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Linting - don't reverse conda channel order #295

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Merged
apeltzer merged 4 commits into from
Apr 6, 2019
Merged

Linting - don't reverse conda channel order #295

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1855d34
Merge pull request #281 from ewels/master
ewels Mar 13, 2019
a5fdbfd
Merge branch 'master' of github.com:nf-core/tools
ewels Apr 6, 2019
570b9ba
Linting: Don't reverse the conda channel order
ewels Apr 6, 2019
9672f50
Changelog
ewels Apr 6, 2019
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,8 @@
* Sorting now works again
* Output is partially coloured (better highlighting out of date pipelines)
* Improved documentation
* Fixed bugs in `nf-core lint`
* The order of conda channels is now correct, avoiding occasional erroneous errors that packages weren't found ([#207](https://github.com/nf-core/tools/issues/207))

## [v1.5](https://github.com/nf-core/tools/releases/tag/1.5) - 2019-03-13 Iron Shark

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4 changes: 3 additions & 1 deletion nf_core/lint.py
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Expand Up @@ -683,7 +683,7 @@ def check_anaconda_package(self, dep):
if '::' in depname:
dep_channels = [depname.split('::')[0]]
depname = depname.split('::')[1]
for ch in reversed(dep_channels):
for ch in dep_channels:
anaconda_api_url = 'https://api.anaconda.org/package/{}/{}'.format(ch, depname)
try:
response = requests.get(anaconda_api_url, timeout=10)
Expand All @@ -701,6 +701,8 @@ def check_anaconda_package(self, dep):
elif response.status_code != 404:
self.warned.append((8, "Anaconda API returned unexpected response code '{}' for: {}\n{}".format(response.status_code, anaconda_api_url, response)))
raise ValueError
elif response.status_code == 404:
logging.debug("Could not find {} in conda channel {}".format(dep, ch))
else:
# We have looped through each channel and had a 404 response code on everything
self.failed.append((8, "Could not find Conda dependency using the Anaconda API: {}".format(dep)))
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