add libjpeg-turbo as dependency to recent LibTIFF easyconfigs, as otherwise the build can pick up the system-wide library

[paulmelis]

(created using eb --new-pr)

[akesandgren]

Minor comment.
It would be nice if you had the name of the software package in the title. Something like
LibTIFF: Add libjpeg-turbo as dependency,...
Or even LibTIFF-4.0.9: ...

Makes it much easier to figure out what it is about.

[paulmelis]

Minor comment.
It would be nice if you had the name of the software package in the title. Something like
LibTIFF: Add libjpeg-turbo as dependency,...
Or even LibTIFF-4.0.9: ...

Makes it much easier to figure out what it is about.

Hmmm, okay, did not realize that it would need to be more specific. I was also half expecting the --new-pr command to take care of that, as you give it an easyconfig file from which it would be able to extract such metadata. Ah well, something to remember for next time.

[migueldiascosta]

@paulmelis --new-pr sets the title automatically if no commit message is set, but since you are modifying an existing message a custom commit message is necessary (although --new-pr could probably be enhanced to add some context also in that case as you mention)

in any case, you can still edit the title at any time

[paulmelis]

@paulmelis --new-pr sets the title automatically if no commit message is set, but since you are modifying an existing message a custom commit message is necessary (although --new-pr could probably be enhanced to add some context also in that case as you mention)

Wait, how am I "modifying an existing message"?

[migueldiascosta]

sorry, I meant "modifying an existing easyconfig" :)

[migueldiascosta]

Test report by @migueldiascosta
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in this PR)
generoso - Linux centos linux 7.6.1810, Intel(R) Xeon(R) CPU E5-2660 v4 @ 2.00GHz, Python 3.6.8
See https://gist.github.com/bbf6345ed217caab04170fab0e025973 for a full test report.

[migueldiascosta]

lgtm

[migueldiascosta]

@paulmelis this was indeed a problem and your PR fixes it, thanks again

would you consider also fixing the other LibTIFF easyconfigs?

[paulmelis]

Travis test report: 5/5 runs failed - see https://travis-ci.org/easybuilders/easybuild-easyconfigs/builds/599019907

Only showing partial log for 1st failed test suite run 17707.1;
full log at https://travis-ci.org/easybuilders/easybuild-easyconfigs/jobs/599019908

...
FAIL: Specific checks only done for the (easyconfig) files that were changed in a pull request.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/travis/build/easybuilders/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 541, in test_changed_files_pull_request
    self.check_https(changed_ecs)
  File "/home/travis/build/easybuilders/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 485, in check_https
    self.assertFalse(failing_checks, '\n'.join(failing_checks))
AssertionError: Found http:// URL in LibTIFF-4.0.9-GCCcore-7.3.0.eb, should be https:// : http://hpcbios.readthedocs.org/en/latest/

You have got to be kidding me? That URL is part of a commented line:

easybuild-easyconfigs/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.9-GCCcore-7.3.0.eb

Line 10 in b031c6a

# http://hpcbios.readthedocs.org/en/latest/

So even though the description of check_https() says it checks URLs used for "homepage/source_urls" it does something different by simply matches any part of the easyconfig text without looking at lines and comments? Seriously?

easybuild-easyconfigs/test/easyconfigs/easyconfigs.py

Lines 459 to 485 in 5b85d4d

	def check_https(self, changed_ecs):
	"""Make sure https:// URL is used (if it exists) for homepage/source_urls (rather than http://)."""
	whitelist = [
	'UCX-', # bad certificate for https://www.openucx.org
	]
	http_regex = re.compile('http://[^"\'\n]+', re.M)
	failing_checks = []
	for ec in changed_ecs:
	ec_fn = os.path.basename(ec.path)
	if any(ec_fn.startswith(x) for x in whitelist):
	continue
	for http_url in http_regex.findall(ec.rawtxt):
	https_url = http_url.replace('http://', 'https://')
	try:
	https_url_works = bool(urlopen(https_url))
	except (HTTPError, URLError):
	https_url_works = False
	if https_url_works:
	failing_checks.append("Found http:// URL in %s, should be https:// : %s" % (ec_fn, http_url))
	self.assertFalse(failing_checks, '\n'.join(failing_checks))

[migueldiascosta]

@paulmelis it does seem a bit too much... would you mind opening an issue about this?

[paulmelis]

@paulmelis it does seem a bit too much... would you mind opening an issue about this?

Done, #9180

[migueldiascosta]

closing and reopening to trigger travis

[boegel]

Thanks a lot for the fix @paulmelis!

We should apply this consistently though, at least to all LibTIFF 4.0.9 & newer easyconfigs (which may involve adding the missing easyconfigs for libjpeg-turbo with other toolchains)...

[boegel]

I looked into making this consistent myself, no missing libjpeg-turbo easyconfigs.

@paulmelis please review/merge sara-nl#3 to update this PR

[boegel]

Test report by @boegel
SUCCESS
Build succeeded for 8 out of 8 (8 easyconfigs in this PR)
node2409.golett.os - Linux centos linux 7.6.1810, Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz, Python 2.7.5
See https://gist.github.com/782d1981013c4fa0407b3bd851aa3804 for a full test report.

[boegel]

Test report by @boegel
SUCCESS
Build succeeded for 8 out of 8 (8 easyconfigs in this PR)
node2414.golett.os - Linux centos linux 7.7.1908, Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz, Python 2.7.5
See https://gist.github.com/f1ddef7056d14838839b186cb61e528d for a full test report.

[boegel]

Going in, thanks @paulmelis!