Use Paramspace to automate the file naming scheme based on wildcards #40
Commits on Jan 20, 2023
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Config key names need to be valid Python
Can't have hyphens. Better to use hyphens to separate params.
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Commits on Jan 25, 2023
Commits on Jan 28, 2023
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Implement 'exclude_param_keys' in config
to give users control over paramspace wildcards
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Move paramspace-related functions to separate script
and write unit tests
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Write get_paramspace_from_config()
Also fix instances_drop_wildcard() so it returns a unique set
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Commits on Jan 29, 2023
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Fix typo for find_feature_importance
Have to use output filepath, not rules.output, because the plot is blank when find_feat_imp is False
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Use 'include' instead of 'import' for snakedeploy
Otherwise, will get a ModuleNotFoundError when deploying this module with snakedeploy
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No need to specify inner_join(by)
Just use all columns that match
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Merge branch 'paramspace' of https://github.com/SchlossLab/mikropml-s…
…nakemake-workflow into paramspace
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Get method,seed,kfold from wildcards not params
Because of this error with snakedeploy: WildcardError in file https://github.com/SchlossLab/mikropml-snakemake-workflow/raw/paramspace/workflow/rules/learn.smk, line 25: Wildcards in params cannot be determined from output files. Note that you have to use a function to deactivate automatic wildcard expansion in params strings, e.g., `lambda wildcards: '{test}'`. Also see https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules: 'method'
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Merge branch 'paramspace' of https://github.com/SchlossLab/mikropml-s…
…nakemake-workflow into paramspace
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Silence snakemake linter warning about abs paths
These are not absolute paths, but the snakemake linter thinks they are. Moving the slash to the end of the regex should fix it. Lints for snakefile /github/workspace/workflow/scripts/functions.py: * Absolute path "/{{0,1}}{wildcard}{paramspace.param_sep}{{{wildcard}}}" in line 36: Do not define absolute paths inside of the workflow, since this renders your workflow irreproducible on other machines. Use path relative to the working directory instead, or make the path configurable via a config file. Also see: https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration * Absolute path "/{{0,1}}{wildcard}{paramspace.param_sep}[a-zA-Z_0-9]*" in line 54: Do not define absolute paths inside of the workflow, since this renders your workflow irreproducible on other machines. Use path relative to the working directory instead, or make the path configurable via a config file. Also see: https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration -
Merge branch 'paramspace' of https://github.com/SchlossLab/mikropml-s…
…nakemake-workflow into paramspace
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New rule to write the paramspace to csv
This may be needed because workflows that use this module with snakedeploy won't have access to the paramspace object
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Merge branch 'paramspace' of https://github.com/SchlossLab/mikropml-s…
…nakemake-workflow into paramspace
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Move write_paramspace code to script to satisfy linter
Nothing was actually wrong with it. Snakemake has a bug (snakemake issue #2035).
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Merge branches 'paramspace' and 'paramspace' of https://github.com/Sc…
…hlossLab/mikropml-snakemake-workflow into paramspace
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Commits on Jan 30, 2023
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Switch from pytest-parallel to pytest-xdist
Got a warning in pytest-parallel, found out it's no longer maintained. kevlened/pytest-parallel#118
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Merge branch 'paramspace' of https://github.com/SchlossLab/mikropml-s…
…nakemake-workflow into paramspace
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Merge branch 'paramspace' of https://github.com/SchlossLab/mikropml-s…
…nakemake-workflow into paramspace
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Merge branch 'paramspace' of https://github.com/SchlossLab/mikropml-s…
…nakemake-workflow into paramspace
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Commits on Jan 31, 2023
Commits on Feb 1, 2023
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Merge branch 'paramspace' of https://github.com/SchlossLab/mikropml-s…
…nakemake-workflow into paramspace
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Merge branch 'paramspace' of https://github.com/SchlossLab/mikropml-s…
…nakemake-workflow into paramspace
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Merge branch 'paramspace' of https://github.com/SchlossLab/mikropml-s…
…nakemake-workflow into paramspace