From 22dc07e68ff8d63d2951c7aff8a9ec4d0bce7db3 Mon Sep 17 00:00:00 2001 From: Ilya_Shlyakhter Date: Thu, 27 Aug 2020 15:32:09 +0000 Subject: [PATCH 1/5] Added a comment: understanding why standalone conda package gets preferred --- .../comment_12_9b0a7c108855d9db63092dd5f93bc5e5._comment | 8 ++++++++ 1 file changed, 8 insertions(+) create mode 100644 doc/forum/building_the_standalone_distribution_from_source/comment_12_9b0a7c108855d9db63092dd5f93bc5e5._comment diff --git a/doc/forum/building_the_standalone_distribution_from_source/comment_12_9b0a7c108855d9db63092dd5f93bc5e5._comment b/doc/forum/building_the_standalone_distribution_from_source/comment_12_9b0a7c108855d9db63092dd5f93bc5e5._comment new file mode 100644 index 0000000000..f576e20470 --- /dev/null +++ b/doc/forum/building_the_standalone_distribution_from_source/comment_12_9b0a7c108855d9db63092dd5f93bc5e5._comment @@ -0,0 +1,8 @@ +[[!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. +"""]] From 2d1b198420c3bc3a53e7df9b495253e8e79f4005 Mon Sep 17 00:00:00 2001 From: cardoso-neto Date: Fri, 28 Aug 2020 00:20:31 +0000 Subject: [PATCH 2/5] Added a comment --- ..._27f987a16d931a02f5a4ab3f80bf327a._comment | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 doc/forum/building_the_standalone_distribution_from_source/comment_13_27f987a16d931a02f5a4ab3f80bf327a._comment diff --git a/doc/forum/building_the_standalone_distribution_from_source/comment_13_27f987a16d931a02f5a4ab3f80bf327a._comment b/doc/forum/building_the_standalone_distribution_from_source/comment_13_27f987a16d931a02f5a4ab3f80bf327a._comment new file mode 100644 index 0000000000..4a16e6c5ec --- /dev/null +++ b/doc/forum/building_the_standalone_distribution_from_source/comment_13_27f987a16d931a02f5a4ab3f80bf327a._comment @@ -0,0 +1,33 @@ +[[!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 +``` +"""]] From b46776917da3e9abf64f01b1f4de2fb1201fed75 Mon Sep 17 00:00:00 2001 From: Ilya_Shlyakhter Date: Fri, 28 Aug 2020 01:02:50 +0000 Subject: [PATCH 3/5] Added a comment --- ...omment_14_44606ec8db82f75f37aabcd7df5c24bb._comment | 10 ++++++++++ 1 file changed, 10 insertions(+) create mode 100644 doc/forum/building_the_standalone_distribution_from_source/comment_14_44606ec8db82f75f37aabcd7df5c24bb._comment diff --git a/doc/forum/building_the_standalone_distribution_from_source/comment_14_44606ec8db82f75f37aabcd7df5c24bb._comment b/doc/forum/building_the_standalone_distribution_from_source/comment_14_44606ec8db82f75f37aabcd7df5c24bb._comment new file mode 100644 index 0000000000..158e70919f --- /dev/null +++ b/doc/forum/building_the_standalone_distribution_from_source/comment_14_44606ec8db82f75f37aabcd7df5c24bb._comment @@ -0,0 +1,10 @@ +[[!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`. +"""]] From c30fc9e7e1abefe3b0e0dbe527f34ecf1a16a882 Mon Sep 17 00:00:00 2001 From: "jcohen@8a78f6f9e293f581b96cd43634328c0e9de6b36e" Date: Fri, 28 Aug 2020 02:12:15 +0000 Subject: [PATCH 4/5] --- ..._synced_from_my_local_repos_to_amazon.mdwn | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 doc/forum/Data_not_synced_from_my_local_repos_to_amazon.mdwn diff --git a/doc/forum/Data_not_synced_from_my_local_repos_to_amazon.mdwn b/doc/forum/Data_not_synced_from_my_local_repos_to_amazon.mdwn new file mode 100644 index 0000000000..b26b3f76e2 --- /dev/null +++ b/doc/forum/Data_not_synced_from_my_local_repos_to_amazon.mdwn @@ -0,0 +1,44 @@ +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 From c1d93e83955882b05ad48cba9e7dac5c75008d9c Mon Sep 17 00:00:00 2001 From: "jcohen@8a78f6f9e293f581b96cd43634328c0e9de6b36e" Date: Fri, 28 Aug 2020 02:12:57 +0000 Subject: [PATCH 5/5] --- doc/forum/Data_not_synced_from_my_local_repos_to_amazon.mdwn | 1 + 1 file changed, 1 insertion(+) diff --git a/doc/forum/Data_not_synced_from_my_local_repos_to_amazon.mdwn b/doc/forum/Data_not_synced_from_my_local_repos_to_amazon.mdwn index b26b3f76e2..39a8ccaa75 100644 --- a/doc/forum/Data_not_synced_from_my_local_repos_to_amazon.mdwn +++ b/doc/forum/Data_not_synced_from_my_local_repos_to_amazon.mdwn @@ -16,6 +16,7 @@ Note: I wanted to do `git annex sync --content amazon` after the commit, accordi 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