global_id
 
-        def set_global_id(self, global_id) -> None:
-            self._global_id = global_id
-
     return Simulation

tests/integration/test_unit_cube/micro_dummy.py

@@ -6,10 +6,11 @@
 
 class MicroSimulation:
 
-    def __init__(self):
+    def __init__(self, sim_id):
         """
         Constructor of MicroSimulation class.
         """
+        self._sim_id = sim_id
         self._micro_scalar_data = None
         self._micro_vector_data = None
         self._checkpoint = None

tests/unit/test_micro_manager.py

@@ -5,7 +5,7 @@
 
 
 class MicroSimulation:
-    def __init__(self):
+    def __init__(self, sim_id):
         self.very_important_value = 0
 
     def initialize(self):
@@ -83,7 +83,7 @@ def test_solve_mico_sims(self):
         """
         manager = micro_manager.MicroManager('micro-manager-config.json')
         manager._local_number_of_sims = 4
-        manager._micro_sims = [MicroSimulation() for _ in range(4)]
+        manager._micro_sims = [MicroSimulation(i) for i in range(4)]
         manager._micro_sims_active_steps = np.zeros(4, dtype=np.int32)
 
         micro_sims_output = manager._solve_micro_simulations(self.fake_read_data)