Update Documentation - Githubissues

Issues to fix:

[x] Python version requirement is now 3.8-3.10, not 3.6
- https://vivarium-core.readthedocs.io/en/latest/getting_started.html#python-3
- https://vivarium-core.readthedocs.io/en/latest/getting_started_dev.html#python-3
[x] Verify that getting started instructions are still valid: https://vivarium-core.readthedocs.io/en/latest/getting_started.html
[x] CONTRIBUTING.md should point to the getting started guide
[x] Verify that the vivarium-template repository is still correct vivarium-collective/vivarium-template#1
[x] Replace "compartment" with "composite" or "composer"
- https://vivarium-core.readthedocs.io/en/latest/getting_started.html#repository-structure
- https://vivarium-core.readthedocs.io/en/latest/getting_started.html#some-terminology-processes-and-compartments
- https://vivarium-core.readthedocs.io/en/latest/guides/compartments.html
- https://vivarium-core.readthedocs.io/en/latest/guides/processes.html
- https://vivarium-core.readthedocs.io/en/latest/tutorials/write_process.html
[x] The getting started guide for developers doesn't really cover how to develop: https://vivarium-core.readthedocs.io/en/latest/getting_started_dev.html
[ ] Verify that the notebook tutorials still work
[x] The "modeling paradigm" guide frames Vivarium as ABM + WCM. Is this still appropriate? https://vivarium-core.readthedocs.io/en/latest/guides/modeling_paradigm.html
[x] Update the processes guide:
- Ports are no longer defined in constructor
- We can now just call super()
- Ports can be wired directly to variables
- Derivers are now steps
- is_deriver() and is_step() methods
- Custom timestep
- Process names
- Conditional updating
[x] Discuss flows in compartments guide: https://vivarium-core.readthedocs.io/en/latest/guides/compartments.html
[ ] Document Composer and MetaComposer better
[ ] Document the available arguments for the Engine constructor
[x] Document the ** syntax: https://vivarium-core.readthedocs.io/en/latest/guides/hierarchy.html
[x] ConveneinceKinetics is now it's own project: https://vivarium-core.readthedocs.io/en/latest/tutorials/write_process.html
[x] Ports no longer declared in constructor: https://vivarium-core.readthedocs.io/en/latest/tutorials/write_process.html#the-constructor
[x] We no longer support the Process.derivers() method: https://vivarium-core.readthedocs.io/en/latest/tutorials/write_process.html
[x] Move steps documentation into processes.rst
[x] In processes.rst, document advanced port schema techniques (*, **)
[ ] In processes.rst, document advanced updater techniques (_add, _delete, _move, {'_updater': ...})
[x] Pull in everything from the paper supplement
[x] Rename "experiment" to "engine"
[x] Fix reference to "compartment" in experiment docs
[x] Document emitters in simulation data format page
[ ] Document analyses
[x] * really belongs with schemas, not paths as it is now in the hierarchy.rst docs
[ ] Document Engine.run_for()

Pages to audit:

Tutorials
Reference Material

vivarium-collective / vivarium-core

Update Documentation #146