cellgraph 0.1.0__py3-none-any.whl

cellgraph/vocabulary.py

@@ -0,0 +1,263 @@
+"""Annotations and the vocabulary a host composes from them (design 4).
+
+An annotation declares its key (and any extra keys it reads), a parser from its
+directive lines to a value, its effects from the closed set in ``effects``, whether
+it is in the definition key, an encoder when its value is not already canonical,
+and an optional validator. The package applies the effects and never interprets
+an annotation beyond them: one with no effects that is not in the key is metadata,
+available to the host as ``cell.annotations[key]``.
+"""
+
+from __future__ import annotations
+
+from collections.abc import Callable, Iterable, Iterator, Mapping, Sequence
+from dataclasses import dataclass, field, replace
+from typing import TYPE_CHECKING, Any
+
+from cellgraph.diagnostics import Diagnostic
+from cellgraph.effects import Effect
+from cellgraph.grammar import GRAMMAR, Directive, Grammar
+
+if TYPE_CHECKING:
+    from cellgraph.analysis import Cell
+
+
+class AnnotationError(ValueError):
+    """A directive that cannot be read as written.
+
+    Raised by a parser, an encoder or a validator. It becomes an error diagnostic,
+    and the cell is not plannable. ``code`` defaults to ``<key>_unreadable``.
+    """
+
+    def __init__(self, message: str, *, code: str | None = None, line: int | None = None):
+        super().__init__(message)
+        self.code = code
+        self.line = line
+
+
+@dataclass(frozen=True)
+class Partial:
+    """What a parser returns when part of an annotation reads: the value, and the errors.
+
+    The annotation is present with ``value`` (its effects and key field apply) and
+    each error becomes a diagnostic, so the cell is not plannable. For lines that
+    cannot be read beside lines that can, as Strata keeps the readable ones.
+    """
+
+    value: Any
+    errors: tuple[AnnotationError, ...]
+
+    def __init__(self, value: Any, errors: Iterable[AnnotationError]) -> None:
+        object.__setattr__(self, "value", value)
+        object.__setattr__(self, "errors", tuple(errors))
+
+
+@dataclass(frozen=True)
+class ValidationContext:
+    """What a validator sees: the cell, its names after effects, and the host's context."""
+
+    cell: Cell
+    defines: tuple[str, ...]
+    references: tuple[str, ...]
+    host: Any = None
+
+
+Parser = Callable[[list[Directive]], Any]
+Validator = Callable[[Any, ValidationContext], Iterable[Diagnostic]]
+CellEffects = Callable[[Mapping[str, Any], Mapping[str, Any]], Iterable[Effect]]
+
+
+_OFF = frozenset({"off", "false", "no", "0"})
+_FLAG_VALUES = frozenset({"", "on", "off", "true", "false", "yes", "no", "1", "0"})
+
+
+def scalar(convert: Callable[[str], Any] = str) -> Parser:
+    """One value; the last directive wins. An empty value or a failed ``convert`` is an error."""
+
+    def parse(directives: list[Directive]) -> Any:
+        last = directives[-1]
+        if not last.value:
+            raise AnnotationError(f"`@{last.key}` needs a value", line=last.line)
+        try:
+            return convert(last.value)
+        except (TypeError, ValueError) as exc:
+            raise AnnotationError(
+                f"`@{last.key} {last.value}` could not be read: {exc}", line=last.line
+            ) from exc
+
+    return parse
+
+
+def flag() -> Parser:
+    """``# @key`` or ``# @key on|off|true|false|yes|no|1|0``; the last directive wins."""
+
+    def parse(directives: list[Directive]) -> bool:
+        last = directives[-1]
+        if last.value.lower() not in _FLAG_VALUES:
+            raise AnnotationError(
+                f"`@{last.key} {last.value}`: expected nothing, or one of on, off, true, "
+                "false, yes, no, 1, 0",
+                line=last.line,
+            )
+        return last.value.strip().lower() not in _OFF
+
+    return parse
+
+
+def stacked(item: Callable[[Directive], Any]) -> Parser:
+    """One value per directive line, in source order; the lines may repeat."""
+
+    def parse(directives: list[Directive]) -> list[Any]:
+        return [item(directive) for directive in directives]
+
+    return mark_stacked(parse)
+
+
+def mark_stacked(parse: Parser) -> Parser:
+    """Mark *parse* as reading repeated lines, so ``set_directive`` refuses its key."""
+    setattr(parse, "stacked", True)  # noqa: B010
+    return parse
+
+
+def is_stacked(parse: Parser) -> bool:
+    """Whether *parse* reads repeated lines (``stacked``), which a single-line edit would drop."""
+    return bool(getattr(parse, "stacked", False))
+
+
+def _default_parse(directives: list[Directive]) -> Any:
+    return scalar(str)(directives)
+
+
+@dataclass(frozen=True)
+class Annotation:
+    """One annotation of a vocabulary.
+
+    - ``parse`` gets every directive of ``key`` and ``also_reads``, in source order.
+    - ``effects`` maps the parsed value to effects; it runs only when a directive is
+      present.
+    - ``in_key``: a present annotation adds one field, named ``key``, to the definition
+      key. The value is ``encode(value)``, or the value itself when it is canonical.
+    - ``validate`` gets the value and a ``ValidationContext`` and returns diagnostics.
+    """
+
+    key: str
+    parse: Parser = _default_parse
+    effects: Callable[[Any], Iterable[Effect]] | None = None
+    in_key: bool = True
+    encode: Callable[[Any], Any] | None = None
+    validate: Validator | None = None
+    also_reads: tuple[str, ...] = ()
+
+    @property
+    def keys(self) -> tuple[str, ...]:
+        """Every directive key this annotation reads."""
+        return (self.key, *self.also_reads)
+
+
+@dataclass(frozen=True)
+class Vocabulary:
+    """A set of annotations with distinct keys, and an optional per-cell host hook.
+
+    ``cell_effects(meta, parsed)`` is called for every cell, with the host's ``meta``
+    and the parsed value of each present annotation. It returns effects that come
+    from host configuration rather than directives; they go through the same phases
+    and conflict rules.
+    """
+
+    annotations: tuple[Annotation, ...] = ()
+    cell_effects: CellEffects | None = None
+    grammar: Grammar = field(default=GRAMMAR, compare=False)
+
+    def __init__(
+        self,
+        annotations: Sequence[Annotation] = (),
+        cell_effects: CellEffects | None = None,
+        grammar: Grammar = GRAMMAR,
+    ) -> None:
+        seen: dict[str, str] = {}
+        for annotation in annotations:
+            for key in annotation.keys:
+                if key in seen:
+                    raise ValueError(
+                        f"directive key {key!r} is claimed by both @{seen[key]} and "
+                        f"@{annotation.key}"
+                    )
+                seen[key] = annotation.key
+        object.__setattr__(self, "annotations", tuple(annotations))
+        object.__setattr__(self, "cell_effects", cell_effects)
+        object.__setattr__(self, "grammar", grammar)
+
+    @classmethod
+    def core(cls) -> Vocabulary:
+        """``@name``, ``@after``, ``@nocache``, ``@variant`` and ``@per_variant`` (design 6)."""
+        from cellgraph.core import core_annotations
+
+        return cls(core_annotations())
+
+    def __or__(self, other: Vocabulary) -> Vocabulary:
+        """Both vocabularies; a key in both is refused, so order never decides a result."""
+        hooks = [hook for hook in (self.cell_effects, other.cell_effects) if hook is not None]
+        combined: CellEffects | None
+        if len(hooks) == 2:
+            first, second = hooks
+
+            def combined(meta: Mapping[str, Any], parsed: Mapping[str, Any]) -> list[Effect]:
+                return [*first(meta, parsed), *second(meta, parsed)]
+
+        else:
+            combined = hooks[0] if hooks else None
+        return Vocabulary([*self.annotations, *other.annotations], cell_effects=combined)
+
+    def __iter__(self) -> Iterator[Annotation]:
+        return iter(self.annotations)
+
+    def __contains__(self, key: object) -> bool:
+        return any(annotation.key == key for annotation in self.annotations)
+
+    def __getitem__(self, key: str) -> Annotation:
+        for annotation in self.annotations:
+            if annotation.key == key:
+                return annotation
+        raise KeyError(key)
+
+    @property
+    def keys(self) -> frozenset[str]:
+        """Every directive key the vocabulary reads, ``also_reads`` keys included."""
+        return frozenset(key for annotation in self.annotations for key in annotation.keys)
+
+    def owner(self, directive_key: str) -> Annotation | None:
+        """The annotation that reads directives of *directive_key*, if any."""
+        for annotation in self.annotations:
+            if directive_key in annotation.keys:
+                return annotation
+        return None
+
+    def without(self, *keys: str) -> Vocabulary:
+        """This vocabulary without the annotations named *keys*."""
+        missing = set(keys) - {a.key for a in self.annotations}
+        if missing:
+            raise KeyError(sorted(missing))
+        return Vocabulary(
+            [a for a in self.annotations if a.key not in keys],
+            cell_effects=self.cell_effects,
+            grammar=self.grammar,
+        )
+
+    def replace(self, key: str, **changes: Any) -> Vocabulary:
+        """This vocabulary with annotation *key* changed, e.g. given a validator."""
+        return Vocabulary(
+            [replace(a, **changes) if a.key == key else a for a in self.annotations],
+            cell_effects=self.cell_effects,
+            grammar=self.grammar,
+        )
+
+    def set_directive(self, source: str, key: str, value: str) -> str:
+        """*source* with one ``# @key value`` set; refused for a stacked annotation's key."""
+        owner = self.owner(key.lower())
+        if owner is not None and is_stacked(owner.parse):
+            raise ValueError(f"@{key} is repeatable; edit the cell source directly")
+        return self.grammar.set_directive(source, key, value)
+
+    def remove_directive(self, source: str, key: str) -> str:
+        """*source* with every ``# @key`` directive removed from its leading block."""
+        return self.grammar.remove_directive(source, key)

cellgraph-0.1.0.dist-info/METADATA

@@ -0,0 +1,63 @@
+Metadata-Version: 2.4
+Name: cellgraph
+Version: 0.1.0
+Summary: The cell graph of a notebook or script: annotations with a host-supplied vocabulary, analysis, the DAG, and the keys that say whether a cell must run.
+Author: Fangchen Li
+Author-email: Fangchen Li <fangchen.li@outlook.com>
+License-Expression: Apache-2.0
+License-File: LICENSE
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Intended Audience :: Developers
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Requires-Python: >=3.12
+Project-URL: Homepage, https://github.com/bearing-research/cellgraph
+Project-URL: Repository, https://github.com/bearing-research/cellgraph
+Project-URL: Changelog, https://github.com/bearing-research/cellgraph/blob/main/CHANGELOG.md
+Description-Content-Type: text/markdown
+
+# cellgraph
+
+The cell graph of a notebook or script. A cell is source with a leading
+`# @key value` block; the set of annotations is the host's, composed from the
+ten effects the package implements (binds, defines, reads, keeps, after, seeds,
+member, fan-out, input, no-cache). `analyze` reads every cell's names and
+annotations, applies their effects, wires the DAG, says which cells can be
+planned and why the others cannot, and keys each cell: a definition key from its
+normalized source and the annotations that change what it computes, and an
+execution key from the outputs and external inputs the host looks up. The
+package has no dependencies and runs nothing; the host executes, stores and
+resolves. It was factored out of Strata's notebook, its first host, whose
+formats it reproduces exactly under `legacy-1`.
+
+```bash
+pip install cellgraph
+```
+
+See [the API](https://github.com/bearing-research/cellgraph/blob/main/docs/api.md).
+
+```python
+import cellgraph as cg
+
+vocab = cg.Vocabulary.core() | cg.Vocabulary(
+    [
+        cg.Annotation("gpu", parse=cg.scalar(str), in_key=False),
+    ]
+)
+analysis = cg.analyze(
+    [cg.Cell("a", "x = 1\n"), cg.Cell("b", "# @gpu A100\ny = x + 1\n")],
+    vocab,
+)
+analysis.cells["b"].annotations["gpu"]  # 'A100'
+analysis.dag.topological_order  # ['a', 'b']
+```
+
+## Development
+
+```bash
+uv sync
+uv run pytest
+uv run pre-commit run --all-files
+```

cellgraph-0.1.0.dist-info/RECORD

@@ -0,0 +1,16 @@
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+cellgraph/analysis.py,sha256=qmilm5Lv-6tUIyKSoh0U7j5Bg4wNqOzWQMfD6z7eXe0,39213
+cellgraph/core.py,sha256=frkhzoSuF66zGyx2p9MI0qEkNOS2ypCWJ1kZoNsfLnY,3157
+cellgraph/diagnostics.py,sha256=8gGUODyP51q2NvDjdT1QQ0oAg3vELHVndgzaO5Q_41I,607
+cellgraph/effects.py,sha256=BHEItUCN5bYUfrrewpO7lIkFgVeqoDMo4I_ACHbyo28,3018
+cellgraph/grammar.py,sha256=WE8vJz7tmtVQ1aXF14Kvb5GX7voFxkFH2eTEo2oky0k,5403
+cellgraph/keys.py,sha256=opDPkcM9qZZ2G6T4ZpE2BroBBoGi56VXd_U30_7hP38,15300
+cellgraph/languages.py,sha256=udq9-GXxfbJ5dOClsQ6cFonbekO1s4XNi4e1gEHAeUE,3623
+cellgraph/plan.py,sha256=IOgFxp7qR0d4TRCEk3aNmHD0Xmpj-F67iMk_Cz_E47Q,1243
+cellgraph/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+cellgraph/python.py,sha256=nku01OPyornnp3_VFJQb__5oM4Finz-BjiQby24Ovu0,27128
+cellgraph/vocabulary.py,sha256=sGpgpsBXUWEeMs18yCc62ZWcCzq5bF60pNnxwzQyvAY,9962
+cellgraph-0.1.0.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+cellgraph-0.1.0.dist-info/WHEEL,sha256=3NO1oYsF7mANFUWVdyEQLM-zmecczWWEmmF5rEbXrWk,80
+cellgraph-0.1.0.dist-info/METADATA,sha256=ZtoifY4ktBzSncolDNlFQRSI6JDF3H0cMoiC8qGgwuU,2322
+cellgraph-0.1.0.dist-info/RECORD,,

cellgraph-0.1.0.dist-info/WHEEL

@@ -0,0 +1,4 @@
+Wheel-Version: 1.0
+Generator: uv 0.13.6
+Root-Is-Purelib: true
+Tag: py3-none-any

cellgraph-0.1.0.dist-info/licenses/LICENSE

@@ -0,0 +1,201 @@
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