Apply ruff formatting

.pre-commit-config.yaml

@@ -7,10 +7,10 @@ repos:
     - id: check-yaml
     - id: end-of-file-fixer
     - id: trailing-whitespace
-# - repo: https://github.com/astral-sh/ruff-pre-commit
-#   rev: v0.4.0
-#   hooks:
-#     - id: ruff-format
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.5.0
+  hooks:
+    - id: ruff-format
 #     - id: ruff
 
 exclude: .bumpversion.cfg

README.md

@@ -942,8 +942,21 @@ clone the repository and create a [pull
 request](https://github.com/MannLabs/alphapeptdeep/pulls) with a new
 branch. For an even more interactive participation, check out the
 [discussions](https://github.com/MannLabs/alphapeptdeep/discussions) and
-the [the Contributors License Agreement](misc/CLA.md).
+the [Contributors License Agreement](misc/CLA.md).
 
+### Notes for developers
+#### pre-commit hooks
+It is highly recommended to use the provided pre-commit hooks, as the CI pipeline enforces all checks therein to
+pass in order to merge a branch.
+
+The hooks need to be installed once by
+```bash
+pre-commit install
+```
+You can run the checks yourself using:
+```bash
+pre-commit run --all-files
+```
 ------------------------------------------------------------------------
 
 ## Changelog

docs/conf.py

@@ -14,14 +14,15 @@
 import sys
 import importlib
 import inspect
-sys.path.insert(0, os.path.abspath('..'))
+
+sys.path.insert(0, os.path.abspath(".."))
 
 
 # -- Project information -----------------------------------------------------
 
-project = 'peptdeep'
-copyright = '2022, Mann Labs, MPIB'
-author = 'Mann Labs, MPIB'
+project = "peptdeep"
+copyright = "2022, Mann Labs, MPIB"
+author = "Mann Labs, MPIB"
 
 release = "1.2.1"
 
@@ -31,34 +32,33 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.napoleon',
+    "sphinx.ext.napoleon",
     "sphinx.ext.intersphinx",
     "sphinx.ext.linkcode",
-    'sphinx.ext.viewcode',
-    'autodocsumm',
-    'nbsphinx',
-    'myst_parser',
+    "sphinx.ext.viewcode",
+    "autodocsumm",
+    "nbsphinx",
+    "myst_parser",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = [
-    '_build', 'Thumbs.db', '.DS_Store',
-    '_modidx,py'
-]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "_modidx,py"]
 
 code_url = f"https://github.com/mannlabs/alphapeptdeep/blob/main"
 
+
 def linkcode_resolve(domain, info):
     # Non-linkable objects from the starter kit in the tutorial.
     if domain == "js" or info["module"] == "connect4":
         return
 
-    if domain != "py": return
+    if domain != "py":
+        return
 
     mod = importlib.import_module(info["module"])
     if "." in info["fullname"]:
@@ -93,16 +93,16 @@ def linkcode_resolve(domain, info):
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'furo'
-html_logo = '_static/peptdeep.png'
-html_favicon = '_static/peptdeep.png'
+html_theme = "furo"
+html_logo = "_static/peptdeep.png"
+html_favicon = "_static/peptdeep.png"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 autodoc_default_options = {
-    'autosummary': True,
-    'special-members': '__init__',  # Include __init__ methods.
+    "autosummary": True,
+    "special-members": "__init__",  # Include __init__ methods.
 }

peptdeep/_modidx.py

@@ -1,2 +1 @@
-d = { 'settings': { },
-  'syms': { }}
+d = {"settings": {}, "syms": {}}

peptdeep/cli.py

@@ -13,17 +13,18 @@
 from peptdeep.settings import global_settings, load_global_settings
 from .cli_argparse import get_parser, parse_args_to_global_settings
 
+
 @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(peptdeep.__version__, "-v", "--version")
 def run(ctx, **kwargs):
     click.echo(
-r'''
+        r"""
      ____             __  ____
     / __ \___  ____  / /_/ __ \___  ___  ____
    / /_/ / _ \/ __ \/ __/ / / / _ \/ _ \/ __ \
@@ -35,48 +36,63 @@ def run(ctx, **kwargs):
 .{url}.
 .{license}.
 ....................................................
-'''.format(
-        version=peptdeep.__version__.center(50),
-        url=peptdeep.__github__.center(50),
-        license=peptdeep.__license__.center(50),
+""".format(
+            version=peptdeep.__version__.center(50),
+            url=peptdeep.__github__.center(50),
+            license=peptdeep.__license__.center(50),
+        )
     )
-)
     if ctx.invoked_subcommand is None:
         click.echo(run.get_help(ctx))
 
+
 @run.command("gui", help="Start graphical user interface.")
-@click.option("--port", default=10077, type=int,
-    show_default=True, help="The web server port."
+@click.option(
+    "--port", default=10077, type=int, show_default=True, help="The web server port."
 )
-@click.option("--settings_yaml", default='', type=str,
-    show_default=True, help="Load default settings yaml file."
+@click.option(
+    "--settings_yaml",
+    default="",
+    type=str,
+    show_default=True,
+    help="Load default settings yaml file.",
 )
 def _gui(port, settings_yaml):
     import peptdeep.gui
     from peptdeep.webui.server import _server
+
     if os.path.isfile(settings_yaml):
         load_global_settings(settings_yaml)
     # start the server to run tasks
     _server.start()
     peptdeep.gui.run(port)
 
+
 @run.command("install-models", help="Install or update peptdeep pre-trained models.")
-@click.option("--model-file", default=None, type=str,
-    show_default=True, help="The model .zip file to install. "
-    "If not set, peptdeep will download the model file from GitHub."
+@click.option(
+    "--model-file",
+    default=None,
+    type=str,
+    show_default=True,
+    help="The model .zip file to install. "
+    "If not set, peptdeep will download the model file from GitHub.",
 )
-@click.option("--overwrite", default=True, type=bool,
-    show_default=True, help="If overwrite existing model file."
+@click.option(
+    "--overwrite",
+    default=True,
+    type=bool,
+    show_default=True,
+    help="If overwrite existing model file.",
 )
 def _install_model(model_file, overwrite):
-    from peptdeep.pretrained_models import (
-        download_models, model_url
-    )
+    from peptdeep.pretrained_models import download_models, model_url
+
     if not model_file:
         download_models(model_url, overwrite=overwrite)
     else:
         download_models(model_file, overwrite=overwrite)
 
+
 _help_str = (
     "\n\nTo get the settings_yaml file,"
     " you can either export from the GUI,"
@@ -94,41 +110,49 @@ def _install_model(model_file, overwrite):
 #     load_global_settings(settings_yaml)
 #     rescore()
 
-@run.command("library", help=
-    "Predict library for DIA search."+_help_str
-)
+
+@run.command("library", help="Predict library for DIA search." + _help_str)
 @click.argument("settings_yaml", type=str)
-def _library(settings_yaml:str):
+def _library(settings_yaml: str):
     from peptdeep.pipeline_api import generate_library
+
     load_global_settings(settings_yaml)
     generate_library()
 
-@run.command("transfer", help=
-    "Transfer learning for different data types."+_help_str
-)
+
+@run.command("transfer", help="Transfer learning for different data types." + _help_str)
 @click.argument("settings_yaml", type=str)
-def _transfer(settings_yaml:str):
+def _transfer(settings_yaml: str):
     from peptdeep.pipeline_api import transfer_learn
+
     load_global_settings(settings_yaml)
     transfer_learn()
 
-@run.command("export-settings", help="Export the default settings to a yaml file. It can be used as the template setting.")
+
+@run.command(
+    "export-settings",
+    help="Export the default settings to a yaml file. It can be used as the template setting.",
+)
 @click.argument("yaml_file", type=str)
-def _export_settings(yaml_file:str):
+def _export_settings(yaml_file: str):
     save_yaml(yaml_file, global_settings)
 
+
 class ParserHelper(click.Command):
     def format_help(self, ctx: Context, formatter: HelpFormatter) -> None:
         parser = get_parser()
         formatter.write(parser.format_help())
 
-@run.command("cmd-flow",
+
+@run.command(
+    "cmd-flow",
     help="Using command line arguments to control the settings",
     cls=ParserHelper,
     context_settings=dict(
-    ignore_unknown_options=True,
-    allow_extra_args=True,
-))
+        ignore_unknown_options=True,
+        allow_extra_args=True,
+    ),
+)
 @click.pass_context
 def _cmd_flow(ctx):
     parser = get_parser()
@@ -138,25 +162,39 @@ def _cmd_flow(ctx):
         parse_args_to_global_settings(parser, ctx.args)
         if "train" in global_settings["task_workflow"]:
             from peptdeep.pipeline_api import transfer_learn
+
             transfer_learn()
-            if os.path.isfile(os.path.join(
-                global_settings["model_mgr"]["transfer"]["model_output_folder"], "ms2.pth"
-            )):
+            if os.path.isfile(
+                os.path.join(
+                    global_settings["model_mgr"]["transfer"]["model_output_folder"],
+                    "ms2.pth",
+                )
+            ):
                 global_settings["model_mgr"]["external_ms2_model"] = os.path.join(
-                    global_settings["model_mgr"]["transfer"]["model_output_folder"], "ms2.pth"
+                    global_settings["model_mgr"]["transfer"]["model_output_folder"],
+                    "ms2.pth",
                 )
-            if os.path.isfile(os.path.join(
-                global_settings["model_mgr"]["transfer"]["model_output_folder"], "rt.pth"
-            )):
+            if os.path.isfile(
+                os.path.join(
+                    global_settings["model_mgr"]["transfer"]["model_output_folder"],
+                    "rt.pth",
+                )
+            ):
                 global_settings["model_mgr"]["external_rt_model"] = os.path.join(
-                    global_settings["model_mgr"]["transfer"]["model_output_folder"], "rt.pth"
+                    global_settings["model_mgr"]["transfer"]["model_output_folder"],
+                    "rt.pth",
+                )
+            if os.path.isfile(
+                os.path.join(
+                    global_settings["model_mgr"]["transfer"]["model_output_folder"],
+                    "ccs.pth",
                 )
-            if os.path.isfile(os.path.join(
-                global_settings["model_mgr"]["transfer"]["model_output_folder"], "ccs.pth"
-            )):
+            ):
                 global_settings["model_mgr"]["external_ccs_model"] = os.path.join(
-                    global_settings["model_mgr"]["transfer"]["model_output_folder"], "ccs.pth"
+                    global_settings["model_mgr"]["transfer"]["model_output_folder"],
+                    "ccs.pth",
                 )
         if "library" in global_settings["task_workflow"]:
             from peptdeep.pipeline_api import generate_library
+
             generate_library()