diff --git a/README.md b/README.md index 63c7b83c..e0a05bfe 100644 --- a/README.md +++ b/README.md @@ -69,6 +69,32 @@ bun run test bun run build ``` +## Paper and documentation site + +The manuscript in `paper/` renders with Quarto. Its Python environment is the +`docs` extra, which holds only the Jupyter kernel and notebook runner that +Quarto's Jupyter engine drives (ipykernel, nbclient, nbformat). See +[`paper/README.md`](paper/README.md) for the other prerequisites. + +```bash +uv sync --extra docs +uv run python paper/render_paper.py +``` + +The operational-docs site in `docs/` builds with Jupyter Book 2, which +`docs/requirements.txt` declares outside `uv.lock`. Build it in a throwaway +environment (Jupyter Book needs Node.js 18, 20 or 22+): + +```bash +cd docs +uv run --no-project --with-requirements requirements.txt jupyter book build --html +``` + +The output lands in `docs/_build/` (gitignored). jupyter-book stays out of the +`docs` extra on purpose: it pulls in jupyter-server, nbconvert, bleach, mistune +and their dependencies, none of which the paper render uses, and every package +in `uv.lock` is in Dependabot's scan whichever extra it belongs to. + ## Benchmark run For paid/public runs, follow the concrete diff --git a/docs/requirements.txt b/docs/requirements.txt index 31024bb2..71cca9fc 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1 +1,4 @@ +# Builds the docs/ site: cd docs && uv run --no-project --with-requirements +# requirements.txt jupyter book build --html. Kept out of pyproject.toml and +# uv.lock on purpose; see "Paper and documentation site" in README.md. jupyter-book>=2.0 diff --git a/paper/README.md b/paper/README.md index d044364a..f2417802 100644 --- a/paper/README.md +++ b/paper/README.md @@ -30,7 +30,11 @@ Notes: to the invoking virtualenv (`render_paper.py` sets `QUARTO_PYTHON` and `JUPYTER_PREFER_ENV_PATH=1`), so it always executes this checkout's `policybench`. No user-level kernelspec needs to be registered. The render - environment lives in the `docs` extra (`uv sync --extra docs`). + environment lives in the `docs` extra (`uv sync --extra docs`): ipykernel, + nbclient and nbformat, the kernel and notebook runner that Quarto's Jupyter + engine drives. It does not include jupyter-book, which builds only the + separate `docs/` site; see "Paper and documentation site" in the top-level + README. - The manuscript tables and figures read from the frozen source run exports under `paper/snapshot/20260501/runs/`. - `app/src/data.json` is the live site export. For this snapshot it must match diff --git a/pyproject.toml b/pyproject.toml index 48de20e3..7aa74caf 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -28,9 +28,12 @@ dev = [ "pytest-cov>=5.0", "ruff>=0.4", ] +# The paper render environment (paper/render_paper.py, .github/workflows/paper.yml): +# the Jupyter kernel and notebook runner that Quarto's Jupyter engine drives. +# jupyter-book, which builds the docs/ site, stays out of uv.lock on purpose: +# docs/requirements.txt declares it (README.md, "Paper and documentation site"). docs = [ "ipykernel>=6.0", - "jupyter-book>=2.0", "nbformat>=5.0", "nbclient>=0.10", ] diff --git a/tests/test_render_environment.py b/tests/test_render_environment.py new file mode 100644 index 00000000..69094c05 --- /dev/null +++ b/tests/test_render_environment.py @@ -0,0 +1,328 @@ +"""The paper render environment stays free of Jupyter Book's server stack. + +The ``docs`` extra is the environment ``paper/render_paper.py`` and the Paper +workflow render the manuscript in. Quarto's Jupyter engine runs the notebook +through nbclient and nbformat on the ipykernel ``python3`` kernel; it never +imports jupyter-book, or the jupyter-server and nbconvert stack behind it. +jupyter-book builds only the docs/ site, from docs/requirements.txt, so it stays +out of uv.lock: Dependabot scans every locked package, whichever extra pulls it +in, and that stack brought bleach, mistune and soupsieve alerts with it. +""" + +from __future__ import annotations + +import codecs +import os +import re +import tomllib +from pathlib import Path + +import pytest +from packaging.requirements import InvalidRequirement, Requirement + +ROOT = Path(__file__).resolve().parents[1] +RENDER_KERNEL = {"ipykernel", "nbclient", "nbformat"} +DOCS_SITE_STACK = {"jupyter-book", "jupyter-server", "nbconvert"} + + +def _name(requirement: str) -> str: + match = re.match(r"\s*([A-Za-z0-9][A-Za-z0-9._-]*)", requirement) + assert match, requirement + return re.sub(r"[-_.]+", "-", match.group(1)).lower() + + +def _extras() -> dict[str, set[str]]: + project = tomllib.loads((ROOT / "pyproject.toml").read_text())["project"] + return { + extra: {_name(requirement) for requirement in requirements} + for extra, requirements in project["optional-dependencies"].items() + } + + +def test_docs_extra_holds_the_render_kernel(): + assert RENDER_KERNEL <= _extras()["docs"] + + +def test_no_extra_declares_the_docs_site_stack(): + for extra, names in _extras().items(): + assert not names & DOCS_SITE_STACK, extra + + +def test_docs_site_stack_is_not_locked(): + lock = tomllib.loads((ROOT / "uv.lock").read_text()) + locked = {package["name"] for package in lock["package"]} + assert not locked & DOCS_SITE_STACK + + +# The line forms _requirement_names reads. pip (req_file.py and +# req/constructors.py) and uv, which builds the docs site, read each of them +# the same way; any other line fails the test rather than being guessed at. +# Elsewhere they differ: on continuation lines, -r spellings, archive-like +# versions, encoding declarations, include cycles, a .. after a symlinked +# directory and include paths ending in /, and uv rejects empty parentheses +# and (in 0.11) a trailing comma that pip accepts. A false marker makes both +# quietly install nothing. So a guess could hide jupyter-book from one or +# both. Absolute include paths and included symlinks are refused too, though +# pip and uv read the cases run so far alike: no file here needs them, and +# refusing them keeps the test independent of the machine's paths and of how +# uv recognizes a file it has already read. +# - blank lines and comments: a # at a line's start or after whitespace, +# except a PEP 263 encoding line among a file's first two, which pip +# applies to the whole file; +# - includes: -r FILE, --requirement FILE or --requirement=FILE, where FILE +# is a relative path, resolved against the including file's directory, +# that names no symlink (read either with .. collapsed, as pip opens it, +# or as the OS resolves it), has no .. after a symlinked directory, +# doesn't end in / or /. and closes no cycle; +# - requirements: a name, optional extras and version specifiers with no +# empty parentheses or trailing comma; no URL, path, marker, archive name +# or per-requirement option. +# Every file is UTF-8 with no byte-order mark. +_COMMENT = re.compile(r"(^|\s+)#.*$") +_INCLUDE = re.compile( + r"(?:-r\s+|--requirement(?:\s+|=))([A-Za-z0-9._][A-Za-z0-9._/-]*)" +) +# pip decodes a file by its byte-order mark, or else by a PEP 263 line among +# its first two that starts with # (_decode_req_file in req_file.py). The +# UTF-16 and UTF-32 marks aren't valid UTF-8, so only UTF-8's needs a check. +_PEP263 = re.compile(rb"coding[:=]\s*([-\w.]+)") +# pip's archive extensions (pip/_internal/utils/filetypes.py), which it +# compares case-insensitively, after stripping extras, to decide that a line +# names a file rather than a project. +_ARCHIVE = (".zip", ".whl", ".tar.bz2", ".tbz", ".tar.gz", ".tgz", ".tar") +_ARCHIVE += (".tar.xz", ".txz", ".tlz", ".tar.lz", ".tar.lzma") + + +def _requirement_names(path: Path, _including: tuple[str, ...] = ()) -> set[str]: + """Names of the packages a requirements file asks pip and uv to install, + following its includes. A line outside the forms above fails the test.""" + real = os.path.realpath(path) + assert real not in _including, f"an include cycle: {path}" + data = path.read_bytes() + assert not data.startswith(codecs.BOM_UTF8), f"a byte-order mark: {path.name}" + for first in data.split(b"\n")[:2]: + assert not (first[:1] == b"#" and _PEP263.search(first)), ( + f"an encoding declaration: {path.name}: {first!r}" + ) + try: + # Decoded from bytes, so a lone carriage return isn't a line break. + text = data.decode() + except UnicodeDecodeError: + raise AssertionError(f"not UTF-8: {path.name}") from None + names = set() + for number, raw in enumerate(text.split("\n"), 1): + raw = raw.removesuffix("\r") + where = f"{path.name}:{number}: {raw!r}" + assert all(c in " \t" for c in raw if c.isspace()), ( + f"whitespace other than spaces and tabs: {where}" + ) + assert not raw.endswith("\\"), f"a continuation line: {where}" + line = _COMMENT.sub("", raw).strip() + if not line: + continue + include = _INCLUDE.fullmatch(line) + if include: + # pathlib drops a trailing / or /., and uv rejects the path. + assert not re.search(r"/\.?$", include.group(1)), ( + f"an include path ending in / or /.: {where}" + ) + target = path.parent / include.group(1) + assert not ( + os.path.islink(target) or os.path.islink(os.path.normpath(target)) + ), f"an include of a symlink: {where}" + # pip collapses .. before opening the file (os.path.abspath), + # while opening it follows a symlink before applying the .. + lexical = os.path.realpath(os.path.normpath(target)) + assert os.path.realpath(target) == lexical, ( + f"an include whose .. crosses a symlink: {where}" + ) + names |= _requirement_names(target, (*_including, real)) + continue + assert not re.match(r"(?:-r\s+|--requirement(?:\s+|=))/", line), ( + f"an absolute include path: {where}" + ) + assert not line.startswith("-"), f"an option: {where}" + assert not re.search(r"\s-", line), f"a per-requirement option: {where}" + assert not re.search(r"[@:/\\]", line), f"a URL or path: {where}" + assert ";" not in line, f"a marker: {where}" + assert "===" not in line, f"arbitrary equality: {where}" + assert not re.search(r",\s*\)?$", line), f"a trailing comma: {where}" + assert not re.search(r"\(\s*\)", line), f"empty parentheses: {where}" + stem = re.sub(r"\s*\[[^\]]+\]$", "", line).lower() + assert not stem.endswith(_ARCHIVE), f"an archive name: {where}" + requirement = Requirement(line) + assert requirement.url is None and requirement.marker is None, where + names.add(_name(requirement.name)) + return names + + +def test_requirement_names_read_the_forms_pip_and_uv_agree_on(tmp_path): + (tmp_path / "sub").mkdir() + (tmp_path / "base.txt").write_text("Included_Pkg\n") + (tmp_path / "sub" / "more.txt").write_text("-r ../deep.txt\n") + (tmp_path / "deep.txt").write_text("deep\n") + (tmp_path / "other.txt").write_text("other\r\n") + (tmp_path / "tabbed.txt").write_text("after-tab\n") + (tmp_path / "requirements.txt").write_text( + "# top\n" + " # indented\n" + "\n" + "foo>=1 # why\n" + "Bar_Baz[extra]\n" + "spaced >= 1.0, < 3\n" + "\tTabbed==1.0\t# a tab before the comment\n" + "-r base.txt\n" + "--requirement sub/more.txt\n" + "--requirement=other.txt\n" + "--requirement\t./tabbed.txt\n" + ) + assert _requirement_names(tmp_path / "requirements.txt") == { + "foo", + "bar-baz", + "spaced", + "tabbed", + "included-pkg", + "deep", + "other", + "after-tab", + } + + +@pytest.mark.parametrize( + ("text", "reason"), + [ + ("jupyter-book>=2.0 \\\n --hash=sha256:00\n", "a continuation line"), + ("jupyter-book \\\n>=2.0\n", "a continuation line"), + # pip joins the next line onto a comment that doesn't start the line. + ("foo # see below \\\njupyter-book\n", "a continuation line"), + ("jupyter-book\x0c>=2.0\n", "whitespace other than"), + ("jupyter-book>=2.0\xa0# note\n", "whitespace other than"), + ("jupyter-book>=2.0\rfoo\n", "whitespace other than"), + # pip decodes the file as UTF-7, so "+AFw" is a backslash that joins the + # jupyter-book line into the comment before it. + ("# coding: utf-7\nfoo # x+AFw\njupyter-book\n", "an encoding declaration"), + ( + "# Docs site; no coding=needed\njupyter-book>=2.0\n", + "an encoding declaration", + ), + ("\n# coding: utf-16\njupyter-book\n", "an encoding declaration"), + ("\ufeffjupyter-book\n", "a byte-order mark"), + (b"jupyter-book # caf\xe9\n", "not UTF-8"), + ("jupyter-book\n".encode("utf-16"), "not UTF-8"), + ("jupyter-book\n".encode("utf-32"), "not UTF-8"), + ("-r requirements.txt\n", "an include cycle"), + ("foo\n-r requirements.txt\n", "an include cycle"), + ("-r base.txt/\n", "an include path ending in /"), + ("-r /abs/base.txt\n", "an absolute include path"), + ("--requirement=/abs/base.txt\n", "an absolute include path"), + ("--requirement=base.txt/.\n", "an include path ending in /"), + ("-r=base.txt\n", "an option"), # pip opens "=base.txt"; uv, base.txt + ("-rbase.txt\n", "an option"), + ("--requirementbase.txt\n", "an option"), + ("--requirements=base.txt\n", "an option"), + ("--requirem base.txt\n", "an option"), + ('-r "base.txt"\n', "an option"), + ("-r base.txt --pre\n", "an option"), + ("-r base.txt -r other.txt\n", "an option"), + ("-r ${DIR}/base.txt\n", "an option"), + ("-r https://example.com/base.txt\n", "an option"), + ("-c base.txt\n", "an option"), + ("-e ./local\n", "an option"), + ("--editable=./local\n", "an option"), + ("--edit ./local\n", "an option"), + ("--pre -e ./local\n", "an option"), + ("--index-url https://example.com/simple\n", "an option"), + ("https://example.com/pkg-1.0-py3-none-any.whl\n", "a URL or path"), + ("git+https://example.com/pkg.git\n", "a URL or path"), + ("./vendor/pkg-1.0.tar.gz\n", "a URL or path"), + ("named @ https://example.com/named-1.0.tar.gz\n", "a URL or path"), + ( + "jupyter-book @ https://h.example/p;v=1/jupyter_book-2.1.7-py3-none-any.whl\n", + "a URL", + ), + ('jupyter-book>=2.0 ; python_version < "3"\n', "a marker"), + ("jupyter-book>=2.0; extra == 'docs'\n", "a marker"), + ("jupyter-book===2.0\n", "arbitrary equality"), + ("jupyter-book===2.0.zip\n", "arbitrary equality"), + ("jupyter-book>=2.0,\n", "a trailing comma"), + ("jupyter-book (>=1, <3 , ) # x\n", "a trailing comma"), + ("jupyter-book ()\n", "empty parentheses"), + ("jupyter-book[docs] ( ) # x\n", "empty parentheses"), + ("jupyter-book>=2.0 --hash=sha256:00\n", "a per-requirement option"), + ("pkg-1.0-py3-none-any.whl\n", "an archive name"), + ("PKG-1.0-py3-none-any.WHL\n", "an archive name"), + ("jupyter-book.txz\n", "an archive name"), + ("jupyter-book==2.0+local.zip\n", "an archive name"), + ("jupyter-book.zip[docs]\n", "an archive name"), + ("jupyter-book.zip [docs]\n", "an archive name"), + # A naive comment rule would read this as "foo". + ("foo#bar\n", None), + ("${PKG}>=2.0\n", None), + ], +) +def test_requirement_names_refuse_every_other_form(tmp_path, text, reason): + (tmp_path / "base.txt").write_text("jupyter-book>=2.0\n") + data = text if isinstance(text, bytes) else text.encode() + (tmp_path / "requirements.txt").write_bytes(data) + if reason is None: + with pytest.raises(InvalidRequirement): + _requirement_names(tmp_path / "requirements.txt") + else: + with pytest.raises(AssertionError, match=re.escape(reason)): + _requirement_names(tmp_path / "requirements.txt") + + +def test_requirement_names_refuse_an_include_whose_dotdot_crosses_a_symlink( + tmp_path, +): + """pip opens -r sub/../base.txt as docs/base.txt; the OS follows sub first.""" + (tmp_path / "elsewhere").mkdir() + (tmp_path / "elsewhere" / "more.txt").write_text("more\n") + (tmp_path / "docs").mkdir() + (tmp_path / "docs" / "sub").symlink_to(tmp_path / "elsewhere") + (tmp_path / "docs" / "base.txt").write_text("foo\n") + (tmp_path / "base.txt").write_text("jupyter-book\n") + requirements = tmp_path / "docs" / "requirements.txt" + requirements.write_text("-r sub/more.txt\n") + assert _requirement_names(requirements) == {"more"} + requirements.write_text("-r sub/../base.txt\n") + with pytest.raises(AssertionError, match="an include whose .. crosses a symlink"): + _requirement_names(requirements) + + +def test_requirement_names_refuse_an_absolute_include(tmp_path): + """Refused whatever characters the machine's temp path holds.""" + (tmp_path / "base.txt").write_text("jupyter-book\n") + requirements = tmp_path / "requirements.txt" + requirements.write_text(f"-r {tmp_path / 'base.txt'}\n") + with pytest.raises(AssertionError, match="an absolute include path"): + _requirement_names(requirements) + + +def test_requirement_names_refuse_an_include_of_a_symlink(tmp_path): + """A symlinked file's own includes resolve against the link's directory.""" + (tmp_path / "a").mkdir() + (tmp_path / "a" / "real.txt").write_text("-r base.txt\n") + (tmp_path / "a" / "base.txt").write_text("foo\n") + (tmp_path / "docs").mkdir() + (tmp_path / "docs" / "link.txt").symlink_to("../a/real.txt") + (tmp_path / "docs" / "base.txt").write_text("jupyter-book\n") + requirements = tmp_path / "docs" / "requirements.txt" + requirements.write_text("-r ../a/real.txt\n") + assert _requirement_names(requirements) == {"foo"} + requirements.write_text("-r link.txt\n") + with pytest.raises(AssertionError, match="an include of a symlink"): + _requirement_names(requirements) + # pip opens docs/x.txt, a symlink; the OS follows sub to e/inner first + # and opens e/x.txt, a regular file, so both read the same file. + (tmp_path / "e" / "inner").mkdir(parents=True) + (tmp_path / "e" / "x.txt").write_text("jupyter-book\n") + (tmp_path / "docs" / "x.txt").symlink_to("../e/x.txt") + (tmp_path / "docs" / "sub").symlink_to("../e/inner") + requirements.write_text("-r sub/../x.txt\n") + with pytest.raises(AssertionError, match="an include of a symlink"): + _requirement_names(requirements) + + +def test_docs_site_requirements_declare_jupyter_book(): + assert 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