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Merge tag '1.0.0' into develop

Release v1.0.0

API changes:
------------

Modules
- Renamed:
  - `compute.big_phi` to `compute.network`
  - `compute.concept` to `compute.subsystem`
  - `models.big_phi` to `models.subsystem`
  - `models.concept` to `models.mechanism`

Functions
- Renamed:
  - `compute.main_complex()` to `compute.major_complex()`
  - `compute.big_mip()` to `compute.sia()`
  - `compute.big_phi()` to `compute.phi()`
  - `compute.constellation()` to `compute.ces()`
  - `compute.conceptual_information()` to `compute.conceptual_info()`
  - `subsystem.core_cause()` to `subsystem.mic()`
  - `subsystem.core_effect()` to `subsystem.mie()`
  - `subsystem.mip_past()` to `subsystem.cause_mip()`
  - `subsystem.phi_mip_past()` to `subsystem.phi_cause_mip()`
  - `subsystem.phi_mip_future()` to `subsystem.phi_effect_mip()`
  - `distance.small_phi_measure()` to `distance.repertoire_distance()`
  - `distance.big_phi_measure()` to `distance.system_repertoire_distance()`
  - For all functions in `convert`:
    - `loli` to `le` (little-endian)
    - `holi` to `be` (big-endian)
- Removed `compute.concept()`; use `Subsystem.concept()` instead.

Arguments
- Renamed `connectivity_matrix` keyword argument of `Network()` to `cm`

Objects
- Renamed `BigMip` to `SystemIrreducibilityAnalysis`
  - Renamed the `unpartitioned_constellation` attribute to `ces`
  - `sia` is used throughout for attributes, variables, and function names
    instead of `big_mip`
- Renamed `Mip` to `RepertoireIrreducibilityAnalysis`
  - Renamed the `unpartitioned_repertoire` attribute to `repertoire`
  - `ria` is used throughout for attributes, variables, and function names
    instead of `mip`
- Renamed `Constellation` to `CauseEffectStructure`
  - `ces` is used throughout for attributes, variables, and function names
    instead of `constellation`
- Renamed `Mice` to `MaximallyIrreducibleCauseOrEffect`
  - `mic` or `mie` are used throughout for attributes, variables, and function
    names instead of `mip`
- Similar changes were made to the `actual` and `models.actual_causation`
  modules.

Configuration settings
- Changed configuration settings as necessary to use the new object names.

Constants
- Renamed `Direction.PAST` to `Direction.CAUSE`
- Renamed `Direction.CAUSE` to `Direction.EFFECT`

API additions:
--------------

Configuration settings
- Added `CACHE_REPERTOIRES` to control whether cause/effect repertoires are
  cached. Single-node cause/effect repertoires are always cached.
- Added `CLEAR_SUBSYSTEM_CACHES_AFTER_COMPUTING_SIA` to control whether
  subsystem caches are cleared after calling `compute.sia()`.

Objects
- Added two new objects, `MaximallyIrreducibleCause` and
  `MaximallyIrreducibleEffect`, that are subclasses of
  `MaximallyIrreducibleCauseOrEffect` with a fixed direction.

Refactor:
---------

- Moved network-level functions in `compute.big_phi` to
  `pyphi.compute.network`
- Moved subsystem-level functions in `compute.big_phi` and `compute.concept` to
  `compute.subsystem`

Documentation:
--------------
- Added a description of TPM representations.
- Improved the explanation of conditional independence and updated the example
  to reflect that PyPhi now raises an error if a conditionally-dependent TPM is
  provided.
- Added detailed installation instructions.
- Little-endian and big-endian replace LOLI and HOLI terminology
- Added documentation for the following modules:
  - `distribution`
  - `cache`
  - `compute.parallel`
  - `compute` top-level module
  - `module` top-level module

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