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Main logged verbose abc
Congm12
reviewed
Nov 27, 2024
| @@ -1,10 +1,12 @@ | |||
| name: calicost_env | |||
| name: calicost | |||
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This corresponds to condo environment name, right? If so, shall we change it back as the README and readthedocs documentations still have conda activate calicost_env in the installation instruction.
Congm12
reviewed
Nov 27, 2024
| @@ -1 +1 @@ | |||
| __version__ = 'v1.0.0' | |||
| __version__ = "v1.0.0" | |||
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How about set the version to v1.1?
Congm12
reviewed
Nov 27, 2024
| start_params=None, | ||
| maxiter=10_000, | ||
| maxfun=5_000, | ||
| write_chain=True, |
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Shall we make write_chain to be False by default? I remember it caused problems when I start multiple CalicoST runs in the same directory and all runs tried to write the fitting details to the same file.
Congm12
reviewed
Nov 27, 2024
Congm12
reviewed
Nov 27, 2024
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This file is not used anywhere and is almost empty
Congm12
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Nov 27, 2024
There was a problem hiding this comment.
This file is not used anywhere.
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Updates the config files to specify the scipy/numpy versions consistently between the environment managers.
Specifies difference between max_iter_outer & max_iter_outer_initial in config file and downstream usage.
no longer specifies a single thread for MKL in calicost supervised.
addition of ARI and Hamming distance for clone convergence in EM.
TBC
Should aim to address:
compatible scipy version for frequent ".A error" in parse_final_snp.py, utils_IO.py, etc. #14