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Initial support for Implicit TPMs#105

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isacdaavid wants to merge 191 commits intofeature/iit-4.0wmayner/pyphi:feature/iit-4.0from feature/tpm-classwmayner/pyphi:feature/tpm-classCopy head branch name to clipboard

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Commits on Jan 3, 2023

• tpm.ProxyMetaclass: Change list to generator expression

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• tpm: Improve documentation

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• Move TPM documentation to tpm.ExplicitTPM class

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Commits on Jan 5, 2023

• tpm.ExplicitTPM: Remove superfluous call to super constructor

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• tpm.ExplicitTPM: Preserve column alignment in string representation.

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Commits on Jan 6, 2023

• subsystem: Complete ExplicitTPM.enforce cleanup

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Commits on Jan 7, 2023

• Refactor Node to use xarray DataArray (accessor namespace for now)

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Commits on Jan 10, 2023

• Node: Add support for multivalued and heterogeneous units

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Commits on Jan 11, 2023

• Node: Fix docstring

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• Node.node: Singleton coords aren't necessarily due to marginalization

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Commits on Jan 12, 2023

• tpm: Add abstract class ImplicitTPM and decorate for xr.Dataset

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Commits on Jan 13, 2023

• Refactor Network and Node for future implicit TPM support

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Commits on Jan 16, 2023

• Send duplicate state space filtering to utils.build_state_space()

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• Network.__init__: Avoid transient storage of nodes beyond the TPM

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• Network.to_json Include state_space attribute.

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• Network.__len__: Go back to counting nodes in the TPM (now a Dataset).

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Commits on Jan 17, 2023

• build_state_space(): Fix Union declaration

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• Fix widespread Union declaration typo

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• Squeeze singleton dimensions in Node

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Commits on Jan 18, 2023

• Implement ImplicitTPM validation

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• Merge remote-tracking branch

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• Update Network __eq__() method.

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• Network: revert to a __repr__ ammenable to JSON serialization.

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• Miscellaneous bug fixes in Node attribute setters and getters.

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• tpm.ImplicitTPM: Implement condition_tpm()

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• Minor import and docstring cleanup in subsystem

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Commits on Jan 27, 2023

• Change state space structure to use a dictionary.

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Commits on Feb 2, 2023

• Revert to using dummy singleton dimensions in multidimensional node TPMs

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• Node._hash: temporary workaround when the TPM array is mutable.

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Commits on Feb 17, 2023

• Implement function to properly unalign DataArray's

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Commits on Feb 20, 2023

• Node.streamline(): use more consistent variable declarations.

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• Avoid xarray Dataset altogether

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• Network.__init__(): Handle network as tpm argument

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• Fix error message

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• Merge pull request #87 from dviggiano/feature/tpm-class

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• Network: Fix build_cm() when None is provided.

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• Network.__init__(): maximum line length.

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Commits on Feb 21, 2023

• Network.__init__(): Pass xarray nodes to the ImplicitTPM constructor.

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• Implement proper indexing for the ImplicitTPM

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Commits on Feb 22, 2023

• Node.project_index(): remove leftover print statements.

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• tpm: miscellaneous cleanup.

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• tpm.ImplicitTPM: implement __len__ method.

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• Node.project_index: make positional indexing consistent with name indexing.

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• tpm.ImplicitTPM: implement ndim property

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• Modularize code to compute the shape of an ImplicitTPM

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Commits on Feb 23, 2023

• tpm: refactor ImplicitTPM.condition_tpm()

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• Handle potential KeyError if user passes nonexisting dimension labels.

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• Subsystem: remove unused property.

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Commits on Feb 24, 2023

• Fix ImplicitTPM.condition_tpm and generalize argument

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• Filter .nodes attribute based on membership to Subsystem.node_indices

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• Call Node directly and DataArray through callback-like reference to parent

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Commits on Feb 27, 2023

• Network.__init__(): Verify nodes against CM

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• Merge branch 'feature/tpm-class' of https://github.com/dviggiano/pyphi into feature/tpm-class

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• Fix bad merge

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• Network: Include attrs in repr, remove redundancy

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• Network.__init__(): Exclude cache

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• Network.__init__(): Properly grab CM columns

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• Update error message

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• Fix operator, error message

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• Fix _state_space assignment

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• Merge pull request #88 from dviggiano/feature/tpm-class

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• Fix bug in tpm.ImplicitTPM.shape

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• Network._build_cm(): Account for multiple nodes

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• Network.__init__(): Assign attributes in all cases

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• Fix redundancy

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• Merge branch 'wmayner:feature/tpm-class' into feature/tpm-class

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• Merge pull request #89 from dviggiano/feature/tpm-class

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• Merge branch 'feature/tpm-class' of github.com:wmayner/pyphi into feature/tpm-class

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Commits on Mar 1, 2023

• network.py: format source code

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• Fix bug in Network._build_cm() for explicit TPMs.

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• Cosmetic refactoring of Network._build_cm()

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• Don't reference self.cm before it has been set.

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• _build_cm(): Should use cm param, not self.cm

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• Merge branch 'feature/tpm-class' of https://github.com/dviggiano/pyphi into feature/tpm-class

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• test_network(): Add test_build_cm_implicit_tpm()

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• Merge pull request #90 from dviggiano/feature/tpm-class

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• test_network: Add test_build_cm_explicit_tpm()

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• DictCache: allow for reconstruction with __repr__

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• test_network.test_build_cm_explicit_tpm(); Allow for DictCache reconstruction with __repr__()

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• test_build_cm_explicit_tpm(): Use np.ones()

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• Merge pull request #92 from dviggiano/feature/tpm-class

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• Don't assume network state_space dict is ordered.

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• test_build_cm(): Combine into one test

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• Merge pull request #93 from dviggiano/feature/tpm-class

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• Network.__repr__(): Only use dict for state_space

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• Merge branch 'wmayner:feature/tpm-class' into feature/tpm-class

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• Merge pull request #94 from dviggiano/feature/tpm-class

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• Set the state of the subsystem nodes.

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• test_network: Add test_init_with_explicit_tpm()

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• Merge pull request #95 from dviggiano/feature/tpm-class

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Commits on Mar 2, 2023

• Change semantics of Node.tpm for direct access to ExplicitTPM methods.

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• Merge branch 'feature/tpm-class' of github.com:wmayner/pyphi into feature/tpm-class

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• Avoid reuse of subsystem nodes after cut

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• Guarantee marginalization of non_inputs when generating Nodes.

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Commits on Mar 3, 2023

• Inherit TPM.tpm_indices() and make it agnostic to state cardinality

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Commits on Mar 4, 2023

• Rehabilitate validate.network()

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Commits on Mar 7, 2023

• test_network.py: add fixture for making implicit TPMs

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• Infer network shape from nodes' last dimension.

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Commits on Mar 8, 2023

• Deduplicate code and turn into ImplicitTPM.shapes attribute

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• Add equals method to ImplicitTPM

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• Merge pull request #96 from dviggiano/feature/tpm-class

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• Fix bug in ImplicitTPM._node_shapes_to_shape()

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• Merge branch 'feature/tpm-class' of github.com:wmayner/pyphi into feature/tpm-class

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• Ibidem

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• Add state space reroute

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• Merge pull request #97 from dviggiano/feature/tpm-class

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• Include state_space in node declarations

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• Merge branch 'wmayner:feature/tpm-class' into feature/tpm-class

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• Merge pull request #98 from dviggiano/feature/tpm-class

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• Use hasattr instead of try-catch

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• Merge pull request #99 from dviggiano/feature/tpm-class

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• Do not use tpm.tpm

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• Merge pull request #100 from dviggiano/feature/tpm-class

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Commits on Mar 10, 2023

• tpm.py: extend subtpm() and reconstitute_tpm()

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• Merge branch 'feature/tpm-class' of github.com:wmayner/pyphi into feature/tpm-class

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Commits on Mar 14, 2023

• test_tpm.py: Convert to np.ndarray when comparing matrices.

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• tpm: inherit infer_cm() and infer_edge from parent class

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• Implement marginalize_out() for ImplicitTPM

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Commits on Mar 15, 2023

• Fix reconstitute_tpm so that it considers singletons

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Commits on Mar 16, 2023

• Implement ImplicitTPM.squeeze

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• Refactor remove_singleton_dimensions()

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Commits on Mar 17, 2023

• Sync macro.py with latest TPM code

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Commits on Mar 19, 2023

• Fix bug in auxilary method _node_shapes_to_shape

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Commits on Mar 20, 2023

• Make node_labels parameter mandatory when building a state space

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• macro.py: cast TPM type if necessary

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• test_node: Convert ImplicitTPMs for generate_nodes

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• MacroSubsystem.nodes(): Reconstitute TPM

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• test_macro.test_pack_attrs(): Fix TPM comparison

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• Merge branch 'feature/tpm-class' of https://github.com/dviggiano/pyphi into feature/tpm-class

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• generate_nodes(): Handle Implicit network TPMs

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• Merge pull request #101 from dviggiano/feature/tpm-class

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• node.py: Avoid circular import

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• Merge branch 'wmayner:feature/tpm-class' into feature/tpm-class

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• Merge pull request #102 from dviggiano/feature/tpm-class

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• Catch calls to ImplicitTPM.array_equals and route accordingly

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• Merge branch 'feature/tpm-class' of github.com:wmayner/pyphi into feature/tpm-class

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• Subsystem: set node TPM state early

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• (Cleanup) Exclude ExplicitTPM from top-level namespace

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Commits on Mar 21, 2023

• TPM: allow tpm_indices to discard singletons

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• macro: tidy remaining references to reconstitute_tpm

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Commits on Mar 22, 2023

• Harmonize {MacroSubsystem._,ImplicitTPM.}squeeze and fix test_blackbox_external

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• validate.state_reachable(): Reconstitute TPM

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• Implement ImplicitTPM.__hash__()

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• Merge pull request #103 from dviggiano/feature/tpm-class

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• ImplicitTPM.__hash__(): Fix syntax

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• Merge branch 'wmayner:feature/tpm-class' into feature/tpm-class

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• Merge pull request #104 from dviggiano/feature/tpm-class

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Commits on Mar 23, 2023

• validate.state_reachable: only cast if necessary

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• Re-enable validation at Subsystem constructor

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• test_validate: Don't refer to tpm.tpm

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Commits on Mar 24, 2023

• Refactor _validate_probabilities (and use utils.eq)

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• distribution.is_unitary: Remove superfluous flattening

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• Make sure node shapes are validated if CM is passed

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• tpm: Remove old ProxyMetaclass code

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Commits on Mar 25, 2023

• Remove validate.node_states, deprecated by Node.state setter

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• Add support for state labels in validate.state_reachable

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• Fix Network creation from existing ImplicitTPM

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• Remove Node.streamline

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• Refactor implicit_tpm fixture

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• Disable state reachability validation until reimplemented in implicit way

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• Merge feature/iit-4.0 into feature/tpm-class

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• tpm: Simplify subtpm method

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• Refactor TPM validation

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• subsystem: Fix proper_tpm

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• Tidy documentation

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• node.py: Improve code formatting

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• Rename DataArray accessor to something more explicit

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• validate: Disable state reachability warning for now

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• tpm: add number_of_units getter in the ImplicitTPM case

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• ImplicitTPM.number_of_units: more efficient implementation

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• test_tpm: validate arguments in implicit_tpm test

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• tpm: implement probability_of_current_state() and backward_tpm() for ImplicitTPMs

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• Refactor backward_tpm as instance methods

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• Rename DataArray accessor to something more expressive

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• test_tpm: Add test_backward_tpm

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• Move Fig 8 counter network to examples

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• utils: Add equivalent_states generator

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• Rework state reachability validation to avoid computing joint prob.

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• Merge branch feature/iit-4.0.

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• Merge branch 'feature/iit-4.0' into feature/tpm-class

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• Only compute potential purviews if not overriden

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• Merge remote-tracking branch 'refs/remotes/origin/feature/tpm-class' into feature/tpm-class

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• validate.state_reachable: Shortcircuit intersection as soon as possible

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• validate.state_reachable: Don't expand equivalence classes, use symbolic intersection.

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• validate.state_reachable: parallelize intersection between symbolic equivalence classes

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• Merge branch 'feature/tpm-class' of github.com:wmayner/pyphi into feature/tpm-class

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• validate: Refactor scope and add documentation/tests.

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• Improve state validation when creating subsystems

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• validate.state_value: Fix off-by-one error

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• Remove parallelization of state_reachable for now

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• Backport unified subsystem interface to tpm-class branch

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