Merge branch 'development' of github.com:wilhelm-lab/spectrum_io into…

… development
wilhelm-lab · Oct 5, 2023 · 40b352e · 40b352e
2 parents 3a3dd72 + 19234f7
commit 40b352e
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Showing 8 changed files with 13 additions and 14 deletions.
diff --git a/.cookietemple.yml b/.cookietemple.yml
@@ -15,5 +15,5 @@ full_name: Mario Picciani
 email: [email protected]
 project_name: spectrum_io
 project_short_description: IO related functionalities for oktoberfest.
-version: 0.3.2
+version: 0.3.3
 license: MIT
diff --git a/.github/release-drafter.yml b/.github/release-drafter.yml
@@ -1,5 +1,5 @@
-name-template: "0.3.2 🌈" # <<COOKIETEMPLE_FORCE_BUMP>>
-tag-template: 0.3.2 # <<COOKIETEMPLE_FORCE_BUMP>>
+name-template: "0.3.3 🌈" # <<COOKIETEMPLE_FORCE_BUMP>>
+tag-template: 0.3.3 # <<COOKIETEMPLE_FORCE_BUMP>>
 exclude-labels:
     - "skip-changelog"
 

diff --git a/cookietemple.cfg b/cookietemple.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.3.2
+current_version = 0.3.3
 
 [bumpversion_files_whitelisted]
 init_file = spectrum_io/__init__.py

diff --git a/docs/conf.py b/docs/conf.py
@@ -53,9 +53,9 @@
 # the built documents.
 #
 # The short X.Y version.
-version = "0.3.2"
+version = "0.3.3"
 # The full version, including alpha/beta/rc tags.
-release = "0.3.2"
+release = "0.3.3"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "spectrum_io"
-version = "0.3.2"  # <<COOKIETEMPLE_FORCE_BUMP>>
+version = "0.3.3"  # <<COOKIETEMPLE_FORCE_BUMP>>
 description = "IO related functionalities for oktoberfest."
 authors = ["Mario Picciani <[email protected]>"]
 license = "MIT"

diff --git a/spectrum_io/__init__.py b/spectrum_io/__init__.py
@@ -2,7 +2,7 @@
 
 __author__ = "Mario Picciani"
 __email__ = "[email protected]"
-__version__ = "0.3.2"
+__version__ = "0.3.3"
 
 import logging
 import logging.handlers

diff --git a/spectrum_io/__main__.py b/spectrum_io/__main__.py
@@ -5,7 +5,7 @@
 
 
 @click.command()
-@click.version_option(version="0.3.2", message=click.style("spectrum_io Version: 0.3.2"))
+@click.version_option(version="0.3.3", message=click.style("spectrum_io Version: 0.3.3"))
 def main() -> None:
     """spectrum_io."""
 

diff --git a/spectrum_io/raw/msraw.py b/spectrum_io/raw/msraw.py
@@ -18,20 +18,19 @@ def check_analyzer(mass_analyzers: Dict[str, str]) -> Dict[str, str]:
     Convert mass analyzer accession ids to internal format.
 
     :param mass_analyzers: dictionary with instrumentConfigurationRef, analyzer accession
-    :raises AssertionError: if the mass analyzer metadata cannot be found in the file or the search
-        was conducted with an unsupported mass analyzer.
-    :return: dictionary with instrumentConfigurationRef, one of (ITMS, FTMS, TOF)
+    :return: dictionary with instrumentConfigurationRef, one of "ITMS", "FTMS", "TOF" or "unknown",
+        in case the analyzer accession cannot be mapped to one of the three groups.
     """
     for elem in mass_analyzers.keys():
         accession = mass_analyzers[elem]
         if accession in ["MS:1000079", "MS:1000484"]:  # fourier transform ion cyclotron, orbitrap
             mass_analyzers[elem] = "FTMS"
-        elif accession in ["MS:1000082", "MS:1000264"]:  # quadrupole ion-trap, io-trap
+        elif accession in ["MS:1000082", "MS:1000264" "MS:1000078"]:  # quadrupole ion-trap, ion-trap, linear ion-trap
             mass_analyzers[elem] = "ITMS"
         elif accession in ["MS:1000084"]:  # TOF
             mass_analyzers[elem] = "TOF"
         else:
-            raise AssertionError(f"The mass analyzer with accession {accession} is not supported.")
+            mass_analyzers[elem] = "unsupported"
     return mass_analyzers