Merge pull request #213 from MannLabs/development

Development

.bumpversion.cfg

@@ -1,9 +1,9 @@
 [bumpversion]
-current_version = 1.2.5
+current_version = 1.3.0
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?
-serialize =
+serialize = 
 	{major}.{minor}.{patch}
 	{major}.{minor}.{patch}
 

.pre-commit-config.yaml

@@ -12,5 +12,7 @@ repos:
   hooks:
     - id: ruff-format
     - id: ruff
+      args:
+        - "--fix"
 
 exclude: .bumpversion.cfg

CHANGELOG.md

@@ -1,5 +1,7 @@
 # Changelog
 
+Note: This changelog is deprecated and will no longer be updated. Please refer to the Release changelogs on github.
+
 Follow the changelog format from https://keepachangelog.com/en/1.0.0/.
 
 ## 1.1.0 - 2023.xx.xx
@@ -10,7 +12,7 @@ Follow the changelog format from https://keepachangelog.com/en/1.0.0/.
 
 ### Changed
 
-- `mod@Any N-term` and `mod@Any_N-term` are both supported, `Any_N-term` is prefered as there are no spaces and hence better for command line tools. The same for `mod@Protein N-term`, `mod@Any C-term`, and `mod@Protein C-term`.
+- `mod@Any_N-term` are both supported, `Any_N-term` is prefered as there are no spaces and hence better for command line tools. The same for `mod@Protein_N-term`, `mod@Any_C-term`, and `mod@Protein_C-term`.
 - Enable customizing dtypes of peak mz and intensty values.
 - `SWATHLibraryReader` to `LibraryBaseReader` in `alphabase.spectral_library.reader`.
 - New `LibraryReaderBase._get_fragment_intensity` implementation which is called at the end of the parsing process in `PSMReaderBase._post_process`. This allows it to operate only on the translated column names. By default, all non-fragment columns will be grouped and part of the final output.

alphabase/__init__.py

@@ -2,7 +2,7 @@
 
 
 __project__ = "alphabase"
-__version__ = "1.2.5"
+__version__ = "1.3.0"
 __license__ = "Apache"
 __description__ = "An infrastructure Python package of the AlphaX ecosystem"
 __author__ = "Mann Labs"

alphabase/constants/_const.py

@@ -1,4 +1,5 @@
 import os
+
 import numpy as np
 
 from alphabase.yaml_utils import load_yaml

alphabase/constants/aa.py

@@ -1,18 +1,17 @@
 import os
-import pandas as pd
-import numpy as np
 import typing
 
-from alphabase.yaml_utils import load_yaml
+import numpy as np
+import pandas as pd
 
+from alphabase.constants._const import CONST_FILE_FOLDER
 from alphabase.constants.atom import (
-    calc_mass_from_formula,
     MASS_H2O,
+    calc_mass_from_formula,
     parse_formula,
     reset_elements,
 )
-
-from alphabase.constants._const import CONST_FILE_FOLDER
+from alphabase.yaml_utils import load_yaml
 
 # We use all 128 ASCII code to represent amino acids for flexible extensions in the future.
 # The amino acid masses are stored in 128-lengh array :py:data:`AA_ASCII_MASS`.
@@ -70,7 +69,7 @@ def reset_AA_df():
 def reset_AA_Composition():
     global AA_Composition
     AA_Composition = {}
-    for aa, formula, mass in AA_DF.values:
+    for aa, formula, _mass in AA_DF.values:
         AA_Composition[aa] = dict(parse_formula(formula))
     return AA_Composition
 

alphabase/constants/atom.py

@@ -1,11 +1,11 @@
 import os
-import numpy as np
-import numba
 import typing
 
-from alphabase.yaml_utils import load_yaml
+import numba
+import numpy as np
 
 from alphabase.constants._const import CONST_FILE_FOLDER, common_const_dict
+from alphabase.yaml_utils import load_yaml
 
 MASS_PROTON: float = common_const_dict["MASS_PROTON"]
 MASS_ISOTOPE: float = common_const_dict["MASS_ISOTOPE"]