Restructure code + reformat

.bazeliskrc

@@ -0,0 +1,3 @@
+BAZELISK_BASE_URL=https://static.aspect.build/aspect
+USE_BAZEL_VERSION=aspect/2025.15.20
+

.bazelrc

@@ -0,0 +1,27 @@
+# =============================================================================
+# Common Settings
+# =============================================================================
+# This makes sure bazel doesn't implicitly create missing __init__.py files.
+build --incompatible_default_to_explicit_init_py
+build --experimental_isolated_extension_usages
+
+# =============================================================================
+# Build Performance
+# =============================================================================
+build --jobs=auto
+build --experimental_remote_merkle_tree_cache
+build --experimental_remote_cache_compression
+build --experimental_remote_cache_async
+build --experimental_guard_against_concurrent_changes
+build --experimental_reuse_sandbox_directories
+
+# =============================================================================
+# Developer Experience
+# =============================================================================
+build --show_progress_rate_limit=0.5
+build --color=yes
+build --terminal_columns=120
+build --show_timestamps
+build --announce_rc  # Show which config files are read
+build --heap_dump_on_oom  # Dump heap on out-of-memory
+test --test_output=all # Show all test output in real time

.bazelversion

@@ -0,0 +1 @@
+7.6.1

.gitignore

@@ -6,9 +6,18 @@ __pycache__/
 # C extensions
 *.so
 
-# CMake
-CMakeCache.txt
-CMakeFiles
+# Bazel
+bazel-*
+MODULE.bazel.lock
+
+# node
+node_modules
+
+# OS X
+.DS_Store
+
+# Pycharm
+.idea/
 
 # Distribution / packaging
 .Python
@@ -107,15 +116,3 @@ ENV/
 
 # IDE settings
 .vscode/
-.idea/
-
-# Output of tests
-dlup/preprocessors/tests/data/test_output
-
-# OS files
-.DS_Store
-
-
-tools/logs
-config/machine_settings/*
-!config/machine_settings/example.yaml

.npmrc

@@ -0,0 +1 @@
+hoist=false

.ruff.toml

@@ -0,0 +1,62 @@
+# Exclude a variety of commonly ignored directories.
+exclude = [
+    ".bzr",
+    ".direnv",
+    ".eggs",
+    ".git",
+    ".git-rewrite",
+    ".hg",
+    ".ipynb_checkpoints",
+    ".mypy_cache",
+    ".nox",
+    ".pants.d",
+    ".pyenv",
+    ".pytest_cache",
+    ".pytype",
+    ".ruff_cache",
+    ".svn",
+    ".tox",
+    ".venv",
+    ".vscode",
+    "__pypackages__",
+    "_build",
+    "buck-out",
+    "build",
+    "dist",
+    "node_modules",
+    "site-packages",
+    "venv",
+]
+
+# Same as Black.
+line-length = 120
+indent-width = 4
+
+target-version = "py311"
+
+[lint]
+# Enable Pyflakes (`F`) and a subset of the pycodestyle (`E`)  codes by default.
+# Unlike Flake8, Ruff doesn't enable pycodestyle warnings (`W`) or
+# McCabe complexity (`C901`) by default.
+select = ["E4", "E7", "E9", "F"]
+ignore = []
+
+# Allow fix for all enabled rules (when `--fix`) is provided.
+fixable = ["ALL"]
+unfixable = []
+
+# Allow unused variables when underscore-prefixed.
+dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
+
+[format]
+# Like Black, use double quotes for strings.
+quote-style = "double"
+
+# Like Black, indent with spaces, rather than tabs.
+indent-style = "space"
+
+# Like Black, respect magic trailing commas.
+skip-magic-trailing-comma = false
+
+# Like Black, automatically detect the appropriate line ending.
+line-ending = "auto"

BUILD.bazel

@@ -0,0 +1,56 @@
+load("@aspect_rules_js//js:defs.bzl", "js_library")
+load("@npm//:defs.bzl", "npm_link_all_packages")
+load("@rules_multirun//:defs.bzl", "multirun")
+load("@rules_uv//uv:pip.bzl", "pip_compile")
+
+package(default_visibility = ["//visibility:public"])
+
+npm_link_all_packages(name = "node_modules")
+
+exports_files(
+    [
+        ".ruff.toml",
+    ],
+    visibility = ["//visibility:public"],
+)
+
+pip_compile(
+    name = "generate_requirements_linux_txt",
+    python_platform = "x86_64-unknown-linux-gnu",
+    requirements_in = "requirements.in",
+    requirements_txt = "requirements_linux.txt",
+)
+
+pip_compile(
+    name = "generate_requirements_darwin_txt",
+    python_platform = "aarch64-apple-darwin",
+    requirements_in = "requirements.in",
+    requirements_txt = "requirements_darwin.txt",
+)
+
+multirun(
+    name = "generate_requirements_lock",
+    commands = [
+        ":generate_requirements_linux_txt",
+        ":generate_requirements_darwin_txt",
+    ],
+    # Running in a single threaded mode allows consecutive `uv` invocations to benefit
+    # from the `uv` cache from the first run.
+    jobs = 1,
+)
+
+js_library(
+    name = "prettierrc",
+    srcs = ["prettier.config.cjs"],
+    visibility = ["//tools/format:__pkg__"],
+    deps = [
+        ":node_modules/@prettier/plugin-xml",
+        ":node_modules/prettier-plugin-gherkin",
+        ":node_modules/prettier-plugin-sql",
+    ],
+)
+
+alias(
+    name = "format",
+    actual = "//tools/format",
+)

MODULE.bazel

@@ -0,0 +1,64 @@
+"""
+This module defines the dependencies and configurations for DIRECT.
+"""
+
+module(name = "stapler")
+
+bazel_dep(name = "platforms", version = "0.0.11")
+bazel_dep(name = "bazel_features", version = "1.23.0")
+bazel_dep(name = "bazel_skylib", version = "1.7.1")
+bazel_dep(name = "gazelle", version = "0.41.0")
+bazel_dep(name = "cython", version = "3.0.11-1")
+bazel_dep(name = "rules_multirun", version = "0.10.0")
+bazel_dep(name = "rules_python", version = "1.4.0-rc0")
+bazel_dep(name = "rules_license", version = "1.0.0")
+bazel_dep(name = "rules_cc", version = "0.1.1")
+bazel_dep(name = "buildifier_prebuilt", version = "8.0.1")
+bazel_dep(name = "aspect_rules_lint", version = "1.2.0")
+bazel_dep(name = "aspect_rules_js", version = "2.0.0")
+bazel_dep(name = "aspect_rules_py", version = "1.3.2")
+
+# We are using this commit because it's not yet released
+# https://github.com/aspect-build/rules_py/commit/6ad466797d8e595016c5a8bec7186268b9ea7f6f
+# This allows sharding of tests and easier setup
+archive_override(
+    module_name = "aspect_rules_py",
+    integrity = "sha256-p7Fo6yMoh96SurOcGt1uLt95vRf/RUeuPvr/1oA6jzw=",
+    strip_prefix = "rules_py-1296c6b88156594543b7f41ceb331bdc9a053055",
+    urls = ["https://github.com/aspect-build/rules_py/archive/1296c6b88156594543b7f41ceb331bdc9a053055.zip"],
+)
+
+bazel_dep(name = "rules_uv", version = "0.65.0", dev_dependency = True)
+
+python = use_extension("@rules_python//python/extensions:python.bzl", "python")
+python.toolchain(
+    is_default = True,
+    python_version = "3.11",
+)
+
+pip = use_extension("@rules_python//python/extensions:pip.bzl", "pip")
+pip.parse(
+    enable_implicit_namespace_pkgs = True,
+    hub_name = "pip",
+    python_version = "3.11",
+    requirements_darwin = ":requirements_darwin.txt",
+    requirements_lock = ":requirements_linux.txt",
+)
+use_repo(pip, "pip")
+
+npm = use_extension("@aspect_rules_js//npm:extensions.bzl", "npm")
+npm.npm_translate_lock(
+    name = "npm",
+    npmrc = ".npmrc",
+    pnpm_lock = "pnpm-lock.yaml",
+    public_hoist_packages = {
+        "typescript-eslint": [""],
+    },
+)
+use_repo(npm, "npm")
+
+pnpm = use_extension("@aspect_rules_js//npm:extensions.bzl", "pnpm")
+
+# Allows developers to use the matching pnpm version, for example:
+# bazelisk run @pnpm -- --dir /home/runner/work/rules_js/rules_js install
+use_repo(pnpm, "pnpm")