From adf80215ffe2791a4722732e50ca7d0121b26af0 Mon Sep 17 00:00:00 2001 From: frthjf Date: Thu, 19 May 2022 13:51:38 -0500 Subject: [PATCH] Adopt pyproject.toml and poetry packaging system --- .editorconfig | 24 + .github/workflows/main.yml | 92 +- .github/workflows/publish-to-pypi.yml | 25 + .pre-commit-config.yaml | 59 +- Makefile | 84 +- docs/conf.py | 5 +- examples/post_processing/spike_detection.py | 11 +- miv/__init__.py | 15 + miv/io/__init__.py | 2 +- miv/io/binary.py | 9 +- miv/io/data.py | 10 +- miv/py.typed | 0 miv/signal/filter/__init__.py | 4 +- miv/signal/filter/butter_bandpass_filter.py | 3 +- miv/signal/filter/filter_collection.py | 11 +- miv/signal/filter/protocol.py | 3 +- miv/signal/spike/__init__.py | 2 +- miv/signal/spike/detection.py | 11 +- miv/signal/spike/protocol.py | 6 +- miv/signal/spike/sorting.py | 17 +- miv/statistics/summarizer.py | 13 +- miv/typing.py | 3 +- miv/version.py | 1 - miv/visualization/fft_domain.py | 5 +- miv/visualization/waveform.py | 17 +- poetry.lock | 1654 +++++++++++++++++ pyproject.toml | 169 ++ requirements.txt | 17 - setup.py | 144 -- tests/filter/mock_filter.py | 1 + tests/filter/test_butterworth.py | 3 +- tests/filter/test_filter_collection.py | 9 +- tests/filter/test_filter_protocol.py | 3 +- tests/io/test_binary_io.py | 8 +- tests/spike/mock_spike_detection.py | 1 + tests/spike/test_spike_detection_protocol.py | 5 +- .../statistics/test_spikestamps_statistics.py | 7 +- tests/test_modules.py | 12 +- tests/visualization/test_fft.py | 3 +- tests/visualization/test_waveform.py | 3 +- 40 files changed, 2114 insertions(+), 357 deletions(-) create mode 100644 .editorconfig create mode 100644 .github/workflows/publish-to-pypi.yml create mode 100644 miv/py.typed delete mode 100644 miv/version.py create mode 100644 poetry.lock create mode 100644 pyproject.toml delete mode 100644 requirements.txt delete mode 100644 setup.py diff --git a/.editorconfig b/.editorconfig new file mode 100644 index 00000000..7f578f15 --- /dev/null +++ b/.editorconfig @@ -0,0 +1,24 @@ +# Check http://editorconfig.org for more information +# This is the main config file for this project: +root = true + +[*] +charset = utf-8 +end_of_line = lf +insert_final_newline = true +indent_style = space +indent_size = 2 +trim_trailing_whitespace = true + +[*.{py, pyi}] +indent_style = space +indent_size = 4 + +[Makefile] +indent_style = tab + +[*.md] +trim_trailing_whitespace = false + +[*.{diff,patch}] +trim_trailing_whitespace = false diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 80a130b0..f5fde272 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -1,97 +1,51 @@ -# This is a basic workflow to help you get started with Actions - name: CI -# Controls when the action will run. Triggers the workflow on push request -# events for the master branch, and pull request events for all branches. -on: - push: - branches: [ main ] - pull_request: - branches: [ '**' ] +on: [push, pull_request] -# A workflow run is made up of one or more jobs that can run sequentially or in parallel jobs: - # This workflow contains a single job called "build" build: - # The type of runner that the job will run on - runs-on: ${{ matrix.os }} #ubuntu-latest - + runs-on: ${{ matrix.os }} strategy: matrix: - os: [ubuntu-latest, macos-latest, windows-latest] # Run macos tests if really required, since they charge 10 times more for macos python-version: ["3.8", "3.9", "3.10"] + os: [ubuntu-latest, macos-latest, windows-latest] # Run macos tests if really required, since they charge 10 times more for macos + include: + - os: ubuntu-latest + path: ~/.cache/pip + - os: macos-latest + path: ~/Library/Caches/pip + - os: windows-latest + path: ~\AppData\Local\pip\Cache - # Steps represent a sequence of tasks that will be executed as part of the job steps: - # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it - uses: actions/checkout@v2 - - # Ref: https://docs.github.com/en/free-pro-team@latest/actions/guides/building-and-testing-python - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 + uses: actions/setup-python@v2.2.2 with: python-version: ${{ matrix.python-version }} - # You can test your matrix by printing the current Python version - - name: Display Python version - run: python -c "import sys; print(sys.version)" + - name: Install poetry + run: make poetry-download - # Cache the pip requirmenets for other tests. If requirements cached use them to speed up the build. - # Ref: https://github.com/actions/cache/blob/main/examples.md#python---pip - - name: Cache pip Linux - uses: actions/cache@v2 - if: startsWith(runner.os, 'Linux') - with: - path: ~/.cache/pip - key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} - restore-keys: | - ${{ runner.os }}-pip- - - name: Cache pip MacOS - uses: actions/cache@v2 - if: startsWith(runner.os, 'macOS') + - name: Set up cache + uses: actions/cache@v3 with: - path: ~/Library/Caches/pip - key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} - restore-keys: | - ${{ runner.os }}-pip- - - - name: Cache pip Windows - uses: actions/cache@v2 - if: startsWith(runner.os, 'Windows') - with: - path: ~\AppData\Local\pip\Cache - key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} + path: ${{ matrix.path }} + key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}-${{ hashFiles('poetry.lock') }} restore-keys: | ${{ runner.os }}-pip- - name: Install dependencies run: | - echo update pip - python -m pip install --upgrade pip - echo update requirments - pip install -r requirements.txt - echo update test requirements - pip install -r tests/requirements.txt - - # Runs a single command using the runners shell - - name: Welcome message - run: echo Hello, world! Welcome MiV-OS Build, lets start testing! + poetry config virtualenvs.in-project true + poetry install - # Formatting test with black and flake8 - - name: Black and Flake8 formatting tests - if: startsWith(runner.os, 'macOS') + - name: Run style checks run: | - if [[ "${{ matrix.python-version }}" == "3.8" ]]; then - black --version - black --check miv tests - flake8 --version - flake8 miv tests - fi + make check-codestyle - # General PyTest for all matrix strategy - - name: PyTest and MyPy + - name: Run tests run: | - make ci + make test # Set environment variables for coverage test. Coverage test is done using python 3.8 # Test MiV-OS using pytest diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yml new file mode 100644 index 00000000..412fc08a --- /dev/null +++ b/.github/workflows/publish-to-pypi.yml @@ -0,0 +1,25 @@ +name: publish + +on: + release: + types: [created] + +jobs: + deploy: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v3 + - name: Set up Python + uses: actions/setup-python@v3.1.0 + with: + python-version: "3.x" + - name: Install Poetry + uses: snok/install-poetry@v1.3 + - name: Build + run: | + poetry build + - name: Publish distribution 📦 to PyPI + if: startsWith(github.ref, 'refs/tags') + uses: pypa/gh-action-pypi-publish@master + with: + password: ${{ secrets.PYPI_API_TOKEN }} diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index d4b57b9f..7e533e09 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,18 +1,43 @@ +default_language_version: + python: python3.8 + +default_stages: [commit, push] + repos: -- repo: https://github.com/pre-commit/pre-commit-hooks - rev: v2.3.0 - hooks: - - id: trailing-whitespace - - id: check-json - - id: end-of-file-fixer - - id: requirements-txt-fixer -- repo: https://github.com/psf/black - rev: 21.12b0 - hooks: - - id: black - additional_dependencies: ['click==8.0.4'] - # args: [--line-length=120] -- repo: https://github.com/pycqa/flake8 - rev: 4.0.0 - hooks: - - id: flake8 + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v2.5.0 + hooks: + - id: trailing-whitespace + - id: check-json + - id: check-yaml + - id: end-of-file-fixer + exclude: LICENSE + + - repo: local + hooks: + - id: pyupgrade + name: pyupgrade + entry: poetry run pyupgrade --py37-plus + types: [python] + language: system + + - repo: local + hooks: + - id: isort + name: isort + entry: poetry run isort --settings-path pyproject.toml + types: [python] + language: system + + - repo: local + hooks: + - id: black + name: black + entry: poetry run black --config pyproject.toml + types: [python] + language: system + + - repo: https://github.com/pycqa/flake8 + rev: 4.0.0 + hooks: + - id: flake8 diff --git a/Makefile b/Makefile index e5d5a257..05819329 100644 --- a/Makefile +++ b/Makefile @@ -1,11 +1,83 @@ +#* Variables +PYTHON := python +PYTHONPATH := `pwd` + +#* Poetry +.PHONY: poetry-download +poetry-download: + curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/install-poetry.py | $(PYTHON) - + +.PHONY: poetry-remove +poetry-remove: + curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/install-poetry.py | $(PYTHON) - --uninstall + +#* Installation +.PHONY: install +install: + poetry lock -n && poetry export --without-hashes > requirements.txt + poetry install -n + -poetry run mypy --install-types --non-interactive ./ + +.PHONY: pre-commit-install +pre-commit-install: + poetry run pre-commit install + +#* Formatters +.PHONY: codestyle +codestyle: + poetry run pyupgrade --exit-zero-even-if-changed --py38-plus **/*.py + poetry run isort --settings-path pyproject.toml ./ + poetry run black --config pyproject.toml ./ + +.PHONY: formatting +formatting: codestyle + +#* Linting +.PHONY: test test: - @python -m pytest + PYTHONPATH=$(PYTHONPATH) poetry run pytest -c pyproject.toml --cov-report=html --cov=miv tests/ + +.PHONY: check-codestyle +check-codestyle: + poetry run isort --diff --check-only --settings-path pyproject.toml ./ + poetry run black --diff --check --config pyproject.toml ./ + poetry run darglint --verbosity 2 miv tests +.PHONY: mypy mypy: - @mypy --ignore-missing-imports miv + poetry run mypy --config-file pyproject.toml ./ + +.PHONY: lint +lint: test check-codestyle mypy check-safety + +.PHONY: update-dev-deps +update-dev-deps: + poetry add -D "isort[colors]@latest" mypy@latest pre-commit@latest pydocstyle@latest pylint@latest pytest@latest pyupgrade@latest coverage@latest pytest-html@latest pytest-cov@latest black@latest + +#* Cleaning +.PHONY: pycache-remove +pycache-remove: + find . | grep -E "(__pycache__|\.pyc|\.pyo$$)" | xargs rm -rf + +.PHONY: dsstore-remove +dsstore-remove: + find . | grep -E ".DS_Store" | xargs rm -rf + +.PHONY: mypycache-remove +mypycache-remove: + find . | grep -E ".mypy_cache" | xargs rm -rf + +.PHONY: ipynbcheckpoints-remove +ipynbcheckpoints-remove: + find . | grep -E ".ipynb_checkpoints" | xargs rm -rf + +.PHONY: pytestcache-remove +pytestcache-remove: + find . | grep -E ".pytest_cache" | xargs rm -rf -coverage: - @pytest --cov=miv tests/ +.PHONY: build-remove +build-remove: + rm -rf build/ -all:test mypy coverage -ci: test mypy +.PHONY: cleanup +cleanup: pycache-remove dsstore-remove mypycache-remove ipynbcheckpoints-remove pytestcache-remove diff --git a/docs/conf.py b/docs/conf.py index 04fa4468..330a7696 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -18,8 +18,7 @@ sys.path.insert(0, os.path.abspath("../")) -from miv.version import VERSION - +from miv import get_version # -- Project information ----------------------------------------------------- @@ -28,7 +27,7 @@ author = "Gazzola Lab" # The full version, including alpha/beta/rc tags -release = VERSION +release = get_version() # -- General configuration --------------------------------------------------- diff --git a/examples/post_processing/spike_detection.py b/examples/post_processing/spike_detection.py index ea7d8f28..b2bc371f 100644 --- a/examples/post_processing/spike_detection.py +++ b/examples/post_processing/spike_detection.py @@ -1,20 +1,19 @@ import os + +import matplotlib.pyplot as plt +import neo import numpy as np import quantities as pq +from viziphant.rasterplot import rasterplot_rates from miv.io import load_data from miv.signal.filter import butter_bandpass_filter from miv.signal.spike import ( + align_to_minimum, compute_spike_threshold, detect_threshold_crossings, - align_to_minimum, ) -import neo -from viziphant.rasterplot import rasterplot_rates - -import matplotlib.pyplot as plt - def main(): """Example spike detection script""" diff --git a/miv/__init__.py b/miv/__init__.py index e69de29b..e7dc41b5 100644 --- a/miv/__init__.py +++ b/miv/__init__.py @@ -0,0 +1,15 @@ +# type: ignore[attr-defined] +"""Python software for analysis and computing framework used in MiV project.""" + +import sys +from importlib import metadata as importlib_metadata + + +def get_version() -> str: + try: + return importlib_metadata.version(__name__) + except importlib_metadata.PackageNotFoundError: # pragma: no cover + return "unknown" + + +version: str = get_version() diff --git a/miv/io/__init__.py b/miv/io/__init__.py index 0ec7ac30..4754678d 100644 --- a/miv/io/__init__.py +++ b/miv/io/__init__.py @@ -1,2 +1,2 @@ -from miv.io.data import * from miv.io.binary import * +from miv.io.data import * diff --git a/miv/io/binary.py b/miv/io/binary.py index 29a10bb8..7c60d0a9 100644 --- a/miv/io/binary.py +++ b/miv/io/binary.py @@ -8,14 +8,15 @@ """ __all__ = ["load_continuous_data", "load_recording", "oebin_read", "apply_channel_mask"] -from typing import Any, Dict, Optional, Union, List, Set, Sequence +from typing import Any, Dict, List, Optional, Sequence, Set, Union import os -import numpy as np from ast import literal_eval from glob import glob -import quantities as pq + import neo +import numpy as np +import quantities as pq from miv.typing import SignalType, TimestampsType @@ -73,7 +74,7 @@ def bits_to_voltage(signal: SignalType, channel_info: Sequence[Dict[str, Any]]): unit_conversion = (recorded_unit / resultant_unit).simplified signal[:, channel] *= bit_to_volt_conversion * unit_conversion if "ADC" in channel_info[channel]["channel_name"]: - signal[:, channel] *= 10 ** 6 + signal[:, channel] *= 10**6 return signal diff --git a/miv/io/data.py b/miv/io/data.py index 5c5ee386..0fb186d5 100644 --- a/miv/io/data.py +++ b/miv/io/data.py @@ -26,18 +26,18 @@ """ __all__ = ["Data", "DataManager"] -from typing import Any, Optional, Iterable, Callable, List, Set +from typing import Any, Callable, Iterable, List, Optional, Set -from collections.abc import MutableSequence import logging - import os +from collections.abc import MutableSequence +from contextlib import contextmanager from glob import glob + import numpy as np -from contextlib import contextmanager from miv.io.binary import load_continuous_data, load_recording -from miv.signal.filter import FilterProtocol +from miv.signal.filter.protocol import FilterProtocol from miv.typing import SignalType diff --git a/miv/py.typed b/miv/py.typed new file mode 100644 index 00000000..e69de29b diff --git a/miv/signal/filter/__init__.py b/miv/signal/filter/__init__.py index fd1bb8f2..73e42400 100644 --- a/miv/signal/filter/__init__.py +++ b/miv/signal/filter/__init__.py @@ -1,3 +1,3 @@ -from miv.signal.filter.protocol import * -from miv.signal.filter.filter_collection import * from miv.signal.filter.butter_bandpass_filter import * +from miv.signal.filter.filter_collection import * +from miv.signal.filter.protocol import * diff --git a/miv/signal/filter/butter_bandpass_filter.py b/miv/signal/filter/butter_bandpass_filter.py index ef29a008..4073a135 100644 --- a/miv/signal/filter/butter_bandpass_filter.py +++ b/miv/signal/filter/butter_bandpass_filter.py @@ -3,11 +3,10 @@ from dataclasses import dataclass +import matplotlib.pyplot as plt import numpy as np import numpy.typing as npt - import scipy.signal as sps -import matplotlib.pyplot as plt from miv.typing import SignalType diff --git a/miv/signal/filter/filter_collection.py b/miv/signal/filter/filter_collection.py index 35338479..bf7109f8 100644 --- a/miv/signal/filter/filter_collection.py +++ b/miv/signal/filter/filter_collection.py @@ -20,14 +20,17 @@ """ __all__ = ["FilterCollection"] -from typing import Union, List -import numpy as np -import numpy.typing as npt +from typing import TYPE_CHECKING, List from collections.abc import MutableSequence +import numpy as np +import numpy.typing as npt + from miv.typing import SignalType -from miv.signal.filter import FilterProtocol + +if TYPE_CHECKING: + from miv.signal.filter import FilterProtocol class FilterCollection(MutableSequence): diff --git a/miv/signal/filter/protocol.py b/miv/signal/filter/protocol.py index 9393f508..ee2c456c 100644 --- a/miv/signal/filter/protocol.py +++ b/miv/signal/filter/protocol.py @@ -2,8 +2,7 @@ __all__ = ["FilterProtocol"] import typing -from typing import Union, Callable, Optional -from typing import Protocol +from typing import Callable, Optional, Protocol, Union import numpy as np import numpy.typing as npt diff --git a/miv/signal/spike/__init__.py b/miv/signal/spike/__init__.py index 7ea090f6..8392de78 100644 --- a/miv/signal/spike/__init__.py +++ b/miv/signal/spike/__init__.py @@ -1,3 +1,3 @@ -from miv.signal.spike.protocol import * from miv.signal.spike.detection import * +from miv.signal.spike.protocol import * from miv.signal.spike.sorting import * diff --git a/miv/signal/spike/detection.py b/miv/signal/spike/detection.py index d179148e..f3578dde 100644 --- a/miv/signal/spike/detection.py +++ b/miv/signal/spike/detection.py @@ -17,17 +17,16 @@ """ __all__ = ["ThresholdCutoff"] -from typing import Union, List, Iterable +from typing import Iterable, List, Union +from dataclasses import dataclass + +import neo import numpy as np import quantities as pq - from tqdm import tqdm -from dataclasses import dataclass -from miv.typing import SignalType, TimestampsType, SpikestampsType - -import neo +from miv.typing import SignalType, SpikestampsType, TimestampsType @dataclass diff --git a/miv/signal/spike/protocol.py b/miv/signal/spike/protocol.py index da092835..1a9d27b3 100644 --- a/miv/signal/spike/protocol.py +++ b/miv/signal/spike/protocol.py @@ -4,12 +4,12 @@ "UnsupervisedFeatureClusteringProtocol", ] -from typing import Protocol, Union, Any, Iterable +from typing import Any, Iterable, Protocol, Union -import numpy as np import neo.core +import numpy as np -from miv.typing import SignalType, TimestampsType, SpikestampsType +from miv.typing import SignalType, SpikestampsType, TimestampsType class SpikeDetectionProtocol(Protocol): diff --git a/miv/signal/spike/sorting.py b/miv/signal/spike/sorting.py index 6c243a86..537833ee 100644 --- a/miv/signal/spike/sorting.py +++ b/miv/signal/spike/sorting.py @@ -54,29 +54,26 @@ "SuperParamagneticClustering", ] -from typing import Any, Union, Optional +from typing import Any, Optional, Union from dataclasses import dataclass +import matplotlib.pyplot as plt +import neo import numpy as np +import pywt +import quantities as pq import scipy import scipy.special -import quantities as pq - -import pywt - -import matplotlib.pyplot as plt - -from sklearn.mixture import GaussianMixture from sklearn.decomposition import PCA +from sklearn.mixture import GaussianMixture from sklearn.preprocessing import StandardScaler -import neo -from miv.typing import SignalType, TimestampsType, SpikestampsType from miv.signal.spike.protocol import ( SpikeFeatureExtractionProtocol, UnsupervisedFeatureClusteringProtocol, ) +from miv.typing import SignalType, SpikestampsType, TimestampsType class SpikeSorting: diff --git a/miv/statistics/summarizer.py b/miv/statistics/summarizer.py index ba540bdc..170dc350 100644 --- a/miv/statistics/summarizer.py +++ b/miv/statistics/summarizer.py @@ -40,15 +40,16 @@ """ __all__ = ["spikestamps_statistics"] -from typing import Any, Optional, Iterable, Union, Dict -import numpy as np -import matplotlib.pyplot as plt +from typing import Any, Dict, Iterable, Optional, Union + import datetime -import scipy -import scipy.signal -import neo import elephant.statistics +import matplotlib.pyplot as plt +import neo +import numpy as np +import scipy +import scipy.signal # FIXME: For now, we provide the free function for simple usage. For more diff --git a/miv/typing.py b/miv/typing.py index e53b1105..40931f5a 100644 --- a/miv/typing.py +++ b/miv/typing.py @@ -1,11 +1,10 @@ # from typing import TypeAlias from typing import Union +import neo import numpy as np import numpy.typing as npt -import neo - SignalType = Union[ np.ndarray, neo.core.AnalogSignal, # npt.DTypeLike diff --git a/miv/version.py b/miv/version.py deleted file mode 100644 index 4d389414..00000000 --- a/miv/version.py +++ /dev/null @@ -1 +0,0 @@ -VERSION = "0.0.3" diff --git a/miv/visualization/fft_domain.py b/miv/visualization/fft_domain.py index 88b2731a..0a1a2c17 100644 --- a/miv/visualization/fft_domain.py +++ b/miv/visualization/fft_domain.py @@ -1,13 +1,12 @@ __all__ = ["plot_frequency_domain"] import os -import numpy as np +import matplotlib.pyplot as plt +import numpy as np from scipy import fftpack from scipy.signal import welch -import matplotlib.pyplot as plt - from miv.typing import SignalType diff --git a/miv/visualization/waveform.py b/miv/visualization/waveform.py index 8dcc9913..ce56fafe 100644 --- a/miv/visualization/waveform.py +++ b/miv/visualization/waveform.py @@ -3,22 +3,19 @@ """ __all__ = ["extract_waveforms", "plot_waveforms"] -from typing import Any, Optional, Union, Tuple, Dict +from typing import Any, Dict, Optional, Tuple, Union import os -import numpy as np +import matplotlib.pyplot as plt +import neo +import numpy as np import quantities as pq - -from sklearn.mixture import GaussianMixture +from scipy.signal import lfilter, savgol_filter from sklearn.decomposition import PCA +from sklearn.mixture import GaussianMixture from sklearn.preprocessing import StandardScaler -from scipy.signal import lfilter, savgol_filter - -import matplotlib.pyplot as plt - -import neo from miv.typing import SignalType, SpikestampsType # TODO: Modularize the entire process. @@ -131,7 +128,7 @@ def plot_waveforms( color, linewidth=1, alpha=0.3, - **plot_kwargs + **plot_kwargs, ) plt.xlabel("Time (ms)") plt.ylabel("Voltage (uV)") diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 00000000..e39234cf --- /dev/null +++ b/poetry.lock @@ -0,0 +1,1654 @@ +[[package]] +name = "antlr4-python3-runtime" +version = "4.9.3" +description = "ANTLR 4.9.3 runtime for Python 3.7" +category = "main" +optional = false +python-versions = "*" + +[[package]] +name = "astroid" +version = "2.11.5" +description = "An abstract syntax tree for Python with inference support." +category = "dev" +optional = false +python-versions = ">=3.6.2" + +[package.dependencies] +lazy-object-proxy = ">=1.4.0" +typing-extensions = {version = ">=3.10", markers = "python_version < \"3.10\""} +wrapt = ">=1.11,<2" + +[[package]] +name = "atomicwrites" +version = "1.4.0" +description = "Atomic file writes." +category = "dev" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" + +[[package]] +name = "attrs" +version = "21.4.0" +description = "Classes Without Boilerplate" +category = "dev" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" + +[package.extras] +dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"] +docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"] +tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "cloudpickle"] +tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "cloudpickle"] + +[[package]] +name = "black" +version = "22.3.0" +description = "The uncompromising code formatter." +category = "dev" +optional = false +python-versions = ">=3.6.2" + +[package.dependencies] +click = ">=8.0.0" +mypy-extensions = ">=0.4.3" +pathspec = ">=0.9.0" +platformdirs = ">=2" +tomli = {version = ">=1.1.0", markers = 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Update me + "Development Status :: 3 - Alpha", + "Intended Audience :: Science/Research", + "Intended Audience :: Education", + "Operating System :: OS Independent", + "License :: OSI Approved :: MIT License", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.7", + "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.9", +] + +include = ["miv/py.typed"] + + +[tool.poetry.dependencies] +python = ">=3.8,<4.0" +elephant = "^0.11.1" +matplotlib = ">=3.3.2" +McsPyDataTools = "^0.4.3" +neo = "^0.10.2" +numba = ">=0.51.0" +numpy = ">=1.19.2" +omegaconf = "^2.2.1" +pandas = "^1.4.2" +Pillow = "^9.1.1" +PyWavelets = "^1.3.0" +quantities = "^0.13.0" +scikit-learn = "^1.1.1" +scipy = ">=1.5.2" +seaborn = "^0.11.2" +sklearn = "^0.0" +tqdm = ">=4.61.1" +[tool.poetry.dev-dependencies] +black = "^22" +isort = {extras = ["colors"], version = "^5.10.1"} +mypy = "^0.910" +mypy-extensions = "^0.4.3" +pre-commit = "^2.15.0" +pydocstyle = "^6.1.1" +pylint = "^2.11.1" +pytest = "^6.2.5" +pyupgrade = "^2.29.1" +coverage = "^6.1.2" +pytest-html = "^3.1.1" +pytest-cov = "^3.0.0" +flake8 = "^4.0.1" +[tool.poetry.extras] +build = [ + "twine" +] +docs = [ + "sphinx", + "sphinx_rtd_theme", + "sphinx-book-theme", + "readthedocs-sphinx-search", + "sphinx-autodoc-typehints", + "myst-parser", + "numpydoc", + "docutils", +] + + + +[tool.black] +# https://github.com/psf/black +target-version = ["py38"] +line-length = 88 +color = true + +exclude = ''' +/( + \.git + | \.hg + | \.mypy_cache + | \.tox + | \.venv + | _build + | buck-out + | build + | dist + | env + | venv +)/ +''' + +[tool.isort] +# https://github.com/timothycrosley/isort/ +py_version = 37 +line_length = 88 + +known_typing = ["typing", "types", "typing_extensions", "mypy", "mypy_extensions"] +sections = ["FUTURE", "TYPING", "STDLIB", "THIRDPARTY", "FIRSTPARTY", "LOCALFOLDER"] +include_trailing_comma = true +profile = "black" +multi_line_output = 3 +indent = 4 +color_output = true + +[tool.mypy] +# https://mypy.readthedocs.io/en/latest/config_file.html#using-a-pyproject-toml-file +python_version = 3.8 +pretty = true +show_traceback = true +color_output = true + +allow_redefinition = false +check_untyped_defs = true +disallow_any_generics = true +disallow_incomplete_defs = true +ignore_missing_imports = true +implicit_reexport = false +no_implicit_optional = true +show_column_numbers = true +show_error_codes = true +show_error_context = true +strict_equality = true +strict_optional = true +warn_no_return = true +warn_redundant_casts = true +warn_return_any = true +warn_unreachable = true +warn_unused_configs = true +warn_unused_ignores = true + + +[tool.pytest.ini_options] +# https://docs.pytest.org/en/6.2.x/customize.html#pyproject-toml +# Directories that are not visited by pytest collector: +norecursedirs =["hooks", "*.egg", ".eggs", "dist", "build", "docs", ".tox", ".git", "__pycache__"] +doctest_optionflags = ["NUMBER", "NORMALIZE_WHITESPACE", "IGNORE_EXCEPTION_DETAIL"] + +# Extra options: +addopts = [ + "--strict-markers", + "--tb=short", + "--doctest-modules", + "--doctest-continue-on-failure", +] + +[tool.coverage.run] +source = ["tests"] + +[coverage.paths] +source = "miv" + +[coverage.run] +branch = true + +[coverage.report] +fail_under = 50 +show_missing = true diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index b4745d26..00000000 --- a/requirements.txt +++ /dev/null @@ -1,17 +0,0 @@ -elephant -matplotlib -matplotlib>=3.3.2 -McsPyDataTools -neo -numba>=0.51.0 -numpy>=1.19.2 -omegaconf -pandas -Pillow -PyWavelets -quantities -scikit-learn -scipy>=1.5.2 -seaborn -sklearn -tqdm>=4.61.1 diff --git a/setup.py b/setup.py deleted file mode 100644 index 09f70807..00000000 --- a/setup.py +++ /dev/null @@ -1,144 +0,0 @@ -#!/usr/bin/env python -# Thanks and credits to https://github.com/navdeep-G/setup.py for setup.py format -import io -import os -import sys -from shutil import rmtree - -from setuptools import Command, find_packages, setup - -from miv.version import VERSION - -# Package meta-data. -NAME = "MiV-OS" -DESCRIPTION = ( - "Python software for analysis and computing framework used in MiV project." -) -URL = "https://github.com/GazzolaLab/MiV-OS" -EMAIL = "skim449@illinois.edu" -AUTHOR = "GazzolaLab" -REQUIRES_PYTHON = ">=3.8.0" - -# What packages are required for this module to be executed? -REQUIRED = [ - "matplotlib", - "matplotlib>=3.3.2", - "McsPyDataTools", - "numba>=0.51.0", - "numpy>=1.19.2", - "omegaconf", - "pandas", - "Pillow", - "quantities", - "scikit-learn", - "scipy>=1.5.2", - "seaborn", - "sklearn", - "tqdm>=4.61.1", -] - -# What packages are optional? -EXTRAS = { - "dev": ["black", "pre-commit", "pytest", "flake8", "mypy"], - "build": ["twine"], - "docs": [ - "sphinx==4.4.0", - "sphinx_rtd_theme==1.0.0", - "sphinx-book-theme", - "readthedocs-sphinx-search==0.1.1", - "sphinx-autodoc-typehints", - "myst-parser", - "numpydoc", - "docutils", - ], -} - -here = os.path.abspath(os.path.dirname(__file__)) - -# Import the README and use it as the long-description. -# Note: this will only work if 'README.md' is present in your MANIFEST.in file! -try: - with io.open(os.path.join(here, "README.md"), encoding="utf-8") as f: - long_description = "\n" + f.read() -except FileNotFoundError: - long_description = DESCRIPTION - -# Load the package's __version__.py module as a dictionary. -about = {} -if not VERSION: - project_slug = NAME.lower().replace("-", "_").replace(" ", "_") - with open(os.path.join(here, project_slug, "__version__.py")) as f: - exec(f.read(), about) -else: - about["__version__"] = VERSION - - -class UploadCommand(Command): - """Support setup.py upload.""" - - description = "Build and publish the package." - user_options = [] - - @staticmethod - def status(s): - """Prints things in bold.""" - print("\033[1m{0}\033[0m".format(s)) - - def initialize_options(self): - pass - - def finalize_options(self): - pass - - def run(self): - try: - self.status("Removing previous builds…") - rmtree(os.path.join(here, "dist")) - except OSError: - pass - - self.status("Building Source and Wheel (universal) distribution…") - os.system("{0} setup.py sdist bdist_wheel --universal".format(sys.executable)) - - self.status("Uploading the package to PyPI via Twine…") - os.system("twine upload dist/*") - - self.status("Pushing git tags…") - os.system("git tag v{0}".format(about["__version__"])) - os.system("git push --tags") - - sys.exit() - - -setup( - name=NAME, - version=about["__version__"], - description=DESCRIPTION, - long_description=long_description, - long_description_content_type="text/markdown", # This is important! - author=AUTHOR, - author_email=EMAIL, - python_requires=REQUIRES_PYTHON, - url=URL, - # packages=["miv"], - package_dir={"miv": "./miv"}, - packages=find_packages(), - license="MIT", - classifiers=[ - # Trove classifiers - # Full list: https://pypi.python.org/pypi?%3Aaction=list_classifiers - "License :: OSI Approved :: MIT License", - "Development Status :: 3 - Alpha", - "Programming Language :: Python", - "Programming Language :: Python :: 3.8", - "Intended Audience :: Science/Research", - "Intended Audience :: Education", - ], - download_url=f"https://github.com/GazzolaLab/MiV-OS/archive/refs/tags/{VERSION}.tar.gz", - install_requires=REQUIRED, - extras_require=EXTRAS, - # $ setup.py publish support: We don't know how to use this part. We already know how to publish.! - cmdclass={ - "upload": UploadCommand, - }, -) diff --git a/tests/filter/mock_filter.py b/tests/filter/mock_filter.py index 2d30af38..d21655b3 100644 --- a/tests/filter/mock_filter.py +++ b/tests/filter/mock_filter.py @@ -1,6 +1,7 @@ from typing import Any, Iterable import numpy as np + from miv.signal.filter import FilterProtocol diff --git a/tests/filter/test_butterworth.py b/tests/filter/test_butterworth.py index ebf2ebe9..5dd224c3 100644 --- a/tests/filter/test_butterworth.py +++ b/tests/filter/test_butterworth.py @@ -1,8 +1,7 @@ +import numpy as np import pytest -import numpy as np from miv.signal.filter import ButterBandpass - from tests.filter.test_filter_protocol import RuntimeFilterProtocol ParameterSet = [ diff --git a/tests/filter/test_filter_collection.py b/tests/filter/test_filter_collection.py index ecd45db3..53e6bbb1 100644 --- a/tests/filter/test_filter_collection.py +++ b/tests/filter/test_filter_collection.py @@ -1,13 +1,10 @@ -from typing import runtime_checkable -from typing import Protocol, Any - -import pytest +from typing import Any, Protocol, runtime_checkable import numpy as np +import pytest -from miv.signal.filter import FilterProtocol, FilterCollection +from miv.signal.filter import FilterCollection, FilterProtocol from tests.filter.mock_filter import mock_filter_list, mock_nonfilter_list - from tests.filter.test_filter_protocol import RuntimeFilterProtocol diff --git a/tests/filter/test_filter_protocol.py b/tests/filter/test_filter_protocol.py index 723a5ce7..16a19f5a 100644 --- a/tests/filter/test_filter_protocol.py +++ b/tests/filter/test_filter_protocol.py @@ -1,5 +1,4 @@ -from typing import runtime_checkable -from typing import Protocol, Any +from typing import Any, Protocol, runtime_checkable import pytest diff --git a/tests/io/test_binary_io.py b/tests/io/test_binary_io.py index 508ea40f..bd589e22 100644 --- a/tests/io/test_binary_io.py +++ b/tests/io/test_binary_io.py @@ -1,14 +1,14 @@ -import pytest - -import tempfile import os +import tempfile + import numpy as np +import pytest from miv.io.binary import ( + apply_channel_mask, load_continuous_data, load_recording, oebin_read, - apply_channel_mask, ) diff --git a/tests/spike/mock_spike_detection.py b/tests/spike/mock_spike_detection.py index 484cdfc2..ba4537b4 100644 --- a/tests/spike/mock_spike_detection.py +++ b/tests/spike/mock_spike_detection.py @@ -1,6 +1,7 @@ from typing import Any, Iterable import numpy as np + from miv.signal.spike import SpikeDetectionProtocol diff --git a/tests/spike/test_spike_detection_protocol.py b/tests/spike/test_spike_detection_protocol.py index 7782bdaa..5a9914a4 100644 --- a/tests/spike/test_spike_detection_protocol.py +++ b/tests/spike/test_spike_detection_protocol.py @@ -1,12 +1,11 @@ -from typing import runtime_checkable -from typing import Protocol, Any +from typing import Any, Protocol, runtime_checkable import pytest from miv.signal.spike import SpikeDetectionProtocol from tests.spike.mock_spike_detection import ( - mock_spike_detection_list, mock_nonspike_detection_list, + mock_spike_detection_list, ) diff --git a/tests/statistics/test_spikestamps_statistics.py b/tests/statistics/test_spikestamps_statistics.py index d24dfba1..8ed09e18 100644 --- a/tests/statistics/test_spikestamps_statistics.py +++ b/tests/statistics/test_spikestamps_statistics.py @@ -1,10 +1,9 @@ -import pytest - import numpy as np +import pytest +import quantities as pq +from neo.core import SpikeTrain from miv.statistics import spikestamps_statistics -from neo.core import SpikeTrain -import quantities as pq SpikestampsTestSet = [ [[1, 2, 3]], diff --git a/tests/test_modules.py b/tests/test_modules.py index 4cdc2e5a..3334f111 100644 --- a/tests/test_modules.py +++ b/tests/test_modules.py @@ -1,16 +1,12 @@ -import pytest import re -import numpy as np - def test_version_regex_match(): - import miv.version - from miv.version import VERSION + from miv import version - re_version = re.search(r"([\d.]+)", VERSION).group(1) - assert re_version == VERSION, "Version numbers should be integer." + re_version = re.search(r"([\d.]+)", version).group(1) + assert re_version == version, "Version numbers should be integer." lead_zero_stripped_version = ".".join([str(int(v)) for v in re_version.split(".")]) assert ( - lead_zero_stripped_version == VERSION + lead_zero_stripped_version == version ), "Version numbers should not have leading zeros." diff --git a/tests/visualization/test_fft.py b/tests/visualization/test_fft.py index b371874a..6e6d7a5a 100644 --- a/tests/visualization/test_fft.py +++ b/tests/visualization/test_fft.py @@ -1,5 +1,4 @@ -import pytest - import numpy as np +import pytest from miv.visualization import plot_frequency_domain diff --git a/tests/visualization/test_waveform.py b/tests/visualization/test_waveform.py index da6dce3f..809efa7b 100644 --- a/tests/visualization/test_waveform.py +++ b/tests/visualization/test_waveform.py @@ -1,5 +1,4 @@ -import pytest - import numpy as np +import pytest from miv.visualization import extract_waveforms, plot_waveforms