Zenodo package (open release) and the PDF rebuilt with the published history's hashes.

make_open_package.py builds the archive from HEAD - source (git archive, LF line ends), the full history (git bundle), both simbracket wheels, README, requirements, reproduce.sh, LICENSE, NOTICE, SHA256SUMS - and refuses if any commit of the branch carries a string from a private list kept outside the repository, or if a text file has CRLF line ends; cleanroom_check.sh verifies the archive on Linux. Appendix D states that the history was rewritten once before publication to remove a server address, and that Table D1 is recomputed from the published history. lib/LICENSE so the wheels carry the licence. Server: verify 548 OK / 0 BAD, regression x2 1239 passed, PDF 32 pages, 0 errors, 0 overfull.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>

article/sim_numerics.md

@@ -718,7 +718,7 @@ Three caveats, all of them limitations of the measurement rather than of the met
 
 ## Appendix D. Advance records and the frozen code
 
-Every rule of §6 and every test of §7 was written down, with its criteria and stop rule, before its code and its run. Table D1 gives, for each document, the commit that first added it and the commit that first added the results its run wrote, both read from git by `check_prereg_order.py`: 25 of the 30 were committed before their results; four were committed together with them, so git cannot order them; one was decided on its smoke run and has no results file. We call these documents advance records, not pre-registrations: they live in the author's repository, and their order relative to the runs is attested only by the author's git history, whose timestamps the author sets; no external registry was used. A deposit with an external timestamp (Zenodo, OSF) before a run would remove that limitation for future tests. The code of A′ was committed (`8027d7f`) after corpus 4 was defined (`657df10`) and before its results (`6d2531e`); `simroot/pure.py` did not change in between.
+Every rule of §6 and every test of §7 was written down, with its criteria and stop rule, before its code and its run. Table D1 gives, for each document, the commit that first added it and the commit that first added the results its run wrote, both read from git by `check_prereg_order.py`: 25 of the 30 were committed before their results; four were committed together with them, so git cannot order them; one was decided on its smoke run and has no results file. We call these documents advance records, not pre-registrations: they live in the author's repository, and their order relative to the runs is attested only by the author's git history, whose timestamps the author sets; no external registry was used. A deposit with an external timestamp (Zenodo, OSF) before a run would remove that limitation for future tests. Before publication the history was rewritten once, to remove infrastructure details (a server address); the commits cited here are those of the published history, in which `check_prereg_order.py` recomputes Table D1. The code of A′ was committed (`8027d7f`) after corpus 4 was defined (`657df10`) and before its results (`6d2531e`); `simroot/pure.py` did not change in between.
 
 **Table D1.** Advance records, in the order they were written.
 

article/sim_numerics.tex

@@ -2400,9 +2400,13 @@ in the author's repository, and their order relative to the runs is
 attested only by the author's git history, whose timestamps the author
 sets; no external registry was used. A deposit with an external
 timestamp (Zenodo, OSF) before a run would remove that limitation for
-future tests. The code of A′ was committed (\texttt{8027d7f}) after
+future tests. Before publication the history was rewritten once, to
-corpus 4 was defined (\texttt{657df10}) and before its results
+remove infrastructure details (a server address); the commits cited here
-(\texttt{6d2531e}); \texttt{simroot/pure.py} did not change in between.
+are those of the published history, in which
+\texttt{check\_prereg\_order.py} recomputes Table D1. The code of A′ was
+committed (\texttt{8027d7f}) after corpus 4 was defined
+(\texttt{657df10}) and before its results (\texttt{6d2531e});
+\texttt{simroot/pure.py} did not change in between.
 
 \textbf{Table D1.} Advance records, in the order they were written.
 

lib/LICENSE

@@ -0,0 +1,202 @@
+
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zenodo/README.md

@@ -0,0 +1,70 @@
+# Root Finding by Similarity and Analogy — code, data and history
+
+Companion archive to the paper *Root Finding by Similarity and Analogy: A Bracketing Method with a
+Data-Selected Decision Layer* (V. Sitnikov). Everything behind the paper is here, under the Apache
+License 2.0: the method's reference implementation, a compiled library of the proposed method A′, the
+benchmark harness, the problem corpora, every results file, the records written before each run, the
+paper itself, and the full development history.
+
+## Contents
+
+| path | what |
+|---|---|
+| `source/` | the repository at the commit the paper was built from: `simroot/` (the reference implementation of the base rule, A′ and every variant the paper measures), `lib/` (the source of the compiled library `simbracket`), the sweep scripts, corpora (`corpus_*.py`), diagnoses, the verifier `verify_article.py`, the tests, every results file (`sweep_*.json`, `results_*.txt`), the records written before the runs (`PREREG_*.md`, `POSTHOC_*.md`), the findings (`FINDINGS_*.md`) and the paper (`article/`) |
+| `sim-numerics.bundle` | the full git history of that branch (`git clone sim-numerics.bundle`); the commits cited in the paper's Appendix D are in it |
+| `wheels/` | `simbracket`, A′ as a compiled library (Python ≥ 3.10; Linux and Windows builds) |
+| `requirements.txt`, `reproduce.sh` | the Python packages used, and the one-command reproduction |
+| `SHA256SUMS` | checksums of every file in the archive |
+
+## Requirements
+
+**Linux x86_64 for reproducing the numbers.** The paper's numbers come from one Linux machine (Ubuntu
+24.04, glibc 2.39, Python 3.12.3). The test functions call the platform's `libm`, whose last digit
+differs between platforms; on Windows, TOMS 748 needs 2635 evaluations on the Alefeld–Potra–Shi set
+instead of 2636, and two of the paper's fresh recomputations move by a few evaluations. Using the
+method needs no particular platform.
+
+## Reproduce
+
+```bash
+./reproduce.sh
+```
+
+creates a virtual environment, installs `requirements.txt` and the `simbracket` wheel, and in `source/`
+runs
+
+1. `python -u verify_article.py` — recomputes or re-reads every number stated in the paper (548) and
+   compares it with the value printed there; it ends with *every number stated in the paper matches the
+   sweep data*;
+2. `python -m pytest tests/test_simbracket_equivalence.py` — the compiled library equals the reference
+   implementation bit for bit, point and evaluation count, on all 868 problems of the six corpora.
+
+Any table can be recomputed from scratch with its sweep script; each script's docstring names the table
+it produces (for example `python -u rescore_uniform.py` for the protocol tables, `python -u
+sweep_fourth.py --fourth` for corpus 4, `python -u sweep_controls.py` and `python -u sweep_estimated.py`
+for the controls). The full test suite is `python -m pytest tests`.
+
+## Use A′ on your own problem
+
+```python
+from simbracket import find_root, evaluation_bound
+
+x, nfev, converged = find_root(f, a, b, xtol=1e-12, maxfev=200)
+# f(a) and f(b) of opposite signs; stops when the bracket is no wider than xtol or f(x) == 0;
+# never more than evaluation_bound(a, b, xtol) = 2*ceil(log2(|b-a|/xtol)) + 3 evaluations
+```
+
+or, from source, `simroot.pure.pure_root` with the configuration named `APRIME` in `sweep_full.py`.
+
+## The records and their order
+
+`PREREG_*.md` were written, and committed, before the runs they describe; `POSTHOC_*.md` after, as
+marked. Appendix D of the paper lists each record with its commit and the commit of its results;
+`check_prereg_order.py` recomputes that table from the history in `sim-numerics.bundle`. The order is
+attested by the author's git history, not by an external registry. Before publication the history was
+rewritten once to remove infrastructure details (a server address); the commit hashes cited in the paper
+are those of the rewritten history in this archive.
+
+## Licence
+
+Apache License 2.0 (`LICENSE`); copyright Valeri Sitnikov (`NOTICE`).

zenodo/cleanroom_check.sh

@@ -0,0 +1,34 @@
+#!/bin/bash
+# Clean-room check of the Zenodo archive on Linux: unzip into an empty directory, install only the
+# simbracket wheel from the archive (dependencies from the existing environment, nothing downloaded),
+# run the verifier and the equivalence test from source/, and recompute Appendix D from the bundled
+# history.  Usage: cleanroom_check.sh <zip>
+set -e
+export OMP_NUM_THREADS=1 OPENBLAS_NUM_THREADS=1 MKL_NUM_THREADS=1
+PY=~/torchenv/bin/python
+Z=$(readlink -f "$1")
+R=~/zenodo_cleanroom
+rm -rf $R && mkdir -p $R && cd $R
+$PY -c "import zipfile,sys; zipfile.ZipFile(sys.argv[1]).extractall('.')" "$Z"
+D=$(ls -d sim-numerics-*/)
+cd $R/$D
+echo "== checksums"; sha256sum -c --quiet SHA256SUMS && echo "all match"
+$PY -m pip install --quiet --no-deps --target $R/site wheels/simbracket-*-linux_x86_64.whl
+cd source
+export PYTHONPATH=$R/site:.
+$PY -c "import simbracket, simroot.pure; print('simbracket', simbracket.__file__); print('reference', simroot.pure.__file__)"
+echo "== verify_article.py"
+$PY -u verify_article.py > $R/verify.log 2>&1 || true
+echo "OK $(grep -c '^  OK' $R/verify.log)  BAD $(grep -c '^  BAD' $R/verify.log)"
+grep '^  BAD' $R/verify.log || true
+grep -A6 '^Traceback' $R/verify.log || true
+tail -1 $R/verify.log
+echo "== equivalence test"
+$PY -m pytest tests/test_simbracket_equivalence.py -q -p no:cacheprovider 2>&1 | tail -1
+echo "== Appendix D from the bundled history"
+cd $R && git clone --quiet $R/$D/sim-numerics.bundle hist && cd hist
+$PY -u check_prereg_order.py | grep '^| `' > $R/appD_from_history.txt
+grep '^| `' $R/$D/source/results_prereg_order.txt > $R/appD_in_archive.txt
+if diff -q $R/appD_from_history.txt $R/appD_in_archive.txt; then echo "Appendix D reproduced from the history: identical"; else echo "Appendix D DIFFERS"; fi
+grep -c '^| `' $R/appD_from_history.txt
+echo "=== CLEANROOM DONE ==="

zenodo/make_open_package.py

@@ -0,0 +1,96 @@
+"""Build the Zenodo archive (open release, Apache-2.0): the repository at HEAD of release
+(`git archive`), its full history (`git bundle`), the simbracket wheels, README, requirements, the
+reproduction script, LICENSE, NOTICE and SHA256SUMS - zipped as sim-numerics-<version>.zip.
+
+Refuses to build if the tree or the bundled history contains the server address or the
+specifics of the next method, if HEAD is not release, or if a text file of the archive has
+Windows line ends.
+
+    python -u zenodo/make_open_package.py 1.0.0
+"""
+from __future__ import annotations
+
+import hashlib
+import os
+import shutil
+import subprocess
+import sys
+import zipfile
+
+ROOT = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
+VERSION = sys.argv[1] if len(sys.argv) > 1 else "1.0.0"
+NAME = f"sim-numerics-{VERSION}"
+OUT = os.path.join(ROOT, "zenodo_build")
+PKG = os.path.join(OUT, NAME)
+# The strings that must appear in no commit are read from a file OUTSIDE the repository (named by
+# $ZENODO_FORBIDDEN): listing them here would put them into the history this check protects.
+FORBIDDEN_FILE = os.environ.get("ZENODO_FORBIDDEN", "")
+WHEELS = ["lib/dist/simbracket-1.0.0-cp310-abi3-linux_x86_64.whl",
+          "lib/dist/simbracket-1.0.0-cp310-abi3-win_amd64.whl"]
+CRLF = bytes([13, 10])
+
+
+def git(*args, **kw):
+    return subprocess.run(["git", "-C", ROOT, *args], check=True, capture_output=True, **kw)
+
+
+def main():
+    branch = git("branch", "--show-current", text=True).stdout.strip()
+    assert branch == "release", branch
+    assert not git("status", "--porcelain", "--untracked-files=no", text=True).stdout.strip(), \
+        "commit everything first: the archive is HEAD"
+    assert FORBIDDEN_FILE and os.path.isfile(FORBIDDEN_FILE), "set ZENODO_FORBIDDEN to the private list"
+    assert not os.path.abspath(FORBIDDEN_FILE).startswith(ROOT), "the list must live outside the repository"
+    forbidden = [ln.strip() for ln in open(FORBIDDEN_FILE, encoding="utf8") if ln.strip()]
+    for s in forbidden:                                          # every commit of the branch
+        hits = subprocess.run(["git", "-C", ROOT, "log", "release", "-p", "-S", s, "--format=%h"],
+                              capture_output=True, text=True, encoding="utf8").stdout.split()
+        assert not hits, (s, hits[:3])
+    if os.path.isdir(OUT):
+        shutil.rmtree(OUT)
+    os.makedirs(os.path.join(PKG, "wheels"))
+    tar = os.path.join(OUT, "source.tar")
+    # core.autocrlf=false: the archive carries the repository's LF line ends, not Windows' CRLF
+    git("-c", "core.autocrlf=false", "archive", "--format=tar", "--prefix=source/", "-o", tar, "HEAD")
+    shutil.unpack_archive(tar, PKG)
+    os.remove(tar)
+    git("bundle", "create", os.path.join(PKG, "sim-numerics.bundle"), "release")
+    for w in WHEELS:
+        shutil.copy(os.path.join(ROOT, w), os.path.join(PKG, "wheels"))
+    src = os.path.join(PKG, "source")          # from the archive: LF, exactly as committed
+    for f in ("README.md", "requirements.txt", "reproduce.sh"):
+        shutil.copy(os.path.join(src, "zenodo", f), os.path.join(PKG, f))
+    for f in ("LICENSE", "NOTICE"):
+        shutil.copy(os.path.join(src, f), os.path.join(PKG, f))
+    bad = []
+    for d, _, files in os.walk(PKG):
+        for f in files:
+            if f.endswith((".py", ".sh", ".md", ".txt")) or f in ("LICENSE", "NOTICE"):
+                if CRLF in open(os.path.join(d, f), "rb").read():
+                    bad.append(os.path.relpath(os.path.join(d, f), PKG))
+    assert not bad, ("Windows line ends", bad[:5])
+    sums = []
+    for d, _, files in os.walk(PKG):
+        for f in sorted(files):
+            p = os.path.join(d, f)
+            rel = os.path.relpath(p, PKG).replace("\\", "/")
+            sums.append(f"{hashlib.sha256(open(p, 'rb').read()).hexdigest()}  {rel}")
+    with open(os.path.join(PKG, "SHA256SUMS"), "w", encoding="ascii", newline="\n") as fh:
+        fh.write("\n".join(sorted(sums, key=lambda s: s[66:])) + "\n")
+    zp = os.path.join(OUT, NAME + ".zip")
+    with zipfile.ZipFile(zp, "w", zipfile.ZIP_DEFLATED) as z:
+        for d, _, files in os.walk(PKG):
+            for f in files:
+                p = os.path.join(d, f)
+                info = zipfile.ZipInfo.from_file(p, os.path.relpath(p, OUT).replace("\\", "/"))
+                if f.endswith(".sh"):
+                    info.external_attr = 0o755 << 16
+                with open(p, "rb") as src_fh:
+                    z.writestr(info, src_fh.read(), zipfile.ZIP_DEFLATED)
+    head = git("rev-parse", "--short", "HEAD", text=True).stdout.strip()
+    print(f"{zp}: {os.path.getsize(zp) / 1e6:.1f} MB, {len(sums)} files, source at {head}")
+    print("zenodo package done")
+
+
+if __name__ == "__main__":
+    main()

zenodo/reproduce.sh

@@ -0,0 +1,16 @@
+#!/bin/sh
+# Reproduce the paper's numbers (Linux x86_64, Python 3.12).  See README.md.
+set -e
+cd "$(dirname "$0")"
+python3.12 -m venv .venv
+. .venv/bin/activate
+python -m pip install --quiet -r requirements.txt
+python -m pip install --quiet --no-deps wheels/simbracket-*-linux_x86_64.whl
+export OMP_NUM_THREADS=1
+cd source
+echo "== verify_article.py (every number stated in the paper) =="
+python -u verify_article.py > ../verify.log 2>&1 || true
+echo "OK $(grep -c '^  OK' ../verify.log)  BAD $(grep -c '^  BAD' ../verify.log)"
+tail -1 ../verify.log
+echo "== simbracket against the reference implementation, bit for bit =="
+python -m pytest tests/test_simbracket_equivalence.py -q -p no:cacheprovider | tail -1

zenodo/requirements.txt

@@ -0,0 +1,5 @@
+numpy==2.4.3
+scipy==1.17.1
+mpmath==1.3.0
+pymodab==1.0.9
+pytest==9.1.1