562 fix codacy on master 1

[ntchen]

No description provided.

[codecov-commenter]

Codecov Report

Attention: 34 lines in your changes are missing coverage. Please review.

Comparison is base (5043785) 95.05% compared to head (2ec4427) 95.12%.

Files	Patch %	Lines
domainlab/algos/trainers/compos/matchdg_match.py	86.95%	6 Missing ⚠️
domainlab/algos/trainers/train_matchdg.py	86.20%	4 Missing ⚠️
domainlab/algos/builder_custom.py	77.77%	2 Missing ⚠️
domainlab/algos/trainers/zoo_trainer.py	50.00%	2 Missing ⚠️
domainlab/utils/u_import_net_module.py	66.66%	2 Missing ⚠️
domainlab/algos/msels/c_msel_oracle.py	0.00%	1 Missing ⚠️
domainlab/arg_parser.py	98.14%	1 Missing ⚠️
domainlab/compos/nn_zoo/net_gated.py	85.71%	1 Missing ⚠️
domainlab/compos/vae/c_vae_recon.py	85.71%	1 Missing ⚠️
...omainlab/compos/vae/compos/encoder_xyd_parallel.py	83.33%	1 Missing ⚠️
... and 13 more

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #741      +/-   ##
==========================================
+ Coverage   95.05%   95.12%   +0.07%     
==========================================
  Files         125      125              
  Lines        4911     4902       -9     
==========================================
- Hits         4668     4663       -5     
+ Misses        243      239       -4     

Flag	Coverage Δ
unittests	95.12% <95.98%> (+0.07%)	⬆️

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[smilesun]

CI is broken

[smilesun]

@ntchen snakemake/snakemake#2607

[smilesun]

https://anaconda.org/bioconda/snakemake

[smilesun]

https://app.codacy.com/gh/marrlab/DomainLab/pullRequest?bid=39739936&prid=13402189&utm_campaign=new_commit&utm_medium=Email&utm_source=Internal&

[ntchen]

https://app.codacy.com/gh/marrlab/DomainLab/pullRequest?bid=39739936&prid=13402189&utm_campaign=new_commit&utm_medium=Email&utm_source=Internal&

It seems that they are not new issues. The file modifications triggered a scan which resulted in the identification of these new issues. The total issues were reduced from 639 to 573.

[ntchen]

`UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:
Specifications:

• bioconda::snakemake -> python[version='3.4.|3.5.|3.6.*|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0']`

[smilesun]

`UnsatisfiableError: The following specifications were found to be incompatible with the existing python installation in your environment: Specifications:

• bioconda::snakemake -> python[version='3.4.|3.5.|3.6.*|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0']`

so we will increase the python version to 3.11, then pip should find snakemake 8.2.0

[smilesun]

If this passed, then we have python3.11 for domainlab and we could install latest snakemake

#743

[ntchen]

https://app.codacy.com/gh/marrlab/DomainLab/pullRequest?bid=39739936&prid=13402189&utm_campaign=new_commit&utm_medium=Email&utm_source=Internal&

It seems that they are not new issues. The file modifications triggered a scan which resulted in the identification of these new issues. The total issues were reduced from 639 to 573.

How shall we merge it after success CI tests? It will not be fast to fix the 573 issues. We can try to adjust settings to focus on the changes made in the merge request rather than scanning all related files. But even though, I think the changed lines include a lot of other issues. is it worth overriding merge checks?

[smilesun]

https://app.codacy.com/gh/marrlab/DomainLab/pullRequest?bid=39739936&prid=13402189&utm_campaign=new_commit&utm_medium=Email&utm_source=Internal&

It seems that they are not new issues. The file modifications triggered a scan which resulted in the identification of these new issues. The total issues were reduced from 639 to 573.

How shall we merge it after success CI tests? It will not be fast to fix the 573 issues. We can try to adjust settings to focus on the changes made in the merge request rather than scanning all related files. But even though, I think the changed lines include a lot of other issues. is it worth overriding merge checks?

some issues are not avoidable:e.g. too many arguments in a function, we could fix other issues manually though. see my latest commits.

[smilesun]

@ntchen

Run pip install pulp<2.8 && install snakemake==7.32.0 && sed -i '1s/^/#!/bin/bash -x -v\n/' run_benchmark_standalone.sh && bash -x -v run_benchmark_standalone.sh examples/benchmark/demo_shared_hyper_grid.yaml && cat zoutput/benchmarks/mnist_benchmark_grid/hyperparameters.csv && cat zoutput/benchmarks/mnist_benchmark_grid/results.csv
/home/runner/work/_temp/0e90565a-d45b-415a-9af3-e86f855f7956.sh: line 1: 2.8: No such file or directory
Error: Process completed with exit code 1.

[ntchen]

@ntchen

Run pip install pulp<2.8 && install snakemake==7.32.0 && sed -i '1s/^/#!/bin/bash -x -v\n/' run_benchmark_standalone.sh && bash -x -v run_benchmark_standalone.sh examples/benchmark/demo_shared_hyper_grid.yaml && cat zoutput/benchmarks/mnist_benchmark_grid/hyperparameters.csv && cat zoutput/benchmarks/mnist_benchmark_grid/results.csv /home/runner/work/_temp/0e90565a-d45b-415a-9af3-e86f855f7956.sh: line 1: 2.8: No such file or directory Error: Process completed with exit code 1.

it should be the missing pip for snakemake. You already fixed it

[smilesun]

@ntchen
Run pip install pulp<2.8 && install snakemake==7.32.0 && sed -i '1s/^/#!/bin/bash -x -v\n/' run_benchmark_standalone.sh && bash -x -v run_benchmark_standalone.sh examples/benchmark/demo_shared_hyper_grid.yaml && cat zoutput/benchmarks/mnist_benchmark_grid/hyperparameters.csv && cat zoutput/benchmarks/mnist_benchmark_grid/results.csv /home/runner/work/_temp/0e90565a-d45b-415a-9af3-e86f855f7956.sh: line 1: 2.8: No such file or directory Error: Process completed with exit code 1.

it should be the missing pip for snakemake. You already fixed it

not really, see the CI run result from my commit