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* yapf for snakefiles (#18)
@ 2016-07-08  7:41 Endre Bakken Stovner
  2016-07-08  8:03 ` Endre Bakken Stovner
                   ` (2 more replies)
  0 siblings, 3 replies; 6+ messages in thread
From: Endre Bakken Stovner @ 2016-07-08  7:41 UTC (permalink / raw)
  To: kyleam/snakemake-mode

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Would you be interested in having [yapf](https://github.com/google/yapf) for snakefiles? If you think it is desirable and feasible, I might start looking into it. I guess at first only yapfing the `rule:` portion should be the goal. 

In the end hacking yapf to analyze snakefiles might be a goal...

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* Re: yapf for snakefiles (#18)
  2016-07-08  7:41 yapf for snakefiles (#18) Endre Bakken Stovner
@ 2016-07-08  8:03 ` Endre Bakken Stovner
  2020-04-14  2:10   ` Kyle Meyer
  2016-07-09 11:18 ` Endre Bakken Stovner
  2016-10-21 21:30 ` Kyle Meyer
  2 siblings, 1 reply; 6+ messages in thread
From: Endre Bakken Stovner @ 2016-07-08  8:03 UTC (permalink / raw)
  To: kyleam/snakemake-mode

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Perhaps the easiest way to do this would be to 

1) replace all the stuff that is snakemake-specific with syntactically valid placeholders,
2) then run yapf on the modified file
3) then re-insert the snakemake specific stuff...

So that the below 
```
rule get_gene_expression:
    input:
        expression_matrix
    output:
        "data/expression/series.csv"
    run:
        expression_matrix = pd.read_table(input[0])
        expression_series = expression_matrix.sum(1).sort_values(ascending=False)
        expression_series.to_csv(output[0], sep=" ")
```

becomes

```
for i in [1]: # snakemake
    for j in [2]: # snakemake
        expression_matrix = pd.read_table(input[0])
        expression_series = expression_matrix.sum(1).sort_values(ascending=False)
        expression_series.to_csv(output[0], sep=" ")
```

which you then can run yapf on. After yapf is run, the placeholder `for i in [1] #snakemake`  is replaced with `rule get_gene_expression:`, `for i in [2] #snakemake` is replaced with ```    input:
        expression_matrix
    output:
        "data/expression/series.csv"
    run:
```.

Just throwing it out there for criticism. It is very, very hackish, but seems like the minimally intrusive way of using yapf with snakefiles.

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* Re: yapf for snakefiles (#18)
  2016-07-08  7:41 yapf for snakefiles (#18) Endre Bakken Stovner
  2016-07-08  8:03 ` Endre Bakken Stovner
@ 2016-07-09 11:18 ` Endre Bakken Stovner
  2020-04-14  2:11   ` Kyle Meyer
  2016-10-21 21:30 ` Kyle Meyer
  2 siblings, 1 reply; 6+ messages in thread
From: Endre Bakken Stovner @ 2016-07-09 11:18 UTC (permalink / raw)
  To: kyleam/snakemake-mode; +Cc: Kyle Meyer, Comment

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It seems harder to extend yapf than to implement my hackish proposal.

But I guess I could create my own Python script which 1) does the transformation, 2) calls yapf and then 3) translates the code into snakemake again.

I should have been clearer about why I posted this here. I was wondering about whether you might accept a PR for such a formatter if I write it. I doubt the yapf projects would be interested in PRs to support a relatively obscure DSL.

Anyways, will be sometime in the future so that I can use and tweak it myself for a while.

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* Re: yapf for snakefiles (#18)
  2016-07-08  7:41 yapf for snakefiles (#18) Endre Bakken Stovner
  2016-07-08  8:03 ` Endre Bakken Stovner
  2016-07-09 11:18 ` Endre Bakken Stovner
@ 2016-10-21 21:30 ` Kyle Meyer
  2 siblings, 0 replies; 6+ messages in thread
From: Kyle Meyer @ 2016-10-21 21:30 UTC (permalink / raw)
  To: kyleam/snakemake-mode; +Cc: Kyle Meyer, Your activity

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Closed #18.

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* Re: yapf for snakefiles (#18)
  2016-07-08  8:03 ` Endre Bakken Stovner
@ 2020-04-14  2:10   ` Kyle Meyer
  0 siblings, 0 replies; 6+ messages in thread
From: Kyle Meyer @ 2020-04-14  2:10 UTC (permalink / raw)
  To: snakemake-mode

------------------------------------------------------------------------
Some replies are missing, as described at

  https://inbox.kyleam.com/snakemake-mode/874ktmyh4u.fsf@kyleam.com/

The text below is copied from

  https://github.com/kyleam/snakemake-mode/issues/18#issuecomment-231516187
------------------------------------------------------------------------

I'm not familiar with yapf, but, at least at first glance, nothing
seems Emacs-specific here. If you extend the command line program to
support Snakemake files, [py-yapf](or a wrapper around it, if
necesary) could be used to call it from Emacs.

Am I missing something?

^ permalink raw reply	[flat|nested] 6+ messages in thread

* Re: yapf for snakefiles (#18)
  2016-07-09 11:18 ` Endre Bakken Stovner
@ 2020-04-14  2:11   ` Kyle Meyer
  0 siblings, 0 replies; 6+ messages in thread
From: Kyle Meyer @ 2020-04-14  2:11 UTC (permalink / raw)
  To: snakemake-mode

------------------------------------------------------------------------
Some replies are missing, as described at

  https://inbox.kyleam.com/snakemake-mode/874ktmyh4u.fsf@kyleam.com/

The text below is copied from

  https://github.com/kyleam/snakemake-mode/issues/18#issuecomment-231539511
------------------------------------------------------------------------

Thanks for the clarification. If you decide the go with elisp for
implementing this, I'd suggest you do it as its own package. If you
find it works well, I'm happy to link to it in Snakemake mode's
README.

^ permalink raw reply	[flat|nested] 6+ messages in thread

end of thread, other threads:[~2020-04-14  2:11 UTC | newest]

Thread overview: 6+ messages (download: mbox.gz / follow: Atom feed)
-- links below jump to the message on this page --
2016-07-08  7:41 yapf for snakefiles (#18) Endre Bakken Stovner
2016-07-08  8:03 ` Endre Bakken Stovner
2020-04-14  2:10   ` Kyle Meyer
2016-07-09 11:18 ` Endre Bakken Stovner
2020-04-14  2:11   ` Kyle Meyer
2016-10-21 21:30 ` Kyle Meyer

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