Merge pull request #217 from DrDaveD/pick-sylabs-2.15.1

Update to sylabs/sif 2.15.1

go.mod

@@ -3,7 +3,7 @@ module github.com/apptainer/sif/v2
 go 1.20
 
 require (
-	github.com/ProtonMail/go-crypto v0.0.0-20230717121422-5aa5874ade95
+	github.com/ProtonMail/go-crypto v0.0.0-20230923063757-afb1ddc0824c
 	github.com/google/go-containerregistry v0.17.0
 	github.com/google/uuid v1.5.0
 	github.com/sebdah/goldie/v2 v2.5.3

go.sum

@@ -1,5 +1,5 @@
-github.com/ProtonMail/go-crypto v0.0.0-20230717121422-5aa5874ade95 h1:KLq8BE0KwCL+mmXnjLWEAOYO+2l2AE4YMmqG1ZpZHBs=
-github.com/ProtonMail/go-crypto v0.0.0-20230717121422-5aa5874ade95/go.mod h1:EjAoLdwvbIOoOQr3ihjnSoLZRtE8azugULFRteWMNc0=
+github.com/ProtonMail/go-crypto v0.0.0-20230923063757-afb1ddc0824c h1:kMFnB0vCcX7IL/m9Y5LO+KQYv+t1CQOiFe6+SV2J7bE=
+github.com/ProtonMail/go-crypto v0.0.0-20230923063757-afb1ddc0824c/go.mod h1:EjAoLdwvbIOoOQr3ihjnSoLZRtE8azugULFRteWMNc0=
 github.com/beorn7/perks v1.0.1 h1:VlbKKnNfV8bJzeqoa4cOKqO6bYr3WgKZxO8Z16+hsOM=
 github.com/bwesterb/go-ristretto v1.2.3/go.mod h1:fUIoIZaG73pV5biE2Blr2xEzDoMj7NFEuV9ekS419A0=
 github.com/cespare/xxhash/v2 v2.2.0 h1:DC2CZ1Ep5Y4k3ZQ899DldepgrayRUGE6BBZ/cd9Cj44=

pkg/sif/create.go

@@ -326,51 +326,6 @@ func CreateContainerAtPath(path string, opts ...CreateOpt) (*FileImage, error) {
 	return f, nil
 }
 
-func zeroData(fimg *FileImage, descr *rawDescriptor) error {
-	// first, move to data object offset
-	if _, err := fimg.rw.Seek(descr.Offset, io.SeekStart); err != nil {
-		return err
-	}
-
-	var zero [4096]byte
-	n := descr.Size
-	upbound := int64(4096)
-	for {
-		if n < 4096 {
-			upbound = n
-		}
-
-		if _, err := fimg.rw.Write(zero[:upbound]); err != nil {
-			return err
-		}
-		n -= 4096
-		if n <= 0 {
-			break
-		}
-	}
-
-	return nil
-}
-
-func resetDescriptor(fimg *FileImage, index int) error {
-	// If we remove the primary partition, set the global header Arch field to HdrArchUnknown
-	// to indicate that the SIF file doesn't include a primary partition and no dependency
-	// on any architecture exists.
-	if fimg.rds[index].isPartitionOfType(PartPrimSys) {
-		fimg.h.Arch = hdrArchUnknown
-	}
-
-	offset := fimg.h.DescriptorsOffset + int64(index)*int64(binary.Size(fimg.rds[0]))
-
-	// first, move to descriptor offset
-	if _, err := fimg.rw.Seek(offset, io.SeekStart); err != nil {
-		return err
-	}
-
-	var emptyDesc rawDescriptor
-	return binary.Write(fimg.rw, binary.LittleEndian, emptyDesc)
-}
-
 // addOpts accumulates object add options.
 type addOpts struct {
 	t time.Time
@@ -452,6 +407,26 @@ func (f *FileImage) isLast(d *rawDescriptor) bool {
 	return isLast
 }
 
+// zeroReader is an io.Reader that returns a stream of zero-bytes.
+type zeroReader struct{}
+
+func (zeroReader) Read(b []byte) (int, error) {
+	for i := range b {
+		b[i] = 0
+	}
+	return len(b), nil
+}
+
+// zero overwrites the data object described by d with a stream of zero bytes.
+func (f *FileImage) zero(d *rawDescriptor) error {
+	if _, err := f.rw.Seek(d.Offset, io.SeekStart); err != nil {
+		return err
+	}
+
+	_, err := io.CopyN(f.rw, zeroReader{}, d.Size)
+	return err
+}
+
 // truncateAt truncates f at the start of the padded data object described by d.
 func (f *FileImage) truncateAt(d *rawDescriptor) error {
 	start := d.Offset + d.Size - d.SizeWithPadding
@@ -535,7 +510,7 @@ func (f *FileImage) DeleteObject(id uint32, opts ...DeleteOpt) error {
 	}
 
 	if do.zero {
-		if err := zeroData(f, d); err != nil {
+		if err := f.zero(d); err != nil {
 			return fmt.Errorf("%w", err)
 		}
 	}
@@ -551,15 +526,17 @@ func (f *FileImage) DeleteObject(id uint32, opts ...DeleteOpt) error {
 	f.h.DescriptorsFree++
 	f.h.ModifiedAt = do.t.Unix()
 
-	index := 0
-	for i, od := range f.rds {
-		if od.ID == id {
-			index = i
-			break
-		}
+	// If we remove the primary partition, set the global header Arch field to HdrArchUnknown
+	// to indicate that the SIF file doesn't include a primary partition and no dependency
+	// on any architecture exists.
+	if d.isPartitionOfType(PartPrimSys) {
+		f.h.Arch = hdrArchUnknown
 	}
 
-	if err := resetDescriptor(f, index); err != nil {
+	// Reset rawDescripter with empty struct
+	*d = rawDescriptor{}
+
+	if err := f.writeDescriptors(); err != nil {
 		return fmt.Errorf("%w", err)
 	}
 

pkg/sif/create_test.go

@@ -552,6 +552,69 @@ func TestDeleteObject(t *testing.T) {
 	}
 }
 
+func TestDeleteObjectAndAddObject(t *testing.T) {
+	tests := []struct {
+		name string
+		id   uint32
+		opts []DeleteOpt
+	}{
+		{
+			name: "Compact",
+			id:   2,
+			opts: []DeleteOpt{
+				OptDeleteCompact(true),
+			},
+		},
+		{
+			name: "NoCompact",
+			id:   2,
+		},
+		{
+			name: "Zero",
+			id:   2,
+			opts: []DeleteOpt{
+				OptDeleteZero(true),
+			},
+		},
+		{
+			name: "ZeroCompact",
+			id:   2,
+			opts: []DeleteOpt{
+				OptDeleteZero(true),
+				OptDeleteCompact(true),
+			},
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			var b Buffer
+
+			f, err := CreateContainer(&b,
+				OptCreateDeterministic(),
+				OptCreateWithDescriptors(
+					getDescriptorInput(t, DataGeneric, []byte("abc")),
+					getDescriptorInput(t, DataGeneric, []byte("def")),
+				),
+			)
+			if err != nil {
+				t.Fatal(err)
+			}
+
+			if err := f.DeleteObject(tt.id, tt.opts...); err != nil {
+				t.Fatal(err)
+			}
+
+			if err := f.AddObject(getDescriptorInput(t, DataGeneric, []byte("ghi"))); err != nil {
+				t.Fatal(err)
+			}
+
+			g := goldie.New(t, goldie.WithTestNameForDir(true))
+			g.Assert(t, tt.name, b.Bytes())
+		})
+	}
+}
+
 func TestSetPrimPart(t *testing.T) {
 	tests := []struct {
 		name       string

pkg/siftool/siftool.go

@@ -80,10 +80,5 @@ func AddCommands(cmd *cobra.Command, opts ...CommandOpt) error {
 		c.getSetPrim(),
 	)
 
-	if c.opts.experimental {
-		cmd.AddCommand(c.getMount())
-		cmd.AddCommand(c.getUnmount())
-	}
-
 	return nil
 }

pkg/siftool/siftool_test.go

@@ -55,6 +55,7 @@ func makeTestSIF(t *testing.T, withDataObject bool) string {
 	return tf.Name()
 }
 
+//nolint:unparam
 func runCommand(t *testing.T, cmd *cobra.Command, args []string, wantErr error) {
 	t.Helper()
 
@@ -123,11 +124,6 @@ func TestAddCommands(t *testing.T) {
 			name: "SetPrim",
 			args: []string{"help", "setprim"},
 		},
-		{
-			name: "Mount",
-			opts: []CommandOpt{OptWithExperimental(true)},
-			args: []string{"help", "mount"},
-		},
 	}
 	for _, tt := range tests {
 		t.Run(tt.name, func(t *testing.T) {