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
As was attempted earlier in the buggy commit 0d2e3058ee
Avoided the bug that had by making the upgrade log be updated after each
upgrade step. So, after upgrade from v8 to v9, the log is updated, and
so Upgrade.V9's timeOfUpgrade check will find that it was upgraded
recently and so won't let it skip ahead to v10.
Sponsored-by: k0ld on Patreon
This reverts commit 0d2e3058ee.
This commit accidentially caused repos that were initialized at v8 to
also upgrade to v10. There is nothing in the upgrade.log for such a
repo..
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
There is nothing in upgrade.log because it was never upgraded to version
9. Before, it would have never autoupgraded to 10, but it's entirely
safe to upgrade to 10 immediately.
Of course, annex.autoupgraderepository = false will prevent that
upgrade. So if someone for some reason really wants v9, they can set
that. I can't think of a reason someone would actually want v9 rather
than v10 though.
Sponsored-by: k0ld on Patreon
This would have prevented old git-annex from ever upgrading from v9 to
v10. Note that a manual `git-annex upgrade` can never run while the
assistant is running, so not <$> assistantrunning was always True,
so no matter what the timestamp of the v9 upgrade in the log, it would
decide there was old process danger.
Sponsored-by: Jack Hill on Patreon
If the content directory does not exist, then it does not make sense to
lock the content file, as it also does not exist, and so it's ok for the
lock operation to fail.
This avoids potential races where the content file exists but is then
deleted/renamed, while another process sees that it exists and goes to
lock it, resulting in a dangling lock file in an otherwise empty object
directory.
Also renamed modifyContent to modifyContentDir since it is not only
necessarily used for modifying content files, but also other files in
the content directory.
Sponsored-by: Dartmouth College's Datalad project
That left the repo in v8, but with filter.annex.process set. Instead,
only warn, and defer the v10 upgrade.
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
The v10 upgrade should almost be safe now. What remains to be done is
notice when the v10 upgrade has occurred, while holding the shared lock,
and switch to using v10 lock files.
Sponsored-by: Dartmouth College's Datalad project
The upgrade from V9 uses this to avoid an automatic upgrade until 1 year
after the V9 update. It can also be used in future such situations.
Sponsored-by: Dartmouth College's Datalad project
v10 will run 1 year after the upgrade to v9, to give time for any v8
processes to die. Until that point, the v10 upgrade will be tried by
every process but deferred, so added support for deferring upgrades.
The upgrade prevention lock file that will be used by v10 is not yet
implemented, so it does not yet defer.
Sponsored-by: Dartmouth College's Datalad project
Seems to work ok. Unsure yet about the actual locking changes being
correct.
This is not the end of the story with upgrades, because it is unsafe for
this upgrade as implemented to run in a repository where an old
git-annex process is already running. The old process would use the old
locking method, and not notice files locked by the new, and this could
result in data loss. This problem will need to be dealt with before this
branch is suitable for merging.
Sponsored-by: Dartmouth College's Datalad project
This is the start of v9, but it's currently identical to v8, and v8 is
not upgraded to it. git-annex upgrade will upgrade to v9 with this
change.
Sponsored-by: Dartmouth College's Datalad project
This adds the overhead of a copy when serializing and deserializing keys.
I have not benchmarked much, but runtimes seem barely changed at all by that.
When a lot of keys are in memory, it improves memory use.
And, it prevents keys sometimes getting PINNED in memory and failing to GC,
which is a problem ByteString has sometimes. In particular, git-annex sync
from a borg special remote had that problem and this improved its memory
use by a large amount.
Sponsored-by: Shae Erisson on Patreon
This eliminates the distinction between decodeBS and decodeBS', encodeBS
and encodeBS', etc. The old implementation truncated at NUL, and the
primed versions had to do extra work to avoid that problem. The new
implementation does not truncate at NUL, and is also a lot faster.
(Benchmarked at 2x faster for decodeBS and 3x for encodeBS; more for the
primed versions.)
Note that filepath-bytestring 1.4.2.1.8 contains the same optimisation,
and upgrading to it will speed up to/fromRawFilePath.
AFAIK, nothing relied on the old behavior of truncating at NUL. Some
code used the faster versions in places where I was sure there would not
be a NUL. So this change is unlikely to break anything.
Also, moved s2w8 and w82s out of the module, as they do not involve
filesystem encoding really.
Sponsored-by: Shae Erisson on Patreon
The pass was needed to populate files when annex.thin was set,
but in commit 73e0cbbb19,
reconcileStaged started to do that. So, this second pass is not needed
any longer.
This makes git checkout and git merge hooks do the work to catch up with
changes that they made to the tree. Rather than doing it at some later
point when the user is not thinking about that past operation.
Sponsored-by: Dartmouth College's Datalad project
Before only unlocked files were included.
The initial scan now scans for locked as well as unlocked files. This
does mean it gets a little bit slower, although I optimised it as well
as I think it can be.
reconcileStaged changed to diff from the current index to the tree of
the previous index. This lets it handle deletions as well, removing
associated files for both locked and unlocked files, which did not
always happen before.
On upgrade, there will be no recorded previous tree, so it will diff
from the empty tree to current index, and so will fully populate the
associated files, as well as removing any stale associated files
that were present due to them not being removed before.
reconcileStaged now does a bit more work. Most of the time, this will
just be due to running more often, after some change is made to the
index, and since there will be few changes since the last time, it will
not be a noticable overhead. What may turn out to be a noticable
slowdown is after changing to a branch, it has to go through the diff
from the previous index to the new one, and if there are lots of
changes, that could take a long time. Also, after adding a lot of files,
or deleting a lot of files, or moving a large subdirectory, etc.
Command.Lock used removeAssociatedFile, but now that's wrong because a
newly locked file still needs to have its associated file tracked.
Command.Rekey used removeAssociatedFile when the file was unlocked.
It could remove it also when it's locked, but it is not really
necessary, because it changes the index, and so the next time git-annex
run and accesses the keys db, reconcileStaged will run and update it.
There are probably several other places that use addAssociatedFile and
don't need to any more for similar reasons. But there's no harm in
keeping them, and it probably is a good idea to, if only to support
mixing this with older versions of git-annex.
However, mixing this and older versions does risk reconcileStaged not
running, if the older version already ran it on a given index state. So
it's not a good idea to mix versions. This problem could be dealt with
by changing the name of the gitAnnexKeysDbIndexCache, but that would
leave the old file dangling, or it would need to keep trying to remove
it.
This adds a separate journal, which does not currently get committed to
an index, but is planned to be committed to .git/annex/index-private.
Changes that are regarding a UUID that is private will get written to
this journal, and so will not be published into the git-annex branch.
All log writing should have been made to indicate the UUID it's
regarding, though I've not verified this yet.
Currently, no UUIDs are treated as private yet, a way to configure that
is needed.
The implementation is careful to not add any additional IO work when
privateUUIDsKnown is False. It will skip looking at the private journal
at all. So this should be free, or nearly so, unless the feature is
used. When it is used, all branch reads will be about twice as expensive.
It is very lucky -- or very prudent design -- that Annex.Branch.change
and maybeChange are the only ways to change a file on the branch,
and Annex.Branch.set is only internal use. That let Annex.Branch.get
always yield any private information that has been recorded, without
the risk that Annex.Branch.set might be called, with a non-private UUID,
and end up leaking the private information into the git-annex branch.
And, this relies on the way git-annex union merges the git-annex branch.
When reading a file, there can be a public and a private version, and
they are just concacenated together. That will be handled the same as if
there were two diverged git-annex branches that got union merged.
This was making it git checkout master when that branch was already
checked out, for apparently no good reason at all. In a 100,000 file
repo, that takes about 1 second.
Note, I'm not sure why it checks out the branch in the Nothing case, so
I left that alone.
9cb250f7be got the ones in RawFilePath,
but there were others that used the one from unix-compat, which fails at
runtime on windows. To avoid this,
import System.PosixCompat.Files hiding removeLink
This commit was sponsored by Ethan Aubin.
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.
nukeFile replaced with removeWhenExistsWith removeLink, which allows
using RawFilePath. Utility.Directory cannot use RawFilePath since setup
does not depend on posix.
This commit was sponsored by Graham Spencer on Patreon.
planned to use for an optimisation
most things using stagedDetails were not expecting to get dup files in a
conflicted merge and deal with them, so converted them to use
inRepoDetails.
And convert parser to attoparsec, probably faster.
Before, a parse failure threw the whole --stage output line in to the
filename, which was certianly a bad idea, so fixed that.
Added annex.skipunknown git config, that can be set to false to change the
behavior of commands like `git annex get foo*`, to not skip over files/dirs
that are not checked into git and are explicitly listed in the command
line.
Significant complexity was needed to handle git-annex add, which uses some
git ls-files calls, but needs to not use --error-unmatch because of course
the files are not known to git.
annex.skipunknown is planned to change to default to false in a
git-annex release in early 2022. There's a todo for that.
37b42e72e7 made it catch exceptions but
thought they were unlikely to be useful to display, which may be right when
a git command fails, but not in the case yoh found.
The only price paid is one additional MVar read per write to the journal.
Presumably writing a journal file dominiates over a MVar read time by
several orders of magnitude.
--batch does not get the speedup because then it needs to notice when
another process has made a change. Also made the assistant and other damon
modes bypass the optimisation, which would not help them anyway.
Remaining things needing converted are in the assistant, and Annex.Ssh.
Every other remaining call to createDirectoryIfMissing True has been
audited and is not relevant. The ones in Build/ of course don't get
included in the program. Others included eg, Remote.Tahoe and
Config.Files which both write to dotfiles under the home directory.
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.
Fix support for repositories tuned with annex.tune.branchhash1=true,
including --all not working and git-annex log not displaying anything for
annexed files.
