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Better testing, and more objective functions #79

Merged
merged 106 commits into from
Nov 1, 2023
Merged

Better testing, and more objective functions #79

merged 106 commits into from
Nov 1, 2023

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miguelgondu
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miguelgondu and others added 30 commits September 4, 2023 12:29
@miguelgondu
Merge pull request #25 from MachineLearningLifeScience/master
9fc4cea 
Merge pull request #24 from MachineLearningLifeScience/dev
@miguelgondu
Updates the environment for lambo, forces registration, adds example
def6565
@miguelgondu
For now, we add dev installation instead of master
6472be8
@RMichae1
Merge pull request #27 from MachineLearningLifeScience/bugfix-cleans-…
bfc0650 
…the-environment-for-lambo

Updates the environment for lambo, forces registration, adds example
@SimonBartels
enabling support for unaligned problems
085afe3 
Closes #16
@SimonBartels
Merge branch 'dev' of github.com:MachineLearningLifeScience/poli into…
6ad8d5f 
… dev
@miguelgondu
adds a description of how to contribute
635102e
@miguelgondu
Merge branch 'dev' of github.com:MachineLearningLifeScience/poli into…
d0359d9 
… dev
@miguelgondu
Adds three lambo objectives, including an example
e04e751
@miguelgondu
Removes the lambo tests, they take too long on GitHub
6ac1f7c
@miguelgondu
Merge pull request #28 from MachineLearningLifeScience/feature-adds-l…
5bb19ec 
…ambo-objectives

Adds three lambo objectives, including an example
@miguelgondu
Updates the readme and example for the ddr3 docking task
0f9310f
@miguelgondu
renames the docking task, fixing a small typo
8628499
@miguelgondu
Adds SA from TDC as an objective, refactors TDC-related black boxes
2fffe6b
@miguelgondu
Forgot about formatting the files
a803b1e
@miguelgondu
Merge pull request #29 from MachineLearningLifeScience/feature-add-sa…
c8f607b 
…-objective

Adds SA from TDC as an objective, refactors TDC-related black boxes
@miguelgondu
Fixes a bug on generating molecules from selfies
7ccdbea
@SimonBartels
fixed broken observer support
bdbb97c
@miguelgondu
Cleans up a repeated operation in tests. Moves a poli-baselines test …
83c3350 
…to poli-baselines
added problem sequence individual fix replacement in wrapper
83ea6a9
black formatting for RFPWrapper
343bd9c
@RMichae1
Merge pull request #31 from MachineLearningLifeScience/30-lambo-basic…
ea39a16 
…-aa-alphabet-breaks-on-problematic-rfp-sequence

added problem sequence individual fix replacement in wrapper
@miguelgondu
Implements repairing using the foldx interface, allows users to pass …
c458cf8 
…zero mutations
@miguelgondu
Merge pull request #32 from MachineLearningLifeScience/feat-improving…
2f13ea8 
…-foldx-interface

Implements repairing using the foldx interface, allows users to pass …
@miguelgondu
Starts implementing an alternate version of foldx to include more tha…
fa76162 
…n one wildtype
@miguelgondu
Fixes a bug on the process wrapper information passing
b9ca64f
@miguelgondu
adds a common black box function for foldx tasks
185c10e
@miguelgondu
Removes unused packages
880437a
@miguelgondu
Merge pull request #33 from MachineLearningLifeScience/feature-more-t…
87c4ec3 
…han-one-wildtype-foldx

More than one wildtype in `foldx` objectives
@miguelgondu
Adds parallelization to the call of the abstract black box
d630e48
@miguelgondu
Implements a black box function for RaSP
437f6cd
@miguelgondu
Implements a black box function for RaSP
11caa69
@miguelgondu
Runs linting
b9fa69b
@miguelgondu
Forgot linting of one file
f3bebb7
@miguelgondu
Implements the problem factory for RaSP
30ff002
@miguelgondu
Makes sure that the position in the variant is accurate by relying on…
dea47d5 
… the residue information
@miguelgondu
Cleans up the warnings thrown by RaSP inference
ffa60bb
@miguelgondu
Refactors the interface and model loading to have more representative…
9d510e4 
… names
@miguelgondu
Adds better error handling and exceptions when running commands on th…
2becc26 
…e terminal in RaSP
@miguelgondu
Implements RaSP for more than one wildtype
9473941
@miguelgondu
Uncomments foldx example and lints
b3e8694
@miguelgondu
Adds an example of how to compute saturation mutagenesis using RaSP
5c25427
@miguelgondu
Implements downloading the cavity and downstream models from RaSPs re…
85f2639 
…pository
@miguelgondu
Adds MD5 checksums to verify the integrity of the models we download
3aa48a9
@miguelgondu
Adds a test for RaSP (which will get skipped in the action, unfortuna…
f871534 
…tely)
@miguelgondu
Updates the conda environment for RaSP
36b39f6
@miguelgondu
Uses pdb tools directly, instead of running a subprocess
e5dcaf2
@miguelgondu
Merge pull request #76 from MachineLearningLifeScience/feature-add-rasp
3273c8f 
Add `RaSP` as an objective function
@miguelgondu
Adds RaSP to testing
89ee670
@miguelgondu
Adds forceful registration to the RaSP test
a905d2e
@miguelgondu
Adds missing dependencies to poli__protein and poli__rasp envs
81f396e
@miguelgondu
Refactors tests, and removes RaSP from testing on dev
dff5441
@miguelgondu
Specifies the ignore paths as posargs in tox
cd0cab0
@miguelgondu
Specifies a different configuration file for dev and master testing
c1985e6
@miguelgondu
Specifies config file for linting in the github action
c982a38
@miguelgondu
Removes the installation of the poli__rasp environment from tox dev
675646e
@miguelgondu
Incorporates these changes to testing in the documentation of how to …
f785116 
…contribute
@miguelgondu
Merge pull request #78 from MachineLearningLifeScience/feature-better…
7074477 
…-testing

Test using `docker` & add `RaSP` to testing
@miguelgondu miguelgondu merged commit 3543b70 into master Nov 1, 2023
2 checks passed
miguelgondu added a commit that referenced this pull request Nov 1, 2023
@miguelgondu
Merge pull request #80 from MachineLearningLifeScience/master
55e348f 
Merge pull request #79 from MachineLearningLifeScience/dev
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3 participants
@miguelgondu @RMichae1 @SimonBartels