Merge branch 'master' into pre-commit-ci-update-config

Author: smoia

.github/dependabot.yml

@@ -0,0 +1,8 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    labels:
+      - "Internal"

.github/workflows/auto-label.yml

@@ -12,4 +12,4 @@ jobs:
       pull-requests: write
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/labeler@v5
+      - uses: actions/labeler@v6

.github/workflows/auto-release.yml

@@ -19,7 +19,7 @@ jobs:
         shell: bash
     steps:
     - name: Checkout source
-      uses: actions/checkout@v4
+      uses: actions/checkout@v5
       with:
         # Fetch all history for all branches and tags
         fetch-depth: 0

.github/workflows/bot.yaml

@@ -0,0 +1,21 @@
+name: bot
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
+  cancel-in-progress: true
+on:  # yamllint disable-line rule:truthy
+  pull_request
+
+permissions:
+  contents: write
+  pull-requests: write
+
+jobs:
+  auto-merge:
+    runs-on: ubuntu-latest
+    if: (github.event.pull_request.user.login == 'dependabot[bot]' || github.event.pull_request.user.login == 'pre-commit-ci[bot]') && github.repository == 'physiopy/peakdet'
+    steps:
+      - name: Enable auto-merge for bot PRs
+        run: gh pr merge --auto --squash "$PR_URL"
+        env:
+          PR_URL: ${{ github.event.pull_request.html_url }}
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/python-publish.yml

@@ -14,9 +14,9 @@ jobs:
 
     steps:
     - name: Checkout source
-      uses: actions/checkout@v4
+      uses: actions/checkout@v5
     - name: Set up Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: 3.11
     - name: Install dependencies

.pre-commit-config.yaml

@@ -1,39 +1,39 @@
+ci:
+    autoupdate_schedule: quarterly
+
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v6.0.0
+    rev: v5.0.0
     hooks:
-    -   id: trailing-whitespace
-    -   id: end-of-file-fixer
-    -   id: check-yaml
-    -   id: check-added-large-files
-    -   id: check-case-conflict
-    -   id: check-merge-conflict
--   repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 25.9.0
-    hooks:
-    -   id: black
--   repo: https://github.com/pycqa/isort
-    rev: 7.0.0
-    hooks:
-    -   id: isort
--   repo: https://github.com/pycqa/flake8
-    rev: 7.3.0
-    hooks:
-    -   id: flake8
--   repo: https://github.com/pycqa/pydocstyle
-    rev: 6.3.0
-    hooks:
-      - id: pydocstyle
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-merge-conflict
+
 -   repo: https://github.com/pre-commit/pygrep-hooks
     rev: v1.10.0
     hooks:
       - id: rst-backticks
       - id: rst-directive-colons
       - id: rst-inline-touching-normal
+
 -   repo: https://github.com/codespell-project/codespell
     rev: v2.4.1
     hooks:
       - id: codespell
         args: ["-L", "trough,troughs"]
+
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.12.2
+  hooks:
+      - id: ruff
+        name: ruff linter
+        args: [--fix]
+        files: peakdet
+      - id: ruff-format
+        name: ruff formatter
+        files: peakdet

peakdet/_version.py

@@ -84,7 +84,7 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=
                 stderr=(subprocess.PIPE if hide_stderr else None),
             )
             break
-        except EnvironmentError:
+        except OSError:
             e = sys.exc_info()[1]
             if e.errno == errno.ENOENT:
                 continue
@@ -97,8 +97,7 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=
             print("unable to find command, tried %s" % (commands,))
         return None, None
     stdout = p.communicate()[0].strip()
-    if sys.version_info[0] >= 3:
-        stdout = stdout.decode()
+    stdout = stdout.decode()
     if p.returncode != 0:
         if verbose:
             print("unable to run %s (error)" % dispcmd)
@@ -116,7 +115,7 @@ def versions_from_parentdir(parentdir_prefix, root, verbose):
     """
     rootdirs = []
 
-    for i in range(3):
+    for _i in range(3):
         dirname = os.path.basename(root)
         if dirname.startswith(parentdir_prefix):
             return {
@@ -147,7 +146,7 @@ def git_get_keywords(versionfile_abs):
     # _version.py.
     keywords = {}
     try:
-        f = open(versionfile_abs, "r")
+        f = open(versionfile_abs)
         for line in f.readlines():
             if line.strip().startswith("git_refnames ="):
                 mo = re.search(r'=\s*"(.*)"', line)
@@ -162,7 +161,7 @@ def git_get_keywords(versionfile_abs):
                 if mo:
                     keywords["date"] = mo.group(1)
         f.close()
-    except EnvironmentError:
+    except OSError:
         pass
     return keywords
 
@@ -524,7 +523,7 @@ def get_versions():
         # versionfile_source is the relative path from the top of the source
         # tree (where the .git directory might live) to this file. Invert
         # this to find the root from __file__.
-        for i in cfg.versionfile_source.split("/"):
+        for _i in cfg.versionfile_source.split("/"):
             root = os.path.dirname(root)
     except NameError:
         return {

peakdet/analytics.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """
 Functions and classes for generating analytics on physiological data
 """

peakdet/cli/run.py

@@ -1,4 +1,5 @@
-# -*- coding: utf-8 -*-
+"""Parser and physio workflow."""
+
 import argparse
 import datetime
 import glob
@@ -40,7 +41,7 @@
 
 
 def get_parser():
-    """Parser for GUI and command-line arguments"""
+    """Parser for GUI and command-line arguments."""
     parser = argparse.ArgumentParser()
     parser.add_argument(
         "file_template",
@@ -53,7 +54,7 @@ def get_parser():
     )
 
     inp_group = parser.add_argument_group(
-        "Inputs", "Options to specify " "format of input files"
+        "Inputs", "Options to specify format of input files"
     )
     inp_group.add_argument(
         "--modality",
@@ -83,7 +84,7 @@ def get_parser():
     )
 
     out_group = parser.add_argument_group(
-        "Outputs", "Options to specify " "format of output files"
+        "Outputs", "Options to specify format of output files"
     )
     out_group.add_argument(
         "-o",
@@ -104,12 +105,12 @@ def get_parser():
         "-s",
         "--savehistory",
         action="store_true",
-        help="Whether to save history of data processing " "for each file.",
+        help="Whether to save history of data processing for each file.",
     )
 
     edit_group = parser.add_argument_group(
         "Workflow arguments (optional!)",
-        "Options to specify modifications " "to workflow",
+        "Options to specify modifications to workflow",
     )
     edit_group.add_argument(
         "-n",
@@ -135,7 +136,10 @@ def get_parser():
         "--debug",
         dest="debug",
         action="store_true",
-        help="Print additional debugging info and error diagnostics to log file. Default is False.",
+        help=(
+            "Print additional debugging info and error diagnostics to log file. "
+            "Default is False."
+        ),
         default=False,
     )
     log_style_group_exclusive.add_argument(
@@ -162,12 +166,12 @@ def workflow(
     savehistory=True,
     noedit=False,
     thresh=0.2,
-    measurements=ATTR_CONV.keys(),
+    measurements=None,
     debug=False,
     quiet=False,
 ):
     """
-    Basic workflow for physiological data
+    Run basic workflow for physiological data.
 
     Parameters
     ----------
@@ -192,12 +196,15 @@ def workflow(
         Whether to disable interactive editing of physio data. Default: False
     thresh : [0, 1] float, optional
         Threshold for peak detection. Default: 0.2
-    measurements : list, optional
+    measurements : None or list, optional
         Which HRV-related measurements to save from data. See ``peakdet.HRV``
-        for available measurements. Default: all available measurements.
+        for available measurements.
+        Default: None, that is all available measurements.
     verbose : bool, optional
-        Whether to include verbose logs when catching exceptions that include diagnostics
+        Whether to include verbose logs when catching exceptions that include diagnostic
     """
+    if measurements is None:
+        measurements = ATTR_CONV.keys()
     outdir = os.path.dirname(output)
     logger.info(f"Current path is {outdir}")
 
@@ -255,9 +262,9 @@ def workflow(
         )
 
     # output file
-    logger.info("OUTPUT FILE:\t\t{}".format(output))
+    logger.info(f"OUTPUT FILE:\t\t{output}")
     # grab files from file template
-    logger.info("FILE TEMPLATE:\t{}".format(file_template))
+    logger.info(f"FILE TEMPLATE:\t{file_template}")
     files = glob.glob(file_template, recursive=True)
 
     # convert measurements to peakdet.HRV attribute friendly names
@@ -277,7 +284,7 @@ def workflow(
     # check if output file exists -- if so, ensure headers will match
     head = "filename," + ",".join(measurements)
     if os.path.exists(output):
-        with open(output, "r") as src:
+        with open(output) as src:
             eheader = src.readlines()[0]
         # if existing output file does not have same measurements are those
         # requested on command line, warn and use existing measurements so
@@ -300,7 +307,7 @@ def workflow(
         # iterate through all files and do peak detection with manual editing
         for fname in files:
             fname = os.path.relpath(fname)
-            logger.info("Currently processing {}".format(fname))
+            logger.info(f"Currently processing {fname}")
 
             # if we want to save history, this is the output name it would take
             outname = os.path.join(
@@ -343,10 +350,12 @@ def workflow(
 
 
 def main():
+    """Run main entrypoint."""
     logger.enable("")
     opts = get_parser().parse_args()
     workflow(**vars(opts))
 
 
 if __name__ == "__main__":
+    """Run main entrypoint."""
     main()

peakdet/editor.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Functions and class for performing interactive editing of physiological data."""
 
 import functools
@@ -63,7 +62,8 @@ def __init__(self, data):
         reject = functools.partial(self.on_edit, method="reject")
         insert = functools.partial(self.on_edit, method="insert")
 
-        # Check matplotlib version rectprops is deprecated with matplotlib 3.5.0 and then obsolete
+        # Check matplotlib version rectprops is deprecated with matplotlib 3.5.0
+        # and then obsolete
         if Version(matplotlib.__version__) >= Version("3.5.0"):
             property_name = "props"
         else: