Release/0.3.3

.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

.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"
 

.readthedocs.yml

@@ -3,19 +3,20 @@
 
 version: 2
 
-# Build documentation in the docs/ directory with Sphinx
+# Set the OS, Python version and other tools you might need
+build:
+    os: ubuntu-22.04
+    tools:
+        python: "3.10"
+
+# Build documentation in the "docs/" directory with Sphinx
 sphinx:
     configuration: docs/conf.py
 
-# Build documentation with MkDocs
-#mkdocs:
-#  configuration: mkdocs.yml
-
 # Optionally build your docs in additional formats such as PDF and ePub
 formats: all
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-    version: 3.8
     install:
         - requirements: docs/requirements.txt

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

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.

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"

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

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."""
 

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