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v1.0.0 alpha #154

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Commits on Jun 10, 2024

  1. added learning for online variational filtering

    @dimarkov
    dimarkov committed Jun 10, 2024
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  2. optimized learning routines to minimize calls to tree_map

    @dimarkov
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  3. fix tests and passing of the results of the learning

    @dimarkov
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  4. fix update state transition

    @dimarkov
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  5. move task.py to jax/envs/env.py

    Tim Verbelen committed Jun 10, 2024
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  6. fix names

    @dimarkov
    dimarkov committed Jun 10, 2024
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  7. notebook for showcasing inference and learning using different methods

    @dimarkov
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  8. Merge pull request #133 from infer-actively/pymdp-move-PymdpEnv 

    move task.py to jax/envs/env.py
    @conorheins
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  9. add a pyproject toml

    @OzanCatalVerses
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  10. move task.py to jax/envs/env.py

    @conorheins
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  11. get a version that passes all tests

    @OzanCatalVerses
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  12. Merge pull request #134 from infer-actively/feature/pyproject-toml 

    Feature/pyproject toml
    @conorheins
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  13. added an example of A tensors and B tensors where smoothing should di… 

    …sambiguate hidden states in the past
    @conorheins
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  14. did first step of inference in the ovf example

    @conorheins
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  15. add a pyproject toml

    @OzanCatalVerses @conorheins
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  16. get a version that passes all tests

    @OzanCatalVerses @conorheins
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  17. add a pyproject toml

    @OzanCatalVerses @conorheins
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  18. get a version that passes all tests

    @OzanCatalVerses @conorheins
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  19. initial graph worlds version

    Tim Verbelen committed Jun 10, 2024
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Commits on Jun 11, 2024

  1. named distribution implementation 

    First past of implementation for named distribution for easy manipulation and inspection of discrete conditional probability distributions.
    @alec-tschantz
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  2. updated example

    @dimarkov
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  3. Merge branch 'full-ovf-with-example' into full-ovf-implementation

    @dimarkov
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  4. removed oudated markdown cell at the end of the smoothing example not… 

    …ebook
    @conorheins
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  5. update graph worlds env

    Tim Verbelen committed Jun 11, 2024
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  6. add a first version of model compilation

    @OzanCatalVerses
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  7. add missing s, add some basic tests

    @OzanCatalVerses
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  8. add unittest

    @OzanCatalVerses
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  9. rename compile to compile_model

    @OzanCatalVerses
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  10. added example notebook

    @alec-tschantz
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  11. add some documentation

    @OzanCatalVerses
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  12. api updates to jax/agent

    @alec-tschantz
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  13. Merge branch 'feature/distribution-api' of https://github.com/infer-a… 

    …ctively/pymdp into feature/distribution-api

# Conflicts:
#	examples/distribution_api.ipynb
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  14. add get_dependencies

    @OzanCatalVerses
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  15. clean up a bit

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  16. add dependency extraction to jax agent

    @alec-tschantz
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  17. acknowledge that the alphabet has an ordering

    @OzanCatalVerses
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  18. end to end test of agent API

    @alec-tschantz
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  19. forgot to push notebook

    @alec-tschantz
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  20. update random_B_matrix to handle complex action dependencies

    @ran-weii
    ran-weii committed Jun 11, 2024
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  21. change config naming to be more consistent

    @OzanCatalVerses
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  22. config naming changes

    @OzanCatalVerses
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  23. make the data argument optional 

    breaking change!!
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  24. updated agent api

    @alec-tschantz
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  25. updated notebook

    @alec-tschantz
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  26. updated init for agent

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  27. add utils to convert combinations to flattened index with test

    @ran-weii
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  28. updated example notebook

    @alec-tschantz
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  29. added complicated example

    @alec-tschantz
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  30. Merge branch 'feature/distribution-api' into feature/complex_act_depe… 

    …ndency
    @ran-weii
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  31. add rollout function and fix graph world env and demo notebook

    Tim Verbelen committed Jun 11, 2024
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  32. initial solution for flattening B action dims

    @ran-weii
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  33. move a copy of combination indexing utils to jax.utils

    @ran-weii
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  34. initial solution for multi action decoding

    @ran-weii
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  35. vectorize combination indexing and update tests

    @ran-weii
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  36. handle no action dependency in B tensor flattening, use vectorized mu… 

    …lti action encoding and decoding
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  37. commit complex_action_dependency notebook

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Commits on Jun 12, 2024

  1. add knapsack_demo notebook, planning not working

    @ran-weii
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  2. add function to construct flattend policies

    @ran-weii
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  3. commit working knapsack demo notebook

    @ran-weii
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  4. add some docstring

    Tim Verbelen committed Jun 12, 2024
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  5. add some more comments in the notebook

    Tim Verbelen committed Jun 12, 2024
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  6. smoothing demo notebook starting to work with sparse BCOO arrays from… 

    … jax.experimental.sparse
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  7. in pymdp/jax/inference.py, added version of joint_dist_factor (sub-… 

    …routine of `smoothing_ovf`) that dispatches on jnp.ndarrays and JAXSparse arrays (e.g., BCOO arrays)
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  8. add multimethod to the dependencies

    @OzanCatalVerses
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  9. Merge pull request #135 from infer-actively/feature/graph_env 

    Rollout function, graph world environment, demo notebook
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  10. named distribution implementation 

    First past of implementation for named distribution for easy manipulation and inspection of discrete conditional probability distributions.
    @alec-tschantz @conorheins
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  11. add a first version of model compilation

    @OzanCatalVerses @conorheins
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  12. add missing s, add some basic tests

    @OzanCatalVerses @conorheins
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  13. add unittest

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  14. rename compile to compile_model

    @OzanCatalVerses @conorheins
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  15. added example notebook

    @alec-tschantz @conorheins
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  16. api updates to jax/agent

    @alec-tschantz @conorheins
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  17. add some documentation

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  18. add get_dependencies

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  19. clean up a bit

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  20. add dependency extraction to jax agent

    @alec-tschantz @conorheins
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  21. acknowledge that the alphabet has an ordering

    @OzanCatalVerses @conorheins
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  22. end to end test of agent API

    @alec-tschantz @conorheins
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  23. forgot to push notebook

    @alec-tschantz @conorheins
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  24. change config naming to be more consistent

    @OzanCatalVerses @conorheins
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  25. config naming changes

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  26. make the data argument optional 

    breaking change!!
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  27. updated agent api

    @alec-tschantz @conorheins
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  28. updated notebook

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  29. updated init for agent

    @alec-tschantz @conorheins
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  30. updated example notebook

    @alec-tschantz @conorheins
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  31. added complicated example

    @alec-tschantz @conorheins
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  32. Merge branch 'feature/distribution-api' of https://github.com/infer-a… 

    …ctively/pymdp into feature/distribution-api

# Conflicts:
#	examples/distribution_api.ipynb
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  33. updated so we do not add a batch by default in agent constructor

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  34. fixed normalize

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  35. function to rol out using jax

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  36. agent action perception loop

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  37. Working state multiple cues

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  38. Updated notebook

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  39. made environment functional and added docstrings

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  40. intermediate state

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  41. bug resolved demo

    @salvatomm @toonvdm
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  42. Clean up notebook for the generalized tmaze

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  43. remove duplicate line

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  44. remove duplicate

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  45. line length agent

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  46. undo linting issues with agent.py

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  47. undo linting issues with agent.py

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  48. smoothing example notebook now working without batch dimensions

    @conorheins
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  49. functional sparse array version of smoothing_ovf in inference.py (doe… 

    …sn't work with vmap!)
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  50. rename B_dependencies back to B_factor_list to not break tests

    @ran-weii
    ran-weii committed Jun 12, 2024
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  51. fixed num_states / num_obs constructors

    @alec-tschantz
    alec-tschantz committed Jun 12, 2024
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  52. update multi action encoding and decoing with test

    @ran-weii
    ran-weii committed Jun 12, 2024
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  53. merge with distribution_api branch and resolve conflict

    @ran-weii
    ran-weii committed Jun 12, 2024
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Commits on Jun 13, 2024

  1. Use new rollout signature

    @toonvdm
    toonvdm committed Jun 13, 2024
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  2. Merge pull request #137 from toonvdm/feature/agent-demo 

    Feature/agent demo
    @dimarkov
    dimarkov authored Jun 13, 2024
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  3. Merge remote-tracking branch 'origin/pymdp-verses-hackathon' into fea… 

    …ture/distribution-api
    @conorheins
    conorheins committed Jun 13, 2024
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  4. Merge pull request #136 from infer-actively/feature/distribution-api 

    Feature/distribution api
    @conorheins
    conorheins authored Jun 13, 2024
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  5. Merge remote-tracking branch 'origin/pymdp-verses-hackathon' into HEAD

    @conorheins
    conorheins committed Jun 13, 2024
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  6. Merge pull request #143 from infer-actively/feature/complex_act_depen… 

    …dency

Feature/complex action dependency for Jax agent (copy of #139)
    @conorheins
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  7. Merge remote-tracking branch 'origin/pymdp-verses-hackathon' into fea… 

    …ture/sparse_tensors_backend
    @conorheins
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  8. don't overwrite C, D, E tensors if apply batch is True

    @toonvdm
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  9. updated poetry.lock

    @toonvdm @conorheins
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  10. beginning of unit test file for sparse tensors backend

    @conorheins
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  11. add sparse spm dot initial version

    @OzanCatalVerses
    OzanCatalVerses committed Jun 13, 2024
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  12. fixes to agent.py in pymdp.jax to deal with: 

    (A) batch expansion issues with C, D, and E
(B) the case where B_action_dependencies is trivial (i.e. provided as None)
    @conorheins
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  13. use apply_batch=False when constructing agent in generalized t maze d… 

    …emo notebook
    @conorheins
    conorheins committed Jun 13, 2024
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  14. add a separate py file for tree searching

    Tim Verbelen committed Jun 13, 2024
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  15. intermediate sharing some tree building

    Tim Verbelen committed Jun 13, 2024
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  16. update

    Tim Verbelen committed Jun 13, 2024
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  17. step function

    @alec-tschantz
    alec-tschantz authored and Tim Verbelen committed Jun 13, 2024
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  18. vmap over policies

    @alec-tschantz
    alec-tschantz authored and Tim Verbelen committed Jun 13, 2024
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  19. integrated alec's new step function

    Tim Verbelen committed Jun 13, 2024
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  20. we have a tree

    Tim Verbelen committed Jun 13, 2024
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  21. added vmap over leaves

    @alec-tschantz
    alec-tschantz authored and Tim Verbelen committed Jun 13, 2024
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  22. merging sophisticated inference backprop

    @alec-tschantz
    alec-tschantz authored and Tim Verbelen committed Jun 13, 2024
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  23. vmap over observations

    @alec-tschantz
    alec-tschantz authored and Tim Verbelen committed Jun 13, 2024
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  24. Merge pull request #144 from infer-actively/fix/error-c-tensor 

    Fix/error c tensor
    @conorheins
    conorheins authored Jun 13, 2024
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  25. fix spm_dot_sparse dims dims modifications

    @OzanCatalVerses
    OzanCatalVerses committed Jun 13, 2024
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  26. add sophisticated tmaze example

    Tim Verbelen committed Jun 13, 2024
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Commits on Jun 14, 2024

  1. Unit test for ovf smoothing using sparse tensors

    @toonvdm
    toonvdm committed Jun 14, 2024
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  2. updated docstring for todense hack

    @toonvdm
    toonvdm committed Jun 14, 2024
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  3. get the inference methods comparison notebook to work with latest hac… 

    …kathon version
    @OzanCatalVerses
    OzanCatalVerses committed Jun 14, 2024
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  4. benchmarking notebook

    @toonvdm
    toonvdm committed Jun 14, 2024
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Commits on Jun 17, 2024

  1. fix multimethod matching

    @OzanCatalVerses
    OzanCatalVerses committed Jun 17, 2024
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Commits on Jun 18, 2024

  1. change array->arraylike in all type signatures

    @OzanCatalVerses
    OzanCatalVerses committed Jun 18, 2024
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Commits on Jun 21, 2024

  1. unit tests for learning + B_dependencies in update_state_transition_d… 

    …irichlet
    @toonvdm
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Commits on Jun 22, 2024

  1. added learning from main + added docstring + unit tested jax implemen… 

    …tation against numpy counterpart
    @toonvdm
    toonvdm committed Jun 22, 2024
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  2. selective update of factors for learning the transition parameters

    @toonvdm
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Commits on Jun 23, 2024

  1. return all transition matrices when factors_to_update is not all

    @toonvdm
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  2. return all transition matrices when factors_to_update is not all

    @toonvdm
    toonvdm committed Jun 23, 2024
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  3. remove legacy comment

    @toonvdm
    toonvdm committed Jun 23, 2024
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Commits on Jun 27, 2024

  1. Merge pull request #148 from infer-actively/feature/learning-unit-tests 

    Feature/learning unit tests
    @dimarkov
    dimarkov authored Jun 27, 2024
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  2. add imageio dependency

    Tim Verbelen committed Jun 27, 2024
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  3. also allow to use Distribution for C and D

    Tim Verbelen committed Jun 27, 2024
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  4. Added Leaf class to register arbitrary objects as leaf

    @toonvdm
    toonvdm committed Jun 27, 2024
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  5. comment policies multi

    @toonvdm
    toonvdm committed Jun 27, 2024
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  6. Resolve merge conflicts

    @toonvdm
    toonvdm committed Jun 27, 2024
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  7. add demo notebooks for the two jax envs

    Tim Verbelen committed Jun 27, 2024
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  8. Merge branch 'feature/sophisticated-jax-rebased' into hackaton-demos

    Tim Verbelen committed Jun 27, 2024
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  9. refactor si code and examples

    Tim Verbelen committed Jun 27, 2024
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  10. move generate graph function to env file

    Tim Verbelen committed Jun 27, 2024
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  11. running sophisticated inference in a generalized tmaze env

    @dimarkov
    dimarkov authored and Tim Verbelen committed Jun 27, 2024
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  12. add mctx based mcts planner

    Tim Verbelen committed Jun 27, 2024
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  13. simpler graph world demo

    Tim Verbelen committed Jun 27, 2024
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  14. use custom scan to use scan signature to iterate over sparse arrays

    @toonvdm
    toonvdm committed Jun 27, 2024
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  15. Merge branch 'feature/sparse_tensors_backend' into hackaton-demos

    Tim Verbelen committed Jun 27, 2024
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  16. create separate subdir for the sparse experiment

    Tim Verbelen committed Jun 27, 2024
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Commits on Jun 28, 2024

  1. Added mctx and mediapy dependencies

    @toonvdm
    toonvdm committed Jun 28, 2024
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  2. generated outputs for benchmark notebook

    @toonvdm
    toonvdm committed Jun 28, 2024
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Commits on Jul 31, 2024

  1. add readable string repr for Distribution

    @tverbele
    tverbele committed Jul 31, 2024
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  2. add Model class for describing the full model in api

    @tverbele
    tverbele committed Jul 31, 2024
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Commits on Aug 2, 2024

  1. fix bug in creating preference distribution

    @tverbele
    tverbele committed Aug 2, 2024
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Commits on Aug 8, 2024

  1. also allow specifying state preferences (H) through model/distribution

    @tverbele
    tverbele committed Aug 8, 2024
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  2. allow to set gamma and make default value 1

    @tverbele
    tverbele committed Aug 8, 2024
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Commits on Aug 9, 2024

  1. use muzero_policy as default instead of the gumbel_muzero_policy

    @tverbele
    tverbele committed Aug 9, 2024
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Commits on Sep 20, 2024

  1. Merge pull request #149 from infer-actively/api_model 

    Add some extra features to the Distribution API
    @conorheins
    conorheins authored Sep 20, 2024
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  2. Merge pull request #151 from infer-actively/si_fixes 

    Si fixes
    @conorheins
    conorheins authored Sep 20, 2024
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  3. Merged @dimarkov's upstream changes to master into hackaton_demos 

    Co-authored-by: Tim Verbelen <[email protected]>
    @conorheins @tverbele
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  4. Merge pull request #152 from infer-actively/hackaton-demos 

    Hackaton demos
    @conorheins
    conorheins authored Sep 20, 2024
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  5. fix Distribution API notebook

    Tim Verbelen committed Sep 20, 2024
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  6. fixed the initialization of the E vector in Agent constructor so th… 

    …at it cannot be a list, must be an array or Distribution instance
    @conorheins
    conorheins committed Sep 20, 2024
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  7. Added apply_batch=False flag to all initializations of an Agent i… 

    …n the `inference_methods_comparison.ipynb` notebook
    @conorheins
    conorheins committed Sep 20, 2024
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  8. fix Graph Worlds demo

    Tim Verbelen committed Sep 20, 2024
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  9. changes to control.py: 

    - moved `t` indexing in `compute_expected_utility` function to end of argument list, default to `0`
- added missing arguments `A_dependencies` and `B_dependencies` into calls of parameter info gain functions
    @conorheins
    conorheins committed Sep 20, 2024
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  10. fixed deprecated syntax of Agent.infer_states in mcts.py and si.py

    @conorheins
    conorheins committed Sep 20, 2024
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  11. fixes to sparse_benchmark.ipynb notebook: 

    - changed deprecated naming of `infer_empirical_prior()` to `update_empirical_prior()`
- changed indexing into `smoothed_dense` tuple during output-plotting, to respect the new output structure of `smoothing_ovf` function
    @conorheins
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Commits on Sep 23, 2024

  1. cleanup the dependencies and poetry .toml

    Tim Verbelen committed Sep 23, 2024
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  2. remove unused pandas import

    Tim Verbelen committed Sep 23, 2024
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  3. fix distribution unit test

    Tim Verbelen committed Sep 23, 2024
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  4. fix update_empirical_prior and infer_states in tests

    Tim Verbelen committed Sep 23, 2024
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  5. configure setuptools using pyproject.toml

    Tim Verbelen committed Sep 23, 2024
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  6. fix typo

    Tim Verbelen committed Sep 23, 2024
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Commits on Sep 24, 2024

  1. declare packages

    @tverbele
    tverbele committed Sep 24, 2024
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  2. remove requirements.txt from README

    @tverbele
    tverbele committed Sep 24, 2024
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  3. added back in decode_multi_actions as method of Agent, originally… 

    … from @ran-weii's `complex_act_dependencies` branch
    @conorheins
    conorheins committed Sep 24, 2024
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  4. added optional factors_to_update argument into `pymdp.jax.learning.… 

    …update_state_likelihood_dirichlet()` function
    @conorheins
    conorheins committed Sep 24, 2024
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  5. fixed unit test test_sparse_smoothing in test_jax_sparse_backend … 

    …to respect new output structure of `pymdp.jax.inference.smoothing_ovf`
    @conorheins
    conorheins committed Sep 24, 2024
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  6. removed calls to np.random.seed(0) in test_learning_jax.py

    @conorheins
    conorheins committed Sep 24, 2024
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  7. added more authors to author list in pyproject.toml (unfinished/WIP)

    @conorheins
    conorheins committed Sep 24, 2024
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  8. fixed update_state_likelihood_dirichlet to allow for `factors_to_up… 

    …date` to work properly, not using `tree_map` anymore
    @conorheins
    conorheins committed Sep 24, 2024
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  9. Refactor of pymdp so that jax is the main backend, and numpy vers… 

    …ion now relegated to a `legacy` folder.

Co-authored-by: Tim Verbelen <[email protected]>
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    conorheins and tverbele committed Sep 24, 2024
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  10. fix refactored packages

    Tim Verbelen committed Sep 24, 2024
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  11. removed field(static=True) option for policies matrix in Agent

    @conorheins
    conorheins committed Sep 24, 2024
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  12. reimplementation of missing line when checking pA in self.validate(… 

    …) method of `Agent`, from commit 1958e4d
    @conorheins
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  13. update to pymdp.Agent: 

    - in case inductive matrix `I` is not present,do not update it when updating transition parameters. This avoids an error in `tree_at` for updating None-valued leaves (`self.I` will be None in case `self.use_inductive = False`)
    @conorheins
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Commits on Sep 30, 2024

  1. changed github workflow configuration .yml to no longer test on Pytho… 

    …n 3.10 and to not assume a requirements.txt file. Authored by @tverbele
    @conorheins
    conorheins committed Sep 30, 2024
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Commits on Oct 2, 2024

  1. - renamed PyMDPEnv to Env throughout the repo 

    - started version of `T-Maze` environment in new jax `Env` class

Co-authored-by: Tim Verbelen <[email protected]>
    @conorheins @tverbele
    conorheins and tverbele committed Oct 2, 2024
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  2. renamed PyMDPEnv to Env in learning_gridworld.ipynb notebook

    @conorheins
    conorheins committed Oct 2, 2024
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  3. renamed PyMDPEnv to Env in graph_worlds.py

    @conorheins
    conorheins committed Oct 2, 2024
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  4. renamed PyMDPEnv to Env in grid_world_demo.ipynb

    @conorheins
    conorheins committed Oct 2, 2024
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  5. started refactoring GeneralizedTMaze(Env) class

    @conorheins
    conorheins committed Oct 2, 2024
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  6. removed .jax module prefixes from imports in pymdp.envs.rollout

    @conorheins
    conorheins committed Oct 2, 2024
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  7. refactor legacy TMaze to jax Env

    Tim Verbelen committed Oct 2, 2024
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  8. add TMaze demo notebook

    Tim Verbelen committed Oct 2, 2024
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  9. refactor PyMDPEnv to Env

    Tim Verbelen committed Oct 2, 2024
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  10. Merge branch 'tmaze' into v1.0.0_alpha

    Tim Verbelen committed Oct 2, 2024
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  11. fix reset

    Tim Verbelen committed Oct 2, 2024
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Commits on Oct 3, 2024

  1. add pymdp.envs.assets to package

    Tim Verbelen committed Oct 3, 2024
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  2. package image files in assets

    Tim Verbelen committed Oct 3, 2024
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  3. fix state initialization on reset

    Tim Verbelen committed Oct 3, 2024
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