Fix CLI not working with monorepos

cmd/deepsource/main.go

@@ -73,21 +73,24 @@ func mainRun() (exitCode int) {
 func run() int {
 	v.SetBuildInfo(version, Date, buildMode)
 
-	// Check for available updates and notify (skip when running "update" itself)
+	// Notify about available updates from a previous check (instant, disk-only read).
+	// Then kick off a background check for the next invocation.
 	isUpdateCmd := len(os.Args) >= 2 && os.Args[1] == "update"
 	if !isUpdateCmd && update.ShouldCheckForUpdate() {
-		client := &http.Client{Timeout: 3 * time.Second}
-		if err := update.CheckForUpdate(client); err != nil {
-			debug.Log("update: %v", err)
-		}
-
 		state, err := update.ReadUpdateState()
 		if err != nil {
 			debug.Log("update: %v", err)
 		}
 		if state != nil {
-			fmt.Fprintln(os.Stderr, pterm.Yellow(fmt.Sprintf("Update available: v%s, run '%s update' to install.", state.Version, filepath.Base(os.Args[0]))))
+			fmt.Fprintln(os.Stderr, pterm.Yellow(fmt.Sprintf("Update available: v%s → v%s, run '%s update' to install.", version, state.Version, filepath.Base(os.Args[0]))))
 		}
+
+		go func() {
+			client := &http.Client{Timeout: 3 * time.Second}
+			if err := update.CheckForUpdate(client); err != nil {
+				debug.Log("update: %v", err)
+			}
+		}()
 	}
 
 	exitCode := 0

command/auth/login/pat_login_flow.go

@@ -9,7 +9,7 @@ import (
 	"github.com/fatih/color"
 )
 
-func (opts *LoginOptions) startPATLoginFlow(svc *authsvc.Service, cfg *config.CLIConfig, token string) error {
+func (_ *LoginOptions) startPATLoginFlow(svc *authsvc.Service, cfg *config.CLIConfig, token string) error {
 	cfg.Token = token
 
 	viewer, err := svc.GetViewer(context.Background(), cfg)

command/issues/issues.go

@@ -252,7 +252,7 @@ func (opts *IssuesOptions) Run(ctx context.Context, cmd *cobra.Command) error {
 	opts.client = client
 	opts.remote = remote
 
-	issuesList, err := opts.resolveIssues(ctx, client, remote)
+	issuesList, err := opts.resolveIssuesWithRetry(ctx, client, remote)
 	if err != nil {
 		return err
 	}
@@ -283,6 +283,41 @@ func (opts *IssuesOptions) Run(ctx context.Context, cmd *cobra.Command) error {
 	return nil
 }
 
+// resolveIssuesWithRetry calls resolveIssues and, for monorepos with an
+// auto-detected sub-repo path, progressively strips path segments on
+// "Repository does not exist" errors until a match is found.
+func (opts *IssuesOptions) resolveIssuesWithRetry(ctx context.Context, client *deepsource.Client, remote *vcs.RemoteData) ([]issues.Issue, error) {
+	issuesList, err := opts.resolveIssues(ctx, client, remote)
+	if err == nil {
+		return issuesList, nil
+	}
+
+	if strings.Contains(err.Error(), "This repository is a monorepo") {
+		return nil, fmt.Errorf("This is a monorepo. Use --repo to specify a sub-project.\n\nHint: %s", err.Error())
+	}
+
+	if !strings.Contains(err.Error(), "Repository does not exist") || remote.SubRepoSuffix == "" {
+		return nil, err
+	}
+
+	parts := strings.Split(remote.SubRepoSuffix, ":")
+	for len(parts) > 1 {
+		parts = parts[:len(parts)-1]
+		remote.SubRepoSuffix = strings.Join(parts, ":")
+		baseName := strings.SplitN(remote.RepoName, ":", 2)[0]
+		remote.RepoName = baseName + ":" + remote.SubRepoSuffix
+
+		issuesList, err = opts.resolveIssues(ctx, client, remote)
+		if err == nil {
+			return issuesList, nil
+		}
+		if !strings.Contains(err.Error(), "Repository does not exist") {
+			return nil, err
+		}
+	}
+	return nil, err
+}
+
 func (opts *IssuesOptions) resolveIssues(ctx context.Context, client *deepsource.Client, remote *vcs.RemoteData) ([]issues.Issue, error) {
 	serverFilters := opts.buildServerFilters()
 	prFilters := opts.buildPRFilters()
@@ -314,7 +349,11 @@ func (opts *IssuesOptions) resolveIssues(ctx context.Context, client *deepsource
 		case ab.PRNumber > 0:
 			opts.PRNumber = ab.PRNumber
 			opts.CommitOid = ab.CommitOid
-			issuesList, err = client.GetPRIssues(ctx, remote.Owner, remote.RepoName, remote.VCSProvider, ab.PRNumber, prFilters)
+			if ab.Fallback {
+				issuesList, err = client.GetRunIssuesFlat(ctx, ab.CommitOid, serverFilters)
+			} else {
+				issuesList, err = client.GetPRIssues(ctx, remote.Owner, remote.RepoName, remote.VCSProvider, ab.PRNumber, prFilters)
+			}
 		case ab.UseRepo:
 			issuesList, err = client.GetIssues(ctx, remote.Owner, remote.RepoName, remote.VCSProvider)
 		default:

command/issues/tests/golden_files/get_analysis_runs_pr_fallback_completed_response.json

@@ -0,0 +1,46 @@
+{
+  "repository": {
+    "analysisRuns": {
+      "edges": [
+        {
+          "node": {
+            "runUid": "run-uid-running-01",
+            "commitOid": "831701c7a1b2c3d4e5f6a7b8c9d0e1f2a3b4c5d6",
+            "branchName": "feature/new-auth",
+            "status": "RUNNING",
+            "createdAt": "2025-03-12T14:00:00Z",
+            "finishedAt": null,
+            "updatedAt": "2025-03-12T14:01:00Z",
+            "summary": {
+              "occurrencesIntroduced": 0,
+              "occurrencesResolved": 0,
+              "occurrencesSuppressed": 0
+            },
+            "reportCard": null
+          }
+        },
+        {
+          "node": {
+            "runUid": "run-uid-completed-01",
+            "commitOid": "862df9f2e3a4b5c6d7e8f9a0b1c2d3e4f5a6b7c8",
+            "branchName": "feature/new-auth",
+            "status": "SUCCESS",
+            "createdAt": "2025-03-12T12:00:00Z",
+            "finishedAt": "2025-03-12T12:05:00Z",
+            "updatedAt": "2025-03-12T12:05:00Z",
+            "summary": {
+              "occurrencesIntroduced": 2,
+              "occurrencesResolved": 0,
+              "occurrencesSuppressed": 0
+            },
+            "reportCard": null
+          }
+        }
+      ],
+      "pageInfo": {
+        "hasNextPage": false,
+        "endCursor": null
+      }
+    }
+  }
+}

command/issues/tests/golden_files/get_analysis_runs_pr_fallback_first_response.json

@@ -0,0 +1,29 @@
+{
+  "repository": {
+    "analysisRuns": {
+      "edges": [
+        {
+          "node": {
+            "runUid": "run-uid-running-01",
+            "commitOid": "831701c7a1b2c3d4e5f6a7b8c9d0e1f2a3b4c5d6",
+            "branchName": "feature/new-auth",
+            "status": "RUNNING",
+            "createdAt": "2025-03-12T14:00:00Z",
+            "finishedAt": null,
+            "updatedAt": "2025-03-12T14:01:00Z",
+            "summary": {
+              "occurrencesIntroduced": 0,
+              "occurrencesResolved": 0,
+              "occurrencesSuppressed": 0
+            },
+            "reportCard": null
+          }
+        }
+      ],
+      "pageInfo": {
+        "hasNextPage": false,
+        "endCursor": null
+      }
+    }
+  }
+}

command/issues/tests/issues_test.go

@@ -420,6 +420,104 @@ func TestIssuesMultipleFilters(t *testing.T) {
 	}
 }
 
+// TestIssuesPRFallbackUsesRunIssues verifies that when auto-branch resolution
+// detects a PR AND the current run is in-progress (fallback), the code fetches
+// issues via GetRunIssuesFlat (commit-scoped) instead of GetPRIssues.
+// Regression test for ticket #6884175.
+func TestIssuesPRFallbackUsesRunIssues(t *testing.T) {
+	cfgMgr := testutil.CreateTestConfigManager(t, "test-token", "deepsource.com", "test@example.com")
+
+	// Load golden files for the multi-step mock.
+	prFoundData, err := os.ReadFile(goldenPath("get_pr_by_branch_found_response.json"))
+	if err != nil {
+		t.Fatalf("failed to read PR golden file: %v", err)
+	}
+	runsFirstData, err := os.ReadFile(goldenPath("get_analysis_runs_pr_fallback_first_response.json"))
+	if err != nil {
+		t.Fatalf("failed to read first runs golden file: %v", err)
+	}
+	runsCompletedData, err := os.ReadFile(goldenPath("get_analysis_runs_pr_fallback_completed_response.json"))
+	if err != nil {
+		t.Fatalf("failed to read completed runs golden file: %v", err)
+	}
+	commitScopeData, err := os.ReadFile(goldenPath("commit_scope_response.json"))
+	if err != nil {
+		t.Fatalf("failed to read commit scope golden file: %v", err)
+	}
+
+	mock := graphqlclient.NewMockClient()
+	analysisRunsCalls := 0
+	mock.QueryFunc = func(_ context.Context, query string, _ map[string]any, result any) error {
+		switch {
+		case strings.Contains(query, "pullRequests("):
+			return json.Unmarshal(prFoundData, result)
+		case strings.Contains(query, "query GetAnalysisRuns("):
+			analysisRunsCalls++
+			if analysisRunsCalls == 1 {
+				// First call (ResolveLatestRunForBranch, limit=1): RUNNING run
+				return json.Unmarshal(runsFirstData, result)
+			}
+			// Second call (ResolveLatestCompletedRun, limit=10): RUNNING + SUCCESS
+			return json.Unmarshal(runsCompletedData, result)
+		case strings.Contains(query, "checks {"):
+			// GetRunIssuesFlat for the fallback commit
+			return json.Unmarshal(commitScopeData, result)
+		default:
+			t.Fatalf("unexpected query: %s", query)
+			return nil
+		}
+	}
+	client := deepsource.NewWithGraphQLClient(mock)
+
+	var buf bytes.Buffer
+	deps := &cmddeps.Deps{
+		Client:    client,
+		ConfigMgr: cfgMgr,
+		Stdout:    &buf,
+		BranchNameFunc: func() (string, error) {
+			return "feature/new-auth", nil
+		},
+		HasUnpushedCommitsFunc:    func() bool { return false },
+		HasUncommittedChangesFunc: func() bool { return false },
+	}
+
+	cmd := issuesCmd.NewCmdIssuesWithDeps(deps)
+	cmd.SetArgs([]string{"--repo", "gh/testowner/testrepo", "--output", "json"})
+
+	if err := cmd.Execute(); err != nil {
+		t.Fatalf("unexpected error: %v", err)
+	}
+
+	got := buf.String()
+
+	// Verify the fallback info message is present.
+	if !strings.Contains(got, "Analysis is running on commit") {
+		t.Errorf("expected fallback info message, got: %q", got)
+	}
+
+	// Extract the JSON array from the output (after the info message line).
+	// The JSON starts at the first '[' character.
+	jsonStart := strings.Index(got, "[")
+	if jsonStart < 0 {
+		t.Fatalf("no JSON array found in output: %s", got)
+	}
+
+	var issues []map[string]any
+	if err := json.Unmarshal([]byte(got[jsonStart:]), &issues); err != nil {
+		t.Fatalf("failed to parse JSON output: %v\nraw output: %s", err, got)
+	}
+
+	// Must NOT be empty — this was the bug.
+	if len(issues) == 0 {
+		t.Fatal("expected non-empty issues from fallback commit, got empty array")
+	}
+
+	// Verify we got the expected issues from commit_scope_response.json.
+	if issues[0]["issue_code"] != "GO-W1007" {
+		t.Errorf("expected first issue GO-W1007, got %v", issues[0]["issue_code"])
+	}
+}
+
 func TestIssuesRunInProgress(t *testing.T) {
 	cfgMgr := testutil.CreateTestConfigManager(t, "test-token", "deepsource.com", "test@example.com")
 	mock := testutil.MockQueryFunc(t, map[string]string{

command/update/update.go

@@ -3,10 +3,12 @@ package update
 import (
 	"fmt"
 	"net/http"
+	"runtime"
 	"time"
 
 	"github.com/deepsourcelabs/cli/buildinfo"
 	"github.com/deepsourcelabs/cli/internal/update"
+	"github.com/pterm/pterm"
 	"github.com/spf13/cobra"
 )
 
@@ -29,7 +31,7 @@ func runUpdate(cmd *cobra.Command) error {
 		return fmt.Errorf("checking for updates: %w", err)
 	}
 
-	state, err := update.ReadUpdateState()
+	state, err := update.PrepareUpdate()
 	if err != nil {
 		return fmt.Errorf("reading update state: %w", err)
 	}
@@ -40,17 +42,25 @@ func runUpdate(cmd *cobra.Command) error {
 		return nil
 	}
 
-	fmt.Fprintf(w, "Updating to v%s...\n", state.Version)
+	fmt.Fprintln(w, pterm.Green("✓")+" Platform: "+runtime.GOOS+"/"+runtime.GOARCH)
+	fmt.Fprintln(w, pterm.Green("✓")+" Version: v"+state.Version)
 
 	applyClient := &http.Client{Timeout: 30 * time.Second}
-	newVer, err := update.ApplyUpdate(applyClient)
+	data, err := update.DownloadUpdate(applyClient, state)
 	if err != nil {
-		return fmt.Errorf("applying update: %w", err)
+		return fmt.Errorf("downloading update: %w", err)
 	}
+	fmt.Fprintln(w, pterm.Green("✓")+" Downloaded")
 
-	if newVer != "" {
-		fmt.Fprintf(w, "Updated to v%s\n", newVer)
+	if err := update.VerifyUpdate(data, state); err != nil {
+		return fmt.Errorf("verifying update: %w", err)
 	}
+	fmt.Fprintln(w, pterm.Green("✓")+" Checksum verified")
+
+	if err := update.ExtractAndInstall(data, state.ArchiveURL); err != nil {
+		return fmt.Errorf("installing update: %w", err)
+	}
+	fmt.Fprintln(w, pterm.Green("✓")+" Installed")
 
 	return nil
 }

config/config.go

@@ -25,7 +25,7 @@ func (cfg *CLIConfig) SetTokenExpiry(str string) {
 	cfg.TokenExpiresIn = t.UTC()
 }
 
-func (cfg CLIConfig) IsExpired() bool {
+func (cfg *CLIConfig) IsExpired() bool {
 	if cfg.TokenExpiresIn.IsZero() {
 		return false
 	}

deepsource/issues/queries/pr_issues.go

@@ -35,6 +35,12 @@ const fetchPRIssuesQuery = `query GetPRIssues(
             category
             severity
             explanation
+            issue {
+              analyzer {
+                name
+                shortcode
+              }
+            }
           }
         }
         pageInfo {
@@ -77,6 +83,12 @@ type PRIssuesListResponse struct {
 						Category   string `json:"category"`
 						Severity   string `json:"severity"`
 						Explanation string `json:"explanation"`
+						Issue       *struct {
+							Analyzer struct {
+								Name      string `json:"name"`
+								Shortcode string `json:"shortcode"`
+							} `json:"analyzer"`
+						} `json:"issue"`
 					} `json:"node"`
 				} `json:"edges"`
 				PageInfo pagination.PageInfo `json:"pageInfo"`
@@ -139,6 +151,12 @@ func (r *PRIssuesListRequest) Do(ctx context.Context) ([]issues.Issue, error) {
 					},
 				},
 			}
+			if node.Issue != nil {
+				issue.Analyzer = issues.AnalyzerMeta{
+					Name:      node.Issue.Analyzer.Name,
+					Shortcode: node.Issue.Analyzer.Shortcode,
+				}
+			}
 			allIssues = append(allIssues, issue)
 		}