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Modern packaging + ruff + numpy 2 compat #187

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Modern packaging + ruff + numpy 2 compat #187

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ceb11fc
Modern packaging + ruff (NPY201)
raphaelvallat Dec 20, 2024
f9fc8d7
move to src folder + ruff
raphaelvallat Dec 20, 2024
5a56bf3
Better pyproject + add tests for 3.12
raphaelvallat Dec 20, 2024
d16a169
Fix install Windows
raphaelvallat Dec 20, 2024
5579bb3
fix ruff for some docstring
raphaelvallat Dec 20, 2024
407609c
Disable docstring formatting
raphaelvallat Dec 21, 2024
35fd3f7
disable py312
raphaelvallat Dec 21, 2024
3bcf7b7
ruff fixes
raphaelvallat Dec 21, 2024
d9d95df
re-enable macos
raphaelvallat Dec 21, 2024
1c9f166
disable macos
raphaelvallat Dec 21, 2024
8b7a19e
fix missing line code block rst
raphaelvallat Dec 21, 2024
f9e8bd2
add tests folder to coverage
raphaelvallat Dec 21, 2024
42fa120
remove test folder from coverage
raphaelvallat Dec 21, 2024
f8cd161
add libomp for macos-latest
raphaelvallat Dec 22, 2024
975ee06
2nd attempt
raphaelvallat Dec 22, 2024
4a639d9
re-enable lspopt
raphaelvallat Dec 22, 2024
2b54270
add setuptools dep
raphaelvallat Dec 22, 2024
319a0fe
fix numpy deprecation
raphaelvallat Dec 22, 2024
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14 changes: 0 additions & 14 deletions .coveragerc
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10 changes: 0 additions & 10 deletions .github/workflows/black.yml
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24 changes: 13 additions & 11 deletions .github/workflows/python_tests.yml
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Expand Up @@ -2,45 +2,47 @@ name: Python tests

on:
push:
branches: [master, develop]
branches: [master]
pull_request:
branches: [master, develop]
branches: [master]
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jobs:
build:
strategy:
fail-fast: false
matrix:
platform: [ubuntu-latest, windows-latest] # macos-latest
python-version: ["3.9", "3.10", "3.11"]
platform: [ubuntu-latest, macos-latest, windows-latest]
python-version: ["3.9", "3.10", "3.11", "3.12"]

runs-on: ${{ matrix.platform }}

env:
FORCE_COLOR: true

steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v4

- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v1
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}

- name: Install libomp (macOS)
if: ${{ matrix.platform == 'macos-latest' }}
run: brew install libomp

- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install -r requirements.txt
pip install -r requirements-test.txt
pip install .
pip install ".[test]"

- name: Test with pytest
run: |
pytest --cov --cov-report=xml --cov-config=setup.cfg --verbose
pytest --cov --cov-report=xml --verbose

- name: Upload coverage report
if: ${{ matrix.platform == 'ubuntu-latest' && matrix.python-version == 3.9 }}
uses: codecov/codecov-action@v1
uses: codecov/codecov-action@v4
with:
token: a58a0c62-fb11-4429-977b-65bec01ecb44
file: ./coverage.xml
13 changes: 13 additions & 0 deletions .github/workflows/ruff.yml
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@@ -0,0 +1,13 @@
name: Ruff
on: [push, pull_request]
jobs:
ruff:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: "Linting"
uses: astral-sh/ruff-action@v1
- name: "Formatting"
uses: astral-sh/ruff-action@v1
with:
args: "format --check"
19 changes: 2 additions & 17 deletions MANIFEST.in
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@@ -1,21 +1,6 @@
# Add README, LICENSE and requirements :
# Add README and LICENSE :
include README.rst
include LICENSE
include requirements.txt

# Add trained classifiers
# v0.4.0
include yasa/classifiers/clf_eeg_lgb_0.4.0.joblib
include yasa/classifiers/clf_eeg+eog_lgb_0.4.0.joblib
include yasa/classifiers/clf_eeg+eog+emg_lgb_0.4.0.joblib
include yasa/classifiers/clf_eeg+eog+emg+demo_lgb_0.4.0.joblib

# v0.5.0
include yasa/classifiers/clf_eeg_lgb_0.5.0.joblib
include yasa/classifiers/clf_eeg+demo_lgb_0.5.0.joblib
include yasa/classifiers/clf_eeg+eog_lgb_0.5.0.joblib
include yasa/classifiers/clf_eeg+eog+demo_lgb_0.5.0.joblib
include yasa/classifiers/clf_eeg+emg_lgb_0.5.0.joblib
include yasa/classifiers/clf_eeg+emg+demo_lgb_0.5.0.joblib
include yasa/classifiers/clf_eeg+eog+emg_lgb_0.5.0.joblib
include yasa/classifiers/clf_eeg+eog+emg+demo_lgb_0.5.0.joblib
recursive-include yasa/classifiers/ *.joblib
13 changes: 13 additions & 0 deletions README.rst
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Expand Up @@ -14,6 +14,10 @@
.. image:: https://pepy.tech/badge/yasa
:target: https://pepy.tech/badge/yasa

.. image:: https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json
:target: https://github.com/astral-sh/ruff
:alt: Ruff

----------------

.. figure:: /docs/pictures/yasa_logo.png
Expand Down Expand Up @@ -48,6 +52,15 @@ Alternatively, YASA can be installed with conda:
conda config --set channel_priority strict
conda install yasa

To build and install from source, clone this repository or download the source archive and decompress the files

.. code-block:: shell

cd yasa
pip install ".[test]" # install the package
pip install --editable ".[test]" # or editable install
pytest # test the package

**What are the prerequisites for using YASA?**

To use YASA, all you need is:
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2 changes: 0 additions & 2 deletions codecov.yml
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4 changes: 3 additions & 1 deletion docs/conf.py
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Expand Up @@ -3,9 +3,11 @@
import os
import sys
import time
import yasa

import sphinx_bootstrap_theme

import yasa

# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
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4 changes: 2 additions & 2 deletions docs/contributing.rst
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Expand Up @@ -12,11 +12,11 @@ Code guidelines

Before starting new code, we highly recommend opening an issue on `GitHub <https://github.com/raphaelvallat/yasa>`_ to discuss potential changes.

* Please use standard `pep8 <https://pypi.python.org/pypi/pep8>`_ and `flake8 <http://flake8.pycqa.org/>`_ Python style guidelines. To test that your code complies with those, you can run:
* Please use standard `pep8 <https://pypi.python.org/pypi/pep8>`_ and `flake8 <http://flake8.pycqa.org/>`_ Python style guidelines. YASA uses `ruff <https://github.com/astral-sh/ruff>`_ for code formatting. Before submitting a PR, please make sure to run the following command in the root folder of YASA:

.. code-block:: bash

$ flake8
$ ruff format --line-length=100

* Use `NumPy style <https://numpydoc.readthedocs.io/en/latest/format.html>`_ for docstrings. Follow existing examples for simplest guidance.

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13 changes: 13 additions & 0 deletions docs/index.rst
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Expand Up @@ -14,6 +14,10 @@
.. image:: https://pepy.tech/badge/yasa
:target: https://pepy.tech/badge/yasa

.. image:: https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json
:target: https://github.com/astral-sh/ruff
:alt: Ruff

----------------

.. figure:: /pictures/yasa_logo.png
Expand Down Expand Up @@ -48,6 +52,15 @@ Alternatively, YASA can be installed with conda:
conda config --set channel_priority strict
conda install yasa

To build and install from source, clone this repository or download the source archive and decompress the files

.. code-block:: shell

cd yasa
pip install ".[test]" # install the package
pip install -e ".[test]" # or editable install
pytest # test the package

**What are the prerequisites for using YASA?**

To use YASA, all you need is:
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6 changes: 6 additions & 0 deletions push_pypi.md
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# Build and upload a new version of YASA

```bash
python -m build
twine upload dist/yasa-<VERSION>
```
134 changes: 131 additions & 3 deletions pyproject.toml
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[tool.black]
[build-system]
requires = ["setuptools>=70.0", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "yasa"
description = "YASA: Analysis of polysomnography recordings."
readme = "README.rst"
license = {text = "BSD (3-clause)"}
authors = [
{name = "Raphael Vallat", email = "[email protected]"},
{name = "Remington Mallett", email = "[email protected]"},
]
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maintainers = [
{name = "Raphael Vallat", email = "[email protected]"},
{name = "Remington Mallett", email = "[email protected]"},
]
classifiers = [
"Intended Audience :: Science/Research",
"Operating System :: MacOS",
"Operating System :: POSIX",
"Operating System :: Unix",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
]
dynamic = ["version"]
requires-python = ">=3.9"
dependencies = [
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Given the failure on python v3.12, should we change this to >=3.9, <3.12?

I think we should go forward as-is without >3.11 support, but given that Python currently supports versions up to 3.13, I would like to not fall that far behind. Maybe I can add a PR on lspopt about this? We could be patient about a fix and then come up with an alternate plan if need be.

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I would keep support for 3.12. I'll investigate the lspopt issue now

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Problem solved here as well. Just needed to add setuptools to the dependencies.

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Note that this still creates a DeprecationWarning in the tests. We should update lspopt at some point:

=============================== warnings summary ===============================
../../../../../opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/site-packages/lspopt/data/__init__.py:11
  /opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/site-packages/lspopt/data/__init__.py:11: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
    from pkg_resources import resource_filename

"numpy>=1.18.1",
"scipy",
"pandas",
"matplotlib",
"seaborn",
"mne>=1.3",
"numba>=0.57.1",
"antropy",
"scikit-learn",
"tensorpac>=0.6.5",
"pyriemann>=0.2.7",
"sleepecg>=0.5.0",
"setuptools>=70",
"lspopt",
"ipywidgets",
"joblib",
"lightgbm",
]

[project.optional-dependencies]
test = [
"pytest>=6",
"pytest-cov",
# Ensure coverage is new enough for `source_pkgs`.
"coverage[toml]>=5.3",
"ruff"
]
docs = [
"sphinx>7.0.0",
"pydata_sphinx_theme",
"numpydoc",
"sphinx-copybutton",
"sphinx-design",
"sphinx-notfound-page",
]

[project.urls]
Homepage = "https://github.com/raphaelvallat/yasa/"
Downloads = "https://github.com/raphaelvallat/yasa/"

[tool.setuptools]
py-modules = ["yasa"]
include-package-data = true

[tool.setuptools.package-data]
yasa = [
"classifiers/*.joblib",
]

[tool.setuptools.packages.find]
namespaces = false
where = ["src"]

[tool.setuptools.dynamic]
version = {attr = "yasa.__version__"}

[tool.pytest.ini_options]
minversion = "6.0"
addopts = "--showlocals --durations=10 --maxfail=2 --cov"
doctest_optionflags= ["NORMALIZE_WHITESPACE", "IGNORE_EXCEPTION_DETAIL"]
filterwarnings = [
"ignore::UserWarning",
"ignore::RuntimeWarning",
"ignore::FutureWarning",
]
markers = ["slow"]

[tool.coverage.run]
branch = true
omit = [
"*/tests/*",
]
source_pkgs = ["yasa"]

[tool.coverage.paths]
source = ["src"]

[tool.coverage.report]
show_missing = true
# sort = "Cover"

[tool.ruff]
line-length = 100
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target-version = ['py311']
include = '\.pyi?$'
target-version = "py311"
# Enable Pyflakes (`F`) and a subset of the pycodestyle (`E`) codes by default.
# Unlike Flake8, Ruff doesn't enable pycodestyle warnings (`W`) or
# McCabe complexity (`C901`) by default.
lint.select = ["E4", "E7", "E9", "F", "I", "NPY201"]
exclude = [
"notebooks", # Skip jupyter notebook examples
"docs",
]

[tool.ruff.lint.per-file-ignores]
"__init__.py" = ["F401", "F403"] # Ignore star and unused import violations for __init__.py files

[tool.ruff.lint.pydocstyle]
convention = "numpy"

[tool.ruff.format]
docstring-code-format = false
docstring-code-line-length = 90
4 changes: 0 additions & 4 deletions requirements-test.txt
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16 changes: 0 additions & 16 deletions requirements.txt
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