openmassspec 1.0.0__tar.gz

openmassspec-1.0.0/LICENSE

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openmassspec-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: openmassspec
+Version: 1.0.0
+Summary: Open mass spectrometry: one install for the OpenMassSpec vendor reader stack (Thermo, Bruker, Waters)
+Author-email: Nathan Riley <git@nathanriley.com>
+License: Apache-2.0
+Project-URL: Homepage, https://github.com/Sigilweaver/OpenMassSpec
+Project-URL: Documentation, https://github.com/Sigilweaver/OpenMassSpec
+Project-URL: Source, https://github.com/Sigilweaver/OpenMassSpec
+Project-URL: Issues, https://github.com/Sigilweaver/OpenMassSpec/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
+License-File: LICENSE
+Requires-Dist: openmassspec-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"
+Dynamic: license-file
+
+# openmassspec
+
+`openmassspec` is a thin Python metapackage that bundles the OpenMassSpec 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 openmassspec[thermo]
+pip install openmassspec[bruker]
+pip install openmassspec[waters]
+```
+
+Or install every supported vendor reader:
+
+```bash
+pip install openmassspec[all]
+```
+
+## Usage
+
+```python
+import openmassspec
+
+kind = openmassspec.detect("/data/sample.raw")     # "thermo" | "bruker" | "waters" | None
+run  = openmassspec.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).

openmassspec-1.0.0/README.md

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+# openmassspec
+
+`openmassspec` is a thin Python metapackage that bundles the OpenMassSpec 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 openmassspec[thermo]
+pip install openmassspec[bruker]
+pip install openmassspec[waters]
+```
+
+Or install every supported vendor reader:
+
+```bash
+pip install openmassspec[all]
+```
+
+## Usage
+
+```python
+import openmassspec
+
+kind = openmassspec.detect("/data/sample.raw")     # "thermo" | "bruker" | "waters" | None
+run  = openmassspec.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).

openmassspec-1.0.0/openmassspec/__init__.py

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+"""OpenMassSpec: open proteomics vendor reader stack.
+
+This metapackage is the single pip install surface for the stack. The
+base install always brings ``openmassspec_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 openmassspec            # openmassspec_io only
+    pip install openmassspec[thermo]    # + opentfraw
+    pip install openmassspec[bruker]    # + opentimstdf
+    pip install openmassspec[waters]    # + openwraw
+    pip install openmassspec[all]       # + all vendor extensions
+
+Top-level helpers fall into two layers:
+
+* ``detect_format``, ``to_mzml``, ``iter_spectra`` are re-exports from
+  ``openmassspec_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
+from importlib.metadata import version as _pkg_version
+from pathlib import Path
+from typing import Optional
+
+try:
+    __version__ = _pkg_version("openmassspec")
+except PackageNotFoundError:  # pragma: no cover - source checkout fallback
+    __version__ = "0.0.0+unknown"
+
+# Re-export the openmassspec_io reader surface so callers can write
+# ``from openmassspec import to_mzml, iter_spectra, detect_format``.
+try:
+    from openmassspec_io import (  # type: ignore[import-not-found]
+        Spectrum,
+        iter_spectra,
+        to_mzml,
+    )
+    from openmassspec_io import detect as detect_format  # type: ignore[import-not-found]
+except ImportError:  # pragma: no cover - openmassspec_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}")

openmassspec-1.0.0/openmassspec.egg-info/PKG-INFO

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+Metadata-Version: 2.4
+Name: openmassspec
+Version: 1.0.0
+Summary: Open mass spectrometry: one install for the OpenMassSpec vendor reader stack (Thermo, Bruker, Waters)
+Author-email: Nathan Riley <git@nathanriley.com>
+License: Apache-2.0
+Project-URL: Homepage, https://github.com/Sigilweaver/OpenMassSpec
+Project-URL: Documentation, https://github.com/Sigilweaver/OpenMassSpec
+Project-URL: Source, https://github.com/Sigilweaver/OpenMassSpec
+Project-URL: Issues, https://github.com/Sigilweaver/OpenMassSpec/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
+License-File: LICENSE
+Requires-Dist: openmassspec-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"
+Dynamic: license-file
+
+# openmassspec
+
+`openmassspec` is a thin Python metapackage that bundles the OpenMassSpec 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 openmassspec[thermo]
+pip install openmassspec[bruker]
+pip install openmassspec[waters]
+```
+
+Or install every supported vendor reader:
+
+```bash
+pip install openmassspec[all]
+```
+
+## Usage
+
+```python
+import openmassspec
+
+kind = openmassspec.detect("/data/sample.raw")     # "thermo" | "bruker" | "waters" | None
+run  = openmassspec.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).

openmassspec-1.0.0/openmassspec.egg-info/SOURCES.txt

@@ -0,0 +1,11 @@
+LICENSE
+README.md
+pyproject.toml
+./openmassspec/__init__.py
+openmassspec/__init__.py
+openmassspec.egg-info/PKG-INFO
+openmassspec.egg-info/SOURCES.txt
+openmassspec.egg-info/dependency_links.txt
+openmassspec.egg-info/requires.txt
+openmassspec.egg-info/top_level.txt
+tests/test_metapackage.py

openmassspec-1.0.0/openmassspec.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

openmassspec-1.0.0/openmassspec.egg-info/requires.txt

@@ -0,0 +1,15 @@
+openmassspec-io
+
+[all]
+opentfraw
+opentimstdf
+openwraw
+
+[bruker]
+opentimstdf
+
+[thermo]
+opentfraw
+
+[waters]
+openwraw

openmassspec-1.0.0/openmassspec.egg-info/top_level.txt

@@ -0,0 +1 @@
+openmassspec

openmassspec-1.0.0/pyproject.toml

@@ -0,0 +1,50 @@
+[build-system]
+requires = ["setuptools>=68", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "openmassspec"
+version = "1.0.0"
+description = "Open mass spectrometry: one install for the OpenMassSpec vendor reader stack (Thermo, Bruker, Waters)"
+readme = "README.md"
+license = { text = "Apache-2.0" }
+authors = [{ name = "Nathan Riley", email = "git@nathanriley.com" }]
+requires-python = ">=3.9"
+keywords = [
+    "mass-spectrometry",
+    "proteomics",
+    "raw",
+    "thermo",
+    "bruker",
+    "waters",
+    "tdf",
+    "mzml",
+]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "License :: OSI Approved :: Apache Software License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Rust",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+dependencies = ["openmassspec-io"]
+
+[project.optional-dependencies]
+# The base install always brings openmassspec-io (the vendor-agnostic Rust
+# reader). Each extra layers on a per-vendor native binding; the `all`
+# extra installs every supported vendor.
+thermo = ["opentfraw"]
+bruker = ["opentimstdf"]
+waters = ["openwraw"]
+all = ["opentfraw", "opentimstdf", "openwraw"]
+
+[project.urls]
+Homepage = "https://github.com/Sigilweaver/OpenMassSpec"
+Documentation = "https://github.com/Sigilweaver/OpenMassSpec"
+Source = "https://github.com/Sigilweaver/OpenMassSpec"
+Issues = "https://github.com/Sigilweaver/OpenMassSpec/issues"
+
+[tool.setuptools]
+packages = ["openmassspec"]
+package-dir = { "" = "." }
+license-files = ["LICENSE"]

openmassspec-1.0.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

openmassspec-1.0.0/tests/test_metapackage.py

@@ -0,0 +1,155 @@
+"""Smoke tests for the `openmassspec` metapackage.
+
+These tests do not require any vendor corpus. They exercise:
+
+* metadata (`__version__`, `__all__`),
+* structural `detect()` against synthesized directories/files,
+* `open_run()` error paths,
+* presence of the `openmassspec_io` re-exports (when installed).
+"""
+
+from __future__ import annotations
+
+from pathlib import Path
+
+import openmassspec
+import pytest
+
+
+def test_version_string():
+    assert isinstance(openmassspec.__version__, str)
+    assert openmassspec.__version__.count(".") >= 1
+
+
+def test_vendors_tuple():
+    assert openmassspec.VENDORS == ("thermo", "bruker", "waters")
+
+
+def test_detect_thermo_file(tmp_path: Path):
+    f = tmp_path / "sample.raw"
+    f.write_bytes(b"")
+    assert openmassspec.detect(f) == "thermo"
+
+
+def test_detect_bruker_d(tmp_path: Path):
+    d = tmp_path / "sample.d"
+    d.mkdir()
+    (d / "analysis.tdf").write_bytes(b"")
+    assert openmassspec.detect(d) == "bruker"
+
+
+def test_detect_waters_raw(tmp_path: Path):
+    d = tmp_path / "sample.raw"
+    d.mkdir()
+    (d / "_HEADER.TXT").write_bytes(b"")
+    assert openmassspec.detect(d) == "waters"
+
+
+def test_detect_unknown_returns_none(tmp_path: Path):
+    p = tmp_path / "something.txt"
+    p.write_bytes(b"hello")
+    assert openmassspec.detect(p) is None
+
+
+def test_detect_missing_path_returns_none(tmp_path: Path):
+    assert openmassspec.detect(tmp_path / "does-not-exist") is None
+
+
+def test_open_run_unknown_raises(tmp_path: Path):
+    p = tmp_path / "nope.txt"
+    p.write_bytes(b"")
+    with pytest.raises(ValueError):
+        openmassspec.open_run(p)
+
+
+def test_openmassspec_io_reexports_present():
+    # The base install pulls openmassspec_io; the re-exports should be
+    # importable callables. If openmassspec_io is genuinely missing the
+    # module falls back to None and we skip.
+    if openmassspec.to_mzml is None:
+        pytest.skip("openmassspec_io not importable in this environment")
+    assert callable(openmassspec.to_mzml)
+    assert callable(openmassspec.iter_spectra)
+    assert callable(openmassspec.detect_format)
+
+
+def test_version_matches_installed_metadata():
+    """Catch ``__version__`` drift from ``pyproject.toml`` early."""
+    from importlib.metadata import PackageNotFoundError, version
+
+    try:
+        installed = version("openmassspec")
+    except PackageNotFoundError:
+        pytest.skip("openmassspec not installed (running from source)")
+    assert openmassspec.__version__ == installed
+
+
+def test_open_run_thermo_dispatch(monkeypatch, tmp_path: Path):
+    """``open_run`` on a thermo file imports opentfraw and calls ``RawFile``."""
+    import sys
+    import types
+
+    f = tmp_path / "sample.raw"
+    f.write_bytes(b"")
+    calls: list[str] = []
+
+    fake = types.ModuleType("opentfraw")
+    fake.RawFile = lambda p: calls.append(("thermo", p)) or "thermo-handle"  # type: ignore[attr-defined]
+    monkeypatch.setitem(sys.modules, "opentfraw", fake)
+
+    assert openmassspec.open_run(f) == "thermo-handle"
+    assert calls == [("thermo", str(f))]
+
+
+def test_open_run_bruker_dispatch(monkeypatch, tmp_path: Path):
+    import sys
+    import types
+
+    d = tmp_path / "sample.d"
+    d.mkdir()
+    (d / "analysis.tdf").write_bytes(b"")
+    calls: list[str] = []
+
+    fake = types.ModuleType("opentimstdf")
+    fake.Reader = lambda p: calls.append(("bruker", p)) or "bruker-handle"  # type: ignore[attr-defined]
+    monkeypatch.setitem(sys.modules, "opentimstdf", fake)
+
+    assert openmassspec.open_run(d) == "bruker-handle"
+    assert calls == [("bruker", str(d))]
+
+
+def test_open_run_waters_dispatch(monkeypatch, tmp_path: Path):
+    import sys
+    import types
+
+    d = tmp_path / "sample.raw"
+    d.mkdir()
+    (d / "_HEADER.TXT").write_bytes(b"")
+    calls: list[str] = []
+
+    fake = types.ModuleType("openwraw")
+    fake.RawReader = lambda p: calls.append(("waters", p)) or "waters-handle"  # type: ignore[attr-defined]
+    monkeypatch.setitem(sys.modules, "openwraw", fake)
+
+    assert openmassspec.open_run(d) == "waters-handle"
+    assert calls == [("waters", str(d))]
+
+
+def test_vendors_is_immutable_tuple():
+    assert isinstance(openmassspec.VENDORS, tuple)
+    with pytest.raises((TypeError, AttributeError)):
+        openmassspec.VENDORS[0] = "nope"  # type: ignore[index]
+
+
+def test_public_api_surface():
+    expected = {
+        "__version__",
+        "VENDORS",
+        "Spectrum",
+        "detect",
+        "detect_format",
+        "iter_spectra",
+        "open_run",
+        "to_mzml",
+    }
+    assert set(openmassspec.__all__) == expected