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Congm12
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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
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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
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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
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Nov 27, 2024
Congm12
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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
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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