Paper branch #69

conorheins · 2022-03-12T15:32:56Z

JOSS manuscript now in paper folder
initial changes based on reviews from @seankmartin (added Summary section to paper, added documentation for Agent API)
other minor tweaks (some minor variable renaming in the internals of Agent)

…step paper

…riginally in arxiv version). In reference to openjournals/joss-reviews#4098 (comment)

… SPM test suite, after changing that function a private member in `agent.py` (to avoid autodocumentation)

…`efe` to `G`

…based on openjournals/joss-reviews#4098 (comment)

conorheins · 2022-03-12T15:40:45Z

The new Agent API autodocumentation was in response to #67 by @seankmartin (see also openjournals/joss-reviews#4098 (comment)). That new documentation can be found on the RTD page specifically for the paper_branch, which can be found here: https://pymdp-rtd.readthedocs.io/en/paper_branch/agent.html

I am not going to close #67 because we still need to add API documentation for the Env base class to the RTD website to fully address @seankmartin's comments..

…tring

conorheins · 2022-03-13T16:39:00Z

In response to #67 and openjournals/joss-reviews#4098 (comment), we have now added a specific sub-section in the APIs documentation section that documents the Env base class and the sub-class implementations. That can be found here: https://pymdp-rtd.readthedocs.io/en/paper_branch/env.html

I think this now fully addresses #67

…ate_state_likelihood_dirichlet()`, to avoid improper index error

…n transition model (B matrix) for 2d grid worlds

…t learning), based on earlier bug with action indexing

- added new section in RTD for notebooks that are inspired by MATLAB code in Step-by-Step tutorial paper

…t for compilation during RTD (for the new VFE tutorial notebook)

…om Step-by-Step paper)

…D error

…ependenciesMerge branch 'paper_branch' into tutorial_scripts_translations

conorheins · 2022-04-02T14:27:15Z

docs/requirements.txt

 sphinx_rtd_theme
 sphinx-autodoc-typehints==1.11.1
 jupyter-sphinx>=0.3.2
 myst-nb
+jinja2==3.0.0


see RDT issue here

…states and two instances of "THe" vs. "the"), to address Issue #71: #71 (comment)

Update paper_branch with new changes in the tutorial_scripts_translations branches (e.g. updates to the index.rst file) # the commit.

- added Verses affil for other co-authors, added Alec's 2nd sussex affiliation

…penjournals/joss-reviews#4098 (comment)

…(comment) - added missing DOIs for particular citations - used official ForneyLab citation from their GitHub page -standardized ArXiv-preprint reference style

…wledgement to be explicit about finding technical error in arxiv version

…s in documentation

…eviews#4098 (comment))

@emdupre

…ralComp one suggested by @emdupre here: openjournals/joss-reviews#4098 (comment)

…nals/joss-reviews#4098 (comment)

… need section, following suggestion from openjournals/joss-reviews#4098 (comment)

…mahault

…mahault (see #73 (comment))

conorheins added 8 commits January 14, 2022 19:25

initial upload for paper submission

811f780

fixed friston_reinforcement_2009 authorship in paper.bib

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fixed typo in end of statement-of-need

8bac708

replaced 'documenting idiosyncrasies' bit when talking about step-by-…

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…step paper

Moved old Usage section above and renamed to Summary (as it was o…

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…riginally in arxiv version). In reference to openjournals/joss-reviews#4098 (comment)

changed reference to infer_states_test() to _infer_states_test in…

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… SPM test suite, after changing that function a private member in `agent.py` (to avoid autodocumentation)

changed references to second return of agent.infer_policies() from …

c1e6fc4

…`efe` to `G`

added documentation to Sphinx autodocumentation for Agent API class, …

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…based on openjournals/joss-reviews#4098 (comment)

conorheins added 5 commits March 12, 2022 16:51

added quick usage example and extra information to Agent class docs…

aef6abf

…tring

removed mdp_search_env environment class

dff20eb

added docstrings for the Env base class and example environments

d92da9e

added env autodocumentation to index.rst

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added reference to env.rst in index.rst

ea83bca

conorheins added 13 commits April 1, 2022 17:57

turn action into integer when indexing into slices of B array in `upd…

fcf1152

…ate_state_likelihood_dirichlet()`, to avoid improper index error

changed output to qB in update_B() function of agent()

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wrapper fn indefault_models() library for building local-navigatio…

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…n transition model (B matrix) for 2d grid worlds

unit-test for update_B() function of Agent (transition model Dirichle…

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…t learning), based on earlier bug with action indexing

- added reference to paper on RTD front page (to address Issue #64)

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- added new section in RTD for notebooks that are inspired by MATLAB code in Step-by-Step tutorial paper

lowercase categorical

a75f945

fixed typo in learning.rst file

ed0658a

Added reference to paper in pymdp fundamentals notebook

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added autograd requirement to reqiurements.txt and setup.py to accoun…

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…t for compilation during RTD (for the new VFE tutorial notebook)

decreased maxdepth of toctree for Additional learning materials folder

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Bayes rule / VFE calculation notebook (companion to MATLAB version fr…

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…om Step-by-Step paper)

update to sphinx and implicitly pin jinja2 dependency to deal with RT…

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…D error

Pull changes from paper_branch relating to sphinx/jinja updates and d…

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…ependenciesMerge branch 'paper_branch' into tutorial_scripts_translations

conorheins commented Apr 2, 2022

View reviewed changes

fix typos in the text of Tutorial 1 (mis-labelling prior over hidden …

6a8e621

…states and two instances of "THe" vs. "the"), to address Issue #71: #71 (comment)

conorheins added 15 commits April 9, 2022 13:44

Merge branch 'tutorial_scripts_translations' into paper_branch

6613db4

Update paper_branch with new changes in the tutorial_scripts_translations branches (e.g. updates to the index.rst file) # the commit.

update release version to 0.0.4 in conf.py for autodocumentation

9b4e707

add middle initial to Iain's name

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- changed Templeton acknowledgement

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- added Verses affil for other co-authors, added Alec's 2nd sussex affiliation

acknowledged Thomas for feedback on manuscript

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changes to main Agent demo to address textual edits raised in #72 and o…

a6729a4

…penjournals/joss-reviews#4098 (comment)

to address JOSS editor comments here: openjournals/joss-reviews#4098 …

74f47b3

…(comment) - added missing DOIs for particular citations - used official ForneyLab citation from their GitHub page -standardized ArXiv-preprint reference style

updated with new string for ForneyLab citation, changed Thomas' ackno…

589f796

…wledgement to be explicit about finding technical error in arxiv version

missing comma after publisher in gregory 1980 citation

b41ddf6

added reference in README.md to growing list of active inference demo…

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…s in documentation

fixed typo in doi of van2021chance reference (see openjournals/joss-r…

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…eviews#4098 (comment))

updated chance-constrained AIF reference/citation to the official Neu…

09acaac

…ralComp one suggested by @emdupre here: openjournals/joss-reviews#4098 (comment)

standardized arxiv references to include fields requested in openjour…

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…nals/joss-reviews#4098 (comment)

added reference to arxiv preprint and github repo in the statement of…

ff7450c

… need section, following suggestion from openjournals/joss-reviews#4098 (comment)

fixed typo in B matrix normalization error message, as pointed out by @…

125042f

…mahault (see #73 (comment))

conorheins merged commit 137cec4 into master Apr 25, 2022

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Paper branch #69

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Paper branch #69

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