CLI argument handler restructuring #16
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| # create data folder | ||
| # raises error if data directory exists (prevents overwriting) | ||
| data_dir_obj = Path("data") | ||
| data_dir_obj.mkdir(exist_ok=False) |
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I do not know if I explained to you about snakemake's ability to track the progress of the workflow and sets up save points for each successful rule. This is beautifully illustrated from this paper on figure 1 far right figure.
if --force where to be false, this indicates that when you re-run cytopipe it will start from where it failed. If --force where to be True, then executing cytopipe run again will cause the workflow to start from the beginning and recreate the files again.
Hopefully that clears any confusion!
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ooohh, so if the directory is created during cytopipe, if the cytopipe run fails, the directory will be deleted?
(i can't see fig 1 b/c paywall)
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Not necessarily. Remember, the data directory is important to maintain. That's how snakemake knows where to put the outputs files. What occurs is that snakemake knows that there are files within the data folder and when --force flag is True, you are telling snakemake (via cytopipe) "Hey, I know there are files there in there, but I want you to start from the beginning and overwrite them"
The data directory does not get deleted. The contents within the data folder gets overwritten.
Hopefully this makes sense!
P.S: I have sent the paper I was referring via Discord!
Co-authored-by: Gregory Way <gregory.way@gmail.com>
Co-authored-by: Gregory Way <gregory.way@gmail.com>
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Hey! @gwaybio I have answered one of your comments here. Hopefully my responses provide some clarity of the implementation. I ended up removing the I will be merging this now! |
Motivation
The motivation of this PR is in regards to how
cytopipehandles user input arguments from the terminal.The issue I was facing when working with the previous version of the
argsmodule was how fragile it was when introducing different argument patterns.For example, if I were to develop a new mode that required some user parameters, the
args_checker()function required to be completely re-written. This has to not to only accommodate new features being implemented but also the previously designed features.approach
To approach this problem, I decided to create a class object known as
CliControlPanel. The class keeps track of all supported parameters, workflows and argument states.A unique feature of this class is usage of
argument_states. These states are simply boolean data type that tellcytopipewhich parameters were selected. This provides easy control flow of different parameters and what operations to execute during run time.In addition, this allows implementing more features much simpler, since we are only dealing with boolean operators!
The majority of the
CliControlPanelimplemenation is done within this commit: bcbf011