Upgrade go-github from v82 to v87 (#2452)

Breaking changes addressed:
- raw.NewClient: Use WithHTTPClient/WithEnterpriseURLs options, pass ctx to
  NewRequest, return (*Client, error)
- internal/ghmcp/server.go: Use functional options for REST client creation,
  replace UserAgent field mutation with UserAgentTransport wrapper, add
  restUATransp field to githubClients struct
- pkg/github/dependencies.go: Use functional options for REST client creation,
  handle raw.NewClient error return
- pkg/github/actions.go: Handle new WorkflowDispatchRunDetails return value
  from CreateWorkflowDispatchEventByID/ByFileName
- pkg/github/issues.go: Replace IssueListOptions with ListOptions for
  SubIssue.ListByIssue
- pkg/github/notifications.go: MarkThreadDone now takes string instead of
  int64; remove ParseInt and strconv import
- pkg/github/projects.go: Remove pointer indirection from
  ListProjectsPaginationOptions and ListProjectsOptions fields
- pkg/github/issues_granular.go: Pass ctx to NewRequest, remove ctx from Do
- Test files: Add mustNewGHClient helper, replace all NewClient calls,
  fix stubClientFnFromHTTP signature, fix lockdown_test.go BaseURL handling,
  fix raw_test.go, remove invalid threadID test case

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

Author: iulia-b

e2e/e2e_test.go

@@ -18,7 +18,7 @@ import (
 	"github.com/github/github-mcp-server/internal/ghmcp"
 	"github.com/github/github-mcp-server/pkg/github"
 	"github.com/github/github-mcp-server/pkg/translations"
-	gogithub "github.com/google/go-github/v82/github"
+	gogithub "github.com/google/go-github/v87/github"
 	"github.com/modelcontextprotocol/go-sdk/mcp"
 	"github.com/stretchr/testify/require"
 )

go.mod

@@ -5,7 +5,7 @@ go 1.25.0
 require (
 	github.com/go-chi/chi/v5 v5.2.5
 	github.com/go-viper/mapstructure/v2 v2.5.0
-	github.com/google/go-github/v82 v82.0.0
+	github.com/google/go-github/v87 v87.0.0
 	github.com/google/jsonschema-go v0.4.2
 	github.com/josephburnett/jd/v2 v2.5.0
 	github.com/lithammer/fuzzysearch v1.1.8

go.sum

@@ -16,8 +16,8 @@ github.com/golang-jwt/jwt/v5 v5.3.1/go.mod h1:fxCRLWMO43lRc8nhHWY6LGqRcf+1gQWArs
 github.com/google/go-cmp v0.6.0/go.mod h1:17dUlkBOakJ0+DkrSSNjCkIjxS6bF9zb3elmeNGIjoY=
 github.com/google/go-cmp v0.7.0 h1:wk8382ETsv4JYUZwIsn6YpYiWiBsYLSJiTsyBybVuN8=
 github.com/google/go-cmp v0.7.0/go.mod h1:pXiqmnSA92OHEEa9HXL2W4E7lf9JzCmGVUdgjX3N/iU=
-github.com/google/go-github/v82 v82.0.0 h1:OH09ESON2QwKCUVMYmMcVu1IFKFoaZHwqYaUtr/MVfk=
-github.com/google/go-github/v82 v82.0.0/go.mod h1:hQ6Xo0VKfL8RZ7z1hSfB4fvISg0QqHOqe9BP0qo+WvM=
+github.com/google/go-github/v87 v87.0.0 h1:9Ck3dcOxWJyfsN8tzdah4YvmqB/7ZsstMglv/PkOsl0=
+github.com/google/go-github/v87 v87.0.0/go.mod h1:hGUoT5pwm/ck5uLL+wroSVQfg8mpe+buxllCcGV4VaM=
 github.com/google/go-querystring v1.2.0 h1:yhqkPbu2/OH+V9BfpCVPZkNmUXhb2gBxJArfhIxNtP0=
 github.com/google/go-querystring v1.2.0/go.mod h1:8IFJqpSRITyJ8QhQ13bmbeMBDfmeEJZD5A0egEOmkqU=
 github.com/google/jsonschema-go v0.4.2 h1:tmrUohrwoLZZS/P3x7ex0WAVknEkBZM46iALbcqoRA8=

internal/ghmcp/server.go

@@ -24,18 +24,19 @@ import (
 	"github.com/github/github-mcp-server/pkg/scopes"
 	"github.com/github/github-mcp-server/pkg/translations"
 	"github.com/github/github-mcp-server/pkg/utils"
-	gogithub "github.com/google/go-github/v82/github"
+	gogithub "github.com/google/go-github/v87/github"
 	"github.com/modelcontextprotocol/go-sdk/mcp"
 	"github.com/shurcooL/githubv4"
 )
 
 // githubClients holds all the GitHub API clients created for a server instance.
 type githubClients struct {
-	rest       *gogithub.Client
-	gql        *githubv4.Client
-	gqlHTTP    *http.Client // retained for middleware to modify transport
-	raw        *raw.Client
-	repoAccess *lockdown.RepoAccessCache
+	rest         *gogithub.Client
+	restUATransp *transport.UserAgentTransport
+	gql          *githubv4.Client
+	gqlHTTP      *http.Client // retained for middleware to modify transport
+	raw          *raw.Client
+	repoAccess   *lockdown.RepoAccessCache
 }
 
 // createGitHubClients creates all the GitHub API clients needed by the server.
@@ -61,10 +62,18 @@ func createGitHubClients(cfg github.MCPServerConfig, apiHost utils.APIHostResolv
 	}
 
 	// Construct REST client
-	restClient := gogithub.NewClient(nil).WithAuthToken(cfg.Token)
-	restClient.UserAgent = fmt.Sprintf("github-mcp-server/%s", cfg.Version)
-	restClient.BaseURL = restURL
-	restClient.UploadURL = uploadURL
+	restUATransport := &transport.UserAgentTransport{
+		Transport: http.DefaultTransport,
+		Agent:     fmt.Sprintf("github-mcp-server/%s", cfg.Version),
+	}
+	restClient, err := gogithub.NewClient(
+		gogithub.WithHTTPClient(&http.Client{Transport: restUATransport}),
+		gogithub.WithAuthToken(cfg.Token),
+		gogithub.WithEnterpriseURLs(restURL.String(), uploadURL.String()),
+	)
+	if err != nil {
+		return nil, fmt.Errorf("failed to create REST client: %w", err)
+	}
 
 	// Construct GraphQL client
 	// We use NewEnterpriseClient unconditionally since we already parsed the API host
@@ -80,7 +89,10 @@ func createGitHubClients(cfg github.MCPServerConfig, apiHost utils.APIHostResolv
 	gqlClient := githubv4.NewEnterpriseClient(graphQLURL.String(), gqlHTTPClient)
 
 	// Create raw content client (shares REST client's HTTP transport)
-	rawClient := raw.NewClient(restClient, rawURL)
+	rawClient, err := raw.NewClient(restClient, rawURL)
+	if err != nil {
+		return nil, fmt.Errorf("failed to create raw client: %w", err)
+	}
 
 	// Set up repo access cache for lockdown mode
 	var repoAccessCache *lockdown.RepoAccessCache
@@ -95,11 +107,12 @@ func createGitHubClients(cfg github.MCPServerConfig, apiHost utils.APIHostResolv
 	}
 
 	return &githubClients{
-		rest:       restClient,
-		gql:        gqlClient,
-		gqlHTTP:    gqlHTTPClient,
-		raw:        rawClient,
-		repoAccess: repoAccessCache,
+		rest:         restClient,
+		restUATransp: restUATransport,
+		gql:          gqlClient,
+		gqlHTTP:      gqlHTTPClient,
+		raw:          rawClient,
+		repoAccess:   repoAccessCache,
 	}, nil
 }
 
@@ -170,7 +183,7 @@ func NewStdioMCPServer(ctx context.Context, cfg github.MCPServerConfig) (*mcp.Se
 		github.RegisterUIResources(ghServer)
 	}
 
-	ghServer.AddReceivingMiddleware(addUserAgentsMiddleware(cfg, clients.rest, clients.gqlHTTP))
+	ghServer.AddReceivingMiddleware(addUserAgentsMiddleware(cfg, clients.restUATransp, clients.gqlHTTP))
 
 	return ghServer, nil
 }
@@ -345,7 +358,7 @@ func createFeatureChecker(enabledFeatures []string, insidersMode bool) inventory
 	}
 }
 
-func addUserAgentsMiddleware(cfg github.MCPServerConfig, restClient *gogithub.Client, gqlHTTPClient *http.Client) func(next mcp.MethodHandler) mcp.MethodHandler {
+func addUserAgentsMiddleware(cfg github.MCPServerConfig, restUATransp *transport.UserAgentTransport, gqlHTTPClient *http.Client) func(next mcp.MethodHandler) mcp.MethodHandler {
 	return func(next mcp.MethodHandler) mcp.MethodHandler {
 		return func(ctx context.Context, method string, request mcp.Request) (result mcp.Result, err error) {
 			if method != "initialize" {
@@ -368,7 +381,7 @@ func addUserAgentsMiddleware(cfg github.MCPServerConfig, restClient *gogithub.Cl
 				userAgent += " (insiders)"
 			}
 
-			restClient.UserAgent = userAgent
+			restUATransp.Agent = userAgent
 
 			gqlHTTPClient.Transport = &transport.UserAgentTransport{
 				Transport: gqlHTTPClient.Transport,

pkg/errors/error.go

@@ -6,7 +6,7 @@ import (
 	"net/http"
 
 	"github.com/github/github-mcp-server/pkg/utils"
-	"github.com/google/go-github/v82/github"
+	"github.com/google/go-github/v87/github"
 	"github.com/modelcontextprotocol/go-sdk/mcp"
 )
 

pkg/errors/error_test.go

@@ -6,7 +6,7 @@ import (
 	"net/http"
 	"testing"
 
-	"github.com/google/go-github/v82/github"
+	"github.com/google/go-github/v87/github"
 	"github.com/stretchr/testify/assert"
 	"github.com/stretchr/testify/require"
 )

pkg/github/actions.go

@@ -16,7 +16,7 @@ import (
 	"github.com/github/github-mcp-server/pkg/scopes"
 	"github.com/github/github-mcp-server/pkg/translations"
 	"github.com/github/github-mcp-server/pkg/utils"
-	"github.com/google/go-github/v82/github"
+	"github.com/google/go-github/v87/github"
 	"github.com/google/jsonschema-go/jsonschema"
 	"github.com/modelcontextprotocol/go-sdk/mcp"
 )
@@ -989,10 +989,10 @@ func runWorkflow(ctx context.Context, client *github.Client, owner, repo, workfl
 	var workflowType string
 
 	if workflowIDInt, parseErr := strconv.ParseInt(workflowID, 10, 64); parseErr == nil {
-		resp, err = client.Actions.CreateWorkflowDispatchEventByID(ctx, owner, repo, workflowIDInt, event)
+		_, resp, err = client.Actions.CreateWorkflowDispatchEventByID(ctx, owner, repo, workflowIDInt, event)
 		workflowType = "workflow_id"
 	} else {
-		resp, err = client.Actions.CreateWorkflowDispatchEventByFileName(ctx, owner, repo, workflowID, event)
+		_, resp, err = client.Actions.CreateWorkflowDispatchEventByFileName(ctx, owner, repo, workflowID, event)
 		workflowType = "workflow_file"
 	}
 

pkg/github/actions_test.go

@@ -8,7 +8,7 @@ import (
 
 	"github.com/github/github-mcp-server/internal/toolsnaps"
 	"github.com/github/github-mcp-server/pkg/translations"
-	"github.com/google/go-github/v82/github"
+	"github.com/google/go-github/v87/github"
 	"github.com/google/jsonschema-go/jsonschema"
 	"github.com/stretchr/testify/assert"
 	"github.com/stretchr/testify/require"
@@ -86,7 +86,7 @@ func Test_ActionsList_ListWorkflows(t *testing.T) {
 
 	for _, tc := range tests {
 		t.Run(tc.name, func(t *testing.T) {
-			client := github.NewClient(tc.mockedClient)
+			client := mustNewGHClient(t, tc.mockedClient)
 			deps := BaseDeps{
 				Client: client,
 			}
@@ -136,7 +136,7 @@ func Test_ActionsList_ListWorkflowRuns(t *testing.T) {
 			}),
 		})
 
-		client := github.NewClient(mockedClient)
+		client := mustNewGHClient(t, mockedClient)
 		deps := BaseDeps{
 			Client: client,
 		}
@@ -185,7 +185,7 @@ func Test_ActionsList_ListWorkflowRuns(t *testing.T) {
 			}),
 		})
 
-		client := github.NewClient(mockedClient)
+		client := mustNewGHClient(t, mockedClient)
 		deps := BaseDeps{
 			Client: client,
 		}
@@ -241,7 +241,7 @@ func Test_ActionsGet_GetWorkflow(t *testing.T) {
 			}),
 		})
 
-		client := github.NewClient(mockedClient)
+		client := mustNewGHClient(t, mockedClient)
 		deps := BaseDeps{
 			Client: client,
 		}
@@ -284,7 +284,7 @@ func Test_ActionsGet_GetWorkflowRun(t *testing.T) {
 			}),
 		})
 
-		client := github.NewClient(mockedClient)
+		client := mustNewGHClient(t, mockedClient)
 		deps := BaseDeps{
 			Client: client,
 		}
@@ -412,7 +412,7 @@ func Test_ActionsRunTrigger_RunWorkflow(t *testing.T) {
 
 	for _, tc := range tests {
 		t.Run(tc.name, func(t *testing.T) {
-			client := github.NewClient(tc.mockedClient)
+			client := mustNewGHClient(t, tc.mockedClient)
 			deps := BaseDeps{
 				Client: client,
 			}
@@ -449,7 +449,7 @@ func Test_ActionsRunTrigger_CancelWorkflowRun(t *testing.T) {
 			}),
 		})
 
-		client := github.NewClient(mockedClient)
+		client := mustNewGHClient(t, mockedClient)
 		deps := BaseDeps{
 			Client: client,
 		}
@@ -480,7 +480,7 @@ func Test_ActionsRunTrigger_CancelWorkflowRun(t *testing.T) {
 			}),
 		})
 
-		client := github.NewClient(mockedClient)
+		client := mustNewGHClient(t, mockedClient)
 		deps := BaseDeps{
 			Client: client,
 		}
@@ -504,7 +504,7 @@ func Test_ActionsRunTrigger_CancelWorkflowRun(t *testing.T) {
 	t.Run("missing run_id for non-run_workflow methods", func(t *testing.T) {
 		mockedClient := MockHTTPClientWithHandlers(map[string]http.HandlerFunc{})
 
-		client := github.NewClient(mockedClient)
+		client := mustNewGHClient(t, mockedClient)
 		deps := BaseDeps{
 			Client: client,
 		}
@@ -556,7 +556,7 @@ func Test_ActionsGetJobLogs_SingleJob(t *testing.T) {
 			}),
 		})
 
-		client := github.NewClient(mockedClient)
+		client := mustNewGHClient(t, mockedClient)
 		deps := BaseDeps{
 			Client:            client,
 			ContentWindowSize: 5000,
@@ -618,7 +618,7 @@ func Test_ActionsGetJobLogs_FailedJobs(t *testing.T) {
 			}),
 		})
 
-		client := github.NewClient(mockedClient)
+		client := mustNewGHClient(t, mockedClient)
 		deps := BaseDeps{
 			Client:            client,
 			ContentWindowSize: 5000,
@@ -668,7 +668,7 @@ func Test_ActionsGetJobLogs_FailedJobs(t *testing.T) {
 			}),
 		})
 
-		client := github.NewClient(mockedClient)
+		client := mustNewGHClient(t, mockedClient)
 		deps := BaseDeps{
 			Client:            client,
 			ContentWindowSize: 5000,

pkg/github/code_scanning.go

@@ -11,7 +11,7 @@ import (
 	"github.com/github/github-mcp-server/pkg/scopes"
 	"github.com/github/github-mcp-server/pkg/translations"
 	"github.com/github/github-mcp-server/pkg/utils"
-	"github.com/google/go-github/v82/github"
+	"github.com/google/go-github/v87/github"
 	"github.com/google/jsonschema-go/jsonschema"
 	"github.com/modelcontextprotocol/go-sdk/mcp"
 )

pkg/github/code_scanning_test.go

@@ -8,7 +8,7 @@ import (
 
 	"github.com/github/github-mcp-server/internal/toolsnaps"
 	"github.com/github/github-mcp-server/pkg/translations"
-	"github.com/google/go-github/v82/github"
+	"github.com/google/go-github/v87/github"
 	"github.com/google/jsonschema-go/jsonschema"
 	"github.com/stretchr/testify/assert"
 	"github.com/stretchr/testify/require"
@@ -80,7 +80,7 @@ func Test_GetCodeScanningAlert(t *testing.T) {
 	for _, tc := range tests {
 		t.Run(tc.name, func(t *testing.T) {
 			// Setup client with mock
-			client := github.NewClient(tc.mockedClient)
+			client := mustNewGHClient(t, tc.mockedClient)
 			deps := BaseDeps{
 				Client: client,
 			}
@@ -206,7 +206,7 @@ func Test_ListCodeScanningAlerts(t *testing.T) {
 	for _, tc := range tests {
 		t.Run(tc.name, func(t *testing.T) {
 			// Setup client with mock
-			client := github.NewClient(tc.mockedClient)
+			client := mustNewGHClient(t, tc.mockedClient)
 			deps := BaseDeps{
 				Client: client,
 			}