Soil

Added
* Control logging level in CLI and simulation
* `Stats` to calculate trial and simulation-wide statistics
* Simulation statistics are stored in a separate table in history (see `History.get_stats` and `History.save_stats`, as well as `soil.stats`)
* Aliased `NetworkAgent.G` to `NetworkAgent.topology`.
Changed
* Templates in config files can be given as dictionaries in addition to strings
* Samplers are used more explicitly
* Removed nxsim dependency. We had already made a lot of changes, and nxsim has not been updated in 5 years.
* Exporter methods renamed to `trial` and `end`. Added `start`.
* `Distribution` exporter now a stats class
* `global_topology` renamed to `topology`
* Moved topology-related methods to `NetworkAgent`
Fixed
* Temporary files used for history in dry_run mode are not longer left open

Changed
* Seed random before environment initialization

Fixed
* Invalid directory names in Windows gsi-upm/soil5

Changed
* Minor change to traceback handling in async simulations
Fixed
* Incomplete example in the docs (example.yml) caused an exception

Fixed
* Bug with newer versions of networkx (0.24) where the Graph.node attribute has been removed. We have updated our calls, but the code in nxsim is not under our control, so we have pinned the networkx version until that issue is solved.
Changed
* Explicit yaml.SafeLoader to avoid deprecation warnings when using yaml.load. It should not break any existing setups, but we could move to the FullLoader in the future if needed.

Fixed
* Bug in `agent.get_agents()` when `state_id` is passed as a string. The tests have been modified accordingly.