Merge pull request #45 from MannLabs/39-code-formatting-2

39 code formatting 2

.bumpversion.cfg

@@ -3,7 +3,7 @@ current_version = 0.4.5
 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}
 

.github/workflows/_run_tests.yml

@@ -51,4 +51,4 @@ jobs:
         cd tests
         python download_test_data.py
         . ./run_tests.sh
-        conda deactivate
+        conda deactivate

.github/workflows/pip_installation.yml

@@ -38,4 +38,4 @@ jobs:
     with:
       os: ${{ matrix.os }}
       python-version: ${{ matrix.python-version }}
-      install-script: "loose_pip_install.sh"
+      install-script: "loose_pip_install.sh"

README.md

@@ -63,7 +63,7 @@ requires you to add the ppa to your trusted sources!
 1.  Install [brew](https://brew.sh).
 2.  Install mono: `brew install mono`.
 3.  If the pseudo mono folder `/Library/Frameworks/Mono.framework/Versions` does not exist, create it by running `sudo mkdir -p /Library/Frameworks/Mono.framework/Versions`.
-4.  Link homebrew mono to pseudo mono folder: `sudo ln -s /opt/homebrew/Cellar/mono/6.12.0.182 /Library/Frameworks/Mono.framework/Versions/Current`. Here, `6.12.0.182` is the brew-installed mono version, please check your installed version. Navigate to `/Library/Frameworks/Mono.framework/Versions` and run `ls -l` to verify that the link `Current` points to `/opt/homebrew/Cellar/mono/6.12.0.182`. If `Current` points to a different installation and/or `/opt/homebrew/Cellar/mono/6.12.0.182` is referenced by a different link, delete the corresponding links and run `sudo ln -s /opt/homebrew/Cellar/mono/6.12.0.182 Current`.     
+4.  Link homebrew mono to pseudo mono folder: `sudo ln -s /opt/homebrew/Cellar/mono/6.12.0.182 /Library/Frameworks/Mono.framework/Versions/Current`. Here, `6.12.0.182` is the brew-installed mono version, please check your installed version. Navigate to `/Library/Frameworks/Mono.framework/Versions` and run `ls -l` to verify that the link `Current` points to `/opt/homebrew/Cellar/mono/6.12.0.182`. If `Current` points to a different installation and/or `/opt/homebrew/Cellar/mono/6.12.0.182` is referenced by a different link, delete the corresponding links and run `sudo ln -s /opt/homebrew/Cellar/mono/6.12.0.182 Current`.
 5.  Install pythonnet: `pip install pythonnet`.
 
 ------------------------------------------------------------------------

alpharaw/__init__.py

@@ -1,23 +1,29 @@
 #!python
 
 import warnings
+
 warnings.filterwarnings("ignore")
 
+
 def register_readers():
     from .ms_data_base import ms_reader_provider
     from .legacy_msdata import mgf
     from .mzml import MzMLReader
     from .wrappers import alphapept_wrapper
+
     try:
         from .sciex import SciexWiffData
         from .thermo import ThermoRawData
     except (RuntimeError, ImportError):
         print("[WARN] pythonnet is not installed")
 
+
 __project__ = "alpharaw"
 __version__ = "0.4.5"
 __license__ = "Apache"
-__description__ = "An open-source Python package to unify raw MS data access and storage."
+__description__ = (
+    "An open-source Python package to unify raw MS data access and storage."
+)
 __author__ = "Mann Labs"
 __author_email__ = "[email protected]"
 __github__ = "https://github.com/MannLabs/alpharaw"
@@ -28,7 +34,7 @@ def register_readers():
     "mass spectrometry",
     "raw data",
     "data access",
-    "data storage"
+    "data storage",
 ]
 __python_version__ = ">=3.8"
 __classifiers__ = [

alpharaw/cli.py

@@ -6,55 +6,66 @@
 from alpharaw.legacy_msdata import mgf
 from alpharaw.mzml import MzMLReader
 from alpharaw.wrappers import alphapept_wrapper
+
 try:
     from alpharaw.sciex import SciexWiffData
     from alpharaw.thermo import ThermoRawData
 except (RuntimeError, ImportError):
     print("[WARN] pythonnet is not installed")
 
+
 @click.group(
     context_settings=dict(
-        help_option_names=['-h', '--help'],
+        help_option_names=["-h", "--help"],
     ),
-    invoke_without_command=True
+    invoke_without_command=True,
 )
 @click.pass_context
 @click.version_option(alpharaw.__version__, "-v", "--version")
 def run(ctx, **kwargs):
     click.echo(
-r'''
-   ___   __     __        ___             
+        r"""
+   ___   __     __        ___
   / _ | / /__  / /  ___ _/ _ \___ __    __
  / __ |/ / _ \/ _ \/ _ `/ , _/ _ `/ |/|/ /
-/_/ |_/_/ .__/_//_/\_,_/_/|_|\_,_/|__,__/ 
-       /_/                                
+/_/ |_/_/ .__/_//_/\_,_/_/|_|\_,_/|__,__/
+       /_/
 ....................................................
 .{version}.
 .{url}.
 .{license}.
 ....................................................
-'''.format(
-        version=alpharaw.__version__.center(50),
-        url=alpharaw.__github__.center(50), 
-        license=alpharaw.__license__.center(50),
+""".format(
+            version=alpharaw.__version__.center(50),
+            url=alpharaw.__github__.center(50),
+            license=alpharaw.__license__.center(50),
+        )
     )
-)
     if ctx.invoked_subcommand is None:
         click.echo(run.get_help(ctx))
 
+
 @run.command("parse", help="Convert raw files into alpharaw hdf5 (.hdf) format.")
 @click.option(
-    "--raw_type", type=str, default="thermo_raw",
-    show_default=True, help=f"Only `thermo_raw`, `sciex_wiff` is supported currently.",
+    "--raw_type",
+    type=str,
+    default="thermo_raw",
+    show_default=True,
+    help=f"Only `thermo_raw`, `sciex_wiff` is supported currently.",
 )
 @click.option(
-    "--raw", multiple=True, default=[],
-    show_default=True, help="Raw files, can be `--raw raw1 --raw raw2 ...`."
+    "--raw",
+    multiple=True,
+    default=[],
+    show_default=True,
+    help="Raw files, can be `--raw raw1 --raw raw2 ...`.",
 )
-def _parse(raw_type:str, raw:list):
+def _parse(raw_type: str, raw: list):
     reader = ms_reader_provider.get_reader(raw_type)
-    if reader is None: 
-        print(f"{raw_type} is not supported, this may be due to the failed installion of PythonNet or other packages")
+    if reader is None:
+        print(
+            f"{raw_type} is not supported, this may be due to the failed installion of PythonNet or other packages"
+        )
     else:
         for raw_file in raw:
             if not os.path.isfile(raw_file):

alpharaw/dia/normal_dia.py

@@ -10,29 +10,32 @@
 from alpharaw.utils.timstof import convert_to_alphatims
 from alphatims.bruker import TimsTOF
 
-class NormalDIAGrouper():
+
+class NormalDIAGrouper:
     def __init__(self, ms_data: MSData_Base):
         self.ms_data = ms_data
-        self.ms_data.spectrum_df[
-            "dia_group"
-        ] = ms_data.spectrum_df.precursor_mz.astype(int)
+        self.ms_data.spectrum_df["dia_group"] = ms_data.spectrum_df.precursor_mz.astype(
+            int
+        )
 
         self.dia_group_dfs = self.ms_data.spectrum_df.groupby("dia_group")
         self.dia_isolation_dict = {}
         for dia_group, df in self.dia_group_dfs:
-            if dia_group == -1: continue
+            if dia_group == -1:
+                continue
             self.dia_isolation_dict[dia_group] = (
                 df.isolation_lower_mz.values[0],
-                df.isolation_upper_mz.values[0]
+                df.isolation_upper_mz.values[0],
             )
         self.dia_groups = np.sort(list(self.dia_isolation_dict.keys()))
 
-    def get_ms_data_for_a_group(self, 
-        dia_group:int=-1, 
-        return_alpharaw_data: bool=True,
-        return_alphatims_data: bool=True,
-    )->typing.Union[MSData_Base, TimsTOF, typing.Tuple[MSData_Base, TimsTOF]]:
-        """ Get compressed MS data for isolation window `dia_group`.
+    def get_ms_data_for_a_group(
+        self,
+        dia_group: int = -1,
+        return_alpharaw_data: bool = True,
+        return_alphatims_data: bool = True,
+    ) -> typing.Union[MSData_Base, TimsTOF, typing.Tuple[MSData_Base, TimsTOF]]:
+        """Get compressed MS data for isolation window `dia_group`.
 
         Args:
             dia_group (int, optional): The DIA group, -1 means ms1. Defaults to -1.
@@ -57,17 +60,15 @@ def get_ms_data_for_a_group(self,
         else:
             ms_data = MSData_Base()
 
-            spec_df, peak_df = remove_unused_peaks(
-                spec_df, self.ms_data.peak_df
-            )
+            spec_df, peak_df = remove_unused_peaks(spec_df, self.ms_data.peak_df)
 
             ms_data.spectrum_df = spec_df
             ms_data.peak_df = peak_df
             return ms_data
 
-    def assign_dia_groups(self, 
-        precursor_mzs
-    )->typing.DefaultDict[typing.List, typing.List]:
+    def assign_dia_groups(
+        self, precursor_mzs
+    ) -> typing.DefaultDict[typing.List, typing.List]:
         dia_precursor_groups = defaultdict(list)
         for i, mz in enumerate(precursor_mzs):
             i_group = np.searchsorted(self.dia_groups, int(mz))
@@ -81,9 +82,9 @@ def assign_dia_groups(self,
                 if mz >= isolation_lower and mz <= isolation_upper:
                     dia_precursor_groups[dia_group].append(i)
                     continue
-            dia_group = self.dia_groups[i_group-1]
+            dia_group = self.dia_groups[i_group - 1]
             if dia_group in self.dia_isolation_dict:
                 isolation_lower, isolation_upper = self.dia_isolation_dict[dia_group]
                 if mz >= isolation_lower and mz <= isolation_upper:
                     dia_precursor_groups[dia_group].append(i)
-        return dia_precursor_groups
+        return dia_precursor_groups

alpharaw/ext/thermo_fisher/THERMO_LICENSE.txt

@@ -6,7 +6,7 @@ These License terms are an agreement between you and Thermo Finnigan LLC ("Licen
 
 1.1. You may install and use this Software on any of your computing devices.
 
-1.2. You may distribute this Software to others, but only in combination with other software components and/or programs that you provide and subject to the distribution requirements and restrictions below. 
+1.2. You may distribute this Software to others, but only in combination with other software components and/or programs that you provide and subject to the distribution requirements and restrictions below.
 
 2.  Use Restrictions:
 
@@ -48,4 +48,4 @@ If you distribute this Software to others, you agree to:
 
 5.8. LICENSOR’S TOTAL LIABILITY TO YOU FOR DIRECT DAMAGES ARISING UNDER THIS LICENSE IS LIMITED TO U.S. $1.00. YOU CANNOT RECOVER ANY OTHER DAMAGES, INCLUDING CONSEQUENTIAL, LOST PROFITS, SPECIAL, INDIRECT OR INCIDENTAL DAMAGES, EVEN IF LICENSOR IS EXPRESSLY MADE AWARE OF THE POSSIBILITY THEREOF OR IS NEGLIGENT. THIS LIMITATION APPLIES TO ANYTHING RELATED TO THIS SOFTWARE, SERVICES, CONTENT (INCLUDING CODE) ON THIRD PARTY INTERNET SITES, OR THIRD PARTY PROGRAMS, AND CLAIMS FOR BREACH OF CONTRACT, BREACH OF WARRANTY, GUARANTEE  OR CONDITION, STRICT LIABILITY, NEGLIGENCE, OR OTHER TORT TO THE EXTENT PERMITTED BY APPLICABLE LAW.
 
-5.9. Use, duplication or disclosure of this Software by the U.S. Government is subject to the restricted rights applicable to commercial computer software (under FAR 52.227019 and DFARS 252.227-7013 or parallel regulations). The manufacturer for this purpose is Thermo Finnigan LLC, 355 River Oaks Parkway, San Jose, California 95134, U.S.A.
+5.9. Use, duplication or disclosure of this Software by the U.S. Government is subject to the restricted rights applicable to commercial computer software (under FAR 52.227019 and DFARS 252.227-7013 or parallel regulations). The manufacturer for this purpose is Thermo Finnigan LLC, 355 River Oaks Parkway, San Jose, California 95134, U.S.A.