Add CPU trellis decoder

AGENTS.md

@@ -3,30 +3,33 @@
 - Use the Bazel build system when interacting with this repository.
 - The CMake build system is available to help users who need it.
 - Keep both the CMake and Bazel builds working at all times.
+- Use at most one CPU core for all builds, tests, and other expensive commands.
+  For Bazel, pass `--jobs=1`. For CMake builds, pass `--parallel 1`. For
+  `make`, pass `-j1`.
 
 ## Building with Bazel
 
 To build all code with bazel:
 ```bash
-bazel build src:all
+bazel build --jobs=1 src:all
 ```
 To build the Tesseract and Simplex main binaries:
 ```bash
-bazel build src:tesseract src:simplex
+bazel build --jobs=1 src:tesseract src:simplex
 ```
 
 ## Running Tests with Bazel
 
 ```bash
-bazel test src/...
+bazel test --jobs=1 src/...
 ```
 
 ## Building with CMake
 
-In case you need to, when building with CMake, use parallel flags to speed up the process.
+In case you need to build with CMake, keep the build single-core.
 
-- When using `cmake --build`, add the `--parallel` flag.
-- When using `make`, add the `-j` flag (e.g., `make -j$(nproc)`).
+- When using `cmake --build`, add `--parallel 1`.
+- When using `make`, add `-j1`.
 
 ## Running Tests with CMake
 
@@ -36,7 +39,7 @@ To run the tests, execute the following commands from the root of the repository
 mkdir -p build
 cd build
 cmake ..
-cmake --build . --parallel
+cmake --build . --parallel 1
 ctest
 ```
 
@@ -49,7 +52,7 @@ To build the Python wheel for `tesseract_decoder` locally, you will need to use
 Use the following command:
 
 ```bash
-bazel build //:tesseract_decoder_wheel --define=VERSION=0.1.1 --define=TARGET_VERSION=py313
+bazel build --jobs=1 //:tesseract_decoder_wheel --define=VERSION=0.1.1 --define=TARGET_VERSION=py313
 ```
 
 - `--define=VERSION=0.1.1`: Sets the version of the wheel. You should replace `0.1.1` with the current version from the `_version.py` file.
@@ -62,7 +65,7 @@ The resulting wheel file will be located in the `bazel-bin/` directory.
 If you change the Python version in `MODULE.bazel`, you will need to regenerate the `requirements_lock.txt` file to ensure all dependencies are compatible. To do this, run the following command:
 
 ```bash
-bazel run //src/py:requirements.update
+bazel run --jobs=1 //src/py:requirements.update
 ```
 
 This will update the `src/py/requirements_lock.txt` file with the correct dependency versions for the new Python environment.

CMakeLists.txt

@@ -98,6 +98,14 @@ target_include_directories(tesseract_lib PUBLIC ${TESSERACT_SRC_DIR})
 target_compile_options(tesseract_lib PRIVATE ${OPT_COPTS})
 target_link_libraries(tesseract_lib PUBLIC utils boost_headers visualization)
 
+add_library(tesseract_trellis_lib
+  ${TESSERACT_SRC_DIR}/tesseract_trellis.cc
+  ${TESSERACT_SRC_DIR}/tesseract_trellis.h
+)
+target_include_directories(tesseract_trellis_lib PUBLIC ${TESSERACT_SRC_DIR})
+target_compile_options(tesseract_trellis_lib PRIVATE ${OPT_COPTS})
+target_link_libraries(tesseract_trellis_lib PUBLIC common utils libstim Threads::Threads)
+
 add_library(simplex ${TESSERACT_SRC_DIR}/simplex.cc ${TESSERACT_SRC_DIR}/simplex.h)
 target_include_directories(simplex PUBLIC ${TESSERACT_SRC_DIR})
 target_compile_options(simplex PRIVATE ${OPT_COPTS})
@@ -108,6 +116,12 @@ add_executable(tesseract ${TESSERACT_SRC_DIR}/tesseract_main.cc)
 target_compile_options(tesseract PRIVATE ${OPT_COPTS})
 target_link_libraries(tesseract PRIVATE tesseract_lib argparse::argparse nlohmann_json::nlohmann_json)
 
+add_executable(tesseract_trellis ${TESSERACT_SRC_DIR}/tesseract_trellis_main.cc)
+target_compile_options(tesseract_trellis PRIVATE ${OPT_COPTS})
+target_link_libraries(tesseract_trellis
+  PRIVATE tesseract_trellis_lib argparse::argparse nlohmann_json::nlohmann_json
+)
+
 add_executable(simplex_bin ${TESSERACT_SRC_DIR}/simplex_main.cc)
 set_target_properties(simplex_bin PROPERTIES OUTPUT_NAME simplex)
 target_compile_options(simplex_bin PRIVATE ${OPT_COPTS})
@@ -137,3 +151,6 @@ add_executable(tesseract_test ${TESSERACT_SRC_DIR}/tesseract.test.cc)
 target_link_libraries(tesseract_test PRIVATE tesseract_lib simplex GTest::gtest_main)
 add_test(NAME tesseract_test COMMAND tesseract_test)
 
+add_executable(tesseract_trellis_test ${TESSERACT_SRC_DIR}/tesseract_trellis.test.cc)
+target_link_libraries(tesseract_trellis_test PRIVATE tesseract_trellis_lib GTest::gtest_main)
+add_test(NAME tesseract_trellis_test COMMAND tesseract_trellis_test)

src/BUILD

@@ -140,6 +140,19 @@ cc_library(
     ],
 )
 
+cc_library(
+    name = "libtesseract_trellis",
+    srcs = ["tesseract_trellis.cc"],
+    hdrs = ["tesseract_trellis.h"],
+    copts = OPT_COPTS,
+    linkopts = OPT_LINKOPTS,
+    deps = [
+        ":libcommon",
+        ":libutils",
+        "@stim//:stim_lib",
+    ],
+)
+
 cc_binary(
     name = "tesseract",
     srcs = ["tesseract_main.cc"],
@@ -153,6 +166,19 @@ cc_binary(
     ],
 )
 
+cc_binary(
+    name = "tesseract_trellis",
+    srcs = ["tesseract_trellis_main.cc"],
+    copts = OPT_COPTS,
+    linkopts = OPT_LINKOPTS,
+    deps = [
+        ":libtesseract_trellis",
+        "@argparse",
+        "@nlohmann_json//:json",
+        "@stim//:stim_lib",
+    ],
+)
+
 cc_test(
     name = "tesseract_tests",
     timeout = "eternal",
@@ -169,6 +195,19 @@ cc_test(
     ],
 )
 
+cc_test(
+    name = "tesseract_trellis_tests",
+    srcs = ["tesseract_trellis.test.cc"],
+    copts = OPT_COPTS,
+    linkopts = OPT_LINKOPTS,
+    deps = [
+        ":libtesseract_trellis",
+        "@gtest",
+        "@gtest//:gtest_main",
+        "@stim//:stim_lib",
+    ],
+)
+
 cc_test(
     name = "common_tests",
     srcs = ["common.test.cc"],

src/simplex_main.cc

@@ -251,6 +251,7 @@ struct Args {
       // Create a writer instance to write the predicted obs to a file
       stim::FileFormatData predictions_out_format = stim::format_name_to_enum_map().at(out_format);
       FILE* predictions_file = stdout;
+      // An output path of "-" means stdout.
       if (out_fname != "-") {
         predictions_file = fopen(out_fname.c_str(), "w");
       }

src/tesseract_main.cc

@@ -317,6 +317,7 @@ struct Args {
       // Create a writer instance to write the predicted obs to a file
       stim::FileFormatData predictions_out_format = stim::format_name_to_enum_map().at(out_format);
       FILE* predictions_file = stdout;
+      // An output path of "-" means stdout.
       if (out_fname != "-") {
         predictions_file = fopen(out_fname.c_str(), "w");
       }