Panqec

Improvement of the `Analysis` class, many refactoring, better documentation and tutorials. This includes:
* `Analysis` can aggregate many results, calculate the threshold, plot threshold curves (including for different sectors), collapse plots and threshold vs bias curves
* Updated Computing Threshold and Adding a New Code with new pipeline
* New XZZX threshold vs bias tutorial
* Documentation API for all the modules, better separation of different sections
* Much more docstrings in general (with a detailed description of almost all codes)

Lots of refactoring as well as many new features, such as:
- New codes: 3D color code, 6.6.6 color code, 4.8.8 color code
- New decoder: xcube matching decoder
- Refactoring of simulations: new `BaseSimulation` class, with `DirectSimulation`, `SplittingSimulation` and `BatchSimulation` as children
- New Analysis class for plots and threshold calculations
- New scripts for the cluster, with parallelization over runs instead of probabilities, a lower number of input and output files, and the compression of output files as the main new features.
- Decoders have a new attribute `allowed_codes` to determine which codes the decoder is tailored to. This is mostly used for the GUI, to avoid having the same list of decoders displayed for all the codes.
- Improvement of unit tests: new `tests/codes` and `tests/decoders` folder, new `DecoderTest` base class, new unit tests for all codes and decoders using base classes.
- New polygon shape in the GUI, that allows to easily have a different polygon for the bulk and for the boundary of a code (see e.g. 2D color codes)