Repository: apptainer/apptainer

Issue:
Update yaml package source
`gopkg.in/yaml.v2` and `gopkg.in/yaml.v3` are not supported anymore.  There's a maintained fork at `github.com/yaml/go-yaml`, we should switch to it.  The preferred reference is `go.yaml.in/yaml/v3` for v3.

Hints from issue comments:
@afbjorklund: There is a go.yaml.in/yaml/v4 now (in RC), both v2 and v3 have been "frozen"

https://github.com/yaml/go-yaml#version-intentions

Solution patch:
diff --git a/LICENSE_DEPENDENCIES.md b/LICENSE_DEPENDENCIES.md
index bfc6cc5a0..c8e35a43a 100644
--- a/LICENSE_DEPENDENCIES.md
+++ b/LICENSE_DEPENDENCIES.md
@@ -16239,6 +16239,217 @@ For more information, please refer to <http://unlicense.org/>
 ```
 
 
+## go.yaml.in/yaml/v4
+
+**License:** Apache-2.0
+
+```
+
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+      by You to the Licensor shall be under the terms and conditions of
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+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
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+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for reasonable and customary use in describing the
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+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
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+      To apply the Apache License to your work, attach the following
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+
+   Copyright 2025 - The go-yaml Project Contributors
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
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+
+```
+
+
 ## golang.org/x/crypto
 
 **License:** BSD-3-Clause
diff --git a/go.mod b/go.mod
index 8d703d809..88bec28ca 100644
--- a/go.mod
+++ b/go.mod
@@ -46,11 +46,11 @@ require (
 	github.com/spf13/pflag v1.0.10
 	github.com/sylabs/json-resp v0.9.5
 	github.com/vbauerster/mpb/v8 v8.11.2
+	go.yaml.in/yaml/v4 v4.0.0-rc.3
 	golang.org/x/crypto v0.45.0
 	golang.org/x/sys v0.38.0
 	golang.org/x/term v0.37.0
 	golang.org/x/text v0.31.0
-	gopkg.in/yaml.v3 v3.0.1
 	gotest.tools/v3 v3.5.2
 	mvdan.cc/sh/v3 v3.12.0
 )
@@ -65,7 +65,6 @@ require (
 	github.com/moby/sys/userns v0.1.0
 	github.com/samber/lo v1.52.0
 	github.com/sirupsen/logrus v1.9.3
-	gopkg.in/yaml.v2 v2.4.0
 )
 
 require (
@@ -172,7 +171,14 @@ require (
 	google.golang.org/genproto/googleapis/rpc v0.0.0-20250313205543-e70fdf4c4cb4 // indirect
 	google.golang.org/grpc v1.72.2 // indirect
 	google.golang.org/protobuf v1.36.10 // indirect
+	gopkg.in/yaml.v2 v2.4.0 // indirect
+	gopkg.in/yaml.v3 v3.0.1 // indirect
 	sigs.k8s.io/knftables v0.0.18 // indirect
 )
 
+replace (
+	gopkg.in/yaml.v2 => go.yaml.in/yaml/v2 v2.4.0
+	gopkg.in/yaml.v3 => go.yaml.in/yaml/v3 v3.0.1
+)
+
 replace oras.land/oras-go => github.com/sylabs/oras-go v1.2.4-0.20230628133146-a64659fc0454
diff --git a/go.sum b/go.sum
index 32bc3aab9..37b0f44fe 100644
--- a/go.sum
+++ b/go.sum
@@ -471,8 +471,14 @@ go.opentelemetry.io/proto/otlp v1.3.1 h1:TrMUixzpM0yuc/znrFTP9MMRh8trP93mkCiDVeX
 go.opentelemetry.io/proto/otlp v1.3.1/go.mod h1:0X1WI4de4ZsLrrJNLAQbFeLCm3T7yBkR0XqQ7niQU+8=
 go.uber.org/automaxprocs v1.6.0 h1:O3y2/QNTOdbF+e/dpXNNW7Rx2hZ4sTIPyybbxyNqTUs=
 go.uber.org/automaxprocs v1.6.0/go.mod h1:ifeIMSnPZuznNm6jmdzmU3/bfk01Fe2fotchwEFJ8r8=
+go.yaml.in/yaml/v2 v2.4.0 h1:1wUho2rqHvQlbIzGvWDqpyuGtd8ClFDJx7sxsblGvig=
+go.yaml.in/yaml/v2 v2.4.0/go.mod h1:RDklbk79AGWmwhnvt/jBztapEOGDOx6ZbXqjP6csGnQ=
+go.yaml.in/yaml/v3 v3.0.1 h1:XDp0bdmK8yhjHY72LqCnqEpEHMlIZgqKewnYfT7YV/U=
+go.yaml.in/yaml/v3 v3.0.1/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM=
 go.yaml.in/yaml/v3 v3.0.4 h1:tfq32ie2Jv2UxXFdLJdh3jXuOzWiL1fo0bu/FbuKpbc=
 go.yaml.in/yaml/v3 v3.0.4/go.mod h1:DhzuOOF2ATzADvBadXxruRBLzYTpT36CKvDb3+aBEFg=
+go.yaml.in/yaml/v4 v4.0.0-rc.3 h1:3h1fjsh1CTAPjW7q/EMe+C8shx5d8ctzZTrLcs/j8Go=
+go.yaml.in/yaml/v4 v4.0.0-rc.3/go.mod h1:aZqd9kCMsGL7AuUv/m/PvWLdg5sjJsZ4oHDEnfPPfY0=
 golang.org/x/crypto v0.0.0-20180904163835-0709b304e793/go.mod h1:6SG95UA2DQfeDnfUPMdvaQW0Q7yPrPDi9nlGo2tz2b4=
 golang.org/x/crypto v0.0.0-20190308221718-c2843e01d9a2/go.mod h1:djNgcEr1/C05ACkg1iLfiJU5Ep61QUkGW8qpdssI0+w=
 golang.org/x/crypto v0.0.0-20190426145343-a29dc8fdc734/go.mod h1:yigFU9vqHzYiE8UmvKecakEJjdnWj3jj499lnFckfCI=
@@ -604,14 +610,6 @@ gopkg.in/check.v1 v1.0.0-20201130134442-10cb98267c6c h1:Hei/4ADfdWqJk1ZMxUNpqntN
 gopkg.in/check.v1 v1.0.0-20201130134442-10cb98267c6c/go.mod h1:JHkPIbrfpd72SG/EVd6muEfDQjcINNoR0C8j2r3qZ4Q=
 gopkg.in/fsnotify.v1 v1.4.7/go.mod h1:Tz8NjZHkW78fSQdbUxIjBTcgA1z1m8ZHf0WmKUhAMys=
 gopkg.in/tomb.v1 v1.0.0-20141024135613-dd632973f1e7/go.mod h1:dt/ZhP58zS4L8KSrWDmTeBkI65Dw0HsyUHuEVlX15mw=
-gopkg.in/yaml.v2 v2.2.1/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI=
-gopkg.in/yaml.v2 v2.2.2/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI=
-gopkg.in/yaml.v2 v2.4.0 h1:D8xgwECY7CYvx+Y2n4sBz93Jn9JRvxdiyyo8CTfuKaY=
-gopkg.in/yaml.v2 v2.4.0/go.mod h1:RDklbk79AGWmwhnvt/jBztapEOGDOx6ZbXqjP6csGnQ=
-gopkg.in/yaml.v3 v3.0.0-20200313102051-9f266ea9e77c/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM=
-gopkg.in/yaml.v3 v3.0.0-20200605160147-a5ece683394c/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM=
-gopkg.in/yaml.v3 v3.0.1 h1:fxVm/GzAzEWqLHuvctI91KS9hhNmmWOoWu0XTYJS7CA=
-gopkg.in/yaml.v3 v3.0.1/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM=
 gotest.tools/v3 v3.5.2 h1:7koQfIKdy+I8UTetycgUqXWSDwpgv193Ka+qRsmBY8Q=
 gotest.tools/v3 v3.5.2/go.mod h1:LtdLGcnqToBH83WByAAi/wiwSFCArdFIUV/xxN4pcjA=
 mvdan.cc/sh/v3 v3.12.0 h1:ejKUR7ONP5bb+UGHGEG/k9V5+pRVIyD+LsZz7o8KHrI=
diff --git a/internal/pkg/checkpoint/dmtcp/dmtcp.go b/internal/pkg/checkpoint/dmtcp/dmtcp.go
index 30d2440fe..acb74587e 100644
--- a/internal/pkg/checkpoint/dmtcp/dmtcp.go
+++ b/internal/pkg/checkpoint/dmtcp/dmtcp.go
@@ -18,7 +18,7 @@ import (
 	"github.com/apptainer/apptainer/internal/pkg/checkpoint"
 	"github.com/apptainer/apptainer/internal/pkg/util/paths"
 	"github.com/apptainer/apptainer/pkg/sylog"
-	"gopkg.in/yaml.v2"
+	"go.yaml.in/yaml/v4"
 )
 
 const (
diff --git a/internal/pkg/remote/remote.go b/internal/pkg/remote/remote.go
index 0ad0a959c..316386afa 100644
--- a/internal/pkg/remote/remote.go
+++ b/internal/pkg/remote/remote.go
@@ -24,7 +24,7 @@ import (
 	remoteutil "github.com/apptainer/apptainer/internal/pkg/remote/util"
 	"github.com/apptainer/apptainer/pkg/syfs"
 	"github.com/apptainer/apptainer/pkg/sylog"
-	"gopkg.in/yaml.v3"
+	"go.yaml.in/yaml/v4"
 )
 
 // ErrNoDefault indicates no default remote being set
diff --git a/mconfig b/mconfig
index 5ed371346..202d0bcc1 100755
--- a/mconfig
+++ b/mconfig
@@ -893,7 +893,7 @@ if [ "$host" = "unix" ]; then
 		while IFS='' read -r REPLY; do
 			if [ "$REPLY" = "@BUNDLED_PROVIDES@" ]; then
 				# Calculate bundled provides
-				awk '{if (index($1, "/") != 0 && ($1 != "//")) {print "Provides: bundled(golang("$1")) = "$2}}' go.mod | sed -e 's/-/_/g' | sort | uniq
+				awk '{if (index($1, "/") != 0 && ($1 != "//") && ($2 != "=>")) {print "Provides: bundled(golang("$1")) = "$2}}' go.mod | sed -e 's/-/_/g' | sort | uniq
 			else
 				echo "$REPLY"
 			fi



Test patch:
diff --git a/internal/app/apptainer/remote_add_test.go b/internal/app/apptainer/remote_add_test.go
index b719791fe..e110da38c 100644
--- a/internal/app/apptainer/remote_add_test.go
+++ b/internal/app/apptainer/remote_add_test.go
@@ -17,7 +17,7 @@ import (
 	"github.com/apptainer/apptainer/internal/pkg/remote"
 	"github.com/apptainer/apptainer/internal/pkg/remote/endpoint"
 	"github.com/apptainer/apptainer/internal/pkg/test"
-	"gopkg.in/yaml.v3"
+	"go.yaml.in/yaml/v4"
 )
 
 const (
diff --git a/internal/pkg/remote/remote_test.go b/internal/pkg/remote/remote_test.go
index 52f2a5627..68b9f9231 100644
--- a/internal/pkg/remote/remote_test.go
+++ b/internal/pkg/remote/remote_test.go
@@ -19,7 +19,7 @@ import (
 
 	"github.com/apptainer/apptainer/internal/pkg/remote/endpoint"
 	useragent "github.com/apptainer/apptainer/pkg/util/user-agent"
-	"gopkg.in/yaml.v3"
+	"go.yaml.in/yaml/v4"
 )
 
 // #nosec G101