Merge branch 'delaysmudge' into v7

Annex/Content.hs

@@ -46,6 +46,7 @@ module Annex.Content (
 	staleKeysPrune,
 	pruneTmpWorkDirBefore,
 	isUnmodified,
+	isUnmodifiedCheap,
 	verifyKeyContent,
 	VerifyConfig(..),
 	Verification(..),
@@ -746,25 +747,38 @@ isUnmodified :: Key -> FilePath -> Annex Bool
 isUnmodified key f = go =<< geti
   where
 	go Nothing = return False
-	go (Just fc) = cheapcheck fc <||> expensivecheck fc
+	go (Just fc) = isUnmodifiedCheap' key fc <||> expensivecheck fc
-	cheapcheck fc = anyM (compareInodeCaches fc)
-		=<< Database.Keys.getInodeCaches key
 	expensivecheck fc = ifM (verifyKeyContent RetrievalAllKeysSecure AlwaysVerify UnVerified key f)
 		( do
+			liftIO $ print "content verified"
 			-- The file could have been modified while it was
 			-- being verified. Detect that.
 			ifM (geti >>= maybe (return False) (compareInodeCaches fc))
 				( do
 					-- Update the InodeCache to avoid
 					-- performing this expensive check again.
+					liftIO $ print "update inode cache"
 					Database.Keys.addInodeCaches key [fc]
 					return True
 				, return False
 				)
-		, return False
+		, do
+			liftIO $ print "content not verified"
+			return False
 		)
 	geti = withTSDelta (liftIO . genInodeCache f)
 
+{- Cheap check if a file contains the unmodified content of the key,
+ - only checking the InodeCache of the key.
+ -}
+isUnmodifiedCheap :: Key -> FilePath -> Annex Bool
+isUnmodifiedCheap key f = maybe (return False) (isUnmodifiedCheap' key) 
+	=<< withTSDelta (liftIO . genInodeCache f)
+
+isUnmodifiedCheap' :: Key -> InodeCache -> Annex Bool
+isUnmodifiedCheap' key fc = 
+	anyM (compareInodeCaches fc) =<< Database.Keys.getInodeCaches key
+
 {- Moves a key out of .git/annex/objects/ into .git/annex/bad, and
  - returns the file it was moved to. -}
 moveBad :: Key -> Annex FilePath

Annex/Hook.hs

@@ -32,6 +32,17 @@ postReceiveHook = Git.Hook "post-receive"
 	[ mkHookScript "git annex post-receive"
 	]
 
+postCheckoutHook :: Git.Hook
+postCheckoutHook = Git.Hook "post-checkout" smudgeHook []
+
+postMergeHook :: Git.Hook
+postMergeHook = Git.Hook "post-merge" smudgeHook []
+
+-- Only run git-annex smudge --update when git-annex supports it.
+-- Older versions of git-annex didn't need this hook.
+smudgeHook :: String
+smudgeHook = mkHookScript "if git annex smudge --update >/dev/null 2>&1; then git-annex smudge --update; fi"
+
 preCommitAnnexHook :: Git.Hook
 preCommitAnnexHook = Git.Hook "pre-commit-annex" "" []
 

Annex/Ingest.hs

@@ -38,7 +38,6 @@ import Logs.Location
 import qualified Annex
 import qualified Annex.Queue
 import qualified Database.Keys
-import qualified Git.Branch
 import Config
 import Utility.InodeCache
 import Annex.ReplaceFile

Annex/Init.hs

@@ -112,6 +112,9 @@ initialize' ai mversion = checkCanInitialize ai $ do
 	whenM versionSupportsUnlockedPointers $ do
 		configureSmudgeFilter
 		scanUnlockedFiles
+		unlessM isBareRepo $ do
+			hookWrite postCheckoutHook
+			hookWrite postMergeHook
 	checkAdjustedClone >>= \case
 		NeedUpgradeForAdjustedClone -> 
 			void $ upgrade True  versionForAdjustedClone

Annex/Locations.hs

@@ -38,6 +38,8 @@ module Annex.Locations (
 	gitAnnexFsckDbDir,
 	gitAnnexFsckDbLock,
 	gitAnnexFsckResultsLog,
+	gitAnnexSmudgeLog,
+	gitAnnexSmudgeLock,
 	gitAnnexExportDbDir,
 	gitAnnexExportLock,
 	gitAnnexScheduleState,
@@ -312,6 +314,14 @@ gitAnnexFsckDbLock u r = gitAnnexFsckDir u r </> "fsck.lck"
 gitAnnexFsckResultsLog :: UUID -> Git.Repo -> FilePath
 gitAnnexFsckResultsLog u r = gitAnnexDir r </> "fsckresults" </> fromUUID u
 
+{- .git/annex/smudge.log is used to log smudges worktree files that need to
+ - be updated. -}
+gitAnnexSmudgeLog :: Git.Repo -> FilePath
+gitAnnexSmudgeLog r = gitAnnexDir r </> "smudge.log"
+
+gitAnnexSmudgeLock :: Git.Repo -> FilePath
+gitAnnexSmudgeLock r = gitAnnexDir r </> "smudge.lck"
+
 {- .git/annex/export/uuid/ is used to store information about
  - exports to special remotes. -}
 gitAnnexExportDir :: UUID -> Git.Repo -> FilePath

CHANGELOG

@@ -21,6 +21,19 @@ git-annex (6.20181012) UNRELEASED; urgency=medium
     get confused about whether a locked file's content was present.
   * Fix concurrency bug that occurred on the first download from an
     exporttree remote.
+  * smudge: The smudge filter no longer provides git with annexed
+    file content, to avoid a git memory leak, and because that did not
+    honor annex.thin. Now git annex smudge --update has to be run
+    after a checkout to update unlocked files in the working tree 
+    with annexed file contents.
+  * init, upgrade: Install git post-checkout and post-merge hooks that run 
+    git annex smudge --update.
+  * precommit: Run git annex smudge --update, because the post-merge
+    hook is not run when there is a merge conflict. So the work tree will
+    be updated when a commit is made to resolve the merge conflict.
+  * Note that git has no hooks run after git stash or git cherry-pick,
+    so the user will have to manually run git annex smudge --update
+    after such commands.
 
  -- Joey Hess <id@joeyh.name>  Sat, 13 Oct 2018 00:52:02 -0400
 

Command/PreCommit.hs

@@ -13,6 +13,7 @@ import Command
 import Config
 import qualified Command.Add
 import qualified Command.Fix
+import qualified Command.Smudge
 import Annex.Direct
 import Annex.Hook
 import Annex.Link
@@ -54,11 +55,21 @@ seek ps = lockPreCommitHook $ ifM isDirect
 				flip withFilesToBeCommitted l $ \f -> commandAction $
 					maybe stop (Command.Fix.start Command.Fix.FixSymlinks f)
 						=<< isAnnexLink f
-				-- inject unlocked files into the annex
+				ifM versionSupportsUnlockedPointers
-				-- (not needed when repo version uses
+					-- after a merge conflict or git
-				-- unlocked pointer files)
+					-- cherry-pick or stash, pointer
-				unlessM versionSupportsUnlockedPointers $
+					-- files in the worktree won't
-					withFilesOldUnlockedToBeCommitted (commandAction . startInjectUnlocked) l
+					-- be populated, so populate them
+					-- here
+					( Command.Smudge.updateSmudged 
+						-- When there's a false index,
+						-- restaging the files won't work.
+						. Restage =<< liftIO Git.haveFalseIndex
+					-- inject unlocked files into the annex
+					-- (not needed when repo version uses
+					-- unlocked pointer files)
+					, withFilesOldUnlockedToBeCommitted (commandAction . startInjectUnlocked) l
+					)
 			)
 		runAnnexHook preCommitAnnexHook
 		-- committing changes to a view updates metadata

Command/Smudge.hs

@@ -8,12 +8,12 @@
 module Command.Smudge where
 
 import Command
-import qualified Annex
 import Annex.Content
 import Annex.Link
 import Annex.FileMatcher
 import Annex.Ingest
 import Annex.CatFile
+import Logs.Smudge
 import Logs.Location
 import qualified Database.Keys
 import qualified Git.BuildVersion
@@ -29,43 +29,46 @@ cmd = noCommit $ noMessages $
 		"git smudge filter"
 		paramFile (seek <$$> optParser)
 
-data SmudgeOptions = SmudgeOptions
+data SmudgeOptions = UpdateOption | SmudgeOptions
 	{ smudgeFile :: FilePath
 	, cleanOption :: Bool
 	}
 
 optParser :: CmdParamsDesc -> Parser SmudgeOptions
-optParser desc = SmudgeOptions
+optParser desc = smudgeoptions <|> updateoption
-	<$> argument str ( metavar desc )
+  where
-	<*> switch ( long "clean" <> help "clean filter" )
+	smudgeoptions = SmudgeOptions
+		<$> argument str ( metavar desc )
+		<*> switch ( long "clean" <> help "clean filter" )
+	updateoption = flag' UpdateOption
+		( long "update" <> help "populate annexed worktree files" )
 
 seek :: SmudgeOptions -> CommandSeek
-seek o = commandAction $
+seek (SmudgeOptions f False) = commandAction (smudge f)
-	(if cleanOption o then clean else smudge) (smudgeFile o)
+seek (SmudgeOptions f True) = commandAction (clean f)
+seek UpdateOption = commandAction update
 
 -- Smudge filter is fed git file content, and if it's a pointer to an
--- available annex object, should output its content.
+-- available annex object, git expects it to output its content.
+--
+-- However, this does not do that. It outputs the pointer, and records
+-- the filename in the smudge log. Git hooks run after commands like checkout
+-- then run git annex smudge --update which populates the work tree files
+-- with annex content. This is done for several reasons:
+--
+-- * To support annex.thin
+-- * Because git currently buffers the whole object received from the
+--   smudge filter in memory, which is a problem with large files.
 smudge :: FilePath -> CommandStart
 smudge file = do
 	b <- liftIO $ B.hGetContents stdin
 	case parseLinkOrPointer b of
-		Nothing -> liftIO $ B.putStr b
+		Nothing -> noop
 		Just k -> do
-			Database.Keys.addAssociatedFile k =<< inRepo (toTopFilePath file)
+			topfile <- inRepo (toTopFilePath file)
-			-- A previous unlocked checkout of the file may have
+			Database.Keys.addAssociatedFile k topfile
-			-- led to the annex object getting modified;
+			void $ smudgeLog k topfile
-			-- don't provide such modified content as it
+	liftIO $ B.putStr b
-			-- will be confusing. inAnnex will detect such
-			-- modifications.
-			ifM (inAnnex k)
-				( do
-					content <- calcRepo (gitAnnexLocation k)
-					whenM (annexThin <$> Annex.getGitConfig) $
-						warning $ "Not able to honor annex.thin when git is checking out " ++ file ++ " (run git annex fix to re-thin files)"
-					liftIO $ B.putStr . fromMaybe b
-						=<< catchMaybeIO (B.readFile content)
-				, liftIO $ B.putStr b
-				)
 	stop
 
 -- Clean filter is fed file content on stdin, decides if a file
@@ -92,20 +95,31 @@ clean file = do
 			if Git.BuildVersion.older "2.5"
 				then B.length b `seq` return ()
 				else liftIO $ hClose stdin
-			-- Look up the backend that was used for this file
+
-			-- before, so that when git re-cleans a file its
+			-- Optimization when the file is already annexed
-			-- backend does not change.
+			-- and is unmodified.
-			let oldbackend = maybe Nothing (maybeLookupBackendVariety . keyVariety) oldkey
+			case oldkey of
-			-- Can't restage associated files because git add
+				Nothing -> ingest oldkey
-			-- runs this and has the index locked.
+				Just ko -> ifM (isUnmodifiedCheap ko file)
-			let norestage = Restage False
+					( liftIO $ emitPointer ko
-			liftIO . emitPointer
+					, ingest oldkey
-				=<< postingest
+					)
-				=<< (\ld -> ingest' oldbackend ld Nothing norestage)
-				=<< lockDown cfg file
 		, liftIO $ B.hPut stdout b
 		)
 	
+	ingest oldkey = do
+		-- Look up the backend that was used for this file
+		-- before, so that when git re-cleans a file its
+		-- backend does not change.
+		let oldbackend = maybe Nothing (maybeLookupBackendVariety . keyVariety) oldkey
+		-- Can't restage associated files because git add
+		-- runs this and has the index locked.
+		let norestage = Restage False
+		liftIO . emitPointer
+			=<< postingest
+			=<< (\ld -> ingest' oldbackend ld Nothing norestage)
+			=<< lockDown cfg file
+
 	postingest (Just k, _) = do
 		logStatus k InfoPresent
 		return k
@@ -151,3 +165,19 @@ getMoveRaceRecovery k file = void $ tryNonAsync $
 		populatePointerFile (Restage False) k obj file >>= \case
 			Nothing -> return ()
 			Just ic -> Database.Keys.addInodeCaches k [ic]
+
+update :: CommandStart
+update = do
+	updateSmudged (Restage True)
+	stop
+
+updateSmudged :: Restage -> Annex ()
+updateSmudged restage = streamSmudged $ \k topf -> do
+	f <- fromRepo $ fromTopFilePath topf
+	whenM (inAnnex k) $ do
+		obj <- calcRepo (gitAnnexLocation k)
+		unlessM (isJust <$> populatePointerFile restage k obj f) $
+			liftIO (isPointerFile f) >>= \case
+				Just k' | k' == k -> toplevelWarning False $
+					"unable to populate worktree file " ++ f
+				_ -> noop

Logs/File.hs

@@ -2,26 +2,59 @@
  -
  - Copyright 2018 Joey Hess <id@joeyh.name>
  -
- - Licensed under the GNU GPL version 3 or higher.
+ - Licensed under the GNU AGPL version 3 or higher.
  -}
 
-module Logs.File where
+module Logs.File (writeLogFile, appendLogFile, streamLogFile) where
 
 import Annex.Common
 import Annex.Perms
+import Annex.LockFile
+import qualified Git
 import Utility.Tmp
 
 -- | Writes content to a file, replacing the file atomically, and
 -- making the new file have whatever permissions the git repository is
 -- configured to use. Creates the parent directory when necessary.
 writeLogFile :: FilePath -> String -> Annex ()
-writeLogFile f c = go `catchNonAsync` \_e -> do
+writeLogFile f c = createDirWhenNeeded f $ viaTmp writelog f c
-	-- Most of the time, the directory will exist, so this is only
-	-- done if writing the file fails.
-	createAnnexDirectory (parentDir f)
-	go
   where
-	go = viaTmp writelog f c
 	writelog f' c' = do
 		liftIO $ writeFile f' c'
 		setAnnexFilePerm f'
+
+-- | Appends a line to a log file, first locking it to prevent
+-- concurrent writers.
+appendLogFile :: FilePath -> (Git.Repo -> FilePath) -> String -> Annex ()
+appendLogFile f lck c = createDirWhenNeeded f $ withExclusiveLock lck $ do
+	liftIO $ withFile f AppendMode $ \h -> hPutStrLn h c
+	setAnnexFilePerm f
+
+-- | Streams lines from a log file, and then empties the file at the end.
+--
+-- If the action is interrupted or throws an exception, the log file is
+-- left unchanged.
+--
+-- Does nothing if the log file does not exist.
+-- 
+-- Locking is used to prevent writes to to the log file while this
+-- is running.
+streamLogFile :: FilePath -> (Git.Repo -> FilePath) -> (String -> Annex ()) -> Annex ()
+streamLogFile f lck a = withExclusiveLock lck $ bracketOnError setup cleanup go
+  where
+	setup = liftIO $ tryWhenExists $ openFile f ReadMode 
+	cleanup Nothing = noop
+	cleanup (Just h) = liftIO $ hClose h
+	go Nothing = noop
+	go (Just h) = do
+		mapM_ a =<< liftIO (lines <$> hGetContents h)
+		liftIO $ hClose h
+		liftIO $ writeFile f ""
+		setAnnexFilePerm f
+
+createDirWhenNeeded :: FilePath -> Annex () -> Annex ()
+createDirWhenNeeded f a = a `catchNonAsync` \_e -> do
+	-- Most of the time, the directory will exist, so this is only
+	-- done if writing the file fails.
+	createAnnexDirectory (parentDir f)
+	a

Logs/Smudge.hs

@@ -0,0 +1,40 @@
+{- git-annex smudge log file
+ -
+ - Copyright 2018 Joey Hess <id@joeyh.name>
+ -
+ - Licensed under the GNU AGPL version 3 or higher.
+ -}
+
+module Logs.Smudge where
+
+import Annex.Common
+import Git.FilePath
+import Logs.File
+
+-- | Log a smudged file.
+smudgeLog :: Key -> TopFilePath -> Annex ()
+smudgeLog k f = do
+	logf <- fromRepo gitAnnexSmudgeLog
+	appendLogFile logf gitAnnexSmudgeLock $ 
+		key2file k ++ " " ++ getTopFilePath f
+
+-- | Streams all smudged files, and then empties the log at the end.
+--
+-- If the action is interrupted or throws an exception, the log file is
+-- left unchanged.
+--
+-- Locking is used to prevent new items being added to the log while this
+-- is running.
+streamSmudged :: (Key -> TopFilePath -> Annex ()) -> Annex ()
+streamSmudged a = do
+	logf <- fromRepo gitAnnexSmudgeLog
+	streamLogFile logf gitAnnexSmudgeLock $ \l -> 
+		case parse l of
+			Nothing -> noop
+			Just (k, f) -> a k f
+  where
+	parse l = 
+		let (ks, f) = separate (== ' ') l
+		in do
+			k <- file2key ks
+			return (k, asTopFilePath f)

Upgrade/V5.hs

@@ -17,6 +17,7 @@ import Annex.Direct
 import Annex.Content
 import Annex.CatFile
 import Annex.WorkTree
+import Annex.Hook
 import qualified Database.Keys
 import qualified Annex.Content.Direct as Direct
 import qualified Git
@@ -63,6 +64,9 @@ upgrade automatic = do
 		 - adjust branch. Instead, update HEAD manually. -}
 		inRepo $ setHeadRef b
 	configureSmudgeFilter
+	unlessM isBareRepo $ do
+		hookWrite postCheckoutHook
+		hookWrite postMergeHook
 	-- Inode sentinal file was only used in direct mode and when
 	-- locking down files as they were added. In v6, it's used more
 	-- extensively, so make sure it exists, since old repos that didn't

doc/git-annex-smudge.mdwn

@@ -6,11 +6,13 @@ git-annex smudge - git filter driver for git-annex
 
 git annex smudge [--clean] file
 
+git annex smudge --update
+
 # DESCRIPTION
 
 This command lets git-annex be used as a git filter driver which lets
-annexed files in the git repository to be unlocked at all times, instead
+annexed files in the git repository to be unlocked, instead
-of being symlinks.
+of being symlinks, and lets `git add` store files in the annex.
 
 When adding a file with `git add`, the annex.largefiles config is
 consulted to decide if a given file should be added to git as-is,
@@ -32,6 +34,16 @@ contents:
 	* filter=annex
 	.* !filter
 
+The smudge filter does not provide git with the content of annexed files,
+because that would be slow and triggers memory leaks in git. Instead,
+it records which worktree files need to be updated, and 
+`git annex smudge --update` later updates the work tree to contain
+the content. That is run by several git hooks, including post-checkout
+and post-merge. However, a few git commands, notably `git stash` and
+`git cherry-pick`, do not run any hooks, so after using those commands
+you can manually run `git annex smudge --update` to update the working
+tree.
+
 # SEE ALSO
 
 [[git-annex]](1)

doc/git-annex.mdwn

@@ -1032,11 +1032,6 @@ Here are all the supported configuration settings.
   After setting (or unsetting) this, you should run `git annex fix` to
   fix up the annexed files in the work tree to be hard links (or copies).
 
-  Note that `annex.thin` is not honored when git updates an annexed file
-  in the working tree. So when `git checkout` or `git merge` updates the
-  working tree, a second copy of annexed files will result. You can run
-  `git-annex fix` to fix up the hard links after running such git commands.
-
 * `annex.delayadd`
 
   Makes the watch and assistant commands delay for the specified number of

git-annex.cabal

@@ -880,6 +880,7 @@ Executable git-annex
     Logs.Schedule
     Logs.SingleValue
     Logs.SingleValue.Pure
+    Logs.Smudge
     Logs.TimeStamp
     Logs.Transfer
     Logs.Transitions