Added annex.adjustedbranchrefresh git config to update adjusted branches
set up by git-annex adjust --unlock-present/--hide-missing.
Note, in a few cases, I was not able to make the adjusted branch
be updated in calls to moveAnnex, because information about what
file corresponds to a key is not available. They are:
* If two files point to one file, then eg, `git annex get foo` will
update the branch to unlock foo, but will not unlock bar, because it
does not know about it. Might be fixable by making `git annex get
bar` do something besides skipping bar?
* git-annex-shell recvkey likewise (so sends over ssh from old versions
of git-annex)
* git-annex setkey
* git-annex transferkey if the user does not use --file
* git-annex multicast sends keys with no associated file info
Doing a single full refresh at the end, after any incremental refresh,
will deal with those edge cases.
All properties changed to use them, except for
prop_encode_c_decode_c_roundtrip, which already filtered to ascii
for other reasons.
A few modules had to be split out, because Setup does not build-depend
on QuickCheck.
Always run Git.Config.store, so when the git config gets reloaded,
the override gets re-added to it, and changeGitRepo then calls extractGitConfig
on it and sees the annex.* settings from the override.
Remove any prior occurance of -c v and add it to the end. This way,
-c foo=1 -c foo=2 -c foo=1 will pass -c foo=1 to git, rather than -c foo=2
Note that, if git had some multiline config that got built up by
multiple -c's, this would not work still. But it never worked because
before the bug got fixed in the first place, the -c value was repeated
many times, so the multivalue thing would have been wrong. I don't think
-c can be used with multiline configs anyway, though git-config does
talk about them?
Fix a deadlock that could occur after git-annex got an unlocked file,
causing the command to hang indefinitely.
Known to happen on vfat filesystems, possibly others.
Note that a deadlock is still theoretically possible, if anything
smudge --clean does causes it to run the git queue for some other
reason.
Apparently that doesn't happen, but will need to keep an eye on it.
Limited to min of -JN or number of CPU cores, because it will often be
CPU bound, once it's read the gitignore file for a directory.
In some situations it's more disk bound, but in any case it's unlikely
to be the main bottleneck that -J is used to avoid. Eg, when dropping,
this is used for numcopies checks, but the main bottleneck will be
accessing the remotes to verify presence. So the user might decide to
-J32 that, but having 32 check-attr processes would just waste however
many filehandles they open, and probably worsen their performance due to
CPU contention.
Note that, I first tried just letting up to the -JN be started. However,
even when it's no bottleneck at all, that still results in all of them
being started. Why? Well, all the worker threads start up nearly
simulantaneously, so there's a thundering herd..
Avoid running a large number of git cat-file child processes when run with
a large -J value.
This implementation takes care to avoid adding any overhead to git-annex
when run without -J. When run with -J, there is a small bit of added
overhead, to manipulate the resource pool. That optimisation added a
fair bit of complexity.
Avoid repeatedly opening keys db when accessing a local git remote and -J
is used.
What was happening was that Remote.Git.onLocal created a new annex state
as each thread started up. The way the MVar was used did not prevent that.
And that, in turn, led to repeated opening of the keys db, as well as
probably other extra work or resource use.
Also managed to get rid of Annex.remoteannexstate, and it turned out there
was an unncessary Maybe in the keysdbhandle, since the handle starts out
closed.
It's important that it be clear that it overrides a config, such that
reloading the git config won't change it, and in particular, setConfig
won't change it.
Most of the calls to changeGitConfig were actually after setConfig,
which was redundant and unncessary. So removed those.
The only remaining one, besides --debug, is in the handling of
repository-global config values. That one's ok, because the
way mergeGitConfig is implemented, it does not override any value that
is set in git config. If a value with a repo-global setting was passed
to setConfig, it would set it in the git config, reload the git config,
re-apply mergeGitConfig, and use the newly set value, which is the right
thing.
annex.largefiles can be configured by git-annex config, to more easily set
a default that will also be used by clones, without needing to shoehorn the
expression into the gitattributes file. The git config and gitattributes
override that.
Whenever something is added to git-annex config, we have to consider what
happens if a user puts a purposfully bad value in there. Or, if a new
git-annex adds some new value that an old git-annex can't parse.
In this case, a global annex.largefiles that can't be parsed currently
makes an error be thrown. That might not be ideal, but the gitattribute
behaves the same, and is almost equally repo-global.
Performance notes:
git-annex add and addurl construct a matcher once
and uses it for every file, so the added time penalty for reading the global
config log is minor. If the gitattributes annex.largefiles were deprecated,
git-annex add would get around 2% faster (excluding hashing), because
looking that up for each file is not fast. So this new way of setting
it is progress toward speeding up add.
git-annex smudge does need to load the log every time. As well as checking
the git attribute. Not ideal. Setting annex.gitaddtoannex=false avoids
both overheads.
This was already optimised before, but profiling found that delEntry was
around 1.5% of the total runtime of git-annex whereis. It was being
called once per environment variable per file processed.
Fixed by better caching. Since withIndexFile is almost always run with
the same .git/annex/index file, it can cache the modified environment,
rather than re-modifying it each time called.
(cherry picked from commit 6535aea49a)
debian oldoldstable has 2.1, and that's what i386ancient uses. It would be
better to require git 2.2, which is needed to use adjusted branches, but
can't do that w/o losing support for some old linux kernels or a
complicated git backport.
When running multiple concurrent actions, the cleanup phase is run in a
separate queue than the main action queue. This can make some commands
faster, because less time is spent on bookkeeping in between each file
transfer.
But as far as I can see, nothing will be sped up much by this yet, because
all the existing cleanup actions are very light-weight. This is just groundwork
for deferring checksum verification to cleanup time.
This change does mean that if the user expects -J2 will mean that they see no
more than 2 jobs running at a time, they may be surprised to see 4 in some
cases (if the cleanup actions are slow enough to notice).
It might also make sense to enable background cleanup without the -J,
for at least one cleanup action. Indeed, that's the behavior that -J1
has now. At some point in the future, it make make sense to make the
behavior with no -J the same as -J1. The only reason it's not currently
is that git-annex can build w/o concurrent-output, and also any bugs
in concurrent-output (such as perhaps misbehaving on non-VT100 compatible
terminals) are avoided by default by only using it when -J is used.
This does not change the overall license of the git-annex program, which
was already AGPL due to a number of sources files being AGPL already.
Legally speaking, I'm adding a new license under which these files are
now available; I already released their current contents under the GPL
license. Now they're dual licensed GPL and AGPL. However, I intend
for all my future changes to these files to only be released under the
AGPL license, and I won't be tracking the dual licensing status, so I'm
simply changing the license statement to say it's AGPL.
(In some cases, others wrote parts of the code of a file and released it
under the GPL; but in all cases I have contributed a significant portion
of the code in each file and it's that code that is getting the AGPL
license; the GPL license of other contributors allows combining with
AGPL code.)
Tested on an older ghc by enabling MonadFailDesugaring globally.
In TransferQueue, the lack of a MonadFail for STM exposed what would
normally be a bug in the pattern matching, although in this case an
earlier check that the queue was not empty avoided a pattern match
failure.
Both Command.Sync and Annex.Ingest had their own versions of this.
The one in Annex.Ingest used Git.Branch.currentUnsafe, but does not seem
to need it. That is only checking to see if it's in an adjusted unlocked
branch, and when in an adjusted branch, the branch does in fact exist,
so the added check that Git.Branch.current does is fine.
This commit was sponsored by Denis Dzyubenko on Patreon.
Probably not noticed until now because the queue is large enough that two
threads each filling theirs at the same time and flushing is unlikely to
happen.
Also made explicit that each worker thread gets its own queue.
I think that was the case before, but if something was put in the queue
before worker threads were forked off, they could have each inherited the
same queue.
Could have gone with a single shared queue, but per-worker queues is more
efficient, because a worker can add lots of stuff to its own queue without
any locking.
This commit was sponsored by Ole-Morten Duesund on Patreon.
Switch to Data.Map.Strict everywhere that used it.
There are still lots of lazy maps in git-annex. I think switching these
is safe. The risk is that there might be a map that is used in a way
that relies on the values not being evaluated to WHNF, and switching to
strict might result in bad performance or memory use. So, I have not
switched everything.
Fix behavior of --json-progress followed by --json, in which
the latter option disabled the former.
This commit was supported by the NSF-funded DataLad project.
And for tab completion, by not unnessessarily statting paths to remotes,
which used to cause eg, spin-up of removable drives.
Got rid of the remotes member of Git.Repo. This was a bit painful.
Remote.Git modifies the list of remotes as it reads their configs,
so still need a persistent list of remotes. So, put it in as
Annex.gitremotes. It's only populated by getGitRemotes, so commands
like examinekey that don't care about remotes won't do so.
This commit was sponsored by Jake Vosloo on Patreon.
Fully working, including --fast/--relaxed.
Note that, while git-annex addurl --relaxed is not going to check
youtube-dl, I kept git annex importfeed --relaxed checking it.
Thinking is that, let's not break people's importfeed cron jobs, and
importfeed does not typically have to check a large number of new items,
so it's ok if it's a little bit slower when used with youtube playlist
feeds.
importfeed's behavior is also improved (?) when a feed has links in it
to non-media files. Before, those were skipped. Now, the content of the
link is downloaded. This had to be done, because trying to use
youtube-dl is slow, and if those were skipped, it would have to check
every time importfeed was run. While this behavior change may not be
desirable for some feeds, that intersperse links to web pages with
enclosures, it will be desirable for other feeds, that have
non-enclosure directy links to media files.
Remove old quvi modules.
This commit was sponsored by Øyvind Andersen Holm.
This avoids all the complication about redundant work discussed in
the previous try at fixing this. At the expense of needing each command
that could have the problem to be patched to simply wrap the action in
onlyActionOn once the key is known. But there do not seem to be many
such commands.
onlyActionOn' should not be used with a CommandStart (or CommandPerform),
although the types do allow it. onlyActionOn handles running the whole
CommandStart chain. I couldn't immediately see a way to avoid mistken
use of onlyActionOn'.
This commit was supported by the NSF-funded DataLad project.
After a false start, I found a fairly non-intrusive way to deal with it.
Although it only handles transfers -- there may be issues with eg
concurrent dropping of the same key, or other operations.
There is no added overhead when -J is not used, other than an added
inAnnex check. When -J is used, it has to maintain and check a small
Set, which should be negligible overhead.
It could output some message saying that the transfer is being done by
another thread. Or it could even display the same progress info for both
files that are being downloaded since they have the same content. But I
opted to keep it simple, since this is rather an edge case, so it just
doesn't say anything about the transfer of the file until the other
thread finishes.
Since the deferred transfer action still runs, actions that do more than
transfer content will still get a chance to do their other work. (An
example of something that needs to do such other work is P2P.Annex,
where the download always needs to receive the content from the peer.)
And, if the first thread fails to complete a transfer, the second thread
can resume it.
But, this unfortunately means that there's a risk of redundant work
being done to transfer a key that just got transferred.
That's not ideal, but should never cause breakage; the same
thing can occur when running two separate git-annex processes.
The get/move/copy/mirror --from commands had extra inAnnex checks added,
inside the download actions. Without those checks, the first thread
downloaded the content, and then the second thread woke up and
downloaded the same content redundantly.
move/copy/mirror --to is left doing redundant uploads for now. It
would need a second checkPresent of the remote inside the upload
to avoid them, which would be expensive. A better way to avoid
redundant work needs to be found..
This commit was supported by the NSF-funded DataLad project.
Added remote configuration settings annex-ignore-command and
annex-sync-command, which are dynamic equivilants of the annex-ignore
and annex-sync configurations.
For this I needed a new DynamicConfig infrastructure. Its implementation
should be as fast as before when there is no dynamic config, and it caches
so shell commands are only run once.
Note that annex-ignore-command exits nonzero when the remote should be ignored.
While that may seem backwards, it allows using the same command for it as
for annex-sync-command when you want to disable both.
This commit was sponsored by Trenton Cronholm on Patreon.
When ssh connection caching is enabled (and when GIT_ANNEX_USE_GIT_SSH is
not set), only one ssh password prompt will be made per host, and only one
ssh password prompt will be made at a time.
This also fixes a race in prepSocket's stale ssh connection stopping
when run with -J. It was possible for one thread to start a cached ssh
connection, and another thread to immediately stop it, resulting in excess
connections being made.
This commit was supported by the NSF-funded DataLad project.
It takes a single key-value backend, rather than the unncessary and confusing list.
The old option still works if set.
Simplified some old old code too.
This commit was sponsored by Thomas Hochstein on Patreon.
It was distributing jobs to remotes that were not being used by any other
job. But, suppose that there are only 2 remotes, and -J10. In such a case,
the first 2 downloads would be distributed amoung the 2 remotes, but
the other 8 would all go to remote #1. Improved by keeping a counter
of how many jobs are assigned to a remote, and prefer remotes with fewer
jobs.
Note use of Data.Map.Strict to avoid blowing up space. I kept the
bang-patterns as-is, although probably not needed with Data.Map.Strict.
This commit was sponsored by Jack Hill on Patreon.
... to control the default behavior in all clones of a repository.
This includes a new Configurable data type, so the GitConfig type indicates
which values can be configured this way.
The implementation should be quite efficient; the config log is only read
once, and only when a Configurable value has not already been set by
git-config.
Indeed, it would be nice in the future to extend this, so that git-config
is itself only read on demand. Some commands may not need to look at the
git configuration at all.
This commit was sponsored by Trenton Cronholm on Patreon.
Any config names can be set using this; git-annex commands will only look
at specific ones that make sense and are worth the overhead of querying the
branch.
This might also be useful for storing whatever other config-type stuff the
user might want to shove into the git-annex branch.
This commit was sponsored by Jochen Bartl on Patreon.
Speeds up commands like "git-annex find --in remote" by over 50%.
Profiling showed that adjustGitEnv was 21% of the time and 37% of the
allocations of that command. It copied the environment each time with
getEnvironment.
The only repeated use of adjustGitEnv is in withIndexFile, which tends to
be run at least once per file. So, it was optimised by keeping a cache of
the environment, which can be reused.
There could be other better ways to optimise this. Maybe get the while
environment once at startup. But, then it would have to be serialized back
out each time running a child process, so I doubt that would be a net win.
It might be better to cache a version of the environment that is
pre-modified to use .git-annex/index. But, profiling doesn't show that
modifying the enviroment is taking any significant time.
This makes -Jn work with --json and --quiet, where before
setting -Jn disabled those options.
Concurrent json output is currently a mess though since threads output
chunks over top of one-another.
Only done in -J mode because only if there's concurrency can downloading
from two remotes be faster. Without concurrency, it's likely the case that
sequential downloads from the same remote are faster than switching back
and forth between two remotes.
There is some hairy MVar code here, but basically it just keeps
the activeremotes MVar full except when deciding which remote to assign
to a thread.
Also affects gets by sync --content -J
This commit was sponsored by Jochen Bartl.
