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Bmti error dev #141

Merged
merged 11 commits into from
Sep 2, 2024
Merged

Bmti error dev #141

merged 11 commits into from
Sep 2, 2024

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charliematteo
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@charliematteo charliematteo commented Jul 30, 2024 •
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Proposed changes

Updated diagonal of inverse cross covariance of the deltaF in density_advanced (used in BMTI) to published version (https://arxiv.org/abs/2407.08094). This includes substantial edits to cython_grads, neighbour_graph and density_advanced.

PLEASE: before accepting pull request see if a fresh install of DADApy cloning this branch succeeds.

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  • [ x] Bugfix (non-breaking change which fixes an issue)
  • [ x ] New feature (non-breaking change which adds functionality)
  • Breaking change (fix or feature that would cause existing functionality to not work as expected)

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  • [ x ] Lint and unit tests pass locally with my changes
  • [ x ] I have added tests that prove my fix is effective or that my feature works

@charliematteo
added neigh_similiarity_index_mat to neigh_graph and to tests
fce3842
@charliematteo
fixed linting
16b7aa6
@charliematteo
fixed test_density_advanced
f323ff9
@charliematteo
updated inversion of deltaFs cross covariance to the latest developme…
a609753 
…nts, but still needs cleanup
@charliematteo
Re-cythonized cython_grads.pyx, now dadapy installs correctly in edit…
1911196 
…able mode with pip install -e .
@charliematteo
linting and updated README with reference
00d3d8a
@charliematteo
modified cython_grads and density advanced but currently unable to in…
d461b9d 
…stall dadapy
@charliematteo
debugged locally cython_grads, runs on a locally compiled version. Fa…
a047b11 
…iling to install dadapy in editable mode
@charliematteo
Removed pearson_mat from density_advanced. Fixed methods for estimati…
a635595 
…ng neigh_similarity_index_array and _mat
@charliematteo
fixed linting and all tests pass
4d080ea
@charliematteo
updated cython_grads.c, now dadapy regularly installson my computer
1e7c738
@charliematteo charliematteo requested a review from AldoGl July 30, 2024 20:52
@charliematteo charliematteo self-assigned this Jul 30, 2024
AldoGl
AldoGl approved these changes Sep 2, 2024
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@AldoGl AldoGl left a comment •
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Looks good to me, and I could install it in a fresh environment, we can merge!

@AldoGl AldoGl merged commit dd8a486 into main Sep 2, 2024
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@AldoGl AldoGl deleted the BMTI_error_dev branch September 2, 2024 13:55
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@AldoGl AldoGl AldoGl approved these changes

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@charliematteo @AldoGl