Adds support to open local repositories and to use file-based object storage (#55)v3.1.0

* remove some comments

* idx writer/reader

* Shut up ssh tests, they are annoying

* Add file scheme test to clients

* Add dummy file client

* Add test fot file client

* Make tests use fixture endpoint

* add parser for packed-refs format

* add parser for packed-refs format

* WIP adding dir.Refs() tests

* Add test for fixture refs

* refs parser for the refs directory

* Documentation

* Add Capabilities to file client

* tgz.Exatract now accpets a path instead of a Reader

* fix bug in idxfile fanout calculation

* remove dead code

* packfile documentation

* clean packfile parser code

* add core.Object.Content() and returns errors for core.ObjectStorage.Iter()

* add seekable storage

* add dir repos to NewRepository

* clean prints

* Add dir client documentation to README

* Organize the README

* README

* Clean tgz package

* Clean temp dirs after tgz tests

* Gometalinter on gitdir

* Clean pattern function

* metalinter tgz

* metalinter gitdir

* gitdir coverage and remove seekable packfile filedescriptor leak

* gitdir Idxfile tests and remove file descriptor leak

* gitdir Idxfile tests when no idx is found

* clean storage/seekable/internal/index and some formats/idxfile API issues

* clean storage/seekable

* clean formats/idx

* turn packfile/doc.go into packfile/doc.txt

* move formats/packfile/reader to decoder

* fix packfile decoder error names

* improve documentation

* comment packfile decoder errors

* comment public API (format/packfile)

* remve duplicated code in packfile decoder test

* move tracking_reader into an internal package and clean it

* use iota for packfile format

* rename packfile parse.go to packfile object_at.go

* clean packfile deltas

* fix delta header size bug

* improve delta documentation

* clean packfile deltas

* clean packfiles deltas

* clean repository.go

* Remove go 1.5 from Travis CI

Because go 1.5 does not suport internal packages.

* change local repo scheme to local://

* change "local://" to "file://" as the local scheme

* fix broken indentation

* shortens names of variables in short scopes

* more shortening of variable names

* more shortening of variable names

* Rename git dir client to "file", as the scheme used for it

* Fix file format ctor name, now that the package name has change

* Sortcut local repo constructor to not use remotes

The object storage is build directly in the repository ctor, instead
of creating a remote and waiting for the user to pull it.

* update README and fix some errors in it

* remove file scheme client

* Local respositories has now a new ctor

This is, they are no longer identified by the scheme of the URL, but are
created different from inception.

* remove unused URL field form Repository

* move all git dir logic to seekable sotrage ctor

* fix documentation

* Make formats/file/dir an internal package to storage/seekable

* change package storage/seekable to storage/fs

* clean storage/fs

* overall storage/fs clean

* more cleaning

* some metalinter fixes

* upgrade cshared to last changes

* remove dead code

* fix test error info

* remove file scheme check from clients

* fix test error message

* fix test error message

* fix error messages

* style changes

* fix comments everywhere

* style changes

* style changes

* scaffolding and tests for local packfiles without ifx files

* outsource index building from packfile to the packfile decoder

* refactor packfile header reading into a new function

* move code to generate index from packfile back to index package

* add header parsing

* fix documentation errata

* add undeltified and OFS delta support for index building from the packfile

* add tests for packfile with ref-deltas

* support for packfiles with ref-deltas and no idx

* refactor packfile format parser to reuse code

* refactor packfile format parser to reuse code

* refactor packfile format parser to reuse code

* refactor packfile format parser to reuse code

* refactor packfile format parser to reuse code

* WIP refactor packfile format parser to reuse code

* refactor packfile format parser to reuse code

* remove prints from tests

* remove prints from tests

* refactor packfile.core into packfile.parser

* rename packfile reader to something that shows it is a recaller

* rename cannot recall error

* rename packfile.Reader to packfile.ReadRecaller and document

* speed up test by using StreamReader instead of SeekableReader when possible

* clean packfile StreamReader

* stream_reader tests

* refactor packfile.StreamReader into packfile.StreamReadRecaller

* refactor packfile.SeekableReader into packfile.SeekableReadRecaller and document it

* generalize packfile.StreamReadRecaller test to all packfile.ReadRecaller implementations

* speed up storage/fs tests

* speed up tests in . by loading packfiles in memory

* speed up repository tests by using and smaller fixture

* restore doc.go files

* rename packfile.ReadRecaller implementations to shorter names

* update comments to type changes

* packfile.Parser test (WIP)

* packfile.Parser tests and add ForgetAll() to packfile.ReadRecaller

* add test for packfile.ReadRecaller.ForgetAll()

* clarify seekable being able to recallByOffset forgetted objects

* use better names for internal maps

* metalinter packfile package

* speed up some tests

* documentation fixes

* change storage.fs package name to storage.proxy to avoid confusion with new filesystem support

* New fs package and os transparent implementation

Now NewRepositoryFromFS receives a fs and a path and tests are
modified accordingly, but it is still not using for anything.

* add fs to gitdir and proxy.store

* reduce fs interface for easier implementation

* remove garbage dirs from tgz tests

* change file name gitdir/dir.go to gitdir/gitdir.go

* fs.OS tests

* metalinter utils/fs

* add NewRepositoryFromFS documentation to README

* Readability fixes to README

* move tgz to an external dependency

* move filesystem impl. example to example dir

* rename proxy/store.go to proxy/storage.go for coherence with memory/storage.go

* rename proxy package to seekable

1 files changed, 116 insertions, 0 deletions

diff --git a/formats/packfile/decoder.go b/formats/packfile/decoder.go
new file mode 100644
index 0000000..e8c5c6a
--- /dev/null
+++ b/formats/packfile/decoder.go
@@ -0,0 +1,116 @@
+package packfile
+
+import (
+	"io"
+
+	"gopkg.in/src-d/go-git.v3/core"
+)
+
+// Format specifies if the packfile uses ref-deltas or ofs-deltas.
+type Format int
+
+// Possible values of the Format type.
+const (
+	UnknownFormat Format = iota
+	OFSDeltaFormat
+	REFDeltaFormat
+)
+
+var (
+	// ErrMaxObjectsLimitReached is returned by Decode when the number
+	// of objects in the packfile is higher than
+	// Decoder.MaxObjectsLimit.
+	ErrMaxObjectsLimitReached = NewError("max. objects limit reached")
+
+	// ErrInvalidObject is returned by Decode when an invalid object is
+	// found in the packfile.
+	ErrInvalidObject = NewError("invalid git object")
+
+	// ErrPackEntryNotFound is returned by Decode when a reference in
+	// the packfile references and unknown object.
+	ErrPackEntryNotFound = NewError("can't find a pack entry")
+
+	// ErrZLib is returned by Decode when there was an error unzipping
+	// the packfile contents.
+	ErrZLib = NewError("zlib reading error")
+)
+
+const (
+	// DefaultMaxObjectsLimit is the maximum amount of objects the
+	// decoder will decode before returning ErrMaxObjectsLimitReached.
+	DefaultMaxObjectsLimit = 1 << 20
+)
+
+// Decoder reads and decodes packfiles from an input stream.
+type Decoder struct {
+	// MaxObjectsLimit is the limit of objects to be load in the packfile, if
+	// a packfile excess this number an error is throw, the default value
+	// is defined by DefaultMaxObjectsLimit, usually the default limit is more
+	// than enough to work with any repository, with higher values and huge
+	// repositories you can run out of memory.
+	MaxObjectsLimit uint32
+
+	p *Parser
+	s core.ObjectStorage
+}
+
+// NewDecoder returns a new Decoder that reads from r.
+func NewDecoder(r ReadRecaller) *Decoder {
+	return &Decoder{
+		MaxObjectsLimit: DefaultMaxObjectsLimit,
+
+		p: NewParser(r),
+	}
+}
+
+// Decode reads a packfile and stores it in the value pointed to by s.
+func (d *Decoder) Decode(s core.ObjectStorage) error {
+	d.s = s
+
+	count, err := d.p.ReadHeader()
+	if err != nil {
+		return err
+	}
+
+	if count > d.MaxObjectsLimit {
+		return ErrMaxObjectsLimitReached.AddDetails("%d", count)
+	}
+
+	err = d.readObjects(count)
+
+	return err
+}
+
+func (d *Decoder) readObjects(count uint32) error {
+	// This code has 50-80 µs of overhead per object not counting zlib inflation.
+	// Together with zlib inflation, it's 400-410 µs for small objects.
+	// That's 1 sec for ~2450 objects, ~4.20 MB, or ~250 ms per MB,
+	// of which 12-20 % is _not_ zlib inflation (ie. is our code).
+	for i := 0; i < int(count); i++ {
+		start, err := d.p.Offset()
+		if err != nil {
+			return err
+		}
+
+		obj, err := d.p.ReadObject()
+		if err != nil {
+			if err == io.EOF {
+				break
+			}
+
+			return err
+		}
+
+		err = d.p.Remember(start, obj)
+		if err != nil {
+			return err
+		}
+
+		_, err = d.s.Set(obj)
+		if err == io.EOF {
+			break
+		}
+	}
+
+	return nil
+}