npc-ephys 0.1.1__tar.gz

npc-ephys-0.1.1/LICENSE

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+MIT
+
+Copyright (c) 2024 Allen Institute for Neural Dynamics
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+

npc-ephys-0.1.1/PKG-INFO

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+Metadata-Version: 2.1
+Name: npc-ephys
+Version: 0.1.1
+Summary: Tools for accessing and processing raw ephys data, compatible with data in the cloud.
+Author-email: Ben Hardcastle <ben.hardcastle@alleninstitue.org>
+License: MIT
+Project-URL: Repository, https://github.com/AllenInstitute/npc_ephys
+Project-URL: Issues, https://github.com/AllenInstitute/npc_ephys/issues
+Classifier: Development Status :: 3 - Alpha
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Operating System :: POSIX :: Linux
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: npc-sync>=0.1.2
+Requires-Dist: zarr>=2.16.1
+Requires-Dist: pandas>=2.2.0
+Requires-Dist: tqdm>=4.66.1
+Requires-Dist: npc-lims>=0.1.115
+Requires-Dist: wavpack-numcodecs>=0.1.5
+
+# npc_ephys
+
+Tools for accessing and processing raw ephys data, compatible with data in the cloud.
+
+[![PyPI](https://img.shields.io/pypi/v/npc_ephys.svg?label=PyPI&color=blue)](https://pypi.org/project/npc_ephys/)
+[![Python version](https://img.shields.io/pypi/pyversions/npc_ephys)](https://pypi.org/project/npc_ephys/)
+
+[![Coverage](https://img.shields.io/codecov/c/github/AllenInstitute/npc_ephys?logo=codecov)](https://app.codecov.io/github/AllenInstitute/npc_ephys)
+[![CI/CD](https://img.shields.io/github/actions/workflow/status/AllenInstitute/npc_ephys/publish.yml?label=CI/CD&logo=github)](https://github.com/AllenInstitute/npc_ephys/actions/workflows/publish.yml)
+[![GitHub issues](https://img.shields.io/github/issues/AllenInstitute/npc_ephys?logo=github)](https://github.com/AllenInstitute/npc_ephys/issues)
+
+# Usage
+```bash
+conda create -n npc_ephys python>=3.9
+conda activate npc_ephys
+pip install npc_ephys
+```
+
+## Windows
+[`wavpack-numcodecs`](https://github.com/AllenNeuralDynamics/wavpack-numcodecs)
+is used to read compressed ephys data from S3 (stored in Zarr format). On Windows, that requires C++
+build tools to be installed: if `pip install npc_ephys` fails you'll likely need to download it [from here](https://visualstudio.microsoft.com/downloads/#build-tools-for-visual-studio-2022).
+
+## Python
+```python
+>>> import npc_ephys
+```
+
+# Development
+See instructions in https://github.com/AllenInstitute/npc_ephys/CONTRIBUTING.md and the original template: https://github.com/AllenInstitute/copier-pdm-npc/blob/main/README.md

npc-ephys-0.1.1/README.md

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+# npc_ephys
+
+Tools for accessing and processing raw ephys data, compatible with data in the cloud.
+
+[![PyPI](https://img.shields.io/pypi/v/npc_ephys.svg?label=PyPI&color=blue)](https://pypi.org/project/npc_ephys/)
+[![Python version](https://img.shields.io/pypi/pyversions/npc_ephys)](https://pypi.org/project/npc_ephys/)
+
+[![Coverage](https://img.shields.io/codecov/c/github/AllenInstitute/npc_ephys?logo=codecov)](https://app.codecov.io/github/AllenInstitute/npc_ephys)
+[![CI/CD](https://img.shields.io/github/actions/workflow/status/AllenInstitute/npc_ephys/publish.yml?label=CI/CD&logo=github)](https://github.com/AllenInstitute/npc_ephys/actions/workflows/publish.yml)
+[![GitHub issues](https://img.shields.io/github/issues/AllenInstitute/npc_ephys?logo=github)](https://github.com/AllenInstitute/npc_ephys/issues)
+
+# Usage
+```bash
+conda create -n npc_ephys python>=3.9
+conda activate npc_ephys
+pip install npc_ephys
+```
+
+## Windows
+[`wavpack-numcodecs`](https://github.com/AllenNeuralDynamics/wavpack-numcodecs)
+is used to read compressed ephys data from S3 (stored in Zarr format). On Windows, that requires C++
+build tools to be installed: if `pip install npc_ephys` fails you'll likely need to download it [from here](https://visualstudio.microsoft.com/downloads/#build-tools-for-visual-studio-2022).
+
+## Python
+```python
+>>> import npc_ephys
+```
+
+# Development
+See instructions in https://github.com/AllenInstitute/npc_ephys/CONTRIBUTING.md and the original template: https://github.com/AllenInstitute/copier-pdm-npc/blob/main/README.md

npc-ephys-0.1.1/pyproject.toml

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+[project]
+name = "npc-ephys"
+description = "Tools for accessing and processing raw ephys data, compatible with data in the cloud."
+authors = [
+    { name = "Ben Hardcastle", email = "ben.hardcastle@alleninstitue.org" },
+]
+readme = "README.md"
+requires-python = ">=3.9"
+dependencies = [
+    "npc-sync>=0.1.2",
+    "zarr>=2.16.1",
+    "pandas>=2.2.0",
+    "tqdm>=4.66.1",
+    "npc-lims>=0.1.115",
+    "wavpack-numcodecs>=0.1.5",
+]
+version = "0.1.1"
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: POSIX :: Linux",
+]
+
+[project.license]
+text = "MIT"
+
+[project.urls]
+Repository = "https://github.com/AllenInstitute/npc_ephys"
+Issues = "https://github.com/AllenInstitute/npc_ephys/issues"
+
+[build-system]
+requires = [
+    "setuptools>=61",
+    "wheel",
+]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools.packages.find]
+where = [
+    "src",
+]
+
+[tool.setuptools.package-data]
+npc_ephys = [
+    "py.typed",
+]
+
+[tool.black]
+target-version = [
+    "py39",
+    "py310",
+    "py311",
+]
+
+[tool.ruff]
+line-length = 100
+select = [
+    "B",
+    "C4",
+    "E",
+    "F",
+    "PGH",
+    "RUF",
+    "W",
+    "YTT",
+    "ANN",
+    "C",
+    "I",
+    "RUF100",
+    "N",
+    "UP",
+]
+src = [
+    "src",
+]
+extend-exclude = [
+    "tests/fixtures",
+]
+target-version = "py39"
+
+[tool.ruff.flake8-tidy-imports]
+ban-relative-imports = "all"
+
+[tool.ruff.mccabe]
+max-complexity = 10
+
+[tool.coverage.paths]
+source = [
+    "src",
+]
+
+[tool.coverage.run]
+branch = true
+source = [
+    "src",
+]
+
+[tool.coverage.report]
+skip_covered = true
+show_missing = true
+skip_empty = true
+exclude_also = [
+    "raise AssertionError",
+    "raise NotImplementedError",
+    "if __name__ == .__main__.:",
+    "@(abc.)?abstractmethod",
+    "@typing.runtime_checkable",
+]
+
+[tool.pytest.ini_options]
+addopts = [
+    "--import-mode=importlib",
+    "--doctest-modules",
+    "--ignore-glob=*scripts*,*examples*,*docs*",
+    "--cov",
+    "--cov-report=html",
+    "--cov-config=pyproject.toml",
+    "--doctest-glob=*README.md",
+    "-x",
+]
+doctest_optionflags = [
+    "NORMALIZE_WHITESPACE",
+    "IGNORE_EXCEPTION_DETAIL",
+    "ELLIPSIS",
+]
+testpaths = [
+    "src",
+    "tests",
+]
+
+[tool.mypy]
+check_untyped_defs = false
+disallow_untyped_defs = false
+disallow_incomplete_defs = false
+disallow_untyped_decorators = false
+disallow_any_unimported = false
+warn_return_any = false
+warn_unused_ignores = true
+no_implicit_optional = true
+show_error_codes = true
+ignore_missing_imports = true
+implicit_reexport = false
+exclude = [
+    "src/npc_ephys/scripts",
+]
+
+[tool.isort]
+profile = "black"
+atomic = true
+skip_glob = [
+    "*/setup.py",
+]
+filter_files = true
+known_first_party = [
+    "npc_ephys",
+]
+
+[tool.pdm]
+plugins = [
+    "pdm-bump",
+    "copier",
+]
+
+[tool.pdm.build]
+package-dir = "src"
+
+[tool.pdm.dev-dependencies]
+dev = [
+    "pytest>=7.4.0",
+    "ruff>=0.0.282",
+    "mypy>=1.4.1",
+    "pytest-cov>=4.1.0",
+    "black>=23.7.0",
+    "git-changelog>=2.3",
+    "parver>=0.3",
+]
+docs = [
+    "markdown-callouts>=0.3",
+    "markdown-exec>=1.7",
+    "mkdocs>=1.5",
+    "mkdocs-coverage>=1.0",
+    "mkdocs-gen-files>=0.5",
+    "mkdocs-git-committers-plugin-2>=1.2",
+    "mkdocs-git-revision-date-localized-plugin>=1.2",
+    "mkdocs-literate-nav>=0.6",
+    "mkdocs-material>=9.4",
+    "mkdocs-minify-plugin>=0.7",
+    "mkdocstrings[python]>=0.23",
+    "tomli>=2.0; python_version < '3.11'",
+]
+
+[tool.pdm.scripts]
+ruff = "ruff check src --fix-only"
+black = "black src"
+pytest = "pytest --cov-report term-missing:skip-covered --cov-report=html"
+mypy = "mypy src --install-types --non-interactive"
+log = "git-changelog -o CHANGELOG.md"
+dryrun = "pdm publish --repository testpypi --dry-run"
+post_init = "pdm install --plugins"
+
+[tool.pdm.scripts.test]
+composite = [
+    "pdm run mypy",
+    "pdm run pytest",
+]
+
+[tool.pdm.scripts.docs]
+shell = "cd docs && mkdocs serve"
+help = "Start the dev server for doc preview"
+
+[tool.pdm.scripts.bumpver]
+composite = [
+    "pdm self add pdm-bump",
+    "pdm bump micro",
+]
+
+[tool.pdm.scripts.tag]
+composite = [
+    "pdm self add pdm-bump",
+    "pdm bump tag",
+]
+
+[tool.pdm.scripts.pre_build]
+composite = [
+    "pdm run black",
+    "pdm run ruff",
+    "pdm run bumpver",
+]
+
+[tool.pdm.scripts.post_build]
+composite = [
+    "git commit -am 'Bump'",
+    "pdm run tag",
+    "pdm run log",
+]

npc-ephys-0.1.1/setup.cfg

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

npc-ephys-0.1.1/src/npc_ephys/__init__.py

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+"""
+    Tools for accessing and processing raw ephys data, compatible with data in the cloud.
+"""
+
+import doctest
+import importlib.metadata
+import logging
+
+from npc_ephys.barcodes import *
+
+# import functions from submodules here:
+from npc_ephys.openephys import *
+from npc_ephys.settings_xml import *
+from npc_ephys.spikeinterface import *
+from npc_ephys.units import *
+
+logger = logging.getLogger(__name__)
+
+__version__ = importlib.metadata.version("npc_ephys")
+logger.debug(f"{__name__}.{__version__ = }")
+
+
+def testmod(**testmod_kwargs) -> doctest.TestResults:
+    """
+    Run doctests for the module, configured to ignore exception details and
+    normalize whitespace.
+
+    Accepts kwargs to pass to doctest.testmod().
+
+    Add to modules to run doctests when run as a script:
+    .. code-block:: text
+        if __name__ == "__main__":
+            from npc_io import testmod
+            testmod()
+
+    """
+    _ = testmod_kwargs.setdefault(
+        "optionflags", doctest.NORMALIZE_WHITESPACE | doctest.ELLIPSIS
+    )
+    return doctest.testmod(**testmod_kwargs)
+
+
+if __name__ == "__main__":
+    testmod()