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
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
git-annex get when run as the first git-annex command in a new repo did not
populate unlocked files. (Reversion in version 8.20210621)
I am not entirely happy with this, because I don't understand how
428c91606b caused the problem in the first
place, and I don't fully understand how skipping calling scanAnnexedFiles
during autoinit avoids the problem.
Kept the explicit call to scanAnnexedFiles during git-annex init,
so that when reconcileStaged is expensive, it can be made to run then,
rather than at some later point when the information is needed.
Sponsored-by: Brock Spratlen 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.
Some uses of linkFromAnnex are inside replaceWorkTreeFile, which was
already safe, but others use it directly on the work tree file, which
was race-prone. Eg, if the work tree file was first removed, then
linkFromAnnex called to populate it, the user could have re-written it in
the interim.
This came to light during an audit of all calls of addInodeCaches,
looking for such races. All the other uses of it seem ok.
Sponsored-by: Brett Eisenberg on Patreon
Clear visible progress bar first.
Removed showSideActionAfter because it can't be used in reconcileStaged
(import loop). Instead, it counts the number of files it
processes and displays it after it's seen a sufficient to know it's
taking a while.
Sponsored-by: Dartmouth College's Datalad project
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
Following commit c941ab6f5b, this avoids
the second, redundant scan when annex.thin is not set.
The benchmark now runs in 35.5 seconds, down from 40 seconds.
Note that the inode cache of the annex object has to be passed to
addInodeCaches now, because it might not already be in the inode caches,
unlike previously.
Sponsored-by: Dartmouth College's Datalad project
reconcileStaged populates the db, so scanAnnexedFiles does not need to
do it again. It still makes a pass over the HEAD tree, but populating
the db was most of the expensive part.
Benchmarking with 100,000 files, git-annex init now takes 40 seconds,
vs 37 seconds with the old, buggy version of this fix. It should be
possible to win those 3 precious seconds per 100k files back, in the
case when when annex.thin is not set, with improvements to reconcileStaged
that avoid needing this second pass.
Sponsored-by: Dartmouth College's Datalad project
This reverts commit 0f10f208a7.
The implementation of this turns out to be unsafe; it can lead to a keys
db deadlock. scanAnnexedFiles injects a call to inAnnex into
reconcileStaged, but inAnnex sometimes needs to read from the keys db,
which will try to re-open it when it's in the process of being opened.
The exclusive lock of gitAnnexKeysDbLock will then deadlock.
This needs to be done in some other way...
reconcileStaged was doing a redundant scan to scannAnnexedFiles.
It would probably make sense to move the body of scannAnnexedFiles
into reconcileStaged, the separation does not really serve any purpose.
Sponsored-by: Dartmouth College's Datalad project
Streaming through git this way speeds it up by around 25%. This is
similar to the optimisations of seeking annexed files.
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.
Not yet used, but allows getting the size of items in the tree fairly
cheaply.
I noticed that CmdLine.Seek uses ls-tree and the feeds the files into
another long-running process to check their size. That would be an
example of a place that might be sped up by using this. Although in that
particular case, it only needs to know the size of unlocked files, not
locked. And since enabling --long probably doubles the ls-tree runtime
or more, the overhead of using it there may outwweigh the benefit.
removeFile changed to removeLink, because AFAICS it should be fine to
remove non-file things here. In particular, it's fine to remove a
symlink, since we're about to write a symlink. (removeLink does not
remove directories, so file, symlink, and unix socket are the only
possibilities.)
Since it was used on both worktree and .git/annex files, split into
multiple functions.
In passing, this also improves permissions of created directories in
.git/annex, using createAnnexDirectory on those.
git-annex find is now RawFilePath end to end, no string conversions.
So is git-annex get when it does not need to get anything.
So this is a major milestone on optimisation.
Benchmarks indicate around 30% speedup in both commands.
Probably many other performance improvements. All or nearly all places
where a file is statted use RawFilePath now.
Adds a dependency on filepath-bytestring, an as yet unreleased fork of
filepath that operates on RawFilePath.
Git.Repo also changed to use RawFilePath for the path to the repo.
This does eliminate some RawFilePath -> FilePath -> RawFilePath
conversions. And filepath-bytestring's </> is probably faster.
But I don't expect a major performance improvement from this.
This is mostly groundwork for making Annex.Location use RawFilePath,
which will allow for a conversion-free pipleline.
Since the sqlite branch uses blobs extensively, there are some
performance benefits, ByteStrings now get stored and retrieved w/o
conversion in some cases like in Database.Export.
Finally builds (oh the agoncy of making it build), but still very
unmergable, only Command.Find is included and lots of stuff is badly
hacked to make it compile.
Benchmarking vs master, this git-annex find is significantly faster!
Specifically:
num files old new speedup
48500 4.77 3.73 28%
12500 1.36 1.02 66%
20 0.075 0.074 0% (so startup time is unchanged)
That's without really finishing the optimization. Things still to do:
* Eliminate all the fromRawFilePath, toRawFilePath, encodeBS,
decodeBS conversions.
* Use versions of IO actions like getFileStatus that take a RawFilePath.
* Eliminate some Data.ByteString.Lazy.toStrict, which is a slow copy.
* Use ByteString for parsing git config to speed up startup.
It's likely several of those will speed up git-annex find further.
And other commands will certianly benefit even more.
It's not necessary. And if the bare repo somehow has a pointer
file in it with the same name as a file in HEAD, that file would be
populated, which would be surprising since the file is not really under
git's control.
Fix bug that lost modifications to unlocked files when init is re-ran in an
already initialized repo.
In retrospect needing scanUnlockedFiles False in the direct mode upgrade
path was a good hint that it was unsafe when used with True.
However, this bug did not affect upgrade from v5. In such an upgrade, an
unlocked file that is modified is left as-is. The only place
scanUnlockedFiles True did overwrite modified unlocked files is during an
git-annex init of a repo that was already initialized by git-annex.
(I also tried a scenario where the repo had not been initialized by
git-annex yet, but was cloned from a v7 repo with an unlocked file, and the
pointer file replaced with some other content, and the data loss did not
occur in that situation.)
Since the fixed scanUnlockedFiles avoids overwriting non-pointer files,
it should be safe to run in any situation, so there's no need any longer
for the parameter.
This is a non-backwards compatable change, so not suitable for merging
w/o a annex.version bump and transition code. Not yet tested.
This improves performance of git-annex benchmark --databases
across the board by 10-25%, since eg Key roundtrips as a ByteString.
(serializeKey' produces a lazy ByteString, so there is still a
copy involved in converting it to a strict ByteString. It may be faster
to switch to using bytestring-strict-builder.)
FilePath and Key are both stored as blobs. This avoids mojibake in some
situations. It would be possible to use varchar instead, if persistent
could avoid converting that to Text, but it seems there is no good
way to do so. See doc/todo/sqlite_database_improvements.mdwn
Eliminated some ugly artifacts of using Read/Show serialization;
constructors and quoted strings are no longer stored in sqlite.
Renamed SRef to SSha to reflect that it is only ever a git sha,
not a ref name. Since it is limited to the characters in a sha,
it is not affected by mojibake, so still uses String.
When upgrading a direct mode repo to v7 with adjusted unlocked branches,
fix a bug that prevented annex.thin from taking effect for the files in
working tree.
The hard links used to be ok, but commit 8e22114735 accidentially
broke them. It repopulates the worktree file, which is already a hard link,
and when it's creating the new file, the link count is already 2, and so it
doesn't make a hard link then.
Turns out that 7be690f326 broke the
test suite on the i386ancient builder. There, git show-ref --verify HEAD
fails with "'HEAD' - not a valid ref". Apparently git 2.1.4 didn't
support that.
headExists works there and does the same thing.
Support running v7 upgrade in a repo where there is no branch checked out,
but HEAD is set directly to some other ref.
This commit was sponsored by Jack Hill on Patreon.
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.)
Added graftTree but it's buggy.
Should use graftTree in Annex.Branch.graftTreeish; it will be faster
than the current implementation there.
Started Annex.Import, but untested and it doesn't yet handle tree
grafting.
If the worktree file already exists, and is annexed and uses the same
key, avoid failing, nothing needs to be done.
Had to add lookupFileNotHidden to handle the case where an adjust --hide-missing
is in use, and the worktree file was hidden due to the object content
being missing. lookupFile would return the key of the hidden file,
but it makes sense that after fromkey succeeds, the worktree must
contain the file it was supposed to set up.
When a file was already unlocked, but the annex object was present, the
upgrade process populated the unlocked file, but neglected to update the
index.
This commit was sponsored by Jochen Bartl on Patreon.
This relies on git ls-files --with-tree, which I'm using in a way that
its man page does not document. Hm. I emailed the git list to try to get
the docs improved, but at least the git test suite does test the same
kind of use case I'm using here.
Performance impact when not in an adjusted branch is limited to some
additional MVar accesses, and a single git call to determine the name of
the current branch. So very minimal.
When in an adjusted branch, the performance impact is
in Annex.WorkTree.lookupFile, which starts doing an equal amount of work
for files that didn't exist as it already did for files that were
unlocked.
This commit was sponsored by Jochen Bartl on Patreon.
This was badly named, it's a not a blob necessarily, but anything that a
tree can refer to.
Also removed the Show instance which was used for serialization to git
format, instead use fmtTreeItemType.
This commit was supported by the NSF-funded DataLad project.
Closes https://github.com/datalad/datalad/issues/1020
The use of runWriter in scanUnlockedFiles broke due to this change;
it failed with blocked indefinitely in mvar, because the database write
handle was taken while linkFromAnnex needed to also write to it (to update
the inode cache). So, switched to using a separate runWriter for each call
to addAssociatedFileFast. A little less efficient, but not greatly; the
writes should all still be cached.
WorkTree.lookupFile was finding a key for a file that's deleted from the
work tree, which is different than the v5 behavior (though perhaps the same
as the direct mode behavior). Fix by checking that the work tree file exists
before catting its key.
Hopefully this won't slow down much, probably the catKey is much more expensive.
I can't see any way to optimise this, except perhaps to make Command.Unused
check if work tree files exist before/after calling lookupFile. But,
it seems better to make lookupFile really only find keys for worktree files;
that's what it's intended to do.
