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Merge branch 'master' of ssh://git-annex.branchable.com into master

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Joey Hess 2020-08-28 12:57:25 -04:00
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Disclaimer: I am not an expert in git-annex.
Hi,
I have cloned the git-annex repos on my laptop, and use it to push on amazon s3. So far, everything was working fine.
Recently, I made some changes on my local repos, and synced it (or I _thought_ I did) to Amazon, by doing the following procedure:
~~~
git commit
git annex sync
~~~
Note: I wanted to do `git annex sync --content amazon` after the commit, according to our [procedure](https://github.com/spine-generic/data-multi-subject/blob/95ae0f390b4d9220760d733a3d6c6b560cc6502e/CONTRIBUTING.md), but it failed (see https://github.com/spine-generic/data-multi-subject/issues/18).
So I went ahead, and opened the PRs on Github, and then rebased+merged them on master.
After merging, I went back to another local copy of the repos (on compute canada cluster), and did the following:
~~~
git pull
git annex get
~~~
But I was not able to retrieve the data that were recently pushed (or that I _thought_ I pushed) from my laptop. For example, I get the following error message:
~~~
[jcohen@gra-login3 data-multi-subject]$ git-annex get sub-cmrra02/anat/sub-cmrra02_T2w.nii.gz
get sub-cmrra02/anat/sub-cmrra02_T2w.nii.gz (not available)
Try making some of these repositories available:
5cdba4fc-8d50-4e89-bb0c-a3a4f9449666 -- julien@julien-macbook.local:~/code/spine-generic/data-multi-subject
(Note that these git remotes have annex-ignore set: origin)
failed
git-annex: get: 1 failed
[jcohen@gra-login3 data-multi-subject]$ git remote
amazon
origin
~~~
If it could be of any help, the full context is available in this [Github issue](https://github.com/spine-generic/data-multi-subject/issues/24).
Thank you for any help you might provide,
Julien

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[[!comment format=mdwn
username="Ilya_Shlyakhter"
avatar="http://cdn.libravatar.org/avatar/1647044369aa7747829c38b9dcc84df0"
subject="understanding why standalone conda package gets preferred"
date="2020-08-27T15:32:05Z"
content="""
@cardoso-neto \"The only dependency that was installed when I conda-installed git-annex was this\" -- do you by chance remember the exact commands used to create that conda environment, before you tried installing git-annex into it? (Or if you have the environment, can you do `conda list --explicit` in it?) I'd like to better understand why `conda install` prefers the standalone package [so often](https://anaconda.org/conda-forge/git-annex/files). I'll ask conda gurus, but first need a reproducible case where that happens seemingly unnecessarily.
"""]]

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doc/forum/building_the_standalone_distribution_from_source/comment_13_27f987a16d931a02f5a4ab3f80bf327a._comment Normal file
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[[!comment format=mdwn
username="cardoso-neto"
avatar="http://cdn.libravatar.org/avatar/d90a656df072f3a29da54302c190c696"
subject="comment 13"
date="2020-08-28T00:20:30Z"
content="""
I checked my .bash_history and it was `conda create -n $myname python=3.8` the command used.
I just reran that and got the same result when I installed git-annex with `conda install -c conda-forge git-annex`.
I also noticed you made the standalone dist warning message much prettier. Thanks for that. However, you forgot the `--channel` argument in your suggested install script. Here is a copypasta of your current message:
```
Executing transaction: /
##############################################################################
# #
# Standalone distribution of git-annex was installed, instead of the #
# standard distribution, likely due to package conflicts in the target #
# environment. The standalone distribution may have issues (e.g. be slower, #
# or not pass the expected environment to some external programs); #
# the standard distribution should be used when possible. #
# You can force installation of the standard version by adding =alldep* to #
# the build string, e.g. #
# conda install git-annex=*=alldep* #
# #
# For more info on the standalone git-annex distribution see #
# https://git-annex.branchable.com/install/Linux_standalone/ #
# #
##############################################################################
done
```
"""]]

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[[!comment format=mdwn
username="Ilya_Shlyakhter"
avatar="http://cdn.libravatar.org/avatar/1647044369aa7747829c38b9dcc84df0"
subject="comment 14"
date="2020-08-28T01:02:48Z"
content="""
Thanks for point out the channel omission in the message.
I was able to reproduce the issue, but only with `conda create --override-channels -c defaults -n new-test-env-03 python=3.8 ` . When I instead create the initial environment with `-c conda-forge`, the issue doesn't recur. I guess it makes sense: packages in conda-forge are pinned to be more compatible with each other, but not necessarily with packages in `defaults`.
"""]]