New style

[neil-glikin]

Broadly gives IonSim a more "functional" programming feel.

Some major changes:

• Introduces functions for accessing all relevant fields of IonSim structs. Both for retreiving and setting field values. This changes the preferred way to interface with IonSim structs, which is through these functions. For example, rather than calling chamber.iontrap.ions, we call should call ions(chamber).
• Sets conventions for function names (Name indicates what is returned, and underscores are avoided where possible. Phrases "get" and "set" generally avoided; functions which set values indicate this with a ! at the end of the function name. Setter functions always take in the object that's being modified as the first argument.)
• Sample of some name changes:
  • Trap -> Chamber
  • IonConfiguration -> IonTrap
  • stark_shift -> manualshift
  • vibrational_modes -> selectedmodes
• Changes laser strength to be in terms of intensity rather than E-field amplitude

Some minor changes:

• Default value of keyword argument timescale in hamiltonian changed from 1e-6 to 1 (however, there is a problem when timescale=1 is actually used; see #104)
• Allows mode size to be set in LinearChain constructor
• Allows Ions to be constructed with sublevel aliases
• Allows all functions which take in both a Chamber and a Laser and/or Ion to optionally index the Laser/Ion with an Int
• Ordering of some functions rearranged

[neil-glikin]

Format check will fail; I think we should get rid of this for now, since it does a few undesirable things, for example spacing around math operators and spacing around the = in keyword arguments.

[codecov[bot]]

Codecov Report

Base: 91.5% // Head: 88.5% // Decreases project coverage by -3.0% :warning:

Coverage data is based on head (f6f9e1c) compared to base (9df6d9e). Patch coverage: 80.7% of modified lines in pull request are covered.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #106 +/- ## ======================================== - Coverage 91.5% 88.5% -3.0% ======================================== Files 15 15 Lines 1166 1240 +74 ======================================== + Hits 1067 1098 +31 - Misses 99 142 +43 ``` | [Impacted Files](https://codecov.io/gh/HaeffnerLab/IonSim.jl/pull/106?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=HaeffnerLab) | Coverage Δ | | |---|---|---| | [src/IonSim.jl](https://codecov.io/gh/HaeffnerLab/IonSim.jl/pull/106?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=HaeffnerLab#diff-c3JjL0lvblNpbS5qbA==) | `100.0% <ø> (ø)` | | | [src/timeevolution.jl](https://codecov.io/gh/HaeffnerLab/IonSim.jl/pull/106?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=HaeffnerLab#diff-c3JjL3RpbWVldm9sdXRpb24uamw=) | `100.0% <ø> (ø)` | | | [src/iontraps.jl](https://codecov.io/gh/HaeffnerLab/IonSim.jl/pull/106?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=HaeffnerLab#diff-c3JjL2lvbnRyYXBzLmps) | `87.9% <56.7%> (ø)` | | | [src/chambers.jl](https://codecov.io/gh/HaeffnerLab/IonSim.jl/pull/106?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=HaeffnerLab#diff-c3JjL2NoYW1iZXJzLmps) | `71.3% <71.3%> (ø)` | | | [src/lasers.jl](https://codecov.io/gh/HaeffnerLab/IonSim.jl/pull/106?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=HaeffnerLab#diff-c3JjL2xhc2Vycy5qbA==) | `81.0% <73.8%> (-16.9%)` | :arrow_down: | | [src/ions.jl](https://codecov.io/gh/HaeffnerLab/IonSim.jl/pull/106?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=HaeffnerLab#diff-c3JjL2lvbnMuamw=) | `87.8% <84.5%> (+5.8%)` | :arrow_up: | | [src/vibrationalmodes.jl](https://codecov.io/gh/HaeffnerLab/IonSim.jl/pull/106?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=HaeffnerLab#diff-c3JjL3ZpYnJhdGlvbmFsbW9kZXMuamw=) | `90.3% <90.3%> (ø)` | | | [src/analyticfunctions.jl](https://codecov.io/gh/HaeffnerLab/IonSim.jl/pull/106?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=HaeffnerLab#diff-c3JjL2FuYWx5dGljZnVuY3Rpb25zLmps) | `100.0% <100.0%> (ø)` | | | [src/hamiltonians.jl](https://codecov.io/gh/HaeffnerLab/IonSim.jl/pull/106?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=HaeffnerLab#diff-c3JjL2hhbWlsdG9uaWFucy5qbA==) | `93.3% <100.0%> (+2.3%)` | :arrow_up: | | [src/operators.jl](https://codecov.io/gh/HaeffnerLab/IonSim.jl/pull/106?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=HaeffnerLab#diff-c3JjL29wZXJhdG9ycy5qbA==) | `98.6% <100.0%> (ø)` | | | ... and [8 more](https://codecov.io/gh/HaeffnerLab/IonSim.jl/pull/106?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=HaeffnerLab) | | Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=HaeffnerLab). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=HaeffnerLab)

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[jbroz11]

update docs