Psyneulink

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

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)

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 not use shared memory for inputs (2731)

Llvm/execution

- Generalize parameter writeback function (2643)
- Improve writeback handling of history and empty structures
- Do not write back "random_state" parameter
- Do not construct numpy arrays of empty structures
- Use "state" instead of context/CTX in debug print
- Print information about composition input struct if enabled
- Print information about "evaluate" output structure if enabled

Registry

- Apply prefix to autogenerated names for the first instance (2640)

Requirements

- Bump minimum numpy version to 1.19.0 (2583)
- Update pytest requirement from <7.2.1 to <7.2.2 (2586)
- Update pandas requirement from <1.5.3 to <1.5.4 (2588)
- Update pytest-xdist requirement from <3.2.0 to <3.3.0 (2599)
- Update matplotlib requirement from <3.6.4 to <3.7.1 (2602)
- Update toposort requirement from <1.10 to <1.11 (2605)
- Update pytest requirement from <7.2.2 to <7.2.3 (2606)
- Update matplotlib requirement from <3.7.1 to <3.7.2 (2607)
- Update elfi requirement from <0.8.5 to <0.8.7 (2608)
- Update networkx requirement from <3.1 to <3.2 (2620)
- Update pillow requirement from <9.5.0 to <9.6.0 (2618)
- Update pandas requirement from <1.5.4 to <2.0.1 (2619)
- Use sharp inequality for bear type upper bound
- Fix dill dependency upper bound
- Use sharp inequality for leabra-psyneulink upper bound
- Sort alphabetically
- Add protobuf to dependency list
- Drop grpcio-tools
- Use sharp upper bounds and maintain alphabetical order (2624)
- Update pytest requirement from <7.2.3 to <7.3.1 (2627)
- Update beartype requirement from <0.13.0 to <0.14.0 (2625)
- Update pytest requirement from <7.3.1 to <7.3.2 (2635)
- Update pandas requirement from <2.0.1 to <2.0.2 (2646)
- Update graph-scheduler requirement (2638)
- Update fastkde requirement (2649)
- Update torch requirement from >=1.8.0,<1.14.0 to >=1.8.0,<2.1.0 (2652)
- Update beartype requirement from <0.14.0 to <0.15.0 (2658)
- Update llvmlite requirement from <0.40 to <0.41 (2657)
- Use exclusive upper bound for optuna (2661)
- Update pint requirement from <0.21.0 to <0.22.0 (2655)
- Update pytest-xdist requirement from <3.3.0 to <3.4.0 (2669)
- Update numpy requirement from <1.22.5 to <1.23.6
- Update numpy requirement from <1.22.5 to <1.23.6 (2672)
- Update pytest-cov requirement from <4.0.1 to <4.1.1 (2678)
- Update pandas requirement from <2.0.2 to <2.0.3 (2682)
- Update numpy requirement
- Update optuna requirement from <3.2.0 to <3.3.0 (2683)
- Update grpcio requirement from <1.43.0 to <1.56.0 (2676)
- Update pytest requirement from <7.3.2 to <7.3.3 (2696)
- Update autograd requirement from <1.6 to <1.7 (2704)
- Update grpcio requirement from <1.56.0 to <1.57.0 (2705)
- Update pytest requirement from <7.3.3 to <7.4.1 (2706)
- Update pandas requirement from <2.0.3 to <2.0.4 (2708)
- Update pillow requirement from <9.6.0 to <10.1.0 (2715)
- Update matplotlib requirement from <3.7.2 to <3.7.3 (2719)
- Update fastkde requirement (2747)

Setup

- Add Python 3.11 to the list of supported versions

Torch

- Check status of torch numpy bindings instead of specific version

Treewide

- Inherit all component Exceptions from ComponentError (2595)

Utilities

- Handle numpy 1.24 rugged arrays

Warnings

- Ignore PNLInternalWarning by default

Wip

- Fit evaluate

{dev,tutorial}_requirements

- Use sharp inequality for jupyter upper bound

Documentation

- Remove invalid escape sequences ([2531](https://github.com/PrincetonUniversity/PsyNeuLink/issues/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](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2512))

Testing

- Use the correct execution mode in test_transfer_mech_integration_rate_0_8 ([2471](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2471))
- Tests, treewide: Add missing "composition" marks ([2472](https://github.com/PrincetonUniversity/PsyNeuLink/issues/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](https://github.com/PrincetonUniversity/PsyNeuLink/issues/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](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2542))
- Do not check for string value of numpy error embedded in MechanismError ([2569](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2569))
- Use mac/windows results for numpy>=1.22 and AVX512 CPUs

TransferFunction

- Add support for computing derivatives using base function output ([2538](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2538))

Function/SoftMax

- Use correct dimensionality when calculating full Jacobian ([2539](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2539))

Functions/DriftDiffusionAnalytical

- Re-associate floating point operations

Functions/ReLU,SoftMax

- Restore functionality broken in 2528 ([2532](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2532))

Functions/SoftMax

- Restore correct computation of derivation
- Add support for 2d inputs to SoftMax derivative ([2534](https://github.com/PrincetonUniversity/PsyNeuLink/issues/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](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2482))
- Restrict scipy to <1.9.2 on x86 ([2502](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2502))
- Use environment files to set outputs ([2506](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2506))
- Restrict scikit-learn to <1.1.3 on x86 ([2511](https://github.com/PrincetonUniversity/PsyNeuLink/issues/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](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2513))
- Restrict statsmodels to <0.13.3 on x86 ([2516](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2516))
- Run only the latest instance of the main CI workflows ([2537](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2537))
- Check env var to tag selected OSes to run on self-hosted runners ([2546](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2546))
- Generalize package name extraction from dependabot branch name ([2566](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2566))

Github-actions/codeql

- Skip CI job on pushes that only update documentation ([2560](https://github.com/PrincetonUniversity/PsyNeuLink/issues/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](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2555))

Github-actions/install-pnl/dependabot_pr

- Cleanup installation of the bumped package before installing PNL ([2481](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2481))
- Skip package version check for not installed packages ([2483](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2483))

Library/AutodiffComposition

- Drop empty docstring ([2567](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2567))

Llvm

- Add sin, cos builtins
- Implement compiled Angle and SoftMax derivative Functions ([2528](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2528))

Llvm/builtins

- Implement binomial distribution for N==1 ([2552](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2552))

Llvm/codegen

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

Maint

- Ignore mdf test autogenerated files ([2527](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2527))

Models/Botvinnick

- Use top level import

Registry

- Add configurable prefix to auto generated component names

Requirements

- Restrict modeci_mdf to 64bit cpython ([2473](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2473))
- Update pytest requirement from <7.1.3 to <7.1.4 ([2478](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2478))
- Update pandas requirement from <1.4.4 to <1.4.5 ([2477](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2477))
- Update matplotlib requirement from <3.5.4 to <3.6.1 ([2486](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2486))
- Update pandas requirement from <1.4.5 to <1.5.1 ([2488](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2488))
- Update autograd requirement from <1.5 to <1.6 ([2493](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2493))
- Update pytest-cov requirement from <3.0.1 to <4.0.1 ([2492](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2492))
- Update pandas requirement from <1.5.1 to <1.5.2 ([2503](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2503))
- Update matplotlib requirement from <3.6.1 to <3.6.2 ([2497](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2497))
- Update torch requirement from >=1.8.0,<1.12.0 to >=1.8.0,<1.13.0 ([2504](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2504))
- Update pytest-xdist requirement from <2.6.0 to <3.1.0 ([2510](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2510))
- Update pytest-benchmark requirement from <3.4.2 to <4.0.1 ([2507](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2507))
- Update pint requirement from <0.20.0 to <0.21.0 ([2509](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2509))
- Update pillow requirement from <9.3.0 to <9.4.0 ([2515](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2515))
- Update pytest requirement from <7.1.4 to <7.2.1 ([2508](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2508))
- Update matplotlib requirement from <3.6.2 to <3.6.3 ([2525](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2525))
- Update pandas requirement from <1.5.2 to <1.5.3 ([2548](https://github.com/PrincetonUniversity/PsyNeuLink/issues/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](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2553))
- Update pytest-xdist requirement from <3.1.0 to <3.2.0 ([2554](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2554))
- Use upper and lower bound for fastkde ([2561](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2561))
- Update pillow requirement from <9.4.0 to <9.5.0 ([2565](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2565))
- Bump fastkde from 1.0.19 to 1.0.20 ([2559](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2559))
- Update networkx requirement from <2.9 to <3.1 ([2570](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2570))
- Update toposort requirement from <1.8 to <1.9 ([2573](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2573))
- Update toposort requirement from <1.9 to <1.10 ([2575](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2575))
- Update matplotlib requirement from <3.6.3 to <3.6.4 ([2576](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2576))
- Update numpy requirement to <1.22.5
- Reassociate operations in the DriftDiffusionAnalytical function and update numpy to <1.22.5 ([2476](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2476))

Treewide

- Drop mentions of ControlMechanismRegistry
- Drop mentions of GatingMechanismRegistry
- Cleanup. Reduce the number of warnings issued during test execution ([2541](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2541))

Utilities

- Check that the compared value is not an empty list
- Add fastpath when checking if object is compatible with itself
- Safe_equals: handle dict-like objects in np arrays ([2551](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2551))

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](https://github.com/PrincetonUniversity/PsyNeuLink/issues/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](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2467))

Llvm/helpers

- Reuse type of index variable

Requirements

- Update matplotlib requirement from <3.5.3 to <3.5.4 ([2463](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2463))

Github-actions/install-pnl

- Move upgrade of pip+wheel to its own step ([2461](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2461))

Requirements

- Update modelspec requirement from <0.2.6 to <0.2.7 ([2458](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2458))

Treewide

- Add missing whitespace after keyword ([2460](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2460))