Deepcave

Quality of Life
- Improve documentation on installation of extra requirements.
- Add licence information to all source files.

Converters
- Add support for AMLTK.
- Add support for Optuna.
- Add support for adding a run in DataFrame format (137).
- BOHB: Consider missing state as valid state as state is not provided by default (65).

Version-Updates
- ConfigSpace from 0.6.1 to 1.2.0
- Numpy from 1.26.4 to 2.0.1
- pyPDPPartitioner from to 0.1.8 to 0.1.9

Ablation Paths Plugin
- Added ablation paths as a plugin.
- Added ablation as a evaluator to use for the plugin.
- Added tests as well as documentation.
- Modified the RandomForest surrogate model, so it can be passed the number of trees.

Move plugins
- Moved the Configuration cube and the parallel coordinates plugin from objective to hyperparameter.
- Changed layout accordingly as well as the documentation.

Bug-Fixes
- Upgrade pyPDPPartitioner to 0.1.9 as a requirement which fixes a bug related to copying config space objects (111).

Quality of Life
- Update the documentation to reflect the new changes.
- Disable warnings during RunHandler initialization to avoid showing warnings with respect to previously loaded runs.
- Remove option to use docker (not yet supported).
- Add SMAC3v2 multi-fidelity example runs.
- Add more useful SMAC3v2 multi-objective example run.
- Remove defective matplotlib button and associated functionalities.

Quality of Life
- Runs now get displayed with their parent directory for better distinguishability.
- Increase plot font sizes.
- Add a simple loading bar functionality for longer runs.

General
- Seed is now required in the Recorder.

Bug-Fixes
- Use normalized LPI importance via variance instead of importance over mean (152)
- Return nan as importance values if variance is 0. for a hyperparameter / budget (152)

Plugins
- Show a run's hoover-text for the actual budget of a trial in Cost over Time with Combined budget (154).
- Use highest budget as default budget for Cost over Time instead of Combined.
- Show best value / config for each objective instead of merged objective in Overview (159).
- Use chosen objective instead of merged objective to get the incumbent for the calculation of LPI importance (159).
- Add total runtime in overview (155).

Plugins
- Add symbolic explanations plugin (46).
- It is now possible to view multiple unequal runs at once in Cost over Time and Pareto (93).
- Runs with unequal objectives cannot be displayed together.
- Added an enum for displaying according warning messages.

Enhancements
- Fix lower bounds of dependency versions.
- Allow to load multi-objective SMAC3v2 and add example (69).
- Allow to load runs with multiple seeds and add examples (70).
- Correct incumbent calculation when single objective should be maximized.
- Correct range of configuration cube slider for number of configs.
- Do not disable existing loggers.
- Update author email.
- Add exit button which first deletes running jobs and then terminates DeepCave.
- Nicer handling of Keyboard Interrupt.
- Disable debug mode.
- Save plotly plots in higher resolution upon download.
- Get hovertext per budget in Footprint, Config Cube, Cost over Time, and Pareto Front.

Bug-Fixes
- Fix missing objective specification in LPI evaluator (71).
- Don't convert BOHB runs with status 'running' (consistent with SMAC).
- Fix api examples (68).
- Reset inputs to fix error when subsequently selecting runs with different configspaces, objectives or budgets (106).
- Fix errors due to changing inputs before runselection (64).
- For fANOVA, remove constant hyperparameters from configspace (9).
- When getting budget, objectives etc from multiple runs in Cost over Time and Pareto Front:
- Instead of taking the first run as comparative value,
- take the one with the lowest budget, else the index for the budgets could be out of bounds.
- For PCP, show hyperparameters with highest importance closest to the cost, i.e. right (124).
- Add init files to all test directories.
- Correct LPI importance tests.
- Free port when exiting via the exit button (52).

Documentation
- Add How to Contribute section.
- Expand documentation for partial dependence plugin.

Version-Updates
- Black version from 23.1.0 to 23.3.0
- Mypy from 0.930 to 1.5.1

Mypy
- Updated args so there are no missing imports
- Updated additional dependencies, so mypy can check all types
- Note: If the installs in requirements change, it has to be adapted in additional dependencies
- Added many type annotations
- In some cases internal refactoring for variables, due to typing

Pydocstyle and Linter
- Major overhaul of docstrings in various files
- Removed unused imports and variables

Groups
- Groups now get a default name, if no name was entered by the user.
- Groups get sorted alphabetically to appear more ordered.

Additional Changes
- Added a "make install examples" in Makefile

Bug-Fixes
- Fix seaborn style name (82).
- Remove potential sources of nondeterminism in evaluators by not setting seeds randomly (75).
- Exchange SMAC log examples to fix issue with PDP (54).
- Fix error when requesting more than 10 colors in a plot (36 colors available now).

Bug-Fixes
- Fix configspace version.