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

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Joey Hess 2019-05-20 09:50:56 -04:00
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doc/bugs/Android_install_doesn__39__t_permanently_add_to___36__PATH/comment_4_d8cec7fae740e82c5da1da47037e2da6._comment Normal file
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[[!comment format=mdwn
username="branchable@bafd175a4b99afd6ed72501042e364ebd3e0c45e"
nickname="branchable"
avatar="http://cdn.libravatar.org/avatar/ae41dba34ee6000056f00793c695be75"
subject=".profile doesn't take effect"
date="2019-05-18T19:46:09Z"
content="""
Ah, interesting. Very odd that the install script doesn't do that directly. I do have the same contents in my `~/.profile`, but Termux happily ignores it, so `$PATH` is unaltered. Does it really work for you? What version of Termux do you have?
"""]]

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### Please describe the problem.
There appears to be no way of getting the current configuration of special remotes (e.g. url, keyid). Maybe there should be git-annex-showremote (or similar).
### What steps will reproduce the problem?
Configure the special remote (e.g. webdav), and then forget what settings you specified ;)
### What version of git-annex are you using? On what operating system?
7.20190129-3 (Debian)

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[[!comment format=mdwn
username="derobert"
avatar="http://cdn.libravatar.org/avatar/05b48b72766177b3b0a6ff4afdb70790"
subject="comment 1"
date="2019-05-16T08:12:45Z"
content="""
Did you try `git-annex info «remote»` (where «remote» could be the name or the UUID).
"""]]

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[[!comment format=mdwn
username="aragilar"
avatar="http://cdn.libravatar.org/avatar/7390f7c0dd07d43ca827a5446b65c102"
subject="comment 2"
date="2019-05-16T08:26:28Z"
content="""
Weird, I tried that on the same remote on a different system, and it gave what I wanted... I'll have to work out why that didn't work the first time. Thanks @derobert!
"""]]

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### Please describe the problem.
The man page for [[`git-annex-init`|git-annex-init]] suggests that it is idempotent. But, when run with no args, it will overwrite an existing repo description with an automatically-generated one. Same for [[`git-annex-describe`|git-annex-describe]].
### What version of git-annex are you using? On what operating system?
(master_env_v135_py36) 13:44 [r2] $ git annex version
git-annex version: 7.20190507-g0c2cc3d
build flags: Assistant Webapp Pairing S3 WebDAV Inotify DBus DesktopNotify TorrentParser MagicMime Feeds Testsuite
dependency versions: aws-0.21.1 bloomfilter-2.0.1.0 cryptonite-0.25 DAV-1.3.3 feed-1.0.1.0 ghc-8.4.2 http-client-0.5.14 persistent-sq\
lite-2.9.2 torrent-10000.1.1 uuid-1.3.13 yesod-1.6.0
key/value backends: SHA256E SHA256 SHA512E SHA512 SHA224E SHA224 SHA384E SHA384 SHA3_256E SHA3_256 SHA3_512E SHA3_512 SHA3_224E SHA3_\
224 SHA3_384E SHA3_384 SKEIN256E SKEIN256 SKEIN512E SKEIN512 BLAKE2B256E BLAKE2B256 BLAKE2B512E BLAKE2B512 BLAKE2B160E BLAKE2B160 BLA\
KE2B224E BLAKE2B224 BLAKE2B384E BLAKE2B384 BLAKE2S256E BLAKE2S256 BLAKE2S160E BLAKE2S160 BLAKE2S224E BLAKE2S224 BLAKE2SP256E BLAKE2SP\
256 BLAKE2SP224E BLAKE2SP224 SHA1E SHA1 MD5E MD5 WORM URL
remote types: git gcrypt p2p S3 bup directory rsync web bittorrent webdav adb tahoe glacier ddar hook external
operating system: linux x86_64
supported repository versions: 5 7
upgrade supported from repository versions: 0 1 2 3 4 5 6
local repository version: 5
(master_env_v135_py36) 13:47 [r2] $ uname -a
Linux ip-172-31-90-58.ec2.internal 4.14.114-105.126.amzn2.x86_64 #1 SMP Tue May 7 02:26:40 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

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It seems that the [[issue with parallel git-annex-add|bugs/withOtherTmp_file_escapes]] is not yet quite fixed; I'm seeing it in the git-annex version 7.20190507-g0c2cc3d . Repeating the git-annex-add command succeeds in adding the files that failed the first time.
[[!format sh """
add benchmarks/rabies200/analysis-FK7BF7Q0761xKv6V3z3gzZgK/benchmark_variants/v1.23.0_spades-3.13.0-trinity-metaspades-01/inputs-local.json
git-annex: .git/annex/othertmp/inge11793-2931: rename: permission denied (Permission denied)
failed
add benchmarks/rabies200/analysis-FK7BKGj0761VgPb22550gfBX/benchmark_variants/v1.23.0_spades-3.13.0-trinity-metaspades-01/inputs-local.json
git-annex: .git/annex/othertmp/inge11793-3330: rename: permission denied (Permission denied)
failed
git-annex: add: 2 failed
"""]]
### Have you had any luck using git-annex before? (Sometimes we get tired of reading bug reports all day and a lil' positive end note does wonders)
git-annex has become an essential tool for organizing my bioinformatics data analyses. It scales well to large repos. It lets me keep track of analyses without
locking myself into any specific cloud platform. It lets me quickly free up space on demand by moving data to cheaper storage, with the assurance that nothing will get lost.
Thanks @joeyh for all your work on it.

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[[!comment format=mdwn
username="ply"
avatar="http://cdn.libravatar.org/avatar/1270501a59ed4a4042366b00295fe236"
subject="comment 3"
date="2019-05-17T20:55:48Z"
content="""
Hello, I have similar problem, but with exFAT on macOS 10.13.6. Output is not stripped, it's no filename there:
```
$ git annex info --fast --debug
[2019-05-17 22:42:09.997466] read: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"show-ref\",\"git-annex\"]
[2019-05-17 22:42:12.914831] process done ExitSuccess
[2019-05-17 22:42:12.915017] read: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"show-ref\",\"--hash\",\"refs/heads/git-annex\"]
[2019-05-17 22:42:12.953171] process done ExitSuccess
[2019-05-17 22:42:12.953815] read: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"log\",\"refs/heads/git-annex..a0409bc558f0ed6679bf591e80f9782f1cd81da3\",\"--pretty=%H\",\"-n1\"]
[2019-05-17 22:42:12.995305] process done ExitSuccess
[2019-05-17 22:42:12.996023] chat: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"hash-object\",\"-w\",\"--stdin-paths\",\"--no-filters\"]
[2019-05-17 22:42:13.014492] chat: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"cat-file\",\"--batch\"]
[2019-05-17 22:42:13.029075] chat: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"cat-file\",\"--batch-check=%(objectname) %(objecttype) %(objectsize)\"]
[2019-05-17 22:42:13.043862] feed: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"update-index\",\"-z\",\"--index-info\"]
[2019-05-17 22:42:13.050909] read: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"diff-index\",\"--raw\",\"-z\",\"-r\",\"--no-renames\",\"-l0\",\"--cached\",\"refs/heads/git-annex\",\"--\"]
[2019-05-17 22:42:14.066638] process done ExitSuccess
[2019-05-17 22:42:14.08207] process done ExitSuccess
[2019-05-17 22:42:14.090912] feed: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"update-index\",\"-z\",\"--index-info\"]
[2019-05-17 22:42:15.852868] process done ExitSuccess
(recording state in git...)
[2019-05-17 22:42:15.868392] read: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"write-tree\"]
[2019-05-17 22:42:17.763573] process done ExitSuccess
[2019-05-17 22:42:17.763746] chat: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"commit-tree\",\"20ab70e8f50d62cc8d9657eaaff71cce88dfaa21\",\"--no-gpg-sign\",\"-p\",\"refs/heads/git-annex\"]
[2019-05-17 22:42:17.800472] process done ExitSuccess
[2019-05-17 22:42:17.800747] call: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"update-ref\",\"refs/heads/git-annex\",\"e0259808f7fbed2ce7cf0d8080dabb8d208c0da1\"]
[2019-05-17 22:42:17.867585] process done ExitSuccess
git-annex: openFile: resource busy (file is locked)
failed
[2019-05-17 22:42:17.870299] process done ExitSuccess
[2019-05-17 22:42:17.875024] process done ExitSuccess
[2019-05-17 22:42:17.886388] process done ExitSuccess
```
I tried `sudo dtruss -f git annex info --fast --debug`, and this is an excerpt from the terminal:
```
82503/0x1b0045: write(0x2, \"[2019-05-17 22:29:55.91659] process done ExitSuccess\n\0\", 0x35) = 53 0
82503/0x1b0045: mkdir(\".git/annex\0\", 0x1FF, 0x0) = -1 Err#17
82503/0x1b0045: stat64(\".git/annex\0\", 0x4200038E40, 0x0) = 0 0
82503/0x1b0045: getpid(0x0, 0x0, 0x0) = 82503 0
82503/0x1b0045: open(\".git/annex/index.lck82503-2.tmp\0\", 0x20A06, 0x180) = 13 0
82503/0x1b0045: fstat64(0xD, 0x420004D050, 0x0) = 0 0
82503/0x1b0045: stat64(\".git/annex\0\", 0x420004D1D0, 0x0) = 0 0
82503/0x1b0045: mkdir(\".git/annex\0\", 0x1FF, 0x0) = -1 Err#17
82503/0x1b0045: stat64(\".git/annex\0\", 0x420004D3A0, 0x0) = 0 0
82503/0x1b0045: open(\".git/annex/index.lck82503-3.tmp\0\", 0x20A06, 0x180) = 21 0
82503/0x1b0045: fstat64(0x15, 0x420004D580, 0x0) = 0 0
82503/0x1b0045: close(0xC) = 0 0
82503/0x1b0045: poll(0x7FFEEC5CC810, 0x1, 0x0) = 1 0
82503/0x1b0045: write(0x1, \"\n\0\", 0x1) = 1 0
82503/0x1b0045: poll(0x7FFEEC5CC810, 0x1, 0x0) = 1 0
82503/0x1b0045: write(0x2, \"git-annex: openFile: resource busy (file is locked)\n\0\", 0x34) = 52 0
```
Removing `.git/annex/*.lck*` hadn't helped.
I use git-annex version 7.20190322 from Homebrew:
```
build flags: Assistant Webapp Pairing S3(multipartupload)(storageclasses) WebDAV FsEvents TorrentParser MagicMime Feeds Testsuite
dependency versions: aws-0.19 bloomfilter-2.0.1.0 cryptonite-0.25 DAV-1.3.3 feed-1.0.1.0 ghc-8.2.2 http-client-0.5.14 persistent-sqlite-2.6.4 torrent-10000.1.1 uuid-1.3.13 yesod-1.4.5
key/value backends: SHA256E SHA256 SHA512E SHA512 SHA224E SHA224 SHA384E SHA384 SHA3_256E SHA3_256 SHA3_512E SHA3_512 SHA3_224E SHA3_224 SHA3_384E SHA3_384 SKEIN256E SKEIN256 SKEIN512E SKEIN512 BLAKE2B256E BLAKE2B256 BLAKE2B512E BLAKE2B512 BLAKE2B160E BLAKE2B160 BLAKE2B224E BLAKE2B224 BLAKE2B384E BLAKE2B384 BLAKE2S256E BLAKE2S256 BLAKE2S160E BLAKE2S160 BLAKE2S224E BLAKE2S224 BLAKE2SP256E BLAKE2SP256 BLAKE2SP224E BLAKE2SP224 SHA1E SHA1 MD5E MD5 WORM URL
remote types: git gcrypt p2p S3 bup directory rsync web bittorrent webdav adb tahoe glacier ddar hook external
operating system: darwin x86_64
supported repository versions: 5 7
upgrade supported from repository versions: 0 1 2 3 4 5 6
local repository version: 7
```
"""]]