v0.15.3.0

[0.15.3.0] - 2024-12-05

Bug Fixes

• Fix/standard_output_ports_calculate (#3114)

• • recurrenttransfermechanism.py
  • _instantiate_attributes_after_function(): fix assignment of StabilityFunction, and force update of default_variable for output_port

• _instantiate_attributes_after_function:
  revise call to _update_default_variable to use energy.variable instead of value

• • test_recurrent_transfer_mechanism.py
  • TestStandardOutputPorts:
    test_rtn_energy()
    test_rtn_entropy()
• • recurrenttransfermechanism.py
    _instantiate_attributes_after_function():
    refactor to assign functions for ENERGY and ENTROPY standard_output_ports before call to super()

• Fix/lccontrolmechanism_objectivemechanism (#3134)

• • composition.py
  • suppress warning about adding CONTROL_OBJECTIVE NodeRole if ObjectiveMechanism is already associated with a ControlMechanism

• lccontrolmechanism.py

  • _instantiate_objective_mechanism(): implement default ObjectiveMechanism with CombineMeans
  • _instantiate_control_signals:
    complete implementation of ALL
• • test_control_mechanism.py
    test_lc_control_monitored_and_modulated_mechanisms_composition(): augmented to test implementation of ObjectiveMechanism

Component

• Make deprecated arg error via illegal args; deprecate 'size' (#3123)

Functions/OneHot

• Fix "DETERMINISITC" typo
• Use local PRNG to randomly select extreme index

Mechanism

• If any port has default_input, get variable from input_ports

Parameter

• Correct .set post-initialization check (#3116)

Port

• Use default_input before checking projections

Refactor

• Refactor/emcomposition_field_handling (#3122)

• • emcomposition.py
    _parse_fields: clean up assignment of self.num_fields

• test_emcomposition.py
  add test_assign_field_weights_and_0_vs_None()
  add test_field_weights_all_None_and_or_0

• emcomposition.py

  • revamp docstring to document new mods
  • add fields arg to specify field_naes, field_weights, learn_field_weights
  • implement fields arg to specify field_names, field_weights, learn_field_weights in dict format
  • implement support for field-specific learn_field_weight specifications
  • _identify_target_nodes():
    refactor to use target_fields instead of learn_field_weights
  • add target_fields to fields specification dict
  • add dict spec for entries in fields arg
  • start adding field_idx to all components
  • add self._field_index_map

• pytorchEMcompositionwrapper.py

  • store_memory(): use self._field_index_map to assign memories to fields

• test_emcomposition.py

  • test_backpropagation_of_error_in_learning(): use EGO model to test for error backpropagation through EMCompoistion
  • test_field_args_and_map_assignments(): flesh out _field_index_map validation
• • emcomposition.py
  • update docstring figs
  • add purge_by_field_weights Parameter
• • autodiffcomposition.py
  • infer_backpropagation_learning_pathways(): add NodeRole.BIAS to pathways consructed for learning

Testing

• Split softmax_choice test
• Add mode=DETERMINISTIC tests
• Test more int32 samples in MT builtin test
• Use array_equal to test integer results

Broken_trans_deps

• Block coverage==7.6.5 (#3118)

Ci

• Test-release: add matrix.dist to test result artifact
• Test-release: exclude macos-11 on py3.7

Ci/ga

• Use console_output_style=count (#3132)

Llvm

• Convert recursive array iterator into contextmanager
• Implement range integer generation to match Numpy's
• Implement range integer generation to match old Numpy's

Llvm/Component

• Allow 'indicator' and 'abs_val' parameters in OneHot DETERMINISTIC mode

Llvm/DictionaryMemory

• Remove OneHot mode workarounds

Llvm/Mechanism

• Reinit integrator_function in Mechanism reset if present (#3112)

Llvm/OneHot

• Isolate handling of PROB and PROB_INDICATOR modes
• Refactor to match Python behaviour for modes != DETERMINISTIC
• Add basic implementation of DETERMINISTIC mode
• Implement support for RANDOM tie resolution
• Simplify PROB/PROB_INDICATOR implementation
• Implement all modes (#3124)

Requirements

• Update optuna requirement from <4.1.0 to <4.2.0 (#3110)
• Update grpcio requirement from <1.68.0 to <1.69.0 (#3120)
• Update pytest-profiling requirement from <1.8.1 to <1.8.2 (#3135)
• Update pytest requirement from <8.3.4 to <8.3.5 (#3138)

v0.15.2.0

[0.15.2.0] - 2024-11-11

Bug Fixes

• Fix/ego_update_figs (#3108)

• EGO CSW Model: update figures

CombineMeans

• Avoid creating unecessary object dtype for means

Component

• Only explicitly set new parameter defaults
• Check for existing parameter by name before getattr
• _initialize_parameters: allow creating Parameters dynamically
• _get_current_parameter_value: pass modulated=True to _get
• Always shallow copy owner
• Handle hybrid copy in deepcopy
• deepcopy remove no_shared in memo
• deepcopy add copy to memo
• Copy default variable if not passed to execute
• _validate_variable: copy default variable if used
• Copy matrix default value if used
• Store set of containing Compositions
• Rework size argument to accept and validate numpy shapes

Composition

• Inherit Parameters from parent class
• Fix bug storing results
• Do not delete value Parameter
• Remove compiled writeback of matrix during learning

CompositionInterfaceMechanism

• Use standard default_variable assignment

DDM

• Codestyle

DictionaryMemory

• Consolidate default entry creation

Documentation

• Fix table formatting
• Extend short title underlines
• Fix "strong" markup
• Fix literal markup
• Fix Inline emphasis markup
• Fix external links
• Fix inline interpreted markup
• Fix table vs. substitution conflict
• Fix basic rst formatting errors (#2958)
• Rename figure to match docstring reference (#3009)
• Add quotation to pip install (#3051)
• Use pattern rule to execute generator scripts (#3087)

DriftDiffusionAnalytical

• Specify dependence of bias on starting_value, threshold

DriftOnASphereIntegrator

• Fix initializer assignment
• Correct default initializer

EMComposition

• Reduce calls to memory_getter in init

EMStorageMechanism

• Add 'fields' as Parameter
• Do not set value in _execute
• Fix dot-notation access
• Explicitly update field_projection matrices

EMstorageMechanism

• Replace internal use of Parameter.get with _get

Function

• Copy variable on external .function call
• Do not process the value, or reset PRNG when syncing seed

Function_Base

• Don't catch and re-raise ValueError

IntegratorMechanism

• Correct broken size argument (#3046)

MDF

• Condition: handle np.number and np.array types as arguments
• Handle parameters/args in list and dict format

MaskedMappingProjection

• Also set matrix parameter port value

Mechanism

• Use np ones instead of list multiplication
• Copy defaults before executing with them
• Drop beartype decorator on internal function

OptimizationControlMechanism

• Correct non-stateful use of num_estimates

OptimizationFunction

• Make grid stateful

PECOptimizationFunction

• Make initial_seed shared and use context

Parameter

• Fix arg comment
• _set_default_value: add 'directly' to bypass parse/validate
• Bypass any setters when making uninherited
• deepcopy: always deepcopy non-inherited default_value
• Store source and final_source as self
• Faster contains
• getattr: call _parent fewer times
• Replace equivalent code with copy_parameter_value
• _set, _set_value: reformat arg list
• _set: make skip_delivery kwarg explicit
• On set, update compatible numpy arrays in place

ParameterEstimationComposition

• Make seed parameters shared
• Empty results on new run, not clear

ParameterPortList

• Reduce excess slow str formats

Parameters

• Clean up getter dev docs
• Check for alias using name

ParametersBase

• Cache names of attrs that do not exist
• Break throw_attr into separate method
• Do not getattr on parent for missing parameter attrs

ParametersTemplate

• Replace _children with WeakSet
• Add _params check in _is_parameter

Port

• Refactor is_modulated -> has_modulation

Projection_Base

• Copy sender default value if used as default

RecurrentTransferMechanism

• Make recurrent_projection a Parameter (#2940)

Refactor

• Refactor/emcomposition_softmax_after_dot (#3095)

• • emcomposition.py
  • move softmax operation to after combining weighted dot products
  • update use_gating_for_weighting and softmax CONTROL option to work with refactoring
  • validate that use_gating_for_weighting is False when learn_field_weights is True
  • docstring updates

• Update Environment.py

• test_emcomposition.py

  • update test_execution

• Refactor/linearmatrix_matrixtransform (#3101)

• combinationfunctions(.py) -> transformfunctions(.py)

• transferfunctions.py:

  • rename LinearCombination as MatrixTransform and move to transformfunctions.py

• transformfunctions:

  • MatrixTransform: add operation parameter

• recurrenttransfermechanism.py

  • correct names for standard_outputports ENERGY and ENTROPY

• lccontrolmechanism.py:

  • add keywords for modulable fitzhugh-nagumo params

• emcomposition.py:

  • use MatrixTransform(operation=L0) w/o normalization for retrieval if len(key)==1

• 'EGO Model - CSW with Simple Integrator.py':

  • Younes' script corrections, now functions propery!

Report

• Store report parameters on the instance instead of the class

SampleIterator

• Make generate_current_value instance-method-like

Scheduler

• Fix false add_condition replace warning (#3107)

StatefulFunction

• Correct previous_value shape with ragged variable

Testing

• Replace some assert == with numpy.testing.assert_array_equal
• Correct assert shape mismatch
• TestControlTimeScales: correct silent shape mismatch in results
• Check shape of results as well as the values
• Check shape of results as well as the values
• Use assert_array_equal to check array shape and values (#2922)
• Fix AVX512 detection on Numpy>=1.26 (#2932)
• Allow writeback on compiled tests.
• Remove result shape workaround
• Add test of dependency after DDM finished
• Control: split result assertions
• Auto test all numeric values wrapped in np array
• Add missing 'composition' marks (#2967)
• Narrow down the allowed exceptions in compilation fallback test
• Codestyle
• Use numpy prod instead of product
• Use fixture to preserve environment (#2987)
• Add leak check test (#2992)
• Remove leftover debug code
• Test show_graph in the leak test
• Fix show_graph leak and extend the leak test (#2997)
• Skip running ExecutionMode.LLVM instead of xfail
• Clarify failure in xfail test
• Cleanup some xfail tests (#2998)
• Adjust expected result based on scipy version
• Update OCM controller tests
• Use numpy arrays for fixed size arguments
• Use numpy arrays for fixed size arguments
• Use numpy arrays for fixed size arguments
• Use numpy arrays for fixed size arguments
• Cleanup
• Cleanup use of ExecutionMode.Python
• Cleanup
• Add llvm_not_implemented mark.
• Add llvm_not_implemented mark (#3075)
• Use issubclass to check Function class
• Convert dict test arguments to an immutable MappingProxyType
• Use MappingProxyType to pass dict test parameters (#3076)
• Drop unused ctypes import
• Use top level module import of ExecutionMode
• Drop unused import of core.llvm
• Comment out imports only used in commented out code
• Drop unused imports
• Drop unused imports (#3083)
• Move condition construction args to test parametrization
• Enable testing in per-node compiled mode

UserDefinedFunction

• Do not modify cust_fct_params attr on function call
• Rework creation of custom Parameters
• Use external Parameter.set for custom parameters

Broken_trans_deps

• Block beartype==0.17.1 (#2914)

Ci

• Split windows x86 job (#2943)
• Test-release: add --verbose to twine upload
• Test-release: use github cli to create github release
• Test-release: include python 3.10, 3.11, 3.12

Ci/ga

• Use native python architecture for macos python 3.8 job
• Use native python version on macos-arm64 runners (#2953)
• Simplify documentaitons ci jobs (#2957)
• Use single variable to check for self-hosted runners availability (#2965)
• Drop python-3.7 macos documentation build
• Require custom runners to have "enabled" flag (#2989)

Ci/ga/docs

• Use default python-architecture for each platform to build docs
• Represent correct os version in matrix.os
• Generate version matrix dimension based on GA event

Ci/github-actions

• Add python 3.12 docs building jobs
• Add python 3.12 jobs

Composition

• Create a copy of 'controller_condition'

Condition

• Add python interface from graph_scheduler
• Fix pnl-specific names in condition.py stub and all (#3089)

Conditions

• Add When alias for Condition
• Explicitly specify pnl Conditions in all

Conftest

• Clear graph scheduler cache in test teardown
• Inherit the original class of the benchmark fixture (#3093)

Dependabot

• Allow up to 25 open pull requests (#2944)

Deps/fastkde

• Bump minimum version to >=2.0.0

Fitfunctions

• Try using underscore name to construct fastKDE object

Function

• Replace FunctionOutputType.RAW_NUMBER with NP_0D_ARRAY

Functions

• Return numpy array as output for multi-item functions

Ga

• Move wheel/sdist creation to install-pnl action (#3085)

Llvm

• Move matrices of learnable projections to compiled state
• Move learnable matrices from RO params to RW params (#2933)
• Enable state writeback on all compiled Functions and Mechanisms (#2938)
• AutoassociativeProjection is a PNL param of the owning Mechanism (#2941)
• Add cleanup destruction check
• Consolidate construction and sync of compiled structures (#2973)
• Rearrange members of the Mersenne-Twister state structure
• Use int16 instead of int1 for flag in Philox state
• Use known type instead of...

v0.15.1.0

[0.15.1.0] - 2024-02-02

Functions/MemoryFunctions

• Do not use comparisons to empty list

Functions/UniformToNormalDist

• Do not check for scipy at runtime

MDF

• Write_mdf_file: clarify documentation on fmt arg
• Write_mdf_file: fix bug in detecting filename extension
• Add NodeRole.LEARNING as an exclusion for mechanisms
• Fix bug in detecting imported modules in script

PECOptimizationFunction

• Use opt_func instead of self.method to construct optuna study

Port/_parse_port_spec

• Convert value to string to compare to keyword

Security

• Only purge python cache if CODEQL_PYTHON is set (#2888)

Testing

• Use fixed seed for optuna sampler instances
• Seed optuna samplers (#2875)
• Check that running/executing with no inputs produces a warning
• Enable node_spec_types test.
• Add invocation wrapper to use in benchmark fixture
• Only consider first 10 values in checks
• Remove spurious return statement
• Don't use deprecated pytest.warns(None)
• Escape special characters in regexp
• MDF: correct implicit use of locals in exec
• MDF: test equivalence using np assert_array_equal
• MDF: standardize model_backprop object naming
• MDF: rework. share code. correct shared state
• MDF: replace use of json-named functions with mdf-named
• MDF: use tempfile instead of manually named files
• MDF: rename
• Use matrix.modulated or get_mod_matrix() instead of mod_matrix
• Do not apply marks to a fixture (#2901)

Broken_trans_deps

• Block sphinxcontrib-applehelp>=1.0.8
• Block sphinxcontrib-devhelp>=1.0.6
• Block sphinxcontrib-htmlhelp>=2.0.5
• Block sphinxcontrib-serializinghtml>=1.1.10
• Block sphinxcontrib-qthelp>=1.0.7

Ci/ga

• Upload pr_number only once
• Do not upload distfile for version restricted run
• Add version restriction to test artifact name
• Bump versions of actions/{download,upload}-artifact (#2893)
• Print additional CPU and memory info on all runners (#2898)
• Use all logical cores to run tests (#2900)

Ci/github-actions

• Make sure the uploaded artifacts are unique (#2892)

Deps

• Block sphinxcontrib-* that silently depend on sphinx >=5 (#2880)

Github-actions

• Bump actions/download-artifact from 3 to 4 (#2865)
• Bump actions/cache from 3 to 4 (#2879)

Llvm

• Codestyle
• Use checked/universal API to access binary structures (#2873)

Requirements

• Update grpcio requirement from <1.60.0 to <1.61.0 (#2855)
• Bump pycuda to <2024 (#2869)
• Update pytest requirement from <7.4.4 to <7.4.5 (#2870)
• Update pillow requirement from <10.2.0 to <10.3.0 (#2872)
• Add scipy to requirements file
• Update beartype requirement from <0.16.0 to <0.17.0 (#2804)
• Update pandas requirement from <2.1.5 to <2.2.1 (#2890)
• Update dill requirement from <0.3.8 to <0.3.9 (#2891)
• Update pytest requirement from <7.4.5 to <8.0.1 (#2896)

Setup

• Remove stale warning filter.
• Error on SyntaxWarnings

Treewide

• Assign values to ".base" attribute of a modulated Parameter

v0.15.0.0

Features

• add handling of partial differentials ("covariates") for BackPropagation learning (#2766)
• support learning nested AutodiffCompositions (#2801)
• support graph-scheduler graph structure conditions (#2864)
• add form of episodic / external memory with EMComposition (#2735)

Fixes

• log: nparray, nparray_dictionary: add report_all_executions option that reports all executions for a given TIME_STEP (#2844)

v0.14.0.0

[0.14.0.0] - 2023-07-26

AutoAssociativeProjection

• Only pass initial_shared 'matrix' to function

Bug Fixes

• Fix for some tests that expect runtime type checks
• Fix some lgtm errors

Component

• Add prefix to autogenerated names in deferred init
• Add predefined prefix to autogenerated names in deferred init (#2664)
• _initialize_parameters: simplify user specified check
• Improve illegal argument detection
• Improve param_defaults
• Fix detecting constructor args during init
• Don't prune args to function init
• Don't try copying defaults with value None
• Fully disallow name when constructor arg present
• Rework constructor argument validation
• Parse to combine alt param specifications
• Skip assigning defaults of aliases
• Add unused learning parameters to compilation blocklist (#2642)

Composition

• Assert for non-nested Composition run without input
• Correct context passing of pathways/add_node
• Correct context passing through add_projection
• Remove non-user-added projections from processing graph
• Fix INPUT roles for ControlMechanism -> inner Composition

ContentAddressableMemory

• Allow specifying selection_function in constructor
• Remove extraneous function instantiation checks
• Correct _parse_distance_function_variable as used in _validate
• _validate: remove function instantiation and default setting
• _validate: check result of each combo of granularity and field_weights
• Make selection_function dependent on distance_function
• _parse_distance_function_variable: use variable argument

ControlMechanism

• Remove extraneous output_ports arg
• Fix control_allocation initialization
• Correct _parse_output_ports
• Remove init parsing of monitor_for_control
• Remove init parsing of control

ControlSignal

• Do not recalculate costs on Port._update (#2722)

CostFunctions

• Use Flags instead of IntFlags for cost function enum

DictionaryMemory

• Reset: handle empty previous_value

Documentation

• Doc fixes on OptimizationFunction

EpisodicMemoryMechanism

• Make memory (_memory_init) a FunctionParameter

GradientOptimization

• Fix potentially uninitialized local variable
• Fix error on default bounds

LCAMechanism

• _validate_competition: fix reference to component name

LearningMechanism

• Remove unused LEARNED_PARAM

MDF

• Function: handle param mdf names for initializers
• Implement FitzHughNagumoIntegrator

OrnsteinUhlenbeckIntegrator

• Avoid producing 3d value (#2590)

Parameters

• Don't suppress AttributeError in _parse/_validate methods
• Rework parse and validation method interface
• Handle Parameters as dependencies

PredictionErrorMechanism

• Pass up only sample and target

SampleIterator

• Fix incorrect use of curly brackets in error strings (#2690)

Testing

• Remove blank line at the end of file
• Correct transfer mech initial_value override test (#2557)
• Add helper to tests that include parallel compiled execution (#2591)
• Add missing composition tags. Remove redundant Scheduler instances. (#2611)
• Extra role tests for pathway ending in control mechanism
• Use np.testing.assert_allclose to check resutls (#2621)
• Use np.testing.assert_equal instead of assert np.all(==)
• Prefer np.testing.assert_equal to assert np.all(==)
• Use np.testing.assert_equal instead of np.all (#2628)
• Convert to use autodiff_mode
• FP32 should only be used in compiled tests
• Check for execution mode PyTorch in test_optimizer specs
• Add helper function to return the first set of learning results
• Test_documentation_models: reenable parametrizations
• Allclose changes
• Test_nested_composition_run_trials_inputs: undo disable test parametrizations
• Test_nested_transfer_mechanism_composition_parallel shape mismatch
• TestRunInputSpecifications test_run_2_mechanisms_reuse_input: fix allclose
• TestRun test_run_2_mechanisms_reuse_input: fix allclose
• TestInputSpecifications test_run_2_mechanisms_reuse_input: fix allclose
• Test_connect_compositions_with_simple_states: fix allclose
• Test_linear_combination_function_in_mechanism: fix allclose
• Test_user_def_func_numpy: match 2d output to 2d input
• Test_LCAMechanism_threshold: fix allclose
• Test_output_ports: fix allclose
• Tests_output_port_variable_spec_composition: fix allclose
• Test_integrator_multiple_input: fix allclose
• TestRunInputSpecifications::test_2_mechanisms_input_5: fix allclose
• Test_assign_value: fix allclose
• Test_buffer_standalone: fix allclose
• Test_example_11: fix allclose
• Test_input_not_provided_to_run: fix allclose
• Test_input_specification_multiple_nested_compositions: fix allclose
• Test_transfer_mech_func: fix allclose
• Test_target_dict_spec_single_trial_scalar_and_lists_rl: fix allclose
• Test_AGTUtility_valid: fix allclose
• Test_connect_outer_composition_to_only_input_node_in_inner_comp_option2: fix allclose
• Test_single_array: fix allclose
• Test_transfer_mech_array_var_normal_array_noise: fix allclose
• Test_reset_run_2darray: fix allclose
• Test_rpy.py test_multilayer: fix allclose
• Test_log: fix allclose shape
• Test_gating_with_composition: fix allclose
• Replace assert np.allclose with np.testing.assert_allclose where tolerance fails
• Replace all unaffected assert np.allclose with np.testing.assert_allclose
• Remove asserts using zip loops where possible
• Adjust expected shape based on execution type
• Adjust shape of expected results based on execution mode
• Assert on results in "heterogenous_variable" tests
• Convert more tests to np.testing.assert_allclose (#2633)
• Tighten tolerance for compiled results (#2653)
• Test_call_after_construction_with_learning_pathway: fix missing assert (#2647)
• Check expected learning results
• Use worksteal xdist balancer (#2670)
• Add a 3rd set of expected results for small drift rate
• Ensure seed change test uses new seed (#2675)
• Use pytest.param id instead of fake parameter
• Drop redundant return statements
• Use full precision expected result instead of changing tolerance
• Skip on CUDA
• Sanitize PEC tests (#2688)
• Don't check newline encoding in the printf test (#2691)
• Extract mechanism values to form homogeneous array
• Illegal kwargs: add missing asserts
• Integrator mech: fix variable->default_variable
• Remove duplicate 'const_data' debug flag
• Add a helper to generate power set
• Add helper to generate power set and use it to test compiler debug options (#2707)
• Style
• Add TransferWithCosts test with all combinations of costs
• Do not include CostFunctions.ALL when constructing power set (#2714)
• Enable GPU tests
• Add for invalid function_params
• Mark em_composition TestExecution as pytorch
• Mark test_import_composition as pytorch
• Use overlooked helper function
• Rename test Component

Autodiff

• Make sure inputs to cross entropy loss are at least 2d for torch<=1.11.x

Autodiff_composition

• Use torch 1.11 with python3.10 and Windows (#2667)

Broken_trans_deps

• Add all python3.10 win32 torch wheels >=1.12.0
• Add cattrs==23.1.1 to broken deps list (#2686)

Ci

• Run all tests using --fp-precision=fp32 (#2629)
• Add run using --benchmark-enable (#2630)
• Add ipython 8.13.0 to blocklist for python <3.9 (#2651)
• Add --forked run to test autogenerated names
• Don't build "base" version of docs using python 3.10 or 3.11
• Don't use latest python on macos for building docs
• Don't use python 3.7.17 on macos to build docs (#2703)
• Disable pytest-xdist in benchmark ci job (#2710)

Components

• Add methods to return/filter projections between components

Dependencies

• Update to numpy<1.24.4 (#2693)

Deps

• Add onnx==1.14.0 to broken_trans_deps (#2663)
• Add pytest-forked to 'dev' requirements
• Restrict contourpy to <1.1.0 on x86 (32-bit) (#2700)
• Restrict pillow to <10.0.0 on x86 (32-bit) (#2716)

Dev_requirements

• Use sharp inequality of pytest-profiling upper bound

Functions/MaxLikelihoodEstimator

• Add support for storing all simulated results

Functions/TransferFunction

• Add support for 'per-item' mode derivative

Github-actions

• Use constraints file instead of pre-installing packages on x86 (#2584)
• Constraint broken transitive dependencies (#2603)
• Add fp32 compilation only test job (#2612)
• Run all tests with --fp-precision=fp32
• Add job running --benchmark-enable
• Add python 3.11 to docs CI
• Bump top python version 3.10->3.11

Github-actions/pnl-ci

• Print numpy and CPU info before running tests

Integratorfunctions

• _parse_initializer: cast initializer to numpy array

Llvm

• Pass number of inputs to 'evaluate' function
• Convert shape mismatch warning to PNLCompilerWarning category
• Use WeakRefDictionary for node wrappers
• Add human readable name to _node_wrapper instances
• Use weak references and proxy objects in _node_wrapper objects (#2613)
• Remove unnecessary data shape checks and workarounds (#2634)
• Update and extend the collection of code generation statistics (#2687)
• Represent integer types as unsigned in ctype
• Only write back shareable data (#2718)
• Add more structure stat messages (#2729)

Llvm/CUDA/function

• Sync stateful params back to CPU at the end of cuda_execute

Llvm/builder_context

• Use proxy object for _node_wrapper owning composition
• Move stats printing to LLVMBuilderContext destructor
• Include 'function' in cache stats for generated LLVM functions
• Collect statistics for number of cached and generated struct types
• Calculate and print cache hit rates
• Clarify output of module scope stats

Llvm/codegen

• E713 test for membership should be 'not in'

Llvm/cuda

• Do not upload inputs to shared memory.
• Do n...

v0.13.0.0

[0.13.0.0] - 2023-01-13

Documentation

• Remove invalid escape sequences (#2531)

MDF

• OutputPort: include shape and type
• Improve handling of more complex Functions
• Set up stateful parameter index handling
• Implement DriftDiffusionIntegrator

Parameters

• Allow validate methods to reference other parameters (#2512)

Testing

• Use the correct execution mode in test_transfer_mech_integration_rate_0_8 (#2471)
• Tests, treewide: Add missing "composition" marks (#2472)
• MDF: make onnx noise generation more flexible
• Drop extra 'monitor' mechanism from the threshold modulation test
• Use numpy instead of python math module
• Use lambda function to get the name of tested function
• Consolidate Buffer Function test
• Use more than one iteration in test using stateful functions
• Run more than one iteration in tests that use stateful Functions
• Consolidate test of different input formats
• Consolidate testing of different mechanism functions
• Run more than one iteration in tests that use integrator mode
• Use 'num_trials' instead of manually calling 'execute'
• Overload 'benchmark' fixture with custom invocation
• Use the benchmark fixture unconditionally
• Use the benchmark fixture unconditionally
• Use the benchmark fixture unconditionally
• Use the benchmark fixture unconditionally
• Use custom benchmark fixture (#2529)
• Don't use the same position in default variable
• Add derivative test when using OUTPUT_MDOE=ALL
• Use keywords instead of hardcoded strings as parameters
• Add type of output to names of SoftMax tests
• Assert that func_mode is only one of the three valid options
• Tests, functions/SoftMax: Don't use nested 'params' dir to set parameters
• Use 'size' instead of 'content_size' in construction
• Check for compiled variant sooner
• Check for warning messages when there's a conflict between mech and function parameter
• Drop 'DECISION_TIME' output port
• Add custom name prefix to all components with default names generated during test collection
• Use custom name prefix for Components instantiated during test enumeration (#2542)
• Do not check for string value of numpy error embedded in MechanismError (#2569)
• Use mac/windows results for numpy>=1.22 and AVX512 CPUs

TransferFunction

• Add support for computing derivatives using base function output (#2538)

Function/SoftMax

• Use correct dimensionality when calculating full Jacobian (#2539)

Functions/DriftDiffusionAnalytical

• Re-associate floating point operations

Functions/ReLU,SoftMax

• Restore functionality broken in #2528 (#2532)

Functions/SoftMax

• Restore correct computation of derivation
• Add support for 2d inputs to SoftMax derivative (#2534)
• Use "ALL" results to calculate derivative directly
• Use 'squeezed' version of output when calculating Jacobian

Functions/Transfer

• Consider 'bias' parameter in 0 check in ReLU derivative function

Functions/TransferFunction/Angle

• Optimize python version

Functios/ReLU

• Rename 'variable' arguemnt to 'input'

Github-actions

• Add hash of requirements.txt to cache key of built pip packages (#2482)
• Restrict scipy to <1.9.2 on x86 (#2502)
• Use environment files to set outputs (#2506)
• Restrict scikit-learn to <1.1.3 on x86 (#2511)
• Fix setting of outputs
• Consider 'doc_requirements.txt' when generating cache key in doc CI jobs
• Consider 'dev_requirements.txt' when generating cache key in CI jobs
• Fix detection of wheel cache directory location (#2513)
• Restrict statsmodels to <0.13.3 on x86 (#2516)
• Run only the latest instance of the main CI workflows (#2537)
• Check env var to tag selected OSes to run on self-hosted runners (#2546)
• Generalize package name extraction from dependabot branch name (#2566)

Github-actions/codeql

• Skip CI job on pushes that only update documentation (#2560)

Github-actions/coedql

• Run codeql analysis on PRs to devel

Github-actions/install-pnl

• Only check version of a new package if it's in a requirements file
• Restrict jupyter-server to <2 (#2555)

Github-actions/install-pnl/dependabot_pr

• Cleanup installation of the bumped package before installing PNL (#2481)
• Skip package version check for not installed packages (#2483)

Library/AutodiffComposition

• Drop empty docstring (#2567)

Llvm

• Add sin, cos builtins
• Implement compiled Angle and SoftMax derivative Functions (#2528)

Llvm/builtins

• Implement binomial distribution for N==1 (#2552)

Llvm/codegen

• Use visit_Constant instead of visit_{Num,NamedConstant} if available

Maint

• Ignore mdf test autogenerated files (#2527)

Models/Botvinnick

• Use top level import

Registry

• Add configurable prefix to auto generated component names

Requirements

• Restrict modeci_mdf to 64bit cpython (#2473)
• Update pytest requirement from <7.1.3 to <7.1.4 (#2478)
• Update pandas requirement from <1.4.4 to <1.4.5 (#2477)
• Update matplotlib requirement from <3.5.4 to <3.6.1 (#2486)
• Update pandas requirement from <1.4.5 to <1.5.1 (#2488)
• Update autograd requirement from <1.5 to <1.6 (#2493)
• Update pytest-cov requirement from <3.0.1 to <4.0.1 (#2492)
• Update pandas requirement from <1.5.1 to <1.5.2 (#2503)
• Update matplotlib requirement from <3.6.1 to <3.6.2 (#2497)
• Update torch requirement from >=1.8.0,<1.12.0 to >=1.8.0,<1.13.0 (#2504)
• Update pytest-xdist requirement from <2.6.0 to <3.1.0 (#2510)
• Update pytest-benchmark requirement from <3.4.2 to <4.0.1 (#2507)
• Update pint requirement from <0.20.0 to <0.21.0 (#2509)
• Update pillow requirement from <9.3.0 to <9.4.0 (#2515)
• Update pytest requirement from <7.1.4 to <7.2.1 (#2508)
• Update matplotlib requirement from <3.6.2 to <3.6.3 (#2525)
• Update pandas requirement from <1.5.2 to <1.5.3 (#2548)
• Update torch requirement from >=1.8.0,<1.13.0 to >=1.8.0,<1.14.0
• Update torch requirement from >=1.8.0,<1.13.0 to >=1.8.0,<1.14.0 (#2553)
• Update pytest-xdist requirement from <3.1.0 to <3.2.0 (#2554)
• Use upper and lower bound for fastkde (#2561)
• Update pillow requirement from <9.4.0 to <9.5.0 (#2565)
• Bump fastkde from 1.0.19 to 1.0.20 (#2559)
• Update networkx requirement from <2.9 to <3.1 (#2570)
• Update toposort requirement from <1.8 to <1.9 (#2573)
• Update toposort requirement from <1.9 to <1.10 (#2575)
• Update matplotlib requirement from...

v0.12.1.0

[0.12.1.0] - 2022-08-17

Testing

• Use np.where instead of opencoding it using map
• Refactor for better code reuse

Functions/UDF

• Use 'dir(builtins)' instead of 'builtins'

Llvm

• Switch compiled 'evaluate' to use composition simulation input (#2466)

Llvm/OptimizationControlMechanism

• Move construction of simulation input out of "evaluate" function

Llvm/cuda/execution

• Use bytes instead of bytearray for RO access to ctype structures

Llvm/execution

• Fix typo "variale" -> "variable"
• Use 'evaluate' function params when constructing simulation input (#2467)

Llvm/helpers

• Reuse type of index variable

Requirements

• Update matplotlib requirement from <3.5.3 to <3.5.4 (#2463)

v0.12.0.1

[0.12.0.1] - 2022-08-05

Github-actions/install-pnl

• Move upgrade of pip+wheel to its own step (#2461)

Requirements

• Update modelspec requirement from <0.2.6 to <0.2.7 (#2458)

Treewide

• Add missing whitespace after keyword (#2460)

v0.12.0.0

[0.12.0.0] - 2022-07-27

Component

• Don't exclude _init_args from deepcopy (#2380)
• Set correct Parameter owner on Component deepcopy

Composition

• Fix TERMINAL node detection (#2384)
• Add_projection: also detect feedback from node roles (#2429)

ControlMechanism

• Set function default to Identity
• Set monitor_for_control default to []

DriftOnASphereIntegrator

• Change default dimension to 3 (#2428)

JSON/MDF

• Determine fixed onnx noise values at test time (#2441)

KWTAMechanism

• Set matrix according to tests (#2398)

MDF

• Support v0.3.4; import from MDF classes
• Update interface methods
• Add yaml_summary
• Rename JSONDumpable to MDFSerializable
• Update all documentation from JSON to MDF
• Rename json files to mdf
• Remove manual arg substitution in expressions

MemoryFunction

• Use Buffer _update_default_variable fix
• _update_default_variable: handle ragged arrays

Parameter

• Remove delivery_condition from _additional_param_attr_properties
• Add specify_none flag

Parameters

• Fix Parameter inheritance when setting attributes (#2402)
• Allow specification in inner class or init

Testing

• Add checks for ControlMechanism allocation parameter
• Make sure all 'cuda' marked tests are also marked 'llvm'
• Add cmdline option to select compiler fp precision
• Add fp32 variant
• Consolidate matrix ops tests
• Drop fixed dimension vector matrix multiply
• Use pnlvm.ir instead of importing llvmlite ir again
• Convert arguments to the correct fp precision
• Consolidate spelling of 'Philox' to easily identify philox tests
• Convert parameters to correct type in PTX tests
• Parameters: add check for _additional_param_attr_properties
• Make sure inputs are representable in fp32
• Use higher tolerance when running in fp32 mode
• Refactor test parameters
• Add fp32 expected values
• Add Philox fp32 results
• Remove dead code
• Add fp32 results
• Add testing for fp32 results and fp32 precision
• Adjust probabilities for storage/retrieve
• Pass PRNG type as explicit test parameter
• Add special case result for PTX fp32 test
• Refactor tests to use pytest.param(id=)
• MDF: correct os-specific filepaths

Components

• Add default_variable as constructor_argument where missing
• Add check_user_specified decorator for _user_specified

Function/OptimizationFunction

• Allow array based SampleIterator in compiled code path
• Move Python specific code to non-compiled else branch

Functions/GridSearch

• Rename '_run_grid' -> '_search_grid'
• Refactor parallel compiled path to reuse existing '_evaluate' implementation
• Refactor parallel compiled path to reuse existing '_evaluate' implementation (#2445)

Functions/OptimizationFunction

• Disable aggregation in compiled mode

Github-actions

• Use v0.0.0.0 as dummy tag to compare documentation on pull requests (#2376)
• Bump actions/github-script from 5 to 6 (#2317)
• Bump actions/download-artifact from 2 to 3 (#2378)
• Bump actions/setup-python from 3 to 4 (#2425)
• Install latest pip and wheel when testing new dependencies (#2444)
• Drop python3.7 macos job (#2453)

Github-actions/install-pnl

• Fix lookup of dep packages (#2392)

Github-actions/pnl-ci-docs

• Skip removing zero tag if the tag creation was skipped (#2393)

Github-actions/pnl-install

• Check if a newly bumped dependency is rolled back during installation (#2390)

Llvm

• Split allocating new space in params with history from populating it
• Add support for different floating point precision conversions
• Add option to use 32bit floating point representation (#2400)
• Add support for more SoftMax output types (#2418)
• Always emit debuginfo with LLVM IR
• Cleanup codegen of mechanisms that modify function return value (#2421)
• Improve parallel execution handling (#2443)

Llvm/ConditionGenerator

• Refactor structure/initializer methods to not use type to detect composition

Llvm/UDF

• Reuse metadata from variable builder in codegen builder
• Update debug code location for every parsed AST node
• Add detailed line debugging information to generated IR (#2419)

Llvm/builder_context

• Use llvm.ir module directly
• Simplify debug info handling
• Use load_extract_scalar_array_one helper to load PRNG seed

Llvm/builtins

• Split 'is_close' builtin implementation by type
• Change 'tanh' formula to better handle large input
• Change 'coth' formula to better handle large input
• Change 'csch' formula to better handle large input
• Drop dead code

Llvm/debug

• Print parallel execution time when "time_stat" is set

Llvm/execution

• Add support for structs to _element_dtype
• Check for errors in jobs submitted to thread pool executor

Mechanism/ControlMechanism

• Drop DefaultAllocationFunction
• Remove obsolete workaround

Mechanisms/ControlMechanism

• Drop unused import of psyneulink.llvm

Requirements

• Update pillow requirement from <9.1.0 to <9.2.0 (#2370)
• Update pandas requirement from <=1.4.1 to <1.4.3 (#2373)
• Update autograd requirement from <=1.3 to <1.5 (#2379)
• Update graphviz requirement from <0.20.0 to <0.21.0 (#2389)
• Update networkx requirement from <2.8 to <2.9 (#2383)
• Update pytest requirement from <7.1.2 to <7.1.3 (#2396)
• Update psyneulink-sphinx-theme requirement (#2426)
• Update graph-scheduler requirement (#2391)
• Update pillow requirement from <9.2.0 to <9.3.0 (#2436)
• Update pandas requirement from <1.4.3 to <1.4.4 (#2434)
• Update elfi requirement from <0.8.4 to <0.8.5 (#2427)
• Update matplotlib requirement from <3.5.2 to <3.5.3 (#2403)
• Update torch requirement from <1.9.0 to <1.12.0 (#2446)
• Update pint requirement from <0.18 to <0.20 (#2447)
• Update llvmlite requirement from <0.39 to <0.40 (#2451)
• Bump pycuda to <2023 (#2452)
• Update numpy requirement from <1.21.4 to <1.21.7 (#2454)

Utilities

• Combine signature caches

Release v0.11.0.0

What's Changed

• requirements: update grpcio requirement from <1.35.0 to <1.41.0 by @dependabot in #2115
• requirements: update grpcio-tools requirement from <1.35.0 to <1.41.0 by @dependabot in #2116
• requirements: update rich requirement from <10.10,>=10.1 to >=10.1,<10.11 by @dependabot in #2123
• requirements: update pytest-xdist requirement from <2.4.0 to <2.5.0 by @dependabot in #2124
• tests/models/Predator-Prey: Use attractor/repeller forces to select the next move by @jvesely in #2121
• github-actions(deps): bump actions/github-script from 4.1 to 5 by @dependabot in #2125
• requirements: update toposort requirement from <1.7 to <1.8 by @dependabot in #2129
• treewide: codestyle fixes by @jvesely in #2131
• requirements: update rich requirement from <10.11,>=10.1 to >=10.1,<10.12 by @dependabot in #2126
• Reset random state on seed change by @jvesely in #2130
• Use IntFlag for cost functions by @jvesely in #2133
• Parameters: exclude more types from copying by @kmantel in #2134
• requirements: update pytest-cov requirement from <2.12.2 to <3.0.1 by @dependabot in #2135
• UDF improvements by @kmantel in #2132
• llvm: Add missing functionality to OCM by @jvesely in #2137
• llvm: Add helper function to retrieve and optionally reseed random state by @jvesely in #2138
• github-actions: Restrict main CI run to macos-10.15 by @jvesely in #2139
• functions: _is_identity: add option for defaults by @kmantel in #2136
• llvm, mechanism: Use Parameter class to build a list of needed parameter ports by @jvesely in #2140
• requirements: update rich requirement from <10.12,>=10.1 to >=10.1,<10.13 by @dependabot in #2141
• SharedParameter: improve source detection by @kmantel in #2142
• requirements: update grpcio requirement from <1.41.0 to <1.42.0 by @dependabot in #2127
• requirements: update grpcio-tools requirement from <1.41.0 to <1.42.0 by @dependabot in #2128
• SharedParameter: direct get_previous, get_delta to source Parameter by @kmantel in #2143
• llvm, ports/ControlSignal: Always call 'combine_costs' when calculating costs by @jvesely in #2146
• LCAMechanism: allow user-input integrator_function by @kmantel in #2148
• requirements: update sphinx requirement from <4.1.3 to <4.2.1 by @dependabot in #2120
• github-actions(deps): bump actions/checkout from 2.3.4 to 2.3.5 by @dependabot in #2149
• requirements: update pillow requirement from <8.4.0 to <8.5.0 by @dependabot in #2150
• requirements: update elfi requirement from <0.8.1 to <0.8.3 by @dependabot in #2147
• github-actions: Bump python-3.{8,9} to macos-latest. by @jvesely in #2151
• requirements: update graph-scheduler requirement from <=1.0.0rc2 to <1.0.1 by @kmantel in #2153
• requirements: update numpy requirement from <1.21.3 to <1.21.4 by @dependabot in #2152
• functions/TransferWithCosts: Change default cost options to CostFunctions.NONE by @jvesely in #2156
• github-actions: Drop maxprocesses settings by @jvesely in #2158
• github-actions: Add code coverage job by @jvesely in #2159
• github-actions: Do not check for GITHUB_TOKEN env var when uploading coveralls result by @jvesely in #2163
• github-actions: Allow RW permissions for jobs updating the online docs by @jvesely in #2160
• Component: add all_dependent_parameters by @kmantel in #2162
• github-actions(deps): bump actions/checkout from 2.3.5 to 2.4.0 by @dependabot in #2165
• Refactor/pec by @jdcpni in #2166
• github-actions/install-pnl: Support persistent runners by @jvesely in #2167
• maint: remove freeze.txt by @kmantel in #2182
• github-actions/release: Consolidate by @jvesely in #2185
• Refactor/controlmech and ocm by @jdcpni in #2186
• Docs/comp ctlmech ocm pec by @jdcpni in #2187
• llvm: Initialize builder context and jit engines on demand by @jvesely in #2188
• github-actions/pnl-ci-docs: Force creation of temporary version tag by @jvesely in #2192
• llvm: Add support for Philox PRNG by @jvesely in #2194
• tests/ddm: Disable Bogacz test with Philox prng by @jvesely in #2195
• github-actions/comment: Add PR write permission and use github.rest.* for rest API by @jvesely in #2196
• llvm: Check for correct use of get_{param,state}_ptr helpers by @jvesely in #2198
• tests/models/predator-prey: Restore checks of results by @jvesely in #2202
• llvm, ports/ControlSignal: Add support for CostFunctions.NONE by @jvesely in #2203
• tests/predator-prey: Mark the 101 level test instance as 'stress' test by @jvesely in #2204
• tests/llvm: Add Philox PRNG tests with different seeds by @jvesely in #2205
• pnl-ci: build docs-only branches by @kmantel in #2206
• requirements: update psyneulink-sphinx-theme requirement from <1.2.2.2 to <1.2.3.1 by @dependabot in #2201
• GatingMechanism: properly set gating_allocation as value alias by @kmantel in #2191
• ControlProjection: correct control_signal to SharedParameter by @kmantel in #2212
• github-actions(deps): bump actions/setup-python from 2.2.2 to 2.3.0 by @dependabot in #2209
• llvm: Cleanup execution of compiled functions by @jvesely in #2214
• github-actions(deps): bump actions/cache from 2.1.6 to 2.1.7 by @dependabot in #2213
• setup/coverage: Correct option name multiprocess -> multiprocessing by @jvesely in #2219
• github-actions(deps): bump actions/setup-python from 2.3.0 to 2.3.1 by @dependabot in #2215
• tests/show_graph: Strip whitespace before comparing expected dot output by @jvesely in #2220
• requirements: update graphviz requirement from <0.18.0 to <0.20.0 by @dependabot in #2218
• Refactor/ocm/state input ports by @jdcpni in #2221
• Misc/ocm/docs and tests by @jdcpni in #2223
• requirements: update grpcio-tools requirement from <1.42.0 to <1.43.0 by @dependabot in #2210
• Docs/ocm/revs by @jdcpni in #2225
• Docs/ocm/revs by @jdcpni in #2227
• tests/report: cleanup by @jvesely in #2228
• Feat/ocm/random params by @jdcpni in #2231
• github-actions(deps): bump actions/upload-artifact from 2.2.4 to 2.3.0 by @dependabot in https://github....