secs-gem/docs/30_repository_tour.md

# 30 — Repository tour

← [19 E42 + E148 + S9 — Misc](19_e42_e148_s9_misc.md) | [Back to index](00_index.md) | Next: [31 Spec-as-data + codegen](31_spec_as_data_and_codegen.md) →

You've seen what every SEMI standard *does*.  Now we shift to how
this **codebase** is laid out.  This chapter answers: when you
`git clone` this repo, what are you looking at?

The repo is small — about 15 k lines of C++ + tests + tooling.  It
fits in your head with a little patience.  By the end of this
chapter you'll know:

- What each top-level directory contains.
- Which binaries get built.
- The dependency graph between modules.
- How the build system finds and links them.

---

## Top-level layout

```
secs-gem/
├── README.md                One-page project summary.
├── LICENSE                  Proprietary terms.
├── CMakeLists.txt           Build config (CMake 3.16+, single file).
├── Dockerfile               Ubuntu 24.04 + g++-13 + libasio + yaml-cpp.
├── docker-compose.yml       Multi-container demo wiring.
├── .gitea/workflows/ci.yml  CI pipeline.
│
├── include/secsgem/         Public headers.  All API here.
│   ├── secs2/               E5 codec + SML.
│   ├── hsms/                E37 transport (TCP + framing).
│   ├── secsi/               E4 transport (FSM + TCP tunnel).
│   ├── config/              YAML loader + multi-error validator.
│   ├── metrics/             Prometheus exporter.
│   ├── endpoint.hpp         asio::ip::tcp::endpoint factory.
│   └── gem/                 E30 + every GEM 300 standard.
│       ├── store/           Per-domain bundles (SVIDs, alarms, …).
│       └── *.hpp            State machines + composers.
│
├── src/                     Implementations.  Mirrors include/.
│   ├── secs2/{codec,sml}.cpp
│   ├── hsms/{header,connection}.cpp
│   ├── secsi/{header,block,protocol,tcp_transport}.cpp
│   ├── config/...
│   ├── gem/...
│   └── endpoint.cpp
│
├── apps/                    Standalone binaries.
│   ├── secs_server.cpp      Passive equipment (demo + integration target).
│   ├── secs_client.cpp      Active host driving the demo flow.
│   ├── secs_conformance.cpp 47-check wire-level conformance harness.
│   ├── secs_interop_probe.cpp Probe against secsgem-py passive equip.
│   ├── secs_bench.cpp       Throughput / latency / memory bench.
│   ├── fuzz_secs2_decode.cpp libFuzzer harness for secs2::decode.
│   └── fuzz_sml_parse.cpp    libFuzzer harness for try_parse_sml.
│
├── tests/                   doctest unit + integration tests.
│   └── test_*.cpp           55 files, 473 cases, 3087 assertions.
│
├── data/                    YAML configs (the spec-as-data).
│   ├── messages.yaml        SECS-II message catalog (164 msgs).
│   ├── control_state.yaml   E30 §6.2 transition table.
│   ├── process_job_state.yaml  E40 transition table.
│   ├── control_job_state.yaml  E94 transition table.
│   └── equipment.yaml       Demo SVIDs/ECIDs/CEIDs/alarms/recipes.
│
├── tools/                   Build-time scripts.
│   └── gen_messages.py      Codegen: messages.yaml → messages.hpp.
│
├── interop/                 External-validator harnesses.
│   ├── README.md            Harness-by-harness detail.
│   ├── host_vs_cpp_server.py    secsgem-py active host driving us.
│   ├── passive_equipment.py     secsgem-py passive equipment for us to drive.
│   ├── raw_gem300_harness.py    Raw S3/S14/S16/S12 round-trip.
│   ├── tshark_validate.sh       pcap + tshark HSMS dissector check.
│   ├── secs4j_validate.sh       secs4java8 (Java) cross-validation.
│   └── secs4j/                  Dockerfile + harness for secs4java8.
│
├── examples/
│   └── pvd_tool/            Worked vendor example: fictional PVD tool.
│       ├── README.md        What the example shows.
│       ├── equipment.yaml   Realistic SVIDs/ECIDs/CEIDs/alarms/recipes.
│       └── main.cpp         Sensor sim, recipe runner, alarm monitor.
│
└── docs/                    This guide + reference docs.
    ├── 00_index.md          The series TOC.
    ├── 01–51_*.md           Tutorial chapters.
    ├── ARCHITECTURE.md      One-page architecture overview.
    ├── COMPLIANCE.md        Per-capability audit.
    ├── INTEGRATION.md       Vendor-side production deploy.
    ├── PROOFS.md            8 commands proving feature-completeness.
    ├── VERIFICATION.md      External-validator test plan.
    ├── BENCHMARKS.md        Performance envelope.
    ├── MES_INTEROP.md       Commercial-MES day-1 punch list.
    ├── SECURITY.md          nftables / stunnel / minisign configs.
    ├── GLOSSARY.md          SEMI vocabulary cheat sheet.
    └── FAQ.md               Canonical answers.
```

---

## The dependency graph

```
                            data/*.yaml
                                │
                  ┌─────────────┼──────────────────┐
                  │  (codegen)  │   (runtime load) │
                  ▼             ▼                  ▼
       generated/messages.hpp                  config::loader
                  │                                │
                  └──────────► gem::EquipmentDataModel
                                       │
                                       │ used by
                                       ▼
                                  gem::Router
                                       │
                                       │ wraps
                                       ▼
                               secs2::Message  ◄─── codec / SML
                                       │
                                       │ over
                                       ▼
                           hsms::Connection  /  secsi::TcpTransport
                                       │
                                       ▼
                                   TCP socket
```

Read it bottom-up: a TCP socket carries bytes; `hsms::Connection`
frames them into `secs2::Message`s; `gem::Router` dispatches by
`(stream, function)` to handlers; handlers read/write
`EquipmentDataModel`; the model composes per-domain stores; the
stores were built from the YAML at startup.

No layer ever calls *up* the graph.  `secs2::Item` has no idea
HSMS exists.  `hsms::Connection` doesn't know about CEIDs.
`gem::Router` doesn't know whether the bytes came over HSMS or
SECS-I.  Strict layering is what keeps the codebase small.

---

## The binaries

Built by [`CMakeLists.txt`](../CMakeLists.txt) (one file, ~250
lines).  Each binary lives in `build/` after `cmake --build`.

| Binary               | Source                                                          | What it does                                          |
|----------------------|-----------------------------------------------------------------|-------------------------------------------------------|
| `secs_server`        | [`apps/secs_server.cpp`](../apps/secs_server.cpp)               | Passive equipment.  Listens on TCP, dispatches via Router. |
| `secs_client`        | [`apps/secs_client.cpp`](../apps/secs_client.cpp)               | Active host.  Drives ~24 transactions in the demo.    |
| `secs_conformance`   | [`apps/secs_conformance.cpp`](../apps/secs_conformance.cpp)     | 47 wire-level conformance checks against a live server. |
| `secs_interop_probe` | [`apps/secs_interop_probe.cpp`](../apps/secs_interop_probe.cpp) | Active host probing a secsgem-py passive equipment.   |
| `secs_bench`         | [`apps/secs_bench.cpp`](../apps/secs_bench.cpp)                 | Throughput / latency / memory harness.                |
| `secsgem_tests`      | All `tests/*.cpp`                                               | The 473-case doctest binary.                          |
| `secs_gemd`          | `apps/secs_gemd.cpp` + `proto/secsgem/v1`                       | The gRPC daemon: HSMS equipment + name-based tool API. |
| `secs_gemd_tests`    | `tests/test_daemon_service.cpp`                                 | In-process gRPC service tests (built when grpc++ is). |
| `fuzz_secs2_decode`  | [`apps/fuzz_secs2_decode.cpp`](../apps/fuzz_secs2_decode.cpp)   | libFuzzer (clang only, opt-in `-DSECSGEM_FUZZ=ON`).   |
| `fuzz_sml_parse`     | [`apps/fuzz_sml_parse.cpp`](../apps/fuzz_sml_parse.cpp)         | libFuzzer for the SML parser.                         |

A worked example binary `pvd_tool` (from `examples/pvd_tool/`) is
also built by the same `CMakeLists.txt` when the example is
included.

---

## How the build system finds everything

`CMakeLists.txt` does five things in order:

1. **Pull in dependencies** — `find_package(Threads)`,
   `find_package(yaml-cpp)`, `FetchContent` for doctest.  Standalone
   Asio is header-only (no link step).
2. **Run codegen** — invokes `tools/gen_messages.py` to turn
   `data/messages.yaml` into `build/generated/secsgem/gem/messages.hpp`.
   Listed as a custom command so it re-runs when `messages.yaml`
   changes.
3. **Build the library** — `add_library(secsgem ...)` with every
   source under `src/` plus the generated header.
4. **Build the apps** — one `add_executable` per `apps/*.cpp`,
   each linking against `secsgem`.
5. **Build the tests** — `add_executable(secsgem_tests ...)` with
   every `tests/*.cpp`, linked against doctest + `secsgem`.

Build flags:

- **`-DSECSGEM_TSAN=ON`** — adds `-fsanitize=thread` to a
  separate build dir.  CI runs this lane.
- **`-DSECSGEM_FUZZ=ON`** — requires clang; adds libFuzzer + ASan +
  UBSan; builds the two fuzz harnesses.

Everything else (Release / Debug, parallelism, output dirs) is
standard CMake.

---

## Test layout

50 test files; 473 test cases; 3 087 assertions.  One file per
concern.  Naming is `test_<thing>.cpp` consistently:

- `test_secs2.cpp`, `test_e5_kat.cpp`, `test_sml.cpp`,
  `test_messages.cpp` — codec.
- `test_hsms*.cpp` (5 files), `test_secsi*.cpp` (3 files) — transport.
- `test_control_state.cpp`, `test_communication_state.cpp`,
  `test_data_model.cpp`, `test_host_handler.cpp`, `test_loader.cpp`,
  `test_config_validate.cpp` — E30.
- `test_process_jobs.cpp`, `test_control_jobs.cpp`,
  `test_carriers.cpp`, `test_substrates.cpp`, `test_ept.cpp`,
  `test_modules.cpp`, `test_cem_objects.cpp`, `test_e84*.cpp`,
  `test_e42_formatted_pp.cpp` — GEM 300.
- `test_*_persistence.cpp` (4) — file-backed journal.
- `test_robustness_fuzz.cpp` — randomized property test.
- `test_thread_safety.cpp` — TSan-validated single-threaded contract.
- `test_metrics_prometheus.cpp` — Prometheus exporter.
- `test_wire_ceid_emission.cpp` — CEID firings observed on a real socket.
- `test_live_gem300.cpp`, `test_gem300_scenario.cpp` — multi-FSM cascades.

Full per-standard breakdown:
[`docs/PROOFS.md`](PROOFS.md) "Per-standard test coverage" table.

---

## Where to go next

Now that you know what's where, the next chapter explains the
*philosophy* that makes the codebase this small: the **spec-as-data**
principle, and how the YAML files + codegen + runtime loader work
together so adding a new SVID / state / message rarely requires C++.

Next: [→ 31 Spec-as-data + codegen](31_spec_as_data_and_codegen.md)