Make nf-core modules update --save-diff work when files are created or removed

[ErikDanielsson]

As I reported in #1694, nf-core modules update --save-file simply ignored files that were created or removed between updates. I've fixed this by letting the output .diff file be more similar to the output from git diff:

• Created or removed files are shown to originate from/end up in /dev/null
• "from" and "to" file paths are prefixed with a/ and b/ respectively.

I've moved the diff methods in update to a separate static class to make the update code a bit cleaner also

PR checklist

• This comment contains a description of changes (with reason)
• CHANGELOG.md is updated
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated

[codecov]

Codecov Report

Merging #1698 (88c29a1) into dev (d47574f) will decrease coverage by 0.00%.
The diff coverage is 68.64%.

@@            Coverage Diff             @@
##              dev    #1698      +/-   ##
==========================================
- Coverage   68.24%   68.23%   -0.01%     
==========================================
  Files          56       57       +1     
  Lines        6694     6746      +52     
==========================================
+ Hits         4568     4603      +35     
- Misses       2126     2143      +17     

Impacted Files	Coverage Δ
nf_core/modules/update.py	73.14% <52.63%> (-0.62%)	⬇️
nf_core/modules/modules_differ.py	71.71% <71.71%> (ø)

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[mirpedrol]

I think it looks good! I found a small error while testing the command that should be addressed.

Also, I've seen that when I create a file to test what happens when a file needs to be removed, it works fine with --preview or updating directly, but it's not removed with the option --save-diff.
To reproduce:

git clone https://github.com/nf-core/rnaseq.git
cd rnaseq
nf-core modules update cat/fastq --sha 49da8642876ae4d91128168cd0db4f1c858d7792


touch modules/nf-core/modules/cat/fastq/test.yml
nf-core modules update --save-diff diff.file cat/fastq
grep "test.yml" diff.file
# test.yml file is not listed in diff.file
# Note that functions.py file is indeed removed as expected

nf-core modules update --preview cat/fastq
# test.yml file is listed in the preview and removed

If you think this is out of this PR scope, we can take a look in a different one :)

[ErikDanielsson]

Good points, I've added recursive checking of the module directory now.

Regarding the your first example: The issue here is that the test.yml file is empty, and identical to /dev/null; there is therefore no diff to generate. I tried adding things like

--- modules/nf-core/modules/cat/fastq/test.yml
+++ /dev/null
@@ -0,0 +0,0 @@

to try to coerce git apply into removing the file, but then it only reports that the patch is corrupt. So I think we'll have to accept that empty files can't be removed by the command.

[mirpedrol]

I see the problem. Let's assume we won't usually have empty files :)

[ErikDanielsson]

Sounds good! If it becomes a major issue somewhere, we can have a second look at it.