chore: WIP get unit_test passing with py311 deps

docker/requirements.in

@@ -8,7 +8,7 @@ gspread
 h5py
 humanize
 ipykernel
-ipympl==0.8.6
+ipympl==0.9.3
 ipysheet
 ipywidgets
 jupyter-client

docker/requirements.txt

@@ -117,7 +117,7 @@ ipykernel==6.25.2
     # via
     #   -r requirements.in
     #   jupyterlab
-ipympl==0.8.6
+ipympl==0.9.3
     # via -r requirements.in
 ipysheet==0.7.0
     # via -r requirements.in

metatlas/tools/cheminfo.py

@@ -7,7 +7,8 @@
 import matchms
 import numpy as np
 
-from matchms.filtering.load_adducts import load_adducts_dict
+from matchms.filtering.filter_utils.load_known_adducts import (
+    load_known_adducts)
 from rdkit import Chem
 
 from metatlas.interfaces.compounds import structure_cleaning as cleaning
@@ -28,21 +29,23 @@ def get_parent_mass(precursor_mz: float, adduct: str) -> float:
 @functools.lru_cache
 def get_precursor_mz(parent_mass: float, adduct: str) -> float:
     """For an input molecule with parent_mass that generates adduct, return the resutling precursor_mz"""
-    adducts = load_adducts_dict()
-    if adduct not in adducts:
+    adducts = load_known_adducts()
+    if adduct not in adducts["adduct"].values:
         raise KeyError("Adduct '%s' is not supported")
-    multiplier = adducts[adduct]["mass_multiplier"]
-    correction_mass = adducts[adduct]["correction_mass"]
+    row = adducts.loc[adducts["adduct"] == adduct].iloc[0]
+    multiplier = row["mass_multiplier"]
+    correction_mass = row["correction_mass"]
     return (parent_mass + correction_mass) / multiplier
 
 
 @functools.lru_cache
 def is_positive_mode(adduct: str) -> bool:
     """Returns True if the MS mode for an adduct is positive"""
-    adducts = load_adducts_dict()
-    if adduct not in adducts:
+    adducts = load_known_adducts()
+    if adduct not in adducts["adduct"].values:
         raise KeyError("Adduct '%s' is not supported")
-    return adducts[adduct]["ionmode"] == "positive"
+    row = adducts.loc[adducts["adduct"] == adduct].iloc[0]
+    return row["ionmode"] == "positive"
 
 
 @functools.lru_cache
@@ -149,7 +152,7 @@ def valid_adduct(value: str) -> bool:
     True if the value is an adduct listed supported by the matchms package
     This is not a comprehensive list, so it will return False for some uncommon adducts
     """
-    adducts = load_adducts_dict()
+    adducts = load_known_adducts()
     return value in adducts
 
 

metatlas/tools/config.py

@@ -77,7 +77,7 @@ class BaseNotebookParameters(BaseModel):
     project_directory: Path = Path().home() / "metabolomics_data"
     max_cpus: int = 4
     log_level: str = "INFO"
-    resolve_msms_matches_by = "distance"
+    resolve_msms_matches_by: str = "distance"
 
     def update(self, override_parameters: Dict) -> None:
         """update all parameters with any non-None values in override_parameters"""

noxfile.py

@@ -6,18 +6,18 @@
 
 import nox
 
-py_versions = ["3.8", "3.9"]
+py_versions = ["3.11"]
 
 nox.options.sessions = [
     "flake8",
     "black",
-    "pylint-3.8",
-    "mypy-3.8",
-    "unit_tests-3.8",
+    "pylint-3.11",
+    "mypy-3.11",
+    "unit_tests-3.11",
     "flake8_nb",
     "black_nb",
-    "pylint_nb-3.8",
-    "system_tests-3.8",
+    "pylint_nb-3.11",
+    "system_tests-3.11",
     "update_git_hooks",
 ]
 
@@ -69,15 +69,10 @@
 ]
 
 pytest_deps = [
-    "attrs==22.1.0",
     "coverage==7.0.5",
     "iniconfig==2.0.0",
-    "numpy==1.22.4",
-    "packaging==21.3",
-    "pandas==1.4.2",
     "pluggy==1.0.0",
     "py==1.11.0",
-    "pyparsing==3.0.9",
     "pytest==7.2.1",
     "pytest-cov==3.0.0",
     "pytest-mock==3.10.0",

tests/unit/test_cheminfo.py

@@ -1,6 +1,7 @@
 # pylint: disable=missing-function-docstring, missing-module-docstring, line-too-long
 
-from matchms.filtering.load_adducts import load_adducts_dict
+from matchms.filtering.filter_utils.load_known_adducts import (
+    load_known_adducts)
 from rdkit import Chem
 
 from metatlas.tools import cheminfo
@@ -11,11 +12,11 @@
 
 
 def test_get_parent_mass01():
-    adducts = load_adducts_dict()
+    adducts = load_known_adducts()
     original_parent = 100
-    for name in adducts:
-        pre = cheminfo.get_precursor_mz(original_parent, name)
-        parent = cheminfo.get_parent_mass(pre, name)
+    for _, row in adducts.iterrows():
+        pre = cheminfo.get_precursor_mz(original_parent, row["adduct"])
+        parent = cheminfo.get_parent_mass(pre, row["adduct"])
         assert abs(original_parent - parent) < 1e-7