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CLP tutorial 1 small patch#773

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PhilippPlank merged 40 commits intolava-nc:mainfrom
elvinhajizada:clp_tutorial_01_patch
Sep 21, 2023
Merged

CLP tutorial 1 small patch#773
PhilippPlank merged 40 commits intolava-nc:mainfrom
elvinhajizada:clp_tutorial_01_patch

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Issue Number:

Objective of pull request:
A small patch to fix few minor issues with the CLP tutorial 1.

Pull request checklist

Your PR fulfills the following requirements:

  • Issue created that explains the change and why it's needed
  • Tests are part of the PR (for bug fixes / features)
  • Docs reviewed and added / updated if needed (for bug fixes / features)
  • PR conforms to Coding Conventions
  • PR applys BSD 3-clause or LGPL2.1+ Licenses to all code files
  • Lint (flakeheaven lint src/lava tests/) and (bandit -r src/lava/.) pass locally
  • Build tests (pytest) passes locally

Pull request type

Please check your PR type:

  • Bugfix
  • Feature
  • Code style update (formatting, renaming)
  • Refactoring (no functional changes, no api changes)
  • Build related changes
  • Documentation changes
  • Other (please describe):

What is the current behavior?

  • The first cell is a leftover from development
  • The last figure is partially wrong
  • One or two spelling mistakes

What is the new behavior?

  • All the above issues are fixed

Does this introduce a breaking change?

  • Yes
  • No

Supplemental information

elvinhajizada and others added 30 commits May 30, 2023 22:44
This reverts commit bde4fa9.
@elvinhajizada elvinhajizada added the 1-bug Something isn't working label Aug 14, 2023
@elvinhajizada elvinhajizada self-assigned this Aug 14, 2023
@PhilippPlank PhilippPlank merged commit 1c8f799 into lava-nc:main Sep 21, 2023
@elvinhajizada elvinhajizada deleted the clp_tutorial_01_patch branch September 21, 2023 12:00
epaxon pushed a commit that referenced this pull request Oct 25, 2023
* CLP initial commit: PrototypeLIF, NoveltyDetector, Readout procs/tests

* small linting fix

* Novelty detector upgraded to target next neuron; codacy errors fixed

* integration test; small fixes

* removed duplicate code in prototypeLIF process; linting fixes

* linting fixes

* Linting and codacy fixes

* remove duplicate test; some more codacy fixes

* PrototypeLIF spikes when it recieves a 3rd factor input

* a test for PrototypeLIF output spike after 3rd factor input

* Allocation & prototype id tracking is abstracted away from
NoveltyDetector

* Allocator process; Readout proc sends allocation trigger if error

* introduce learning rate Var in PrototypeLIF

* updated integration tests; full system test included

* Linting fixes

* Another small lintint fix

* PrototypeLIF hard reset capability to enable faster temporal  WTA

* allocation mechanism changed; proc interfaces changes; dense conns
added; lr var removed

* small linting fix

* small codacy fix

* prints removed, spelling mistakes fixed

* ignoring one check in an integration test

* Revert "small linting fix"

This reverts commit bde4fa9.

* Fix linting in test_models.py

* Test fix in utils.py

* Fix test of bug fix in utils.py

* Fix utils.py

* Implemented individual threadsafe random call

Signed-off-by: bamsumit <[email protected]>

* fix figures, removed redundant cell

---------

Signed-off-by: bamsumit <[email protected]>
Co-authored-by: PhilippPlank <[email protected]>
Co-authored-by: Marcus G K Williams <[email protected]>
Co-authored-by: bamsumit <[email protected]>
epaxon added a commit that referenced this pull request Jun 25, 2024
* prod neuron

* trying to get prod neuron to work...

* trying to get prod neuron cpu to work...

* prod neuron process cpu backend working with unit test

* remove init file from prod_neuron

* gradedvec process and test

* working on norm vec

* fixed prod neuron license headers

* invsqrt model and tests, reconfigured to process and models

* normvecdelay and tests, timing weirdness with normvecdelay

* test for second channel of norm vec

* renamed to prodneuron.

* fixing some linting errors

* cleanup

* frameworks and networks added to lava-nc

* adding some docstring, fixing unused imports

* Fix partition parse bug for internal vLab (#741)

* Adding deprecated lava.utils.system.

* Update system.py

* Update system.py

* Bugfix for missing fields in sinfo.

---------

Co-authored-by: PhilippPlank <[email protected]>

* Add linting tutorials folder (#742)

* serialization first try

* first try

* serialization implementation + unittests

* fix linting

* fix bandit

* fix unittest

* fix codacy

* added tutorial

* Update tutorial11_serialization.ipynb

* added notebook to unit tests

* Fixed broken link in tutorial.

* fix linting

* add tutorials folder to CI linting check

* Update ci.yml

* fix bug

---------

Co-authored-by: Mathis Richter <[email protected]>

* Iterator callback fx signature fix (#743)

* update refport unittest to always wait when it writes to port for consistent behavior

Signed-off-by: bamsumit <[email protected]>

* Removed pyproject changes

Signed-off-by: bamsumit <[email protected]>

* Fix to convolution tests. Fixed imcompatible mnist_pretrained for old python versions.

Signed-off-by: bamsumit <[email protected]>

* Missing moudle parent fix

Signed-off-by: bamsumit <[email protected]>

* Added ConvVarModel

* Added iterable callback function

Signed-off-by: bamsumit <[email protected]>

* Fix codacy issues in callback_fx.py

* Fix linting in callback_fx.py

* Fix codacy sig issue in callback_fx.py

---------

Signed-off-by: bamsumit <[email protected]>
Co-authored-by: Joyesh Mishra <[email protected]>
Co-authored-by: Marcus G K Williams <[email protected]>

* Bugfix to pass the args by keyword (#744)

* CLP Tutorial 01 Only (#746)

* CLP initial commit: PrototypeLIF, NoveltyDetector, Readout procs/tests

* small linting fix

* Novelty detector upgraded to target next neuron; codacy errors fixed

* integration test; small fixes

* removed duplicate code in prototypeLIF process; linting fixes

* linting fixes

* Linting and codacy fixes

* remove duplicate test; some more codacy fixes

* clp tutorial01 v1

* PrototypeLIF spikes when it recieves a 3rd factor input

* a test for PrototypeLIF output spike after 3rd factor input

* clp tutorial01 ready to be roughly finished

* linting, license and utils fixes

* CLP on COIL-100, extracted features from 42 objects, tutorial01 fixes

* Allocation & prototype id tracking is abstracted away from
NoveltyDetector

* Allocator process; Readout proc sends allocation trigger if error

* introduce learning rate Var in PrototypeLIF

* updated integration tests; full system test included

* Linting fixes

* Another small lintint fix

* clp tutorial 2, 20 class experiments (Coil-100)

* PrototypeLIF hard reset capability to enable faster temporal  WTA

* allocation mechanism changed; proc interfaces changes; dense conns
added; lr var removed

* small linting fix

* small codacy fix

* prints removed, spelling mistakes fixed

* ignoring one check in an integration test

* Revert "small linting fix"

This reverts commit bde4fa9.

* CLP tutorial 1 is finalized

* Fix linting in test_models.py

* Test fix in utils.py

* Fix test of bug fix in utils.py

* Fix utils.py

* Implemented individual threadsafe random call

Signed-off-by: bamsumit <[email protected]>

* tutorial 2 use new abstracted CLP class

* CLP tutorial 2: unsupervised and supervised experiments are seperated

* addressed reviewer's requests, added tests, removed pics etc

* Update clp.py

fix linting

* Update tutorial01_one-shot_learning_with_novelty_detection.ipynb

* Update tutorial02_clp_on_coil100.ipynb

* Update tutorial01_one-shot_learning_with_novelty_detection.ipynb

* Update tutorial02_clp_on_coil100.ipynb

* Removed sklearn dependency. Now np data gen.

* rm COIL tutorial, dataset, tests from branch

---------

Signed-off-by: bamsumit <[email protected]>
Co-authored-by: Elvin Hajizada <[email protected]>
Co-authored-by: PhilippPlank <[email protected]>
Co-authored-by: Marcus G K Williams <[email protected]>
Co-authored-by: bamsumit <[email protected]>

* Update release job, add pypi upload, github release creation (#737)

* Add pypi upload, github release creation in cd.yml

* Set version to 0.8.0.dev0

* Add readme to pyproject.toml

* use v1.3 of composite action

* Test run of release creation/pypi pub in cd.yml

* Run tests from py 3.10 in cd.yml

* Fix export of output vars in cd.yml

---------

Co-authored-by: PhilippPlank <[email protected]>

* Update release job, pypi auth

Signed-off-by: Marcus G K Williams <Marcus G K Williams [email protected]>

* Use github pypi auth in release job (#747)

* Update release job, pypi auth

Signed-off-by: Marcus G K Williams <Marcus G K Williams [email protected]>

* Add id-token to cd.yml

---------

Signed-off-by: Marcus G K Williams <Marcus G K Williams [email protected]>
Co-authored-by: Marcus G K Williams <Marcus G K Williams [email protected]>

* Release 0.8.0

Signed-off-by: Marcus G K Williams <Marcus G K Williams [email protected]>

* Fix conv python model to send() before recv() (#751)

Co-authored-by: Gavin Parpart <[email protected]>

* Adds support for Monitor a Port to observe if it is blocked (#755)

* Adds support for Monitor a Port to observe if it is blocked

* Fix lint issues

* Redesigned Watchdog to use Multiprocessing Manager; Invoke only 2 Event Monitors and use 2 queues for watching events; Configs are piped in via compiler now

* Incorporate Codacy Suggestions

* Fix lint comments

* Fix failing unit tests to add the watchdog builder

* Code review comments

* Set version to dev0 in pyproject.toml

* Update README.md

Updated version in install instructions.

* Update README.md (#758)

Updated the installation branch to the most recent version.

Co-authored-by: PhilippPlank <[email protected]>

* Fix DelayDense buffer issue (#767)

* update refport unittest to always wait when it writes to port for consistent behavior

Signed-off-by: bamsumit <[email protected]>

* Removed pyproject changes

Signed-off-by: bamsumit <[email protected]>

* Fix to convolution tests. Fixed imcompatible mnist_pretrained for old python versions.

Signed-off-by: bamsumit <[email protected]>

* Missing moudle parent fix

Signed-off-by: bamsumit <[email protected]>

* Added ConvVarModel

* Added iterable callback function

Signed-off-by: bamsumit <[email protected]>

* Fix codacy issues in callback_fx.py

* Fix linting in callback_fx.py

* Fix codacy sig issue in callback_fx.py

* Bugfix to pass the args by keyword

* Delay Dense PyModel fix

Signed-off-by: bamsumit <[email protected]>

* Fixed unittests

Signed-off-by: bamsumit <[email protected]>

* Fixed sparse delay

Signed-off-by: bamsumit <[email protected]>

---------

Signed-off-by: bamsumit <[email protected]>
Co-authored-by: Joyesh Mishra <[email protected]>
Co-authored-by: Marcus G K Williams <[email protected]>

* Allow np.array as input weights for Sparse (#772)

* ndarray as input weights for Sparse

* docs

* codacy

* remove implementation details from docstring and from tests

* move tests to corresponding classes

* put weight casting into extra method

* Removed unused import

---------

Co-authored-by: Mathis Richter <[email protected]>

* Bump tornado from 6.3.2 to 6.3.3 (#778)

Bumps [tornado](https://github.com/tornadoweb/tornado) from 6.3.2 to 6.3.3.
- [Changelog](https://github.com/tornadoweb/tornado/blob/master/docs/releases.rst)
- [Commits](tornadoweb/tornado@v6.3.2...v6.3.3)

---
updated-dependencies:
- dependency-name: tornado
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump cryptography from 41.0.2 to 41.0.3 (#779)

Bumps [cryptography](https://github.com/pyca/cryptography) from 41.0.2 to 41.0.3.
- [Changelog](https://github.com/pyca/cryptography/blob/main/CHANGELOG.rst)
- [Commits](pyca/cryptography@41.0.2...41.0.3)

---
updated-dependencies:
- dependency-name: cryptography
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Mathis Richter <[email protected]>

* small docstring, typing and other formatting changes

* Update README.md (#758)

Updated the installation branch to the most recent version.

Co-authored-by: PhilippPlank <[email protected]>

* small docstring, typing and other formatting changes

* doc strings for graded vec

* Bump gitpython from 3.1.32 to 3.1.35 (#785)

Bumps [gitpython](https://github.com/gitpython-developers/GitPython) from 3.1.32 to 3.1.35.
- [Release notes](https://github.com/gitpython-developers/GitPython/releases)
- [Changelog](https://github.com/gitpython-developers/GitPython/blob/main/CHANGES)
- [Commits](gitpython-developers/GitPython@3.1.32...3.1.35)

---
updated-dependencies:
- dependency-name: gitpython
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* fixing merge conflicts on prodneuron

* Merge Spike IO (#786)

* Made changes to channel builder for SpikeIO

* Added ChannelStub to configure channels

* Added NcSpikeIOVarModel

* Refined the NcSpikeIOVarModel

* Add interface_type and populate it in SpikeIOVarModel

* Add Interface Type

* Test PyNcChannel for Dense and Sparse Data using Unix Message Queues

* Faster encoding for sparse csp_port.send

* Added msg_queue_id to NcSpikeIOVarModel

* Added defaults for ByteEncoder

* Add advance_io API to PyOutPort

* Rename and refactor ConnectionConfig

* Only create channels for ChannelBuilderPyNc; Ignore ChannelBuilderNx

* Added spike_io_port to connection config and var model

* Integrate lower C level code, fix Lava bugs

* Fix merge

* Add enum for spike io mode and add it to ConnectionConfig and SpikeIO Var Model

* Fix indices dtype in sparse send to int32

* Add advance_time API to PyLoihiProcessModel

* Initial commit for spikeio output mode

* Rename to advance_to_time_step API

* Switch to TIME_COMPARE mode as default

* Commit for Spike Block Output Mode

* Move the axon allocation to 2 instead of 1 for output side

* Create a new config for watchdog and print warning; Set PyProcCompiler SpikeCounter Offset to None when object gets deleted

* Expose Mac Address, Num Input Buckets and Use Ethernet Interface from ConnectionConfig

* Fix lint specific errors

* fix codacy errors

* Fix an issue with length of connection_config list

* Fix unit tests

---------

Co-authored-by: yashward <[email protected]>
Co-authored-by: Julia <[email protected]>

* CLP tutorial 1 small patch (#773)

* CLP initial commit: PrototypeLIF, NoveltyDetector, Readout procs/tests

* small linting fix

* Novelty detector upgraded to target next neuron; codacy errors fixed

* integration test; small fixes

* removed duplicate code in prototypeLIF process; linting fixes

* linting fixes

* Linting and codacy fixes

* remove duplicate test; some more codacy fixes

* PrototypeLIF spikes when it recieves a 3rd factor input

* a test for PrototypeLIF output spike after 3rd factor input

* Allocation & prototype id tracking is abstracted away from
NoveltyDetector

* Allocator process; Readout proc sends allocation trigger if error

* introduce learning rate Var in PrototypeLIF

* updated integration tests; full system test included

* Linting fixes

* Another small lintint fix

* PrototypeLIF hard reset capability to enable faster temporal  WTA

* allocation mechanism changed; proc interfaces changes; dense conns
added; lr var removed

* small linting fix

* small codacy fix

* prints removed, spelling mistakes fixed

* ignoring one check in an integration test

* Revert "small linting fix"

This reverts commit bde4fa9.

* Fix linting in test_models.py

* Test fix in utils.py

* Fix test of bug fix in utils.py

* Fix utils.py

* Implemented individual threadsafe random call

Signed-off-by: bamsumit <[email protected]>

* fix figures, removed redundant cell

---------

Signed-off-by: bamsumit <[email protected]>
Co-authored-by: PhilippPlank <[email protected]>
Co-authored-by: Marcus G K Williams <[email protected]>
Co-authored-by: bamsumit <[email protected]>

* CLP Tutorial 02: COIL-100 (#721)

* CLP initial commit: PrototypeLIF, NoveltyDetector, Readout procs/tests

* small linting fix

* Novelty detector upgraded to target next neuron; codacy errors fixed

* integration test; small fixes

* removed duplicate code in prototypeLIF process; linting fixes

* linting fixes

* Linting and codacy fixes

* remove duplicate test; some more codacy fixes

* clp tutorial01 v1

* PrototypeLIF spikes when it recieves a 3rd factor input

* a test for PrototypeLIF output spike after 3rd factor input

* clp tutorial01 ready to be roughly finished

* linting, license and utils fixes

* CLP on COIL-100, extracted features from 42 objects, tutorial01 fixes

* Allocation & prototype id tracking is abstracted away from
NoveltyDetector

* Allocator process; Readout proc sends allocation trigger if error

* introduce learning rate Var in PrototypeLIF

* updated integration tests; full system test included

* Linting fixes

* Another small lintint fix

* clp tutorial 2, 20 class experiments (Coil-100)

* PrototypeLIF hard reset capability to enable faster temporal  WTA

* allocation mechanism changed; proc interfaces changes; dense conns
added; lr var removed

* small linting fix

* small codacy fix

* prints removed, spelling mistakes fixed

* ignoring one check in an integration test

* Revert "small linting fix"

This reverts commit bde4fa9.

* CLP tutorial 1 is finalized

* Fix linting in test_models.py

* Test fix in utils.py

* Fix test of bug fix in utils.py

* Fix utils.py

* Implemented individual threadsafe random call

Signed-off-by: bamsumit <[email protected]>

* tutorial 2 use new abstracted CLP class

* CLP tutorial 2: unsupervised and supervised experiments are seperated

* addressed reviewer's requests, added tests, removed pics etc

* Update clp.py

fix linting

* Update tutorial01_one-shot_learning_with_novelty_detection.ipynb

* Update tutorial02_clp_on_coil100.ipynb

* Update tutorial01_one-shot_learning_with_novelty_detection.ipynb

* Update tutorial02_clp_on_coil100.ipynb

* CLP class and experiments improved; pytorch dependency removed;
feature extraction added

* Allocator accepts arbitrary initial index as param

* New experiments; improved CLP class; continuous experimentation; new
features for COIL-100; toch as optional dependency

* linting fixes

* Temporarily skipping CLP tutorials test till sk-learn is added

* scikit-learn added to poetry; tutorial tst is re-enabled

---------

Signed-off-by: bamsumit <[email protected]>
Co-authored-by: PhilippPlank <[email protected]>
Co-authored-by: Marcus G K Williams <[email protected]>
Co-authored-by: bamsumit <[email protected]>

* Bump cryptography from 41.0.3 to 41.0.4 (#790)

Bumps [cryptography](https://github.com/pyca/cryptography) from 41.0.3 to 41.0.4.
- [Changelog](https://github.com/pyca/cryptography/blob/main/CHANGELOG.rst)
- [Commits](pyca/cryptography@41.0.3...41.0.4)

---
updated-dependencies:
- dependency-name: cryptography
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Generalize int shape check in injector and extractor to take numpy ints (#792)

* update refport unittest to always wait when it writes to port for consistent behavior

Signed-off-by: bamsumit <[email protected]>

* Removed pyproject changes

Signed-off-by: bamsumit <[email protected]>

* Fix to convolution tests. Fixed imcompatible mnist_pretrained for old python versions.

Signed-off-by: bamsumit <[email protected]>

* Missing moudle parent fix

Signed-off-by: bamsumit <[email protected]>

* Added ConvVarModel

* Added iterable callback function

Signed-off-by: bamsumit <[email protected]>

* Fix codacy issues in callback_fx.py

* Fix linting in callback_fx.py

* Fix codacy sig issue in callback_fx.py

* Bugfix to pass the args by keyword

* Delay Dense PyModel fix

Signed-off-by: bamsumit <[email protected]>

* Fixed unittests

Signed-off-by: bamsumit <[email protected]>

* Fixed sparse delay

Signed-off-by: bamsumit <[email protected]>

* IO modules fixes

Signed-off-by: bamsumit <[email protected]>

* IO modules fixes

Signed-off-by: bamsumit <[email protected]>

---------

Signed-off-by: bamsumit <[email protected]>
Co-authored-by: Joyesh Mishra <[email protected]>
Co-authored-by: Marcus G K Williams <[email protected]>

* Resfire (#787)

* resfire process and fixed process model

* changed vth->uth in RFZero. Added tests.

* removed unused imports

* unused imports, copyright statement.

* bsd license on resfire models.py

* Bump pillow from 10.0.0 to 10.0.1 (#794)

Bumps [pillow](https://github.com/python-pillow/Pillow) from 10.0.0 to 10.0.1.
- [Release notes](https://github.com/python-pillow/Pillow/releases)
- [Changelog](https://github.com/python-pillow/Pillow/blob/main/CHANGES.rst)
- [Commits](python-pillow/Pillow@10.0.0...10.0.1)

---
updated-dependencies:
- dependency-name: pillow
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: PhilippPlank <[email protected]>

* Bump urllib3 from 1.26.16 to 1.26.17 (#793)

Bumps [urllib3](https://github.com/urllib3/urllib3) from 1.26.16 to 1.26.17.
- [Release notes](https://github.com/urllib3/urllib3/releases)
- [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst)
- [Commits](urllib3/urllib3@1.26.16...1.26.17)

---
updated-dependencies:
- dependency-name: urllib3
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: PhilippPlank <[email protected]>

* mulitply for threshvec, fixes to frameworks imports, fixes for resfire network

* rename ThreshVec to GradedVec and fixes.

* lava VA tutorials.

* slight updates to lava_va tutorials and removed csr_matrix cast

* super needed, formatting, fixed test_network

* Automatically create identity connections when using lva to connect vectors

* NetworkList to keep track of + Networks. More flexibility in algebra syntax.

* Updated tutorial 1 to demo automatic vec2vec connections and better + overloading

* Updates to Tutorial01 that show automatic identity connections when connecting AlgebraicVectors and syntax.

* Comments, docstrings, typing clean-up.

* changing embedded io import location, in case theres no lava-loihi.

* small codacy fixes. Test lava va tutorials.

* Cleanup comments on test_graded.py and test_tutorials-lva.py

---------

Signed-off-by: bamsumit <[email protected]>
Signed-off-by: Marcus G K Williams <Marcus G K Williams [email protected]>
Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: Tim Shea <[email protected]>
Co-authored-by: PhilippPlank <[email protected]>
Co-authored-by: Mathis Richter <[email protected]>
Co-authored-by: bamsumit <[email protected]>
Co-authored-by: Joyesh Mishra <[email protected]>
Co-authored-by: Marcus G K Williams <[email protected]>
Co-authored-by: Danielle Rager <[email protected]>
Co-authored-by: Elvin Hajizada <[email protected]>
Co-authored-by: Marcus G K Williams <Marcus G K Williams [email protected]>
Co-authored-by: Gavin Parpart <[email protected]>
Co-authored-by: Gavin Parpart <[email protected]>
Co-authored-by: Alexander Henkes <[email protected]>
Co-authored-by: Svea Marie Meyer <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: yashward <[email protected]>
Co-authored-by: Julia <[email protected]>
monkin77 pushed a commit to monkin77/thesis-lava that referenced this pull request Jul 12, 2024
* CLP initial commit: PrototypeLIF, NoveltyDetector, Readout procs/tests

* small linting fix

* Novelty detector upgraded to target next neuron; codacy errors fixed

* integration test; small fixes

* removed duplicate code in prototypeLIF process; linting fixes

* linting fixes

* Linting and codacy fixes

* remove duplicate test; some more codacy fixes

* PrototypeLIF spikes when it recieves a 3rd factor input

* a test for PrototypeLIF output spike after 3rd factor input

* Allocation & prototype id tracking is abstracted away from
NoveltyDetector

* Allocator process; Readout proc sends allocation trigger if error

* introduce learning rate Var in PrototypeLIF

* updated integration tests; full system test included

* Linting fixes

* Another small lintint fix

* PrototypeLIF hard reset capability to enable faster temporal  WTA

* allocation mechanism changed; proc interfaces changes; dense conns
added; lr var removed

* small linting fix

* small codacy fix

* prints removed, spelling mistakes fixed

* ignoring one check in an integration test

* Revert "small linting fix"

This reverts commit bde4fa9.

* Fix linting in test_models.py

* Test fix in utils.py

* Fix test of bug fix in utils.py

* Fix utils.py

* Implemented individual threadsafe random call

Signed-off-by: bamsumit <[email protected]>

* fix figures, removed redundant cell

---------

Signed-off-by: bamsumit <[email protected]>
Co-authored-by: PhilippPlank <[email protected]>
Co-authored-by: Marcus G K Williams <[email protected]>
Co-authored-by: bamsumit <[email protected]>
monkin77 pushed a commit to monkin77/thesis-lava that referenced this pull request Jul 12, 2024
* prod neuron

* trying to get prod neuron to work...

* trying to get prod neuron cpu to work...

* prod neuron process cpu backend working with unit test

* remove init file from prod_neuron

* gradedvec process and test

* working on norm vec

* fixed prod neuron license headers

* invsqrt model and tests, reconfigured to process and models

* normvecdelay and tests, timing weirdness with normvecdelay

* test for second channel of norm vec

* renamed to prodneuron.

* fixing some linting errors

* cleanup

* frameworks and networks added to lava-nc

* adding some docstring, fixing unused imports

* Fix partition parse bug for internal vLab (lava-nc#741)

* Adding deprecated lava.utils.system.

* Update system.py

* Update system.py

* Bugfix for missing fields in sinfo.

---------

Co-authored-by: PhilippPlank <[email protected]>

* Add linting tutorials folder (lava-nc#742)

* serialization first try

* first try

* serialization implementation + unittests

* fix linting

* fix bandit

* fix unittest

* fix codacy

* added tutorial

* Update tutorial11_serialization.ipynb

* added notebook to unit tests

* Fixed broken link in tutorial.

* fix linting

* add tutorials folder to CI linting check

* Update ci.yml

* fix bug

---------

Co-authored-by: Mathis Richter <[email protected]>

* Iterator callback fx signature fix (lava-nc#743)

* update refport unittest to always wait when it writes to port for consistent behavior

Signed-off-by: bamsumit <[email protected]>

* Removed pyproject changes

Signed-off-by: bamsumit <[email protected]>

* Fix to convolution tests. Fixed imcompatible mnist_pretrained for old python versions.

Signed-off-by: bamsumit <[email protected]>

* Missing moudle parent fix

Signed-off-by: bamsumit <[email protected]>

* Added ConvVarModel

* Added iterable callback function

Signed-off-by: bamsumit <[email protected]>

* Fix codacy issues in callback_fx.py

* Fix linting in callback_fx.py

* Fix codacy sig issue in callback_fx.py

---------

Signed-off-by: bamsumit <[email protected]>
Co-authored-by: Joyesh Mishra <[email protected]>
Co-authored-by: Marcus G K Williams <[email protected]>

* Bugfix to pass the args by keyword (lava-nc#744)

* CLP Tutorial 01 Only (lava-nc#746)

* CLP initial commit: PrototypeLIF, NoveltyDetector, Readout procs/tests

* small linting fix

* Novelty detector upgraded to target next neuron; codacy errors fixed

* integration test; small fixes

* removed duplicate code in prototypeLIF process; linting fixes

* linting fixes

* Linting and codacy fixes

* remove duplicate test; some more codacy fixes

* clp tutorial01 v1

* PrototypeLIF spikes when it recieves a 3rd factor input

* a test for PrototypeLIF output spike after 3rd factor input

* clp tutorial01 ready to be roughly finished

* linting, license and utils fixes

* CLP on COIL-100, extracted features from 42 objects, tutorial01 fixes

* Allocation & prototype id tracking is abstracted away from
NoveltyDetector

* Allocator process; Readout proc sends allocation trigger if error

* introduce learning rate Var in PrototypeLIF

* updated integration tests; full system test included

* Linting fixes

* Another small lintint fix

* clp tutorial 2, 20 class experiments (Coil-100)

* PrototypeLIF hard reset capability to enable faster temporal  WTA

* allocation mechanism changed; proc interfaces changes; dense conns
added; lr var removed

* small linting fix

* small codacy fix

* prints removed, spelling mistakes fixed

* ignoring one check in an integration test

* Revert "small linting fix"

This reverts commit bde4fa9.

* CLP tutorial 1 is finalized

* Fix linting in test_models.py

* Test fix in utils.py

* Fix test of bug fix in utils.py

* Fix utils.py

* Implemented individual threadsafe random call

Signed-off-by: bamsumit <[email protected]>

* tutorial 2 use new abstracted CLP class

* CLP tutorial 2: unsupervised and supervised experiments are seperated

* addressed reviewer's requests, added tests, removed pics etc

* Update clp.py

fix linting

* Update tutorial01_one-shot_learning_with_novelty_detection.ipynb

* Update tutorial02_clp_on_coil100.ipynb

* Update tutorial01_one-shot_learning_with_novelty_detection.ipynb

* Update tutorial02_clp_on_coil100.ipynb

* Removed sklearn dependency. Now np data gen.

* rm COIL tutorial, dataset, tests from branch

---------

Signed-off-by: bamsumit <[email protected]>
Co-authored-by: Elvin Hajizada <[email protected]>
Co-authored-by: PhilippPlank <[email protected]>
Co-authored-by: Marcus G K Williams <[email protected]>
Co-authored-by: bamsumit <[email protected]>

* Update release job, add pypi upload, github release creation (lava-nc#737)

* Add pypi upload, github release creation in cd.yml

* Set version to 0.8.0.dev0

* Add readme to pyproject.toml

* use v1.3 of composite action

* Test run of release creation/pypi pub in cd.yml

* Run tests from py 3.10 in cd.yml

* Fix export of output vars in cd.yml

---------

Co-authored-by: PhilippPlank <[email protected]>

* Update release job, pypi auth

Signed-off-by: Marcus G K Williams <Marcus G K Williams [email protected]>

* Use github pypi auth in release job (lava-nc#747)

* Update release job, pypi auth

Signed-off-by: Marcus G K Williams <Marcus G K Williams [email protected]>

* Add id-token to cd.yml

---------

Signed-off-by: Marcus G K Williams <Marcus G K Williams [email protected]>
Co-authored-by: Marcus G K Williams <Marcus G K Williams [email protected]>

* Release 0.8.0

Signed-off-by: Marcus G K Williams <Marcus G K Williams [email protected]>

* Fix conv python model to send() before recv() (lava-nc#751)

Co-authored-by: Gavin Parpart <[email protected]>

* Adds support for Monitor a Port to observe if it is blocked (lava-nc#755)

* Adds support for Monitor a Port to observe if it is blocked

* Fix lint issues

* Redesigned Watchdog to use Multiprocessing Manager; Invoke only 2 Event Monitors and use 2 queues for watching events; Configs are piped in via compiler now

* Incorporate Codacy Suggestions

* Fix lint comments

* Fix failing unit tests to add the watchdog builder

* Code review comments

* Set version to dev0 in pyproject.toml

* Update README.md

Updated version in install instructions.

* Update README.md (lava-nc#758)

Updated the installation branch to the most recent version.

Co-authored-by: PhilippPlank <[email protected]>

* Fix DelayDense buffer issue (lava-nc#767)

* update refport unittest to always wait when it writes to port for consistent behavior

Signed-off-by: bamsumit <[email protected]>

* Removed pyproject changes

Signed-off-by: bamsumit <[email protected]>

* Fix to convolution tests. Fixed imcompatible mnist_pretrained for old python versions.

Signed-off-by: bamsumit <[email protected]>

* Missing moudle parent fix

Signed-off-by: bamsumit <[email protected]>

* Added ConvVarModel

* Added iterable callback function

Signed-off-by: bamsumit <[email protected]>

* Fix codacy issues in callback_fx.py

* Fix linting in callback_fx.py

* Fix codacy sig issue in callback_fx.py

* Bugfix to pass the args by keyword

* Delay Dense PyModel fix

Signed-off-by: bamsumit <[email protected]>

* Fixed unittests

Signed-off-by: bamsumit <[email protected]>

* Fixed sparse delay

Signed-off-by: bamsumit <[email protected]>

---------

Signed-off-by: bamsumit <[email protected]>
Co-authored-by: Joyesh Mishra <[email protected]>
Co-authored-by: Marcus G K Williams <[email protected]>

* Allow np.array as input weights for Sparse (lava-nc#772)

* ndarray as input weights for Sparse

* docs

* codacy

* remove implementation details from docstring and from tests

* move tests to corresponding classes

* put weight casting into extra method

* Removed unused import

---------

Co-authored-by: Mathis Richter <[email protected]>

* Bump tornado from 6.3.2 to 6.3.3 (lava-nc#778)

Bumps [tornado](https://github.com/tornadoweb/tornado) from 6.3.2 to 6.3.3.
- [Changelog](https://github.com/tornadoweb/tornado/blob/master/docs/releases.rst)
- [Commits](tornadoweb/tornado@v6.3.2...v6.3.3)

---
updated-dependencies:
- dependency-name: tornado
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump cryptography from 41.0.2 to 41.0.3 (lava-nc#779)

Bumps [cryptography](https://github.com/pyca/cryptography) from 41.0.2 to 41.0.3.
- [Changelog](https://github.com/pyca/cryptography/blob/main/CHANGELOG.rst)
- [Commits](pyca/cryptography@41.0.2...41.0.3)

---
updated-dependencies:
- dependency-name: cryptography
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Mathis Richter <[email protected]>

* small docstring, typing and other formatting changes

* Update README.md (lava-nc#758)

Updated the installation branch to the most recent version.

Co-authored-by: PhilippPlank <[email protected]>

* small docstring, typing and other formatting changes

* doc strings for graded vec

* Bump gitpython from 3.1.32 to 3.1.35 (lava-nc#785)

Bumps [gitpython](https://github.com/gitpython-developers/GitPython) from 3.1.32 to 3.1.35.
- [Release notes](https://github.com/gitpython-developers/GitPython/releases)
- [Changelog](https://github.com/gitpython-developers/GitPython/blob/main/CHANGES)
- [Commits](gitpython-developers/GitPython@3.1.32...3.1.35)

---
updated-dependencies:
- dependency-name: gitpython
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* fixing merge conflicts on prodneuron

* Merge Spike IO (lava-nc#786)

* Made changes to channel builder for SpikeIO

* Added ChannelStub to configure channels

* Added NcSpikeIOVarModel

* Refined the NcSpikeIOVarModel

* Add interface_type and populate it in SpikeIOVarModel

* Add Interface Type

* Test PyNcChannel for Dense and Sparse Data using Unix Message Queues

* Faster encoding for sparse csp_port.send

* Added msg_queue_id to NcSpikeIOVarModel

* Added defaults for ByteEncoder

* Add advance_io API to PyOutPort

* Rename and refactor ConnectionConfig

* Only create channels for ChannelBuilderPyNc; Ignore ChannelBuilderNx

* Added spike_io_port to connection config and var model

* Integrate lower C level code, fix Lava bugs

* Fix merge

* Add enum for spike io mode and add it to ConnectionConfig and SpikeIO Var Model

* Fix indices dtype in sparse send to int32

* Add advance_time API to PyLoihiProcessModel

* Initial commit for spikeio output mode

* Rename to advance_to_time_step API

* Switch to TIME_COMPARE mode as default

* Commit for Spike Block Output Mode

* Move the axon allocation to 2 instead of 1 for output side

* Create a new config for watchdog and print warning; Set PyProcCompiler SpikeCounter Offset to None when object gets deleted

* Expose Mac Address, Num Input Buckets and Use Ethernet Interface from ConnectionConfig

* Fix lint specific errors

* fix codacy errors

* Fix an issue with length of connection_config list

* Fix unit tests

---------

Co-authored-by: yashward <[email protected]>
Co-authored-by: Julia <[email protected]>

* CLP tutorial 1 small patch (lava-nc#773)

* CLP initial commit: PrototypeLIF, NoveltyDetector, Readout procs/tests

* small linting fix

* Novelty detector upgraded to target next neuron; codacy errors fixed

* integration test; small fixes

* removed duplicate code in prototypeLIF process; linting fixes

* linting fixes

* Linting and codacy fixes

* remove duplicate test; some more codacy fixes

* PrototypeLIF spikes when it recieves a 3rd factor input

* a test for PrototypeLIF output spike after 3rd factor input

* Allocation & prototype id tracking is abstracted away from
NoveltyDetector

* Allocator process; Readout proc sends allocation trigger if error

* introduce learning rate Var in PrototypeLIF

* updated integration tests; full system test included

* Linting fixes

* Another small lintint fix

* PrototypeLIF hard reset capability to enable faster temporal  WTA

* allocation mechanism changed; proc interfaces changes; dense conns
added; lr var removed

* small linting fix

* small codacy fix

* prints removed, spelling mistakes fixed

* ignoring one check in an integration test

* Revert "small linting fix"

This reverts commit bde4fa9.

* Fix linting in test_models.py

* Test fix in utils.py

* Fix test of bug fix in utils.py

* Fix utils.py

* Implemented individual threadsafe random call

Signed-off-by: bamsumit <[email protected]>

* fix figures, removed redundant cell

---------

Signed-off-by: bamsumit <[email protected]>
Co-authored-by: PhilippPlank <[email protected]>
Co-authored-by: Marcus G K Williams <[email protected]>
Co-authored-by: bamsumit <[email protected]>

* CLP Tutorial 02: COIL-100 (lava-nc#721)

* CLP initial commit: PrototypeLIF, NoveltyDetector, Readout procs/tests

* small linting fix

* Novelty detector upgraded to target next neuron; codacy errors fixed

* integration test; small fixes

* removed duplicate code in prototypeLIF process; linting fixes

* linting fixes

* Linting and codacy fixes

* remove duplicate test; some more codacy fixes

* clp tutorial01 v1

* PrototypeLIF spikes when it recieves a 3rd factor input

* a test for PrototypeLIF output spike after 3rd factor input

* clp tutorial01 ready to be roughly finished

* linting, license and utils fixes

* CLP on COIL-100, extracted features from 42 objects, tutorial01 fixes

* Allocation & prototype id tracking is abstracted away from
NoveltyDetector

* Allocator process; Readout proc sends allocation trigger if error

* introduce learning rate Var in PrototypeLIF

* updated integration tests; full system test included

* Linting fixes

* Another small lintint fix

* clp tutorial 2, 20 class experiments (Coil-100)

* PrototypeLIF hard reset capability to enable faster temporal  WTA

* allocation mechanism changed; proc interfaces changes; dense conns
added; lr var removed

* small linting fix

* small codacy fix

* prints removed, spelling mistakes fixed

* ignoring one check in an integration test

* Revert "small linting fix"

This reverts commit bde4fa9.

* CLP tutorial 1 is finalized

* Fix linting in test_models.py

* Test fix in utils.py

* Fix test of bug fix in utils.py

* Fix utils.py

* Implemented individual threadsafe random call

Signed-off-by: bamsumit <[email protected]>

* tutorial 2 use new abstracted CLP class

* CLP tutorial 2: unsupervised and supervised experiments are seperated

* addressed reviewer's requests, added tests, removed pics etc

* Update clp.py

fix linting

* Update tutorial01_one-shot_learning_with_novelty_detection.ipynb

* Update tutorial02_clp_on_coil100.ipynb

* Update tutorial01_one-shot_learning_with_novelty_detection.ipynb

* Update tutorial02_clp_on_coil100.ipynb

* CLP class and experiments improved; pytorch dependency removed;
feature extraction added

* Allocator accepts arbitrary initial index as param

* New experiments; improved CLP class; continuous experimentation; new
features for COIL-100; toch as optional dependency

* linting fixes

* Temporarily skipping CLP tutorials test till sk-learn is added

* scikit-learn added to poetry; tutorial tst is re-enabled

---------

Signed-off-by: bamsumit <[email protected]>
Co-authored-by: PhilippPlank <[email protected]>
Co-authored-by: Marcus G K Williams <[email protected]>
Co-authored-by: bamsumit <[email protected]>

* Bump cryptography from 41.0.3 to 41.0.4 (lava-nc#790)

Bumps [cryptography](https://github.com/pyca/cryptography) from 41.0.3 to 41.0.4.
- [Changelog](https://github.com/pyca/cryptography/blob/main/CHANGELOG.rst)
- [Commits](pyca/cryptography@41.0.3...41.0.4)

---
updated-dependencies:
- dependency-name: cryptography
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Generalize int shape check in injector and extractor to take numpy ints (lava-nc#792)

* update refport unittest to always wait when it writes to port for consistent behavior

Signed-off-by: bamsumit <[email protected]>

* Removed pyproject changes

Signed-off-by: bamsumit <[email protected]>

* Fix to convolution tests. Fixed imcompatible mnist_pretrained for old python versions.

Signed-off-by: bamsumit <[email protected]>

* Missing moudle parent fix

Signed-off-by: bamsumit <[email protected]>

* Added ConvVarModel

* Added iterable callback function

Signed-off-by: bamsumit <[email protected]>

* Fix codacy issues in callback_fx.py

* Fix linting in callback_fx.py

* Fix codacy sig issue in callback_fx.py

* Bugfix to pass the args by keyword

* Delay Dense PyModel fix

Signed-off-by: bamsumit <[email protected]>

* Fixed unittests

Signed-off-by: bamsumit <[email protected]>

* Fixed sparse delay

Signed-off-by: bamsumit <[email protected]>

* IO modules fixes

Signed-off-by: bamsumit <[email protected]>

* IO modules fixes

Signed-off-by: bamsumit <[email protected]>

---------

Signed-off-by: bamsumit <[email protected]>
Co-authored-by: Joyesh Mishra <[email protected]>
Co-authored-by: Marcus G K Williams <[email protected]>

* Resfire (lava-nc#787)

* resfire process and fixed process model

* changed vth->uth in RFZero. Added tests.

* removed unused imports

* unused imports, copyright statement.

* bsd license on resfire models.py

* Bump pillow from 10.0.0 to 10.0.1 (lava-nc#794)

Bumps [pillow](https://github.com/python-pillow/Pillow) from 10.0.0 to 10.0.1.
- [Release notes](https://github.com/python-pillow/Pillow/releases)
- [Changelog](https://github.com/python-pillow/Pillow/blob/main/CHANGES.rst)
- [Commits](python-pillow/Pillow@10.0.0...10.0.1)

---
updated-dependencies:
- dependency-name: pillow
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: PhilippPlank <[email protected]>

* Bump urllib3 from 1.26.16 to 1.26.17 (lava-nc#793)

Bumps [urllib3](https://github.com/urllib3/urllib3) from 1.26.16 to 1.26.17.
- [Release notes](https://github.com/urllib3/urllib3/releases)
- [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst)
- [Commits](urllib3/urllib3@1.26.16...1.26.17)

---
updated-dependencies:
- dependency-name: urllib3
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: PhilippPlank <[email protected]>

* mulitply for threshvec, fixes to frameworks imports, fixes for resfire network

* rename ThreshVec to GradedVec and fixes.

* lava VA tutorials.

* slight updates to lava_va tutorials and removed csr_matrix cast

* super needed, formatting, fixed test_network

* Automatically create identity connections when using lva to connect vectors

* NetworkList to keep track of + Networks. More flexibility in algebra syntax.

* Updated tutorial 1 to demo automatic vec2vec connections and better + overloading

* Updates to Tutorial01 that show automatic identity connections when connecting AlgebraicVectors and syntax.

* Comments, docstrings, typing clean-up.

* changing embedded io import location, in case theres no lava-loihi.

* small codacy fixes. Test lava va tutorials.

* Cleanup comments on test_graded.py and test_tutorials-lva.py

---------

Signed-off-by: bamsumit <[email protected]>
Signed-off-by: Marcus G K Williams <Marcus G K Williams [email protected]>
Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: Tim Shea <[email protected]>
Co-authored-by: PhilippPlank <[email protected]>
Co-authored-by: Mathis Richter <[email protected]>
Co-authored-by: bamsumit <[email protected]>
Co-authored-by: Joyesh Mishra <[email protected]>
Co-authored-by: Marcus G K Williams <[email protected]>
Co-authored-by: Danielle Rager <[email protected]>
Co-authored-by: Elvin Hajizada <[email protected]>
Co-authored-by: Marcus G K Williams <Marcus G K Williams [email protected]>
Co-authored-by: Gavin Parpart <[email protected]>
Co-authored-by: Gavin Parpart <[email protected]>
Co-authored-by: Alexander Henkes <[email protected]>
Co-authored-by: Svea Marie Meyer <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: yashward <[email protected]>
Co-authored-by: Julia <[email protected]>
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