Merge remote-tracking branch 'refs/remotes/origin/feature/iit-4.0' in…

…to feature/iit-4.0

Merge remote-tracking branch 'refs/remotes/origin/feature/iit-4.0' in…

…to feature/iit-4.0

relations: Consolidate phi schemes

- Remove congruence ratio logic
- Update AnalyticalRelations.sum_phi() for new phi schemes

Add Ray configuration

conf: Use 4.0 defaults

Hotfix v1.2.1

Fix wmayner#38: configuration in subprocesses

Configuration options that had been directly assigned within the
interpreter were not respected in subprocesses spawned by `MapReduce`
instances because of a change in the system call used by
`multiprocessing`. In Python 3.8 and above, it's `spawn` instead of
`fork`, so the subprocess no longer has access to the parent's memory,
and a new configuration object is created. Now `MapReduce` will pass the
parent's config object to the subprocess, which loads it.

Note:
  - the issue still arises when parallelization is done by the user
    utside of PyPhi.
  - the issue only affects direct assignment to the config object; using
    the `pyphi_config.yml` file still works as intended in both cases.

Bump version to 1.2.1

Release v1.2.0

Fixes:
- Fixed a bug introduced into `pyphi.utils.load_data()` by a breaking
  change in recent versions of NumPy that caused an error on import.
- Fixed a bug where changing `config.PRECISION` dynamically did not
  change `constants.EPSILON`, causing some comparisons that relied on
  `constants.EPSILON` to not reflect the new precision.
- Changing `config.FS_CACHE_DIRECTORY` and `config.FS_CACHE_VERBOSITY`
  now causes a new `joblib.Memory` cache to be created. Previously,
  changing these options dynamically had no effect.
- Made test suite compatible with stricter usage of `pytest` fixtures
  required by recent versions of `pytest`.

API additions:
- Added `pyphi.tpm.reconstitute_tpm()`.

API changes:
- Renamed `pyphi.partition.partition_registry` to
`pyphi.partition.partition_types`.
- Renamed `pyphi.distance.bld()` to `pyphi.distance.klm()`.
- Fixed the connectivity matrix of the
  `disjunction_conjunction_network()`.
- Removed `'expanded_*_reperotire'` attributes of JSON-serialized
  `Concept`s.

Config:
- Added the `WELCOME_OFF` option to turn off the new welcome message.

Documentation:
- Added documentation for the `partition_types` registry.
- Added documentation for the filesystem and database caches.

Release v1.1.0

Fixes:
- Fixed a memory leaked when concepts returned by parallel CES computations
  were returned with distinct subsystem objects. Now all objects in a CES share
  the same subsystem reference.
- Fixed a race condition caused by newly introduced `tqdm` synchronization.
  Removed the existing `ProgressBar` implementation and pinned `tqdm` to
  version >= 4.20.0.
- Made model hashes deterministic (6b59061). This fixes an issue with the Redis
  MICE cache in which cached values were not shared between processes and
  program invokations.

API additions:
- Added a `NodeLabels` object for managing the labels of network elements. Most
  models now carry a `NodeLabels` instance that is used for string formatting.
- Added the `cut_node_labels` property to `Subsystem` and `MacroSubsystem`.
- Added `utils.time_annotated` decorator to measure execution speed.

API changes:
- Specifying the nodes of a `Subsystem` is now optional. If not provided, the
  subsystem will cover the entire network.
- Removed the `labels2indices`, `indices2labels` and `parse_node_indices`
  methods from `Network`, and the `indices2labels` method from `Subsystem`.
- Renamed `config.load_config_file` to `config.load_file`, and
  `config.load_config_dict` to `config.load_dict`
- Removed backwards-compatible `Direction` import from `constants` module.
- Renamed `macro.coarse_grain` to `coarse_graining`.
- Exposed `coarse_grain`, `blackbox`, `time_scale`, `network_state` and
  `micro_node_indices` as attributes of `MacroSubsystem`.

Config:
- Removed the `LOG_CONFIG_ON_IMPORT` configuration option.

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