copy: When --from and --to are combined and the content is already present
on the destination remote, update location tracking as necessary.
Sponsored-by: Dartmouth College's DANDI project
A repository can have a newline in its description due to being in a
directory containing a newline, or due to git-annex describe being
passed a string with a newline in it for some reason. Putting that
newline in uuid.log breaks its format.
So, escape the newline when it enters uuid.log, to \n
This is a one-way escaping, it is not converted back to a newline
when reading the log. If it were, commands like git-annex info and
whereis would display a multi-line description, which could be confusing
to read.
And, implementing roundtripping would necessarily cause problems if an
old version of git-annex were used to set a description that contained
whatever special character is used to escape the \n. Eg, a \ or if
it used the ! prefix before base64 data that is used in some other logs,
the ! character. Then the description set by the old git-annex would not
roundtrip.
There just doesn't seem to be any benefit of roundtripping newlines through,
so why bother? And, git often displays \n for newline when a filename
contains a newline, so git-annex doing it in this case seems sorta ok
by analogy to git.
(Some other git-annex logs can also have newlines put into them if the
user really wants to break git-annex. For example:
git-annex config annex.largefiles "foo
bar"
The full list is probably config.log, remote.log, group.log,
preferred-content.log, required-content.log,
group-preferred-content.log, schedule.log. Probably there is no
good reason to use a newline in any of these, and the breakage is
probably limited to the bad data the user put in not coming back out.
And users can write any garbage to log files themselves manually in any
case. So, I am not going to address all of those at this time. If a
problem such as this one with the newline in the repository path comes
up, it can be dealt with on a case by case basis.)
Sponsored-by: Dartmouth College's Datalad project
When importing a bunch of feeds, this makes it more clear what it's working
on. Also, I sometimes want to delete a particular feed from a list of feeds
but don't know which url belongs to the feed, and this solves that.
Control characters are filtered out just to protect against some feed
putting escape character stuff in the feed, which could be a
security problem. (Control characters also get filtered out of
importfeed filenames.)
Sponsored-by: Luke Shumaker on Patreon
Added arm64 build for ancient kernels, needed to support Android phones
whose kernels are too old to support kernels used by the current arm64
build.
Updated Android/git-annex-install to use it. (Also made it use i386-ancient
because that seems like a good idea.)
Sponsored-by: Noam Kremen on Patreon
sync: Fix a reversion that prevented sending files to exporttree=yes
remotes when annex-tracking-branch was configured to branch:subdir
(Introduced in version 10.20230214)
Sponsored-by: Kevin Mueller on Patreon
Works around this bug in unix-compat:
https://github.com/jacobstanley/unix-compat/issues/56
getFileStatus and other FilePath using functions in unix-compat do not do
UNC conversion on Windows.
Made Utility.RawFilePath use convertToWindowsNativeNamespace to do the
necessary conversion on windows to support long filenames.
Audited all imports of System.PosixCompat.Files to make sure that no
functions that operate on FilePath were imported from it. Instead, use
the equvilants from Utility.RawFilePath. In particular the
re-export of that module in Common had to be removed, which led to lots
of other changes throughout the code.
The changes to Build.Configure, Build.DesktopFile, and Build.TestConfig
make Utility.Directory not be needed to build setup. And so let it use
Utility.RawFilePath, which depends on unix, which cannot be in
setup-depends.
Sponsored-by: Dartmouth College's Datalad project
As far as I can see, git-annex status was added to support direct mode, and
like other things added for that, it ought to be deprecated.
Behavior is similar to git status --short, though not identical in a few
cases eg renamed files.
I think datalad does not use this command, although it might have in the
past. Could not find any use of it in the current datalad code.
A deprecation warning at runtime would be the next step, probably will wait
and do that for all the deprecated commands together (except findref).
Well, perhaps it could be documented better, but it's a compositional
feature so users who need it will probably try it and be happy to find
that it works.
When generating the view, check if the key is present.
When syncing in a view branch with an adjustment, run adjustedBranchRefreshFull
the same as is done when syncing in other adjusted branches. This is
needed because the docs for git-annex adjust --unlock-present suggest
using git-annex sync to update the branch when annex.adjustedbranchrefresh
is not set.
Note that, with annex.adjustedbranchrefresh set, it just works! The
adjusted branch gets updated in the usual way and it doesn't matter that
there's a view branch underneath.
And of course, re-running git-annex adjut --unlock-present also works,
as suggested in the docs.
Sponsored-by: Erik Bjäreholt on Patreon
Old message was:
sqlite query crashed: thread blocked indefinitely in an MVar operation
New message is eg:
sqlite worker thread crashed: SQLite3 returned ErrorCan'tOpen while attempting to perform open ".git/annex/keysdb/db".
The worker thread used to throw an exception. But before that
exception was seen by anything waiting on the worker thread to
finish, the takeMVar in queryDb would have crashed with
BlockedIndefinitelyOnMVar.
Sponsored-by: k0ld on Patreon
git-annex.cabal: Move webapp build deps under the Assistant build flag so
git-annex can be built again without yesod etc installed.
Commit 78440ca37d got rid of the webapp build
flag to work around what was apparently a cabal bug. It moved the webapp
build deps to the main build-depends list. But that prevents building
git-annex when yesod etc are not installed.
Putting them under the Assistant build flag seems to not tickle that cabal
bug, and lets git-annex build automatically with the assistant disabled
when the webapp build deps are not installed.
I hypotehesize that the problem may have involved build-depends nested
behind two build flags. Also, cabal clean may need to be run in order
for cabal to find the right solution after this change, when building in
a directory where cabal configure had been run before.
Also moved 3 modules that are needed to build git-annex w/o the assistant
out from under the Assistant build flag.
Sponsored-by: Brock Spratlen on Patreon
This reverts commit 648e59cac2.
Failed to build on windows, because
In the dependencies for haskeline-0.8.2:
Win32-2.11.1.0 from Stack configuration does not match >=2.1 && <2.10 || >=2.12 (latest
matching version is 2.13.4.0)
jkniiv did find a solution that builds:
-- Win32-2.11.1.0
+- Win32-2.9.0.0
+- Cabal-3.6.3.0
+- directory-1.3.7.1
+- process-1.6.17.0
+- time-1.11.1.2
But that is a quite old version of Win32 and risks bugs from it, and bumping
Cabal and directory to newer than lts-19.33 has seems also likely to be risky.
So, I've given up. aws-0.24 won't be able to be in the stack build until
there's a stackage lts (or nightly) that has filepath (>=1.4.100.0),
which will not happen until sometime after the next ghc release.
info: Fix reversion in last release involving handling of unsupported input
by continuing to handle any other inputs, before exiting nonzero at the
end.
Sponsored-by: Dartmouth College's Datalad project
view: Fix a reversion in 10.20230214 that omitted a file from a view when
the file had no metadata set, but the view only used path fields.
Sponsored-by: Jack Hill on Patreon
This enables some new features that need the new aws.
Win32 downgraded from the version in lts-19.33 because git-annex does not build
with that version, and newer versions of Win32 need a newer filepath version,
which can't be upgraded while using lts-19.33.
Sponsored-By: Brett Eisenberg on Patreon
path to a bare repo when git config is not allowed to list the configs
due to the CVE-2022-24765 fix.
That resulted in a confusing error message, and prevented the nice
message that explains how to mark the repo as safe to use.
Made isBare a tristate so that the case where core.bare is not returned can
be handled.
The handling in updateLocation is to check if the directory
contains config and objects and if so assume it's bare.
Note that if that heuristic is somehow wrong, it would construct a repo
that thinks it's bare but is not. That could cause follow-on problems,
but since git-annex then checks checkRepoConfigInaccessible, and skips
using the repo anyway, a wrong guess should not be a problem.
Sponsored-by: Luke Shumaker on Patreon
Used to fail with a bad error message, indicating there was no
repository with the specified name, or something like that. Now, suggest
they use the uuid to disambiguate.
* info, enableremotemote, renameremote: Avoid a confusing message when more
than one repository matches the user provided name.
* info: Exit nonzero when the input is not supported.
Sponsored-by: Kevin Mueller on Patreon
A benchmark in my sound repository with `git-annex view feedtitle=*`
took 2:52 wall clock time before and 1:58 after. Though it still only used
130% of CPU.
This is the same kind of optimisation that is in seekFilteredKeys, though
that precaches location logs while this streams the metadata logs direct
to parsing them.
seekFilteredKeys contains more streaming, to find the annexed files, and
this could be further sped up with similar streaming.
Sponsored-by: Nicholas Golder-Manning on Patreon
sync: Fix a bug that caused files to be removed from an importtree=yes
exporttree=yes special remote when the remote's annex-tracking-branch was
not the currently checked out branch.
Sponsored-by: Max Thoursie on Patreon
* sync: When run in a view branch, refresh the view branch to reflect any
changes that have been made to the parent branch or metadata.
This is basically working, but probably needs some more work to deal with
all the edge cases of things sync does.
Sponsored-by: Lawrence Brogan on Patreon
* sync: Avoid pushing view branches to remotes.
* Changed the name of view branches to include the parent branch.
Existing view branches checked out using an old name will still work.
It does not seem useful for sync to push view branches around, because
the information in a view branch can entirely be derived from other
information in git. And sync doesn't push adjusted branches around either.
The better view branch names make it more in line with adjusted branch
names, but were also needed to make fromViewBranch be able to return the
original branch name.
Kept the old view branch names still working. But, when those branches
exist in a repo, sync will still try to push them as before. Avoiding
that would need more complicated and/or expensive changes to sync.
Sponsored-By: Boyd Stephen Smith Jr. on Patreon
* view: New field?=glob and ?tag syntax that includes a directory "_"
in the view for files that do not have the specified metadata set.
* Added annex.viewunsetdirectory git config to change the name of the
"_" directory in a view.
When in a view using the new syntax, old git-annex will fail to parse the
view log. It errors with "Not in a view.", which is not ideal. But that
only affects view commands.
annex.viewunsetdirectory is included in the View for a couple of reasons.
One is to avoid needing to warn the user that it should not be changed when
in a view, since that would confuse git-annex. Another reason is that it
helped with plumbing the value through to some pure functions.
annex.viewunsetdirectory is actually mangled the same as any other view
directory. So if it's configured to something like "N/A", there won't be
multiple levels of directories, which would also confuse git-annex.
Sponsored-By: Jack Hill on Patreon
S3: Support a region= configuration useful for some non-Amazon S3
implementations. This feature needs git-annex to be built with aws-0.24.
datacenter= sets both the AWS hostname and region in one setting, which is
easy when using AWS, but not useful for other hosts. So kept datacenter
as-is, but added this additional config.
Sponsored-By: Brett Eisenberg on Patreon
Allowing --from and --to as an alternative to --from or --to
is hard to do with optparse-applicative!
The obvious approach of (pfrom <|> pto <|> pfromandto) does not work
when pfromandto uses the same option names as pfrom and pto do.
It compiles but the generated parser does not work for all desired
combinations.
Instead, have to parse optionally from and optionally to. When neither
is provided, the parser succeeds, but it's a result that can't be
handled. So, have to giveup after option parsing. There does not seem to
be a way to make an optparse-applicative Parser give up internally
either.
Also, need seek' because I first tried making fto be a where binding,
but that resulted in a hang when git-annex move was run without --from
or --to. I think because startConcurrency was not expecting the stages
value to contain an exception and so ended up blocking.
Sponsored-by: Dartmouth College's DANDI project
I've long been asked for `git-annex find --all` or something like that,
but pushed back on it because I feel that the command is analagous to
find(1) and so it would be surprising for it to list keys rather than
files. So instead, add a new findkeys subcommand.
Note that the use of withKeyOptions is rather strange because usually
that is used to fall back to --all rather than listing files, but here
it's made to default to --all like behavior and never list files.
A performance thing that could be improved is that withKeyOptions
always reads and caches location logs. But findkeys with no options does
not need them, so it could be made faster. That caching does speed up
options like --in though. This is really just a subset of a more general
performance thing that --all reads location logs sometimes unncessarily.
Anyway, it needs to read the location log in order to checkDead,
and it seems good that findkeys does skip dead keys.
Also, cleaned up comments on git-annex-find man page asking for --all
option.
Sponsored-by: Dartmouth College's DANDI project
Note that when this is specified and an older git-annex is used to
enableremote such a special remote, it will simply ignore the cost= field
and use whatever the default cost is.
In passing, fixed adb to support the remote.name.cost and
remote.name.cost-command configs.
Sponsored-by: Dartmouth College's DANDI project
Allow initremote of additional special remotes with type=web, in addition
to the default web special remote.
When --sameas=web is used, these provide additional names for the web
special remote, and may also have their own additional configuration
(once there is any for the web special remote) and cost.
Sponsored-by: Dartmouth College's DANDI project
AFAICS all git-annex builds are using the git-lfs library not the vendored
copy.
Debian stable does have a too old haskell-git-lfs package to be able to
build git-annex from source, but there is not currently a backport of a
recent git-annex to Debian stable. And if they update the backport at some
point, they should be able to backport the library too.
Sponsored-by: Svenne Krap on Patreon
In Makefile, listed additional deps of Build/Standalone. Without that,
it does not get updated for the change to Utility/LinuxMkLibs.hs when
compiling incrementally.
Sponsored-by: Dartmouth College's DANDI project
Speed up git-annex upgrade (from v5) and init in a repository that has
submodules. Setting the config does not affect the submodules, so avoid
the work of getting status in them, which may involve using the smudge
filter etc.
Sponsored-By: the NIH-funded NICEMAN (ReproNim TR&D3) project
Added --anything (and --nothing). Eg, git-annex find --anything will list
all annexed files whether or not the content is present. This is slightly
faster and clearer than --include=* or --exclude=*
While I can't imagine how --nothing will be used, preferred content
expressions already had anything and nothing, so might as well support both
as matching options as well.
Sponsored-by: Dartmouth College's Datalad project
Improve handling of some .git/annex/ subdirectories being on other
filesystems, in the bittorrent special remote, and youtube-dl integration,
and git-annex addurl.
The only one of these that I've confirmed to be a problem is in the
bittorrent special remote when .git/annex/tmp and .git/annex/othertmp are
on different filesystems.
As well as auditing for renameFile, also audited for createLink, all of
those are ok as are the other remaining renameFile calls. Also audited all
code paths that use .git/annex/othertmp, and did not find any other
cross-device problems. So, removing mention of othertmp needing to be on
the same device.
Sponsored-by: Dartmouth College's Datalad project
Change --metadata comparisons < > <= and >= to fall back to lexicographical
comparisons when one or both values being compared are not numbers.
Sponsored-by: Erik Bjäreholt on Patreon
Fix a hang that occasionally occurred during commands such as move.
(A bug introduced in 10.20220927, in
commit 6a3bd283b8)
The restage.log was kept locked while running a complex index refresh
action. In an unusual situation, that action could need to write to the
restage log, which caused a deadlock.
The solution is a two-stage process. First the restage.log is moved to a
work file, which is done with the lock held. Then the content of the work
file is read and processed, which happens without the lock being held.
This is all done in a crash-safe manner.
Note that streamRestageLog may not be fully safe to run concurrently
with itself. That's ok, because restagePointerFiles uses it with the
index lock held, so only one can be run at a time.
streamRestageLog does delete the restage.old file at the end without
locking. If a calcRestageLog is run concurrently, it will either see the
file content before it was deleted, or will see it's missing. Either is
ok, because at most this will cause calcRestageLog to report more
work remains to be done than there is.
Sponsored-by: Dartmouth College's Datalad project
Debian is going to drop youtube-dl which is not active upstream, and yt-dlp
is the replacement. This will make it be used if youtube-dl gets removed.
If an old version of youtube-dl remains installed, git-annex will still use
it. That might not be desirable, but changing git-annex to use yt-dlp in
preference to youtube-dl when both are installed risks breaking when
the user has annex.youtube-dl-options set to something that is supported
by youtube-dl, but not by yt-dlp.
Sponsored-by: Boyd Stephen Smith Jr. on Patreon
init: Avoid scanning for annexed files, which can be lengthy in a
large repository. Instead that scan is done on demand. This lets git-annex
init be run and some query commands be used in a repository without
waiting.
Note that autoinit already behaved this way, so while this will mean some
commands like git-annex get/unlock/add will do the scan the first time run,
that is not really a significant behavior change.
And, it's really better to have a consistent behavior. The reason for
the inconsistency was a strange bug discussed in
b3c4579c79. Avoiding reconcileStaged in
init will keep avoiding whatever that was.
Sponsored-by: Dartmouth College's DANDI project
Increasing the size of the queue 10x makes git-annex init 7% faster in a
repository with 86000 annexed files.
The memory use goes up, from 70876 kb to 85376 kb.
Avoids database querying overhead when the database is newly created.
In the large repository where git-annex init took 24 seconds, this sped it
up to 20.47 seconds, a speedup of around 15%.
Sponsored-by: Dartmouth College's DANDI project
This reverts commit 15dd7fe84b.
aws 0.23 is not used any longer, so read-only S3 import won't be
supported yet when building with stack.
That commit broke the build on windows, because the new version of Win32 that
was included (because the old one does not work with this lts version)
needs a version of filepath that is newer than the one bundled with the
ghc in that lts version. It is not possible to override that to a newer
filepath.
Seems that the only solution to get aws 0.23 will be to wait for a ghc that
contains filepath 1.4.100.0. No ghc yet contains it. (Backporting the Win32
fix to a point release version that does not include this bleeding edge
filepath would also resolve it, but seems unlikely to happen.)
Sponsored-by: Jarkko Kniivilä on Patreon
export: Fix a bug that left a file on a special remote when two files with
the same content were both deleted in the exported tree.
Case of the wrong data structure leading to the wrong result.
The DiffMap now contains all the old filenames, and all the new filenames.
Note that, when 2 files with the same content are both renamed,
it only renames the first, but deletes and re-exports the second.
Improving that is possible, but it would need to use a different temporary
filename. Anyway, that is an unusual case, and there are known to be other
unusual cases where export does not rename with maximum efficiency, IIRC.
(Or maybe this is the case that I remember?)
Sponsored-by: Dartmouth College's OpenNeuro project
This allows building with aws-0.23
Win32-2.13.4.0 contains a function that is not in lts-19.32 yet. Adding
it to stack.yaml does not seem to cause problems when building on linux.
aws-0.23 has been released.
When built with an older aws, initremote will error out when run
with signature=anonymous. And when a remote has been initialized with
that by a version of git-annex that does support it, older versions will
fail when the remote is accessed, with a useful error message.
Sponsored-by: Dartmouth College's DANDI project
Clean the standalone environment before running the su command
to run "sh". Otherwise, PATH leaked through, causing it to run
git-annex.linux/bin/sh, but GIT_ANNEX_DIR was not set,
which caused that script to not work:
[2022-10-26 15:07:02.145466106] (Utility.Process) process [938146] call: pkexec ["sh","-c","cd '/home/joey/tmp/git-annex.linux/r' && '/home/joey/tmp/git-annex.linux/git-annex' 'enable-tor' '1000'"]
/home/joey/tmp/git-annex.linux/bin/sh: 4: exec: /exe/sh: not found
Changed programPath to not use GIT_ANNEX_PROGRAMPATH,
but instead run the scripts at the top of GIT_ANNEX_DIR.
That works both when the standalone environment is set up, and when it's
not.
Sponsored-by: Kevin Mueller on Patreon
Make --batch mode handle unstaged annexed files consistently whether the
file is unlocked or not. Before this, a unstaged locked file
would have the symlink on disk examined and operated on in --batch mode,
while an unstaged unlocked file would be skipped.
Note that, when not in batch mode, unstaged files are skipped over too.
That is actually somewhat new behavior; as late as 7.20191114 a
command like `git-annex whereis .` would operate on unstaged locked
files and skip over unstaged unlocked files. That changed during
optimisation of CmdLine.Seek with apparently little fanfare or notice.
Turns out that rmurl still behaved that way when given an unstaged file
on the command line. It was changed to use lookupKeyStaged to
handle its --batch mode. That also affected its non-batch mode, but
since that's just catching up to the change earlier made to most
other commands, I have not mentioed that in the changelog.
It may be that other uses of lookupKey should also change to
lookupKeyStaged. But it may also be that would slow down some things,
or lead to unwanted behavior changes, so I've kept the changes minimal
for now.
An example of a place where the use of lookupKey is better than
lookupKeyStaged is in Command.AddUrl, where it looks to see if the file
already exists, and adds the url to the file when so. It does not matter
there whether the file is staged or not (when it's locked). The use of
lookupKey in Command.Unused likewise seems good (and faster).
Sponsored-by: Nicholas Golder-Manning on Patreon
While ErrorBusy and other exceptions were caught and the write retried for
up to 10 seconds, it was still possible for git-annex to eventually
give up and error out without writing to the database. Now it will retry
as long as necessary.
This does mean that, if one git-annex process is suspended just as sqlite
has locked the database for writing, another git-annex that tries to write
it it might get stuck retrying forever. But, that could already happen when
opening the sqlite database, which retries forever on ErrorBusy. This is an
area where git-annex is known to not behave well, there's a todo about the
general case of it.
Sponsored-by: Dartmouth College's Datalad project
When running eg git-annex get, for each file it has to read from and
write to the keys database. But it's reading exclusively from one table,
and writing to a different table. So, it is not necessary to flush the
write to the database before reading. This avoids writing the database
once per file, instead it will buffer 1000 changes before writing.
Benchmarking getting 1000 small files from a local origin,
git-annex get now takes 13.62s, down from 22.41s!
git-annex drop now takes 9.07s, down from 18.63s!
Wowowowowowowow!
(It would perhaps have been better if there were separate databases for
the two tables. At least it would have avoided this complexity. Ah well,
this is better than splitting the table in a annex.version upgrade.)
Sponsored-by: Dartmouth College's Datalad project
When importing from versioned remotes, fix tracking of the content of
deleted files.
Only S3 supports versioning so far, so only it was affected.
But, the draft import/export interface for external remotes also seemed to
need a change, so that versionedExport could be set.
S3: Speed up importing from a large bucket when fileprefix= is set by only
asking for files under the prefix.
getBucket still returns the files with the prefix included, so the rest of
the fileprefix stripping still works unchanged.
Sponsored-by: Dartmouth College's DANDI project
This can be used, for example, with importtree=yes to import from a public
bucket.
This needs a patch that has not yet landed in the aws library, and will
need to be adjusted to support compiling with old versions of the library,
so is not yet suitable for merging.
See https://github.com/aristidb/aws/pull/281
The stack.yaml changes are provided to show how to build against the aws
fork and will need to be reverted as well.
Sponsored-by: Dartmouth College's DANDI project
move: Fix openFile crash with -J
This does make them a bit slower, although usually the log file is not
very big, so even when it's being rewritten, they will not block for
long taking the lock. Still, little slowdowns may add up when moving a lot
file files.
A less expensive fix would be to use something lower level than openFile
that does not check if the file is already open for write by another
thread. But GHC does not seem to provide anything convenient; even mkFD
checks for a writing thread.
fullLines is no longer necessary since these functions no longer will
read the file while it's being written.
Sponsored-by: Dartmouth College's DANDI project
* trust, untrust, semitrust, dead: Fix behavior when provided with
multiple repositories to operate on.
* trust, untrust, semitrust, dead: When provided with no parameters,
do not operate on a repository that has an empty name.
The man page and usage already indicated that multiple repos could be
provided to these commands, but they actually used unwords to combine
everything into string, and found a repo matching that string. This was
especially bad when no parameters resulted in the empty string and some
repo happened to have an empty description.
This does change the behavior, and it's possible someone relied on the
current behavior to eg, trust a repo by name with the name not quoted into
a single parameter. But fixing the empty string bug and matching the
documentation are worth breaking that usage.
Note that git-annex init/reinit do still unwords multiple parameters when
provided to them. That is inconsistent behavior, but it certianly seems
possible that something does run git-annex init with an unquoted
description, and I don't think it's worth breaking that just to make it more
consistent with these other commands.
Sponsored-by: Boyd Stephen Smith Jr. on Patreon
Avoids displaying warning about git-annex restage needing to be run in
situations where it does not.
Closing a handle flushes it anyway, so no need for an explict flush. The
handle does get closed twice, but that's fine, the second one does nothing.
Sponsored-by: Dartmouth College's DANDI project
Well, actually, fix a typo that has always been in the implementation of
that. "inbacked" used to work, but let's not tell users about that; they
might try to use it and expect git-annex to keep supporting the typo..
Sponsored-by: Jack Hill on Patreon
p2p: Pass wormhole the --appid option before the receive/send command, as
it does not accept that option after the command
I'm left wondering, did I get this wrong from the beginning, or did
wormhole change its option parser? I'm reminded of the change in 0.8.2
where it silently changed what FD the pairing code was output to.
But, looking at the wormhole source, it was at least putting --appid before
send in its test suite from the introduction of the option.
So I think probably this has always been broken. On 2021-12-31 the --appid
option was enabled, and it took until now for someone to try
git-annex p2p --pair and notice that flag day broke it..
Sponsored-by: Svenne Krap on Patreon
Let GIT_DIR and --git-dir override git's protection against operating in a
repository owned by another user.
This is the same behavior other git commands have.
Sponsored-by: Jarkko Kniivilä on Patreon
This is much easier and less failure-prone than having the user run
git update-index --refresh themselves.
Sponsored-by: Dartmouth College's DANDI project
Fixes updating git index file after getting an unlocked file when
annex.stalldetection is set.
The transferrer may want to send additional protocol messages when it's
shut down. Closing the read handle prevented it from doing that, and caused
it to crash rather than cleanly shutting down.
Draining the handle without processing the protocol seemed ok to do,
because anything it outputs is going to be some side message displayed
at shutdown. Displaying those once per transferrer process that is running
seems unncessary.
Sponsored-by: Dartmouth College's DANDI project
When concurrency is enabled, there can be worker threads still running
when the time limit is checked. Exiting right there does not
give those threads time to finish what they're doing. Instead, the seeking
is wrapped up, and git-annex then shuts down cleanly.
The whole point of --time-limit existing, rather than using timeout(1)
when running git-annex is to let git-annex finish the action(s) it is
working on when the time limit is reached, and shut down cleanly.
I noticed this problem when investigating why restagePointerFile might
not have run after get/drop of an unlocked file. With --time-limit -J,
a worker thread may have finished updating a work tree file, and be killed
by the time limit check before it can run restagePointerFile. So despite
--time-limit running the shutdown actions, the work tree file didn't get
restaged.
Sponsored-by: Dartmouth College's DANDI project
It's hard to know what's a good default for this. But 1 mb seems way too
small, because it's very easy for a git pull or some similar operation
that we don't think of as using much space to use up 1 mb of space.
Most people would want to free up some space if a filesystem only had 100
mb free. But on a small VPS, it's probably not uncommon to have only 1 gb
free. So 1 gb is too large for annex.diskreserve.
While old 1 gb USB keys are around, it's unlikely that anyone is
relying on them to shuttle annex data around; it would be worth anyone's
time to upgrade to a 32 gb or larger cheap modern USB key ($5).
Sponsored-by: Kevin Mueller on Patreon
Fix a reversion that prevented git-annex from working in a repository when
--git-dir or GIT_DIR is specified to relocate the git directory to
somewhere else. (Introduced in version 10.20220525)
checkRepoConfigInaccessible could still run git config --list, just passing
--git-dir. It seems not necessary, because I know that passing --git-dir
bypasses git's check for repo ownership. I suppose it might be that git
eventually changes to check something about the ownership of the working
tree, so passing --git-dir without --work-tree would still be worth doing.
But for now this is the simple fix.
Sponsored-by: Nicholas Golder-Manning on Patreon
Combined with commit 0ffc59d341, this
fixes the case where there are duplicate files on the special remote,
and the first gets modified/deleted, while the second is still present.
directory, adb: Fixed a bug when importtree=yes, and multiple files in the
special remote have the same content, that caused it to refuse to get a
file from the special remote, incorrectly complaining that it had changed,
due to only accepting the inode+mtime of one file (that was since modified
or deleted) and not accepting the inode+mtime of other duplicate files.
Sponsored-by: Max Thoursie on Patreon
Improve handling of directory special remotes with importtree=yes whose
ignoreinode setting has been changed. (By either enableremote or by
upgrading to commit 3e2f1f73cbc5fc10475745b3c3133267bd1850a7.)
When getting a file from such a remote, accept the content that would have
been accepted with the previous ignoreinode setting.
After a change to ignoreinode, importing a tree from the remote will
re-import and generate new content identifiers using the new config. So
when ignoreinode has changed to no, the inodes will be learned, and after
that point, a change in an inode will be detected as a change. Before
re-importing, a change in an inode will be ignored, as it was before the
ignoreinode change. This seems acceptble, because the user can re-import
immediately if they urgently need to add inodes. And if not, they'll
do it sometime, presumably, and the change will take effect then.
Sponsored-by: Erik Bjäreholt on Patreon
Fix a reversion that made dead keys not be skipped when operating on all
keys via --all or in a bare repo. (Introduced in version 8.20200720)
Also, improved the documentation of git-annex-dead, it does not only apply
to fsck --all.
Also, made git-annex fsck, when run on a file whose key is dead, display
that. Before, it displayed that only when run with --all, but with this
fix, it skips dead keys with --all. But it can still be run on a file that
uses a dead key, and displaying "This key is dead" explains to the user
why it does not consider missing content for it to be a problem.
Sponsored-by: k0ld on Patreon
Use curl for downloads from git remotes when annex.url-options and other
git configs are set.
If the url needs a password, curl will fail, and git credential will not be
used to prompt for it. But the user can set --netrc in url-options and
put the password in the netrc file.
This also means that url-options settings like -4 will take effect.
That was the case before commit 1883f7ef8f
forced conduit to be used.
When accessing a git remote over http needs a git credential prompt for a
password, cache it for the lifetime of the git-annex process, rather than
repeatedly prompting.
The git-lfs special remote already caches the credential when discovering
the endpoint. And presumably commands like git pull do as well, since they
may download multiple urls from a remote.
The TMVar CredentialCache is read, so two concurrent calls to
getBasicAuthFromCredential will both prompt for a credential.
There would already be two concurrent password prompts in such a case,
and existing uses of `prompt` probably avoid it. Anyway, it's no worse
than before.
Fix crash importing from a directory special remote that contains a broken
symlink.
The crash was in listImportableContentsM but some other places in
Remote.Directory also seemed like they could have the same problem.
Also audited for other places that have such a problem. Not all calls
to getFileStatus are bad, in some cases it's better to crash on something
unexpected. For example, `git-annex import path` when the path is a broken
symlink should crash, the same as when it does not exist. Many of the
getFileStatus calls are like that, particularly when they involve
.git/annex/objects which should never have a broken symlink in it.
Fixed a few other possible cases of the problem.
Sponsored-by: Lawrence Brogan on Patreon
Trick the linker into not doing unncessary work searching for optimised
libraries that are not present, by symlinking the directories where
optimised libs would be to the main lib dir.
This reduces the ENOENT of git-annex init by about 1/2. The linker always
finds the files where it looks first time now. I have not looked at what
the wall clock speedup might be, it's probably rather small.
If a x86-64-v5 comes to be, the list will need to be extended. And there
may be other directories used on some machines that I have missed. Not done
for arm64 yet, or any uncommon architectures.
Sponsored-by: Dartmouth College's Datalad project
For some reason, cabal 3.4.1.0 builds w/o the assistant and webapp,
even when the flag is explicitly turned on. Moving the build-depends from
inside the if flag section to the main build-depends somehow fixes this.
Since the webapp build deps are thus always available, there is no reason
not to build the webapp when building the assistant. So, got rid of the
webapp build flag. Kept the assistant build flag for now, since building
without it does at least still speed up the build.
Sponsored-by: Brock Spratlen on Patreon
Too big a footgun.
This does not prevent attackers who can write to the directory being
imported from racing the check. But they can cause anything to be imported
anyway, so would be limited to getting the legacy import to follow into a
directory they do not write to, and move files out of it into the annex.
(The directory special remote does not have that problem since it does not
move files.)
Sponsored-by: Jack Hill on Patreon
Fix a regression in 10.20220624 that caused git-annex add to crash when
there was an unstaged deletion.
Sponsored-by: Dartmouth College's Datalad project
Use curl when annex.security.allowed-url-schemes includes an url scheme not
supported by git-annex internally, as long as
annex.security.allowed-ip-addresses is configured to allow using curl.
Sponsored-by: Luke Shumaker on Patreon
WIP: This is mostly complete, but there is a problem: createDirectoryUnder
throws an error when annex.dbdir is set to outside the git repo.
annex.dbdir is a workaround for filesystems where sqlite does not work,
due to eg, the filesystem not properly supporting locking.
It's intended to be set before initializing the repository. Changing it
in an existing repository can be done, but would be the same as making a
new repository and moving all the annexed objects into it. While the
databases get recreated from the git-annex branch in that situation, any
information that is in the databases but not stored in the branch gets
lost. It may be that no information ever gets stored in the databases
that cannot be reconstructed from the branch, but I have not verified
that.
Sponsored-by: Dartmouth College's Datalad project
Since bup split is not concurrency safe.
Used a lock file so that 2 git-annex processes only run one bup split
between them (per bup repo).
(Concurrent writes from different git-annex repository clones to the same
bup repo could still have concurrency problems.)
Sponsored-by: Noam Kremen on Patreon
It seems worth noting here that I emailed bup's author about bup split
being noisy on stderr even with -q in approximately 2011. That never got
fixed. Its current repo on github only accepts pull requests, not bug
reports. Needing to add such complexity to deal with such a longstanding
unfixed issue is not fun.
Sponsored-by: Kevin Mueller on Patreon
bup split outputs to stderr even with -q. This was discarded when using -J,
but it was still outputting when not using -J, and so was git-annex.
Sponsored-by: Nicholas Golder-Manning on Patreon
Work around bug in git 2.37 that causes a segfault when when
core.untrackedCache is set, and broke git-annex init.
Depending on when git gets fixed and how widely the buggy versions are
used, this could be reverted quite soon, or need to linger for a long time.
It only makes git-annex init a tiny bit slower in a new repo.
Sponsored-by: Max Thoursie on Patreon
This is intended for users who want to see what it would output in order to
eg, check if a file would be added to git or the annex. It is not intended
as a way for scripts to get information.
Sponsored-by: Dartmouth College's Datalad project
Last try at this broke on windows with a problem installing ghc, but I
wanted to try again.
Also this has a version of aws that allows using aeson 2.0, which has a
potential security fix.
(And v9 later on to v10.)
When v9/v10 were added, making v8 automatically upgrade was deferred
"for a few months" to prevent interoperability problems if users also
have an old version of git-annex. Of course that could still be the
case, but there has been a good amount of time and this can't be put off
forever.
Allow setting annex.autoupgraderepository to false to avoid this upgrade.
Previously, that only prevented upgrades from no longer supported git-annex
versions, but v8 is still supported, and users may want to keep on v8 to
interoperate with an old git-annex version.
Sponsored-by: Boyd Stephen Smith Jr. on Patreon
I would like for a new repo version to enable appends, but to do so
safely would need a v11 followed by a 1 year delay followed by a v12
that does it. Since a similar v9 and v10 transition is currently
happening, and is less than 6 months along in most repos, it does not
feel wise to stack up another year-long transition behind that. What if
I need to hurry up a new repo version for some other change?
Added todo so I remember to make this change at some time when a v11
and probably v12 repo version do make sense.
Sponsored-by: Dartmouth College's DANDI project
Added annex.alwayscompact setting which can be unset to speed up writes to
the git-annex branch in some cases.
Sponsored-by: Dartmouth College's DANDI project
Fix a reversion that prevented --batch commands (and the assistant)
from noticing data written to the journal by other commands.
I have not identified which commit broke this for sure,
but probably it was aeca7c2207
--batch commands that wrote to the journal avoided the problem since
journalIgnorable sets unset on write. It's a little bit surprising that
nobody noticed that query --batch commands did not see data written by
other commands.
Sponsored-by: Dartmouth College's DANDI project
It does not make sense for either; importing from an existing bucket should
not write to it. And the user may not have write access at all. And exporting to
a bucket should not write other files.
Also this prevents the uuid file being imported after being written.
Sponsored-by: Dartmouth College's DANDI project
To avoid using find -printf, which was first supported in Android around
2019-2020.
Probing seems too fragile, and execing stat once per file is too slow to do
when there's a faster way available, which brought me to an option...
Sponsored-by: Brett Eisenberg on Patreon
This caused git to complain that filter-process failed and kill it with
signal 15. Because it wrote an extra flushPkt for an empty file, which
git did not expect, and so git saw an unexpected response to the next
request.
Luckily, filter-process is only used by default in v9 and up, and v8 is
still the default. Also, git had to be updating an empty file, followed
by another file, which is a fairly unlikely situation. And git restarts
filter-process after this happens and uses it to filter the rest of the
files. So this isn't a crippling bug.
Sponsored-by: Luke Shumaker on Patreon
This reverts commit d2bc268317.
That seemed to break building on windows, before it starts building
git-annex at all, it tried to install ghc and something blew up:
Processing archive: C:\Users\runneradmin\AppData\Local\Programs\stack\x86_64-windows\ghc-9.0.2.tar.xz
Extracting ghc-9.0.2.tar
...
Extracted total of 11790 files from ghc-9.0.2.tar
C:\Users\runneradmin\AppData\Local\Programs\stack\x86_64-windows\ghc-9.0.2-tmp-6d0fbe7f3b29e56c\ghc-9.0.2\: renameDirectory:pathIsDirectory:CreateFile "\\\\?\\C:\\Users\\runneradmin\\AppData\\Local\\Programs\\stack\\x86_64-windows\\ghc-9.0.2-tmp-6d0fbe7f3b29e56c\\ghc-9.0.2\\": does not exist (The system cannot find the file specified.)
Hopefully a newer ghc version or updated stackage version will fix this
at some point, in the meantime revert it.
The webapp modules cannot build with the assistant disabled, so make the
webapp be under the assistant build flag.
Sponsored-by: Jarkko Kniivilä on Patreon
--backend is no longer a global option, and is only accepted by commands
that actually need it.
Three commands that used to support backend but don't any longer are
watch, webapp, and assistant. It would be possible to make them support it,
but I doubt anyone used the option with these. And in the case of webapp
and assistant, the option was handled inconsistently, only taking affect
when the command is run with an existing git-annex repo, not when it
creates a new one.
Also, renamed GlobalOption etc to AnnexOption. Because there are many
options of this type that are not actually global (any more) and get
added to commands that need them.
Sponsored-by: Kevin Mueller on Patreon
Improve handling of parallelization with -J when copying content from/to a
git remote that is a local path.
Sponsored-by: Nicholas Golder-Manning on Patreon
When adding a small file, it does not get locked down, so can be modified
after git-annex checks that it's small. The use of queued git add made the
race window nice and wide too.
Fixed by checking if the file has changed, and by not using git add.
Instead, have to recapitulate git add's handling of things like symlinks
and executable files.
Sponsored-by: Jochen Bartl on Patreon
The remaining callers all did not rely on it checking gitignore, so were
easy to convert.
They were susceptable to the same overwrite race as add and fix,
although less likely to have it and a narrower window than add's race.
Command.Rekey in passing got an unncessary call to removeFile deleted.
addSymlink handles deleting any existing worktree file.
Similar to git-annex add, git-annex fix queued git add, so if a file
got modified before git add ran, the wrong content would be staged,
perhaps a large file content.
Sponsored-by: Brock Spratlen on Patreon
This is not a complete fix for all such races, only the one where a
large file gets changed while adding and gets added to git rather than
to the annex.
addLink needs to go away, any caller of it is probably subject to the
same kind of race. (Also, addLink itself fails to check gitignore when
symlinks are not supported.)
ingestAdd no longer checks gitignore. (It didn't check it consistently
before either, since there were cases where it did not run git add!)
When git-annex import calls it, it's already checked gitignore itself
earlier. When git-annex add calls it, it's usually on files found
by withFilesNotInGit, which handles checking ignores.
There was one other case, when git-annex add --batch calls it. In that
case, old git-annex behaved rather badly, it would seem to add the file,
but git add would later fail, leaving the file as an unstaged annex symlink.
That behavior has also been fixed.
Sponsored-by: Brett Eisenberg on Patreon
move: Improve resuming a move that succeeded in transferring the content,
but where dropping failed due to eg a network problem, in cases where
numcopies checks prevented the resumed move from dropping the object from
the source repository.
This was earlier done for moves that got interrupted during the drop stage.
Sponsored-by: Svenne Krap on Patreon
Fix retrival of an empty file that is stored in a special remote with
chunking enabled.
The speculative chunk stuff caused a reversion by adding an empty list for
the empty file. Which is just wrong; the empty file is still stored on the
remote, and should be retrieved like any other file. It uses 1 chunk, so
`max 1` is the simple fix.
Sponsored-by: Noam Kremen on Patreon
rather than matching path of an existing remote to find the uuid.
The main benefit of this is that locations not using ssh:// will work
now, including both paths and host:/path
The other benefit is that it's a simpler interface, no need to have an
existing remote with the same url and some other name. Although that
will still work of course.
This does rely on tryGitConfigRead working when given a Git.Repo that is
not a remote. Luckily, it works fine that way.
Also, tryGitConfigRead will auto-init a local repo that has a git-annex
branch. I did not enable auto-init of ssh repos though.
The uuid discovery actually happens twice; initremote discovers it,
and uses it to store the special remote config, but does not set it in the
git remote it creates. So the next run of git-annex does uuid discovery
again, and caches it that time. This could be improved for a tiny
speedup, but I didn't want to complicate things for that in this
commit.
Sponsored-by: Dartmouth College's DANDI project
Use cases include using git-annex init --no-autoenable and then going back
and enabling the special remotes that have autoenable configured. As well
as just querying to remember which ones have it enabled.
It lists all special remotes that have autoenable=yes whether currently
enabled or not. And it can be used with --json.
I pondered making this "git-annex info autoenable", but that seemed wrong
because then if the use has a directory named "autoenable", it's unclear
what they are asking for. (Although "git-annex info remote" may be
similarly unclear.) Making it an option does mean that it can't be provided
via --batch though.
Sponsored-by: Dartmouth College's Datalad project
Someone may disagree with what repositories are set to autoenable and
it's good to have local overrides.
See https://github.com/datalad/datalad/issues/6634
Sponsored-by: Dartmouth College's Datalad project
test: When limiting tests to run with -p, work around tasty limitation by
automatically including dependent tests.
This fixes a reversion because it didn't used to use dependencies and
forced tasty to run the init tests first. That changed when parallelizing
the test suite.
It will sometimes do a little more work than strictly required,
because it adds init tests deps when limited to eg quickcheck tests,
which don't depend on them. But this only adds a few seconds work.
Sponsored-by: Dartmouth College's Datalad project
Deal with git's recent changes to fix CVE-2022-24765, which prevent using
git in a repository owned by someone else.
That makes git config --list not list the repo's configs, only global
configs. So annex.uuid and annex.version are not visible to git-annex.
It displayed a message about that, which is not right for this situation.
Detect the situation and display a better message, similar to the one other
git commands display.
Also, git-annex init when run in that situation would overwrite annex.uuid
with a new one, since it couldn't see the old one. Add a check to prevent
it running too in this situation. It may be that this fix has security
implications, if a config set by the malicious user who owns the repo
causes git or git-annex to run code. I don't think any git-annex configs
get run by git-annex init. It may be that some git config of a command
does get run by one of the git commands that git-annex init runs. ("git
status" is the command that prompted the CVE-2022-24765, since
core.fsmonitor can cause it to run a command). Since I don't know how
to exploit this, I'm not treating it as a security fix for now.
Note that passing --git-dir makes git bypass the security check. git-annex
does pass --git-dir to most calls to git, which it does to avoid needing
chdir to the directory containing a git repository when accessing a remote.
So, it's possible that somewhere in git-annex it gets as far as running git
with --git-dir, and git reads some configs that are unsafe (what
CVE-2022-24765 is about). This seems unlikely, it would have to be part of
git-annex that runs in git repositories that have no (visible) annex.uuid,
and git-annex init is the only one that I can think of that then goes on to
run git, as discussed earlier. But I've not fully ruled out there being
others..
The git developers seem mostly worried about "git status" or a similar
command implicitly run by a shell prompt, not an explicit use of git in
such a repository. For example, Ævar Arnfjörð Bjarma wrote:
> * There are other bits of config that also point to executable things,
> e.g. core.editor, aliases etc, but nothing has been found yet that
> provides the "at a distance" effect that the core.fsmonitor vector
> does.
>
> I.e. a user is unlikely to go to /tmp/some-crap/here and run "git
> commit", but they (or their shell prompt) might run "git status", and
> if you have a /tmp/.git ...
Sponsored-by: Jarkko Kniivilä on Patreon
The purpose of this is to fix situations where the annex object file is
stored in a directory structure other than where annex symlinks point to.
But it will also move object files from the hashdirmixed back to
hashdirlower if the repo configuration makes that the normal location.
It would have been more work to avoid that than to let it do it.
Sponsored-by: Dartmouth College's Datalad project
Commit 36133f27c0 had a boolean flip in it,
aaargh.
Special remotes with importtree=yes or exporttree=yes are once again
treated as untrusted, since files stored in them can be deleted or modified
at any time.
Sponsored-by: Kevin Mueller on Patreon
Added support for "megabit" and related bandwidth units in
annex.stalldetection and everywhere else that git-annex parses data units.
Note that the short form is "Mbit" not "Mb" because that differs from "MB"
only in case, and git-annex parses units case-insensitively. It would be
horrible if two different versions of git-annex parsed the same value
differently, so I don't think "Mb" can be supported.
See comment for bonus sad story from my childhood.
Sponsored-by: Nicholas Golder-Manning
Avoid treating refs/annex/last-index or other refs that are not commit
objects as evidence of repository corruption.
The repair code checks to find bad refs by trying to run `git log` on
them, and assumes that no output means something is broken. But git log
on a tree object is empty.
This was worth fixing generally, not as a special case, since it's certainly
possible that other things store tree or other objects in refs.
Sponsored-by: Max Thoursie on Patreon
rsync 3.2.4 broke backwards-compatability by preventing exposing filenames
to the shell. Made the rsync and gcrypt special remotes detect this and
disable shellescape.
An alternative fix would have been to always set RSYNC_OLD_ARGS=1.
Which would avoid the overhead of probing rsync --help for each affected
remote. But that is really very fast to run, and it seemed better to switch
to the modern code path rather than keeping on using the bad old code path.
Sponsored-by: Tobias Ammann on Patreon
Using removePathForcibly avoids concurrent removal problems.
The i386ancient build still uses an old version of ghc and directory that
do not include removePathForcibly though.
Sponsored-by: Dartmouth College's Datalad project
assistant: When annex.autocommit is set, notice commits that the user makes
manually, and push them out to remotes promptly.
Sponsored-by: Boyd Stephen Smith Jr. on Patreon
Ignore annex.numcopies set to 0 in gitattributes or git config, or by
git-annex numcopies or by --numcopies, since that configuration would make
git-annex easily lose data. Same for mincopies.
This is a continuation of the work to make data only be able to be lost
when --force is used. It earlier led to the --trust option being disabled,
and similar reasoning applies here.
Most numcopies configs had docs that strongly discouraged setting it to 0
anyway. And I can't imagine a use case for setting to 0. Not that there
might not be one, but it's just so far from the intended use case of
git-annex, of managing and storing your data, that it does not seem like
it makes sense to cater to such a hypothetical use case, where any
git-annex drop can lose your data at any time.
Using a smart constructor makes sure every place avoids 0. Note that this
does mean that NumCopies is for the configured desired values, and not the
actual existing number of copies, which of course can be 0. The name
configuredNumCopies is used to make that clear.
Sponsored-by: Brock Spratlen on Patreon
Removed vendored copy of http-client-restricted, and removed the
HttpClientRestricted build flag that avoided that dependency.
http-client-restricted is in Debian stable, and the i386ancient build also
uses it, so I think this vendored copy is no longer needed.
Sponsored-by: Noam Kremen on Patreon
add: Avoid unncessarily converting a newly unlocked file to be stored
in git when it is not modified, even when annex.largefiles does not
match it.
This fixes a reversion in version 10.20220222, where git-annex unlock
followed by git-annex add, followed by git commit file could result in
git thinking the file was modified after the commit.
I do have half a mind to remove the withUnmodifiedUnlockedPointers part
of git-annex add. It seems weird, despite that old bug report arguing
a case of consistency that it ought to behave that way. When git-annex
add surpises me, it seems likely it's wrong.. But for now, this is the
smallest possible fix.
Sponsored-by: Dartmouth College's Datalad project
Directory special remotes with importtree=yes have changed to once more
take inodes into account. This will cause extra work when importing from a
directory on a FAT filesystem that changes inodes on every mount.
To avoid that extra work, set ignoreinodes=yes when initializing a new
directory special remote, or change the configuration of your existing
remote: git-annex enableremote foo ignoreinodes=yes
This will mean a one-time re-import of all contents from every directory
special remote due to the changed setting.
73df633a62 thought
it was too unlikely that there would be modifications that the inode number
was needed to notice. That was probably right; it's very unlikely that a
file will get modified and end up with the same size and mtime as before.
But, what was not considered is that a program like NextCloud might write
two files with different content so closely together that they share the
mtime. The inode is necessary to detect that situation.
Sponsored-by: Max Thoursie on Patreon
Default to the number of CPU cores, which seems about optimal
on my laptop. Using one more saves me 2 seconds actually.
Better packing of workers improves speed significantly.
In 2 tests runs, I saw segfaulting workers despite my attempt
to work around that issue. So detect when a worker does, and re-run it.
Removed installSignalHandlers again, because I was seeing an
error "lost signal due to full pipe", which I guess was somehow caused
by using it.
Sponsored-by: Dartmouth College's Datalad project
Avoid git-annex test being very slow when run from within the standalone
linux tarball or OSX app.
It may not really be necessary to add to PATH the directory where the
git-annex binary resides, but it can't hurt. Most places where the test
suite or git-annex run git-annex, they use programPath, so won't need
a modified PATH. But I'm not sure if that's always the case.
Sponsored-by: Dartmouth College's Datalad project
Propagate nonzero exit status from git ls-files when a specified file does
not exist, or a specified directory does not contain any files checked into
git.
The recent completion of the annex.skipunknown transition exposed this
bug, that has unfortunately been lurking all along.
It is also possible that git ls-files errors out for some other reason
-- perhaps a permission problem -- and this will also fix error propagation
in such situations.
Sponsored-by: Dartmouth College's Datalad project
When annex.freezecontent-command is set, and the filesystem does not
support removing write bits, avoid treating it as a crippled filesystem.
The hook may be enough to prevent writing on its own, and some filesystems
ignore attempts to remove write bits.
Sponsored-by: Dartmouth College's Datalad project
It will then proceed to add the file the same as if it were any other
file containing possibly annexable content. Usually the file is one that
was annexed before, so the new, probably corrupt content will also be added
to the annex. If the file was not annexed before, the content will be added
to git.
It's not possible for the smudge filter to throw an error here, because
git then just adds the file to git anyway.
Sponsored-by: Dartmouth College's Datalad project
This format is designed to detect accidental appends, while having some
room for future expansion.
Detect when an unlocked file whose content is not present has gotten some
other content appended to it, and avoid treating it as a pointer file, so
that appended content will not be checked into git, but will be annexed
like any other file.
Dropped the max size of a pointer file down to 32kb, it was around 80 kb,
but without any good reason and certianly there are no valid pointer files
anywhere that are larger than 8kb, because it's just been specified what it
means for a pointer file with additional data even looks like.
I assume 32kb will be good enough for anyone. ;-) Really though, it needs
to be some smallish number, because that much of a file in git gets read
into memory when eg, catting pointer files. And since we have no use cases
for the extra lines of a pointer file yet, except possibly to add
some human-visible explanation that it is a git-annex pointer file, 32k
seems as reasonable an arbitrary number as anything. Increasing it would be
possible, eg to 64k, as long as users of such jumbo pointer files didn't
mind upgrading all their git-annex installations to one that supports the
new larger size.
Sponsored-by: Dartmouth College's Datalad project
File matching options like --include will be rejected in situations where
there is no filename to match against. (Or where there is a filename but
it's not relative to the cwd, or otherwise seemed too bothersome to match
against.)
The addition of listKeys' was necessary to avoid using more memory in the
common case of "git-annex info". Adding a filterM would have caused the
list to buffer in memory and not stream. This is an ugly hack, but listKeys
had previously run Annex operations inside unafeInterleaveIO (for direct
mode). And matching against a matcher should hopefully not change any Annex
state.
This does allow for eg `git-annex info somefile --include=*.ext`
although why someone would want to do that I don't really know. But it
seems to make sense to allow it.
But, consider: `git-annex info ./somefile --include=somefile`
This does not match, so will not display info about somefile.
If the user really wants to, they can `--include=./somefile`.
Using matching options like --copies or --in=remote seems likely to be
slower than git-annex find with those options, because unlike such
commands, info does not have optimised streaming through the matcher.
Note that `git-annex info remote` is not the same as
`git-annex info --in remote`. The former shows info about all files in
the remote. The latter shows local keys that are also in that remote.
The output should make that clear, but this still seems like a point
where users could get confused.
Sponsored-by: Jochen Bartl on Patreon
Implemented by making Git.Queue have a FlushAction, which can accumulate
along with another action on files, and runs only once the other action has
run.
This lets git-annex unlock queue up git update-index actions, without
conflicting with the restagePointerFiles FlushActions.
In a repository with filter-process enabled, git-annex unlock will
often not take any more time than before, though it may when the files are
large. Either way, it should always slow down less than git-annex status
speeds up.
When filter-process is not enabled, git-annex unlock will slow down as much
as git status speeds up.
Sponsored-by: Jochen Bartl on Patreon
annex.skipunknown now defaults to false, so commands like `git annex get foo*`
will not silently skip over files/dirs that are not checked into git.
Sponsored-by: Brock Spratlen on Patreon
* registerurl, unregisterurl: Improved output when reading from stdin
to be more like other batch commands.
* registerurl, unregisterurl: Added --json and --json-error-messages options.
Note that this did change the --batch output in a way that could possibly
break something that expected the old output to never change. I think it's
acceptable to break that because there has never been a guarantee of
unchanging output format except with --batch for most commands. The old
output was just really weird too!
One possible wart is that "git-annex registerurl" with no options now
seems to just hang, since it's waiting for stdin input. Before, it said
"registerurl (stdin)" which was clearer about what's happenening. But this
is a deprecated mode anyway, --batch makes clear what's happening. If
anything, this problem would be a reason to eventually remove the support
for reading from stdin w/o --batch.
Sponsored-by: Dartmouth College's Datalad project
takeByteString can only be used at the end of a parser, not before other
input. This was a dumb enough mistake that I audited the rest of the
code base for similar mistakes. Pity that attoparsec cannot avoid it at
the type level.
Fixes git-annex forget propagation between repositories. (reversion
introduced in version 7.20190122)
Sponsored-by: Brock Spratlen on Patreon
Seems that --no-ext-diff and -c diff.external= are not enough to disable
external diff command when gitattributes textconv specifies it.
I'm pretty sure that --no-ext-diff and -c diff.external= are not both
needed, but not 100%. Something about -G may need the latter to fully
disable diffs in some cases. So kept that part as it was.
Sponsored-by: Dartmouth College's Datalad project
The "+" argument only runs the command once, so is not safe to use. Using
";" instead would have been the simplest fix, but also the slowest.
Since my phone has an xargs that supports -0, I piped find to xargs
instead. Unsure how portable this will be, perhaps some android's don't
have xargs -0 or find -printf to send null terminated output.
The business with pipefail is necessary to make a failure of find cause the
import to fail. Probably this works on all androids, but if not, it will
probably just result in a failure of find being ignored. It would be
possible to make ignorefinderror just disable setting pipefail, but then
if some android has a shell that has pipefail enabled by default, ignorefinderror
would not work, so I kept the || true approach for that.
Sponsored-by: Max Thoursie on Patreon
Reject combinations of --batch (or --batch-keys) with options like --all or
--key or with filenames.
Most commands ignored the non-batch items when batch mode was enabled.
For some reason, addurl and dropkey both processed first the specified
non-batch items, followed by entering batch mode. Changed them to also
error out, for consistency.
Sponsored-by: Dartmouth College's Datalad project
This has tradeoffs, but is generally a win, and users who it causes git add to
slow down unacceptably for can just disable it again.
It needed to happen in an upgrade, since there are git-annex versions
that do not support it, and using such an old version with a v8
repository with filter.annex.process set will cause bad behavior.
By enabling it in v9, it's guaranteed that any git-annex version that
can use the repository does support it. Although, this is not a perfect
protection against problems, since an old git-annex version, if it's
used with a v9 repository, will cause git add to try to run
git-annex filter-process, which will fail. But at least, the user is
unlikely to have an old git-annex in path if they are using a v9
repository, since it won't work in that repository.
Sponsored-by: Dartmouth College's Datalad project
Do not populate the keys database with associated files,
because a bare repo has no working tree, and so it does not make sense to
populate it.
Queries of associated files in the keys database always return empty lists
in a bare repo, even if it's somehow populated. One way it could be
populated is if a user converts a non-bare repo to a bare repo.
Note that Git.Config.isBare does a string comparison, so this is not free!
But, that string comparison is very small compared to a sqlite query.
Sponsored-by: Erik Bjäreholt on Patreon
On a phone with Calyxos, adb find in /sdcard complains:
find: ./Android/data/com.android.providers.downloads.ui: Permission denied
But otherwise works, so this option makes import and export work ok, except
for that one app's data.
Sponsored-by: Graham Spencer
Recover from corrupted content being received from a git remote due eg to a
wire error, by deleting the temporary file when it fails to verify. This
prevents a retry from failing again.
Reversion introduced in version 8.20210903, when incremental verification
was added.
Only the git remote seems to be affected, although it is certianly
possible that other remotes could later have the same issue. This only
affects things passed to getViaTmp that return (False, UnVerified) due to
verification failing. As far as getViaTmp can tell, that could just as well
mean that the transfer failed in a way that would resume, so it cannot
delete the temp file itself. Remote.Git and P2P.Annex use getViaTmp internally,
while other remotes do not, which is why only it seems affected.
A better fix perhaps would be to improve the types of the callback
passed to getViaTmp, so that some other value could be used to indicate
the state where the transfer succeeded but verification failed.
Sponsored-by: Boyd Stephen Smith Jr.
Before it would pick one at random, though preferring ones that were not
dead over dead ones.
Now, if one is dead and the other not, it will use the non-dead one. But if
both are not dead, or both dead, it will error out, suggesting the user
clarify what they want to enable.
Sponsored-by: Luke Shumaker on Patreon
So that importing does not replace them with plain files.
This works similarly to how the previous handling of submodules and
matchers did, except that annexed symlinks still get exported as plain
files of course, it's only non-annexed symlinks that it does not make sense
to export.
When symlinks have previously been exported, updating the export will
unexport them after upgrading to this commit.
Sponsored-by: Kevin Mueller on Patreon
Improved support for using git-annex in a read-only repository, git-annex
branch information from remotes that cannot be merged into the git-annex
branch will now not crash it, but will be merged in memory.
To avoid this making git-annex behave one way in a read-only repository,
and another way when it can write, it's important that Annex.Branch.get
return the same thing (modulo log file compaction) in both cases.
This manages that mostly. There are some exceptions:
- When there is a transition in one of the remote git-annex branches
that has not yet been applied to the local or other git-annex branches.
Transitions are not handled.
- `git-annex log` runs git log on the git-annex branch, and so
it will not be able to show information coming from the other, not yet
merged branches.
- Annex.Branch.files only looks at files in the git-annex branch and not
unmerged branches. This affects git-annex info output.
- Annex.Branch.hs.overBranchFileContents ditto. Affects --all and
also importfeed (but importfeed cannot work in a read-only repo
anyway).
- CmdLine.Seek.seekFilteredKeys when precaching location logs.
Note use of Annex.Branch.fullname
- Database.ContentIdentifier.needsUpdateFromLog and updateFromLog
These warts make this not suitable to be merged yet.
This readonly code path is more expensive, since it has to query several
branches. The value does get cached, but still large queries will be
slower in a read-only repository when there are unmerged git-annex
branches.
When annex.merge-annex-branches=false, updateTo skips doing anything,
and so the read-only repository code does not get triggered. So a user who
is bothered by the extra work can set that.
Other writes to the repository can still result in permissions errors.
This includes the initial creation of the git-annex branch, and of course
any writes to the git-annex branch.
Sponsored-by: Dartmouth College's Datalad project
sync: Better error message when unable to export to a remote because
remote.name.annex-tracking-branch is configured to a ref that does not
exist.
It does not suggest how to fix the problem because there are several
possible solutions: Change the git config to point to something that does
exist, git add some files, or put files on the special remote that will be
imported and so populate the ref.
I considered just silently not doing anything, which is what it does
when annex-tracking-branch = master and nothing has been committed to
master yet. But it seems better to be explicit about it, since this is a
fairly confusing situation to find yourself in.
Sponsored-By: Max Thoursie on Patreon
So that eg, addurl of several large files that take time to download will
update the index for each file, rather than deferring the index updates to
the end.
In cases like an add of many smallish files, where a new file is being
added every few seconds. In that case, the queue will still build up a
lot of changes which are flushed at once, for best performance. Since
the default queue size is 10240, often it only gets flushed once at the
end, same as before. (Notice that updateQueue updated _lastchanged
when adding a new item to the queue without flushing it; that is
necessary to avoid it flushing the queue every 5 minutes in this case.)
But, when it takes more than a 5 minutes to add a file, the overhead of
updating the index immediately is probably small, so do it after each
file. This avoids git-annex potentially taking a very very long time
indeed to stage newly added files, which can be annoying to the user who
would like to get on with doing something with the files it's already
added, eg using git mv to rename them to a better name.
This is only likely to cause a problem if it takes say, 30 seconds to
update the index; doing an extra 30 seconds of work after every 5
minute file add would be less optimal. Normally, updating the index takes
significantly less time than that. On a SSD with 100k files it takes
less than 1 second, and the index write time is bound by disk read and
write so is not too much worse on a hard drive. So I hope this will not
impact users, although if it does turn out to, the time limit could be
made configurable.
A perhaps better way to do it would be to have a background worker
thread that wakes up every 60 seconds or so and flushes the queue.
That is made somewhat difficult because the queue can contain Annex
actions and so this would add a new source of concurrency issues.
So I'm trying to avoid that approach if possible.
Sponsored-by: Erik Bjäreholt on Patreon
Continuing along the same lines as commit
2739adc258, it seems that
while Remote -> Retriever expands to the same data type this changes
it to, ghc 9.0.1 refuses to consider them equiviant. I guess it has
something to do with the forall?
The rest of the build all succeeds, although the stack build then crashes:
Linking .stack-work/dist/x86_64-linux-tinfo6/Cabal-3.4.0.0/build/git-annex/git-annex ...
Completed 233 action(s).
Prelude.chr: bad argument: 2214592520
This issue seems likely to be about it:
https://github.com/commercialhaskell/stack/pull/5508
I'm building with stack from debian, version 2.3.3, so a newer stack
probably avoids that. Anyway, despite that stack problem,
the git-annex binary is built, and works.
The stack.yaml I used for this build was patched as follows:
diff --git a/stack.yaml b/stack.yaml
index 8dac87c15..62c4b5b9d 100644
--- a/stack.yaml
+++ b/stack.yaml
@@ -1,6 +1,6 @@
flags:
git-annex:
- production: true
+ production: false
assistant: true
pairing: true
torrentparser: true
@@ -14,7 +14,7 @@ flags:
httpclientrestricted: true
packages:
- '.'
-resolver: lts-18.13
+resolver: nightly-2021-09-07
extra-deps:
- IfElse-0.85
- aws-0.22
Sponsored-by: Graham Spencer on Patreon
This reverts commit 66b2536ea0.
I misunderstood commit ac56a5c2a0
and caused a FD leak when pid locking is not used.
A LockHandle contains an action that will close the underlying lock
file, and that action is run when it is closed. In the case of a shared
lock, the lock file is opened once for each LockHandle, and only
the one for the LockHandle that is being closed will be closed.
