Merge pull request #67 from maestroque/add-pre-commit

Add .pre-commit-config.yaml

.github/ISSUE_TEMPLATE/ISSUE_TEMPLATE_BUGS.md

@@ -26,8 +26,8 @@ assignees:
 
 ## Specifications
 <!--- Point out the version of peakdet you are running and your OS version -->
-    - Python version: 
-    - phys2bids version:
+    - Python version:
+    - peakdet version:
     - Platform:
 
 ## Possible solution

.github/ISSUE_TEMPLATE/ISSUE_TEMPLATE_DISCUSSION.md

@@ -1,6 +1,6 @@
 ---
 name: Discussion
-about: Use this template to start a discussion issue, i.e. an issue that 
+about: Use this template to start a discussion issue, i.e. an issue meant to open a community debate over a topic
 title: ''
 labels: Discussion
 assignees: ''
@@ -22,6 +22,6 @@ I'm opening this discussion because/I think that/I noticed that...
 <!--- Repeat the concept in a very few, short (max 3) questions -->
 <!--- Remember that the aim is not to give a "tldr", but to help address salient points. -->
 
-    - 
-    - 
-    - 
+    -
+    -
+    -

.github/ISSUE_TEMPLATE/ISSUE_TEMPLATE_GENERAL.md

@@ -18,6 +18,6 @@ assignees: ''
 ## Next Steps
 <!--- Provide possible steps to take in order to address the issue -->
 
-    * 
-    * 
-    * 
+    *
+    *
+    *

.pre-commit-config.yaml

@@ -0,0 +1,39 @@
+# 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: v4.6.0
+    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
+    rev: 24.4.2
+    hooks:
+    -   id: black
+-   repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+    -   id: isort
+-   repo: https://github.com/pycqa/flake8
+    rev: 6.1.0
+    hooks:
+    -   id: flake8
+-   repo: https://github.com/pycqa/pydocstyle
+    rev: 6.3.0
+    hooks:
+      - id: pydocstyle
+-   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: v2.2.6
+    hooks:
+      - id: codespell
+        args: ["-L", "trough,troughs"]

README.md

@@ -72,4 +72,4 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
 
 <!-- ALL-CONTRIBUTORS-LIST:END -->
 
-This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind welcome!
+This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind welcome!

docs/conf.py

@@ -10,19 +10,22 @@
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 import os
 import sys
+
 import matplotlib as mpl
-mpl.use('Agg')
+
+mpl.use("Agg")
 
 # -- Project information -----------------------------------------------------
 
 # Add project name, copyright holder, and author(s)
-project = 'peakdet'
-copyright = '2018, peakdet developers'
-author = 'Ross Markello'
+project = "peakdet"
+copyright = "2018, peakdet developers"
+author = "Ross Markello"
 
 # Import project to get version info
 sys.path.insert(0, os.path.abspath(os.path.pardir))
 import peakdet  # noqa
+
 # The short X.Y version
 version = peakdet.__version__
 # The full version, including alpha/beta/rc tags
@@ -34,14 +37,14 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'matplotlib.sphinxext.plot_directive',
-    'sphinx.ext.autodoc',
-    'sphinx.ext.autosummary',
-    'sphinx.ext.doctest',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.mathjax',
-    'sphinx.ext.napoleon',
-    'sphinx.ext.viewcode',
+    "matplotlib.sphinxext.plot_directive",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.doctest",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.viewcode",
 ]
 
 # Generate the API documentation when building
@@ -50,13 +53,13 @@
 autoclass_content = "class"
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix(es) of source filenames.
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -68,17 +71,18 @@
 # 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']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 import sphinx_rtd_theme  # noqa
-html_theme = 'sphinx_rtd_theme'
+
+html_theme = "sphinx_rtd_theme"
 html_show_sourcelink = False
 
 # Theme options are theme-specific and customize the look and feel of a theme
@@ -89,18 +93,18 @@
 # 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"]
 
 # -- Options for HTMLHelp output ---------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'peakdetdoc'
+htmlhelp_basename = "peakdetdoc"
 
 # -- Extension configuration -------------------------------------------------
 intersphinx_mapping = {
-    'matplotlib': ('https://matplotlib.org', None),
-    'numpy': ('https://docs.scipy.org/doc/numpy', None),
-    'scipy': ('https://docs.scipy.org/doc/scipy/reference', None),
+    "matplotlib": ("https://matplotlib.org", None),
+    "numpy": ("https://docs.scipy.org/doc/numpy", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy/reference", None),
 }
 
 doctest_global_setup = """
@@ -110,6 +114,7 @@
 """
 
 from peakdet.tests.utils import get_test_data_path  # noqa
+
 plot_working_directory = get_test_data_path()
 plot_include_source = True
 plot_formats = [("png", 90)]

docs/requirements.txt

@@ -2,4 +2,3 @@
 pandas
 sphinx>=1.2
 sphinx_rtd_theme
-

docs/user_guide/loading.rst

@@ -9,7 +9,7 @@ with the built-in :py:mod:`peakdet` IO functions.
 
 The :py:meth:`peakdet.load_physio` function is the most simple of these
 functions, and accepts data stored as single-column text file. For example, if
-we have a file `ECG.csv` that we might normally load with :py:mod:`numpy`:
+we have a file ``ECG.csv`` that we might normally load with :py:mod:`numpy`:
 
 .. doctest::
 

docs/user_guide/physio.rst

@@ -9,7 +9,7 @@
 The ``Physio`` data object
 --------------------------
 
-The primary funtionality of :py:mod:`peakdet` relies on its operations being
+The primary functionality of :py:mod:`peakdet` relies on its operations being
 performed on physiological data loaded into a :py:class:`peakdet.Physio`
 object. So, before we get into using :py:mod:`peakdet`, its best to understand
 a little bit about this helper class!

peakdet/__init__.py

@@ -1,18 +1,36 @@
 __all__ = [
-    'delete_peaks', 'edit_physio', 'filter_physio', 'interpolate_physio',
-    'peakfind_physio', 'plot_physio', 'reject_peaks',
-    'load_physio', 'save_physio', 'load_history', 'save_history',
-    'load_rtpeaks', 'Physio', 'HRV', '__version__'
+    "delete_peaks",
+    "edit_physio",
+    "filter_physio",
+    "interpolate_physio",
+    "peakfind_physio",
+    "plot_physio",
+    "reject_peaks",
+    "load_physio",
+    "save_physio",
+    "load_history",
+    "save_history",
+    "load_rtpeaks",
+    "Physio",
+    "HRV",
+    "__version__",
 ]
 
-from peakdet.analytics import (HRV)
-from peakdet.external import (load_rtpeaks)
-from peakdet.io import (load_physio, save_physio, load_history, save_history)
-from peakdet.operations import (delete_peaks, edit_physio, filter_physio,
-                                interpolate_physio, peakfind_physio,
-                                plot_physio, reject_peaks)
-from peakdet.physio import (Physio)
+from peakdet.analytics import HRV
+from peakdet.external import load_rtpeaks
+from peakdet.io import load_history, load_physio, save_history, save_physio
+from peakdet.operations import (
+    delete_peaks,
+    edit_physio,
+    filter_physio,
+    interpolate_physio,
+    peakfind_physio,
+    plot_physio,
+    reject_peaks,
+)
+from peakdet.physio import Physio
 
 from ._version import get_versions
-__version__ = get_versions()['version']
-del get_versions
+
+__version__ = get_versions()["version"]
+del get_versions