Merge pull request #2 from CINPLA/modernize

Modernize and release

.github/workflows/full_tests.yml

@@ -0,0 +1,26 @@
+name: Test on Ubuntu
+
+on:
+  pull_request:
+      branches: [dev]
+      types: [synchronize, opened, reopened]
+
+
+jobs:
+  build-and-test:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.10"
+    - name: Install package
+      run: |
+        python -m pip install --upgrade pip
+        pip install .[test]
+    - name: Pytest
+      run: |
+        pytest -v

.github/workflows/publish-to-pypi.yml

@@ -0,0 +1,28 @@
+name: Release to PyPI
+
+on:
+  push:
+    tags:
+       - '*'
+jobs:
+  release:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.10"
+    - name: Install Tools
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine build
+    - name: Package and Upload
+      env:
+        STACKMANAGER_VERSION: ${{ github.event.release.tag_name }}
+        TWINE_USERNAME: __token__
+        TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
+      run: |
+        python -m build --sdist --wheel
+        twine upload dist/*

.pre-commit-config.yaml

@@ -0,0 +1,32 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: fix-encoding-pragma
+        exclude: tests/test_data
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-docstring-first
+      - id: debug-statements
+      - id: check-toml
+      - id: check-yaml
+      - id: requirements-txt-fixer
+      - id: detect-private-key
+      - id: check-merge-conflict
+
+  - repo: https://github.com/psf/black
+    rev: 24.4.2
+    hooks:
+      - id: black
+      - id: black-jupyter
+
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+        args: ["--profile", "black"]
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.4
+    hooks:
+      - id: ruff

pyproject.toml

@@ -0,0 +1,59 @@
+[project]
+name = "head_direction"
+version = "0.1.0"
+authors = [
+    { name = "Mikkel Lepperod", email = "[email protected]" },
+    { name = "Alessio Buccino", email = "[email protected]" },
+]
+
+description = "Analysis of head direction cells."
+readme = "README.md"
+requires-python = ">=3.10"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+]
+
+dependencies = [
+    "numpy<2",
+    "scipy",
+    "astropy",
+    "pycircstat",
+    "pandas",
+    "elephant",
+    "matplotlib",
+    "nose"
+]
+
+[project.urls]
+homepage = "https://github.com/CINPLA/head-directopm"
+repository = "https://github.com/CINPLA/head-direction"
+
+[build-system]
+requires = ["setuptools>=62.0"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.packages.find]
+where = ["src"]
+include = ["head_direction*"]
+namespaces = false
+
+[project.optional-dependencies]
+dev = ["pre-commit", "black[jupyter]", "isort", "ruff"]
+test = ["pytest", "pytest-cov", "pytest-dependency", "mountainsort5"]
+docs = ["sphinx-gallery", "sphinx_rtd_theme"]
+full = [
+    "head_direction[dev]",
+    "head_direction[test]",
+    "head_direction[docs]",
+]
+
+[tool.coverage.run]
+omit = ["tests/*"]
+
+[tool.black]
+line-length = 120

setup.py

@@ -1,31 +1,6 @@
 # -*- coding: utf-8 -*-
-from setuptools import setup
-import os
 
-from setuptools import setup, find_packages
+import setuptools
 
-long_description = open("README.md").read()
-
-install_requires = [
-    'numpy>=1.9',
-    'scipy',
-    'astropy',
-    'pandas>=0.14.1',
-    'elephant',
-    'matplotlib']
-extras_require = {
-    'testing': ['pytest'],
-    'docs': ['numpydoc>=0.5',
-             'sphinx>=1.2.2',
-             'sphinx_rtd_theme']
-}
-
-setup(
-    name="head_direction",
-    install_requires=install_requires,
-    tests_require=install_requires,
-    extras_require=extras_require,
-    packages=find_packages(),
-    include_package_data=True,
-    version='0.1',
-)
+if __name__ == "__main__":
+    setuptools.setup()

src/head_direction/__init__.py

@@ -0,0 +1,4 @@
+# -*- coding: utf-8 -*-
+from .head import head_direction as head_direction
+from .head import head_direction_rate as head_direction_rate
+from .head import head_direction_score as head_direction_score

head_direction/head.py → src/head_direction/head.py

@@ -1,9 +1,10 @@
+# -*- coding: utf-8 -*-
 import numpy as np
+
 from .tools import moving_average
 
 
-def head_direction_rate(spike_train, head_angles, t,
-                        n_bins=36, avg_window=4):
+def head_direction_rate(spike_train, head_angles, t, n_bins=36, avg_window=4):
     """
     Calculeate firing rate at head direction in binned head angles for time t.
     Moving average filter is applied on firing rate
@@ -37,7 +38,7 @@ def head_direction_rate(spike_train, head_angles, t,
     spikes_in_ang, _ = np.histogram(head_angles, weights=spikes_in_bin, bins=ang_bins)
     time_in_ang, _ = np.histogram(head_angles, weights=time_in_bin, bins=ang_bins)
 
-    with np.errstate(divide='ignore', invalid='ignore'):
+    with np.errstate(divide="ignore", invalid="ignore"):
         rate_in_ang = np.divide(spikes_in_ang, time_in_ang)
     rate_in_ang = moving_average(rate_in_ang, avg_window)
     return ang_bins[:-1], rate_in_ang
@@ -59,8 +60,8 @@ def head_direction_score(head_angle_bins, rate):
     out : float, float
         mean angle, mean vector length
     """
-    import math
     import pycircstat as pc
+
     nanIndices = np.where(np.isnan(rate))
     head_angle_bins = np.delete(head_angle_bins, nanIndices)
     mean_ang = pc.mean(head_angle_bins, w=rate)
@@ -69,7 +70,7 @@ def head_direction_score(head_angle_bins, rate):
     return mean_ang, mean_vec_len
 
 
-def head_direction(x1, y1, x2, y2, t, filt=2.):
+def head_direction(x1, y1, x2, y2, t, filt=2.0):
     """
     Calculeate head direction in angles or radians for time t
 
@@ -98,7 +99,7 @@ def head_direction(x1, y1, x2, y2, t, filt=2.):
     r = np.linalg.norm(dr, axis=0)
     r_mean = np.mean(r)
     r_std = np.std(r)
-    mask = (r > r_mean - filt*r_std)
+    mask = r > r_mean - filt * r_std
     x1 = x1[mask]
     y1 = y1[mask]
     x2 = x2[mask]

head_direction/tools.py → src/head_direction/tools.py

@@ -1,9 +1,9 @@
+# -*- coding: utf-8 -*-
 import numpy as np
-import scipy.signal as sig
 
 
 def unit_vector(v):
-    """ Return unit vector of v
+    """Return unit vector of v
     modified from David Wolever,
     https://stackoverflow.com/questions/2827393/angles
     -between-two-n-dimensional-vectors-in-python
@@ -47,11 +47,11 @@ def moving_average(vector, N):
     if N * 2 > len(vector):
         raise ValueError('Window must be at least half of "len(vector)"')
     vector = np.concatenate((vector[-N:], vector, vector[:N]))
-    return np.convolve(vector, np.ones((N,)) / N, mode='same')[N:-N]
+    return np.convolve(vector, np.ones((N,)) / N, mode="same")[N:-N]
 
 
 def angle_between_vectors(v1, v2):
-    """ Returns the angle in radians between vectors 'v1' and 'v2'
+    """Returns the angle in radians between vectors 'v1' and 'v2'
     modified from David Wolever,
     https://stackoverflow.com/questions/2827393/angles
     -between-two-n-dimensional-vectors-in-python

head_direction/tests/test_head.py → tests/test_head.py

@@ -1,75 +1,74 @@
-import pytest
+# -*- coding: utf-8 -*-
 import numpy as np
-import math
+
+from head_direction.head import (
+    head_direction,
+    head_direction_rate,
+    head_direction_score,
+)
+
 
 def test_head_direction_45():
-    from head_direction.head import head_direction
-    x1 = np.linspace(.01,1,10)
+    x1 = np.linspace(0.01, 1, 10)
     y1 = x1
-    x2 = x1 + .01 # 1cm between
-    y2 = x1 - .01
+    x2 = x1 + 0.01  # 1cm between
+    y2 = x1 - 0.01
     t = x1
     a, t = head_direction(x1, y1, x2, y2, t)
     assert np.allclose(a, np.pi / 4)
 
 
 def test_head_direction_135():
-    from head_direction.head import head_direction
-    x1 = np.linspace(.01,1,10)[::-1]
+    x1 = np.linspace(0.01, 1, 10)[::-1]
     y1 = x1[::-1]
-    x2 = x1 - .01 # 1cm between
-    y2 = y1 - .01
+    x2 = x1 - 0.01  # 1cm between
+    y2 = y1 - 0.01
     t = x1
     a, t = head_direction(x1, y1, x2, y2, t)
     assert np.allclose(a, np.pi - np.pi / 4)
 
 
 def test_head_direction_225():
-    from head_direction.head import head_direction
-    x1 = np.linspace(.01,1,10)[::-1]
+    x1 = np.linspace(0.01, 1, 10)[::-1]
     y1 = x1
-    x2 = x1 - .01 # 1cm between
-    y2 = y1 + .01
+    x2 = x1 - 0.01  # 1cm between
+    y2 = y1 + 0.01
     t = x1
     a, t = head_direction(x1, y1, x2, y2, t)
     assert np.allclose(a, np.pi + np.pi / 4)
 
 
 def test_head_direction_reverse_315():
-    from head_direction.head import head_direction
-    x1 = np.linspace(.01,1,10)
+    x1 = np.linspace(0.01, 1, 10)
     y1 = x1[::-1]
-    x2 = x1 + .01 # 1cm between
-    y2 = y1 + .01
+    x2 = x1 + 0.01  # 1cm between
+    y2 = y1 + 0.01
     t = x1
     a, t = head_direction(x1, y1, x2, y2, t)
     assert np.allclose(a, 2 * np.pi - np.pi / 4)
 
 
 def test_head_rate():
-    from head_direction.head import head_direction, head_direction_rate
-    x1 = np.linspace(.01,1,10)
+    x1 = np.linspace(0.01, 1, 10)
     y1 = x1
-    x2 = x1 + .01 # 1cm between
-    y2 = x1 - .01
-    t = np.linspace(0,1,10)
+    x2 = x1 + 0.01  # 1cm between
+    y2 = x1 - 0.01
+    t = np.linspace(0, 1, 10)
     a, t = head_direction(x1, y1, x2, y2, t)
-    sptr = np.linspace(0,1,100)
+    sptr = np.linspace(0, 1, 100)
     bins, rate = head_direction_rate(sptr, a, t, n_bins=8, avg_window=1)
     assert bins[1] == np.pi / 4
-    assert abs(rate[1] - 100) < .5
+    assert abs(rate[1] - 100) < 0.5
 
 
 def test_head_score():
-    from head_direction.head import (
-        head_direction, head_direction_rate, head_direction_score)
-    x1 = np.linspace(.01,1,10)
+    x1 = np.linspace(0.01, 1, 10)
     y1 = x1
-    x2 = x1 + .01 # 1cm between
-    y2 = x1 - .01
-    t = np.linspace(0,1,10)
+    x2 = x1 + 0.01  # 1cm between
+    y2 = x1 - 0.01
+    t = np.linspace(0, 1, 10)
     a, t = head_direction(x1, y1, x2, y2, t)
-    sptr = np.linspace(0,1,100)
+    sptr = np.linspace(0, 1, 100)
     bins, rate = head_direction_rate(sptr, a, t, n_bins=100, avg_window=2)
     ang, score = head_direction_score(bins, rate)
     assert abs(score - 1) < 0.001