Merge branch 'compute'

Annex/AdjustedBranch.hs

@@ -308,16 +308,12 @@ updateAdjustedBranch adj (AdjBranch currbranch) origbranch
 		-- adjustment is stable.
 		return True
 
-{- Passed an action that, if it succeeds may get or drop the Key associated
+{- Passed an action that, if it succeeds may get or drop a key.
- - with the file. When the adjusted branch needs to be refreshed to reflect
+ - When the adjusted branch needs to be refreshed to reflect
  - those changes, it's handled here.
- -
- - Note that the AssociatedFile must be verified by this to point to the
- - Key. In some cases, the value was provided by the user and might not
- - really be an associated file.
  -}
-adjustedBranchRefresh :: AssociatedFile -> Annex a -> Annex a
+adjustedBranchRefresh :: Annex a -> Annex a
-adjustedBranchRefresh _af a = do
+adjustedBranchRefresh a = do
 	r <- a
 	go
 	return r

Annex/Content.hs

@@ -376,16 +376,16 @@ lockContentUsing contentlocker key fallback a = withContentLockFile key $ \mlock
 {- Runs an action, passing it the temp file to get,
  - and if the action succeeds, verifies the file matches
  - the key and moves the file into the annex as a key's content. -}
-getViaTmp :: RetrievalSecurityPolicy -> VerifyConfig -> Key -> AssociatedFile -> Maybe FileSize -> (OsPath -> Annex (Bool, Verification)) -> Annex Bool
+getViaTmp :: RetrievalSecurityPolicy -> VerifyConfig -> Key -> Maybe FileSize -> (OsPath -> Annex (Bool, Verification)) -> Annex Bool
-getViaTmp rsp v key af sz action =
+getViaTmp rsp v key sz action =
 	checkDiskSpaceToGet key sz False $
-		getViaTmpFromDisk rsp v key af action
+		getViaTmpFromDisk rsp v key action
 
 {- Like getViaTmp, but does not check that there is enough disk space
  - for the incoming key. For use when the key content is already on disk
  - and not being copied into place. -}
-getViaTmpFromDisk :: RetrievalSecurityPolicy -> VerifyConfig -> Key -> AssociatedFile -> (OsPath -> Annex (Bool, Verification)) -> Annex Bool
+getViaTmpFromDisk :: RetrievalSecurityPolicy -> VerifyConfig -> Key -> (OsPath -> Annex (Bool, Verification)) -> Annex Bool
-getViaTmpFromDisk rsp v key af action = checkallowed $ do
+getViaTmpFromDisk rsp v key action = checkallowed $ do
 	tmpfile <- prepTmp key
 	resuming <- liftIO $ doesPathExist tmpfile
 	(ok, verification) <- action tmpfile
@@ -400,7 +400,7 @@ getViaTmpFromDisk rsp v key af action = checkallowed $ do
 		else verification
 	if ok
 		then ifM (verifyKeyContentPostRetrieval rsp v verification' key tmpfile)
-			( pruneTmpWorkDirBefore tmpfile (moveAnnex key af)
+			( pruneTmpWorkDirBefore tmpfile (moveAnnex key)
 			, do
 				verificationOfContentFailed tmpfile
 				return False
@@ -507,8 +507,8 @@ withTmp key action = do
  - accepted into the repository. Will display a warning message in this
  - case. May also throw exceptions in some cases.
  -}
-moveAnnex :: Key -> AssociatedFile -> OsPath -> Annex Bool
+moveAnnex :: Key -> OsPath -> Annex Bool
-moveAnnex key af src = ifM (checkSecureHashes' key)
+moveAnnex key src = ifM (checkSecureHashes' key)
 	( do
 #ifdef mingw32_HOST_OS
 		{- Windows prevents deletion of files that are not
@@ -523,7 +523,7 @@ moveAnnex key af src = ifM (checkSecureHashes' key)
   where
 	storeobject dest = ifM (liftIO $ doesPathExist dest)
 		( alreadyhave
-		, adjustedBranchRefresh af $ modifyContentDir dest $ do
+		, adjustedBranchRefresh $ modifyContentDir dest $ do
 			liftIO $ moveFile src dest
 			-- Freeze the object file now that it is in place.
 			-- Waiting until now to freeze it allows for freeze
@@ -776,7 +776,7 @@ removeAnnex (ContentRemovalLock key) = withObjectLoc key $ \file ->
 	-- it's unmodified.
 	resetpointer file = unlessM (liftIO $ isSymbolicLink <$> R.getSymbolicLinkStatus (fromOsPath file)) $
 		ifM (isUnmodified key file)
-			( adjustedBranchRefresh (AssociatedFile (Just file)) $
+			( adjustedBranchRefresh $ 
 				depopulatePointerFile key file
 			-- Modified file, so leave it alone.
 			-- If it was a hard link to the annex object,

Annex/Export.hs

@@ -11,16 +11,13 @@ module Annex.Export where
 
 import Annex
 import Annex.CatFile
+import Annex.GitShaKey
 import Types
-import Types.Key
 import qualified Git
 import qualified Types.Remote as Remote
 import Git.Quote
 import Messages
 
-import Data.Maybe
-import qualified Data.ByteString.Short as S (fromShort, toShort)
-
 -- From a sha pointing to the content of a file to the key
 -- to use to export it. When the file is annexed, it's the annexed key.
 -- When the file is stored in git, it's a special type of key to indicate
@@ -31,31 +28,6 @@ exportKey sha = mk <$> catKey sha
 	mk (Just k) = k
 	mk Nothing = gitShaKey sha
 
--- Encodes a git sha as a key. This is used to represent a non-annexed
--- file that is stored on a special remote, which necessarily needs a
--- key.
---
--- This is not the same as a SHA1 key, because the mapping needs to be
--- bijective, also because git may not always use SHA1, and because git
--- takes a SHA1 of the file size + content, while git-annex SHA1 keys
--- only checksum the content.
-gitShaKey :: Git.Sha -> Key
-gitShaKey (Git.Ref s) = mkKey $ \kd -> kd
-	{ keyName = S.toShort s
-	, keyVariety = OtherKey "GIT"
-	}
-
--- Reverse of gitShaKey
-keyGitSha :: Key -> Maybe Git.Sha
-keyGitSha k
-	| fromKey keyVariety k == OtherKey "GIT" =
-		Just (Git.Ref (S.fromShort (fromKey keyName k)))
-	| otherwise = Nothing
-
--- Is a key storing a git sha, and not used for an annexed file?
-isGitShaKey :: Key -> Bool
-isGitShaKey = isJust . keyGitSha
-
 warnExportImportConflict :: Remote -> Annex ()
 warnExportImportConflict r = do
 	isimport <- Remote.isImportSupported r

Annex/GitShaKey.hs

@@ -0,0 +1,41 @@
+{- Encoding a git sha as a Key
+ -
+ - Copyright 2017-2025 Joey Hess <id@joeyh.name>
+ -
+ - Licensed under the GNU AGPL version 3 or higher.
+ -}
+
+{-# LANGUAGE OverloadedStrings #-}
+
+module Annex.GitShaKey where
+
+import Types
+import Types.Key
+import qualified Git
+
+import Data.Maybe
+import qualified Data.ByteString.Short as S (fromShort, toShort)
+
+-- Encodes a git sha as a Key. This is used to represent a non-annexed
+-- file. For example, when storing a git sha on a special remote.
+--
+-- This is not the same as a SHA1 key, because the mapping needs to be
+-- bijective, also because git may not always use SHA1, and because git
+-- takes a SHA1 of the file size + content, while git-annex SHA1 keys
+-- only checksum the content.
+gitShaKey :: Git.Sha -> Key
+gitShaKey (Git.Ref s) = mkKey $ \kd -> kd
+	{ keyName = S.toShort s
+	, keyVariety = OtherKey "GIT"
+	}
+
+-- Reverse of gitShaKey
+keyGitSha :: Key -> Maybe Git.Sha
+keyGitSha k
+	| fromKey keyVariety k == OtherKey "GIT" =
+		Just (Git.Ref (S.fromShort (fromKey keyName k)))
+	| otherwise = Nothing
+
+-- Is a key storing a git sha, and not used for an annexed file?
+isGitShaKey :: Key -> Bool
+isGitShaKey = isJust . keyGitSha

Annex/Import.hs

@@ -38,12 +38,12 @@ import qualified Annex
 import Annex.Link
 import Annex.LockFile
 import Annex.Content
-import Annex.Export
 import Annex.RemoteTrackingBranch
 import Annex.HashObject
 import Annex.Transfer
 import Annex.CheckIgnore
 import Annex.CatFile
+import Annex.GitShaKey
 import Annex.VectorClock
 import Annex.SpecialRemote.Config
 import Command
@@ -863,7 +863,7 @@ importKeys remote importtreeconfig importcontent thirdpartypopulated importablec
 					ia loc [cid] tmpfile
 					(Left k)
 					(combineMeterUpdate p' p)
-				ok <- moveAnnex k af tmpfile
+				ok <- moveAnnex k tmpfile
 				when ok $
 					logStatus NoLiveUpdate k InfoPresent
 				return (Just (k, ok))
@@ -906,7 +906,7 @@ importKeys remote importtreeconfig importcontent thirdpartypopulated importablec
 				p
 			case keyGitSha k of
 				Nothing -> do
-					ok <- moveAnnex k af tmpfile
+					ok <- moveAnnex k tmpfile
 					when ok $ do
 						recordcidkey cidmap cid k
 						logStatus NoLiveUpdate k InfoPresent

Annex/Ingest.hs

@@ -198,17 +198,11 @@ ingest' preferredbackend meterupdate (Just (LockedDown cfg source)) mk restage =
 		| otherwise = gounlocked key mcache
 
 	golocked key mcache =
-		tryNonAsync (moveAnnex key naf (contentLocation source)) >>= \case
+		tryNonAsync (moveAnnex key (contentLocation source)) >>= \case
 			Right True -> success key mcache
 			Right False -> giveup "failed to add content to annex"
 			Left e -> restoreFile (keyFilename source) key e
 
-	-- moveAnnex uses the AssociatedFile provided to it to unlock
-	-- locked files when getting a file in an adjusted branch.
-	-- That case does not apply here, where we're adding an unlocked
-	-- file, so provide it nothing.
-	naf = AssociatedFile Nothing
-
 	gounlocked key (Just cache) = do
 		-- Remove temp directory hard link first because
 		-- linkToAnnex falls back to copying if a file
@@ -377,7 +371,7 @@ addAnnexedFile matcher file key mtmp = ifM (addUnlocked matcher mi (isJust mtmp)
 		stagePointerFile file mode =<< hashPointerFile key
 		Database.Keys.addAssociatedFile key =<< inRepo (toTopFilePath file)
 		case mtmp of
-			Just tmp -> ifM (moveAnnex key af tmp)
+			Just tmp -> ifM (moveAnnex key tmp)
 				( linkunlocked mode >> return True
 				, writepointer mode >> return False
 				)
@@ -388,11 +382,10 @@ addAnnexedFile matcher file key mtmp = ifM (addUnlocked matcher mi (isJust mtmp)
 	, do
 		addSymlink file key Nothing
 		case mtmp of
-			Just tmp -> moveAnnex key af tmp
+			Just tmp -> moveAnnex key tmp
 			Nothing -> return True
 	)
   where
-	af = AssociatedFile (Just file)
 	mi = case mtmp of
 		Just tmp -> MatchingFile $ FileInfo
 			{ contentFile = tmp

Annex/Transfer.hs

@@ -78,7 +78,7 @@ download r key f d witness =
 		Just StallDetectionDisabled -> go Nothing
 		Just sd -> runTransferrer sd r key f d Download witness
   where
-	go sd = getViaTmp (Remote.retrievalSecurityPolicy r) vc key f Nothing $ \dest ->
+	go sd = getViaTmp (Remote.retrievalSecurityPolicy r) vc key Nothing $ \dest ->
 		download' (Remote.uuid r) key f sd d (go' dest) witness
 	go' dest p = verifiedAction $
 		Remote.retrieveKeyFile r key f dest p vc

Backend.hs

@@ -10,13 +10,14 @@
 module Backend (
 	builtinList,
 	defaultBackend,
-	defaultHashBackend,
+	hashBackend,
 	genKey,
 	getBackend,
 	chooseBackend,
 	lookupBackendVariety,
 	lookupBuiltinBackendVariety,
 	maybeLookupBackendVariety,
+	unknownBackendVarietyMessage,
 	isStableKey,
 	isCryptographicallySecureKey,
 	isCryptographicallySecure,
@@ -54,6 +55,15 @@ defaultBackend = maybe cache return =<< Annex.getState Annex.backend
 	valid name = not (null name)
 	lookupname = lookupBackendVariety . parseKeyVariety . encodeBS
 
+{- A hashing backend. Takes git config into account, but
+ - guarantees the backend is cryptographically secure. -}
+hashBackend :: Annex Backend
+hashBackend = do
+	db <- defaultBackend
+	return $ if isCryptographicallySecure db
+		then db
+		else defaultHashBackend
+
 {- Generates a key for a file. -}
 genKey :: KeySource -> MeterUpdate -> Backend -> Annex (Key, Backend)
 genKey source meterupdate b = case B.genKey b of

Backend/VURL/Utilities.hs

@@ -10,10 +10,8 @@ module Backend.VURL.Utilities where
 import Annex.Common
 import Types.Key
 import Types.Backend
-import Types.KeySource
 import Logs.EquivilantKeys
 import qualified Backend.Hash
-import Utility.Metered
 
 migrateFromURLToVURL :: Key -> Backend -> AssociatedFile -> Bool -> Annex (Maybe Key)
 migrateFromURLToVURL oldkey newbackend _af inannex
@@ -41,18 +39,3 @@ migrateFromVURLToURL oldkey newbackend _af _
 			(keyData oldkey)
 				{ keyVariety = URLKey }
 	| otherwise = return Nothing
-
--- The Backend must use a cryptographically secure hash.
-generateEquivilantKey :: Backend -> OsPath -> Annex (Maybe Key)
-generateEquivilantKey b f =
-	case genKey b of
-		Just genkey -> do
-			showSideAction (UnquotedString Backend.Hash.descChecksum)
-			Just <$> genkey source nullMeterUpdate
-		Nothing -> return Nothing
-  where
-	source = KeySource
-		{ keyFilename = mempty -- avoid adding any extension
-		, contentLocation = f
-		, inodeCache = Nothing
-		}

CHANGELOG

@@ -1,5 +1,9 @@
 git-annex (10.20250116) UNRELEASED; urgency=medium
 
+  * Added the compute special remote.
+  * addcomputed: New command, adds a file that is generated by a compute
+    special remote.
+  * recompute: New command, recomputes computed files.
   * Support help.autocorrect settings "prompt", "never", and "immediate".
   * Allow setting remote.foo.annex-tracking-branch to a branch name
     that contains "/", as long as it's not a remote tracking branch.

CmdLine/GitAnnex.hs

@@ -133,6 +133,8 @@ import qualified Command.ExtendCluster
 import qualified Command.UpdateProxy
 import qualified Command.MaxSize
 import qualified Command.Sim
+import qualified Command.AddComputed
+import qualified Command.Recompute
 import qualified Command.Version
 import qualified Command.RemoteDaemon
 #ifdef WITH_ASSISTANT
@@ -265,6 +267,8 @@ cmds testoptparser testrunner mkbenchmarkgenerator = map addGitAnnexCommonOption
 	, Command.UpdateProxy.cmd
 	, Command.MaxSize.cmd
 	, Command.Sim.cmd
+	, Command.AddComputed.cmd
+	, Command.Recompute.cmd
 	, Command.Version.cmd
 	, Command.RemoteDaemon.cmd
 #ifdef WITH_ASSISTANT

CmdLine/GitRemoteAnnex.hs

@@ -927,7 +927,7 @@ downloadGitBundle rmt k = getKeyExportLocations rmt k >>= \case
 
 	getexport loc = catchNonAsync (getexport' loc) (const (pure False))
 	getexport' loc =
-		getViaTmp rsp vc k (AssociatedFile Nothing) Nothing $ \tmp -> do
+		getViaTmp rsp vc k Nothing $ \tmp -> do
 			v <- Remote.retrieveExport (Remote.exportActions rmt)
 				k loc tmp nullMeterUpdate
 			return (True, v)
@@ -986,7 +986,7 @@ generateGitBundle rmt bs manifest =
 			tmp nullMeterUpdate
 		if (bundlekey `notElem` inManifest manifest)
 			then do
-				unlessM (moveAnnex bundlekey (AssociatedFile Nothing) tmp) $
+				unlessM (moveAnnex bundlekey tmp) $
 					giveup "Unable to push"
 				return (bundlekey, uploadaction bundlekey)
 			else return (bundlekey, noop)

Command/AddComputed.hs

@@ -0,0 +1,236 @@
+{- git-annex command
+ -
+ - Copyright 2025 Joey Hess <id@joeyh.name>
+ -
+ - Licensed under the GNU AGPL version 3 or higher.
+ -}
+
+{-# LANGUAGE OverloadedStrings #-}
+
+module Command.AddComputed where
+
+import Command
+import qualified Git
+import qualified Git.Types as Git
+import qualified Git.Ref as Git
+import qualified Annex
+import qualified Remote.Compute
+import qualified Types.Remote as Remote
+import Backend
+import Annex.CatFile
+import Annex.Content.Presence
+import Annex.Ingest
+import Annex.UUID
+import Annex.GitShaKey
+import Types.KeySource
+import Types.Key
+import Messages.Progress
+import Logs.Location
+import Logs.EquivilantKeys
+import Utility.Metered
+import Backend.URL (fromUrl)
+
+import qualified Data.Map as M
+import Data.Time.Clock
+
+cmd :: Command
+cmd = notBareRepo $ withAnnexOptions [backendOption] $
+	command "addcomputed" SectionCommon "add computed files to annex"
+		(paramRepeating paramExpression)
+		(seek <$$> optParser)
+
+data AddComputedOptions = AddComputedOptions
+	{ computeParams :: CmdParams
+	, computeRemote :: DeferredParse Remote
+	, reproducible :: Maybe Reproducible
+	}
+
+optParser :: CmdParamsDesc -> Parser AddComputedOptions
+optParser desc = AddComputedOptions
+	<$> cmdParams desc
+	<*> (mkParseRemoteOption <$> parseToOption)
+	<*> parseReproducible
+
+newtype Reproducible = Reproducible { isReproducible :: Bool }
+
+parseReproducible :: Parser (Maybe Reproducible)
+parseReproducible = r <|> unr
+  where
+	r  = flag Nothing (Just (Reproducible True))
+		( long "reproducible"
+		<> short 'r'
+		<> help "computation is fully reproducible"
+		)
+	unr = flag Nothing (Just (Reproducible False))
+		( long "unreproducible"
+		<> short 'u'
+		<> help "computation is not fully reproducible"
+		)
+
+seek :: AddComputedOptions -> CommandSeek
+seek o = startConcurrency commandStages (seek' o)
+
+seek' :: AddComputedOptions -> CommandSeek
+seek' o = do
+	r <- getParsed (computeRemote o)
+	unless (Remote.Compute.isComputeRemote r) $
+		giveup "That is not a compute remote."
+
+	commandAction $ start o r
+
+start :: AddComputedOptions -> Remote -> CommandStart
+start o r = starting "addcomputed" ai si $ perform o r
+  where
+	ai = ActionItemUUID (Remote.uuid r) (UnquotedString (Remote.name r))
+	si = SeekInput (computeParams o)
+
+perform :: AddComputedOptions -> Remote -> CommandPerform
+perform o r = do
+	program <- Remote.Compute.getComputeProgram r
+	repopath <- fromRepo Git.repoPath
+	subdir <- liftIO $ relPathDirToFile repopath (literalOsPath ".")
+	let state = Remote.Compute.ComputeState
+		{ Remote.Compute.computeParams = computeParams o ++
+			Remote.Compute.defaultComputeParams r
+		, Remote.Compute.computeInputs = mempty
+		, Remote.Compute.computeOutputs = mempty
+		, Remote.Compute.computeSubdir = subdir
+		}
+	fast <- Annex.getRead Annex.fast
+	Remote.Compute.runComputeProgram program state
+		(Remote.Compute.ImmutableState False)
+		(getInputContent fast)
+		Nothing
+		(addComputed (Just "adding") True r (reproducible o) chooseBackend Just fast)
+	next $ return True
+
+addComputed
+	:: Maybe StringContainingQuotedPath
+	-> Bool
+	-> Remote
+	-> Maybe Reproducible
+	-> (OsPath -> Annex Backend)
+	-> (OsPath -> Maybe OsPath)
+	-> Bool
+	-> Remote.Compute.ComputeProgramResult
+	-> OsPath
+	-> NominalDiffTime
+	-> Annex ()
+addComputed maddaction stagefiles r reproducibleconfig choosebackend destfile fast result tmpdir ts = do
+	when (M.null outputs) $
+		giveup "The computation succeeded, but it did not generate any files."
+	oks <- forM (M.keys outputs) $ \outputfile -> do
+		case maddaction of
+			Just addaction -> showAction $
+				addaction <> " " <> QuotedPath outputfile
+			Nothing -> noop
+		k <- catchNonAsync (addfile outputfile)
+			(\err -> giveup $ "Failed to ingest output file " ++ fromOsPath outputfile ++ ": " ++ show err)
+		return (outputfile, Just k)
+	let state' = state
+		{ Remote.Compute.computeOutputs = M.fromList oks
+		}
+	forM_ (mapMaybe snd oks) $ \k -> do
+		Remote.Compute.setComputeState
+			(Remote.remoteStateHandle r)
+			k ts state'
+
+		let u = Remote.uuid r
+		unlessM (elem u <$> loggedLocations k) $
+			logChange NoLiveUpdate k u InfoPresent
+  where
+	state = Remote.Compute.computeState result
+	
+	outputs = Remote.Compute.computeOutputs state
+	
+	addfile outputfile
+		| fast = do
+			case destfile outputfile of
+				Nothing -> noop
+				Just f
+					| stagefiles -> addSymlink f stateurlk Nothing
+					| otherwise -> makelink f stateurlk
+			return stateurlk
+		| isreproducible = do
+			sz <- liftIO $ getFileSize outputfile'
+			metered Nothing sz Nothing $ \_ p ->
+				case destfile outputfile of
+					Just f -> ingesthelper f p Nothing
+					Nothing -> genkey outputfile p
+		| otherwise = case destfile outputfile of
+			Just f -> ingesthelper f nullMeterUpdate
+				(Just stateurlk)
+			Nothing -> return stateurlk
+	  where
+	  	stateurl = Remote.Compute.computeStateUrl r state outputfile
+		stateurlk = fromUrl stateurl Nothing True
+		outputfile' = tmpdir </> outputfile
+		ld f = LockedDown ldc (ks f)
+		ks f = KeySource
+			{ keyFilename = f
+			, contentLocation = outputfile'
+			, inodeCache = Nothing
+			}
+		genkey f p = do
+			backend <- choosebackend outputfile
+			fst <$> genKey (ks f) p backend
+		makelink f k = void $ makeLink f k Nothing
+		ingesthelper f p mk
+			| stagefiles = ingestwith $ do
+				k <- maybe (genkey f p) return mk
+				ingestAdd' p (Just (ld f)) (Just k)
+			| otherwise = ingestwith $ do
+				k <- maybe (genkey f p) return mk
+				mk' <- fst <$> ingest p (Just (ld f)) (Just k)
+				maybe noop (makelink f) mk'
+				return mk'
+		ingestwith a = a >>= \case
+			Nothing -> giveup "ingestion failed"
+			Just k -> do
+				u <- getUUID
+				unlessM (elem u <$> loggedLocations k) $
+					logStatus NoLiveUpdate k InfoPresent
+				when (fromKey keyVariety k == VURLKey) $ do
+					hb <- hashBackend
+					void $ addEquivilantKey hb k 
+						=<< calcRepo (gitAnnexLocation k)
+				return k
+	
+	ldc = LockDownConfig
+		{ lockingFile = True
+		, hardlinkFileTmpDir = Nothing
+		, checkWritePerms = True
+		}
+	
+	isreproducible = case reproducibleconfig of
+		Just v -> isReproducible v
+		Nothing -> Remote.Compute.computeReproducible result
+	
+getInputContent :: Bool -> OsPath -> Annex (Key, Maybe (Either Git.Sha OsPath))
+getInputContent fast p = catKeyFile p >>= \case
+	Just inputkey -> getInputContent' fast inputkey filedesc
+	Nothing -> inRepo (Git.fileRef p) >>= \case
+		Just fileref -> catObjectMetaData fileref >>= \case
+			Just (sha, _, t)
+				| t == Git.BlobObject ->
+					getInputContent' fast (gitShaKey sha) filedesc
+				| otherwise ->
+					badinput $ ", not a git " ++ decodeBS (Git.fmtObjectType t)
+			Nothing -> notcheckedin
+		Nothing -> notcheckedin
+  where
+	filedesc = fromOsPath p
+	badinput s = giveup $ "The computation needs an input file " ++ s ++ ": " ++ fromOsPath p
+	notcheckedin = badinput "that is not checked into the git repository"
+
+getInputContent' :: Bool -> Key -> String -> Annex (Key, Maybe (Either Git.Sha OsPath))
+getInputContent' fast inputkey filedesc
+	| fast = return (inputkey, Nothing)
+	| otherwise = case keyGitSha inputkey of
+		Nothing -> ifM (inAnnex inputkey)
+			( do
+				obj <- calcRepo (gitAnnexLocation inputkey)
+				return (inputkey, Just (Right obj))
+			, giveup $ "The computation needs the content of an annexed file which is not present: " ++ filedesc
+			)
+		Just sha -> return (inputkey, Just (Left sha))

Command/Export.hs

@@ -26,6 +26,7 @@ import Types.Remote
 import Types.Export
 import Annex.Export
 import Annex.Content
+import Annex.GitShaKey
 import Annex.Transfer
 import Annex.CatFile
 import Annex.FileMatcher

Command/Multicast.hs

@@ -213,7 +213,7 @@ storeReceived f = do
 			warning $ "Received a file " <> QuotedPath f <> " that is not a git-annex key. Deleting this file."
 			liftIO $ removeWhenExistsWith removeFile f
 		Just k -> void $ logStatusAfter NoLiveUpdate k $
-			getViaTmpFromDisk RetrievalVerifiableKeysSecure AlwaysVerify k (AssociatedFile Nothing) $ \dest -> unVerified $
+			getViaTmpFromDisk RetrievalVerifiableKeysSecure AlwaysVerify k $ \dest -> unVerified $
 				liftIO $ catchBoolIO $ do
 					renameFile f dest
 					return True

Command/ReKey.hs

@@ -128,7 +128,7 @@ linkKey file oldkey newkey = ifM (isJust <$> isAnnexLink file)
  - and vulnerable to corruption. -}
 linkKey' :: VerifyConfig -> Key -> Key -> Annex Bool
 linkKey' v oldkey newkey =
-	getViaTmpFromDisk RetrievalAllKeysSecure v newkey (AssociatedFile Nothing) $ \tmp -> unVerified $ do
+	getViaTmpFromDisk RetrievalAllKeysSecure v newkey $ \tmp -> unVerified $ do
 		oldobj <- calcRepo (gitAnnexLocation oldkey)
 		isJust <$> linkOrCopy' (return True) newkey oldobj tmp Nothing
 

Command/Recompute.hs

@@ -0,0 +1,209 @@
+{- git-annex command
+ -
+ - Copyright 2025 Joey Hess <id@joeyh.name>
+ -
+ - Licensed under the GNU AGPL version 3 or higher.
+ -}
+
+{-# LANGUAGE OverloadedStrings #-}
+
+module Command.Recompute where
+
+import Command
+import qualified Remote.Compute
+import qualified Remote
+import qualified Types.Remote as Remote
+import qualified Git.Ref as Git
+import Annex.Content
+import Annex.UUID
+import Annex.CatFile
+import Annex.GitShaKey
+import Git.FilePath
+import Logs.Location
+import Command.AddComputed (Reproducible(..), parseReproducible, getInputContent, getInputContent', addComputed)
+import Backend (maybeLookupBackendVariety, unknownBackendVarietyMessage)
+import Types.Key
+
+import qualified Data.Map as M
+
+cmd :: Command
+cmd = notBareRepo $ 
+	command "recompute" SectionCommon "recompute computed files"
+		paramPaths (seek <$$> optParser)
+
+data RecomputeOptions = RecomputeOptions
+	{ recomputeThese :: CmdParams
+	, originalOption :: Bool
+	, reproducible :: Maybe Reproducible
+	, computeRemote :: Maybe (DeferredParse Remote)
+	}
+
+optParser :: CmdParamsDesc -> Parser RecomputeOptions
+optParser desc = RecomputeOptions
+	<$> cmdParams desc
+	<*> switch
+		( long "original"
+		<> help "recompute using original content of input files"
+		)
+	<*> parseReproducible
+	<*> optional (mkParseRemoteOption <$> parseRemoteOption)
+
+seek :: RecomputeOptions -> CommandSeek
+seek o = startConcurrency commandStages (seek' o)
+
+seek' :: RecomputeOptions -> CommandSeek
+seek' o = do
+	computeremote <- maybe (pure Nothing) (Just <$$> getParsed)
+		(computeRemote o)
+	let seeker = AnnexedFileSeeker
+		{ startAction = const $ start o computeremote
+		, checkContentPresent = Nothing
+		, usesLocationLog = True
+		}
+	withFilesInGitAnnex ww seeker
+		=<< workTreeItems ww (recomputeThese o)
+  where
+	ww = WarnUnmatchLsFiles "recompute"
+
+start :: RecomputeOptions -> Maybe Remote -> SeekInput -> OsPath -> Key -> CommandStart
+start o (Just computeremote) si file key = 
+	stopUnless (elem (Remote.uuid computeremote) <$> loggedLocations key) $
+		start' o computeremote si file key		
+start o Nothing si file key = do
+	rs <- catMaybes <$> (mapM Remote.byUUID =<< loggedLocations key)
+	case sortOn Remote.cost $ filter Remote.Compute.isComputeRemote rs of
+		[] -> stop
+		(r:_) -> start' o r si file key
+
+start' :: RecomputeOptions -> Remote -> SeekInput -> OsPath -> Key -> CommandStart
+start' o r si file key =
+	Remote.Compute.getComputeState
+		(Remote.remoteStateHandle r) key >>= \case
+			Nothing -> stop
+			Just state -> shouldrecompute state >>= \case
+				Nothing -> stop
+				Just mreason -> starting "recompute" ai si $ do
+					maybe noop showNote mreason
+					perform o r file key state
+  where
+	ai = mkActionItem (key, file)
+
+	shouldrecompute state
+		| originalOption o = return (Just Nothing)
+		| otherwise = firstM (inputchanged state)
+			(M.toList (Remote.Compute.computeInputs state))
+			>>= return . \case
+				Nothing -> Nothing
+				Just (inputfile, _) -> Just $ Just $
+					QuotedPath inputfile <> " changed"
+
+	inputchanged state (inputfile, inputkey) = do
+		-- Note that the paths from the remote state are not to be
+		-- trusted to point to a file in the repository, but using
+		-- the path with git cat-file will only succeed if it
+		-- is checked into the repository.
+		p <- fromRepo $ fromTopFilePath $ asTopFilePath $
+			Remote.Compute.computeSubdir state </> inputfile
+		case keyGitSha inputkey of
+			Nothing -> 
+				catKeyFile p >>= return . \case
+					Just k -> k /= inputkey
+					Nothing -> inputfilemissing
+			Just inputgitsha -> inRepo (Git.fileRef p) >>= \case
+				Just fileref -> catObjectMetaData fileref >>= return . \case
+					Just (sha, _, _) -> sha /= inputgitsha
+					Nothing -> inputfilemissing
+				Nothing -> return inputfilemissing
+	  where
+		-- When an input file is missing, go ahead and recompute.
+		-- This way, the user will see the computation fail,
+		-- with an error message that explains the problem.
+		-- Or, if the input file is only optionally used by the
+		-- computation, it might succeed.
+		inputfilemissing = True
+
+perform :: RecomputeOptions -> Remote -> OsPath -> Key -> Remote.Compute.ComputeState -> CommandPerform
+perform o r file origkey origstate = do
+	program <- Remote.Compute.getComputeProgram r
+	reproducibleconfig <- getreproducibleconfig
+	showOutput
+	Remote.Compute.runComputeProgram program origstate
+		(Remote.Compute.ImmutableState False)
+		(getinputcontent program)
+		Nothing
+		(go program reproducibleconfig)
+	next cleanup
+  where
+	go program reproducibleconfig result tmpdir ts = do
+		checkbehaviorchange program
+			(Remote.Compute.computeState result)
+		addComputed Nothing False r reproducibleconfig
+			choosebackend destfile False result tmpdir ts
+
+	checkbehaviorchange program state = do
+		let check s w a b = forM_ (M.keys (w a)) $ \f ->
+			unless (M.member f (w b)) $
+				Remote.Compute.computationBehaviorChangeError program s f
+		
+		check "not using input file"
+			Remote.Compute.computeInputs origstate state
+		check "outputting"
+			Remote.Compute.computeOutputs state origstate
+		check "not outputting"
+			Remote.Compute.computeOutputs origstate state
+
+	getinputcontent program p
+		| originalOption o =
+			case M.lookup p (Remote.Compute.computeInputs origstate) of
+				Just inputkey -> getInputContent' False inputkey
+					(fromOsPath p ++ "(key " ++ serializeKey inputkey ++ ")")
+				Nothing -> Remote.Compute.computationBehaviorChangeError program
+					"requesting a new input file" p
+		| otherwise = getInputContent False p
+	
+	destfile outputfile
+		| Just outputfile == origfile = Just file
+		| otherwise = Nothing
+	
+	origfile = headMaybe $ M.keys $ M.filter (== Just origkey)
+		(Remote.Compute.computeOutputs origstate)
+
+	origbackendvariety = fromKey keyVariety origkey
+	
+	recomputingvurl = case origbackendvariety of
+		VURLKey -> True
+		_ -> False
+
+	getreproducibleconfig = case reproducible o of
+		Just (Reproducible True) -> return (Just (Reproducible True))
+		-- A VURL key is used when the computation was
+		-- unreproducible. So recomputing should too, but that
+		-- will result in the same VURL key. Since moveAnnex
+		-- will prefer the current annex object to a new one,
+		-- delete the annex object first, so that if recomputing
+		-- generates a new version of the file, it replaces
+		-- the old version.
+		v -> if recomputingvurl
+			then do
+				lockContentForRemoval origkey noop removeAnnex
+				return (Just (Reproducible False))
+			else return v
+	
+	cleanup = do
+		case reproducible o of
+			Just (Reproducible True) -> noop
+			-- in case computation failed, update
+			-- location log for removal done earlier
+			_ -> when recomputingvurl $ do
+				u <- getUUID
+				unlessM (elem u <$> loggedLocations origkey) $
+					logStatus NoLiveUpdate origkey InfoMissing
+		return True
+
+	choosebackend _outputfile
+		-- Use the same backend as was used to compute it before,
+		-- so if the computed file is the same, there will be
+		-- no change.
+		| otherwise = maybeLookupBackendVariety origbackendvariety >>= \case
+			Just b -> return b
+			Nothing -> giveup $ unknownBackendVarietyMessage origbackendvariety

Command/RecvKey.hs

@@ -28,7 +28,7 @@ start :: (SeekInput, Key) -> CommandStart
 start (_, key) = fieldTransfer Download key $ \_p -> do
 	-- This matches the retrievalSecurityPolicy of Remote.Git
 	let rsp = RetrievalAllKeysSecure
-	ifM (getViaTmp rsp DefaultVerify key (AssociatedFile Nothing) Nothing go)
+	ifM (getViaTmp rsp DefaultVerify key Nothing go)
 		( do
 			logStatus NoLiveUpdate key InfoPresent
 			_ <- quiesce True

Command/Reinject.hs

@@ -129,7 +129,7 @@ perform src key = do
 		)
   where
 	move = checkDiskSpaceToGet key Nothing False $
-		moveAnnex key (AssociatedFile Nothing) src
+		moveAnnex key src
 
 cleanup :: Key -> CommandCleanup
 cleanup key = do

Command/SetKey.hs

@@ -36,7 +36,7 @@ perform file key = do
 	-- the file might be on a different filesystem, so moveFile is used
 	-- rather than simply calling moveAnnex; disk space is also
 	-- checked this way.
-	ok <- getViaTmp RetrievalAllKeysSecure DefaultVerify key (AssociatedFile Nothing) Nothing $ \dest -> unVerified $
+	ok <- getViaTmp RetrievalAllKeysSecure DefaultVerify key Nothing $ \dest -> unVerified $
 		if dest /= file
 			then liftIO $ catchBoolIO $ do
 				moveFile file dest

Command/TestRemote.hs

@@ -301,7 +301,7 @@ test runannex mkr mkk =
 			Just verifier -> do
 				loc <- Annex.calcRepo (gitAnnexLocation k)
 				verifier k loc
-	get r k = logStatusAfter NoLiveUpdate k $ getViaTmp (Remote.retrievalSecurityPolicy r) (RemoteVerify r) k (AssociatedFile Nothing) Nothing $ \dest ->
+	get r k = logStatusAfter NoLiveUpdate k $ getViaTmp (Remote.retrievalSecurityPolicy r) (RemoteVerify r) k Nothing $ \dest ->
 		tryNonAsync (Remote.retrieveKeyFile r k (AssociatedFile Nothing) dest nullMeterUpdate (RemoteVerify r)) >>= \case
 			Right v -> return (True, v)
 			Left _ -> return (False, UnVerified)
@@ -375,13 +375,13 @@ testUnavailable runannex mkr mkk =
 	, check (`notElem` [Right True, Right False]) "checkPresent" $ \r k ->
 		Remote.checkPresent r k
 	, check (== Right False) "retrieveKeyFile" $ \r k ->
-		logStatusAfter NoLiveUpdate k $ getViaTmp (Remote.retrievalSecurityPolicy r) (RemoteVerify r) k (AssociatedFile Nothing) Nothing $ \dest ->
+		logStatusAfter NoLiveUpdate k $ getViaTmp (Remote.retrievalSecurityPolicy r) (RemoteVerify r) k Nothing $ \dest ->
 			tryNonAsync (Remote.retrieveKeyFile r k (AssociatedFile Nothing) dest nullMeterUpdate (RemoteVerify r)) >>= \case
 				Right v -> return (True, v)
 				Left _ -> return (False, UnVerified)
 	, check (== Right False) "retrieveKeyFileCheap" $ \r k -> case Remote.retrieveKeyFileCheap r of
 		Nothing -> return False
-		Just a -> logStatusAfter NoLiveUpdate k $ getViaTmp (Remote.retrievalSecurityPolicy r) (RemoteVerify r) k (AssociatedFile Nothing) Nothing $ \dest -> 
+		Just a -> logStatusAfter NoLiveUpdate k $ getViaTmp (Remote.retrievalSecurityPolicy r) (RemoteVerify r) k Nothing $ \dest -> 
 			unVerified $ isRight
 				<$> tryNonAsync (a k (AssociatedFile Nothing) dest)
 	]
@@ -443,7 +443,7 @@ randKey sz = withTmpFile (literalOsPath "randkey") $ \f h -> do
 	k <- case Types.Backend.genKey Backend.Hash.testKeyBackend of
 		Just a -> a ks nullMeterUpdate
 		Nothing -> giveup "failed to generate random key (backend problem)"
-	_ <- moveAnnex k (AssociatedFile Nothing) f
+	_ <- moveAnnex k f
 	return k
 
 getReadonlyKey :: Remote -> OsPath -> Annex Key

Command/TransferKey.hs

@@ -63,7 +63,7 @@ toPerform key af remote = go Upload af $
 fromPerform :: Key -> AssociatedFile -> Remote -> CommandPerform
 fromPerform key af remote = go Upload af $
 	download' (uuid remote) key af Nothing stdRetry $ \p ->
-		logStatusAfter NoLiveUpdate key $ getViaTmp (retrievalSecurityPolicy remote) vc key af Nothing $ \t ->
+		logStatusAfter NoLiveUpdate key $ getViaTmp (retrievalSecurityPolicy remote) vc key Nothing $ \t ->
 			tryNonAsync (Remote.retrieveKeyFile remote key af t p vc) >>= \case
 				Right v -> return (True, v)	
 				Left e -> do

Command/TransferKeys.hs

@@ -50,7 +50,7 @@ start = do
 						return True
 		| otherwise = notifyTransfer direction af $
 			download' (Remote.uuid remote) key af Nothing stdRetry $ \p ->
-				logStatusAfter NoLiveUpdate key $ getViaTmp (Remote.retrievalSecurityPolicy remote) (RemoteVerify remote) key af Nothing $ \t -> do
+				logStatusAfter NoLiveUpdate key $ getViaTmp (Remote.retrievalSecurityPolicy remote) (RemoteVerify remote) key Nothing $ \t -> do
 					r <- tryNonAsync (Remote.retrieveKeyFile remote key af t p (RemoteVerify remote)) >>= \case
 						Left e -> do
 							warning (UnquotedString (show e))

Command/Transferrer.hs

@@ -55,7 +55,7 @@ start = do
 		-- so caller is responsible for doing notification
 		-- and for retrying, and updating location log,
 		-- and stall canceling.
-		let go p = getViaTmp (Remote.retrievalSecurityPolicy remote) (RemoteVerify remote) key af Nothing $ \t -> do
+		let go p = getViaTmp (Remote.retrievalSecurityPolicy remote) (RemoteVerify remote) key Nothing $ \t -> do
 			Remote.verifiedAction (Remote.retrieveKeyFile remote key af t p (RemoteVerify remote))
 		in download' (Remote.uuid remote) key af Nothing noRetry go 
 			noNotification
@@ -72,7 +72,7 @@ start = do
 	runner (AssistantDownloadRequest _ key (TransferAssociatedFile file)) remote =
 		notifyTransfer Download file $
 			download' (Remote.uuid remote) key file Nothing stdRetry $ \p ->
-				logStatusAfter NoLiveUpdate key $ getViaTmp (Remote.retrievalSecurityPolicy remote) (RemoteVerify remote) key file Nothing $ \t -> do
+				logStatusAfter NoLiveUpdate key $ getViaTmp (Remote.retrievalSecurityPolicy remote) (RemoteVerify remote) key Nothing $ \t -> do
 					r <- tryNonAsync (Remote.retrieveKeyFile remote key file t p (RemoteVerify remote)) >>= \case
 						Left e -> do
 							warning (UnquotedString (show e))

Git/Types.hs

@@ -145,7 +145,7 @@ newtype RefDate = RefDate String
 
 {- Types of objects that can be stored in git. -}
 data ObjectType = BlobObject | CommitObject | TreeObject
-	deriving (Show)
+	deriving (Show, Eq)
 
 readObjectType :: S.ByteString -> Maybe ObjectType
 readObjectType "blob" = Just BlobObject

Logs/EquivilantKeys.hs

@@ -1,6 +1,6 @@
 {- Logs listing keys that are equivalent to a key.
  -
- - Copyright 2024 Joey Hess <id@joeyh.name>
+ - Copyright 2024-2025 Joey Hess <id@joeyh.name>
  -
  - Licensed under the GNU AGPL version 3 or higher.
  -}
@@ -10,6 +10,9 @@
 module Logs.EquivilantKeys (
 	getEquivilantKeys,
 	setEquivilantKey,
+	updateEquivilantKeys,
+	addEquivilantKey,
+	generateEquivilantKey,
 ) where
 
 import Annex.Common
@@ -17,6 +20,11 @@ import qualified Annex
 import Logs
 import Logs.Presence
 import qualified Annex.Branch
+import qualified Backend.Hash
+import Types.KeySource
+import Types.Backend
+import Types.Remote (Verification(..))
+import Utility.Metered
 
 getEquivilantKeys :: Key -> Annex [Key]
 getEquivilantKeys key = do
@@ -29,3 +37,34 @@ setEquivilantKey key equivkey = do
 	config <- Annex.getGitConfig
 	addLog (Annex.Branch.RegardingUUID []) (equivilantKeysLogFile config key)
 		InfoPresent (LogInfo (serializeKey' equivkey))
+
+-- This returns Verified when when an equivilant key has been added to the
+-- log (or was already in the log). This is to avoid hashing the object
+-- again later.
+updateEquivilantKeys :: Backend -> OsPath -> Key -> [Key] -> Annex (Maybe Verification)
+updateEquivilantKeys b obj key eks = generateEquivilantKey b obj >>= \case
+	Nothing -> return Nothing
+	Just ek -> do
+		unless (ek `elem` eks) $
+			setEquivilantKey key ek
+		return (Just Verified)
+
+addEquivilantKey :: Backend -> Key -> OsPath -> Annex (Maybe Verification)
+addEquivilantKey b key obj = 
+	updateEquivilantKeys b obj key
+		=<< getEquivilantKeys key
+
+-- The Backend must use a cryptographically secure hash.
+generateEquivilantKey :: Backend -> OsPath -> Annex (Maybe Key)
+generateEquivilantKey b obj =
+	case genKey b of
+		Just genkey -> do
+			showSideAction (UnquotedString Backend.Hash.descChecksum)
+			Just <$> genkey source nullMeterUpdate
+		Nothing -> return Nothing
+  where
+	source = KeySource
+		{ keyFilename = mempty -- avoid adding any extension
+		, contentLocation = obj
+		, inodeCache = Nothing
+		}

P2P/Annex.hs

@@ -81,7 +81,7 @@ runLocal runst runner a = case a of
 			iv <- startVerifyKeyContentIncrementally DefaultVerify k
 			let runtransfer ti = 
 				Right <$> transfer download' k af Nothing (\p ->
-					logStatusAfter NoLiveUpdate k $ getViaTmp rsp DefaultVerify k af Nothing $ \tmp ->
+					logStatusAfter NoLiveUpdate k $ getViaTmp rsp DefaultVerify k Nothing $ \tmp ->
 						storefile tmp o l getb iv validitycheck p ti)
 			let fallback = return $ Left $
 				ProtoFailureMessage "transfer already in progress, or unable to take transfer lock"

Remote.hs

@@ -319,22 +319,11 @@ remoteFromUUID u = ifM ((==) u <$> getUUID)
 		remotesChanged
 		findinmap
 
-{- Filters a list of remotes to ones that have the listed uuids. -}
-remotesWithUUID :: [Remote] -> [UUID] -> [Remote]
-remotesWithUUID rs us = filter (\r -> uuid r `elem` us) rs
-
-{- Filters a list of remotes to ones that do not have the listed uuids. -}
-remotesWithoutUUID :: [Remote] -> [UUID] -> [Remote]
-remotesWithoutUUID rs us = filter (\r -> uuid r `notElem` us) rs
-
 {- List of repository UUIDs that the location log indicates may have a key.
  - Dead repositories are excluded. -}
 keyLocations :: Key -> Annex [UUID]
 keyLocations key = trustExclude DeadTrusted =<< loggedLocations key
 
-{- Whether to include remotes that have annex-ignore set. -}
-newtype IncludeIgnored = IncludeIgnored Bool
-
 {- Cost ordered lists of remotes that the location log indicates
  - may have a key.
  -
@@ -342,33 +331,16 @@ newtype IncludeIgnored = IncludeIgnored Bool
  -}
 keyPossibilities :: IncludeIgnored -> Key -> Annex [Remote]
 keyPossibilities ii key = do
-	u <- getUUID
+	locations <- keyLocations key
-	-- uuids of all remotes that are recorded to have the key
+	keyPossibilities' ii key locations =<< remoteList
-	locations <- filter (/= u) <$> keyLocations key
-	speclocations <- map uuid
-		. filter (remoteAnnexSpeculatePresent . gitconfig)
-		<$> remoteList
-	-- there are unlikely to be many speclocations, so building a Set
-	-- is not worth the expense
-	let locations' = speclocations ++ filter (`notElem` speclocations) locations
-	fst <$> remoteLocations ii locations' []
 
 {- Given a list of locations of a key, and a list of all
  - trusted repositories, generates a cost-ordered list of
  - remotes that contain the key, and a list of trusted locations of the key.
  -}
 remoteLocations :: IncludeIgnored -> [UUID] -> [UUID] -> Annex ([Remote], [UUID])
-remoteLocations (IncludeIgnored ii) locations trusted = do
+remoteLocations ii locations trusted = 
-	let validtrustedlocations = nub locations `intersect` trusted
+	remoteLocations' ii locations trusted =<< remoteList
-
-	-- remotes that match uuids that have the key
-	allremotes <- remoteList 
-		>>= if not ii
-			then filterM (not <$$> liftIO . getDynamicConfig . remoteAnnexIgnore . gitconfig)
-			else return
-	let validremotes = remotesWithUUID allremotes locations
-
-	return (sortBy (comparing cost) validremotes, validtrustedlocations)
 
 {- Displays known locations of a key and helps the user take action
  - to make them accessible. -}

Remote/Compute.hs

@@ -0,0 +1,709 @@
+{- Compute remote.
+ -
+ - Copyright 2025 Joey Hess <id@joeyh.name>
+ -
+ - Licensed under the GNU AGPL version 3 or higher.
+ -}
+
+{-# LANGUAGE OverloadedStrings #-}
+
+module Remote.Compute (
+	remote,
+	isComputeRemote,
+	ComputeState(..),
+	setComputeState,
+	getComputeState,
+	computeStateUrl,
+	ComputeProgram,
+	getComputeProgram,
+	runComputeProgram,
+	ImmutableState(..),
+	ComputeProgramResult(..),
+	computationBehaviorChangeError,
+	defaultComputeParams,
+) where
+
+import Annex.Common
+import qualified Annex
+import Types.Remote
+import Types.ProposedAccepted
+import Types.MetaData
+import Types.Creds
+import Config
+import Config.Cost
+import Remote.Helper.Special
+import Remote.Helper.ExportImport
+import Remote.List.Util
+import Annex.SpecialRemote.Config
+import Annex.UUID
+import Annex.Content
+import Annex.Tmp
+import Annex.GitShaKey
+import Annex.CatFile
+import Annex.RepoSize.LiveUpdate
+import qualified Annex.Transfer
+import Logs.MetaData
+import Logs.EquivilantKeys
+import Logs.Location
+import Messages.Progress
+import Utility.Metered
+import Utility.TimeStamp
+import Utility.Env
+import Utility.Tmp.Dir
+import Utility.Url
+import Utility.MonotonicClock
+import Types.Key
+import Backend
+import qualified Git
+import qualified Utility.FileIO as F
+import qualified Utility.SimpleProtocol as Proto
+
+import Network.HTTP.Types.URI
+import Data.Time.Clock
+import Text.Read
+import Control.Concurrent.STM
+import Control.Concurrent.Async
+import qualified Data.Map as M
+import qualified Data.Set as S
+import qualified Data.ByteString as B
+import qualified Data.Text as T
+import qualified Data.Text.Encoding as T
+
+remote :: RemoteType
+remote = RemoteType
+	{ typename = "compute"
+	, enumerate = const $ findSpecialRemotes "compute"
+	, generate = gen
+	, configParser = computeConfigParser
+	, setup = setupInstance
+	, exportSupported = exportUnsupported
+	, importSupported = importUnsupported
+	, thirdPartyPopulated = False
+	}
+
+isComputeRemote :: Remote -> Bool
+isComputeRemote r = typename (remotetype r) == typename remote
+
+gen :: Git.Repo -> UUID -> RemoteConfig -> RemoteGitConfig -> RemoteStateHandle -> Annex (Maybe Remote)
+gen r u rc gc rs = case getComputeProgram' rc of
+	Left _err -> return Nothing
+	Right program -> do
+		c <- parsedRemoteConfig remote rc
+		cst <- remoteCost gc c veryExpensiveRemoteCost
+		return $ Just $ mk program c cst
+  where
+	mk program c cst = Remote
+		{ uuid = u
+		, cost = cst
+		, name = Git.repoDescribe r
+		, storeKey = storeKeyUnsupported
+ 		, retrieveKeyFile = computeKey rs program
+		, retrieveKeyFileInOrder = pure True
+		, retrieveKeyFileCheap = Nothing
+		, retrievalSecurityPolicy = RetrievalAllKeysSecure
+		, removeKey = dropKey rs
+		, lockContent = Nothing
+		, checkPresent = checkKey rs
+		, checkPresentCheap = False
+		, exportActions = exportUnsupported
+		, importActions = importUnsupported
+		, whereisKey = Nothing
+		, remoteFsck = Nothing
+		, repairRepo = Nothing
+		, config = c
+		, gitconfig = gc
+		, localpath = Nothing
+		, getRepo = return r
+		, readonly = True
+		, appendonly = False
+		, untrustworthy = False
+		, availability = pure LocallyAvailable
+		, remotetype = remote
+		, mkUnavailable = return Nothing
+		, getInfo = return []
+		, claimUrl = Nothing
+		, checkUrl = Nothing
+		, remoteStateHandle = rs
+		}
+
+setupInstance :: SetupStage -> Maybe UUID -> Maybe CredPair -> RemoteConfig -> RemoteGitConfig -> Annex (RemoteConfig, UUID)
+setupInstance ss mu _ c _ = do
+	ComputeProgram program <- either giveup return $ getComputeProgram' c
+	allowedprograms <- maybe [] words . annexAllowedComputePrograms
+		<$> Annex.getGitConfig
+	case ss of
+		Init -> noop
+		_ -> unless (program `elem` allowedprograms) $ do
+			let remotename = fromMaybe "(unknown)" (lookupName c)
+			giveup $ unwords
+				[ "Unable to enable compute special remote"
+				, remotename
+				, "because its compute program"
+				, program
+				, "is not listed in annex.security-allowed-compute-programs"
+				]
+	unlessM (liftIO $ inSearchPath program) $
+		giveup $ "Cannot find " ++ program ++ " in PATH"
+	u <- maybe (liftIO genUUID) return mu
+	gitConfigSpecialRemote u c [("compute", "true")]
+	return (c, u)
+
+computeConfigParser :: RemoteConfig -> Annex RemoteConfigParser
+computeConfigParser _ = return $ RemoteConfigParser
+	{ remoteConfigFieldParsers = 
+		[ optionalStringParser programField
+			(FieldDesc $ "compute program (must start with \"" ++ safetyPrefix ++ "\")")
+		]
+	-- Pass through all other params, which git-annex addcomputed adds
+	-- to the input params.
+	, remoteConfigRestPassthrough = Just
+		( const True
+		, [("*", FieldDesc "all other parameters are passed to compute program")]
+		)
+	}
+
+defaultComputeParams :: Remote -> [String]
+defaultComputeParams = map mk . M.toList . getRemoteConfigPassedThrough . config
+  where
+	mk (f, v) = fromProposedAccepted f ++ '=' : v
+
+newtype ComputeProgram = ComputeProgram String
+	deriving (Show)
+
+getComputeProgram :: Remote -> Annex ComputeProgram
+getComputeProgram r = 
+	case getComputeProgram' (unparsedRemoteConfig (config r)) of
+		Right program -> return program
+		Left err -> giveup $ 
+			"Problem with the configuration of compute remote " ++ name r ++ ": " ++ err
+
+getComputeProgram' :: RemoteConfig -> Either String ComputeProgram
+getComputeProgram' c = case fromProposedAccepted <$> M.lookup programField c of
+	Just program
+		| safetyPrefix `isPrefixOf` program ->
+			Right (ComputeProgram program)
+		| otherwise -> Left $
+			"The program's name must begin with \"" ++ safetyPrefix ++ "\""
+	Nothing -> Left "Specify program="
+
+-- Limiting the program to "git-annex-compute-" prefix is important for
+-- security, it prevents autoenabled compute remotes from running arbitrary
+-- programs.
+safetyPrefix :: String
+safetyPrefix = "git-annex-compute-"
+
+programField :: RemoteConfigField
+programField = Accepted "program"
+
+data ProcessCommand
+	= ProcessInput FilePath
+	| ProcessOutput FilePath
+	| ProcessReproducible
+	| ProcessProgress PercentFloat
+	deriving (Show, Eq)
+
+instance Proto.Receivable ProcessCommand where
+	parseCommand "INPUT" = Proto.parse1 ProcessInput
+	parseCommand "OUTPUT" = Proto.parse1 ProcessOutput
+	parseCommand "REPRODUCIBLE" = Proto.parse0 ProcessReproducible
+	parseCommand "PROGRESS" = Proto.parse1 ProcessProgress
+	parseCommand _ = Proto.parseFail
+
+newtype PercentFloat = PercentFloat Float
+	deriving (Show, Eq)
+
+instance Proto.Serializable PercentFloat where
+	serialize (PercentFloat p) = show p ++ "%"
+	deserialize s = do
+		s' <- reverse <$> stripPrefix "%" (reverse s)
+		PercentFloat <$> readMaybe s'
+
+data ComputeState = ComputeState
+	{ computeParams :: [String]
+	, computeInputs :: M.Map OsPath Key
+	, computeOutputs :: M.Map OsPath (Maybe Key)
+	, computeSubdir :: OsPath
+	}
+	deriving (Show, Eq)
+
+{- Formats a ComputeState as an URL query string.
+ -
+ - Prefixes computeParams with 'p', computeInputs with 'i',
+ - and computeOutputs with 'o'. Uses "d" for computeSubdir.
+ -
+ - When the passed Key is an output, rather than duplicate it
+ - in the query string, that output has no value.
+ -
+ - Example: "psomefile&pdestfile&pbaz&isomefile=WORM--foo&odestfile=&d=subdir"
+ -
+ - The computeParams are in the order they were given. The computeInputs
+ - and computeOutputs are sorted in ascending order for stability.
+ -}
+formatComputeState :: Key -> ComputeState -> B.ByteString
+formatComputeState k = formatComputeState' (Just k)
+
+formatComputeState' :: Maybe Key -> ComputeState -> B.ByteString
+formatComputeState' mk st = renderQuery False $ concat
+	[ map formatparam (computeParams st)
+	, map formatinput (M.toAscList (computeInputs st))
+	, mapMaybe formatoutput (M.toAscList (computeOutputs st))
+	, [("d", Just (fromOsPath (computeSubdir st)))]
+	]
+  where
+	formatparam p = ("p" <> encodeBS p, Nothing)
+	formatinput (file, key) =
+		("i" <> fromOsPath file, Just (serializeKey' key))
+	formatoutput (file, (Just key)) = Just $
+		("o" <> fromOsPath file,
+			if Just key == mk
+				then Nothing
+				else Just (serializeKey' key)
+		)
+	formatoutput (_, Nothing) = Nothing
+
+parseComputeState :: Key -> B.ByteString -> Maybe ComputeState
+parseComputeState k b =
+	let st = go emptycomputestate (parseQuery b)
+	in if st == emptycomputestate then Nothing else Just st
+  where
+	emptycomputestate = ComputeState 
+		{ computeParams = mempty
+		, computeInputs = mempty
+		, computeOutputs = mempty
+		, computeSubdir = literalOsPath "."
+		}
+	
+	go :: ComputeState -> [QueryItem] -> ComputeState
+	go c [] = c { computeParams = reverse (computeParams c) }
+	go c ((f, v):rest) = 
+		let c' = fromMaybe c $ case decodeBS f of
+			('p':p) -> Just $ c
+				{ computeParams = p : computeParams c
+				}
+			('i':i) -> do
+				key <- deserializeKey' =<< v
+				Just $ c
+					{ computeInputs = 
+						M.insert (toOsPath i) key
+							(computeInputs c)
+					}
+			('o':o) -> case v of
+				Just kv -> do
+					key <- deserializeKey' kv
+					Just $ c
+						{ computeOutputs =
+							M.insert (toOsPath o)
+								(Just key)
+								(computeOutputs c)
+						}
+				Nothing -> Just $ c
+					{ computeOutputs = 
+						M.insert (toOsPath o)
+							(Just k)
+							(computeOutputs c)
+					}
+			('d':[]) -> do
+				subdir <- v
+				Just $ c
+					{ computeSubdir = toOsPath subdir
+					}
+			_ -> Nothing
+		in go c' rest
+
+{- A compute: url for a given output file of a computation. -}
+computeStateUrl :: Remote -> ComputeState -> OsPath -> URLString
+computeStateUrl r st p = 
+	"annex-compute:" ++ fromUUID (uuid r) ++ "/" ++ fromOsPath p ++ "?" 
+		++ decodeBS (formatComputeState' Nothing st')
+  where
+	-- Omit computeOutputs, so this gives the same result whether
+	-- it's called on a ComputeState with the computeOutputs 
+	-- Keys populated or not.
+	st' = st { computeOutputs = mempty }
+
+{- The per remote metadata is used to store ComputeState. This allows
+ - recording multiple ComputeStates that generate the same key.
+ -
+ - The metadata fields are numbers (prefixed with "t" to make them legal
+ - field names), which are estimates of how long it might take to run
+ - the computation (in seconds).
+ -
+ - Avoids redundantly recording a ComputeState when the per remote metadata
+ - already contains it.
+ -}
+setComputeState :: RemoteStateHandle -> Key -> NominalDiffTime -> ComputeState -> Annex ()
+setComputeState rs k ts st = do
+	l <- map snd <$> getComputeStatesUnsorted rs k
+	unless (st `elem` l) go
+  where
+	go = addRemoteMetaData k rs $ MetaData $ M.singleton
+		(mkMetaFieldUnchecked $ T.pack ('t':show (truncateResolution 1 ts)))
+		(S.singleton (MetaValue (CurrentlySet True) (formatComputeState k st)))
+
+{- When multiple ComputeStates have been recorded for the same key,
+ - this returns one that is probably less expensive to compute,
+ - based on the original time it took to compute it. -}
+getComputeState :: RemoteStateHandle -> Key -> Annex (Maybe ComputeState)
+getComputeState rs k = headMaybe . map snd . sortOn fst
+	<$> getComputeStatesUnsorted rs k
+
+getComputeStatesUnsorted :: RemoteStateHandle -> Key -> Annex [(NominalDiffTime, ComputeState)]
+getComputeStatesUnsorted rs k = do
+	RemoteMetaData _ (MetaData m) <- getCurrentRemoteMetaData rs k
+	return $ go [] (M.toList m)
+  where
+	go c [] = concat c
+	go c ((f, s) : rest) =
+		let sts = mapMaybe (parseComputeState k . fromMetaValue)
+			(S.toList s)
+		in case parsePOSIXTime (T.encodeUtf8 (T.drop 1 (fromMetaField f))) of
+			Just ts -> go (zip (repeat ts) sts : c) rest
+			Nothing -> go c rest
+
+computeProgramEnvironment :: ComputeState -> Annex [(String, String)]
+computeProgramEnvironment st = do
+	environ <- filter (caninherit . fst) <$> liftIO getEnvironment
+	let addenv = mapMaybe go (computeParams st)
+	return $ environ ++ addenv
+  where
+	envprefix = "ANNEX_COMPUTE_"
+	caninherit v = not (envprefix `isPrefixOf` v)
+	go p
+		| '=' `elem` p =
+			let (f, v) = separate (== '=') p
+			in Just (envprefix ++ f, v)
+		| otherwise = Nothing
+
+newtype ImmutableState = ImmutableState Bool
+
+data ComputeProgramResult = ComputeProgramResult
+	{ computeState :: ComputeState
+	, computeInputsUnavailable :: Bool
+	, computeReproducible :: Bool
+	}
+
+runComputeProgram
+	:: ComputeProgram
+	-> ComputeState
+	-> ImmutableState
+	-> (OsPath -> Annex (Key, Maybe (Either Git.Sha OsPath)))
+	-- ^ get input file's content, or Nothing the input file's
+	-- content is not available
+	-> Maybe (Key, MeterUpdate)
+	-- ^ update meter for this key
+	-> (ComputeProgramResult -> OsPath -> NominalDiffTime -> Annex v)
+	-> Annex v
+runComputeProgram (ComputeProgram program) state (ImmutableState immutablestate) getinputcontent meterkey cont =
+	withOtherTmp $ \othertmpdir ->
+		withTmpDirIn othertmpdir (literalOsPath "compute") go
+  where
+	go tmpdir = do
+		environ <- computeProgramEnvironment state
+		subdir <- liftIO $ getsubdir tmpdir
+		let pr = (proc program (computeParams state))
+			 { cwd = Just (fromOsPath subdir)
+			 , std_in = CreatePipe
+			 , std_out = CreatePipe
+			 , env = Just environ
+			 }
+		showOutput
+		starttime <- liftIO currentMonotonicTimestamp
+		let startresult = ComputeProgramResult state False False
+		result <- withmeterfile $ \meterfile -> bracket
+			(liftIO $ createProcess pr)
+			(liftIO . cleanupProcess)
+			(getinput tmpdir subdir startresult meterfile)
+		endtime <- liftIO currentMonotonicTimestamp
+		cont result subdir (calcduration starttime endtime)
+		
+	getsubdir tmpdir = do
+		let subdir = tmpdir </> computeSubdir state
+		ifM (dirContains <$> absPath tmpdir <*> absPath subdir)
+			( do
+				createDirectoryIfMissing True subdir
+				return subdir
+			-- Ignore unsafe value in state.
+			, return tmpdir
+			)
+	
+	getinput tmpdir subdir result meterfile p = 
+		liftIO (hGetLineUntilExitOrEOF (processHandle p) (stdoutHandle p)) >>= \case
+			Just l
+				| null l -> getinput tmpdir subdir result meterfile p
+				| otherwise -> do
+					result' <- parseoutput p tmpdir subdir result meterfile l
+					getinput tmpdir subdir result' meterfile p
+			Nothing -> do
+				liftIO $ hClose (stdoutHandle p)
+				liftIO $ hClose (stdinHandle p)
+				unlessM (liftIO $ checkSuccessProcess (processHandle p)) $
+					giveup $ program ++ " exited unsuccessfully"
+				return result
+	
+	parseoutput p tmpdir subdir result meterfile l = case Proto.parseMessage l of
+		Just (ProcessInput f) -> do
+			let f' = toOsPath f
+			let knowninput = M.member f'
+				(computeInputs (computeState result))
+			checksafefile tmpdir subdir f' "input"
+			checkimmutable knowninput "inputting" f' $ do
+				(k, inputcontent) <- getinputcontent f'
+				mp <- case inputcontent of
+					Nothing -> pure Nothing
+					Just (Right f'') -> liftIO $
+						Just <$> relPathDirToFile subdir f''
+					Just (Left gitsha) ->
+						Just <$> (liftIO . relPathDirToFile subdir 
+							=<< populategitsha gitsha tmpdir)
+				liftIO $ hPutStrLn (stdinHandle p) $
+					maybe "" fromOsPath mp
+				liftIO $ hFlush (stdinHandle p)
+				let result' = result
+					{ computeInputsUnavailable = 
+						isNothing mp || computeInputsUnavailable result
+					}
+				return $ if immutablestate
+					then result'
+					else modresultstate result' $ \s -> s
+						{ computeInputs = 
+							M.insert f' k
+								(computeInputs s)
+						}
+		Just (ProcessOutput f) -> do
+			let f' = toOsPath f
+			checksafefile tmpdir subdir f' "output"
+			knownoutput <- case M.lookup f' (computeOutputs $ computeState result) of
+				Nothing -> return False
+				Just mk -> do
+					when (mk == fmap fst meterkey) $
+						meterfile (subdir </> f')
+					return True
+			checkimmutable knownoutput "outputting" f' $ 
+				return $ if immutablestate
+					then result
+					else modresultstate result $ \s -> s
+						{ computeOutputs = 
+							M.insert f' Nothing
+								(computeOutputs s)
+							}
+		Just (ProcessProgress percent) -> do
+			liftIO $ updatepercent percent
+			return result
+		Just ProcessReproducible ->
+			return $ result { computeReproducible = True }
+		Nothing -> giveup $
+			program ++ " output an unparseable line: \"" ++ l ++ "\""
+
+	modresultstate result f = 
+		result { computeState = f (computeState result) }
+
+	checksafefile tmpdir subdir f fileaction = do
+		let err problem = giveup $
+			program ++ " tried to " ++ fileaction ++ " a file that is " ++ problem ++ ": " ++ fromOsPath f
+		unlessM (liftIO $ dirContains <$> absPath tmpdir <*> absPath (subdir </> f)) $
+			err "outside the git repository"
+		when (any (\p -> dropTrailingPathSeparator p == literalOsPath ".git") (splitPath f)) $
+			err "inside the .git directory"
+
+	checkimmutable True _ _ a = a
+	checkimmutable False requestdesc p a
+		| not immutablestate = a
+		| otherwise = computationBehaviorChangeError (ComputeProgram program) requestdesc p
+	
+	calcduration (MonotonicTimestamp starttime) (MonotonicTimestamp endtime) =
+		fromIntegral (endtime - starttime) :: NominalDiffTime
+
+	-- Writes to a .git/objects/ file in the tmpdir, rather than
+	-- using the input filename, to avoid exposing the input filename
+	-- to the program as a parameter, which could parse it as a dashed
+	-- option or other special parameter.
+	populategitsha gitsha tmpdir = do
+		let f = tmpdir </> literalOsPath ".git" </> literalOsPath "objects"
+			</> toOsPath (Git.fromRef' gitsha)
+		liftIO $ createDirectoryIfMissing True $ takeDirectory f
+		liftIO . F.writeFile f =<< catObject gitsha
+		return f
+
+	withmeterfile a = case meterkey of
+		Nothing -> a (const noop)
+		Just (_, progress) -> do
+			filev <- liftIO newEmptyTMVarIO
+			endv <- liftIO $ newEmptyTMVarIO
+			let meterfile = void . liftIO 
+				. atomically . tryPutTMVar filev
+			let endmeterfile = atomically $ putTMVar endv ()
+			tid <- liftIO $ async $ do
+				v <- liftIO $ atomically $ 
+					(Right <$> takeTMVar filev)
+						`orElse`
+					(Left <$> takeTMVar endv)
+				case v of
+					Right f -> watchFileSize f progress $ \_ ->
+						void $ liftIO $ atomically $
+							takeTMVar endv
+					Left () -> return ()
+			a meterfile 
+				`finally` liftIO (endmeterfile >> wait tid)
+			
+	updatepercent (PercentFloat percent) = case meterkey of
+		Nothing -> noop
+		Just (k, progress) -> case fromKey keySize k of
+			Nothing -> noop
+			Just sz ->
+				progress $ BytesProcessed $ floor $ 
+					fromIntegral sz * percent / 100
+
+computationBehaviorChangeError :: ComputeProgram -> String -> OsPath -> Annex a
+computationBehaviorChangeError (ComputeProgram program) requestdesc p =
+	giveup $ program ++ " is not behaving the same way it used to, now " ++ requestdesc ++ ": " ++ fromOsPath p
+
+computeKey :: RemoteStateHandle -> ComputeProgram -> Key -> AssociatedFile -> OsPath -> MeterUpdate -> VerifyConfig -> Annex Verification
+computeKey rs (ComputeProgram program) k _af dest meterupdate vc =
+	getComputeState rs k >>= \case
+		Just state ->
+			case computeskey state of
+				Just keyfile -> go state keyfile
+				Nothing -> missingstate
+		Nothing -> missingstate
+  where
+	missingstate = giveup "Missing compute state"
+
+	go state keyfile = metered (Just meterupdate) k Nothing $ \_ p ->
+		runComputeProgram (ComputeProgram program) state
+			(ImmutableState True)
+			(getinputcontent state)
+			(Just (k, p))
+			(postcompute keyfile)
+
+	getinputcontent state f =
+		case M.lookup f (computeInputs state) of
+			Just inputkey -> case keyGitSha inputkey of
+				Nothing -> 
+					let retkey = do
+						obj <- calcRepo (gitAnnexLocation inputkey)
+						return (inputkey, Just (Right obj))
+					in ifM (inAnnex inputkey)
+						( retkey
+						, ifM (getinputcontent' f inputkey)
+							( retkey
+							, return (inputkey, Nothing)
+							)
+						)
+				Just gitsha ->
+					return (inputkey, Just (Left gitsha))
+			Nothing -> error "internal"
+	
+	getinputcontent' f inputkey = do
+		remotes <- avoidCycles [k] inputkey
+			=<< keyPossibilities inputkey
+		anyM (getinputcontentfrom f inputkey) remotes
+	
+	getinputcontentfrom f inputkey r = do
+		showAction $ "getting input " <> QuotedPath f
+			<> " from " <> UnquotedString (name r)
+		lu <- prepareLiveUpdate Nothing inputkey AddingKey
+		logStatusAfter lu inputkey $
+			Annex.Transfer.download r inputkey (AssociatedFile (Just f))
+				Annex.Transfer.stdRetry Annex.Transfer.noNotification
+
+	computeskey state = 
+		case M.keys $ M.filter (== Just k) (computeOutputs state) of
+			(keyfile : _) -> Just keyfile
+			[] -> Nothing
+
+	postcompute keyfile result tmpdir _ts
+		| computeInputsUnavailable result = 
+			giveup "Input file(s) unavailable."
+		| otherwise =
+			postcompute' keyfile (computeState result) tmpdir
+
+	postcompute' keyfile state tmpdir = do
+		hb <- hashBackend
+		let updatevurl key getobj = 
+			if (fromKey keyVariety key == VURLKey)
+				then addEquivilantKey hb key =<< getobj
+				else return Nothing
+
+		let keyfile' = tmpdir </> keyfile
+		unlessM (liftIO $ doesFileExist keyfile') $
+			giveup $ program ++ " exited sucessfully, but failed to write the computed file"
+		catchNonAsync (liftIO $ moveFile keyfile' dest)
+			(\err -> giveup $ "failed to move the computed file: " ++ show err)
+		mverification <- updatevurl k (pure dest)
+
+		-- Try to move any other computed object files into the annex.
+		forM_ (M.toList $ computeOutputs state) $ \case
+			(file, (Just key)) ->
+				when (k /= key) $ do
+					let file' = tmpdir </> file
+					whenM (liftIO $ doesFileExist file') $ do
+						whenM (verifyKeyContentPostRetrieval RetrievalAllKeysSecure vc MustVerify key file') $ do
+							moved <- moveAnnex key file' `catchNonAsync` const (pure False)
+							when moved $
+								void $ updatevurl key (calcRepo (gitAnnexLocation key))
+			_ -> noop
+
+		-- The program might not be reproducible,
+		-- so require strong verification.
+		return $ fromMaybe MustVerify mverification
+		
+keyPossibilities :: Key -> Annex [Remote]
+keyPossibilities key = do
+	remotelist <- Annex.getState Annex.remotes
+	locs <- loggedLocations key
+	keyPossibilities' (IncludeIgnored False) key locs remotelist
+
+{- Filter out any remotes that, in order to compute the inputkey, would
+ - need to get the outputkey from some remote.
+ -
+ - This only finds cycles of compute special remotes, not any other
+ - similar type of special remote that might have its own input keys.
+ - There are no other such special remotes in git-annex itself, so this
+ - is the best that can be done.
+ -
+ - Note that, in a case where a compute special remote needs the outputkey
+ - to compute the inputkey, but could get the outputkey from either this
+ - remote, or some other, non-compute remote, that is filtered out as a
+ - cycle because it's not possible to prevent that remote getting from this
+ - remote.
+ -}
+avoidCycles :: [Key] -> Key -> [Remote] -> Annex [Remote]
+avoidCycles outputkeys inputkey = filterM go
+  where
+	go r
+		| iscomputeremote r = 
+			getComputeState (remoteStateHandle r) inputkey >>= \case
+				Nothing -> return True
+				Just state
+					| inputsoutput state -> return False
+					| otherwise -> checkdeeper state
+		| otherwise = return True
+	
+	iscomputeremote r = remotetype r == remote
+
+	inputsoutput state = not $ M.null $
+		M.filter (`elem` outputkeys)
+			(computeInputs state)
+	
+	checkdeeper state =
+		flip allM (M.elems (computeInputs state)) $ \inputkey' -> do
+			rs <- keyPossibilities inputkey'
+			rs' <- avoidCycles (inputkey:outputkeys) inputkey' rs
+			return (rs' == rs)
+
+-- Make sure that the compute state exists.
+checkKey :: RemoteStateHandle -> Key -> Annex Bool
+checkKey rs k = do
+	states <- getComputeStatesUnsorted rs k
+	if null states
+		then giveup "Missing compute state"
+		else return True
+
+-- Unsetting the compute state will prevent computing the key.
+dropKey :: RemoteStateHandle -> Maybe SafeDropProof -> Key -> Annex ()
+dropKey rs _ k = do
+	RemoteMetaData _ old <- getCurrentRemoteMetaData rs k
+	addRemoteMetaData k rs (modMeta old DelAllMeta)
+
+storeKeyUnsupported :: Key -> AssociatedFile -> Maybe OsPath -> MeterUpdate -> Annex ()
+storeKeyUnsupported _ _ _ _ = giveup "transfer to compute remote not supported; use git-annex addcomputed instead"

Remote/Git.hs

@@ -682,7 +682,7 @@ copyToRemote' repo r st@(State connpool duc _ _ _) key af o meterupdate
 				let checksuccess = liftIO checkio >>= \case
 					Just err -> giveup err
 					Nothing -> return True
-				logStatusAfter NoLiveUpdate key $ Annex.Content.getViaTmp rsp verify key af (Just sz) $ \dest ->
+				logStatusAfter NoLiveUpdate key $ Annex.Content.getViaTmp rsp verify key (Just sz) $ \dest ->
 					metered (Just (combineMeterUpdate meterupdate p)) key bwlimit $ \_ p' -> 
 						copier object dest key p' checksuccess verify
 			)

Remote/List.hs

@@ -40,6 +40,7 @@ import qualified Remote.Borg
 import qualified Remote.Rclone
 import qualified Remote.Hook
 import qualified Remote.External
+import qualified Remote.Compute
 
 remoteTypes :: [RemoteType]
 remoteTypes = map adjustExportImportRemoteType
@@ -63,6 +64,7 @@ remoteTypes = map adjustExportImportRemoteType
 	, Remote.Rclone.remote
 	, Remote.Hook.remote
 	, Remote.External.remote
+	, Remote.Compute.remote
 	]
 
 {- Builds a list of all Remotes.

Remote/List/Util.hs

@@ -1,6 +1,6 @@
 {- git-annex remote list utils
  -
- - Copyright 2011-2020 Joey Hess <id@joeyh.name>
+ - Copyright 2011-2025 Joey Hess <id@joeyh.name>
  -
  - Licensed under the GNU AGPL version 3 or higher.
  -}
@@ -10,6 +10,11 @@ module Remote.List.Util where
 import Annex.Common
 import qualified Annex
 import qualified Git.Config
+import Annex.UUID
+import Types.Remote
+import Config.DynamicConfig
+
+import Data.Ord
 
 {- Call when remotes have changed. Re-reads the git config, and
  - invalidates the cache so the remoteList will be re-generated next time
@@ -22,3 +27,44 @@ remotesChanged = do
 		, Annex.gitremotes = Nothing
 		, Annex.repo = newg
 		}
+
+{- Whether to include remotes that have annex-ignore set. -}
+newtype IncludeIgnored = IncludeIgnored Bool
+
+keyPossibilities'
+	:: IncludeIgnored
+	-> Key
+	-> [UUID]
+	-- ^ uuids of remotes that are recorded to have the key
+	-> [Remote]
+	-- ^ all remotes
+	-> Annex [Remote]
+keyPossibilities' ii _key remotelocations rs = do
+	u <- getUUID
+	let locations = filter (/= u) remotelocations
+	let speclocations = map uuid
+		$ filter (remoteAnnexSpeculatePresent . gitconfig) rs
+	-- there are unlikely to be many speclocations, so building a Set
+	-- is not worth the expense
+	let locations' = speclocations ++ filter (`notElem` speclocations) locations
+	fst <$> remoteLocations' ii locations' [] rs
+
+remoteLocations' :: IncludeIgnored -> [UUID] -> [UUID] -> [Remote] -> Annex ([Remote], [UUID])
+remoteLocations' (IncludeIgnored ii) locations trusted rs = do
+	let validtrustedlocations = nub locations `intersect` trusted
+
+	-- remotes that match uuids that have the key
+	allremotes <- if not ii
+			then filterM (not <$$> liftIO . getDynamicConfig . remoteAnnexIgnore . gitconfig) rs
+			else return rs
+	let validremotes = remotesWithUUID allremotes locations
+
+	return (sortBy (comparing cost) validremotes, validtrustedlocations)
+
+{- Filters a list of remotes to ones that have the listed uuids. -}
+remotesWithUUID :: [Remote] -> [UUID] -> [Remote]
+remotesWithUUID rs us = filter (\r -> uuid r `elem` us) rs
+
+{- Filters a list of remotes to ones that do not have the listed uuids. -}
+remotesWithoutUUID :: [Remote] -> [UUID] -> [Remote]
+remotesWithoutUUID rs us = filter (\r -> uuid r `notElem` us) rs

Remote/Web.hs

@@ -30,7 +30,6 @@ import Annex.SpecialRemote.Config
 import Logs.Remote
 import Logs.EquivilantKeys
 import Backend
-import Backend.VURL.Utilities (generateEquivilantKey)
 
 import qualified Data.Map as M
 
@@ -169,18 +168,8 @@ downloadKey urlincludeexclude key _af dest p vc =
 		| otherwise = return (Just v)
 	
 	recordvurlkey eks = do
-		-- Make sure to pick a backend that is cryptographically
+		b <- hashBackend
-		-- secure.
+		updateEquivilantKeys b dest key eks
-		db <- defaultBackend
-		let b = if isCryptographicallySecure db
-			then db
-			else defaultHashBackend
-		generateEquivilantKey b dest >>= \case
-			Nothing -> return Nothing
-			Just ek -> do
-				unless (ek `elem` eks) $
-					setEquivilantKey key ek
-				return (Just Verified)
 
 uploadKey :: Key -> AssociatedFile -> Maybe OsPath -> MeterUpdate -> Annex ()
 uploadKey _ _ _ _ = giveup "upload to web not supported"

Types/GitConfig.hs

@@ -146,6 +146,7 @@ data GitConfig = GitConfig
 	, annexAllowedUrlSchemes :: S.Set Scheme
 	, annexAllowedIPAddresses :: String
 	, annexAllowUnverifiedDownloads :: Bool
+	, annexAllowedComputePrograms :: Maybe String
 	, annexMaxExtensionLength :: Maybe Int
 	, annexMaxExtensions :: Maybe Int
 	, annexJobs :: Concurrency
@@ -261,6 +262,8 @@ extractGitConfig configsource r = GitConfig
 		getmaybe (annexConfig "security.allowed-http-addresses") -- old name
 	, annexAllowUnverifiedDownloads = (== Just "ACKTHPPT") $
 		getmaybe (annexConfig "security.allow-unverified-downloads")
+	, annexAllowedComputePrograms =
+		getmaybe (annexConfig "security.allowed-compute-programs")
 	, annexMaxExtensionLength = getmayberead (annexConfig "maxextensionlength")
 	, annexMaxExtensions = getmayberead (annexConfig "maxextensions")
 	, annexJobs = fromMaybe NonConcurrent $ 

Upgrade/V0.hs

@@ -25,8 +25,7 @@ upgrade = do
 	olddir <- fromRepo gitAnnexDir
 	keys <- getKeysPresent0 olddir
 	forM_ keys $ \k ->
-		moveAnnex k (AssociatedFile Nothing)
+		moveAnnex k (olddir </> toOsPath (keyFile0 k))
-			(olddir </> toOsPath (keyFile0 k))
 
 	-- update the symlinks to the key files
 	-- No longer needed here; V1.upgrade does the same thing

Upgrade/V1.hs

@@ -85,7 +85,7 @@ moveContent = do
 		let d = parentDir f
 		liftIO $ allowWrite d
 		liftIO $ allowWrite f
-		_ <- moveAnnex k (AssociatedFile Nothing) f
+		_ <- moveAnnex k f
 		liftIO $ removeDirectory d
 
 updateSymlinks :: Annex ()

doc/design/compute_special_remote_interface.mdwn

@@ -23,14 +23,17 @@ that is in the form "foo=bar" will also result in an environment variable
 being set, eg `ANNEX_COMPUTE_passes=10` or `ANNEX_COMPUTE_--level=9`.
 
 For security, the program should avoid exposing user input to the shell
-unprotected, or otherwise executing it.
+unprotected, or otherwise executing it. And when running a command, make
+sure that whatever user input is passed to it can result in only safe and
+expected behavior.
 
 The program is run in a temporary directory, which will be cleaned up after
-it exits.
+it exits. Note that it may be run in a subdirectory of a temporary
+directory. This is done when `git-annex addcomputed` was run in a subdirectory
+of the git repository.
 
-The content of any annexed file in the repository can be an input
+The content of any file in the repository can be an input to the
-to the computation. The program requests an input by writing a line to
+computation. The program requests an input by writing a line to stdout:
-stdout:
 
     INPUT file.raw
 
@@ -38,8 +41,8 @@ Then it can read a line from stdin, which will be the path to the content
 (eg a `.git/annex/objects/` path).
 
 If the program needs multiple input files, it should output multiple
-`INPUT` lines at once, and then read multiple paths from stdin. This
+`INPUT` lines first, and then read multiple paths from stdin. This
-allows retrival of the inputs to potentially run in parallel.
+allows retrieval of the inputs to potentially run in parallel.
 
 If an input file is not available, the program's stdin will be closed
 without a path being written to it. So when reading from stdin fails, 
@@ -90,16 +93,17 @@ An example `git-annex-compute-foo` shell script follows:
     #!/bin/sh
     set -e
     if [ "$1" != "convert" ]; then
-        echo "Usage: convert input output [passes=n]" >&2
+    	echo "Usage: convert input output [passes=n]" >&2
-        exit 1
+     	exit 1
     fi
-    if [ -z "$ANNEX_COMPUTE_passes" ];
+    if [ -z "$ANNEX_COMPUTE_passes" ]; then
-        ANNEX_COMPUTE_passes=1
+    	ANNEX_COMPUTE_passes=1
     fi
-    echo "INPUT "$2"
+    echo "INPUT $2"
     read input
     echo "OUTPUT $3"
     echo REPRODUCIBLE
     if [ -n "$input" ]; then
-       frobnicate --passes="$ANNEX_COMPUTE_passes" <"$input" >"$3"
+        mkdir -p "$(dirname "$3")"
+        frobnicate --passes="$ANNEX_COMPUTE_passes" <"$input" >"$3"
     fi

doc/git-annex-addcomputed.mdwn

@@ -0,0 +1,103 @@
+# NAME
+
+git-annex addcomputed - adds computed files to the repository
+
+# SYNOPSIS
+
+git annex addcomputed `--to=remote -- ...`
+
+# DESCRIPTION
+
+Adds files to the annex that are computed from input files in the
+repository, using a compute special remote.
+
+Once a file has been added to a compute remote, commands
+like `git-annex get` will use it to compute the content of the file.
+
+The syntax of this command after the `--` is up to the program that
+the compute special remote is set up to run to perform the comuptation.
+
+To see the program's usage, you can run:
+
+    git-annex addcomputed --to=foo
+
+Generally you will provide an input file (or files), and often also an
+output filename, and additional parameters to control the computation.
+
+There can be more than one input file that are combined to compute an
+output file. And multiple output files can be computed at the same time.
+
+Some examples of how this might look:
+
+    git-annex addcomputed --to=x -- convert file.raw file.jpeg passes=10
+    git-annex addcomputed --to=y -- compress foo --level=9
+    git-annex addcomputed --to=z -- clip foo 2:01-3:00 combine with bar to baz
+
+Note that parameters that were passed to `git-annex initremote` 
+when setting up the compute special remote will be appended to the end of
+the parameters provided to `git-annex addcomputed`.
+
+# OPTIONS
+
+* `--to=remote`
+
+  Specify which remote will compute the files. 
+
+  This must be a compute remote. For example, one can be
+  initialized with:
+
+    git-annex initremote photoconv type=compute \
+        program=git-annex-compute-photoconv
+
+  For details about compute remotes, and a list of some
+  of the programs that are available, see
+  <https://git-annex.branchable.com/special_remotes/compute/>
+
+* `--fast`
+
+  Adds computed files to the repository, without doing any work yet to
+  compute their content.
+
+  This implies `--unreproducible`, because even if the compute remote
+  produces reproducible output, it's not available.
+
+* `--unreproducible`, `-u`
+
+  Indicate that the computation is not expected to be fully reproducible.
+  It can vary, in ways that produce files that equivilant enough to
+  be interchangeable, but are not necessarily identical.
+
+  This is the default unless the compute remote indicates that it produces
+  reproducible output.
+
+* `--reproducible`, `-r`
+
+  Indicate that the computation is expected to be fully reproducible.
+
+  This is the default when the compute remote indicates that it produces
+  reproducible output (except when using `--fast`).
+
+  If a computation turns out not to be fully reproducible, then getting
+  a computed file from the compute remote will later fail with a
+  checksum verification error. One thing that can be done then is to use 
+  `git-annex recompute --original --unreproducible`.
+
+* `--backend`
+
+  Specifies which key-value backend to use.
+
+*  Also the [[git-annex-common-options]](1) can be used.
+
+# SEE ALSO
+
+[[git-annex]](1)
+
+[[git-annex-recompute]](1)
+
+[[git-annex-initremote]](1)
+
+# AUTHOR
+
+Joey Hess <id@joeyh.name>
+
+Warning: Automatically converted into a man page by mdwn2man. Edit with care.

doc/git-annex-initremote.mdwn

@@ -52,7 +52,7 @@ want to use `git annex renameremote`.
 
 	git annex initremote mys3 type=S3 --whatelse
 
-  For a machine-readable list of the parameters, use this with --json.
+  For a machine-readable list of the parameters, use this with `--json`.
 
 * `--fast`
 

doc/git-annex-recompute.mdwn

@@ -0,0 +1,69 @@
+# NAME
+
+git-annex recompute - recompute computed files
+
+# SYNOPSIS
+
+git-annex recompute [path ...]`
+
+# DESCRIPTION
+
+This updates computed files that were added with
+[[git-annex-addcomputed]](1). 
+
+By default, this only recomputes files whose input files have changed.
+The new contents of the input files are used to re-run the computation.
+
+When the output of the computation is different, the computed file is
+updated with the new content. The updated file is written to the worktree,
+but is not staged, in order to avoid overwriting any staged changes.
+
+# OPTIONS
+
+* `--original`
+
+  Re-run the computation with the original input files.
+
+* `--remote=name`
+
+  Only recompute files that were computed by this compute remote.
+
+  When this option is not used, all computed files are recomputed using
+  whatever compute remote was originally used to add them. (In cases where
+  a file can be computed by multiple remotes, the one with the lowest
+  configured cost is used.)
+
+* `--unreproducible`, `-u`
+
+  Indicate that the computation is not expected to be fully reproducible.
+  It can vary, in ways that produce files that equivilant enough to
+  be interchangeable, but are not necessarily identical.
+
+  This is the default unless the compute remote indicates that it produces
+  reproducible output.
+
+* `--reproducible`, `-r`
+
+  Indicate that the computation is expected to be fully reproducible.
+
+  This is the default when the compute remote indicates that it produces
+  reproducible output.
+
+* matching options
+
+  The [[git-annex-matching-options]](1) can be used to control what
+  files to recompute.
+
+*  Also the [[git-annex-common-options]](1) can be used.
+
+# SEE ALSO
+
+[[git-annex]](1)
+
+[[git-annex-addcomputed]](1)
+
+# AUTHOR
+
+Joey Hess <id@joeyh.name>
+
+Warning: Automatically converted into a man page by mdwn2man. Edit with care.

doc/git-annex.mdwn

@@ -186,6 +186,18 @@ content from the key-value store.
   
   See [[git-annex-undo]](1) for details.
 
+* `addcomputed`
+
+  Adds computed files to the repository.
+
+  See [[git-annex-addcomputed]](1) for details.
+
+* `recompute`
+
+  Recomputes computed files.
+
+  See [[git-annex-recompute]](1) for details.
+
 * `multicast`
 
   Multicast file distribution.
@@ -1945,6 +1957,11 @@ Remotes are configured using these settings in `.git/config`.
   the location of the borg repository to use. Normally this is automatically
   set up by `git annex initremote`, but you can change it if needed.
 
+* `remote.<name>.annex-compute`
+  
+  Used to identify compute special remotes.
+  Normally this is automatically set up by `git annex initremote`.
+
 * `remote.<name>.annex-ddarrepo`
 
   Used by ddar special remotes, this configures
@@ -2184,6 +2201,13 @@ Remotes are configured using these settings in `.git/config`.
 
   Per-remote configuration of annex.security.allow-unverified-downloads.
 
+* `annex.security.allowed-compute-programs`
+
+  This is a space separated list of compute programs eg
+  "git-annex-compute-foo git-annex-compute-bar". Listing a compute
+  program here allows compute special remotes that use that program to be
+  enabled by `git-annex enableremote` or autoenabled.
+
 # CONFIGURATION OF ASSISTANT
 
 * `annex.delayadd`

doc/special_remotes.mdwn

@@ -11,6 +11,7 @@ the content of files.
 * [[Amazon_Glacier|glacier]]
 * [[bittorrent]]
 * [[bup]]
+* [[compute]]
 * [[ddar]]
 * [[directory]]
 * [[gcrypt]] (encrypted git repositories!)

doc/special_remotes/compute.mdwn

@@ -0,0 +1,37 @@
+While other remotes store the contents of annexed files somewhere,
+this special remote uses a program to compute the contents of annexed
+files.
+
+To add a file to a compute special remote, use the [[git-annex-addcomputed]]
+command. Once a file has been added to a compute special remote, commands
+like `git-annex get` will use it to compute the content of the file.
+
+To enable an instance of this special remote:
+
+    # git-annex initremote myremote type=compute program=git-annex-compute-foo
+
+The `program` parameter is the only required parameter. It is the name of the
+program to use to compute the contents of annexed files. It must start with
+"git-annex-compute-". The program needs to be installed somewhere in the
+`PATH`.
+
+Any program can be passed to `git-annex initremote`. However, when enabling
+a compute special remote later with `git-annex enableremote` or due to
+"autoenable=true", the program must be listed in the git config
+`annex.security.allowed-compute-programs`.
+
+All other "field=value" parameters passed to `initremote` will be passed
+to the program when running [[git-annex-addcomputed]]. Note that when the
+program takes a dashed option, it can be provided after "--":
+
+    # git-annex initremote myremote type=compute program=git-annex-compute-foo -- --level=9
+
+## compute programs
+
+To write programs used by the compute special remote, see the 
+[[design/compute_special_remote_interface]].
+
+Have you written a generally useful (and secure) compute program?
+List it here!
+
+* ...

doc/todo/compute_special_remote/comment_21_2546562f7a00e082cd0500debc904cf3._comment

@@ -0,0 +1,22 @@
+[[!comment format=mdwn
+ username="joey"
+ subject="""Re: DataLad exploration of the compute on demand space"""
+ date="2025-03-06T17:39:04Z"
+ content="""
+Thanks for explaining the design points of datalad-remake. Some
+different design choices than I have made, but mostly they strike me as
+implementing what is easier/possible from outside git-annex. 
+
+Eg, storing the compute inputs under `.datalad` in the branch is fine --
+and might even be useful if you want to make a branch that changes
+something in there -- but of course in the git-annex implementation it
+stores the equvilant thing in the git-annex branch.
+
+I do hope I'm not closing off the design space from such differences
+by dropping a compute special remote right into git-annex. But I also
+expect that having a standard and easy way for at least simple
+computations will lead to a lot of contributions as others use it.
+
+Your fMRI case seems like one that my compute remote could handle well
+and easily.
+"""]]

doc/todo/compute_special_remote/comment_22_d1561153a3916411ed8caa92fa53893c._comment

@@ -0,0 +1,69 @@
+[[!comment format=mdwn
+ username="joey"
+ subject="""comment 22"""
+ date="2025-03-06T17:54:50Z"
+ content="""
+I've merged the compute special remote now.
+See [[special_remotes/compute]], [[git-annex-addcomputed]]
+and [[git-annex-recompute]].
+
+I have opened [[todo/compute_special_remote_remaining_todos]] with
+some various ways that I want to improve it further. Including, notably,
+computing on inputs from submodules, which is not currently supported at
+all.
+
+----
+
+Here I'll go down mih's original and quite useful design criteria and see
+how the compute special remote applies to them:
+
+### Generate annex keys (that have never existed)
+
+`git-annex addcomputed --fast`
+
+### Re-generate annex keys
+
+`git-annex addcomputed` optionally with the --reproducible option,
+followed by a later `git-annex get`
+
+Another thing that fits under this heading is when one of the original
+input files has gotten modified, and you want to compute a new version of
+the output file from it, using the same method as was used to compute it
+before. That's `git-annex recompute $output_file`
+
+### Worktree provisioning?
+
+This is the main thing I didn't implement. Given that git-annex is working
+with large files and needs to support various filesystems and OS's that
+lack hardlinks and softlinks, it's hard to do this inexpensively.
+
+Also, it turned out to make sense for the compute program to request
+the input files it needs, since this lets git-annex learn what the input
+files are, so it can make them available when regenerating a computed file
+later. And so the protocol just has git-annex respond with the path to
+the content of the file.
+
+### Request one key, receive many
+
+This is supported. (So is using multiple inputs to produce one (or more)
+outputs.)
+
+### Instruction deposition
+
+`git-annex addcomputed`
+
+### Storage redundancy tests
+
+It did make sense to have it automatically `git-annex get` the inputs.
+Well, I think it makes sense in most cases, this may become a tunable
+setting of the compute special remote.
+
+### Trust
+
+Handled by requiring the user install a `git-annex-compute-foo` command
+in PATH, and provide the name of the command to `initremote`.
+
+And for later `enableremote` or `autoenable=true`, it will only
+allow programs that are listed in the annex.security.allowed-compute-programs
+git config.
+"""]]

doc/todo/compute_special_remote_remaining_todos.mdwn

@@ -0,0 +1,69 @@
+This is the remainder of my todo list while I was building the
+compute special remote. --[[Joey]]
+
+* write a tip showing how to use this
+
+* Write some simple compute programs so we have something to start with.
+
+  - convert between images eg jpeg to png
+  - run a command in a singularity container (that is one of the inputs)
+  - run a wasm binary (that is one of the inputs)
+
+* compute on input files in submodules
+
+* annex.diskreserve can be violated if getting a file computes it but also
+  some other output files, which get added to the annex.
+
+* would be nice to have a way to see what computations are used by a
+  compute remote for a file. Put it in `whereis` output? But it's not an
+  url. Maybe a separate command? That would also allow querying for eg,
+  what files are inputs for another file. Or it could be exposed in the
+  Remote interface, and made into a file matching option.
+
+* "getting input from <file>" message uses the original filename,
+  but that file might have been renamed. Would be more clear to use
+  whatever file in the tree currently points to the key it's getting
+  (what if there is not one?)
+
+* allow git-annex enableremote with program= explicitly specified,
+  without checking annex.security.allowed-compute-programs
+
+* addcomputed should honor annex.addunlocked.
+
+  What about recompute? It seems it should either write the new version of
+  the file as an unlocked file when the old version was unlocked, or also
+  honor annex.addunlocked.
+  
+  Problem: Since recompute does not stage the file, it would have to write
+  the content to the working tree. And then the user would need to
+  git-annex add. But then, if the key was a VURL key, it would add it with
+  the default backend instead, and the file would no longer use a computed
+  key. 
+
+  So it, seems that, for this to be done, recompute would need to stage the
+  pointer file.
+
+* recompute could ingest keys for other files than the one being
+  recomputed, and remember them. Then recomputing those files could just
+  use those keys, without re-running a computation. (Better than --others
+  which got removed.)
+
+* `git-annex recompute foo bar baz`, when foo depends on bar which depends
+  on baz, and when baz has changed, will not recompute foo, because bar has
+  not changed. It then recomputes bar. So running the command again is
+  needed to recompute foo. 
+
+  What it could do is, after it recomputes bar, notice that it already
+  considered foo, and revisit foo, and recompute it then. It could either
+  use a bloom filter to remember the files it considered but did not
+  compute, or it could just notice that the command line includes foo
+  (or includes a directory that contains foo), and then foo is not
+  modified.
+
+  Or it could build a DAG and traverse it, but building a DAG of a large
+  directory tree has its own problems.
+
+* Should addcomputed honor annex.smallfiles? That would seem to imply
+  that recompute should also support recomputing non-annexed files.
+  Otherwise, adding a file and then recomputing it would vary in
+  what the content of the file is, depending on annex.smallfiles setting.

git-annex.cabal

@@ -562,6 +562,7 @@ Executable git-annex
     Annex.FileMatcher
     Annex.Fixup
     Annex.GitOverlay
+    Annex.GitShaKey
     Annex.HashObject
     Annex.Hook
     Annex.Import
@@ -654,6 +655,7 @@ Executable git-annex
     CmdLine.Usage
     Command
     Command.Add
+    Command.AddComputed
     Command.AddUnused
     Command.AddUrl
     Command.Adjust
@@ -727,6 +729,7 @@ Executable git-annex
     Command.Proxy
     Command.Pull
     Command.Push
+    Command.Recompute
     Command.ReKey
     Command.ReadPresentKey
     Command.RecvKey
@@ -930,6 +933,7 @@ Executable git-annex
     Remote.BitTorrent
     Remote.Borg
     Remote.Bup
+    Remote.Compute
     Remote.Ddar
     Remote.Directory
     Remote.Directory.LegacyChunked