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…init status (#3456) some methods like _update_default_variable are called elsewhere after initialization of the actual object, and this can cause state side-effects. avoids incrementing some integrators, as in the duration_cost_fct for OptimizationControlMechanism in test_modulation_simple or test_control.py::TestControlSpecification::test_deferred_init test results are modified; adding extra executions in the None context prior to running the compositions reproduces the previous results: test_deferred_init: `comp.controller.state_input_ports[0].function.execute([1.1]` `comp.controller.state_input_ports[1].function.execute([2.2]` test_modulation_simple: `comp.controller.control_signals[0].function.duration_cost_fct.execute([3]` see #2721
intended to allow non-Component objects also maintain Parameters objects
used to retrieve projection objects by name
intended to allow throwing a consistent error in multiple places other than just Parameter._validate
When a Parameter is tracking compiled struct storage, its current value may be an ndarray view into LLVM param memory. Setting that param from a Python scalar can fail the intended in-place update path and leave compiled memory stale. Coerce scalar sources to np.asarray(...) only when: - _tracking_compiled_struct is True, and - target_value is an ndarray. This preserves in-place mutation via update_array_in_place without changing Python-only scalar behavior. Fixes compiled-mode control-param updates (notably execute_until_finished), which affected LCA step/time reporting in tests/mechanisms/test_lca.py::TestLCA::test_LCAMechanism_standard_output_ports.
…Link into feat/lca/standard_output_ports_DEVEL_pec_fix
- In RecurrentTransferMechanism LLVM reset, stop zeroing `old_val`. - After integrator reset, run the primary transfer function and update output ports from that result, so recurrent feedback state is seeded from reset outputs. - This removes the LLVM/Python step-count divergence in `test_LCAMechanism_standard_output_ports` (LLVM now matches 56/.056). tests: simplify LCA standard_output_ports mode handling - Replace `return True` with `pytest.skip(...)` for unsupported execution modes. - Collapse redundant `comp_mode` conditionals and duplicate expected-value branches. - Update LLVM expected tuple to `(1, 56, .056)` to match aligned behavior. chore: clean comment wrapping/whitespace in Parameter in-place update block
- single location/standardization of parsing and validation that does not modify existing parameter values - partial integration with Parameter classes (TBI: refactoring as a sublcass of Parameter) - projections: implement ProxyProjection - formal class for the 'virtual' projections that span a Composition and a nested Composition that each represent two projections: one from a node in one Composition to a CIM and one from that CIM to another node in the other Composition. - Simplifies storage of learning_rate/optimization parameters using SharedParameter functional WIP with remaining tasks: - generalize optimization parameters as subclass of Parameter, handling more than learning_rate - generalize optimization parameter dict spec to accept Mechanism/Composition, not just Projection
#3466) - single location/standardization of parsing and validation that does not modify existing parameter values - partial integration with Parameter classes (TBI: refactoring as a sublcass of Parameter) - projections: implement ProxyProjection - formal class for the 'virtual' projections that span a Composition and a nested Composition that each represent two projections: one from a node in one Composition to a CIM and one from that CIM to another node in the other Composition. - Simplifies storage of learning_rate/optimization parameters using SharedParameter functional WIP with remaining tasks: - generalize optimization parameters as subclass of Parameter, handling more than learning_rate - generalize optimization parameter dict spec to accept Mechanism/Composition, not just Projection
…ps://github.com/PrincetonUniversity/PsyNeuLink into feat/lca/standard_output_ports_DEVEL_pec_fix
Updates the requirements on [pandas](https://github.com/pandas-dev/pandas) to permit the latest version. - [Release notes](https://github.com/pandas-dev/pandas/releases) - [Commits](pandas-dev/pandas@v3.0.0...v3.0.1) --- updated-dependencies: - dependency-name: pandas dependency-version: 3.0.1 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 6 to 7. - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](actions/upload-artifact@v6...v7) --- updated-dependencies: - dependency-name: actions/upload-artifact dependency-version: '7' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [actions/download-artifact](https://github.com/actions/download-artifact) from 7 to 8. - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](actions/download-artifact@v7...v8) --- updated-dependencies: - dependency-name: actions/download-artifact dependency-version: '8' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Updates the requirements on [protobuf](https://github.com/protocolbuffers/protobuf) to permit the latest version. - [Release notes](https://github.com/protocolbuffers/protobuf/releases) - [Commits](https://github.com/protocolbuffers/protobuf/commits) --- updated-dependencies: - dependency-name: protobuf dependency-version: 7.34.0 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
…Link into fix/fhn-output-port-index
…y in a Mechanism (#3560) ## Summary Fixes two related bugs affecting `FitzHughNagumoIntegrator` (and multi-stateful integrators generally) when used inside a `Mechanism`. Both surfaced from the reproducer below. ### Reproducer ```python import psyneulink as pnl inp = pnl.ProcessingMechanism(input_shapes=1) lc = pnl.TransferMechanism( input_shapes=1, integrator_mode=True, integrator_function=pnl.FitzHughNagumoIntegrator(), function=pnl.Linear(), output_ports=[{pnl.VARIABLE: (pnl.OWNER_VALUE, 1)}], reset_stateful_function_when=pnl.AtTrialStart(), ) comp = pnl.Composition() comp.add_nodes([inp, lc]) comp.add_projection(sender=inp, receiver=lc) comp.run(inputs={inp: [[1.0]]}) # IndexError in Python mode; worked in LLVMRun ``` ## Bug 1 — `IndexError` on reset (`mechanism.py`) On reset, the Mechanism rebuilt its value from the integrator's reset output but kept only element `[0]`: ```python new_input = self.integrator_function.reset(...)[0] ``` `StatefulFunction.reset()` returns one entry per stateful attribute. For single-attribute integrators (`AdaptiveIntegrator` → `[previous_value]`) the `[0]` correctly unwraps. For `FitzHughNagumoIntegrator` → `[v, w, time]` it discarded `w` and `time`, leaving the value with a single element, so an `OutputPort` selecting `(OWNER_VALUE, 1)` indexed past the end → `IndexError`. Compiled mode was unaffected (statically-typed value buffer; reset only rewrites the integrator state). **Fix:** keep all stateful terms when there is more than one. ## Bug 2 — value-shape inconsistency between Python and compiled (`integratorfunctions.py`) Even after Bug 1, the mechanism's value shape differed between modes: Python produced `(3, 1, 1)`, compiled `(3, 1)` (and `defaults.value` was `(3, 1)`). FHN stacks its three stateful terms; in a Mechanism, `variable` is the Mechanism's 2d variable `(1, 1)` while the stateful values are 1d, so broadcasting during execution inflated each term to 2d → `(3, 1, 1)`. During initialization (which sizes `value`) the un-broadcast 1d state is returned → `(3, 1)`. Compiled unwraps the same leading dimension (`helpers.unwrap_2d_array`), so it stays `(3, 1)`. **Fix:** conform `variable` to the rank of the stateful values at the start of `_function` (drop the leading singleton input-port dimension), so Python matches both the advertised default and compiled execution at `(3, 1)`. Standalone use with a genuinely 2d variable (and 2d stateful values) is unaffected. This required no compiled-codegen changes. ## Testing - `test_reset_multi_stateful_integrator_with_owner_value_output_port` runs across Python and all compiled modes, asserts the value shape is `(3, 1)`, and asserts a shared value reference (tolerance covers fp32 compiled CI). - `test_FitzHughNagumo_simple_scalar` previously added a dimension to the Python expected result to work around the shape mismatch; that workaround is removed (Python now matches compiled). - `test_FitzHughNagumo_valid` and the gilzenrat figure-2 test were updated from the inflated `(3, 1, 1)` indexing to `(3, 1)` (values unchanged). - Full FHN / transfer / integrator / processing / LCA / mdf suites pass in Python and compiled. ## Notes - `OrnsteinUhlenbeckIntegrator` has a similar shape inconsistency (plus extra quirks and no existing compiled coverage). It is intentionally left out of this PR and tracked separately. - The construction-dependent FHN shape (`(3,1,1)` when the class, rather than an instance, is passed) is a separate pre-existing issue (the existing `xfail`) and is untouched here. 🤖 Generated with [Claude Code](https://claude.com/claude-code)
Updates the requirements on [scipy](https://github.com/scipy/scipy) to permit the latest version. - [Release notes](https://github.com/scipy/scipy/releases) - [Commits](scipy/scipy@v1.17.0...v1.18.0) --- updated-dependencies: - dependency-name: scipy dependency-version: 1.18.0 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Signed-off-by: Jan Vesely <jan.vesely@rutgers.edu>
Signed-off-by: Jan Vesely <jan.vesely@rutgers.edu>
Ignore generated files. Ignore rules that do not currently pass. Signed-off-by: Jan Vesely <jan.vesely@rutgers.edu>
Ignore line length check. Signed-off-by: Jan Vesely <jan.vesely@rutgers.edu>
Signed-off-by: Jan Vesely <jan.vesely@rutgers.edu>
… a line Signed-off-by: Jan Vesely <jan.vesely@rutgers.edu>
Signed-off-by: Jan Vesely <jan.vesely@rutgers.edu>
Signed-off-by: Jan Vesely <jan.vesely@rutgers.edu>
Signed-off-by: Jan Vesely <jan.vesely@rutgers.edu>
No longer supported (pytest-pydocstyle repository is archived). Use Ruff D* checks instead. Signed-off-by: Jan Vesely <jan.vesely@rutgers.edu>
Runs monthly or on dispatch. The dispatch ref will be used. If it is left on its default value (master), it will be set to devel.
pytest-pydocstyle is archived and no longer maintained.
Fixes: 536883e ("Remove pydocstyle") Signed-off-by: Jan Vesely <jan.vesely@rutgers.edu>
Updates the requirements on [pytest](https://github.com/pytest-dev/pytest) to permit the latest version. - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst) - [Commits](pytest-dev/pytest@9.0.0...9.1.1) --- updated-dependencies: - dependency-name: pytest dependency-version: 9.1.1 dependency-type: direct:development ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Updates the requirements on [pillow](https://github.com/python-pillow/Pillow) to permit the latest version. - [Release notes](https://github.com/python-pillow/Pillow/releases) - [Changelog](https://github.com/python-pillow/Pillow/blob/main/CHANGES.rst) - [Commits](python-pillow/Pillow@12.2.0...12.3.0) --- updated-dependencies: - dependency-name: pillow dependency-version: 12.3.0 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Updates the requirements on [llvmlite](https://github.com/numba/llvmlite) to permit the latest version. - [Release notes](https://github.com/numba/llvmlite/releases) - [Commits](numba/llvmlite@v0.47.0...v0.48.0) --- updated-dependencies: - dependency-name: llvmlite dependency-version: 0.48.0 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
UserDefinedFunction is allowed in the check following the crash
Updates the requirements on [grpcio](https://github.com/grpc/grpc) to permit the latest version. - [Release notes](https://github.com/grpc/grpc/releases) - [Commits](grpc/grpc@v1.81.0...v1.82.1) --- updated-dependencies: - dependency-name: grpcio dependency-version: 1.82.1 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
…3.0,<2.14.0 (#3597) Updates the requirements on [pytorch](https://github.com/pytorch/pytorch) to permit the latest version. - [Release notes](https://github.com/pytorch/pytorch/releases/tag/v2.13.1) - [Commits](pytorch/pytorch@v2.12.0...v2.13.1) Signed-off-by: Jan Vesely <jan.vesely@rutgers.edu>
![github-advanced-security[bot]](https://avatars.githubusercontent.com/in/57789?s=60&v=4){kind=small}
| 'concatenate_queries': False, | ||
| 'enable_learning': True, | ||
| 'softmax_temperature': 0.1, | ||
| 'softmax_threshold': 1e-5, |
| IDENTITY_MATRIX, INPUT_PORT, MAPPING_PROJECTION, MATRIX, OUTPUT_PORT, VALUE) | ||
| from psyneulink.core.globals.log import ContextFlags | ||
| from psyneulink.core.globals.parameters import FunctionParameter, Parameter, check_user_specified, copy_parameter_value | ||
| from psyneulink.core.globals.parameters import FunctionParameter, Parameter, SharedParameter, check_user_specified, copy_parameter_value |
| # defer initialization until they are added | ||
| elif agent_rep.componentCategory=='Composition': | ||
| from psyneulink.core.compositions.composition import NodeRole | ||
| from psyneulink.core.compositions.noderoles import NodeRole |
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| # if isinstance(scale, numbers.Number): | ||
| # # scalar scale | ||
| # product = combination * scale | ||
| # else: | ||
| # # Hadamard scale | ||
| # product = np.prod([combination, scale], axis=0) | ||
| # | ||
| # if isinstance(offset, numbers.Number): | ||
| # # scalar offset | ||
| # result = product + offset | ||
| # else: | ||
| # # Hadamard offset | ||
| # result = np.sum([product, offset], axis=0) |
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| # elif loss == Loss.MSE: | ||
| # self.loss_function = Distance(metric=EUCLIDEAN, normalize=normalize) | ||
| # elif loss == Loss.CROSS_ENTROPY: | ||
| # self.loss_function = Distance(metric=CROSS_ENTROPY, normalize=normalize) |
| # to prevent immediate NaN propagation due to zero inputs. | ||
| GRU_INITIAL_STATE = np.random.uniform(low=-0.01, high=0.01, size=HIDDEN_DIMENSION) | ||
| try: gru_hidden_node.parameters.initial_value.set(GRU_INITIAL_STATE) | ||
| except Exception: pass |
| import numpy as np | ||
| import torch | ||
| import torch.nn as nn | ||
| import torch.nn.functional as F |
| import psyneulink as pnl | ||
| import numpy as np | ||
| import torch | ||
| import torch.nn as nn |
| @@ -0,0 +1,221 @@ | |||
| import psyneulink as pnl | |||
| import numpy as np | |||
| import torch | |||
|
|
||
| assert 0 <= integration_rate <= 1, \ | ||
| f"integrator_retrieval_weight must be a number from 0 to 1" | ||
| enable_learning = learning_rate > 0 |
|
This PR causes the following changes to the html docs (ubuntu-latest-3.11): See CI logs for the full diff. |
kmantel
self-requested a review
July 17, 2026 07:02
kmantel
approved these changes
Jul 17, 2026
|
coverage: 83.925% (-0.7%) from 84.591% — devel into master |
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