Merge branch 'releases' of https://github.com/compomics/ms2pip_c into…

… fix/deps

README.rst

@@ -44,7 +44,7 @@ Python and C.
    ``DVAQIFNNILR/2``.
 
 You can install MS²PIP on your machine by following the
-`installation instructions <https://ms2pip.readthedocs.io/installation/>`_. For a more
+`installation instructions <https://ms2pip.readthedocs.io/en/latest/installation/>`_. For a more
 user-friendly experience, go to the `MS²PIP web server <https://iomics.ugent.be/ms2pip>`_. There,
 you can easily upload a list of peptide sequences, after which the corresponding predicted MS2
 spectra can be downloaded in multiple file formats. The web server can also be contacted through

docs/source/usage.rst

@@ -65,7 +65,7 @@ For instance:
 
 .. code-block:: sh
 
-    ms2pip correlate results.sage.tsv --spectrum-file spectra.mgf
+    ms2pip correlate --psm-filetype sage results.sage.tsv spectra.mgf
 
 
 ``get-training-data``

ms2pip/spectrum_input.py

@@ -29,11 +29,12 @@ def read_spectrum_file(spectrum_file: str) -> Generator[ObservedSpectrum, None,
         If the file extension is not supported.
 
     """
-    file_extension = Path(spectrum_file).suffix.lower()
-    if file_extension not in [".mgf", ".mzml", ".d"] and not _is_minitdf(spectrum_file):
-        raise UnsupportedSpectrumFiletypeError(file_extension)
+    try:
+        spectra = get_ms2_spectra(str(spectrum_file))
+    except ValueError:
+        raise UnsupportedSpectrumFiletypeError(Path(spectrum_file).suffixes)
 
-    for spectrum in get_ms2_spectra(str(spectrum_file)):
+    for spectrum in spectra:
         obs_spectrum = ObservedSpectrum(
             mz=np.array(spectrum.mz, dtype=np.float32),
             intensity=np.array(spectrum.intensity, dtype=np.float32),
@@ -50,15 +51,3 @@ def read_spectrum_file(spectrum_file: str) -> Generator[ObservedSpectrum, None,
         ):
             continue
         yield obs_spectrum
-
-
-def _is_minitdf(spectrum_file: str) -> bool:
-    """
-    Check if the spectrum file is a Bruker miniTDF folder.
-
-    A Bruker miniTDF folder has no fixed name, but contains files matching the patterns
-    ``*ms2spectrum.bin`` and ``*ms2spectrum.parquet``.
-    """
-    files = set(Path(spectrum_file).glob("*ms2spectrum.bin"))
-    files.update(Path(spectrum_file).glob("*ms2spectrum.parquet"))
-    return len(files) >= 2