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V3: complete overhaul #372

Merged
merged 410 commits into from
Jul 26, 2024
Merged

V3: complete overhaul #372

merged 410 commits into from
Jul 26, 2024
This pull request is big! We’re only showing the most recent 250 commits.

Commits on Oct 14, 2023

  1. Remove redundant definitions

    @kahaaga
    kahaaga committed Oct 14, 2023
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  2. Use new syntax for CMI examples

    @kahaaga
    kahaaga committed Oct 14, 2023
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  3. Documentation examples

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  4. Docs...

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  5. References from ComplexityMeasures.jl

    @kahaaga
    kahaaga committed Oct 14, 2023
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  6. Rearrange docs

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    kahaaga committed Oct 14, 2023
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  7. More docs

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  8. Discretization using CosineSimilarityBinning

    @kahaaga
    kahaaga committed Oct 14, 2023
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  9. Delete example system docs

    @kahaaga
    kahaaga committed Oct 14, 2023
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  10. Docs for core

    @kahaaga
    kahaaga committed Oct 14, 2023
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  11. Migrate conditional entropy examples

    @kahaaga
    kahaaga committed Oct 14, 2023
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  12. Missing @docs tag

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    kahaaga committed Oct 14, 2023
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  13. More docs

    @kahaaga
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  14. Docs

    @kahaaga
    kahaaga committed Oct 14, 2023
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  15. Remove some text

    @kahaaga
    kahaaga committed Oct 14, 2023
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  16. Fix SurrogateAssociationTest for transfer entropy

    @kahaaga
    kahaaga committed Oct 14, 2023
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  17. Fix various transfer entropy related issues and docs

    @kahaaga
    kahaaga committed Oct 14, 2023
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  18. Add compatible OutcomeSpaces to docstring

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    kahaaga committed Oct 14, 2023
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  19. More transfer entropy tests

    @kahaaga
    kahaaga committed Oct 14, 2023
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  20. Test Lindner

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  21. New API

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    kahaaga committed Oct 14, 2023
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Commits on Oct 15, 2023

  1. New API for cross mappings (estimators contain measure)

    @kahaaga
    kahaaga committed Oct 15, 2023
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  2. More docs

    @kahaaga
    kahaaga committed Oct 15, 2023
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  3. New syntax

    @kahaaga
    kahaaga committed Oct 15, 2023
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  4. Include closeness and cross mapping files

    @kahaaga
    kahaaga committed Oct 15, 2023
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  5. Some doc restructuring

    @kahaaga
    kahaaga committed Oct 15, 2023
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  6. Include relevant deprecations

    @kahaaga
    kahaaga committed Oct 15, 2023
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  7. correct field name

    @kahaaga
    kahaaga committed Oct 15, 2023
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  8. Fix crossmap doc example

    @kahaaga
    kahaaga committed Oct 15, 2023
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  9. Add explicit error messages

    @kahaaga
    kahaaga committed Oct 15, 2023
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  10. Changelog for cross mappings

    @kahaaga
    kahaaga committed Oct 15, 2023
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  11. More "deprecations"

    @kahaaga
    kahaaga committed Oct 15, 2023
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  12. update changelog

    @kahaaga
    kahaaga committed Oct 15, 2023
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  13. Move utility method to relevant file

    @kahaaga
    kahaaga committed Oct 15, 2023
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  14. Remove obsolete tests

    @kahaaga
    kahaaga committed Oct 15, 2023
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  15. Remove duplicated header

    @kahaaga
    kahaaga committed Oct 15, 2023
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Commits on Oct 16, 2023

  1. Explicit imports

    @kahaaga
    kahaaga committed Oct 16, 2023
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  2. Make formal API

    @kahaaga
    kahaaga committed Oct 16, 2023
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  3. Add note on measures defines also in Distances.jl

    @kahaaga
    kahaaga committed Oct 16, 2023
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  4. Reintroduce correlation measures

    @kahaaga
    kahaaga committed Oct 16, 2023
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  5. Correlation API

    @kahaaga
    kahaaga committed Oct 16, 2023
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  6. Move counting and discretization to information measures

    @kahaaga
    kahaaga committed Oct 16, 2023
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  7. Crossmap API

    @kahaaga
    kahaaga committed Oct 16, 2023
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  8. Correlation examples

    @kahaaga
    kahaaga committed Oct 16, 2023
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  9. Reintroduce closeness measures

    @kahaaga
    kahaaga committed Oct 16, 2023
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  10. Reintroduce JointDistanceDistributionTest

    @kahaaga
    kahaaga committed Oct 16, 2023
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Commits on Jan 2, 2024

  1. Adhere to latest ComplexityMeasures api

    @kahaaga
    kahaaga committed Jan 2, 2024
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Commits on Jan 20, 2024

  1. WIP

    @kahaaga
    kahaaga committed Jan 20, 2024
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  2. Don't run compathelper so often

    @kahaaga
    kahaaga committed Jan 20, 2024
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  3. Fix some missing refs

    @kahaaga
    kahaaga committed Jan 20, 2024
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  4. Temporarily use local build_docs_with_style

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Commits on Jun 6, 2024

  1. Start reorganizing docs mirroring ComplexityMeasures.jl

    @kahaaga
    kahaaga committed Jun 6, 2024
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  2. docs

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    kahaaga committed Jun 6, 2024
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Commits on Jun 7, 2024

  1. Move crossmap api

    @kahaaga
    kahaaga committed Jun 7, 2024
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Commits on Jul 5, 2024

  1. Aim for 1.11 while developing (tests/docs build faster)

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  2. WIP: docs...

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Commits on Jul 6, 2024

  1. wip: Unify syntax, better docs, etc..

    @kahaaga
    kahaaga committed Jul 6, 2024
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  2. Update docs

    @kahaaga
    kahaaga committed Jul 6, 2024
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  3. WIP...

    @kahaaga
    kahaaga committed Jul 6, 2024
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Commits on Jul 7, 2024

  1. Preserve axis information when taking marginals

    @kahaaga
    kahaaga committed Jul 7, 2024
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Commits on Jul 14, 2024

  1. Add coverage files to gitignore

    @kahaaga
    kahaaga committed Jul 14, 2024
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  2. deprecations

    @kahaaga
    kahaaga committed Jul 14, 2024
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  3. deprecations

    @kahaaga
    kahaaga committed Jul 14, 2024
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  4. Multidimensional surrogates

    @kahaaga
    kahaaga committed Jul 14, 2024
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  5. Fix import

    @kahaaga
    kahaaga committed Jul 14, 2024
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  6. Headers

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  7. Add reference

    @kahaaga
    kahaaga committed Jul 14, 2024
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  8. Refer to abstract types

    @kahaaga
    kahaaga committed Jul 14, 2024
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  9. deprecations

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  10. WIP...

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Commits on Jul 21, 2024

  1. organize a bit better

    @kahaaga
    kahaaga committed Jul 21, 2024
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  2. update const name

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  3. move to utils

    @kahaaga
    kahaaga committed Jul 21, 2024
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  4. Use cov/cor from StateSpaceSets 1.5

    @kahaaga
    kahaaga committed Jul 21, 2024
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  5. Update package versions, add StyledStrings and set julia to 1.10

    @kahaaga
    kahaaga committed Jul 21, 2024
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  6. Remove redundant tests

    @kahaaga
    kahaaga committed Jul 21, 2024
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  7. fix tests...

    @kahaaga
    kahaaga committed Jul 21, 2024
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  8. fix tests

    @kahaaga
    kahaaga committed Jul 21, 2024
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  9. fix tests

    @kahaaga
    kahaaga committed Jul 21, 2024
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  10. Typo

    @kahaaga
    kahaaga committed Jul 21, 2024
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  11. Convenience union

    @kahaaga
    kahaaga committed Jul 21, 2024
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  12. Remove unnecessary print

    @kahaaga
    kahaaga committed Jul 21, 2024
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  13. Fix syntax

    @kahaaga
    kahaaga committed Jul 21, 2024
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  14. Update changelog

    @kahaaga
    kahaaga committed Jul 21, 2024
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  15. Fix tests

    @kahaaga
    kahaaga committed Jul 21, 2024
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  16. faster tests with fewer sample

    @kahaaga
    kahaaga committed Jul 21, 2024
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  17. fix tests

    @kahaaga
    kahaaga committed Jul 21, 2024
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  18. cosmetics

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  19. input validation

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  20. cosmetics

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  21. remove integration

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  22. remove redundant ContingencyMatrix

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    kahaaga committed Jul 21, 2024
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  23. Add test dep

    @kahaaga
    kahaaga committed Jul 21, 2024
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  24. Test systems

    @kahaaga
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  25. update deps

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  26. clean up main file

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    kahaaga committed Jul 21, 2024
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  27. remove redundant test

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  28. test cross mapping independence tests

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  29. Fix tests

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  30. remove redundant file

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  31. Faster tests using fewer samples

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  32. Fewer samples -> faster tests

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  33. input checks for all information measures

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  34. fix tests and faster tests

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  35. faster tests

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  36. Fix reference

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  37. Part mutual information tests

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  38. fix discretization for 1d state space sets

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    kahaaga committed Jul 21, 2024
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  39. pmi tests and fix implementation

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  40. more tests

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  41. remove dev deps from project

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    kahaaga committed Jul 21, 2024
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  42. fewer samples, faster tests

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  43. Remove unnecessary deps from doc build

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    kahaaga committed Jul 21, 2024
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  44. LabelledArrays is needed

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    kahaaga committed Jul 21, 2024
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  45. Fix example

    @kahaaga
    kahaaga committed Jul 21, 2024
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  46. Fix OCE and PC

    @kahaaga
    kahaaga committed Jul 21, 2024
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  47. Consistent syntax

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  48. Necessary imports

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  49. consistent syntax

    @kahaaga
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  50. Reintroduce network graph tests

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    kahaaga committed Jul 21, 2024
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  51. Reintroduce example for graphs

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Commits on Jul 22, 2024

  1. improve figures

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    kahaaga committed Jul 22, 2024
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  2. update docs

    @kahaaga
    kahaaga committed Jul 22, 2024
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  3. fix tests and remove outdated syntax

    @kahaaga
    kahaaga committed Jul 22, 2024
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  4. less samples, faster tests

    @kahaaga
    kahaaga committed Jul 22, 2024
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  5. actually test recurrence-based methods

    @kahaaga
    kahaaga committed Jul 22, 2024
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  6. more crossmap tests

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    kahaaga committed Jul 22, 2024
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  7. use rng

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    kahaaga committed Jul 22, 2024
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  8. correct syntax

    @kahaaga
    kahaaga committed Jul 22, 2024
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  9. use rng

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    kahaaga committed Jul 22, 2024
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  10. EntropyDecomposition tests

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    kahaaga committed Jul 22, 2024
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  11. Fix tests

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    kahaaga committed Jul 22, 2024
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  12. Un-support TransferOperator estimation of transfer entropy

    @kahaaga
    kahaaga committed Jul 22, 2024
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  13. type parameterize outcome spaces, so we can dispatch properly

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    kahaaga committed Jul 22, 2024
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  14. Fix transfer entropy estimation using TransferOperator

    @kahaaga
    kahaaga committed Jul 22, 2024
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  15. Generic dispatch for codifying marginals 

    New outcome spaces that implements `codify` now works automagically.
    @kahaaga
    kahaaga committed Jul 22, 2024
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  16. node labels

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    kahaaga committed Jul 22, 2024
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  17. Examples

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  18. Add estimator to docstring

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    kahaaga committed Jul 22, 2024
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  19. more examples

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    kahaaga committed Jul 22, 2024
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  20. fix test

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    kahaaga committed Jul 22, 2024
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  21. remove reference to convenience func

    @kahaaga
    kahaaga committed Jul 22, 2024
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  22. More examples

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  23. More examples

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    kahaaga committed Jul 22, 2024
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  24. examples for joint entropy

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    kahaaga committed Jul 22, 2024
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  25. Add more examples

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    kahaaga committed Jul 22, 2024
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  26. Update docs and test

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    kahaaga committed Jul 22, 2024
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  27. Update tests

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    kahaaga committed Jul 22, 2024
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Commits on Jul 23, 2024

  1. Keep important info in docstrings

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    kahaaga committed Jul 23, 2024
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  2. Clean-up

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    kahaaga committed Jul 23, 2024
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  3. Add tests

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    kahaaga committed Jul 23, 2024
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  4. Add comments for clarity

    @kahaaga
    kahaaga committed Jul 23, 2024
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  5. Clean up docs

    @kahaaga
    kahaaga committed Jul 23, 2024
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  6. Clean up docs

    @kahaaga
    kahaaga committed Jul 23, 2024
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  7. Polish cross-map docs

    @kahaaga
    kahaaga committed Jul 23, 2024
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  8. fix references

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    kahaaga committed Jul 23, 2024
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  9. typo

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    kahaaga committed Jul 23, 2024
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  10. Clean cross mapping stuff

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    kahaaga committed Jul 23, 2024
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  11. rng

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    kahaaga committed Jul 23, 2024
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  12. Cross map docs

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    kahaaga committed Jul 23, 2024
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  13. ccm docs

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    kahaaga committed Jul 23, 2024
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  14. missing references

    @kahaaga
    kahaaga committed Jul 23, 2024
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  15. Clean up cross map stuff 

    Also DO export the predict and crossmap methods.
    @kahaaga
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  16. Clean up index.md

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    kahaaga committed Jul 23, 2024
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  17. cross map stuff

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    kahaaga committed Jul 23, 2024
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  18. add missing reference

    @kahaaga
    kahaaga committed Jul 23, 2024
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  19. fix codify method

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    kahaaga committed Jul 23, 2024
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  20. add conversion method

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    kahaaga committed Jul 23, 2024
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  21. add method for JointProbabilities

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    kahaaga committed Jul 23, 2024
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  22. Add Hilbert

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    kahaaga committed Jul 23, 2024
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  23. add tests

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    kahaaga committed Jul 23, 2024
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  24. docs..

    @kahaaga
    kahaaga committed Jul 23, 2024
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  25. test coverage for MCR and RMCD

    @kahaaga
    kahaaga committed Jul 23, 2024
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  26. remove redundant code

    @kahaaga
    kahaaga committed Jul 23, 2024
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  27. remove redundant docstring

    @kahaaga
    kahaaga committed Jul 23, 2024
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  28. Add hilbert rerference in docs

    @kahaaga
    kahaaga committed Jul 23, 2024
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  29. Example and docs for recurrence measures

    @kahaaga
    kahaaga committed Jul 23, 2024
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  30. Remove redundant docs

    @kahaaga
    kahaaga committed Jul 23, 2024
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  31. Rename

    @kahaaga
    kahaaga committed Jul 23, 2024
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  32. docs

    @kahaaga
    kahaaga committed Jul 23, 2024
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  33. fix tutorial

    @kahaaga
    kahaaga committed Jul 23, 2024
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  34. Fix examples

    @kahaaga
    kahaaga committed Jul 23, 2024
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  35. SymbolicTransferEntropy convenience

    @kahaaga
    kahaaga committed Jul 23, 2024
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  36. Fix docs

    @kahaaga
    kahaaga committed Jul 23, 2024
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  37. Better example

    @kahaaga
    kahaaga committed Jul 23, 2024
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  38. typo

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    kahaaga committed Jul 23, 2024
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  39. Test SymbolicTransferEntropy

    @kahaaga
    kahaaga committed Jul 23, 2024
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  40. test coverage

    @kahaaga
    kahaaga committed Jul 23, 2024
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  41. more tests

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    kahaaga committed Jul 23, 2024
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  42. More tests

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    kahaaga committed Jul 23, 2024
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Commits on Jul 24, 2024

  1. tests

    @kahaaga
    kahaaga committed Jul 24, 2024
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  2. remove reference to deleted file

    @kahaaga
    kahaaga committed Jul 24, 2024
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  3. tests...

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  4. more tests

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    kahaaga committed Jul 24, 2024
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  5. todo

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  6. bbnue.. wip

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    kahaaga committed Jul 24, 2024
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  7. wip..

    @kahaaga
    kahaaga committed Jul 24, 2024
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  8. outer constructor

    @kahaaga
    kahaaga committed Jul 24, 2024
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  9. remove deprecations

    @kahaaga
    kahaaga committed Jul 24, 2024
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  10. remove methods not finished yet

    @kahaaga
    kahaaga committed Jul 24, 2024
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  11. fewer samples, faster tests

    @kahaaga
    kahaaga committed Jul 24, 2024
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  12. Remove not finished bbnue

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    kahaaga committed Jul 24, 2024
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  13. remove unfinished code

    @kahaaga
    kahaaga committed Jul 24, 2024
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  14. duplicate call

    @kahaaga
    kahaaga committed Jul 24, 2024
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  15. remove unfinished code

    @kahaaga
    kahaaga committed Jul 24, 2024
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  16. add tests

    @kahaaga
    kahaaga committed Jul 24, 2024
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  17. remove unused methods

    @kahaaga
    kahaaga committed Jul 24, 2024
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  18. more tests

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    kahaaga committed Jul 24, 2024
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  19. remove unfinished code

    @kahaaga
    kahaaga committed Jul 24, 2024
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  20. Alias

    @kahaaga
    kahaaga committed Jul 24, 2024
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  21. include forgotten test file

    @kahaaga
    kahaaga committed Jul 24, 2024
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  22. remove unfinished code

    @kahaaga
    kahaaga committed Jul 24, 2024
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  23. Remember to export

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    kahaaga committed Jul 24, 2024
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  24. more tests

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    kahaaga committed Jul 24, 2024
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  25. remove redundant code

    @kahaaga
    kahaaga committed Jul 24, 2024
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  26. explicit access

    @kahaaga
    kahaaga committed Jul 24, 2024
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  27. remember to export

    @kahaaga
    kahaaga committed Jul 24, 2024
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  28. more efficient TE tests for independence

    @kahaaga
    kahaaga committed Jul 24, 2024
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  29. Don't use deprecated syntax

    @kahaaga
    kahaaga committed Jul 24, 2024
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  30. Error throwing handled at higher level

    @kahaaga
    kahaaga committed Jul 24, 2024
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  31. More test coverage

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    kahaaga committed Jul 24, 2024
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  32. More tests

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    kahaaga committed Jul 24, 2024
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  33. fix test

    @kahaaga
    kahaaga committed Jul 24, 2024
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  34. add rng to test

    @kahaaga
    kahaaga committed Jul 24, 2024
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  35. Remove redundant code

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    kahaaga committed Jul 24, 2024
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  36. remove redundant utils

    @kahaaga
    kahaaga committed Jul 24, 2024
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  37. more tests

    @kahaaga
    kahaaga committed Jul 24, 2024
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  38. pretty printing

    @kahaaga
    kahaaga committed Jul 24, 2024
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  39. better printing of decomposition estimators

    @kahaaga
    kahaaga committed Jul 24, 2024
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  40. short-form printing

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    kahaaga committed Jul 24, 2024
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  41. typo

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    kahaaga committed Jul 24, 2024
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  42. more tests

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    kahaaga committed Jul 24, 2024
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  43. clean up @show statements

    @kahaaga
    kahaaga committed Jul 24, 2024
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  44. remove redundant code

    @kahaaga
    kahaaga committed Jul 24, 2024
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  45. more tests

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  46. more tests

    @kahaaga
    kahaaga committed Jul 24, 2024
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  47. Reorganize

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  48. Docs.

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  49. docs...

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  50. doc fixes...

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Commits on Jul 25, 2024

  1. Fix doc warnings..

    @kahaaga
    kahaaga committed Jul 25, 2024
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  2. Eliminate documentation warnings

    @kahaaga
    kahaaga committed Jul 25, 2024
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  3. Add DocumenterInterLinks

    @kahaaga
    kahaaga committed Jul 25, 2024
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  4. docs..

    @kahaaga
    kahaaga committed Jul 25, 2024
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  5. finalize docs

    @kahaaga
    kahaaga committed Jul 25, 2024
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  6. codify for multiple outcome spaces

    @kahaaga
    kahaaga committed Jul 25, 2024
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  7. Add note

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Commits on Jul 26, 2024

  1. enable breaking docs on fails again

    @kahaaga
    kahaaga committed Jul 26, 2024
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  2. fix broken link

    @kahaaga
    kahaaga committed Jul 26, 2024
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  3. remove empty file

    @kahaaga
    kahaaga committed Jul 26, 2024
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