Psyneulink

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))

Component

- Don't exclude _init_args from deepcopy ([2380](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2380))
- Set correct Parameter owner on Component deepcopy

Composition

- Fix TERMINAL node detection ([2384](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2384))
- Add_projection: also detect feedback from node roles ([2429](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2429))

ControlMechanism

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

DriftOnASphereIntegrator

- Change default dimension to 3 ([2428](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2428))

JSON/MDF

- Determine fixed onnx noise values at test time ([2441](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2441))

KWTAMechanism

- Set matrix according to tests ([2398](https://github.com/PrincetonUniversity/PsyNeuLink/issues/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](https://github.com/PrincetonUniversity/PsyNeuLink/issues/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](https://github.com/PrincetonUniversity/PsyNeuLink/issues/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](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2376))
- Bump actions/github-script from 5 to 6 ([2317](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2317))
- Bump actions/download-artifact from 2 to 3 ([2378](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2378))
- Bump actions/setup-python from 3 to 4 ([2425](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2425))
- Install latest pip and wheel when testing new dependencies ([2444](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2444))
- Drop python3.7 macos job ([2453](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2453))

Github-actions/install-pnl

- Fix lookup of dep packages ([2392](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2392))

Github-actions/pnl-ci-docs

- Skip removing zero tag if the tag creation was skipped ([2393](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2393))

Github-actions/pnl-install

- Check if a newly bumped dependency is rolled back during installation ([2390](https://github.com/PrincetonUniversity/PsyNeuLink/issues/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](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2400))
- Add support for more SoftMax output types ([2418](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2418))
- Always emit debuginfo with LLVM IR
- Cleanup codegen of mechanisms that modify function return value ([2421](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2421))
- Improve parallel execution handling ([2443](https://github.com/PrincetonUniversity/PsyNeuLink/issues/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](https://github.com/PrincetonUniversity/PsyNeuLink/issues/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](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2370))
- Update pandas requirement from <=1.4.1 to <1.4.3 ([2373](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2373))
- Update autograd requirement from <=1.3 to <1.5 ([2379](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2379))
- Update graphviz requirement from <0.20.0 to <0.21.0 ([2389](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2389))
- Update networkx requirement from <2.8 to <2.9 ([2383](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2383))
- Update pytest requirement from <7.1.2 to <7.1.3 ([2396](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2396))
- Update psyneulink-sphinx-theme requirement ([2426](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2426))
- Update graph-scheduler requirement ([2391](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2391))
- Update pillow requirement from <9.2.0 to <9.3.0 ([2436](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2436))
- Update pandas requirement from <1.4.3 to <1.4.4 ([2434](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2434))
- Update elfi requirement from <0.8.4 to <0.8.5 ([2427](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2427))
- Update matplotlib requirement from <3.5.2 to <3.5.3 ([2403](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2403))
- Update torch requirement from <1.9.0 to <1.12.0 ([2446](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2446))
- Update pint requirement from <0.18 to <0.20 ([2447](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2447))
- Update llvmlite requirement from <0.39 to <0.40 ([2451](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2451))
- Bump pycuda to <2023 ([2452](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2452))
- Update numpy requirement from <1.21.4 to <1.21.7 ([2454](https://github.com/PrincetonUniversity/PsyNeuLink/issues/2454))

Utilities

- Combine signature caches

What's Changed
* requirements: update grpcio requirement from <1.35.0 to <1.41.0 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2115
* requirements: update grpcio-tools requirement from <1.35.0 to <1.41.0 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2116
* requirements: update rich requirement from <10.10,>=10.1 to >=10.1,<10.11 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2123
* requirements: update pytest-xdist requirement from <2.4.0 to <2.5.0 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2124
* tests/models/Predator-Prey: Use attractor/repeller forces to select the next move by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2121
* github-actions(deps): bump actions/github-script from 4.1 to 5 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2125
* requirements: update toposort requirement from <1.7 to <1.8 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2129
* treewide: codestyle fixes by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2131
* requirements: update rich requirement from <10.11,>=10.1 to >=10.1,<10.12 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2126
* Reset random state on seed change by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2130
* Use IntFlag for cost functions by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2133
* Parameters: exclude more types from copying by kmantel in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2134
* requirements: update pytest-cov requirement from <2.12.2 to <3.0.1 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2135
* UDF improvements by kmantel in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2132
* llvm: Add missing functionality to OCM by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2137
* llvm: Add helper function to retrieve and optionally reseed random state by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2138
* github-actions: Restrict main CI run to macos-10.15 by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2139
* functions: _is_identity: add option for defaults by kmantel in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2136
* llvm, mechanism: Use Parameter class to build a list of needed parameter ports by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2140
* requirements: update rich requirement from <10.12,>=10.1 to >=10.1,<10.13 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2141
* SharedParameter: improve source detection by kmantel in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2142
* requirements: update grpcio requirement from <1.41.0 to <1.42.0 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2127
* requirements: update grpcio-tools requirement from <1.41.0 to <1.42.0 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2128
* SharedParameter: direct get_previous, get_delta to source Parameter by kmantel in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2143
* llvm, ports/ControlSignal: Always call 'combine_costs' when calculating costs by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2146
* LCAMechanism: allow user-input integrator_function by kmantel in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2148
* requirements: update sphinx requirement from <4.1.3 to <4.2.1 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2120
* github-actions(deps): bump actions/checkout from 2.3.4 to 2.3.5 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2149
* requirements: update pillow requirement from <8.4.0 to <8.5.0 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2150
* requirements: update elfi requirement from <0.8.1 to <0.8.3 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2147
* github-actions: Bump python-3.{8,9} to macos-latest. by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2151
* requirements: update graph-scheduler requirement from <=1.0.0rc2 to <1.0.1 by kmantel in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2153
* requirements: update numpy requirement from <1.21.3 to <1.21.4 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2152
* functions/TransferWithCosts: Change default cost options to CostFunctions.NONE by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2156
* github-actions: Drop maxprocesses settings by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2158
* github-actions: Add code coverage job by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2159
* github-actions: Do not check for GITHUB_TOKEN env var when uploading coveralls result by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2163
* github-actions: Allow RW permissions for jobs updating the online docs by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2160
* Component: add all_dependent_parameters by kmantel in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2162
* github-actions(deps): bump actions/checkout from 2.3.5 to 2.4.0 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2165
* Refactor/pec by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2166
* github-actions/install-pnl: Support persistent runners by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2167
* maint: remove freeze.txt by kmantel in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2182
* github-actions/release: Consolidate by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2185
* Refactor/controlmech and ocm by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2186
* Docs/comp ctlmech ocm pec by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2187
* llvm: Initialize builder context and jit engines on demand by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2188
* github-actions/pnl-ci-docs: Force creation of temporary version tag by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2192
* llvm: Add support for Philox PRNG by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2194
* tests/ddm: Disable Bogacz test with Philox prng by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2195
* github-actions/comment: Add PR write permission and use github.rest.* for rest API by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2196
* llvm: Check for correct use of get_{param,state}_ptr helpers by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2198
* tests/models/predator-prey: Restore checks of results by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2202
* llvm, ports/ControlSignal: Add support for CostFunctions.NONE by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2203
* tests/predator-prey: Mark the 101 level test instance as 'stress' test by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2204
* tests/llvm: Add Philox PRNG tests with different seeds by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2205
* pnl-ci: build docs-only branches by kmantel in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2206
* requirements: update psyneulink-sphinx-theme requirement from <1.2.2.2 to <1.2.3.1 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2201
* GatingMechanism: properly set gating_allocation as value alias by kmantel in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2191
* ControlProjection: correct control_signal to SharedParameter by kmantel in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2212
* github-actions(deps): bump actions/setup-python from 2.2.2 to 2.3.0 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2209
* llvm: Cleanup execution of compiled functions by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2214
* github-actions(deps): bump actions/cache from 2.1.6 to 2.1.7 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2213
* setup/coverage: Correct option name multiprocess -> multiprocessing by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2219
* github-actions(deps): bump actions/setup-python from 2.3.0 to 2.3.1 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2215
* tests/show_graph: Strip whitespace before comparing expected dot output by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2220
* requirements: update graphviz requirement from <0.18.0 to <0.20.0 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2218
* Refactor/ocm/state input ports by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2221
* Misc/ocm/docs and tests by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2223
* requirements: update grpcio-tools requirement from <1.42.0 to <1.43.0 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2210
* Docs/ocm/revs by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2225
* Docs/ocm/revs by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2227
* tests/report: cleanup by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2228
* Feat/ocm/random params by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2231
* github-actions(deps): bump actions/upload-artifact from 2.2.4 to 2.3.0 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2230
* Control by kmantel in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2226
* requirements: update grpcio requirement from <1.42.0 to <1.43.0 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2211
* Feat/ocm/node role probe by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2232
* Feat/composition/probes by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2235
* requirements: update pytest-xdist requirement from <2.5.0 to <2.6.0 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2233
* Feat/composition/probes by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2236
* llvm: export compiler control options via PNL_LLVM_DEBUG env var by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2239
* Docs/cim by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2240
* PEC: fix constructor context execution_id by kmantel in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2234
* Refactor RANDOMIZATION_CONTROL_SIGNAL creation by kmantel in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2241
* dependabot: Do not autorebase pending PRs by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2242
* github-actions(deps): bump actions/upload-artifact from 2.3.0 to 2.3.1 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2243
* llvm/debug: Document cuda_max_regs option by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2244
* logging: don't throw exception when called from Function parameter by kmantel in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2245
* SharedParameter improvements by kmantel in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2246
* Component: _initialize_parameters: always ensure None context set by kmantel in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2249
* Feat/comp/mult proj between nodes by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2251
* Docs/cim figure by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2252
* functions: set fallback_default=True for seed parameter by kmantel in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2250
* Feat/comp/inputs by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2256
* Create ParameterPorts for all functions of functions by kmantel in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2255
* Feat/comp/inputs by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2257
* Feat/comp/inputs by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2259
* Feat/comp/inputs by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2260
* Fix/control/bugs by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2261
* Tests/control/warnings by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2262
* Fix/comp/proj warnings by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2264
* requirements: update pytest-helpers-namespace requirement from <2021.4.30 to <2021.12.30 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2263
* Fix/ocm/misc by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2267
* Feat/show graph/probe color by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2268
* Feat/control signal/add control arg by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2272
* Refactor/keyword control to control by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2273
* devel with history by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2269
* Refactor/control specs by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2276
* requirements: update pillow requirement from <8.5.0 to <9.1.0 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2274
* Fix/comp/build predicted input dicts by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2277
* requirements: update sphinx-autodoc-typehints requirement from <1.13.0 to <1.15.0 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2278
* Fix/show graph/cim by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2280
* Feat/ocm/state and state dict by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2281
* requirements: update sphinx-autodoc-typehints requirement from <1.15.0 to <1.16.0 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2283
* LLVM: Add support for compiling lambda functions used in UDF by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2284
* OCM: improve simulation context setup by kmantel in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2279
* llvm, functions/OneHot: MAX_ABS_VAL should return absolute value of the greatest magnitude by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2287
* OCM: cleanup fix to e41f205316 by kmantel in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2286
* requirements: update llvmlite requirement from <0.38 to <0.39 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2288
* functions: noise properties based on numeric or function by kmantel in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2258
* Feat/ocm/state feat dict by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2291
* Feat/ocm/state features by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2292
* llvm: Cleanup by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2295
* llvm, functions/AccumulatorIntegrator: Add compilation support by kmantel in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2294
* github-actions/intall-pnl: Update Ubuntu package database before installing graphviz by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2297
* llvm: Drop redundant parameters from compiled structures by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2296
* requirements: update sphinx-autodoc-typehints requirement from <1.16.0 to <1.17.0 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2298
* Feat/ocm/state features by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2299
* requirements: update matplotlib requirement from <3.4.4 to <3.5.2 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2238
* Feat/ocm/state features by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2301
* Feat/ocm/state features by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2302
* Test/ocm/state feat fct dict by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2303
* TransferMechanism: fix integration_rate validation by kmantel in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2304
* llvm/helpers: all_close should compare elements from both input arrays by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2309
* github-actions(deps): bump actions/setup-python from 2.3.1 to 2.3.2 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2306
* requirements: update pytest requirement from <6.2.6 to <7.0.1 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2307
* Fix/comp and mech/input variable by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2310
* llvm/{cuda,}: Reduce and optimize data copies in model execution by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2311
* llvm/debug: Cleanup debug options by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2312
* llvm/jit_engine: Fix typo in debug option check by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2313
* Feat/comp/get input format by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2315
* Fix/misc/jdc by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2316
* requirements: update pytest requirement from <7.0.1 to <7.0.2 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2318
* requirements: update sphinx-autodoc-typehints requirement from <1.17.0 to <1.18.0 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2319
* tests: small cleanup by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2320
* llvm: Reduce the amount of data copied due to parameter modulation by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2321
* Component: use shared_type copying for parameter spec by kmantel in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2322
* Refactor/ocm/state features param by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2323
* requirements: update elfi requirement from <0.8.3 to <0.8.4 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2325
* Refactor/ports/restrict projections by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2327
* llvm/cuda: Optimize memory copies in memory execution by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2328
* Fix/ocm/state features for nested comps by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2329
* github-actions(deps): bump actions/setup-python from 2.3.2 to 3 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2330
* github-actions(deps): bump actions/checkout from 2.4.0 to 3 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2331
* requirements: update networkx requirement from <2.6 to <2.8 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2332
* github-actions(deps): bump actions/upload-artifact from 2.3.1 to 3 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2333
* Threshold condition by kmantel in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2305
* Parameter fitting of compositions using MLE via probability density approximation by davidt0x in https://github.com/PrincetonUniversity/PsyNeuLink/pull/1920
* llvm, mechanism: Eliminate redundant copies of port input data by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2336
* llvm/cuda: Enable function inlining in CUDA path by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2338
* llvm: Remove unused parameters from compiled structures by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2339
* requirements: update pytest requirement from <7.0.2 to <7.1.1 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2341
* requirements: update pytest-pydocstyle requirement from <=2.2.0 to <2.4.0 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2342
* requirements: update pytest-pycodestyle requirement from <=2.2.0 to <2.4.0 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2340
* llvm: Implement printf helper on windows by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2346
* Refactor/ocm/state features all as input ports by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2345
* tests: uncomment disabled json tests by kmantel in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2347
* requirements: update pytest requirement from <7.1.1 to <7.1.2 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2348
* Refactor/ocm/state features all as input ports by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2350
* MDF compatibility by kmantel in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2154
* Refactor/ocm/state features all as input ports by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2351
* Refactor/ocm/state features all as input ports by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2352
* requirements: update graph-scheduler requirement from <1.0.1,>=0.2.0 to >=0.2.0,<1.1.1 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2343
* github-actions(deps): bump actions/cache from 2.1.7 to 3 by dependabot in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2353
* Refactor/ocm/state features all as input ports by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2355
* Refactor/ocm/state features all as input ports by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2356
* Refactor/ocm/state features all as input ports by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2359
* Refactor/ocm/state features all as input ports by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2360
* Refactor/composition/ validate input keys by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2361
* componenets/OutputPort: Add support for using 'num_executions' in output port variable spec by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2362
* Add node removal to Compositions by kmantel in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2364
* requirements: restrict modelspec to working by kmantel in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2366
* Test/compositon/ validate input dict keys by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2365
* llvm: More descriptive variable names by jvesely in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2367
* Refactor/ocm/state features all as input ports by jdcpni in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2369
* Devel by kmantel in https://github.com/PrincetonUniversity/PsyNeuLink/pull/2354


**Full Changelog**: https://github.com/PrincetonUniversity/PsyNeuLink/compare/v0.10.0.0...v0.11.0.0

New features and fixed bugs

New features and fixed bugs