This is to avoid inserting a cluster uuid into the location log when
only dead nodes in the cluster contain the content of a key.
One reason why this is necessary is Remote.keyLocations, which excludes
dead repositories from the list. But there are probably many more.
Implementing this was challenging, because Logs.Location importing
Logs.Cluster which imports Logs.Trust which imports Remote.List resulted
in an import cycle through several other modules.
Resorted to making Logs.Location not import Logs.Cluster, and instead
it assumes that Annex.clusters gets populated when necessary before it's
called.
That's done in Annex.Startup, which is run by the git-annex command
(but not other commands) at early startup in initialized repos. Or,
is run after initialization.
Note that is Remote.Git, it is unable to import Annex.Startup, because
Remote.Git importing Logs.Cluster leads the the same import cycle.
So ensureInitialized is not passed annexStartup in there.
Other commands, like git-annex-shell currently don't run annexStartup
either.
So there are cases where Logs.Location will not see clusters. So it won't add
any cluster UUIDs when loading the log. That's ok, the only reason to do
that is to make display of where objects are located include clusters,
and to make commands like git-annex get --from treat keys as being located
in a cluster. git-annex-shell certainly does not do anything like that,
and I'm pretty sure Remote.Git (and callers to Remote.Git.onLocalRepo)
don't either.
Dunno how useful this will be, since about all that's accessible from
the json is whether it succeeded or failed, and the error messages
which were already on stderr.
Note that, when autoenabling a special remote, it would be possible for
one to stop and prompt or output not using Messages and so not output as
part of the json. I don't think that happens, but I'm not 100% sure
something doesn't manage to break it. Of course, the same could be the
case for commands that transfer objects. Using Annex.Init.autoEnableSpecialRemotes
in --json mode would avoid the problem, but I've chosen to wait until I
know it's needed to use it.
Sponsored-By: the NIH-funded NICEMAN (ReproNim TR&D3) project
Added StringContainingQuotedPath, which is used for ActionItemOther.
In the process, checked every ActionItemOther for those containing
filenames, and made them use quoting.
Sponsored-by: Graham Spencer 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
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
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
No behavior changes (hopefully), just adding SeekInput and plumbing it
through to the JSON display code for later use.
Over the course of 2 grueling days.
withFilesNotInGit reimplemented in terms of seekHelper
should be the only possible behavior change. It seems to test as
behaving the same.
Note that seekHelper dummies up the SeekInput in the case where
segmentPaths' gives up on sorting the expanded paths because there are
too many input paths. When SeekInput later gets exposed as a json field,
that will result in it being a little bit wrong in the case where
100 or more paths are passed to a git-annex command. I think this is a
subtle enough problem to not matter. If it does turn out to be a
problem, fixing it would require splitting up the input
parameters into groups of < 100, which would make git ls-files run
perhaps more than is necessary. May want to revisit this, because that
fix seems fairly low-impact.
Try to enable special remotes configured with autoenable=yes when git-annex
auto-initialization happens in a new clone of an existing repo. Previously,
git-annex init had to be explicitly run to enable them. That was a bit of a
wart of a special case for users to need to keep in mind.
Special remotes cannot display anything when autoenabled this way, to avoid
interfering with the output of git-annex query commands.
Any error messages will be hidden, and if it fails, nothing is displayed.
The user will realize the remote isn't enable when they try to use it,
and can run git-annex init manually then to try the autoenable again and
see what failed.
That seems like a reasonable approach, and it's less complicated than
communicating something across a pipe in order to display it as a side
message. Other reason not to do that is that, if the first command the
user runs is one like git-annex find that has machine readable output,
any message about autoenable failing would need to not be displayed anyway.
So better to not display a failure message ever, for consistency.
(Had to split out Remote.List.Util to avoid an import cycle.)
The 'fail' method has been moved to the 'MonadFail' class. I made the changes
so that the code still compiles with previous versions of 'base' that don't
have the new MonadFail class exported by Prelude yet.
The goal is to be able to run CommandStart in the main thread when -J is
used, rather than unncessarily passing it off to a worker thread, which
incurs overhead that is signficant when the CommandStart is going to
quickly decide to stop.
To do that, the message it displays needs to be displayed in the worker
thread, after the CommandStart has run.
Also, the change will mean that CommandStart will no longer necessarily
run with the same Annex state as CommandPerform. While its docs already
said it should avoid modifying Annex state, I audited all the
CommandStart code as part of the conversion. (Note that CommandSeek
already sometimes runs with a different Annex state, and that has not been
a source of any problems, so I am not too worried that this change will
lead to breakage going forward.)
The only modification of Annex state I found was it calling
allowMessages in some Commands that default to noMessages. Dealt with
that by adding a startCustomOutput and a startingUsualMessages.
This lets a command start with noMessages and then select the output it
wants for each CommandStart.
One bit of breakage: onlyActionOn has been removed from commands that used it.
The plan is that, since a StartMessage contains an ActionItem,
when a Key can be extracted from that, the parallel job runner can
run onlyActionOn' automatically. Then commands won't need to worry about
this detail. Future work.
Otherwise, this was a fairly straightforward process of making each
CommandStart compile again. Hopefully other behavior changes were mostly
avoided.
In a few cases, a command had a CommandStart that called a CommandPerform
that then called showStart multiple times. I have collapsed those
down to a single start action. The main command to perhaps suffer from it
is Command.Direct, which used to show a start for each file, and no
longer does.
Another minor behavior change is that some commands used showStart
before, but had an associated file and a Key available, so were changed
to ShowStart with an ActionItemAssociatedFile. That will not change the
normal output or behavior, but --json output will now include the key.
This should not break it for anyone using a real json parser.
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.)
Avoid performing repository fixups for submodules and git-worktrees
when there's a .noannex file that will prevent git-annex from being
used in the repository.
This change is ok as long as the .noannex file is really going to prevent
git-annex from being used. But, init --force could override the file.
Which would result in the repo being initialized without the fixups
having run.
To avoid that situation decided to change init, to not let --force be used
to override a .noannex file. Instead the user can just delete the file.
This makes --version=6 still work, despite v6 not being in
supportedVersions. Which is useful for scripts that use it.
I didn't document it on the man page, because it's indistinguishable
from an automatic upgrade after initting as v6.
Install new git hooks in this version.
This does beg the question of what to do if git later gets eg a
post-smudge hook, that could run git-annex smudge --update. I think the
thing to do in that case would be to make git-annex smudge --update
install the new hooks. That way, as the user uses git-annex, the hook
would be created pretty quickly and without needing any extra syscalls
except for when git-annex smudge --update is called.
I considered doing something like that for installation of the
post-checkout and post-merge hooks, which would have avoided the need
for v7. But the only place it was cheap to do it would be in git-annex smudge
which could cheaply notice that smudge.log didn't exist yet and so know
the hooks needed to be installed. But since smudge used to populate pointer
files, it would be quite surprising if a single git checkout/merge failed
to update the work tree, and so that idea didn't work out.
The other reason for v7 is psychological -- users don't need to worry
about whether they might be running an old version of git-annex that
doesn't support their v7 repository very well. And bug reports about
"v6" have gotten a bit of a bad association in my head since they often
hit one of the known limitations and didn't realize it was experimental.
newtyped RepoVersion Int to avoid needing 2 comparisons in
versionSupportsUnlockedPointers etc. Also it's just nicer.
This commit was sponsored by John Pellman on Patreon.
A top-level .noannex file will prevent git-annex init from being used in a
repository. This is useful for repositories that have a policy reason not
to use git-annex. The content of the file will be displayed to the user who
tries to run git-annex init.
This also affects git annex reinit and initialization via the webapp.
It does not affect automatic inits, when there's a sibling git-annex branch
already.
This commit was supported by the NSF-funded DataLad project.
Clean up some uses of showStart with "" for the file,
or in some cases, a non-filename description string. That would
generate bad json, although none of the commands doing that
supported --json.
Using "" for the file resulted in output like "foo rest";
now the extra space is eliminated.
This commit was sponsored by Fernando Jimenez on Patreon.
This is a work in progress. It compiles and is able to do basic command
dispatch, including git autocorrection, while using optparse-applicative
for the core commandline parsing.
* Many commands are temporarily disabled before conversion.
* Options are not wired in yet.
* cmdnorepo actions don't work yet.
Also, removed the [Command] list, which was only used in one place.
I've been disliking how the command seek actions were written for some
time, with their inversion of control and ugly workarounds.
The last straw to fix it was sync --content, which didn't fit the
Annex [CommandStart] interface well at all. I have not yet made it take
advantage of the changed interface though.
The crucial change, and probably why I didn't do it this way from the
beginning, is to make each CommandStart action be run with exceptions
caught, and if it fails, increment a failure counter in annex state.
So I finally remove the very first code I wrote for git-annex, which
was before I had exception handling in the Annex monad, and so ran outside
that monad, passing state explicitly as it ran each CommandStart action.
This was a real slog from 1 to 5 am.
Test suite passes.
Memory usage is lower than before, sometimes by a couple of megabytes, and
remains constant, even when running in a large repo, and even when
repeatedly failing and incrementing the error counter. So no accidental
laziness space leaks.
Wall clock speed is identical, even in large repos.
This commit was sponsored by an anonymous bitcoiner.
This is my own damn fault for not making UUID a real type, and then relying
on the type checker to ensure my refactoring was correct -- which it wasn't!
I should probably add code to clean up bogus entries in the uuid.log, but
right now I want to get the fix out there to prevent people experiencing
this bug.
I should also make UUID a real data type.
This new approach allows filtering out checks from the default set that are
not appropriate for a command, rather than having to list every check
that is appropriate. It also reduces some boilerplate.
Haskell does not define Eq for functions, so I had to go a long way around
with each check having a unique id. Meh.
These were a mistake, they make the type signatures harder to read and
less flexible. The CommandSeek, CommandStart, CommandPerform, and
CommandCleanup types were a good idea, but composing them with the
parameters expected is going too far.
when a git repository is first being created. Clones will automatically
notice that git-annex is in use and automatically perform a basic
initalization. It's still recommended to run "git annex init" in any
clones, to describe them.
Do not set annex.version whenever any command is run. Just do it in init.
This ensures that, if a repo has annex.version=3, it has a git-annex
branch, so we don't have to run a command every time to check for the
branch.
Remove the old ad-hoc logic for v0 and v1, to simplify version checking.
