vector-mtrl 0.2.0__py3-none-any.whl

mtrl/transformations/__init__.py

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+"""Compatibility shim for the transformation interface.
+
+The live code moved to `mtrl.operations`. The `mtrl.transformations` import path stays
+available until Stage 3.
+"""
+
+from importlib import import_module
+from typing import TYPE_CHECKING, Any
+
+__all__ = ["DEFAULT_PARAMETERS", "TRANSFORMATIONS", "apply"]
+
+if TYPE_CHECKING:
+    from mtrl.operations.base import DEFAULT_PARAMETERS, TRANSFORMATIONS, apply
+
+
+def __getattr__(name: str) -> Any:
+    """Load the compatibility transformation interface only when a caller requests it."""
+    if name not in __all__:
+        raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
+
+    base_module = import_module("mtrl.operations.base")
+    return getattr(base_module, name)

mtrl/transformations/base.py

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+"""Compatibility re-export of the transformation base module.
+
+The live code moved to `mtrl.operations.base`. This shim keeps the documented
+`mtrl.transformations.base` import path working until Stage 3.
+"""
+
+from mtrl._provenance import _hash_function
+from mtrl.operations._identity import identity
+from mtrl.operations.base import DEFAULT_PARAMETERS, TRANSFORMATIONS, apply
+
+__all__ = [
+    "DEFAULT_PARAMETERS",
+    "TRANSFORMATIONS",
+    "_hash_function",
+    "apply",
+    "identity",
+]

mtrl/units.py

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+"""Units of measure for the Mtrl package, against the QUDT standard.
+
+QUDT (Quantities, Units, Dimensions and Types) gives every unit a stable term. This package
+keeps the reader's own text with that term. A unit that this package cannot match stays in
+the record.
+"""
+
+from pydantic import BaseModel, ConfigDict
+
+QUDT_TERMS_BY_RAW_UNIT: dict[str, tuple[str, str]] = {
+    "cm⁻¹": ("PER-CentiM", "InverseLength"),
+    "cm^-1": ("PER-CentiM", "InverseLength"),
+    "1/cm": ("PER-CentiM", "InverseLength"),
+    "s": ("SEC", "Time"),
+    "second": ("SEC", "Time"),
+    "a.u.": ("UNITLESS", "Dimensionless"),
+}
+"""QUDT terms for each spelling of a unit that a reader can report.
+
+Each value holds the QUDT unit and the QUDT quantity kind. Each entry holds one spelling,
+because a reader can spell the same unit in more than one way.
+"""
+
+
+# @lat: [[domain-model#Units of measure]]
+class Unit(BaseModel):
+    """A unit of measure, as a reader reported it and as QUDT identifies it.
+
+    A Unit is frozen. A checkpoint and the checkpoints that come from it can share one
+    Unit. Replace a Unit when a checkpoint must hold a different one.
+
+    Attributes:
+        raw: The unit as the reader reported it, e.g. "cm⁻¹".
+        qudt_unit: The local name of the QUDT unit, if known, e.g. "PER-CentiM". It gives
+            the measure of the quantity.
+        qudt_quantity_kind: The local name of the QUDT quantity kind, if known, e.g.
+            "InverseLength". It names the property.
+    """
+
+    model_config = ConfigDict(frozen=True)
+
+    raw: str
+    qudt_unit: str | None = None
+    qudt_quantity_kind: str | None = None
+
+    @classmethod
+    def from_raw(cls, raw_unit: str | None) -> Unit | None:
+        """Build a Unit from the text that a reader reported for a unit.
+
+        Args:
+            raw_unit: The unit as the reader reported it, e.g. "cm⁻¹".
+
+        Returns:
+            A Unit that holds `raw_unit`, and the QUDT terms where this package knows them.
+            None, when `raw_unit` is empty or absent.
+        """
+        if not raw_unit:
+            return None
+        qudt_unit, qudt_quantity_kind = QUDT_TERMS_BY_RAW_UNIT.get(raw_unit, (None, None))
+        return cls(raw=raw_unit, qudt_unit=qudt_unit, qudt_quantity_kind=qudt_quantity_kind)

vector_mtrl-0.2.0.dist-info/METADATA

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+Metadata-Version: 2.5
+Name: vector-mtrl
+Version: 0.2.0
+Summary: Materials research tools for spectra and archive workflows.
+Author-email: Fuzzy Labs <info@fuzzylabs.ai>
+License-Expression: MPL-2.0
+License-File: LICENSE
+License-File: NOTICE
+Requires-Python: <4.0,>=3.14
+Requires-Dist: numpy>=2.5.2
+Requires-Dist: pydantic>=2.13.4
+Requires-Dist: rfc8785==0.1.4
+Provides-Extra: excel
+Requires-Dist: openpyxl>=3.1.5; extra == 'excel'
+Requires-Dist: pandas>=3.0.5; extra == 'excel'
+Provides-Extra: interp
+Requires-Dist: scipy>=1.16; extra == 'interp'
+Provides-Extra: tabular
+Requires-Dist: pandas>=3.0.5; extra == 'tabular'
+Description-Content-Type: text/markdown
+
+# vector-mtrl
+
+`mtrl` reads, checks, and writes materials data archives. It records each scientific result as an
+immutable record with exact lineage.
+
+## What you get
+
+- Immutable committed records with stable identities and complete lineage.
+- Bounded `.mtrl` archives with an integrity manifest, external receipts, and forensic inspection.
+- NumPy-only operations: identity, scale, offset, peak normalisation, zero-at-point, and linear
+  resample, beside mean and median aggregates.
+- Explicit analysis grids and a read-only alignment report.
+- A read-only replay plan, a capability view, and a detached rerun for committed chains.
+- Author disclosure that stays inert: stored environment records and passive source bundles that
+  MTRL never imports or executes.
+- CSV export without pandas.
+- Optional extras add SciPy resampling, pandas conversion, and Excel export.
+
+## Install
+
+`vector-mtrl` requires Python 3.14 or newer, below Python 4. The base install depends only on
+NumPy, Pydantic, and RFC 8785 canonical JSON. Create one environment and install the core:
+
+```sh
+uv venv --python 3.14
+uv pip install --python .venv/bin/python vector-mtrl
+```
+
+## Quick start
+
+Commit one synthetic spectrum, normalise it, save an archive, verify it, load it, and export
+CSV. The base install alone runs every step.
+
+### Example: Quick start
+
+**Required install:** `vector-mtrl`
+
+```python
+from pathlib import Path
+from tempfile import TemporaryDirectory
+
+import numpy as np
+
+from mtrl import InstrumentRun, MaterialData, Mtrl, verify_archive
+
+application = Mtrl(sample_id="sample-01")
+run = InstrumentRun(run_name="replicate-01")
+axis = np.array([2000.0, 2100.0, 2200.0])
+content = np.empty(axis.size, dtype=[("wavenumber", "<f8"), ("absorbance", "<f8")])
+content["wavenumber"] = axis
+content["absorbance"] = [0.1, 0.2, 0.3]
+checkpoint = MaterialData(
+    content=content,
+    type="raw",
+    checkpoint_name="spectrum",
+)
+run.add_checkpoint(checkpoint)
+application.add(run)
+
+normalised = application.transform(
+    run.run_id,
+    checkpoint.checkpoint_id,
+    "normalise_peak",
+)
+print(normalised.lineage.provenance.qualified_identifier)
+
+with TemporaryDirectory() as directory:
+    archive_path = application.save(Path(directory) / "sample.mtrl")
+    verification = verify_archive(archive_path)
+    print(verification.structural_status.value, verification.hash_status.value)
+
+    loaded = Mtrl.load(archive_path)
+    print(loaded.sample_id, loaded.get_run(run.run_id) is not None)
+    csv_path = loaded.export_checkpoint(
+        run.run_id,
+        normalised.checkpoint_id,
+        Path(directory) / "signal.csv",
+    )
+    exported = np.genfromtxt(csv_path, delimiter=",", names=True)
+    np.testing.assert_allclose(exported["absorbance"], [1 / 3, 2 / 3, 1])
+    print(csv_path.is_file())
+```
+
+`Mtrl.add()` commits a detached copy, so later changes to your arrays cannot alter the record.
+Every mutation, including the transform above, creates one new revision.
+
+## Guides
+
+The expanded guides ship in the source archive under `docs/user/`. Download the archive for a
+release from https://pypi.org/project/vector-mtrl/#files, then read:
+
+- `docs/user/getting-started.md` for installation, first records, and the save, load, verify,
+  and export loop.
+- `docs/user/workflows.md` for corrections, replacements, transforms, resampling, aggregates,
+  alignment reports, replay, receipts, forensic inspection, disclosure, exports, and registry
+  control.
+- `docs/user/reference.md` for every public route, the stable typed imports, the exact
+  package-root export list, registry names, format features, and the archive safety contract.
+
+## Archive and provenance limits
+
+MTRL reads `.mtrl` archives inside configured size and member limits, and it validates paths,
+entries, JSON, references, payloads, and integrity before it returns data. It does not extract
+archive files.
+
+Archive content does not install packages, does not import operation code, does not change a
+registry, does not execute stored source, and does not change committed records directly.
+Committed records are immutable: use `Mtrl` methods to create a new record version or change the
+active view.
+
+New archives require integrity coverage. Keep a receipt outside the archive if you need to
+detect a complete rewrite. A receipt has no signature, so send it through a separate trusted
+channel. `forensic_inspect()` reports damaged archive facts, but it does not return damaged data
+for normal analysis. MTRL verifies digests and never verifies your execution environment:
+environment records are author claims, not checked facts.
+
+## Licence
+
+The core is licensed under the MPL-2.0. Read the licence text in `LICENSE` and the inherited
+notices in `NOTICE`, both included in this distribution. The upstream licence reference is
+https://www.mozilla.org/en-US/MPL/2.0/.

vector_mtrl-0.2.0.dist-info/RECORD

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vector_mtrl-0.2.0.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: hatchling 1.32.0
+Root-Is-Purelib: true
+Tag: py3-none-any