Run go fmt

**What type of PR is this?**

Documentation

**What does this PR do? Why is it needed?**

Although godoc and comments are well-written in `encoding/ssz/query`
package, we (@rkapka, @fernantho, @syjn99)
[agreed](https://discord.com/channels/476244492043812875/1387734369527136297/1466075406523174944)
that it would be great to have human-readable documentation.

**Which issues(s) does this PR fix?**

Part of  #15587 & #15598 

**Other notes for review**

This documentation is first drafted by Claude Code, and then has a few
rounds of self-review.

**Acknowledgements**

- [x] I have read
[CONTRIBUTING.md](https://github.com/prysmaticlabs/prysm/blob/develop/CONTRIBUTING.md).
- [x] I have included a uniquely named [changelog fragment
file](https://github.com/prysmaticlabs/prysm/blob/develop/CONTRIBUTING.md#maintaining-changelogmd).
- [x] I have added a description with sufficient context for reviewers
to understand this PR.
- [ ] I have tested that my changes work as expected and I added a
testing plan to the PR description (if applicable).

---------

Co-authored-by: fernantho <fernantho1@gmail.com>
Co-authored-by: Radosław Kapka <radoslaw.kapka@gmail.com>

beacon-chain/db/kv/custody_test.go

@@ -67,7 +67,6 @@ func getSubscriptionStatusFromDB(t *testing.T, db *Store) bool {
 	return subscribed
 }
 
-
 func TestUpdateCustodyInfo(t *testing.T) {
 	ctx := t.Context()
 

beacon-chain/rpc/eth/beacon/handlers_pool_test.go

@@ -26,8 +26,8 @@ import (
 	"github.com/OffchainLabs/prysm/v7/beacon-chain/operations/voluntaryexits/mock"
 	p2pMock "github.com/OffchainLabs/prysm/v7/beacon-chain/p2p/testing"
 	"github.com/OffchainLabs/prysm/v7/beacon-chain/rpc/core"
-	mockSync "github.com/OffchainLabs/prysm/v7/beacon-chain/sync/initial-sync/testing"
 	state_native "github.com/OffchainLabs/prysm/v7/beacon-chain/state/state-native"
+	mockSync "github.com/OffchainLabs/prysm/v7/beacon-chain/sync/initial-sync/testing"
 	"github.com/OffchainLabs/prysm/v7/config/params"
 	"github.com/OffchainLabs/prysm/v7/consensus-types/primitives"
 	"github.com/OffchainLabs/prysm/v7/crypto/bls"

beacon-chain/verification/data_column_test.go

@@ -1027,10 +1027,10 @@ func TestGetVerifyingStateEdgeCases(t *testing.T) {
 				sc: signatureCache,
 				sr: &mockStateByRooter{sbr: sbrErrorIfCalled(t)}, // Should not be called
 				hsp: &mockHeadStateProvider{
-					headRoot: parentRoot[:],     // Same as parent
-					headSlot: 32,                // Epoch 1
-					headState: fuluState.Copy(), // HeadState (not ReadOnly) for ProcessSlots
-					headStateReadOnly: nil,      // Should not use ReadOnly path
+					headRoot:          parentRoot[:],    // Same as parent
+					headSlot:          32,               // Epoch 1
+					headState:         fuluState.Copy(), // HeadState (not ReadOnly) for ProcessSlots
+					headStateReadOnly: nil,              // Should not use ReadOnly path
 				},
 				fc: &mockForkchoicer{
 					// Return same root for both to simulate same chain
@@ -1045,8 +1045,8 @@ func TestGetVerifyingStateEdgeCases(t *testing.T) {
 		// Wrap to detect HeadState call
 		originalHsp := initializer.shared.hsp.(*mockHeadStateProvider)
 		wrappedHsp := &mockHeadStateProvider{
-			headRoot: originalHsp.headRoot,
-			headSlot: originalHsp.headSlot,
+			headRoot:  originalHsp.headRoot,
+			headSlot:  originalHsp.headSlot,
 			headState: originalHsp.headState,
 		}
 		initializer.shared.hsp = &headStateCallTracker{

changelog/jtraglia-add-specrefs-readme.md

@@ -0,0 +1,3 @@
+### Added
+
+- Added README for maintaining specrefs.

changelog/jtraglia-nightly-reftests-with-run-id.md

@@ -0,0 +1,3 @@
+### Added
+
+- The ability to download the nightly reference tests from a specific day.

changelog/syjn99_docs-ssz-ql.md

@@ -0,0 +1,3 @@
+### Ignored
+
+- Add handy documentation for SSZ Query package (`encoding/ssz/query`).

changelog/tt_run-gofmt.md

@@ -0,0 +1,2 @@
+### Ignored
+Run go fmt

encoding/ssz/query/doc.md

@@ -0,0 +1,190 @@
+# SSZ Query Package
+
+The `encoding/ssz/query` package provides a system for analyzing and querying SSZ ([Simple Serialize](https://github.com/ethereum/consensus-specs/blob/master/ssz/simple-serialize.md)) data structures, as well as generating Merkle proofs from them. It enables runtime analysis of SSZ-serialized Go objects with reflection, path-based queries through nested structures, generalized index calculation, and Merkle proof generation.
+
+This package is designed to be generic. It operates on arbitrary SSZ-serialized Go values at runtime, so the same query/proof machinery applies equally to any SSZ type, including the BeaconState/BeaconBlock.
+
+## Usage Example
+
+```go
+// 1. Analyze an SSZ object
+block := &ethpb.BeaconBlock{...}
+info, err := query.AnalyzeObject(block)
+
+// 2. Parse a path
+path, err := query.ParsePath(".body.attestations[0].data.slot")
+
+// 3. Get the generalized index
+gindex, err := query.GetGeneralizedIndexFromPath(info, path)
+
+// 4. Generate a Merkle proof
+proof, err := info.Prove(gindex)
+
+// 5. Get offset and length to slice the SSZ-encoded bytes
+sszBytes, _ := block.MarshalSSZ()
+_, offset, length, err := query.CalculateOffsetAndLength(info, path)
+// slotBytes contains the SSZ-encoded value at the queried path
+slotBytes := sszBytes[offset : offset+length]
+```
+
+## Exported API
+
+The main exported API consists of:
+
+```go
+// AnalyzeObject analyzes an SSZ object and returns its structural information
+func AnalyzeObject(obj SSZObject) (*SszInfo, error)
+
+// ParsePath parses a path string like ".field1.field2[0].field3"
+func ParsePath(rawPath string) (Path, error)
+
+// CalculateOffsetAndLength computes byte offset and length for a path within an SSZ object
+func CalculateOffsetAndLength(sszInfo *SszInfo, path Path) (*SszInfo, uint64, uint64, error)
+
+// GetGeneralizedIndexFromPath calculates the generalized index for a given path
+func GetGeneralizedIndexFromPath(info *SszInfo, path Path) (uint64, error)
+
+// Prove generates a Merkle proof for a target generalized index
+func (s *SszInfo) Prove(gindex uint64) (*fastssz.Proof, error)
+```
+
+## Type System
+
+### SSZ Types
+
+The package now supports [all standard SSZ types](https://github.com/ethereum/consensus-specs/blob/master/ssz/simple-serialize.md#typing) except `ProgressiveList`, `ProgressiveContainer`, `ProgressiveBitlist`, `Union`, and `CompatibleUnion`.
+
+### Core Data Structures
+
+#### `SszInfo`
+
+The `SszInfo` structure contains complete structural metadata for an SSZ type:
+
+```go
+type SszInfo struct {
+   sszType       SszType           // SSZ Type classification
+   typ           reflect.Type      // Go reflect.Type
+   source        SSZObject         // Original SSZObject reference. Mostly used for reusing SSZ methods like `HashTreeRoot`.
+   isVariable    bool              // True if contains variable-size fields
+
+   // Composite types have corresponding metadata. Other fields would be nil except for the current type.
+   containerInfo *containerInfo
+   listInfo      *listInfo
+   vectorInfo    *vectorInfo
+   bitlistInfo   *bitlistInfo
+   bitvectorInfo *bitvectorInfo
+}
+```
+
+#### `Path`
+
+The `Path` structure represents navigation paths through SSZ structures. It supports accessing a field by field name, accessing an element by index (list/vector type), and finding the length of homogenous collection types. The `ParsePath` function parses a raw string into a `Path` instance, which is commonly used in other APIs like `CalculateOffsetAndLength` and `GetGeneralizedIndexFromPath`.
+
+```go
+type Path struct {
+   Length   bool           // Flag for length queries (e.g., len(.field))
+   Elements []PathElement  // Sequence of field accesses and indices
+}
+
+type PathElement struct {
+   Name  string  // Field name
+   Index *uint64 // list/vector index (nil if not an index access)
+}
+```
+
+## Implementation Details
+
+### Type Analysis (`analyzer.go`)
+
+The `AnalyzeObject` function performs recursive type introspection using Go reflection:
+
+1. **Type Inspection** - Examines Go `reflect.Value` to determine SSZ type
+   - Basic types (`uint8`, `uint16`, `uint32`, `uint64`, `bool`): `SSZType` constants
+   - Slices: Determined from struct tags (`ssz-size` for vectors, `ssz-max` for lists). There is a related [write-up](https://hackmd.io/@junsong/H101DKnwxl) regarding struct tags.
+   - Structs: Analyzed as Containers with field ordering from JSON tags
+   - Pointers: Dereferenced automatically
+
+2. **Variable-Length Population** - Determines actual sizes at runtime
+   - For lists: Iterates elements, caches sizes for variable-element lists
+   - For containers: Recursively populates variable fields, adjusts offsets
+   - For bitlists: Decodes bit length from bitvector
+
+3. **Offset Calculation** - Computes byte positions within serialized data
+   - Fixed-size fields: Offset = sum of preceding field sizes
+   - Variable-size fields: Offset stored as 4-byte pointer entries
+
+### Path Parsing (`path.go`)
+
+The `ParsePath` function parses path strings with the following rules:
+
+- **Dot notation**: `.field1.field2` for field access
+- **Array indexing**: `[0]`, `[42]` for element access
+- **Length queries**: `len(.field)` for list/vector lengths
+- **Character set**: Only `[A-Za-z0-9._\[\]\(\)]` allowed
+
+Example:
+```go
+path, _ := ParsePath(".nested.array_field[5].inner_field")
+// Returns: Path{
+//   Elements: [
+//     PathElement{Name: "nested"},
+//     PathElement{Name: "array_field", Index: <Pointer to uint64(5)>},
+//     PathElement{Name: "inner_field"}
+//   ]
+// }
+```
+
+### Generalized Index Calculation (`generalized_index.go`)
+
+The generalized index is a tree position identifier. This package follows the [Ethereum consensus-specs](https://github.com/ethereum/consensus-specs/blob/master/ssz/merkle-proofs.md#generalized-merkle-tree-index) to calculate the generalized index.
+
+### Merkle Proof Generation (`merkle_proof.go`, `proof_collector.go`)
+
+The `Prove` method generates Merkle proofs using a single-sweep merkleization algorithm:
+
+#### Algorithm Overview
+
+**Key Terms:**
+
+- **Target gindex** (generalized index): The position of the SSZ element you want to prove, expressed as a generalized Merkle tree index. Stored in `Proof.Index`.
+  - Note: The generalized index for root is 1.
+- **Registered gindices**: The set of tree positions whose node hashes must be captured during merkleization in order to later assemble the proof.
+- **Sibling node**: The node that shares the same parent as another node.
+- **Leaf value**: The 32-byte hash of the target node (the node being proven). Stored in `Proof.Leaf`.
+
+**Phases:**
+
+1. **Registration Phase** (`addTarget`)
+> Goal: determine exactly which sibling hashes are needed for the proof.
+
+   - Record the target gindex as the proof target.
+   - Starting from the target node, walk the Merkle tree from the leaf (target gindex) to the root (gindex = 1).
+   - At each step:
+     - Compute and register the sibling gindex (`i XOR 1`) as “must collect”.
+     - Move to the parent (`i = i/2`).
+   - This produces the full set of registered gindices (the sibling nodes on the target-to-root path).
+
+2. **Merkleization Phase** (`merkleize`)
+> Goal: recursively merkleize the tree and capture the needed hashes.
+
+   - Recursively traverse the SSZ structure and compute Merkle tree node hashes from leaves to root.
+   - Whenever the traversal computes a node whose gindex is in registered gindices, store that node’s hash for later proof construction.
+
+3. **Proof Assembly Phase** (`toProof`)
+> Goal: create the final `fastssz.Proof` object in the correct format and order.
+
+```go
+// Proof represents a merkle proof against a general index.
+type Proof struct {
+	Index  int
+	Leaf   []byte
+	Hashes [][]byte
+}
+```
+
+   - Set `Proof.Index` to the target gindex.
+   - Set `Proof.Leaf` to the 32-byte hash of the target node.
+   - Build `Proof.Hashes` by walking from the target node up to (but not including) the root:
+     - At node `i`, append the stored hash for the sibling (`i XOR 1`).
+     - Move to the parent (`i = i/2`).
+   - The resulting `Proof.Hashes` is ordered from the target level upward, containing one sibling hash per tree level on the path to the root.

monitoring/prometheus/service_test.go

@@ -26,21 +26,21 @@ func TestLifecycle(t *testing.T) {
 	port := 1000 + rand.Intn(1000)
 	prometheusService := NewService(t.Context(), fmt.Sprintf(":%d", port), nil)
 	prometheusService.Start()
-    // Actively wait until the service responds on /metrics (faster and less flaky than a fixed sleep)
-    deadline := time.Now().Add(3 * time.Second)
-    for {
-        if time.Now().After(deadline) {
-            t.Fatalf("metrics endpoint not ready within timeout")
-        }
-        resp, err := http.Get(fmt.Sprintf("http://localhost:%d/metrics", port))
-        if err == nil {
-            _ = resp.Body.Close()
-            if resp.StatusCode == http.StatusOK {
-                break
-            }
-        }
-        time.Sleep(50 * time.Millisecond)
-    }
+	// Actively wait until the service responds on /metrics (faster and less flaky than a fixed sleep)
+	deadline := time.Now().Add(3 * time.Second)
+	for {
+		if time.Now().After(deadline) {
+			t.Fatalf("metrics endpoint not ready within timeout")
+		}
+		resp, err := http.Get(fmt.Sprintf("http://localhost:%d/metrics", port))
+		if err == nil {
+			_ = resp.Body.Close()
+			if resp.StatusCode == http.StatusOK {
+				break
+			}
+		}
+		time.Sleep(50 * time.Millisecond)
+	}
 
 	// Query the service to ensure it really started.
 	resp, err := http.Get(fmt.Sprintf("http://localhost:%d/metrics", port))
@@ -49,18 +49,18 @@ func TestLifecycle(t *testing.T) {
 
 	err = prometheusService.Stop()
 	require.NoError(t, err)
-    // Actively wait until the service stops responding on /metrics
-    deadline = time.Now().Add(3 * time.Second)
-    for {
-        if time.Now().After(deadline) {
-            t.Fatalf("metrics endpoint still reachable after timeout")
-        }
-        _, err = http.Get(fmt.Sprintf("http://localhost:%d/metrics", port))
-        if err != nil {
-            break
-        }
-        time.Sleep(50 * time.Millisecond)
-    }
+	// Actively wait until the service stops responding on /metrics
+	deadline = time.Now().Add(3 * time.Second)
+	for {
+		if time.Now().After(deadline) {
+			t.Fatalf("metrics endpoint still reachable after timeout")
+		}
+		_, err = http.Get(fmt.Sprintf("http://localhost:%d/metrics", port))
+		if err != nil {
+			break
+		}
+		time.Sleep(50 * time.Millisecond)
+	}
 
 	// Query the service to ensure it really stopped.
 	_, err = http.Get(fmt.Sprintf("http://localhost:%d/metrics", port))

specrefs/README.md

@@ -0,0 +1,35 @@
+# Specification References
+
+This directory contains specification reference tracking files managed by
+[ethspecify](https://github.com/jtraglia/ethspecify).
+
+## Installation
+
+Install `ethspecify` with the following command:
+
+```bash
+pipx install ethspecify
+```
+
+> [!NOTE]
+> You can run `ethspecify <cmd>` in the `specrefs` directory or
+> `ethspecify <cmd> --path=specrefs` from the project's root directory.
+
+## Maintenance
+
+When adding support for a new specification version, follow these steps:
+
+0. Change directory into the `specrefs` directory.
+1. Update the version in `.ethspecify.yml` configuration.
+2. Run `ethspecify process` to update/populate specrefs.
+3. Run `ethspecify check` to check specrefs.
+4. If there are errors, use the error message as a guide to fix the issue. If
+   there are new specrefs with empty sources, implement/locate each item and
+   update each specref source list. If you choose not to implement an item,
+   add an exception to the appropriate section the the `.ethspecify.yml`
+   configuration.
+5. Repeat steps 3 and 4 until `ethspecify check` passes.
+6. Run `git diff` to view updated specrefs. If an object/function/etc has
+   changed, make the necessary updates to the implementation.
+7. Lastly, in the project's root directory, run `act -j check-specrefs` to
+   ensure everything is correct.

testing/endtoend/endtoend_test.go

@@ -225,9 +225,9 @@ func (r *testRunner) testDepositsAndTx(ctx context.Context, g *errgroup.Group,
 		if err := helpers.ComponentsStarted(ctx, []e2etypes.ComponentRunner{r.depositor}); err != nil {
 			return errors.Wrap(err, "testDepositsAndTx unable to run, depositor did not Start")
 		}
-        go func() {
-            if r.config.TestDeposits {
-                log.Info("Running deposit tests")
+		go func() {
+			if r.config.TestDeposits {
+				log.Info("Running deposit tests")
 				// The validators with an index < minGenesisActiveCount all have deposits already from the chain start.
 				// Skip all of those chain start validators by seeking to minGenesisActiveCount in the validator list
 				// for further deposit testing.
@@ -238,12 +238,12 @@ func (r *testRunner) testDepositsAndTx(ctx context.Context, g *errgroup.Group,
 						r.t.Error(errors.Wrap(err, "depositor.SendAndMine failed"))
 					}
 				}
-            }
-            // Only generate background transactions when relevant for the test.
-            if r.config.TestDeposits || r.config.TestFeature || r.config.UseBuilder {
-                r.testTxGeneration(ctx, g, keystorePath, []e2etypes.ComponentRunner{})
-            }
-        }()
+			}
+			// Only generate background transactions when relevant for the test.
+			if r.config.TestDeposits || r.config.TestFeature || r.config.UseBuilder {
+				r.testTxGeneration(ctx, g, keystorePath, []e2etypes.ComponentRunner{})
+			}
+		}()
 		if r.config.TestDeposits {
 			return depositCheckValidator.Start(ctx)
 		}

testing/endtoend/minimal_e2e_test.go

@@ -38,8 +38,8 @@ func TestEndToEnd_MinimalConfig(t *testing.T) {
 	r := e2eMinimal(t, cfg,
 		types.WithCheckpointSync(),
 		types.WithEpochs(10),
-		types.WithExitEpoch(4),    // Minimum due to ShardCommitteePeriod=4
-		types.WithLargeBlobs(),    // Use large blob transactions for BPO testing
+		types.WithExitEpoch(4), // Minimum due to ShardCommitteePeriod=4
+		types.WithLargeBlobs(), // Use large blob transactions for BPO testing
 	)
 	r.run()
-}
+}

testing/spectest/README.md

@@ -21,10 +21,14 @@ There are tests for mainnet and minimal config, so for each config we will add a
 
 ## Running nightly spectests
 
-Since [PR 15312](https://github.com/OffchainLabs/prysm/pull/15312), Prysm has support to download "nightly" spectests from github via a starlark rule configuration by environment variable. 
-Set `--repo_env=CONSENSUS_SPEC_TESTS_VERSION=nightly` when running spectest to download the "nightly" spectests. 
-Note: A GITHUB_TOKEN environment variable is required to be set. The github token must be a [fine grained token](https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/managing-your-personal-access-tokens#creating-a-fine-grained-personal-access-token).
+Since [PR 15312](https://github.com/OffchainLabs/prysm/pull/15312), Prysm has support to download "nightly" spectests from github via a starlark rule configuration by environment variable.
+Set `--repo_env=CONSENSUS_SPEC_TESTS_VERSION=nightly` or `--repo_env=CONSENSUS_SPEC_TESTS_VERSION=nightly-<run_id>` when running spectest to download the "nightly" spectests.
+Note: A GITHUB_TOKEN environment variable is required to be set. The github token does not need to be associated with your main account; it can be from a "burner account". And the token does not need to be a fine-grained token; it can be a classic token.
 
 ```
 bazel test //... --test_tag_filters=spectest --repo_env=CONSENSUS_SPEC_TESTS_VERSION=nightly
 ```
+
+```
+bazel test //... --test_tag_filters=spectest --repo_env=CONSENSUS_SPEC_TESTS_VERSION=nightly-21422848633
+```

tools/download_spectests.bzl

@@ -1,5 +1,6 @@
 # bazel build @consensus_spec_tests//:test_data
 # bazel build @consensus_spec_tests//:test_data --repo_env=CONSENSUS_SPEC_TESTS_VERSION=nightly
+# bazel build @consensus_spec_tests//:test_data --repo_env=CONSENSUS_SPEC_TESTS_VERSION=nightly-<run_id>
 
 def _get_redirected_url(repository_ctx, url, headers):
     if not repository_ctx.which("curl"):
@@ -24,7 +25,7 @@ def _impl(repository_ctx):
     version = repository_ctx.getenv("CONSENSUS_SPEC_TESTS_VERSION") or repository_ctx.attr.version
     token = repository_ctx.getenv("GITHUB_TOKEN") or ""
 
-    if version == "nightly":
+    if version == "nightly" or version.startswith("nightly-"):
         print("Downloading nightly tests")
         if not token:
             fail("Error GITHUB_TOKEN is not set")
@@ -34,16 +35,22 @@ def _impl(repository_ctx):
             "Accept": "application/vnd.github+json",
         }
 
-        repository_ctx.download(
-            "https://api.github.com/repos/%s/actions/workflows/%s/runs?branch=%s&status=success&per_page=1"
-                % (repository_ctx.attr.repo, repository_ctx.attr.workflow, repository_ctx.attr.branch),
-            headers = headers,
-            output = "runs.json"
-        )
+        if version.startswith("nightly-"):
+            run_id = version.split("nightly-", 1)[1]
+            if not run_id:
+                fail("Error invalid run id")
+        else:
+            repository_ctx.download(
+                "https://api.github.com/repos/%s/actions/workflows/%s/runs?branch=%s&status=success&per_page=1"
+                    % (repository_ctx.attr.repo, repository_ctx.attr.workflow, repository_ctx.attr.branch),
+                headers = headers,
+                output = "runs.json"
+            )
 
-        run_id = json.decode(repository_ctx.read("runs.json"))["workflow_runs"][0]["id"]
-        repository_ctx.delete("runs.json")
+            run_id = json.decode(repository_ctx.read("runs.json"))["workflow_runs"][0]["id"]
+            repository_ctx.delete("runs.json")
 
+        print("Run id:", run_id)
         repository_ctx.download(
             "https://api.github.com/repos/%s/actions/runs/%s/artifacts"
                 % (repository_ctx.attr.repo, run_id),
@@ -108,8 +115,8 @@ consensus_spec_tests = repository_rule(
         "version": attr.string(mandatory = True),
         "flavors": attr.string_dict(mandatory = True),
         "repo": attr.string(default = "ethereum/consensus-specs"),
-        "workflow": attr.string(default = "generate_vectors.yml"),
-        "branch": attr.string(default = "dev"),
+        "workflow": attr.string(default = "nightly-reftests.yml"),
+        "branch": attr.string(default = "master"),
         "release_url_template": attr.string(default = "https://github.com/ethereum/consensus-specs/releases/download/%s"),
     },
 )