[WIP] Try using anaconda to run travis tests on OSX #234
Conversation
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@AndreasHeger this almost works. If you look deeply in the OSX logs, the tests are actually failing due to linker import errors similar to what I found in #231 |
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I think I fixed the linker problem on OS X in PR #233. |
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I just merged in your changes but still see linker issues here: https://travis-ci.org/pysam-developers/pysam/jobs/111003944 |
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My changes only fixed the linker problem under Python 3.5. It looks like you're using Python 3.3. I also saw linker failures on Python 3.4 using that approach and was unable to spend anymore time to track them down. Any chance you can try with Python 3.5? |
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n/m. I see that Travis is testing multiple versions. |
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When I get home tonight I'll look through your PR to see if I can figure anything else out. |
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Good news is that Python 3.5 worked. Check out these lines in setup.py: if IS_PYTHON3:
import sysconfig
if sys.version_info.minor >= 5:
internal_htslib_libraries = ["chtslib.{}".format(
sysconfig.get_config_var('SOABI'))]
else:
# KBJ: This doesn't work for me on OS X with Python 3.4. Libs have no platform tags.
internal_htslib_libraries = ["chtslib.{}{}".format(
sys.implementation.cache_tag,
sys.abiflags)]
else:
internal_htslib_libraries = ["chtslib"] |
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Actually, even the ones that "appear" to work are having some LD library path issues that I'll fix later---probably just need to set environment variables. For example, py35 on OSX: https://travis-ci.org/pysam-developers/pysam/jobs/111003946:L2484#L2530 |
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FWIW, it's probably a bug in our CI if linker errors are happening silently and still giving green lights on Travis... |
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Actually, the current build for linux has some test failures that could be related to your latest commits: |
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Note that the build has nosetest failures but still reports travis success, which is not quite right either... |
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Thanks. Seems I broke the unit tests on travis. |
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Almost there: with the latest changes from master, I'm down to the following: |
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Thanks, this is down to me. I will fix it tonight and merge. Best wishes, On 24/02/16 01:07, Kyle Beauchamp wrote:
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Actually i still need to fix a few more issues with osx before merging this.
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OK, I disabled libcurl on travis and it now seems to build OK on OSX. There are still some test failures, however, similar to what I show below. |
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Actually, there are build issues on py3K python versions on OSX. Py27 builds fine but dies during tests. |
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Thanks. I will check for open without close cases. |
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Thanks! As all linux tests pass, I will now merge and comment out the osx section to be fixed in a separate branch. |
[WIP] Try using anaconda to run travis tests on OSX
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Sounds good. Note that I also added the bioconda recipe to this pull request. I figured I might as well try to get that working as well. |
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PS: if you open a [WIP] pull request with your OSX branch, I can try to comment on any travis failures that you see. |
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