* Add pyproject.toml

* Further changes to the pyproject.toml

* Add adaptivity module explicitly to the pyproject.toml

* Adding package information to pyproject.toml

* Reintroduce micro_manager.adaptivity to packaged in pyproject.toml

* Add scikit-learn as a dependency in pyproject.toml

* Change package name to micro_manager_precice

* Go back to using micro_manager in the unit tests

* Upgrade pip before installing the Micro Manager in the unit tests CI

* Make executable name the same as the package name

…ecice#104)

* Use initial macro data to initialize micro simulations

* Explicitly define the local variable is_initial_data_required

* Correctly check number of input arguments of the initialiez() function of the micro simulation library

* Add comment on the boolean which states the requirement of initial data in the micro simulation class

* Make initialize() a public method

* Add pull request template

* Modify tests to use public function initialize(), and add github PR template

* Use version compatible format to state dependency version in pyroject.toml

* Use original way of defining dependency version

* Remove run_micro_manager.py from examples and tests

* Upgrade pip3 in the adaptivity tests workflow

* Remove LD_LIBRARY_PATH setting from adaptivity test workflow to check if it works

* Change order of execution in local adaptivity test workflow

* Use micro-manager-precice in running scripts of tests

* Revert to old way of updating pip

* Make the steps about upgrading pip and installing dependencies for the Micro Manager consistent in all workflows

* Try to run dummy without updating pip

* Explicitly install setuptools and wheel before installing the Micro Manager

* Add local bin folder to path to be able to execute the micro-manager-precice executable

* Don't set the PATH and install the Micro Manager without the --user flag

* Restructure Micro Manager config files in the examples/ directly so that the executable can be used to run the solver dummy

* Add CHANGELOG entries

* Remove ./ from precice-config file path in one of the Micro Manager configs

…#106)

* Add documentation for handling of crashing micro simulations

* Rewording

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Co-authored-by: Ishaan Desai <[email protected]>

…e the version

…ut action of the publishing workflow

…cking

…that the adaptivity computation requires (precice#109)

* Check if initial data returned from the micro simulation is the data that the adaptivity computation requires

* Add CHANGELOG entry

* Rephrase exception

* Add documentation about initializing micro simulations

…ialize()` function (precice#110)

* Handle exceptions from the initialize() function call from wrapped functions

* Rework comments and add CHANGELOG entry

* Restructure execution with main

* Add base class and abstract base class to unify common properties

* Add expected return-type to main

* Adapt class descriptions

* Change class descriptions and imports

* Update Changelog

* Update CHANGELOG.md

Co-authored-by: Ishaan Desai <[email protected]>

---------

Co-authored-by: Ishaan Desai <[email protected]>

* Add option for the user to provide initial time window size of the micro simulation

* Put config parameter micro_time_window_size in coupling_params group

* Paasing dt correctly

* Fix unit tests

* Fix crash handling tests

* Add CHANGELOG entry

* Use micro_dt instead of micro_time_window_size

* Use dt=0 when reading initial data

…e configuration (precice#114)

* Move micro_dt from coupling_params to simulation_params in the JSON config

* Update CHANGELOG

* Make sklearn an optional dependency

* Fix optional crash handling

* Fix trailing white space in  config

* Make sklearn an optional dependency

* Fix optional crash handling

* Fix trailing white space in  config

* Apply suggestions from code review

Co-authored-by: Ishaan Desai <[email protected]>

* Add comment regarding parameters potentially configurable by the user

* Resolve conflict in CHANGELOG

---------

Co-authored-by: Ishaan Desai <[email protected]>

* Initial commit for snapshot commputation

* Snapshot: change import of module

* Adapt SnapshotComputation further

* Adapt Snapshot test

* Snapshot: Formatting

* Prepare Snapshot class further

* First working version of snapshot computation

* Add snapshot test, improve snapshot and restructure

* Add snapshot test, improve snapshot and restructure part 2

* Improve logging, comments and minor structural improvements

* Snapshot: extend setup and github actions

* Move Snapshot into Micro Manager and update execution

* Add post-processing script option and restructure snapshot example

* Add post-processing to snapshot config file

* Make snapshot executable and rename snapshot files

* Restructure snapshot computation

* Restructure config

* Update snapshot computation still without chunking

* Remove unintentional print statement

* Update comments in tests

* Read only the necessary input on each process

* Clarify text and names

* Add HDF5 dependency

* Make h5py optional dependency

* Fix h5py optional

* Initial commit for snapshot commputation

* Snapshot: change import of module

* Adapt SnapshotComputation further

* Snapshot: Formatting

* Prepare Snapshot class further

* First working version of snapshot computation

* Add snapshot test, improve snapshot and restructure

* Add snapshot test, improve snapshot and restructure part 2

* Improve logging, comments and minor structural improvements

* Move Snapshot into Micro Manager and update execution

* Add post-processing script option and restructure snapshot example

* Make snapshot executable and rename snapshot files

* Restructure snapshot computation

* Restructure config

* Update snapshot computation still without chunking

* Remove unintentional print statement

* Update comments in tests

* Make h5py optional dependency

* Fix h5py optional

* Change snapshot case in main

* Move dt to simulation parameters in Snapshot and snapshot specific dt

* Fix init

* Fix issue of using member variable in Config class

* Fix tests

* Apply suggestions from code review

Co-authored-by: Ishaan Desai <[email protected]>

* Apply review suggestions

* Remove output dir from gitignore

* Extend CHANGELOG.md

* Update CHANGELOG.md

---------

Co-authored-by: Ishaan Desai <[email protected]>

* Explicitly check if the time window has completed

* Add CHANGELOG entry

…#116)

* Add snapshot docs and update micro manager docs

* Add snapshot configuration docs

* Adapt documentation

* Update postprocessing description

* Remove next step

* Apply suggestions from code review

Co-authored-by: Ishaan Desai <[email protected]>

* Move snapshot mention to -what can it do?-

---------

Co-authored-by: Ishaan Desai <[email protected]>

…recice#123)

* Allow to compute snapshots on single object

* Update snapshot documentation and CHANGELOG

* Apply suggestions from code review

Co-authored-by: Ishaan Desai <[email protected]>

* Add note when to use a single object

---------

Co-authored-by: Ishaan Desai <[email protected]>

…s in adaptivity (precice#125)

* When taking relative norm differences in similarity calculation, use absolute values to get the normalizing factor

* Fix comments with respect to earlier changes

* Add CHANGELOG entry