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anesthetic style plotting functions #35

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a864de9
bump version to 0.12.0
williamjameshandley Dec 7, 2023
a6cafd4
rvs and logpdf working
williamjameshandley Dec 7, 2023
eda4482
Now broadcasting for cov and mean
williamjameshandley Dec 7, 2023
c204e64
predict, condition and marginalise now working
williamjameshandley Dec 7, 2023
280c79c
bijector now tested
williamjameshandley Dec 7, 2023
d57bbfb
Halfway through mixture upgrade
williamjameshandley Dec 8, 2023
5cf4a5b
Extended predict tests
williamjameshandley Dec 8, 2023
5d90763
Now not unecessarily flattening covariance matrices
williamjameshandley Dec 8, 2023
7cbc65f
Merge branch 'multivariate_normal_temp' into multivariate_normal
williamjameshandley Dec 8, 2023
52155bd
rvs working
williamjameshandley Dec 9, 2023
32d847b
Neater version of logpdf and rvs without flatten
williamjameshandley Dec 10, 2023
d0cdd9d
Removed _flatten completely
williamjameshandley Dec 10, 2023
7cd4bdd
condition now running
williamjameshandley Dec 10, 2023
c154533
bijector now tested and working
williamjameshandley Dec 10, 2023
30f456d
Commented and corrected the predict function for mixtures
williamjameshandley Dec 10, 2023
f5cc946
Added cleverer defaults to multivariate_normal
williamjameshandley Dec 10, 2023
015f5e5
Added checks for the new default system
williamjameshandley Dec 10, 2023
c548fb6
Better defaults for b
williamjameshandley Dec 11, 2023
6849ad3
Lazy expansion of mean now working
williamjameshandley Dec 12, 2023
5636294
lazy covariance tests now completing
williamjameshandley Dec 12, 2023
a7e4304
Fixed rvs
williamjameshandley Dec 12, 2023
a080991
A and b now lazily evaluating
williamjameshandley Dec 12, 2023
eaae7d1
Lazy A and b now working
williamjameshandley Dec 12, 2023
403e48c
Tests passing
williamjameshandley Dec 17, 2023
e86652a
re-graded to not bother with checking for scalar means and covariances
williamjameshandley Dec 18, 2023
735ad0d
Minor update to stats
williamjameshandley Dec 26, 2023
a6895f0
First draft of model
williamjameshandley Dec 27, 2023
e62f52c
Begun switch to diagonal_cov strategy
williamjameshandley Dec 28, 2023
03881eb
Removed special treatment of M for now
williamjameshandley Jan 6, 2024
c9fe98a
Tests now passing
williamjameshandley Jan 6, 2024
6ecffaa
Reinstated more efficient calculations
williamjameshandley Jan 6, 2024
1d29ff4
Major test suite completed
williamjameshandley Jan 8, 2024
634cecf
Test suite now too large to fit in memory. Need a different strategy
williamjameshandley Jan 8, 2024
c05c314
Got stats_1 tests now running
williamjameshandley Jan 13, 2024
17a9a64
Predict now passing with diagonal_A extension
williamjameshandley Jan 14, 2024
7fc035b
mixture predict now allows changing the mixture actively
williamjameshandley Jan 14, 2024
d2b32f3
Refactored stats_1
williamjameshandley Jan 14, 2024
cbdbbb9
stats_1 no longer needs skips
williamjameshandley Jan 14, 2024
c1230dd
LinearModel now tested with simple tests
williamjameshandley Jan 14, 2024
ac6541e
Mixture models passing
williamjameshandley Jan 14, 2024
53d60b1
Test suite now covers most things
williamjameshandley Jan 14, 2024
2e9ef64
Minor renaming
williamjameshandley Jan 14, 2024
0724b1a
Need to reduce sensitivity of ks checks
williamjameshandley Jan 15, 2024
46b3f89
Fixed bug in rvs for mixtures with new tests
williamjameshandley Jan 17, 2024
7508774
stats now passing
williamjameshandley Jan 28, 2024
263b953
rvs now testing and fast
williamjameshandley Feb 3, 2024
c68e8e7
Lowered pvalue
williamjameshandley Feb 3, 2024
ced80f6
Added a broadcast argument to logpdf
williamjameshandley Feb 3, 2024
f057566
Broadcasting now working
williamjameshandley Feb 3, 2024
24f2ad5
Test suite now passing
williamjameshandley Feb 6, 2024
55e9bd0
Executed renaming
williamjameshandley Feb 6, 2024
b80bba1
Corrected tests
williamjameshandley Feb 6, 2024
1a57580
Corrected imports for Reduced classes
williamjameshandley Feb 6, 2024
3a6cd87
Updated for black 24.1.1
williamjameshandley Feb 6, 2024
036142f
Reordered theta D for joint
williamjameshandley Feb 6, 2024
4bc07c5
Removed partial code
williamjameshandley Feb 6, 2024
f54a8d1
Corrected transposition error
williamjameshandley Feb 6, 2024
26633ee
Corrected sphinx docstrings
williamjameshandley Feb 6, 2024
1d56c8c
Made covariance calculations more reliable
williamjameshandley Feb 7, 2024
5758456
Removed now unused function
williamjameshandley Feb 7, 2024
00a338a
Aiming for 100% coverage
williamjameshandley Feb 7, 2024
c73d43e
Corrected syntax error in assert
williamjameshandley Feb 9, 2024
8e8b6de
Actually corrected typos
williamjameshandley Feb 9, 2024
a0bda84
Updated
williamjameshandley Feb 9, 2024
941e151
Corrected docstrings for sphinx
williamjameshandley Feb 9, 2024
32acdab
bump version to 0.13.0
williamjameshandley Feb 9, 2024
0046a25
Now testing model.k
williamjameshandley Feb 9, 2024
11ba9c2
Now covering k
williamjameshandley Feb 9, 2024
c84390e
Changed from np.choose to np.take_along_axis
williamjameshandley Feb 13, 2024
6bc0e22
Added cleaner defaults
williamjameshandley Feb 14, 2024
31924fe
Cursed greek letter option
williamjameshandley Feb 14, 2024
deedd4e
Added in aliases and logw
williamjameshandley Feb 14, 2024
5680036
Reverted Reduced models for now
williamjameshandley Feb 14, 2024
e393908
Improved alias functionality
williamjameshandley Feb 15, 2024
d6c3996
Added a test for alias and model kwargs
williamjameshandley Feb 15, 2024
0bb9009
Corrected black
williamjameshandley Feb 15, 2024
448cb05
Corrected isort
williamjameshandley Feb 15, 2024
046174f
Corrected test_linear_model_init
williamjameshandley Feb 15, 2024
03f4e05
Corrections of conversions
williamjameshandley Feb 16, 2024
1bb3d6b
Fixed normalisation
williamjameshandley Feb 16, 2024
19dd841
Added tests to cover ppd and update
williamjameshandley Feb 16, 2024
2aaeaf8
Now passing on diagonal
williamjameshandley Feb 16, 2024
6d38b67
Now covering ppd
williamjameshandley Feb 16, 2024
9a26f37
Added a KL divergence
williamjameshandley Feb 18, 2024
91ff25f
Implemented broadcasting for mixture models
williamjameshandley Feb 18, 2024
082db82
Fixed broadcasting tests
williamjameshandley Feb 18, 2024
4da731d
Actually fixed broadcasting now
williamjameshandley Feb 19, 2024
b9362cb
Removed in the end unecessary broadcasting code
williamjameshandley Feb 19, 2024
9e94da2
Re-instated rvs with broadcast=True
williamjameshandley Feb 20, 2024
6382422
Removed unusual conversion
williamjameshandley Feb 22, 2024
75827e8
Added plotting functions
williamjameshandley Feb 23, 2024
dc4922a
Added a plot member function to stats
williamjameshandley Feb 23, 2024
8747add
Merge branch 'multivariate_normal' into plot
williamjameshandley Feb 23, 2024
7404e40
Updated plot and stats to be recursive
williamjameshandley Feb 23, 2024
5714e56
Merge branch 'master' into plot
williamjameshandley Feb 28, 2024
28f87e5
1d->2d error
williamjameshandley Feb 28, 2024
d2f73a1
updated black adjustment
williamjameshandley Feb 29, 2024
c5d41ad
Updated sphinx documentation
williamjameshandley Feb 29, 2024
e1add3f
Added anesthetic to plot optional dependency
williamjameshandley Mar 1, 2024
5efce71
Added anesthetic as a dependency
williamjameshandley Mar 1, 2024
8cc25cc
tests now available
williamjameshandley Mar 1, 2024
ea8e6e0
Restricted tests to valid sections
williamjameshandley Mar 1, 2024
e468392
Halfway through stats
williamjameshandley Mar 5, 2024
6127eb5
implemented Bayesian model dimensionality
williamjameshandley Mar 5, 2024
d28419e
Added mutual information and total dimensionality
williamjameshandley Mar 6, 2024
99b4f46
Updated model dimensionality for tests
williamjameshandley Mar 6, 2024
9a15e22
Tests now passing
williamjameshandley Mar 6, 2024
5bf5fb4
added monte carlo error estimates
williamjameshandley Mar 6, 2024
ca4d0d2
Trying to debug underestimate of dimensionality error
williamjameshandley Mar 6, 2024
5a82db7
Made some notes about bmd error estimation. To naut. Let's just give …
williamjameshandley Mar 6, 2024
c091a36
Cleaned up stats.py
williamjameshandley Mar 6, 2024
d0e083b
Tests now up to date
williamjameshandley Mar 6, 2024
362b06a
bump version to 0.13.0
williamjameshandley Mar 6, 2024
ba3abce
Fixed documentation
williamjameshandley Mar 6, 2024
d3dbcc8
Merge branch 'master' into plot
williamjameshandley Apr 30, 2024
6974b7a
Corrected cholesky
williamjameshandley May 13, 2024
b0e2205
Updated plotting for mixtures
williamjameshandley May 14, 2024
f766620
Merge branch 'master' into plot
williamjameshandley May 14, 2024
1c94fc1
remove torch dep
yallup Jul 4, 2024
1a46863
merge
yallup Jul 4, 2024
b28d8b3
Removed BMD changes
williamjameshandley Jul 25, 2024
674b296
Merge branch 'network_refactor' into plot
williamjameshandley Jul 25, 2024
1293df3
removed temporary file
williamjameshandley Jul 25, 2024
704c556
Merge branch 'network_refactor' into plot
williamjameshandley Jul 25, 2024
7b26ed0
Updates post imperial talk
williamjameshandley Sep 15, 2024
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3 changes: 1 addition & 2 deletions README.rst
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ lsbi: Linear Simulation Based Inference
=======================================
:lsbi: Linear Simulation Based Inference
:Author: Will Handley & David Yallup
:Version: 0.12.2
:Version: 0.13.0
:Homepage: https://github.com/handley-lab/lsbi
:Documentation: http://lsbi.readthedocs.io/

Expand Down Expand Up @@ -134,7 +134,6 @@ There are many ways you can contribute via the `GitHub repository <https://githu

- You can `open an issue <https://github.com/handley-lab/lsbi/issues>`__ to report bugs or to propose new features.
- Pull requests are very welcome. Note that if you are going to propose major changes, be sure to open an issue for discussion first, to make sure that your PR will be accepted before you spend effort coding it.
- Adding models and data to the grid. Contact `Will Handley <mailto:[email protected]>`__ to request models or ask for your own to be uploaded.


Questions/Comments
Expand Down
8 changes: 5 additions & 3 deletions docs/source/lsbi.rst
Original file line number Diff line number Diff line change
Expand Up @@ -16,12 +16,13 @@ lsbi.model module
:show-inheritance:


lsbi.network module
-------------------
lsbi.plot module
----------------

.. automodule:: lsbi.network
.. automodule:: lsbi.plot
:members:
:undoc-members:
:show-inheritance:


lsbi.stats module
Expand All @@ -30,6 +31,7 @@ lsbi.stats module
.. automodule:: lsbi.stats
:members:
:undoc-members:
:show-inheritance:


lsbi.utils module
Expand Down
2 changes: 1 addition & 1 deletion lsbi/_version.py
Original file line number Diff line number Diff line change
@@ -1 +1 @@
__version__ = "0.12.2"
__version__ = "0.13.0"
205 changes: 0 additions & 205 deletions lsbi/network.py

This file was deleted.

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