newlines formatting

[Smeds]

I have some questions about the number of new lines required by snakefmt

Example

if config["programs"]["Duplicates"] == "fgbio":

    include: "../rules/Alignment/fgbio.smk"
    print("Test")
    include: "../rules/SNV/freebayes.smk"
else:
    if config["programs"]["markduplicate"] == "GPU":

        include: "../rules/Alignment/GPU_alignment.smk"
    else:

        include: "../rules/Alignment/bwa-mem.smk"
        include: "../rules/Alignment/MarkDuplicates.smk"
include: "../rules/SNV/freebayes.smk"
include: "../rules/SNV/mutect2.smk"

would change to

  if config["programs"]["Duplicates"] == "fgbio":
  
      include: "../rules/Alignment/fgbio.smk"
 
 
 print("Test")
 
      include: "../rules/SNV/freebayes.smk"
 
 
  else:
      if config["programs"]["markduplicate"] == "GPU":
  
          include: "../rules/Alignment/GPU_alignment.smk"
 
 
      else:
  
          include: "../rules/Alignment/bwa-mem.smk"
 
          include: "../rules/Alignment/MarkDuplicates.smk"
  include: "../rules/SNV/freebayes.smk"
  include: "../rules/SNV/mutect2.smk"

How many new lines are required seems to be a bit inconsistent and sometimes a bit excessive, atleast for if/else code blocks:

1. Why is 2 new lines added after an "include" inside a if/else code block?
2. Why is the indentation removed for print("Test") and two new lines added?
3. Why is a new line introduced between the include statements in the last else block but not for the two last lines?
4. Shouldn't there be new lines after the last "else" code block?

[bricoletc]

Hi again @Smeds, these are good points, thank you for going into this level of detail.

1. We decided to separate distinct snakemake keywords by two newlines, but perhaps inside such a block should be one.
2. Is definitely a bug
3. This is deliberate (I'll dig into why) but could conceivably be changed
4. I agree

[bricoletc]

Ok, 6fb3400 implements your points 2, 3, and 4. (digging into 3, can't find a good justification for it).

For point 1, we are actually mirroring black:

if p:

    class p:
        elem1 = 2


else:

    class a:
        pass

And I find this readable so will keep it.

If (for readability) you place your print statement before the includes, it will now look like:

if config["programs"]["Duplicates"] == "fgbio":

    print("Test")

    include: "../rules/Alignment/fgbio.smk"
    include: "../rules/SNV/freebayes.smk"


else:
    if config["programs"]["markduplicate"] == "GPU":

        include: "../rules/Alignment/GPU_alignment.smk"


    else:

        include: "../rules/Alignment/bwa-mem.smk"
        include: "../rules/Alignment/MarkDuplicates.smk"


include: "../rules/SNV/freebayes.smk"
include: "../rules/SNV/mutect2.smk"

What do you think @Smeds ?

[mbhall88]

Agree with @bricoletc on all accounts

[Smeds]

Looks great!