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fix: check PSSMs #401

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merged 45 commits into from May 11, 2023
Merged

fix: check PSSMs #401

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f8bbdd1
aa profile sorted by 3-letter code
DaniBodor Mar 19, 2023
4a9b7f0
move/remove amino_acids_by_letter
DaniBodor Mar 19, 2023
01b80bb
delete dummy pssm file
DaniBodor Mar 19, 2023
75691df
Merge branch 'main' into 332_pssmformat_dbodor
DaniBodor Mar 21, 2023
8db7189
allow excluding feature modules
DaniBodor Mar 21, 2023
380a188
test exception if no pssm is present
DaniBodor Mar 21, 2023
b509895
test exclude features
DaniBodor Mar 21, 2023
a3996d6
improve error message for no pssm file found
DaniBodor Mar 21, 2023
4bf6740
allow specifying chain ids in build_testgraph
DaniBodor Mar 21, 2023
bac0683
fix linting
DaniBodor Mar 21, 2023
835cd4e
ensure that excluding works if extension is included
DaniBodor Mar 21, 2023
e47ca22
actually make it work with extension
DaniBodor Mar 21, 2023
5a1a10f
allow strings for feature modules in QC
DaniBodor Mar 21, 2023
e3f3c7e
Merge branch 'main' into 332_pssmformat_dbodor
DaniBodor Mar 26, 2023
78f30db
fix exclude with .py
DaniBodor Mar 26, 2023
cfab145
fix bug for `exclude_feature_modules = None`
DaniBodor Apr 3, 2023
d0c46ee
aa nomenclature conversion
DaniBodor Apr 3, 2023
e12e27e
start on sanity check
DaniBodor Apr 3, 2023
ee21e7f
check pssm function should work
DaniBodor Apr 3, 2023
d51f9ab
docstring and passing chain id
DaniBodor Apr 3, 2023
02011ec
call pssm check
DaniBodor Apr 3, 2023
bc027d2
do not turn into list
DaniBodor Apr 3, 2023
32c6974
better error message
DaniBodor Apr 3, 2023
6b497ee
remove unused import
DaniBodor Apr 3, 2023
570429d
test bad pssms - not working
DaniBodor Apr 24, 2023
b27da6d
fix test by adding build()
DaniBodor May 4, 2023
77e2f19
Merge branch 'main' into 332_testmerge
DaniBodor May 4, 2023
ac6f783
remove PATH_TEST
DaniBodor May 4, 2023
d318e05
remove exclude_feature_modules parameter
DaniBodor May 11, 2023
6a52bf1
update default feature modules
DaniBodor May 11, 2023
bf98c79
set defaults in single code block
DaniBodor May 11, 2023
6cb9638
inlcude feaure log info and improve error message
DaniBodor May 11, 2023
c799c23
remove exclude option from error message
DaniBodor May 11, 2023
afcc5e1
remove exclude_feature_modules from test
DaniBodor May 11, 2023
e36ea2c
add _assert_correct_modules helper function
DaniBodor May 11, 2023
7e846fc
revamp single feature test
DaniBodor May 11, 2023
b8866ae
separate tests for default and all features
DaniBodor May 11, 2023
4044b70
fix test integration
DaniBodor May 11, 2023
5d4012c
wheel does not exist for pytorch 2.0.1
DaniBodor May 11, 2023
07a380b
fix typo and update readme
DaniBodor May 11, 2023
b48baa6
do not allow None for feature modules in query.process
DaniBodor May 11, 2023
0ecf7ca
correct versions of torchvision and torchaudio
DaniBodor May 11, 2023
9ffaacb
fix tests
DaniBodor May 11, 2023
e5f6176
Merge branch 'main' into 332_pssmformat_dbodor
DaniBodor May 11, 2023
febbd25
correct commands for installing pytorch 2.0.0
DaniBodor May 11, 2023
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2 changes: 1 addition & 1 deletion .github/actions/install-python-and-package/action.yml
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Expand Up @@ -60,7 +60,7 @@ runs:
# Only way to install msms is through conda
conda install -c bioconda msms
# Safest way to install PyTorch and PyTorch Geometric is through conda
conda install pytorch torchvision torchaudio cpuonly -c pytorch
conda install pytorch torchvision torchaudio cpuonly -c pytorch==2.0.0
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Great! I've also just noticed that in one of my branches. Also I had a question: why is the line 66 needed? (# Install optional pyg dependencies) Shouldn't conda install pyg -c pyg take care of the pyg dependencies?

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@DaniBodor DaniBodor May 11, 2023 •
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Don't know why, but it doesn't. I guess because they are optional?

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With conda, from their website it should not be necessary. Only with pip. So if it doesn't work using only conda install pyg -c pyg their docs are wrong

conda install pyg -c pyg
# Install optional pyg dependencies
python3 -m pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-$(python3 -c "import torch; print(torch.__version__)")+cpu.html
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