Merge branch 'develop' into joss-submission

CONTRIBUTING.md

@@ -0,0 +1,11 @@
+# Contributing to the Micro Manager
+
+Contributions to the Micro Manager are most welcome! Please have a look at the page [contributing to preCICE](https://precice.org/community-contribute-to-precice.html) and also this page for more details.
+
+## Automatic checks
+
+We check every contribution with a few GitHub Actions workflows that report at the bottom of each pull request. For example, we have an Action to check if the contributed code is formatting correctly according to [autopep8](https://pypi.org/project/autopep8/).
+
+## Changelog
+
+We maintain a `CHANGELOG.md` where all major changes and contributions are entered.

examples/README.md

@@ -47,7 +47,3 @@ python cpp-dummy/run_micro_manager.py
 
 When changing the C++ solverdummy to your own solver, make sure to change the `PYBIND11_MODULE` in `micro_cpp_dummy.cpp` to the name that you want to compile to.
 For example, if you want to import the module as `my_solver`, change the line to `PYBIND11_MODULE(my_solver, m) {`. Then, change the `micro_file_name` in `micro-manager-config.json` to `my_solver`.
-
-### Adaptivity
-
-For the case of adaptivity, the deepcopy function also has to be implemented for the C++ class. An example is provided in the `cpp-dummy` directory.

examples/cpp-dummy/micro_cpp_dummy.hpp

@@ -17,7 +17,6 @@ class MicroSimulation
     MicroSimulation();
     // 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);
-    MicroSimulation __deepcopy__(py::dict memo);
 
     void set_state(py::list state);
     py::list get_state() const;