Read and write idXML files using pyopenms

docs/source/conf.py

@@ -21,6 +21,7 @@
     "sphinx.ext.autodoc",
     "sphinx.ext.autosectionlabel",
     "sphinx.ext.autosummary",
+    "sphinx.ext.intersphinx",
     "sphinx.ext.napoleon",
     "sphinx_rtd_theme",
     "sphinx_mdinclude",
@@ -40,6 +41,15 @@
 autodoc_member_order = "bysource"
 autoclass_content = "init"
 
+# Intersphinx options
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3", None),
+    "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
+    "pyteomics": ("https://pyteomics.readthedocs.io/en/latest/", None),
+    "pyopenms": ("https://pyopenms.readthedocs.io/en/latest/", None),
+}
+
 
 def setup(app):
     config = {

online/pages/2_PSM_file_conversion.py

@@ -68,9 +68,10 @@ def _convert(self):
                 st.success("PSM file successfully converted!")
 
                 # Construct output filename with new extension
-                output_filename = Path(
-                    st.session_state["convert_input_file"].name
-                ).stem + FILETYPES[st.session_state["convert_output_filetype"]]["extension"]
+                output_filename = (
+                    Path(st.session_state["convert_input_file"].name).stem
+                    + FILETYPES[st.session_state["convert_output_filetype"]]["extension"]
+                )
 
                 # Open converted file in memory for download button
                 with open("output_filename", "rb") as file:

psm_utils/io/__init__.py

@@ -9,6 +9,7 @@
 from rich.progress import track
 
 import psm_utils.io.idxml as idxml
+import psm_utils.io.ionbot as ionbot
 import psm_utils.io.maxquant as maxquant
 import psm_utils.io.msamanda as msamanda
 import psm_utils.io.mzid as mzid
@@ -18,7 +19,6 @@
 import psm_utils.io.sage as sage
 import psm_utils.io.tsv as tsv
 import psm_utils.io.xtandem as xtandem
-import psm_utils.io.ionbot as ionbot
 from psm_utils.io._base_classes import WriterBase
 from psm_utils.io.exceptions import PSMUtilsIOException
 from psm_utils.psm import PSM
@@ -27,7 +27,7 @@
 FILETYPES = {
     "idxml": {
         "reader": idxml.IdXMLReader,
-        "writer": None,
+        "writer": idxml.IdXMLWriter,
         "extension": ".idXML",
         "filename_pattern": r"^.*\.idxml$",
     },
@@ -120,7 +120,7 @@ def _supports_write_psm(writer: WriterBase):
             supports_write_psm = True
         else:
             supports_write_psm = True
-        Path(temp_file.name).unlink()
+            Path(temp_file.name).unlink()
         return supports_write_psm
 
 

psm_utils/io/_pd_msf_tables.py

@@ -17,6 +17,7 @@
     UniqueConstraint,
     text,
 )
+
 try:
     from sqlalchemy.orm import declarative_base
 except ImportError: