BF: Let `save -a` commit modified submodules too (closes: gh-636) #739

mih · 2016-08-29T18:03:35Z

No description provided.

yarikoptic · 2016-08-29T18:24:11Z

I think symlinks strike back
Osx


======================================================================
ERROR: datalad.interface.tests.test_save.test_save
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/datalad/buildslave/datalad-pr-dl-osx-64/build/venv-ci/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/Users/datalad/buildslave/datalad-pr-dl-osx-64/build/datalad/tests/utils.py", line 666, in newfunc
    t(*(arg + (uri,)), **kw)
  File "/Users/datalad/buildslave/datalad-pr-dl-osx-64/build/datalad/interface/tests/test_save.py", line 56, in test_save
    subds = Dataset(opj(ds.path, 'sub ds')).create(add_to_super=True)
  File "/Users/datalad/buildslave/datalad-pr-dl-osx-64/build/datalad/distribution/dataset.py", line 438, in apply_func
    return f(**kwargs)
  File "/Users/datalad/buildslave/datalad-pr-dl-osx-64/build/datalad/distribution/create.py", line 172, in __call__
    annex_init_opts=annex_init_opts)
  File "/Users/datalad/buildslave/datalad-pr-dl-osx-64/build/datalad/distribution/dataset.py", line 297, in create_subdataset
    raise ValueError("path %s outside dataset %s" % (path, self))
ValueError: path /var/folders/90/vkz4dwlx0ss72djd8hywgppc0000gp/T/datalad_temp_clone_url_0oZrqP/sub ds outside dataset <Dataset path=/private/var/folders/90/vkz4dwlx0ss72djd8hywgppc0000gp/T/datalad_temp_clone_url_0oZrqP>
-------------------- >> begin captured logging << --------------------
datalad.cmd: ERROR: Failed to start ['git', 'rev-parse', '--show-toplevel']" under '/var/folders/90/vkz4dwlx0ss72djd8hywgppc0000gp/T/datalad_temp_clone_url_0oZrqP/sub ds/..'": [Errno 2] No such file or directory: '/var/folders/90/vkz4dwlx0ss72djd8hywgppc0000gp/T/datalad_temp_clone_url_0oZrqP/sub ds/..' [subprocess.py:_execute_child:1335]
datalad.cmd: ERROR: Failed to start ['git', 'rev-parse', '--show-toplevel']" under '/var/folders/90/vkz4dwlx0ss72djd8hywgppc0000gp/T/datalad_temp_clone_url_0oZrqP/sub ds'": [Errno 2] No such file or directory: '/var/folders/90/vkz4dwlx0ss72djd8hywgppc0000gp/T/datalad_temp_clone_url_0oZrqP/sub ds' [subprocess.py:_execute_child:1335]
--------------------- >> end captured logging << ---------------------

----------------------------------------------------------------------
Ran 504 tests in 586.519s

coveralls · 2016-08-29T18:25:57Z

Coverage increased (+0.02%) to 86.591% when pulling 785b833 on hanke:bf-saveall into 5bbbe2f on datalad:master.

mih · 2016-08-29T18:34:04Z

Hmm, I have no idea. Is there any records of how to deal with this?

On Aug 29, 2016 20:24, "Yaroslav Halchenko" notifications@github.com
wrote:

I think symlinks strike back
Osx

ERROR: datalad.interface.tests.test_save.test_save

Traceback (most recent call last):
File "/Users/datalad/buildslave/datalad-pr-dl-osx-64/build/venv-ci/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(self.arg)
File "/Users/datalad/buildslave/datalad-pr-dl-osx-64/build/datalad/tests/utils.py", line 666, in newfunc
t((arg + (uri,)), **kw)
File "/Users/datalad/buildslave/datalad-pr-dl-osx-64/build/datalad/interface/tests/test_save.py", line 56, in test_save
subds = Dataset(opj(ds.path, 'sub ds')).create(add_to_super=True)
File "/Users/datalad/buildslave/datalad-pr-dl-osx-64/build/datalad/distribution/dataset.py", line 438, in apply_func
return f(**kwargs)
File "/Users/datalad/buildslave/datalad-pr-dl-osx-64/build/datalad/distribution/create.py", line 172, in call
annex_init_opts=annex_init_opts)
File "/Users/datalad/buildslave/datalad-pr-dl-osx-64/build/datalad/distribution/dataset.py", line 297, in create_subdataset
raise ValueError("path %s outside dataset %s" % (path, self))
ValueError: path /var/folders/90/vkz4dwlx0ss72djd8hywgppc0000gp/T/datalad_temp_clone_url_0oZrqP/sub ds outside dataset
-------------------- >> begin captured logging << --------------------
datalad.cmd: ERROR: Failed to start ['git', 'rev-parse', '--show-toplevel']" under '/var/folders/90/vkz4dwlx0ss72djd8hywgppc0000gp/T/datalad_temp_clone_url_0oZrqP/sub ds/..'": [Errno 2] No such file or directory: '/var/folders/90/vkz4dwlx0ss72djd8hywgppc0000gp/T/datalad_temp_clone_url_0oZrqP/sub ds/..' [subprocess.py:_execute_child:1335]
datalad.cmd: ERROR: Failed to start ['git', 'rev-parse', '--show-toplevel']" under '/var/folders/90/vkz4dwlx0ss72djd8hywgppc0000gp/T/datalad_temp_clone_url_0oZrqP/sub ds'": [Errno 2] No such file or directory: '/var/folders/90/vkz4dwlx0ss72djd8hywgppc0000gp/T/datalad_temp_clone_url_0oZrqP/sub ds' [subprocess.py:_execute_child:1335]
--------------------- >> end captured logging << ---------------------

Ran 504 tests in 586.519s

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mih · 2016-08-29T18:52:03Z

I cannot replicate the travis failure with TMPDIR=/tmp/sym link. It seems to resolve just fine on my machine...

yarikoptic · 2016-08-29T22:32:47Z

Just to make sure, you did have that directory a symlink to /tmp right?
NB github refuses to format it properly for me :-/

> ln -sf /tmp /tmp/symlink; TMPDIR=/tmp/symlink nosetests -s -v datalad.interface.tests.test_save 
datalad.interface.tests.test_save.test_save ... ERROR

======================================================================
ERROR: datalad.interface.tests.test_save.test_save
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/home/yoh/proj/datalad/datalad/datalad/tests/utils.py", line 666, in newfunc
    t(*(arg + (uri,)), **kw)
  File "/home/yoh/proj/datalad/datalad/datalad/interface/tests/test_save.py", line 56, in test_save
    subds = Dataset(opj(ds.path, 'sub ds')).create(add_to_super=True)
  File "/home/yoh/proj/datalad/datalad/datalad/distribution/dataset.py", line 438, in apply_func
    return f(**kwargs)
  File "/home/yoh/proj/datalad/datalad/datalad/distribution/create.py", line 172, in __call__
    annex_init_opts=annex_init_opts)
  File "/home/yoh/proj/datalad/datalad/datalad/distribution/dataset.py", line 297, in create_subdataset
    raise ValueError("path %s outside dataset %s" % (path, self))
ValueError: path /tmp/symlink/datalad_temp_clone_url_vyYYDq/sub ds outside dataset <Dataset path=/tmp/datalad_temp_clone_url_vyYYDq>

yarikoptic · 2016-08-30T01:12:43Z

https://github.com/datalad/datalad/pull/743/files#diff-3947667888c8ff9d4bfc6c26f2be70f9R391 (pushed a temp PR -- didn't finish messing with it yet) might help with it... feel free to absorb that piece of code if does

mih · 2016-08-30T05:37:00Z

FTR: this issue sits deeper than expected. Even in the construction of
testrepos there are inappropriate uses of realpath() IMHO. We should talk
about this.

On Aug 30, 2016 03:12, "Yaroslav Halchenko" notifications@github.com
wrote:

https://github.com/datalad/datalad/pull/743/files#diff-
3947667888c8ff9d4bfc6c26f2be70f9R391 (pushed a temp PR -- didn't finish
messing with it yet) might help with it... feel free to absorb that piece
of code if does

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codecov-io · 2016-08-31T11:32:43Z

Current coverage is 86.79% (diff: 100%)

Merging #739 into master will increase coverage by 0.05%

@@             master       #739   diff @@
==========================================
  Files           198        198          
  Lines         17890      17898     +8   
  Methods           0          0          
  Messages          0          0          
  Branches          0          0          
==========================================
+ Hits          15517      15534    +17   
+ Misses         2373       2364     -9   
  Partials          0          0

Powered by Codecov. Last update 8c42f85...b53b583

coveralls · 2016-08-31T11:53:18Z

Coverage increased (+0.02%) to 86.622% when pulling 0842ef3 on mih:bf-saveall into 64730e6 on datalad:master.

coveralls · 2016-09-01T20:45:17Z

Coverage increased (+0.06%) to 86.792% when pulling b53b583 on mih:bf-saveall into 8c42f85 on datalad:master.

yarikoptic mentioned this pull request Aug 30, 2016

BF: messing with realpaths, fixing up install tests (no creativism), etc #743

Merged

mih force-pushed the bf-saveall branch from 785b833 to 0842ef3 Compare August 31, 2016 11:32

mih added 2 commits September 1, 2016 20:30

BF: Let save -a commit modified submodules too (closes: dataladgh-636)

2d6149b

Evasive maneuver (symlink issue, unrelated to this PR)

b53b583

mih force-pushed the bf-saveall branch from 0842ef3 to b53b583 Compare September 1, 2016 18:30

mih merged commit b53b583 into datalad:master Sep 2, 2016

mih deleted the bf-saveall branch June 24, 2017 10:34

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BF: Let `save -a` commit modified submodules too (closes: gh-636) #739

BF: Let `save -a` commit modified submodules too (closes: gh-636) #739

mih commented Aug 29, 2016

yarikoptic commented Aug 29, 2016

coveralls commented Aug 29, 2016 •

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mih commented Aug 29, 2016

ERROR: datalad.interface.tests.test_save.test_save

mih commented Aug 29, 2016

yarikoptic commented Aug 29, 2016 •

edited

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yarikoptic commented Aug 30, 2016

mih commented Aug 30, 2016

codecov-io commented Aug 31, 2016 •

edited

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coveralls commented Aug 31, 2016 •

edited

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coveralls commented Sep 1, 2016 •

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BF: Let save -a commit modified submodules too (closes: gh-636) #739

BF: Let save -a commit modified submodules too (closes: gh-636) #739

Conversation

mih commented Aug 29, 2016

yarikoptic commented Aug 29, 2016

coveralls commented Aug 29, 2016 • edited Loading

mih commented Aug 29, 2016

ERROR: datalad.interface.tests.test_save.test_save

mih commented Aug 29, 2016

yarikoptic commented Aug 29, 2016 • edited Loading

yarikoptic commented Aug 30, 2016

mih commented Aug 30, 2016

codecov-io commented Aug 31, 2016 • edited Loading

Current coverage is 86.79% (diff: 100%)

coveralls commented Aug 31, 2016 • edited Loading

coveralls commented Sep 1, 2016 • edited Loading

BF: Let `save -a` commit modified submodules too (closes: gh-636) #739

BF: Let `save -a` commit modified submodules too (closes: gh-636) #739

coveralls commented Aug 29, 2016 •

edited

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yarikoptic commented Aug 29, 2016 •

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codecov-io commented Aug 31, 2016 •

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coveralls commented Aug 31, 2016 •

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coveralls commented Sep 1, 2016 •

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