oxymake 0.1.0__tar.gz

oxymake-0.1.0/.gitignore

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+# Build
+/target/
+/target-linux/
+# Nested Cargo target dirs (e.g. a crate compiled in isolation) — never track
+# build artifacts anywhere in the tree. Anchored `/target/` alone misses these.
+**/target/
+**/*.rs.bk
+
+# mdBook build output (docs/book/book/) — generated by `mdbook build docs/book`,
+# published to Cloudflare Pages. Never tracked; rebuilt in CI on every deploy.
+docs/book/book/
+
+# IDE
+.idea/
+.vscode/
+*.swp
+*.swo
+*~
+
+# OS
+.DS_Store
+Thumbs.db
+
+# OxyMake runtime (for testing)
+.oxymake/
+
+# Mutation testing
+mutants.out/
+mutants.out.old/
+
+# Coverage
+lcov.info
+tarpaulin-report.html
+.beads/
+.claude/
+.runtime/
+
+# Local agent context — never commit (Gas Town/polecat playbook, operator-private)
+CLAUDE.local.md
+
+# Benchmark generated workloads and timestamped results
+benchmark/perf/workloads/
+benchmark/perf/results-*.md
+
+# Head-to-head bench: transient workloads and per-run measurement data
+bench/snakemake-vs-oxymake/workloads/
+bench/snakemake-vs-oxymake/data/
+
+# Benchmark generated outputs (top-level and per-benchmark)
+benchmark/data/
+benchmark/logs/
+benchmark/results/
+benchmark/*/data/
+benchmark/*/logs/
+benchmark/*/results/
+benchmark/*/benchmarks/
+
+# LaTeX build artifacts (keep only .tex and .pdf in docs/paper/)
+*.aux
+*.log
+*.out
+*.bbl
+*.blg
+*.fls
+*.fdb_latexmk
+*.synctex.gz
+/oxymake-paper.*
+
+# Beads / Dolt files (added by bd init)
+.dolt/
+*.db
+.beads-credential-key
+bench_output/
+__pycache__/
+.oxymake_warm_*.py
+spec/tla/states/
+
+# ── Confidential / author+agent residence — keep OFF the public surface ──
+# These trees hold strategic/relational/inside-baseball docs that must not be
+# tracked on the public surface. The surviving public artefacts are the ADRs,
+# not these minutes/premortems/outreach.
+CLAUDE.local.md
+docs/_private/
+docs/migrated-from-*/
+docs/outreach/
+docs/paper/premortems/
+docs/decisions/
+docs/cosmon-feedback/
+docs/lore/
+
+# Externalized denylist for scripts/release-checklist.sh — holds the confidential
+# alternations (OXYMAKE_FORBID_PATTERN / OXYMAKE_CONF_PATHS) so the guard never
+# names in clear what it forbids (scrub-oxymake-main-tree, D7). Never tracked.
+scripts/.release-denylist.local
+
+# confidential paths, kept off the public surface
+docs/agent/
+docs/health/
+
+# Cross-molecule-board (CMB) correspondence — cross-galaxy inbox/outbox messages.
+# Same residence class as docs/cosmon-feedback/: relational/inside-baseball notes
+# (session origins, third-party names, NDA/strategy context) that must NOT reach
+# the public surface. Keep OFF main; residence is the orphan narration branch.
+docs/cmb/
+
+# TLC model-checker cache (jar downloaded by spec/tla/run-tlc.sh)
+spec/tla/.tlc-cache/
+
+# ...but the archived TLC reference outputs ARE committed (H19):
+# they are what makes the paper's state counts reproducible.
+!spec/tla/runs/*.out
+
+# personal submission helper + internal go/no-go audit (private residence)
+docs/paper/arxiv-metadata.txt
+ops/audits/prerelease-go-2026-06-14.md
+
+# task-20260614-6d66 — confidentiality (Gate 1, public-prep).
+# These two design docs use private, domain-specific methodology as their worked
+# example (internal data scale, private lab paths). That is confidential IP, not
+# a generic OxyMake capability — private residence (noogram/oxymake-private).
+# The generic engine ideas they explore (per-module DAG nodes, in-memory
+# critical path) can be re-documented neutrally on the public surface if needed.
+docs/design/per-alpha-signal-splitting.md
+docs/design/stage2-lab-test-plan.md
+.wrangler/

oxymake-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: oxymake
+Version: 0.1.0
+Summary: Content-addressable workflow engine — git checkout no longer rebuilds everything
+Project-URL: Homepage, https://oxymake.dev
+Project-URL: Repository, https://github.com/noogram/oxymake
+Project-URL: Releases, https://github.com/noogram/oxymake/releases
+Author-email: Emmanuel Sérié <emmanuel@serie.dev>
+License: MIT OR Apache-2.0
+Keywords: build,cache,pipeline,snakemake,workflow
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+
+# OxyMake (Python launcher)
+
+A content-addressable workflow engine. You `git checkout` an old branch, re-run
+your pipeline, and it **does not** rebuild everything — change detection is a
+BLAKE3 hash of file *content*, not timestamps.
+
+```bash
+uv tool install oxymake     # or: pipx install oxymake
+ox --help
+```
+
+This package is a thin launcher: on first run it downloads the prebuilt `ox`
+binary for your platform from the
+[GitHub release](https://github.com/noogram/oxymake/releases/latest), verifies
+its SHA-256, caches it, and execs it. No Rust toolchain required — which is the
+point: bioinformatics and data-science users who live in conda/pip can try
+OxyMake without a source build.
+
+Full documentation: <https://github.com/noogram/oxymake>

oxymake-0.1.0/README.md

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+# OxyMake (Python launcher)
+
+A content-addressable workflow engine. You `git checkout` an old branch, re-run
+your pipeline, and it **does not** rebuild everything — change detection is a
+BLAKE3 hash of file *content*, not timestamps.
+
+```bash
+uv tool install oxymake     # or: pipx install oxymake
+ox --help
+```
+
+This package is a thin launcher: on first run it downloads the prebuilt `ox`
+binary for your platform from the
+[GitHub release](https://github.com/noogram/oxymake/releases/latest), verifies
+its SHA-256, caches it, and execs it. No Rust toolchain required — which is the
+point: bioinformatics and data-science users who live in conda/pip can try
+OxyMake without a source build.
+
+Full documentation: <https://github.com/noogram/oxymake>

oxymake-0.1.0/oxymake_launcher.py

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+"""Thin launcher for the OxyMake `ox` binary.
+
+Installed via `uv tool install oxymake` / `pipx install oxymake`, this module
+exposes the `ox` and `oxymake` console scripts. On first invocation it downloads
+the prebuilt binary matching the host platform from the GitHub release, verifies
+its SHA-256 against the `.sha256` sidecar, caches it under the user cache dir,
+and execs it. No Rust toolchain is required.
+
+This keeps the conda/pip onboarding path open: the audience that lives in Python
+never has to `cargo install` from source.
+"""
+
+from __future__ import annotations
+
+import hashlib
+import os
+import platform
+import stat
+import sys
+import tarfile
+import tempfile
+import urllib.request
+from pathlib import Path
+
+__version__ = "0.1.0"
+
+_REPO = "noogram/oxymake"
+_BASE = f"https://github.com/{_REPO}/releases/download/v{__version__}"
+
+# (sys.platform startswith, machine) -> release target triple
+_TARGETS = {
+    ("darwin", "arm64"): "aarch64-apple-darwin",
+    ("darwin", "x86_64"): "x86_64-apple-darwin",
+    ("linux", "x86_64"): "x86_64-unknown-linux-gnu",
+    ("linux", "amd64"): "x86_64-unknown-linux-gnu",
+}
+
+
+def _target() -> str:
+    key = (sys.platform, platform.machine().lower())
+    target = _TARGETS.get(key)
+    if target is None:
+        raise SystemExit(
+            f"oxymake: no prebuilt binary for {key}. "
+            f"Build from source: https://github.com/{_REPO}#install"
+        )
+    return target
+
+
+def _cache_dir() -> Path:
+    root = os.environ.get("XDG_CACHE_HOME") or str(Path.home() / ".cache")
+    d = Path(root) / "oxymake" / __version__
+    d.mkdir(parents=True, exist_ok=True)
+    return d
+
+
+def _download(url: str, dest: Path) -> None:
+    with urllib.request.urlopen(url) as resp, open(dest, "wb") as fh:  # noqa: S310
+        fh.write(resp.read())
+
+
+def _verify(tarball: Path, target: str) -> None:
+    """Verify the tarball against its published .sha256 sidecar."""
+    expected = _download_text(f"{_BASE}/ox-{target}.tar.gz.sha256").split()[0].strip()
+    actual = hashlib.sha256(tarball.read_bytes()).hexdigest()
+    if actual != expected:
+        raise SystemExit(
+            f"oxymake: checksum mismatch for ox-{target}.tar.gz "
+            f"(expected {expected}, got {actual}). Refusing to run."
+        )
+
+
+def _download_text(url: str) -> str:
+    with urllib.request.urlopen(url) as resp:  # noqa: S310
+        return resp.read().decode()
+
+
+def _ensure_binary() -> Path:
+    target = _target()
+    binary = _cache_dir() / "ox"
+    if binary.exists():
+        return binary
+
+    url = f"{_BASE}/ox-{target}.tar.gz"
+    with tempfile.TemporaryDirectory() as tmp:
+        tarball = Path(tmp) / "ox.tar.gz"
+        _download(url, tarball)
+        _verify(tarball, target)
+        with tarfile.open(tarball) as tf:
+            tf.extract("ox", _cache_dir())  # noqa: S202 - controlled, verified archive
+    binary.chmod(binary.stat().st_mode | stat.S_IEXEC)
+    return binary
+
+
+def main() -> "int":
+    binary = _ensure_binary()
+    os.execv(str(binary), [str(binary), *sys.argv[1:]])
+
+
+if __name__ == "__main__":
+    main()

oxymake-0.1.0/pyproject.toml

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+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "oxymake"
+version = "0.1.0"
+description = "Content-addressable workflow engine — git checkout no longer rebuilds everything"
+readme = "README.md"
+requires-python = ">=3.8"
+license = { text = "MIT OR Apache-2.0" }
+authors = [{ name = "Emmanuel Sérié", email = "emmanuel@serie.dev" }]
+keywords = ["workflow", "pipeline", "snakemake", "build", "cache"]
+
+[project.urls]
+Homepage = "https://oxymake.dev"
+Repository = "https://github.com/noogram/oxymake"
+Releases = "https://github.com/noogram/oxymake/releases"
+
+# This is a thin launcher: it fetches the prebuilt `ox` binary that matches the
+# host platform from the GitHub release on first run, caches it, and execs it.
+# It deliberately has no Rust build dependency so that `uv tool install oxymake`
+# and `pipx install oxymake` work in a pure conda/pip environment.
+
+[project.scripts]
+ox = "oxymake_launcher:main"
+oxymake = "oxymake_launcher:main"
+
+# The distribution name (`oxymake`) does not match the single launcher module
+# (`oxymake_launcher.py`), so hatchling cannot auto-detect what to ship in the
+# wheel — it must be told explicitly, or `python -m build` fails the wheel step.
+[tool.hatch.build.targets.wheel]
+only-include = ["oxymake_launcher.py"]
+
+[tool.hatch.build.targets.sdist]
+include = ["oxymake_launcher.py", "README.md", "pyproject.toml"]