A few bugfixes #19
A few bugfixes #19
Conversation
Codecov Report
@@ Coverage Diff @@
## master #19 +/- ##
==========================================
+ Coverage 98.02% 98.03% +0.01%
==========================================
Files 2 2
Lines 152 153 +1
==========================================
+ Hits 149 150 +1
Misses 3 3
Continue to review full report at Codecov.
|
nf_core/lint.py
Outdated
| @@ -104,7 +104,7 @@ def pf(file_path): | |||
| files = [files] | |||
| if any([os.path.isfile(pf(f)) for f in files]): | |||
| self.passed.append((1, "File found: {}".format(files))) | |||
| self.files.append(f) | |||
| self.files.append(files) | |||
There was a problem hiding this comment.
I think it should be extend(files), as files will be a list.
nf_core/lint.py
Outdated
| @@ -114,7 +114,7 @@ def pf(file_path): | |||
| files = [files] | |||
| if any([os.path.isfile(pf(f)) for f in files]): | |||
| self.passed.append((1, "File found: {}".format(files))) | |||
| self.files.append(f) | |||
| self.files.append(files) | |||
nf_core/lint.py
Outdated
| @@ -269,7 +269,7 @@ def check_readme(self): | |||
| nf_config_version = self.config.get('params.nf_required_version').strip('\'"') | |||
| try: | |||
| assert nf_badge_version == nf_config_version | |||
| except AssertionError, KeyError: | |||
| except (AssertionError, KeyError) as e: | |||
There was a problem hiding this comment.
not necessary imo, cause the exception object is not accessed anywhere
There was a problem hiding this comment.
You're right. I guess writing as e is more of a reflex for me 😄
|
Thanks Remi! Could you also explain what you mean with "work on your Python 3.6" installation? Cause we are running CI with several Python versions. So if something is not working as expected, would be good to know (or even raise an issue) :) |
nf_core/lint.py
Outdated
| @@ -210,7 +210,8 @@ def check_config_vars(self): | |||
| raise AssertionError("`nextflow config` returned non-zero error code: %s,\n %s", e.returncode, e.output) | |||
| else: | |||
| for l in nfconfig_raw.splitlines(): | |||
| k, v = str(l).split(' = ', 1) | |||
| ul = l.decode() | |||
| k, v = ul.split(' = ', 1) | |||
|
Hi Sven. Thanks. I was testing just testing this tool on my Nextflow pipeline and using the version of python I have installed locally ( |
|
Would you mind opening an issue and describe this in detail (StackTrace etc.) Have to look into this, because the CI does not throw the exceptions :( |
|
No worries, Sven. See #20 |
Some changes I made to make linting work on my python 3.6 installation