Bug fix: Re-running git-annex adjust or sync when in an adjusted branch
would overwrite the original branch, losing any commits that had been made
to it since the adjusted branch was created.
When git-annex adjust is run in this situation, it will display a warning
about the diverged branches.
When git-annex sync is run in this situation, mergeToAdjustedBranch
will merge the changes from the original branch to the adjusted branch.
So it does not need to display the divergence warning.
Note that for some reason, I'm needing to run sync twice for that to
happen. The first run does not do the merge and the second does. I'm unsure
why and so am not fully done with this bug.
Sponsored-By: the NIH-funded NICEMAN (ReproNim TR&D3) project
The paragraph just above already shows how to configure .gitattributes
and the necessary git config. So this is redundant. Also, it makes
.gitattributes match *, which is likely not a good idea because those
files are not likely to be all text files.
Running git config --list inside .git then fails, so better to only
do that when --git-dir was specified explicitly. Otherwise, when the
repository is not bare, run the command inside the working tree.
Also make init detect when the uuid it just set cannot be read and fail
with an error, in case git changes something that breaks this later.
I still don't actually understand why git-annex add/assist -J2 was
affected but -J1 was not. But I did show that it was skipping writing to
the location log, because the uuid was NoUUID.
Sponsored-by: Graham Spencer on Patreon
Command.Add.seek starts concurrency with CommandStages. And for
Command.Sync, it needs TransferStages. So, to get both types of concurrency
for the two different parts, it either needs to change the type of
concurrency in between, or just call startConcurrency once for each.
It seems safe enough to call startConcurrency twice, because it does shut
down concurrency (mostly) at the end, and eg the old Annex.workers get
emptied.
Sponsored-by: unqueued on Patreon
This ended up having an interface like sync, rather than like get/copy/drop.
That let it be implemented in terms of sync, which took a lot less code.
Also, it lets it handle many of the edge cases that sync does, such as
getting files that are not visible in a --hide-missing branch, and sending
files to exporttree remotes.
As well as being easier to implement, `git-annex satisfy myremote` makes
sense as it satisfies the preferred content settings of the remote.
`git-annex satisfy somefile` does not form a sentence that makes sense. So
while -C can be a little bit annoying, it still makes sense to have this
syntax.
Note that, while I initially thought this would also satisfy numcopies, it
does not. Arguably it ought to. But, sync does not send files in order to
satisfy numcopies, it only sends files to satisfy preferred content. And
it's important that this transfer the same files as sync does, because
it will probably be used in a workflow where the user sometimes syncs and
sometimes satisfies, and does not expect satisfy to do things that sync
would not do.
(Also opened a new bug that also affects sync et all, not only this command.)
Sponsored-by: Nicholas Golder-Manning on Patreon
This was already possible, but it was rather hard to come up with the
complex shell command needed.
Note that the diff output starts with "diff a/... b/...".
I left off the "--git" because it's not a git format diff.
Fixes a crash by git-annex repair when .git/annex/journal/ does not exist.
Normally the journal directory is created before withJournalHandle gets
run, but git-annex repair can be run in a situation where it does not
exist.
git add will fail if the file got deleted in the meantime. And since it was
queued, there was a window until the queue flushed where a deletion of the
file would cause a crash.
Instead, reuse Command.Add.addFile, which sha1 hashes the file itself
immediately, and then queues the index update. Ignore exceptions that will
happen if the file got deleted already.
Sponsored-by: k0ld on Patreon
Commit b6642dde8a broke it by enabling
non-concurrent display mode while leaving concurrency set in the config
and having already started concurrency earlier.
(I don't actually know if that commit was a good idea.)
Sponsored-By: Brett Eisenberg on Patreon
* config: Added the --show-origin and --for-file options.
* config: Support annex.numcopies and annex.mincopies.
There is a little bit of redundancy here with other code elsewhere that
combines the various configs and selects which to use. But really only
for the special case of annex.numcopies, which is a git config that does
not override the annex branch setting and for annex.mincopies, which does
not have a git config but does have gitattributes settings as well as the
annex branch setting.
That seems small enough, and unlikely enough to grow into a mess that it was
worth supporting annex.numcopies and annex.mincopies in git-annex config
--show-origin. Because these settings are a prime thing that someone might
get confused about and want to know where they were configured.
And, it followed that git-annex config might as well support those two
for --set and --get as well. While this is redundant with the speclialized
commands, it's only a little code and it makes it more consistent.
Note that --set does not have as nice output as numcopies/mincopies
commands in some special cases like setting to 0 or a negative number.
It does avoid setting to a bad value thanks to the smart
constructors (eg configuredNumCopies).
As for other git-annex branch configurations that are not set by git-annex
config, things like trust and wanted that are specific to a repository
don't map to a git config name, so don't really fit into git-annex config.
And they are only configured in the git-annex branch with no local override
(at least so far), so --show-origin would not be useful for them.
Sponsored-by: Dartmouth College's DANDI project
Optimise database to further speed up importing large trees from special
remotes.
See comment for details of why the other index didn't help cid queries.
It would probably be better to manually create an index on only cid, rather
than adding a second uniqueness constraint that is a larger index. But
persitent does not support creating indexes, and an attempt to manually add
it to the migration failed.
Sponsored-by: Nicholas Golder-Manning on Patreon
This avoids bottlenecking on git check-ignore in a particular situation.
Also, there may have been a correctness issue with it not having updated it.
When the exportdb is already up-to-date, this is not expensive. And the
exportdb is updated elsewhere, so usually it is up-to-date.
Sponsored-by: Joshua Antonishen on Patreon
Speeds up eg git-annex sync --content by up to 50%. When it does not need
to transfer or drop anything, it now noops a lot more quickly.
I didn't see anything else in sync --content noop loop that could really
be sped up. It has to cat git objects to keys, stat object files, etc.
Sponsored-by: unqueued on Patreon
Large speed up to importing trees from special remotes that contain a lot
of files, by only processing changed files.
Benchmarks:
Importing from a special remote that has 10000 files, that have all been
imported before, and 1 new file sped up from 26.06 to 2.59 seconds.
An import with no change and 10000 unchanged files sped up from 24.3 to
1.99 seconds.
Going up to 20000 files, an import with no changes sped up from
125.95 to 3.84 seconds.
Sponsored-by: k0ld on Patreon
Speed up importing trees from special remotes somewhat by avoiding
redundant writes to sqlite database.
Before, import would write to both the git-annex branch and also to the
sqlite database. But then the next time it was run, needsUpdateFromLog
would see the branch had changed, so run updateFromLog, which would make
the same writes to the sqlite database a second time.
Now import writes only to the git-annex branch. The next time it's run,
needsUpdateFromLog sees that the branch has changed and so calls
updateFromLog, which updates the sqlite database.
Why defer the write to the sqlite database like this? It seems that it
could write to the database as it goes, and at the end call
recordAnnexBranchTree to indicate that the information in the git-annex
branch has all been written to the cidsdb. That would avoid the second
import doing extra work.
But, there could be other processes running at the same time, and one of
them may update the git-annex branch, eg merging a remote git-annex branch
into it. Any cids logs on that merged git-annex branch would not be
reflected in the cidsdb yet. If the import then called
recordAnnexBranchTree, the cidsdb would never get updated with that merged
information.
I don't think there's a good way to prevent, or to detect that situation.
So, it can't call recordAnnexBranchTree at the end. So it might as well
wait until the next run and do updateFromLog then. It could instead do
updateFromLog at the end, but it's going to check needsUpdateFromLog
at the beginning anyway.
Note that the database writes were queued, so there is already a cidmap
that is used to remember changes that the current process has made.
So, omitting database writes can't change the behavior of the current
process.
Also note that thirdpartypopulatedimport uses recordcidkeyindb, which
reflects what it already did. That code path does not use the cidmap,
but does not need to query it either. It might be possible to make that
code path also only update the git-annex branch and not the db, but I
haven't checked.
Sponsored-by: Noam Kremen on Patreon
