data-annotations 2.1.2__py3-none-any.whl

data_annotations-2.1.2.dist-info/METADATA

@@ -0,0 +1,616 @@
+Metadata-Version: 2.4
+Name: data-annotations
+Version: 2.1.2
+Summary: Annotate generated data artifacts
+Keywords: annotations,data,metadata,provenance,reproducibility
+Author: Rodrigo C.  G.  Pena
+Author-email: Rodrigo C.  G.  Pena <rodrigo.cerqueiragonzalezpena@unibas.ch>
+License-Expression: BSD-3-Clause
+License-File: LICENSE
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Requires-Dist: pydantic>=2.13.1
+Requires-Dist: questionary>=2.1.1 ; extra == 'cli'
+Requires-Dist: typer>=0.16.0 ; extra == 'cli'
+Requires-Python: >=3.12
+Project-URL: Source, https://gitlab.com/ceda-unibas/tools/data-annotations
+Project-URL: Changelog, https://gitlab.com/ceda-unibas/tools/data-annotations/-/blob/main/CHANGELOG.md
+Project-URL: Issues, https://gitlab.com/ceda-unibas/tools/data-annotations/-/issues
+Provides-Extra: cli
+Description-Content-Type: text/markdown
+
+# data-annotations
+
+A small Python package for attaching provenance and structured descriptions to the
+files and directories your workflows produce.
+
+It is designed for lightweight research and reproducibility pipelines where you want
+generated datasets, tables, plots, or reports to carry enough context to explain
+where they came from and what they contain.
+
+The package captures common provenance automatically and writes plain JSON and
+Markdown artifacts that are easy to inspect or archive. The canonical on-disk format
+is now a single annotation document:
+
+- Files use `artifact.ext.meta.json`
+- Directories use `manifest.json`
+
+Each annotation document stores four top-level sections:
+
+- `annotation_version`
+- `subject`
+- `provenance`
+- `description`
+
+See the [changelog](CHANGELOG.md) for release history and upgrade-oriented notes.
+
+## Installation
+
+Install the core library from PyPI with `pip`:
+
+```bash
+pip install data-annotations
+```
+
+Or add it to a project with [uv](https://astral.sh/uv/):
+
+```bash
+uv add data-annotations
+```
+
+The command-line interface uses optional dependencies. Install the package with
+CLI support when you want to run `data-annotations` commands:
+
+```bash
+pip install "data-annotations[cli]"
+uv add "data-annotations[cli]"
+```
+
+For development or unreleased source installs, install directly from GitLab:
+
+```bash
+uv add "data-annotations @ git+https://gitlab.com/ceda-unibas/tools/data-annotations.git"
+pip install "data-annotations @ git+https://gitlab.com/ceda-unibas/tools/data-annotations.git"
+```
+
+Pin a source install to a particular release tag `x.y.z` with:
+
+```bash
+uv add "data-annotations @ git+https://gitlab.com/ceda-unibas/tools/data-annotations.git@x.y.z"
+```
+
+## What gets captured automatically
+
+Every annotation document includes provenance with:
+
+- A UTC creation timestamp
+- Hostname and username
+- The script path and command-line arguments
+- The script path relative to the Git repo root when it can be determined
+- Git commit, branch, dirty state, and canonical repository remote when available
+- The current `SLURM_JOB_ID` when available
+
+You can also attach your own parameters, input file paths, and function names.
+Local filesystem paths in provenance are stored as absolute paths. URI-style inputs
+such as `s3://...` or `https://...` are preserved as provided.
+
+## Quick Start
+
+The recommended way to annotate your data artifacts is to decorate pipeline
+functions that consume some inputs and parameters, then write those artifacts.
+This keeps the artifact-writing logic explicit while letting `data-annotations` capture
+provenance and emit sidecars automatically.
+
+For example, here is a complete file-level annotation workflow using the
+`record_file_annotation(...)` decorator. Once `write_participants` is called, it
+automatically generates sidecars `participants.csv.meta.json` and `participants.csv.README.md`.
+The JSON sidecar will contain provenance and description metadata, and the Markdown sidecar
+will have a human-friendly rendering of the description provided in the decorator.
+
+```python
+from pathlib import Path
+
+from data_annotations.annotations import record_file_annotation
+from data_annotations.description import AllowedValue, FieldDefinition
+
+@record_file_annotation(
+    title="Participant Cohort",
+    summary="Participant-level cohort assignments for the validation split.",
+    fields=[
+        FieldDefinition(
+            name="participant_id",
+            data_type="string",
+            summary="Stable participant identifier.",
+            required=True,
+            nullable=False,
+        ),
+        FieldDefinition(
+            name="group",
+            data_type="string",
+            summary="Assigned study group.",
+            allowed_values=[
+                AllowedValue(value="control"),
+                AllowedValue(value="treatment"),
+            ],
+        ),
+    ],
+    primary_key=["participant_id"],
+    artifact_kind="dataset",
+    acquisition_context={"source": "Study A registry export"},
+    generation_context={"pipeline": "baseline-v1"},
+)
+def write_participants(
+    artifact_path: Path,
+    input_path: Path,
+    split: str,
+) -> Path:
+    participant_ids = [
+        line.strip()
+        for line in input_path.read_text(encoding="utf-8").splitlines()[1:]
+        if line.strip()
+    ]
+    artifact_path.parent.mkdir(parents=True, exist_ok=True)
+    artifact_path.write_text(
+        "\n".join(
+            [
+                "participant_id,group,split",
+                *[
+                    f"{participant_id},control,{split}"
+                    for participant_id in participant_ids
+                ],
+            ]
+        )
+        + "\n",
+        encoding="utf-8",
+    )
+    return artifact_path
+
+# Annotation sidecars are written automatically
+# when the decorated function is called:
+artifact_path = Path("outputs") / "participants.csv"
+write_participants(
+    artifact_path=artifact_path,
+    input_path=Path("data/raw/participants.csv"),
+    split="validation",
+)
+
+print(f"{artifact_path}.meta.json")
+print(f"{artifact_path}.README.md")
+```
+
+### Decorator Contract
+
+You write a normal Python function and the decorator returns that function's
+original return value unchanged.
+
+For provenance-bearing decorators, recorded inputs are inferred from named
+function arguments such as `input_path` and `input_paths`. Those arguments
+should correspond to real data dependencies used inside the wrapped function.
+
+For file decorators:
+
+- `record_file_manifest(...)`
+- `record_file_annotation(...)`
+- `record_file_description(...)`
+
+Your function should:
+
+- accept one argument pointing at the output file path. By default this argument
+  is named `artifact_path`, but you can change the expected name with
+  `artifact_path_arg=...`.
+- use any other normal Python arguments you need for the pipeline step.
+- for provenance-bearing decorators, use argument names listed in `input_args`
+  for real upstream dependencies you want recorded as provenance inputs. By
+  default those names are `("input_path", "input_paths")`.
+
+Your function may return any value. File decorators do not inspect that return
+value. Returning the generated `artifact_path` is recommended because it is
+convenient for callers, but it is not required.
+
+For directory decorators:
+
+- `record_directory_manifest(...)`
+- `record_directory_annotation(...)`
+- `record_directory_description(...)`
+
+Your function should:
+
+- accept one argument pointing at the output directory. By default this argument
+  is named `output_dir`, but you can change the expected name with
+  `output_dir_arg=...`.
+- return a materialized iterable, usually a `list`, describing the files that
+  were produced in that directory.
+- prefer returning a `list` or `tuple` rather than a generator, since the
+  decorator needs to iterate over the outputs to write sidecars.
+
+Accepted directory return items are:
+
+- `DocumentedArtifact` when you want per-artifact title, summary, fields,
+  keys, or missing-value metadata.
+- `ProducedFile` when you only need path, kind, and optional precomputed hash.
+- `(path, kind)` tuples when path and artifact kind are enough.
+- plain path-like values when the artifact kind can default to `"other"`.
+
+For provenance-bearing directory decorators, `input_args` works the same way as
+for file decorators: matching argument names are recorded as inputs, and the
+remaining bound arguments become provenance params.
+
+Here is another decorator pattern example with `record_directory_annotation(...)`:
+
+```python
+from pathlib import Path
+
+from data_annotations.annotations import record_directory_annotation
+from data_annotations.description import DocumentedArtifact, FieldDefinition
+from data_annotations.provenance import ProducedFile
+
+@record_directory_annotation(
+    title="Validation Outputs",
+    summary="Directory-level documentation for the validation run outputs.",
+    acquisition_context={"source": "Study A registry export"},
+    generation_context={"pipeline": "baseline-v1"},
+)
+def build_outputs(
+    output_dir: Path,
+    input_path: Path,
+    split: str,
+):
+    participant_ids = [
+        line.strip()
+        for line in input_path.read_text(encoding="utf-8").splitlines()[1:]
+        if line.strip()
+    ]
+    output_dir.mkdir(parents=True, exist_ok=True)
+
+    table_path = output_dir / "scores.csv"
+    table_path.write_text(
+        "\n".join(
+            [
+                "participant_id,score,split",
+                *[
+                    f"{participant_id},0.94,{split}"
+                    for participant_id in participant_ids
+                ],
+            ]
+        )
+        + "\n",
+        encoding="utf-8",
+    )
+
+    report_path = output_dir / "summary.txt"
+    report_path.write_text(
+        (
+            f"Validated {len(participant_ids)} participants from "
+            f"{input_path.name} for the {split} split.\n"
+        ),
+        encoding="utf-8",
+    )
+
+    plot_path = output_dir / "roc.png"
+    plot_path.write_bytes(
+        (
+            f"plot placeholder derived from {input_path.name} "
+            f"({len(participant_ids)} participants)\n"
+        ).encode("utf-8")
+    )
+
+    return [
+        DocumentedArtifact(
+            path=str(table_path),
+            kind="dataset",
+            title="Metrics Table",
+            fields=[
+                FieldDefinition(
+                    name="metric",
+                    data_type="string",
+                    summary="Metric name.",
+                ),
+                FieldDefinition(
+                    name="value",
+                    data_type="float",
+                    summary="Metric value.",
+                ),
+            ],
+        ),
+        ProducedFile(path=str(report_path), kind="report"),
+        (plot_path, "plot"),
+    ]
+
+
+output_dir = Path("outputs") / "run-001"
+build_outputs(
+    output_dir=output_dir,
+    input_path=Path("data/raw/participants.csv"),
+    split="validation",
+)
+
+print(output_dir / "manifest.json")
+print(output_dir / "README.md")
+```
+
+The decorator and direct APIs write the same canonical document shape. If you need
+metadata to vary per call instead of staying fixed at decoration time, use
+`annotate_file(...)`, `annotate_directory(...)`, `write_file_annotation(...)`, or
+`write_directory_annotation(...)` directly instead. See the example gallery in
+`examples/` for runnable examples of all approaches.
+
+### When To Use Decorators Vs Direct Functions
+
+If a function is only a final serializer for already-prepared data, prefer the
+direct annotation and writer APIs. They let you attach `inputs=[...]` explicitly.
+
+## Canonical Document Shape
+
+File annotations store:
+
+- `subject.path`
+- `subject.kind`
+- `subject.sha256`
+- `provenance.*`
+- `description.title`
+- `description.summary`
+- `description.fields`
+- `description.primary_key`
+- `description.missing_value_codes`
+- `description.acquisition_context`
+- `description.generation_context`
+- `description.description_updated_at`
+
+Directory annotations store:
+
+- `subject.path`
+- `subject.produced_files[]`
+- `provenance.*`
+- `description.title`
+- `description.summary`
+- `description.artifacts[]`
+- `description.acquisition_context`
+- `description.generation_context`
+- `description.description_updated_at`
+
+The `description` section intentionally excludes provenance linkage fields and
+file kinds for directory artifacts. Kinds live in `subject.produced_files`.
+
+## Provenance Decorators And Writers
+
+The `data_annotations.provenance` namespace provides provenance-only entry points.
+Prefer the decorators when you already have a small function that writes artifacts:
+
+```python
+from pathlib import Path
+
+from data_annotations.provenance import record_file_manifest
+
+
+@record_file_manifest(artifact_kind="report")
+def write_report(
+    artifact_path: Path,
+    input_path: Path,
+    threshold: float = 0.5,
+):
+    artifact_path.parent.mkdir(parents=True, exist_ok=True)
+    artifact_path.write_text(
+        f"threshold applied: {threshold}\nsource={input_path.name}\n",
+        encoding="utf-8",
+    )
+
+
+write_report(
+    artifact_path=Path("outputs/summary.txt"),
+    input_path=Path("data/raw/participants.csv"),
+    threshold=0.75,
+)
+```
+
+Use `record_directory_manifest(...)` for directory outputs. Directory decorators
+accept `DocumentedArtifact`, `ProducedFile`, `(path, kind)`, and plain path-like
+return values.
+
+If you want the direct writer approach instead, use `write_file_manifest(...)` and
+`write_directory_manifest(...)` (see `examples/`).
+
+## Description Layer
+
+The `data_annotations.description` sub-package provides the structured description
+models used by annotation writers and the Markdown sidecar renderers.
+Within those models, the primary human-written narrative field is named `summary`.
+
+Key public description models:
+
+- `AllowedValue`
+- `FieldDefinition`
+- `DocumentedArtifact`
+- `ArtifactDescription`
+- `FileDescription`
+- `DirectoryDescription`
+
+Description decorators and helpers:
+
+- `record_file_description(...)`
+- `record_directory_description(...)`
+- `write_file_description(...)`
+- `write_directory_description(...)`
+- `render_file_readme(...)`
+- `render_directory_readme(...)`
+
+Alias helpers `write_file_readme(...)` and `write_directory_readme(...)` are supported.
+
+Use the decorator forms when the description metadata is stable
+for a function, and use the direct helpers when you want to assemble descriptions
+per call.
+
+## Recovery Helpers
+
+Use `artifact_matches_manifest(...)` to verify whether a detached artifact still
+matches an annotation document, and `checkout_manifest_source(...)` to recover the
+recorded code state from Git metadata.
+
+```python
+from pathlib import Path
+
+from data_annotations.provenance import (
+    artifact_matches_manifest,
+    checkout_manifest_source,
+)
+
+annotation_path = Path("outputs/participants.csv.meta.json")
+artifact_path = Path("downloads/participants.csv")
+
+if artifact_matches_manifest(artifact_path, annotation_path):
+    recovered = checkout_manifest_source(annotation_path)
+    print(recovered.checkout_path)
+    print(recovered.script_path)
+```
+
+## Post-Hoc Annotation
+
+The strongest workflow is to create provenance and description at the same time
+as the artifact itself. When annotations are written during generation, the
+package can capture runtime context directly and the resulting records are
+typically more complete, precise, and trustworthy.
+
+For existing artifacts, the CLI provides a post-hoc annotation path so you can
+still attach provenance and description after the fact.
+
+Post-hoc descriptions can still be very useful, but the quality of post-hoc
+provenance depends on how exact the supplied answers are. In particular, fields
+such as the generating script, command, function, Git commit, repository path,
+inputs, and parameters are only as reliable as the information entered during
+annotation.
+
+## CLI Workflow
+
+This package provides a command-line interface (CLI) for retrospective annotation
+and provenance inspection.
+
+For post-hoc annotation:
+
+```bash
+data-annotations annotate file path/to/participants.csv
+data-annotations annotate directory path/to/run-001
+```
+
+These commands prompt for missing details, write `*.meta.json` or `manifest.json`,
+and optionally derive README sidecars. Post-hoc records are marked with
+`capture_mode="post_hoc"`.
+
+For provenance inspection and source recovery:
+
+```bash
+data-annotations provenance match path/to/artifact
+data-annotations provenance checkout path/to/artifact
+```
+
+Command `match` auto-discovers `*.meta.json` for files and `manifest.json` for
+directories, prints a verification summary, and suggests the exact `checkout`
+command to run next when Git recovery metadata is available.
+
+### Run With `uvx`
+
+```bash
+uvx --from "data-annotations[cli]" data-annotations provenance match path/to/participants.csv
+```
+
+### Install And Use With `uv tool`
+
+```bash
+uv tool install "data-annotations[cli]"
+data-annotations provenance match path/to/participants.csv
+```
+
+### Run From Repository Root
+
+From the repository root while developing locally, run `task install` first.
+That task uses `uv sync --extra cli`, so the CLI commands are available in
+the project environment. You can then run:
+
+```bash
+uv run data-annotations annotate file path/to/participants.csv
+uv run data-annotations annotate directory path/to/run-001
+uv run data-annotations provenance match path/to/participants.csv
+uv run data-annotations provenance checkout path/to/participants.csv
+```
+
+## API Overview
+
+### Annotation Models
+
+- `FileArtifactSubject`
+- `DirectoryArtifactSubject`
+- `FileAnnotationDocument`
+- `DirectoryAnnotationDocument`
+- `FileAnnotationResult`
+- `DirectoryAnnotationResult`
+
+### Annotation Decorators
+
+- `record_file_annotation(...)`
+- `record_directory_annotation(...)`
+
+### Annotation Functions
+
+- `write_file_annotation(...)`
+- `write_directory_annotation(...)`
+- `annotate_file(...)`
+- `annotate_directory(...)`
+
+### Description Functions
+
+- `record_file_description(...)`
+- `record_directory_description(...)`
+- `write_file_description(...)`
+- `write_directory_description(...)`
+- `write_file_readme(...)`
+- `write_directory_readme(...)`
+- `render_file_readme(...)`
+- `render_directory_readme(...)`
+
+### Provenance Models
+
+- `ProducedFile`
+- `BaseProvenance`
+- `FileManifest`
+- `DirectoryManifest`
+- `RecoveredSource`
+
+### Provenance Functions
+
+- `record_file_manifest(...)`
+- `record_directory_manifest(...)`
+- `write_file_manifest(...)`
+- `write_directory_manifest(...)`
+- `artifact_matches_manifest(...)`
+- `checkout_manifest_source(...)`
+
+## Examples
+
+Runnable examples live in `examples/` and mirror the README workflows.
+Run them from the repository root with:
+
+```bash
+uv run python examples/record_file_annotation.py
+uv run python examples/record_directory_annotation.py
+uv run python examples/record_file_manifest.py
+uv run python examples/record_directory_manifest.py
+uv run python examples/record_file_description.py
+uv run python examples/record_directory_description.py
+uv run python examples/annotate_file.py
+uv run python examples/annotate_directory.py
+uv run python examples/write_file_manifest.py
+uv run python examples/write_directory_manifest.py
+uv run python examples/write_file_description.py
+uv run python examples/write_directory_description.py
+uv run python examples/recover_provenance.py
+uv run python examples/recover_provenance_cli.py
+```
+
+Each example writes its outputs to a fresh temporary directory and prints the
+location so you can inspect the generated annotation documents and README sidecars.

data_annotations-2.1.2.dist-info/RECORD

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data_annotations-2.1.2.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: uv 0.11.8
+Root-Is-Purelib: true
+Tag: py3-none-any

data_annotations-2.1.2.dist-info/entry_points.txt

@@ -0,0 +1,3 @@
+[console_scripts]
+data-annotations = data_annotations.cli:main
+

data_annotations-2.1.2.dist-info/licenses/LICENSE

@@ -0,0 +1,28 @@
+BSD 3-Clause License
+
+Copyright (c) 2026, CeDA, University of Basel
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.