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.

Discussion:
@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
+
+```
+
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
+      control with that entity. For the purposes of this definition,
+      "control" means (i) the power, direct or indirect, to cause the
+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
+
+      "Source" form shall mean the preferred form for making modifications,
+      including but not limited to software source code, documentation
+      source, and configuration files.
+
+      "Object" form shall mean any form resulting from mechanical
+      transformation or translation of a Source form, including but
+      not limited to compiled object code, generated documentation,
+      and conversions to other media types.
+
+      "Work" shall mean the work of authorship, whether in Source or
+      Object form, made available under the License, as indicated by a
+      copyright notice that is included in or attached to the work
+      (an example is provided in the Appendix below).
+
+      "Derivative Works" shall mean any work, whether in Source or Object
+      form, that is based on (or derived from) the Work and for which the
+      editorial revisions, annotations, elaborations, or other modifications
+      represent, as a whole, an original work of authorship. For the purposes
+      of this License, Derivative Works shall not include works that remain
+      separable from, or merely link (or bind by name) to the interfaces of,
+      the Work and Derivative Works thereof.
+
+      "Contribution" shall mean any work of authorship, including
+      the original version of the Work and any modifications or additions
+      to that Work or Derivative Works thereof, that is intentionally
+      submitted to Licensor for inclusion in the Work by the copyright owner
+      or by an individual or Legal Entity authorized to submit on behalf of
+      the copyright owner. For the purposes of this definition, "submitted"
+      means any form of electronic, verbal, or written communication sent
+      to the Licensor or its representatives, including but not limited to
+      communication on electronic mailing lists, source code control systems,
+      and issue tracking systems that are managed by, or on behalf of, the
+      Licensor for the purpose of discussing and improving the Work, but
+      excluding communication that is conspicuously marked or otherwise
+      designated in writing by the copyright owner as "Not a Contribution."
+
+      "Contributor" shall mean Licensor and any individual or Legal Entity
+      on behalf of whom a Contribution has been received by Licensor and
+      subsequently incorporated within the Work.
+
+   2. Grant of Copyright License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      copyright license to reproduce, prepare Derivative Works of,
+      publicly display, publicly perform, sublicense, and distribute the
+      Work and such Derivative Works in Source or Object form.
+
+   3. Grant of Patent License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      (except as stated in this section) patent license to make, have made,
+      use, offer to sell, sell, import, and otherwise transfer the Work,
+      where such license applies only to those patent claims licensable
+      by such Contributor that are necessarily infringed by their
+      Contribution(s) alone or by combination of their Contribution(s)
+      with the Work to which such Contribution(s) was submitted. If You
+      institute patent litigation against any entity (including a
+      cross-claim or counterclaim in a lawsuit) alleging that the Work
+      or a Contribution incorporated within the Work constitutes direct
+      or contributory patent infringement, then any patent licenses
+      granted to You under this License for that Work shall terminate
+      as of the date such litigation is filed.
+
+   4. Redistribution. You may reproduce and distribute copies of the
+      Work or Derivative Works thereof in any medium, with or without
+      modifications, and in Source or Object form, provided that You
+      meet the following conditions:
+
+      (a) You must give any other recipients of the Work or
+          Derivative Works a copy of this License; and
+
+      (b) You must cause any modified files to carry prominent notices
+          stating that You changed the files; and
+
+      (c) You must retain, in the Source form of any Derivative Works
+          that You distribute, all copyright, patent, trademark, and
+          attribution notices from the Source form of the Work,
+          excluding those notices that do not pertain to any part of
+          the Derivative Works; and
+
+      (d) If the Work includes a "NOTICE" text file as part of its
+          distribution, then any Derivative Works that You distribute must
+          include a readable copy of the attribution notices contained
+          within such NOTICE file, excluding those notices that do not
+          pertain to any part of the Derivative Works, in at least one
+          of the following places: within a NOTICE text file distributed
+          as part of the Derivative Works; within the Source form or
+          documentation, if provided along with the Derivative Works; or,
+          within a display generated by the Derivative Works, if and
+          wherever such third-party notices normally appear. The contents
+          of the NOTICE file are for informational purposes only and
+          do not modify the License. You may add Your own attribution
+          notices within Derivative Works that You distribute, alongside
+          or as an addendum to the NOTICE text from the Work, provided
+          that such additional attribution notices cannot be construed
+          as modifying the License.
+
+      You may add Your own copyright statement to Your modifications and
+      may provide additional or different license terms and conditions
+      for use, reproduction, or distribution of Your modifications, or
+      for any such Derivative Works as a whole, provided Your use,
+      reproduction, and distribution of the Work otherwise complies with
+      the conditions stated in this License.
+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   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
+      origin of the Work and reproducing the content of the NOTICE file.
+
+   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,
+      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+      implied, including, without limitation, any warranties or conditions
+      of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+      PARTICULAR PURPOSE. You are solely responsible for determining the
+      appropriateness of using or redistributing the Work and assume any
+      risks associated with Your exercise of permissions under this License.
+
+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
+      incidental, or consequential damages of any character arising as a
+      result of this License or out of the use or inability to use the
+      Work (including but not limited to damages for loss of goodwill,
+      work stoppage, computer failure or malfunction, or any and all
+      other commercial damages or losses), even if such Contributor
+      has been advised of the possibility of such damages.
+
+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
+      or other liability obligations and/or rights consistent with this
+      License. However, in accepting such obligations, You may act only
+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
+      incurred by, or claims asserted against, such Contributor by reason
+      of your accepting any such warranty or additional liability.
+
+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "[]"
+      replaced with your own identifying information. (Don't include
+      the brackets!)  The text should be enclosed in the appropriate
+      comment syntax for the file format. We also recommend that a
+      file or class name and description of purpose be included on the
+      same "printed page" as the copyright notice for easier
+      identification within third-party archives.
+
+   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
+   limitations under the License.
+
+```
+
+
 ## 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