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fix install for mac osx > 10.9, based on pandas fix for the same #584

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merged 4 commits into from
May 1, 2019

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@bhazelton bhazelton commented Apr 30, 2019

Description

On Mac OSX > 10.9 there can be an issue with properly linking the standard c libraries. This can be fixed by properly setting the MACOSX_DEPLOYMENT_TARGET environment variable. For more detail see: pandas-dev/pandas#23424

This PR is based on the PR that closed that issue on pandas.

Motivation and Context

Fixes a problem seen more than once with installing on mac osx > 10.9. This is the error message:

running build_ext
building 'pyuvdata._miriad' extension
creating build
creating build/temp.macosx-10.7-x86_64-3.6
creating build/temp.macosx-10.7-x86_64-3.6/pyuvdata
creating build/temp.macosx-10.7-x86_64-3.6/pyuvdata/src
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/bryna/anaconda/envs/py36/include -arch x86_64 -I/Users/bryna/anaconda/envs/py36/include -arch x86_64 -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -I/Users/bryna/anaconda/envs/py36/lib/python3.6/site-packages/numpy/core/include -Ipyuvdata/src -I/Users/bryna/anaconda/envs/py36/include/python3.6m -c pyuvdata/src/miriad_wrap.cpp -o build/temp.macosx-10.7-x86_64-3.6/pyuvdata/src/miriad_wrap.o
warning: include path for stdlibc++ headers not found; pass '-stdlib=libc++' on
      the command line to use the libc++ standard library instead
      [-Wstdlibcxx-not-found]
pyuvdata/src/miriad_wrap.cpp:3:10: fatal error: 'string' file not found
#include <string>
         ^~~~~~~~
1 warning and 1 error generated.
error: command 'gcc' failed with exit status 1

Types of changes

  • Bug fix (non-breaking change which fixes an issue)
  • New feature (non-breaking change which adds functionality)
  • Breaking change (fix or feature that would cause existing functionality to change)

Checklist:

  • I have read the contribution guide.
  • My code follows the code style of this project.
  • My change requires a change to the documentation.
    • I have updated the documentation accordingly.
  • My change introduces new functionality that should be highlighted in the tutorial.
    • I have updated the tutorial accordingly.
  • If this is a bug fix, it includes a new test that breaks as a result of the bug (if possible)
  • If this is a breaking change, it includes backwards compatibility and deprecation warnings (if possible)
  • I have added tests to cover my changes.
  • All new and existing tests pass in both python 2 and python 3.
  • My change requires an update to the CHANGELOG.

@bhazelton bhazelton requested a review from plaplant April 30, 2019 23:01
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codecov bot commented May 1, 2019

Codecov Report

Merging #584 into master will not change coverage.
The diff coverage is n/a.

Impacted file tree graph

@@           Coverage Diff           @@
##           master     #584   +/-   ##
=======================================
  Coverage   98.82%   98.82%           
=======================================
  Files          20       20           
  Lines        7830     7830           
=======================================
  Hits         7738     7738           
  Misses         92       92

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Thanks @bhazelton! As a note, we also added a fix to get downstream tests on hera_cal working again, which required installing the hera_sim repo.

@plaplant plaplant merged commit 47ddf9b into master May 1, 2019
@plaplant plaplant deleted the fix_mac_install branch May 1, 2019 21:30
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2 participants