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anesthetic style plotting functions#35

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williamjameshandley wants to merge 125 commits intomasterhandley-lab/lsbi:masterfrom plothandley-lab/lsbi:plotCopy head branch name to clipboard

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Commits on Dec 7, 2023

• bump version to 0.12.0

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• rvs and logpdf working

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• Now broadcasting for cov and mean

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• predict, condition and marginalise now working

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• bijector now tested

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Commits on Dec 8, 2023

• Halfway through mixture upgrade

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• Extended predict tests

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• Now not unecessarily flattening covariance matrices

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• Merge branch 'multivariate_normal_temp' into multivariate_normal

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Commits on Dec 9, 2023

• rvs working

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Commits on Dec 10, 2023

• Neater version of logpdf and rvs without flatten

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• Removed _flatten completely

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• condition now running

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  7cd4bdd

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• bijector now tested and working

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  c154533

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• Commented and corrected the predict function for mixtures

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• Added cleverer defaults to multivariate_normal

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• Added checks for the new default system

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Commits on Dec 11, 2023

• Better defaults for b

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Commits on Dec 12, 2023

• Lazy expansion of mean now working

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• lazy covariance tests now completing

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• Fixed rvs

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• A and b now lazily evaluating

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• Lazy A and b now working

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Commits on Dec 17, 2023

• Tests passing

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Commits on Dec 18, 2023

• re-graded to not bother with checking for scalar means and covariances

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Commits on Dec 26, 2023

• Minor update to stats

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Commits on Dec 27, 2023

• First draft of model

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Commits on Dec 28, 2023

• Begun switch to diagonal_cov strategy

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Commits on Jan 6, 2024

• Removed special treatment of M for now

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• Tests now passing

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• Reinstated more efficient calculations

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Commits on Jan 8, 2024

• Major test suite completed

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• Test suite now too large to fit in memory. Need a different strategy

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Commits on Jan 13, 2024

• Got stats_1 tests now running

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Commits on Jan 14, 2024

• Predict now passing with diagonal_A extension

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• mixture predict now allows changing the mixture actively

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• Refactored stats_1

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• stats_1 no longer needs skips

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• LinearModel now tested with simple tests

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• Mixture models passing

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• Test suite now covers most things

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• Minor renaming

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Commits on Jan 15, 2024

• Need to reduce sensitivity of ks checks

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Commits on Jan 17, 2024

• Fixed bug in rvs for mixtures with new tests

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Commits on Jan 28, 2024

• stats now passing

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Commits on Feb 3, 2024

• rvs now testing and fast

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• Lowered pvalue

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  c68e8e7

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• Added a broadcast argument to logpdf

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• Broadcasting now working

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Commits on Feb 6, 2024

• Test suite now passing

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  24f2ad5

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• Executed renaming

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  55e9bd0

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• Corrected tests

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  b80bba1

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• Corrected imports for Reduced classes

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• Updated for black 24.1.1

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• Reordered theta D for joint

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• Removed partial code

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  4bc07c5

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• Corrected transposition error

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• Corrected sphinx docstrings

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Commits on Feb 7, 2024

• Made covariance calculations more reliable

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  1d56c8c

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• Removed now unused function

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• Aiming for 100% coverage

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Commits on Feb 9, 2024

• Corrected syntax error in assert

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  c73d43e

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• Actually corrected typos

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  8e8b6de

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• Updated

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  a0bda84

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• Corrected docstrings for sphinx

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  941e151

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• bump version to 0.13.0

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  32acdab

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• Now testing model.k

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  0046a25

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• Now covering k

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Commits on Feb 13, 2024

• Changed from np.choose to np.take_along_axis

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Commits on Feb 14, 2024

• Added cleaner defaults

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  6bc0e22

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• Cursed greek letter option

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• Added in aliases and logw

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  deedd4e

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• Reverted Reduced models for now

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Commits on Feb 15, 2024

• Improved alias functionality

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• Added a test for alias and model kwargs

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  d6c3996

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• Corrected black

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• Corrected isort

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• Corrected test_linear_model_init

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Commits on Feb 16, 2024

• Corrections of conversions

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  03f4e05

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• Fixed normalisation

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  1bb3d6b

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• Added tests to cover ppd and update

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  19dd841

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• Now passing on diagonal

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  2aaeaf8

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• Now covering ppd

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Commits on Feb 18, 2024

• Added a KL divergence

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  9a26f37

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• Implemented broadcasting for mixture models

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  91ff25f

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• Fixed broadcasting tests

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Commits on Feb 19, 2024

• Actually fixed broadcasting now

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• Removed in the end unecessary broadcasting code

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Commits on Feb 20, 2024

• Re-instated rvs with broadcast=True

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Commits on Feb 22, 2024

• Removed unusual conversion

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Commits on Feb 23, 2024

• Added plotting functions

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• Added a plot member function to stats

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• Merge branch 'multivariate_normal' into plot

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• Updated plot and stats to be recursive

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Commits on Feb 28, 2024

• Merge branch 'master' into plot

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• 1d->2d error

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Commits on Feb 29, 2024

• updated black adjustment

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• Updated sphinx documentation

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Commits on Mar 1, 2024

• Added anesthetic to plot optional dependency

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• Added anesthetic as a dependency

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• tests now available

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  8cc25cc

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• Restricted tests to valid sections

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  ea8e6e0

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Commits on Mar 5, 2024

• Halfway through stats

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• implemented Bayesian model dimensionality

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Commits on Mar 6, 2024

• Added mutual information and total dimensionality

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• Updated model dimensionality for tests

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  99b4f46

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• Tests now passing

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  9a15e22

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• added monte carlo error estimates

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  5bf5fb4

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• Trying to debug underestimate of dimensionality error

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  ca4d0d2

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• Made some notes about bmd error estimation. To naut. Let's just give it generous error bars

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  5a82db7

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• Cleaned up stats.py

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  c091a36

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• Tests now up to date

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  d0e083b

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• bump version to 0.13.0

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  362b06a

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• Fixed documentation

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Commits on Apr 30, 2024

• Merge branch 'master' into plot

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Commits on May 13, 2024

• Corrected cholesky

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Commits on May 14, 2024

• Updated plotting for mixtures

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• Merge branch 'master' into plot

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Commits on Jul 4, 2024

• remove torch dep

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• merge

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Commits on Jul 25, 2024

• Removed BMD changes

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• Merge branch 'network_refactor' into plot

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• removed temporary file

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• Merge branch 'network_refactor' into plot

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Commits on Sep 15, 2024

• Updates post imperial talk

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