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Add pylint github action #7

Merged
merged 1 commit into from
Mar 29, 2022
Merged

Add pylint github action #7

merged 1 commit into from
Mar 29, 2022

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fgypas
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@fgypas fgypas commented Mar 25, 2022

Pylint GitHub action. Current threshold (0.5)

@fgypas fgypas added the enhancement New feature or request label Mar 25, 2022
@fgypas fgypas self-assigned this Mar 25, 2022
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fgypas commented Mar 29, 2022

Note for me:
mamba create --name scar_test --override-channels cudatoolkit=11.1 pytorch=1.10 torchvision torchaudio tqdm pandas seaborn tensorboard scikit-learn anndata scanpy pyro-ppl --channel nvidia --channel pytorch --channel conda-forge

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fgypas commented Mar 29, 2022

The following example:

import pandas as pd
import scAR
from scAR.main._scAR import model

raw_ADT = pd.read_csv('raw_count.csv', index_col=0)
ambient_profile = pd.read_csv('ambient_profile.csv', index_col=0)

scarObj = model(raw_count=raw_ADT, empty_profile=ambient_profile, scRNAseq_tech='CITEseq', model='binomial')

scarObj.train(epochs=10, batch_size=64)

scarObj.inference()

Works fine and gives the following log:

..Running VAE using the following param set:
......scAR mode:  CITEseq
......count model:  binomial
......num_input_feature:  32
......NN_layer1:  150
......NN_layer2:  100
......latent_space:  15
......dropout_prob:  0
......kld_weight:  1e-05
......lr:  0.001
......lr_step_size:  5
......lr_gamma:  0.97
===========================================
  Training.....
100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████| 10/10 [00:15<00:00,  1.56s/it]
===========================================

@fgypas fgypas merged commit c1331e0 into develop Mar 29, 2022
@fgypas fgypas deleted the pylint-github-action branch April 4, 2022 22:02
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