openproteo 1.0.2__py3-none-any.whl

openproteo/__init__.py

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+"""OpenProteo: open proteomics vendor reader stack.
+
+This metapackage is the single pip install surface for the stack. The
+base install always brings ``openproteo_io`` (the Rust-backed reader
+that converts vendor inputs to mzML / Arrow); the per-vendor extras
+layer on direct Python bindings for each native vendor package:
+
+* ``opentfraw``   - Thermo `.raw` files
+* ``opentimstdf`` - Bruker timsTOF `.d/` bundles
+* ``openwraw``    - Waters MassLynx `.raw/` directories
+
+Install the umbrella::
+
+    pip install openproteo            # openproteo_io only
+    pip install openproteo[thermo]    # + opentfraw
+    pip install openproteo[bruker]    # + opentimstdf
+    pip install openproteo[waters]    # + openwraw
+    pip install openproteo[all]       # + all vendor extensions
+
+Top-level helpers fall into two layers:
+
+* ``detect_format``, ``to_mzml``, ``iter_spectra`` are re-exports from
+  ``openproteo_io`` - the vendor-agnostic reader.
+* ``detect``, ``open_run`` use only structural checks and dispatch to
+  the vendor extension that matches the input path (requires the
+  corresponding extra).
+"""
+
+from __future__ import annotations
+
+import os
+from importlib.metadata import PackageNotFoundError, version as _pkg_version
+from pathlib import Path
+from typing import Optional
+
+try:
+    __version__ = _pkg_version("openproteo")
+except PackageNotFoundError:  # pragma: no cover - source checkout fallback
+    __version__ = "0.0.0+unknown"
+
+# Re-export the openproteo_io reader surface so callers can write
+# ``from openproteo import to_mzml, iter_spectra, detect_format``.
+try:
+    from openproteo_io import (  # type: ignore[import-not-found]
+        Spectrum,
+        iter_spectra,
+        to_mzml,
+    )
+    from openproteo_io import detect as detect_format  # type: ignore[import-not-found]
+except ImportError:  # pragma: no cover - openproteo_io is a hard dep
+    Spectrum = None  # type: ignore[assignment]
+    detect_format = None  # type: ignore[assignment]
+    iter_spectra = None  # type: ignore[assignment]
+    to_mzml = None  # type: ignore[assignment]
+
+__all__ = [
+    "__version__",
+    "VENDORS",
+    "Spectrum",
+    "detect",
+    "detect_format",
+    "iter_spectra",
+    "open_run",
+    "to_mzml",
+]
+
+VENDORS = ("thermo", "bruker", "waters")
+
+
+def detect(path: str | os.PathLike[str]) -> Optional[str]:
+    """Return ``"thermo"``, ``"bruker"``, ``"waters"`` or ``None`` for *path*.
+
+    The check is purely structural (extension + sentinel files); no vendor
+    reader needs to be importable.
+    """
+    p = Path(path)
+    if not p.exists():
+        return None
+    if p.is_file() and p.suffix.lower() == ".raw":
+        return "thermo"
+    if p.is_dir():
+        suffix = p.suffix.lower()
+        if suffix == ".d" and (p / "analysis.tdf").is_file():
+            return "bruker"
+        if suffix == ".raw" and any(
+            (p / name).exists()
+            for name in ("_FUNCTNS.INF", "_extern.inf", "_HEADER.TXT")
+        ):
+            return "waters"
+    return None
+
+
+def open_run(path: str | os.PathLike[str]):
+    """Detect *path*, import the matching vendor package, and open the run.
+
+    Raises ``ImportError`` if the matching vendor extra is not installed and
+    ``ValueError`` if the format cannot be detected.
+    """
+    kind = detect(path)
+    if kind is None:
+        raise ValueError(f"no supported vendor format detected at {path}")
+    if kind == "thermo":
+        import opentfraw  # type: ignore[import-not-found]
+
+        return opentfraw.RawFile(str(path))
+    if kind == "bruker":
+        import opentimstdf  # type: ignore[import-not-found]
+
+        return opentimstdf.Reader(str(path))
+    if kind == "waters":
+        import openwraw  # type: ignore[import-not-found]
+
+        return openwraw.RawReader(str(path))
+    raise ValueError(f"unhandled vendor kind: {kind}")

openproteo-1.0.2.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: openproteo
+Version: 1.0.2
+Summary: Open proteomics: one install for the OpenProteo vendor reader stack (Thermo, Bruker, Waters)
+Author-email: Nathan Riley <git@nathanriley.com>
+License: Apache-2.0
+Project-URL: Homepage, https://github.com/Sigilweaver/OpenProteo
+Project-URL: Documentation, https://github.com/Sigilweaver/OpenProteo
+Project-URL: Source, https://github.com/Sigilweaver/OpenProteo
+Project-URL: Issues, https://github.com/Sigilweaver/OpenProteo/issues
+Keywords: mass-spectrometry,proteomics,raw,thermo,bruker,waters,tdf,mzml
+Classifier: Development Status :: 4 - Beta
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Rust
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+Requires-Dist: openproteo-io
+Provides-Extra: thermo
+Requires-Dist: opentfraw; extra == "thermo"
+Provides-Extra: bruker
+Requires-Dist: opentimstdf; extra == "bruker"
+Provides-Extra: waters
+Requires-Dist: openwraw; extra == "waters"
+Provides-Extra: all
+Requires-Dist: opentfraw; extra == "all"
+Requires-Dist: opentimstdf; extra == "all"
+Requires-Dist: openwraw; extra == "all"
+
+# openproteo
+
+`openproteo` is a thin Python metapackage that bundles the OpenProteo vendor reader stack:
+
+| Vendor | Format         | Underlying package |
+|--------|----------------|--------------------|
+| Thermo | `.raw` file    | `opentfraw`        |
+| Bruker | `.d/` bundle   | `opentimstdf`      |
+| Waters | `.raw/` dir    | `openwraw`         |
+
+## Install
+
+Install just what you need:
+
+```bash
+pip install openproteo[thermo]
+pip install openproteo[bruker]
+pip install openproteo[waters]
+```
+
+Or install every supported vendor reader:
+
+```bash
+pip install openproteo[all]
+```
+
+## Usage
+
+```python
+import openproteo
+
+kind = openproteo.detect("/data/sample.raw")     # "thermo" | "bruker" | "waters" | None
+run  = openproteo.open_run("/data/sample.raw")    # vendor-specific reader object
+```
+
+`open_run` raises `ImportError` if the matching vendor extra is not installed and
+`ValueError` if the format cannot be detected.
+
+## License
+
+Apache-2.0. See [`LICENSE`](../LICENSE).

openproteo-1.0.2.dist-info/RECORD

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+openproteo/__init__.py,sha256=cYrFgRqqSrsOmFXh36i_nHXUgVxh_MlFHISIHxm8wZA,3818
+openproteo-1.0.2.dist-info/METADATA,sha256=xk0xJFzjc2DBNAMPrAxvOuCk_RmnCcbn3QsvltoCdQ4,2244
+openproteo-1.0.2.dist-info/WHEEL,sha256=aeYiig01lYGDzBgS8HxWXOg3uV61G9ijOsup-k9o1sk,91
+openproteo-1.0.2.dist-info/top_level.txt,sha256=3hZgqbVRvdrhPoZ9OxQyxnyk8E8kHbFzcXS5iXemzRQ,11
+openproteo-1.0.2.dist-info/RECORD,,

openproteo-1.0.2.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: setuptools (82.0.1)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

openproteo-1.0.2.dist-info/top_level.txt

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+openproteo