cwl-baseline-plugin 0.1.0__tar.gz

cwl_baseline_plugin-0.1.0/.gitignore

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+# Copyright {{ copyright_year }} {{ author_name }}
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+# Python
+__pycache__/
+*.py[cod]
+*.egg-info/
+.dist/
+build/
+dist/
+.coverage
+coverage.xml
+.pytest_cache/
+.mypy_cache/
+.ruff_cache/
+
+# Environments
+.venv/
+
+# MkDocs
+site/
+
+# Editors
+.idea/
+.vscode/
+.DS_Store
+
+.task
+uv.lock

cwl_baseline_plugin-0.1.0/CHANGELOG.md

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+<!--
+Copyright 2026 Transpiler-Mate
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+-->
+
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+### Added
+
+### Changed
+
+### Deprecated
+
+### Removed
+
+### Fixed
+
+### Security
+
+### Added
+
+- Initial Hatch-based Python project scaffold.
+- Diátaxis documentation structure.
+- MkDocs configuration.
+- Taskfile integration with Terradue remote task utilities.
+
+## [0.1.0] - 2026-01-01
+
+### Added
+
+- Initial project release.
+
+[Unreleased]: https://github.com/Transpiler-Mate/cwl-baseline-plugin/compare/0.1.0...HEAD
+[0.1.0]: https://github.com/Transpiler-Mate/cwl-baseline-plugin/releases/tag/0.1.0

cwl_baseline_plugin-0.1.0/LICENSE

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cwl_baseline_plugin-0.1.0/NOTICE

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+CWL Baseline Transpiler Mate Plugin
+Copyright 2026 Transpiler-Mate
+
+This product includes software developed by Transpiler-Mate.

cwl_baseline_plugin-0.1.0/PKG-INFO

@@ -0,0 +1,340 @@
+Metadata-Version: 2.5
+Name: cwl-baseline-plugin
+Version: 0.1.0
+Summary: CWL Baseline Transpiler Mate Plugin Transpiler-Mate Plugin.
+Project-URL: Homepage, https://github.com/Transpiler-Mate/cwl-baseline-plugin
+Project-URL: Documentation, https://Transpiler-Mate.github.io/cwl-baseline-plugin/
+Project-URL: Repository, https://github.com/Transpiler-Mate/cwl-baseline-plugin
+Project-URL: Issues, https://github.com/Transpiler-Mate/cwl-baseline-plugin/issues
+Project-URL: Changelog, https://github.com/Transpiler-Mate/cwl-baseline-plugin/blob/main/CHANGELOG.md
+Author-email: Transpiler-Mate <info@terradue.com>
+License-Expression: Apache-2.0
+License-File: LICENSE
+License-File: NOTICE
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Classifier: Programming Language :: Python :: Implementation :: PyPy
+Requires-Python: >=3.10
+Requires-Dist: loguru==0.7.3
+Requires-Dist: semver<4,>=3.0.4
+Requires-Dist: transpiler-mate-api==1.0.0
+Description-Content-Type: text/markdown
+
+<!--
+Copyright 2026 Transpiler-Mate
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+-->
+
+# CWL Baseline Transpiler Mate Plugin
+
+[![PyPI - Version](https://img.shields.io/pypi/v/cwl-baseline-plugin.svg)](https://pypi.org/project/cwl-baseline-plugin)
+[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/cwl-baseline-plugin.svg)](https://pypi.org/project/cwl-baseline-plugin)
+
+A standalone plugin implementing the public `transpiler-mate-api` contract.
+It compares every Process in two resolved CWL documents and produces an
+explainable JSON baseline report with a minimum SemVer increment.
+
+## Install
+
+```bash
+python -m pip install cwl-baseline-plugin
+```
+
+For development, install your checkout of the API first if it has not yet been
+published, then install this project:
+
+```bash
+python -m pip install -e ../transpiler-mate-api
+python -m pip install -e .
+hatch run test:test
+```
+
+Requires Python >=3.10, `transpiler-mate-api==1.0.0`, `semver>=3.0.4,<4`, and `loguru==0.7.3`.
+The API supplies cwl-utils and Pydantic. The effective Python requirement also
+depends on the selected versions of those dependencies.
+
+## Integrate with a transpiler-mate runtime
+
+Exported plugin object: `cwl_baseline.baseline_plugin`.
+Plugin name: `baseline`. Options model: `BaselineOptions`.
+
+The package registers `baseline = "cwl_baseline.plugin:baseline_plugin"` in the
+`transpiler_mate.plugins` entry-point group. Install it into the same environment
+as the separately installed runtime. It provides no standalone `cwl_baseline`
+executable. The runtime resolves the current CWL; the plugin resolves only the
+previous release.
+
+```bash
+transpiler-mate baseline examples/current.cwl \
+  --previous examples/previous.cwl --output baseline.json --check
+```
+
+The host CLI resolves its input CWL into `context` and invokes:
+
+```python
+from pathlib import Path
+from transpiler_mate.api import TranspilerContext
+from cwl_baseline import BaselineOptions, baseline_plugin
+
+
+def execute_baseline(context: TranspilerContext) -> None:
+    baseline_plugin.execute(
+        context,
+        BaselineOptions(
+            previous="path-or-URI-to-previous-release.cwl",
+            output=Path("baseline.json"),
+            check=True,
+        ),
+    )
+```
+
+Equivalent options payload for a runtime accepting JSON:
+
+```json
+{
+  "previous": "path-or-URI-to-previous-release.cwl",
+  "output": "baseline.json",
+  "check": true
+}
+```
+
+| Option | Default | Meaning |
+| --- | --- | --- |
+| `previous` | required | Passed unchanged to `context.resolver.resolve()` |
+| `output` | `baseline.json` | JSON destination; its parent directory must exist |
+| `check` | `false` | Fail for unresolved review or insufficient declared version |
+| `review_bump` | `null` | Explicitly classify review findings as `patch`, `minor`, or `major` |
+
+`previous_context = context.resolver.resolve(options.previous)` supplies the
+baseline. `context.document` supplies **all** current Processes, irrespective
+of `context.process_id`. Both versions are read from
+`context.metadata.software_version` on their respective contexts.
+
+The highest applicable bump is applied **once to the previous release** using
+`semver.Version.bump_major()`, `.bump_minor()`, or `.bump_patch()`. The third component is called *patch*.
+Neither CWL document nor either metadata object is mutated.
+
+## Compatibility policy
+
+The current implementation uses fixed static rules plus the global `review_bump`
+classification. It does not yet support configurable per-rule policies. These
+are plugin baselining assumptions, not versioning rules mandated by CWL.
+
+Replacement requires AcceptedInputs(old) ⊆ AcceptedInputs(new) and
+PossibleOutputs(new) ⊆ PossibleOutputs(old). Inputs are contravariant; outputs
+are covariant. Thus `string` → `string | null` is minor for an input but major
+for an output. Identical signatures do not prove compatible behavior.
+
+See the [full compatibility policy](docs/explanation/compatibility.md) for the
+implemented rules and their limitations.
+
+Every Process exposed in `context.document` is treated as public. A Process
+addition is minor; a removal or rename is major. This policy is intentionally
+conservative for documents containing helper tools in their public mapping.
+
+| Change | Minimum bump |
+| --- | --- |
+| Add Process | minor |
+| Remove/rename Process | major |
+| Add input that cannot be omitted | major |
+| Add nullable/defaulted input | minor |
+| Remove/rename input or output | major |
+| Add output | minor; assumes consumers tolerate extra output keys |
+| Widen accepted input values | minor |
+| Narrow accepted input values | major |
+| Widen possible output values | major |
+| Narrow possible output values | patch, with behavioral review |
+| Remove input omission capability | major |
+| Change default | review; independently detect loss of omission capability |
+| Add mandatory execution requirement | major; schema definitions handled separately |
+| Change language version, existing execution requirement, or advisory hint | review |
+| Change command, binding, expression, wiring, container, or step | review |
+| Change `doc`, `label`, schema.org name/description | none |
+| Change unknown extensions | review |
+
+Type comparison is directional: old inputs must be assignable to new inputs;
+new outputs must be assignable to old outputs. It covers primitives, CWL
+numeric promotions, nullability, unions, enums, arrays, records, and named
+schemas. Numeric promotion follows CWL type assignability; it does not claim
+lossless numeric conversion. `Any` excludes null unless explicitly unioned
+with null. Removed record fields are conservatively major for either direction.
+
+Input omission is tracked separately: a serialized default or a nullable type
+allows omission. Removing a default is major only when omission becomes invalid,
+with a separate review finding for the default change. Adding or changing an
+existing parameter's default also requires review.
+
+Hints do not trigger the new mandatory requirement rule. Existing requirement
+changes, including resource/network settings and container images, generally
+receive residual behavioral review. Adding a new mandatory container requirement
+is major. `SchemaDefRequirement` definitions are compared through parameter types;
+unused schema changes require review.
+
+File constraints include `format` and `secondaryFiles`. Literal format subset
+relations can prove compatibility, but relationships between different format
+IRIs may require ontology knowledge and are left for review. Secondary-file
+expressions are also left for review. Existing optional secondary-file outputs
+are not treated as required guarantees. Requiring a new secondary input file or
+weakening a required secondary output guarantee is major; other literal changes
+are minor. Compatible output-format narrowing has a patch floor without an
+independent review flag in the current implementation.
+
+Workflow steps are internal implementation details. They are matched by ID;
+adding/removing one requires behavioral review rather than automatically
+changing the public version. All residual changed DOM fields are reported,
+including embedded `run` objects and unknown extension fields. Lists with
+execution-significant order (arguments, source lists, etc.) retain their order.
+
+## Interpreting the report
+
+```json
+{
+  "schema_version": "1.0",
+  "previous_version": "1.2.3",
+  "current_version": "1.2.3",
+  "minimum_bump": "major",
+  "minimum_version": "2.0.0",
+  "suggested_version": "2.0.0",
+  "review_required": false,
+  "review_bump": null,
+  "declared_version_sufficient": false,
+  "findings": []
+}
+```
+
+The abbreviated example omits findings. Real findings contain a stable rule
+identifier, JSON-Pointer-style comparison path, category, minimum bump,
+before/after values, presence flags, explanation, and review flag. Paths refer
+to the normalized comparison model, not source-file line numbers.
+
+- `minimum_bump` and `minimum_version` express the statically established floor.
+- `suggested_version` is `null` while review remains unresolved. Otherwise it
+  is the minimum proposed release, not an instruction to downgrade a higher
+  already-declared version.
+- A report without changes retains the previous release version.
+- `declared_version_sufficient` is false while review is unresolved, even if the
+  current version is numerically high enough.
+- The full report is written before `check=True` raises `PluginFailureError`.
+- Missing/invalid SemVer metadata and prerelease baselines are domain errors.
+  Current development prereleases are accepted as input, but `1.3.0-dev.1`
+  does not satisfy a required final `1.3.0` release. Build metadata is handled
+  by the semver library.
+
+After reviewing behavioral changes, classify them explicitly:
+
+```python
+options = BaselineOptions(
+    previous="release.cwl",
+    output="baseline.json",
+    review_bump="patch",  # All review findings have been assessed as compatible fixes.
+    check=True,
+)
+baseline_plugin.execute(context, options)
+```
+
+`review_bump` applies to **all** review findings in this invocation. It cannot
+reduce a proven major/minor requirement. Original per-finding review flags are
+retained for auditing, while the report-level flag indicates unresolved review.
+A global classification is not a per-rule waiver mechanism.
+
+For library use without writing files:
+
+```python
+from cwl_baseline import baseline
+
+previous = context.resolver.resolve("release.cwl")
+report = baseline(previous, context)
+print(report.model_dump_json(indent=2))
+```
+
+## Normalization and boundaries
+
+The plugin serializes the existing cwl-utils DOMs using
+`save(relative_uris=False)`. It strips only the owning document's location from
+CWL identity/reference fields, retaining scopes and external URIs. It does not
+rewrite literal defaults, command arguments, expressions, or extension values.
+Unambiguous short named-type references are recognized within a Process;
+ambiguous/unresolved references produce review when their compatibility cannot
+be established. Reachable named schemas are compared through their parameters;
+changes to otherwise unused declarations are reported for review.
+
+The runtime owns CWL parsing, import resolution, graph validation, and metadata
+extraction. This plugin does not execute CWL, evaluate JavaScript, inspect image
+contents, fetch format ontologies, or recursively fetch additional `run` URLs.
+For reproducible baselines, the resolver must provide pinned dependency snapshots
+in `document`. Changes behind an unchanged external reference that is absent
+from the supplied DOMs cannot be detected. Inherited or externally defined
+schemas not present in a Process's available declarations may require review.
+
+Generated serializers may discard source spelling, comments, and explicit null
+defaults. The comparison concerns the effective supplied DOM representation;
+it cannot recover syntax that the parser discarded. Anonymous/generated **public Process** IDs
+should be replaced with stable public IDs before baselining. Generated IDs of
+anonymous inline tools are ignored; their enclosing step/run path identifies
+them.
+
+Static type compatibility does not prove scientific or behavioral equivalence.
+A reviewed major release can still be necessary when output meanings or units
+change without changing CWL types.
+
+## Tests and examples
+
+`tests/` exercises parsed CWL DOMs, plugin resolution and error semantics,
+variance, schema references, record/array changes, file constraints, source
+relocation, ordered arguments, steps, and version aggregation. Test fixtures
+use synthetic source URIs and disable link-existence checking only in their
+fixture loader; production loading remains entirely with the host resolver.
+
+`examples/previous.cwl`, `examples/current.cwl`, and
+`examples/baseline.json` illustrate adding an optional input. Run `hatch run test:test` to execute the configured Python-version test matrix.
+
+Upstream API: https://github.com/transpiler-mate/transpiler-mate-api
+SemVer library: https://pypi.org/project/semver/
+
+## Documentation
+
+Project documentation is published at: https://Transpiler-Mate.github.io/cwl-baseline-plugin/
+
+## Contribute
+
+Submit a [Github issue](https://github.com/Transpiler-Mate/cwl-baseline-plugin/issues) if you have comments or suggestions.
+
+### Local quality checks
+
+Install [Hatch](https://hatch.pypa.io/) and [Taskfiles](https://taskfile.dev/docs/guide) then install the Git hook:
+
+```console
+task quality:pre-commit:install
+```
+
+Every commit runs Ruff (including the configured McCabe complexity limit),
+Ruff formatting, mypy, Bandit, and the pytest suite.
+
+Run the complete hook explicitly with:
+
+```console
+task quality:pre-commit:run
+```
+
+## License
+
+[![Apache License, Version 2.0](https://img.shields.io/badge/license-Apache%20License%202.0-blue)](https://www.apache.org/licenses/LICENSE-2.0)