spikesorted 0.1.0a3__tar.gz

spikesorted-0.1.0a3/.github/workflows/test_and_deploy.yml

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+name: tests
+
+on:
+  push:
+    branches:
+      - '*'
+    tags:
+      - '*'
+  pull_request:
+
+jobs:
+  linting:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: neuroinformatics-unit/actions/lint@v2
+
+  test:
+    needs: [linting]
+    name: ${{ matrix.os }} py${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        # Run all supported Python versions on linux
+        python-version: ["3.11", "3.12", "3.13"]
+        os: [ubuntu-latest]
+        # Include one windows and macos run
+        include:
+        - os: macos-latest
+          python-version: "3.13"
+        - os: windows-latest
+          python-version: "3.13"
+
+    steps:
+      # Run tests
+      - uses: neuroinformatics-unit/actions/test@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+  build_sdist_wheels:
+    name: Build source distribution
+    needs: [test]
+    if: github.event_name == 'push' && github.ref_type == 'tag'
+    runs-on: ubuntu-latest
+    steps:
+    - uses: neuroinformatics-unit/actions/build_sdist_wheels@v2
+
+
+  upload_all:
+    name: Publish build distributions
+    needs: [build_sdist_wheels]
+    runs-on: ubuntu-latest
+    environment: # use Trusted Publisher route
+      name: pypi
+      url: https://pypi.org/p/${{ github.event.repository.name }}
+    permissions:
+      id-token: write # mandatory for trusted publishing
+    steps:
+    - uses: actions/download-artifact@v8
+      with:
+        name: artifact
+        path: dist
+    - uses: pypa/gh-action-pypi-publish@release/v1

spikesorted-0.1.0a3/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask instance folder
+instance/
+
+# Sphinx documentation
+docs/_build/
+
+# MkDocs documentation
+/site/
+
+# PyBuilder
+target/
+
+# Pycharm and VSCode
+.idea/
+venv/
+.vscode/
+
+# IPython Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# OS
+.DS_Store
+
+# written by setuptools-scm
+**/_version.py
+
+/tests/data/neuropixels-1300-openephys/
+/tests/data/neuropixels-2010-spikeglx/
+/tests/data/no-probe-openephys/
+
+/tests/data/cambridge-neurotech-64/
+
+/tests/data/.archives/
+

spikesorted-0.1.0a3/LICENSE

@@ -0,0 +1,28 @@
+
+Copyright (c) 2026, Joe Ziminski
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of spikesorted nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

spikesorted-0.1.0a3/MANIFEST.in

@@ -0,0 +1,8 @@
+include LICENSE
+include README.md
+exclude .pre-commit-config.yaml
+
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
+recursive-exclude docs *
+recursive-exclude tests *

spikesorted-0.1.0a3/PKG-INFO

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+Metadata-Version: 2.4
+Name: spikesorted
+Version: 0.1.0a3
+Summary: `spikesorted` is an end-to-end spike sorting pipeline
+Author-email: Joe Ziminski <joseph.j.ziminski@gmail.com>
+License-Expression: BSD-3-Clause
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.11.0
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: coverage; extra == "dev"
+Requires-Dist: tox; extra == "dev"
+Requires-Dist: mypy; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
+Requires-Dist: ruff==0.16.10; extra == "dev"
+Requires-Dist: codespell; extra == "dev"
+Requires-Dist: check-manifest; extra == "dev"
+Requires-Dist: setuptools-scm; extra == "dev"
+Dynamic: license-file
+
+# spikesorted
+
+An end-to-end pipeline for spike sorting extracellular electrophysiology recordings.
+
+Pre-alpha: the pipeline is under development. This checkout currently contains
+project scaffolding and example modules.

spikesorted-0.1.0a3/README.md

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+# spikesorted
+
+An end-to-end pipeline for spike sorting extracellular electrophysiology recordings.
+
+Pre-alpha: the pipeline is under development. This checkout currently contains
+project scaffolding and example modules.

spikesorted-0.1.0a3/pyproject.toml

@@ -0,0 +1,155 @@
+[project]
+name = "spikesorted"
+authors = [{name = "Joe Ziminski", email= "joseph.j.ziminski@gmail.com"}]
+description = "`spikesorted` is an end-to-end spike sorting pipeline"
+readme = "README.md"
+requires-python = ">=3.11.0"
+dynamic = ["version"]
+
+dependencies = []
+
+license = "BSD-3-Clause"
+
+license-files = ["LICENSE"]
+
+classifiers = [
+    "Development Status :: 2 - Pre-Alpha",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Operating System :: OS Independent",
+]
+
+
+
+[project.optional-dependencies]
+dev = [
+  "pytest",
+  "pytest-cov",
+  "coverage",
+  "tox",
+  "mypy",
+  "pre-commit",
+  "ruff==0.16.10",
+  "codespell",
+  "check-manifest",
+  "setuptools-scm",
+]
+
+[dependency-groups]
+docs = [
+  "linkify-it-py",
+  "myst-parser",
+  "nbsphinx",
+  "pydata-sphinx-theme",
+  "setuptools-scm",
+  "sphinx",
+  "sphinx-autodoc-typehints",
+  "sphinx-sitemap",
+]
+
+[build-system]
+requires = [
+    "setuptools>=77",
+    "wheel",
+    "setuptools-scm[toml]>=8",
+]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.packages.find]
+include = ["spikesorted*"]
+exclude = ["tests", "docs*"]
+
+
+[tool.pytest.ini_options]
+addopts = "--cov=spikesorted"
+filterwarnings = [
+    "error",
+]
+
+[tool.setuptools_scm]
+search_parent_directories = true
+
+[tool.check-manifest]
+ignore = [
+  "*.yaml",
+  "tox.ini",
+  "tests/",
+  "tests/test_unit/",
+  "tests/test_integration/",
+  "docs/",
+  "docs/source/",
+]
+
+
+[tool.ruff]
+line-length = 88
+extend-exclude = ["__init__.py", "build", ".eggs", ".venv-docs"]
+fix = true
+
+[tool.ruff.lint]
+# See https://docs.astral.sh/ruff/rules/
+ignore = [
+  "D203", # one blank line before class
+  "D213", # multi-line-summary second line
+]
+select = [
+  "E",      # pycodestyle errors
+  "F",      # Pyflakes
+  "UP",     # pyupgrade
+  "I",      # isort
+  "B",      # flake8 bugbear
+  "SIM",    # flake8 simplify
+  "C90",    # McCabe complexity
+  "D",      # pydocstyle
+  "NPY201", # checks for syntax that was deprecated in numpy2.0
+]
+per-file-ignores = { "**/tests/**" = [
+  "D100", # missing docstring in public module
+  "D205", # missing blank line between summary and description
+  "D103", # missing docstring in public function
+], "**/examples/**" = [
+  "B018", # Found useless expression
+  "D103", # Missing docstring in public function
+  "D400", # first line should end with a period.
+  "D415", # first line should end with a period, question mark...
+  "D205", # missing blank line between summary and description
+] }
+
+[tool.ruff.format]
+docstring-code-format = true # Also format code in docstrings
+
+[tool.tox]
+legacy_tox_ini = """
+[tox]
+requires =
+    tox>=4
+    tox-gh-actions
+envlist = py{311,312,313}
+isolated_build = True
+
+[gh-actions]
+python =
+    3.11: py311
+    3.12: py312
+    3.13: py313
+
+[testenv]
+passenv =
+    CI
+    GITHUB_ACTIONS
+extras =
+    dev
+commands =
+    pytest -v --color=yes --cov=spikesorted --cov-report=xml
+"""
+
+
+[tool.codespell]
+skip = '.git,.tox,.venv-docs'
+check-hidden = true

spikesorted-0.1.0a3/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

spikesorted-0.1.0a3/spikesorted/__init__.py

@@ -0,0 +1,7 @@
+from importlib.metadata import PackageNotFoundError, version
+
+try:
+    __version__ = version("spikesorted")
+except PackageNotFoundError:
+    # package is not installed
+    pass

spikesorted-0.1.0a3/spikesorted/greetings.py

@@ -0,0 +1,40 @@
+# Define an example class to demonstrate
+# Sphinx's autodoc and autosummary features:
+# https://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html
+# https://www.sphinx-doc.org/en/master/usage/extensions/autosummary.html
+
+# Docstrings are written in NumPy format:
+# https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_numpy.html
+
+
+class Greetings:
+    """
+    A simple example class
+
+    Attributes
+    ----------
+    name : str
+        The name of the person to greet
+
+    Methods
+    -------
+    say_hello
+        Say hello to the person
+    say_goodbye
+        Say goodbye to the person
+    """
+
+    def __init__(self, name):
+        self.name = name
+
+    def say_hello(self):
+        """
+        Say hello to the person
+        """
+        print(f"Hello {self.name}!")
+
+    def say_goodbye(self):
+        """
+        Say goodbye to the person
+        """
+        print(f"Goodbye {self.name}!")

spikesorted-0.1.0a3/spikesorted/math.py

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+# Define some example functions to demonstrate
+# Sphinx's autodoc and autosummary features:
+# https://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html
+# https://www.sphinx-doc.org/en/master/usage/extensions/autosummary.html
+
+# Docstrings are written in NumPy format:
+# https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_numpy.html
+
+
+def add_two_integers(a: int, b: int) -> int:
+    """Add two integer numbers.
+
+    Parameters
+    ----------
+    a : int
+        The first number.
+    b : int
+        The second number.
+
+    Returns
+    -------
+    int
+        The sum of the two numbers.
+    """
+    return a + b
+
+
+def subtract_two_integers(a: int, b: int) -> int:
+    """Subtract two integer numbers.
+
+    Parameters
+    ----------
+    a : int
+        The first number.
+    b : int
+        The second number.
+
+    Returns
+    -------
+    int
+        The difference of the two numbers.
+    """
+    return a - b

spikesorted-0.1.0a3/spikesorted.egg-info/PKG-INFO

@@ -0,0 +1,35 @@
+Metadata-Version: 2.4
+Name: spikesorted
+Version: 0.1.0a3
+Summary: `spikesorted` is an end-to-end spike sorting pipeline
+Author-email: Joe Ziminski <joseph.j.ziminski@gmail.com>
+License-Expression: BSD-3-Clause
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.11.0
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: coverage; extra == "dev"
+Requires-Dist: tox; extra == "dev"
+Requires-Dist: mypy; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
+Requires-Dist: ruff==0.16.10; extra == "dev"
+Requires-Dist: codespell; extra == "dev"
+Requires-Dist: check-manifest; extra == "dev"
+Requires-Dist: setuptools-scm; extra == "dev"
+Dynamic: license-file
+
+# spikesorted
+
+An end-to-end pipeline for spike sorting extracellular electrophysiology recordings.
+
+Pre-alpha: the pipeline is under development. This checkout currently contains
+project scaffolding and example modules.

spikesorted-0.1.0a3/spikesorted.egg-info/SOURCES.txt

@@ -0,0 +1,16 @@
+.gitignore
+LICENSE
+MANIFEST.in
+README.md
+pyproject.toml
+.github/workflows/test_and_deploy.yml
+spikesorted/__init__.py
+spikesorted/greetings.py
+spikesorted/math.py
+spikesorted.egg-info/PKG-INFO
+spikesorted.egg-info/SOURCES.txt
+spikesorted.egg-info/dependency_links.txt
+spikesorted.egg-info/requires.txt
+spikesorted.egg-info/scm_file_list.json
+spikesorted.egg-info/scm_version.json
+spikesorted.egg-info/top_level.txt

spikesorted-0.1.0a3/spikesorted.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

spikesorted-0.1.0a3/spikesorted.egg-info/requires.txt

@@ -0,0 +1,12 @@
+
+[dev]
+pytest
+pytest-cov
+coverage
+tox
+mypy
+pre-commit
+ruff==0.16.10
+codespell
+check-manifest
+setuptools-scm

spikesorted-0.1.0a3/spikesorted.egg-info/scm_file_list.json

@@ -0,0 +1,36 @@
+{
+  "files": [
+    ".github\\workflows\\test_and_deploy.yml",
+    ".gitignore",
+    ".pre-commit-config.yaml",
+    "LICENSE",
+    "MANIFEST.in",
+    "README.md",
+    "docs\\Makefile",
+    "docs\\make.bat",
+    "docs\\source\\_static\\css\\custom.css",
+    "docs\\source\\_static\\css\\docs.css",
+    "docs\\source\\_static\\css\\landing.css",
+    "docs\\source\\_static\\js\\landing.js",
+    "docs\\source\\api_generated\\spikesorted.greetings.Greetings.rst",
+    "docs\\source\\api_generated\\spikesorted.math.add_two_integers.rst",
+    "docs\\source\\api_generated\\spikesorted.math.subtract_two_integers.rst",
+    "docs\\source\\api_index.rst",
+    "docs\\source\\conf.py",
+    "docs\\source\\getting_started.md",
+    "docs\\source\\includes\\home.html",
+    "docs\\source\\index.rst",
+    "docs\\source\\tutorials\\index.md",
+    "docs\\source\\tutorials\\steps\\bad_channel_detection.md",
+    "pyproject.toml",
+    "spikesorted\\__init__.py",
+    "spikesorted\\greetings.py",
+    "spikesorted\\math.py",
+    "tests\\__init__.py",
+    "tests\\data\\README.md",
+    "tests\\data\\fetch_test_data.py",
+    "tests\\test_integration\\__init__.py",
+    "tests\\test_unit\\__init__.py",
+    "tests\\test_unit\\test_placeholder.py"
+  ]
+}

spikesorted-0.1.0a3/spikesorted.egg-info/scm_version.json

@@ -0,0 +1,8 @@
+{
+  "tag": "0.1.0a3",
+  "distance": 0,
+  "node": "g03dfb32c6ff6752c804c5cff0344ae3754797f3c",
+  "dirty": false,
+  "branch": "main",
+  "node_date": "2026-10-20"
+}

spikesorted-0.1.0a3/spikesorted.egg-info/top_level.txt

@@ -0,0 +1 @@
+spikesorted