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[WIP] 207 add the work of neidhart et al as a black box #214

Merged
merged 47 commits into from
Jul 25, 2024
Merged

[WIP] 207 add the work of neidhart et al as a black box #214

merged 47 commits into from
Jul 25, 2024

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RMichae1
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@RMichae1 RMichae1 commented Jul 10, 2024 •
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Add work by Aita et al.
with additions of neidhart et al -> randomness from gen. Pareto instead of Gaussian , and "tunable" c.

Core method implemented as static method to an isolated black-box.

[WIP]

  • add tests logic
  • add tests batched function evaluations

@RMichae1 RMichae1 linked an issue Jul 10, 2024 that may be closed by this pull request
Add the work of Neidhart et al. as a black-box #207
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Looks like the added tests are doing their job +1

@RMichae1 RMichae1 requested a review from miguelgondu July 12, 2024 13:17
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RMichae1 commented Jul 12, 2024 •
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Corrected black-box functionality and added tests for seeding and expected computed values.
Ready for review @miguelgondu .

Might have to rebase on current dev .

@RMichae1 RMichae1 force-pushed the 207-add-the-work-of-neidhart-et-al-as-a-black-box branch from bf19be2 to ae59dfe Compare July 12, 2024 13:45
@RMichae1 RMichae1 marked this pull request as ready for review July 12, 2024 13:47
miguelgondu
miguelgondu reviewed Jul 12, 2024
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tox.ini
@@ -98,7 +98,7 @@ commands=
pytest {tty:--color=yes} -v -m "not slow and poli__dockstring" {posargs}

[testenv:poli-rasp-py39]
description = run the tests with pytest on the dockstring environment for poli
description = run the tests with pytest on the RaSP environment for poli
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Nice catch, thanks!

miguelgondu
miguelgondu requested changes Jul 15, 2024
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Hey Richard! Great job, I left a couple of comments to address.

src/poli/objective_repository/rmf_landscape/isolated_function.py Outdated Show resolved Hide resolved
src/poli/objective_repository/rmf_landscape/register.py Outdated Show resolved Hide resolved
src/poli/objective_repository/rmf_landscape/register.py Outdated Show resolved Hide resolved
src/poli/objective_repository/rmf_landscape/register.py Outdated Show resolved Hide resolved
src/poli/tests/registry/proteins/test_rmf.py Outdated Show resolved Hide resolved
src/poli/tests/registry/proteins/test_rmf.py Show resolved Hide resolved
src/poli/tests/registry/proteins/test_rmf.py Show resolved Hide resolved
Richard Michael and others added 25 commits July 25, 2024 14:19
lint
cf1035c
Add RMF objective, logic, info, and factory
cffffc3
add inner_function on init, add module_to_import to inner_function get
14cd184
correction shape and object types
ad87418
add tests availability, isolation, batch_eval
1f48c49
added random state as class property
ab0f5bc
black, linting
2a86532
add test batch eval
9f78d12
corrections: compute HD, batched results in loop, OH to int encoding
fad4654
add tests seeding and expected values
6e2962f
add environment marker
7c8dacf
add poli-rmf as testenv
d326622
add github workflow
a75927a
isort
5149e06
move imports into env markers
bd83ca8
reblack
c9f737f
@miguelgondu
Modifies the name of the isolated function
d699b85
fix tox test commands
9de1704
no conda runs but shell invoke
695c9ee
__future__ type annotations
5c8b514
Add blackbox docstring
4cbce6e
removed deprecated test
90903ea
lint
68dc275
Merge branch '207-add-the-work-of-neidhart-et-al-as-a-black-box' of g…
666647c 
…ithub.com:MachineLearningLifeScience/poli into 207-add-the-work-of-neidhart-et-al-as-a-black-box
isort on __future__
4738787
miguelgondu
miguelgondu approved these changes Jul 25, 2024
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Looks great! Thanks for addressing the TO-DOs.

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Thanks for the review!:)

@RMichae1 RMichae1 merged commit 664a69b into dev Jul 25, 2024
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@RMichae1 RMichae1 deleted the 207-add-the-work-of-neidhart-et-al-as-a-black-box branch July 25, 2024 12:41
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Add the work of Neidhart et al. as a black-box
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