Modernize package and add actions

.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 +1,36 @@
+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
+        exclude: tests/test_data
+      - id: end-of-file-fixer
+        exclude: tests/test_data
+      - id: check-docstring-first
+      - id: debug-statements
+      - id: check-toml
+      - id: check-yaml
+        exclude: tests/test_data
+      - 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
+        exclude: tests/test_data
+      - 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

examples/tracking_plot.py

@@ -5,10 +5,21 @@
 from scipy.ndimage.measurements import center_of_mass
 
 
-def plot_path(x, y, t, box_size, spike_times=None,
-              color='grey', alpha=0.5, origin='upper',
-              spike_color='r', rate_markersize=False, markersize=10.,
-              animate=False, ax=None):
+def plot_path(
+    x,
+    y,
+    t,
+    box_size,
+    spike_times=None,
+    color="grey",
+    alpha=0.5,
+    origin="upper",
+    spike_color="r",
+    rate_markersize=False,
+    markersize=10.0,
+    animate=False,
+    ax=None,
+):
     """
     Plot path visited
 
@@ -39,8 +50,7 @@ def plot_path(x, y, t, box_size, spike_times=None,
     """
     if ax is None:
         fig = plt.figure()
-        ax = fig.add_subplot(
-            111, xlim=[0, box_size], ylim=[0, box_size], aspect=1)
+        ax = fig.add_subplot(111, xlim=[0, box_size], ylim=[0, box_size], aspect=1)
 
     ax.plot(x, y, c=color, alpha=alpha)
     if spike_times is not None:
@@ -49,20 +59,36 @@ def plot_path(x, y, t, box_size, spike_times=None,
 
         if rate_markersize:
             markersize = spikes_in_bin[is_spikes_in_bin] * markersize
-        ax.scatter(x[:-1][is_spikes_in_bin], y[:-1][is_spikes_in_bin],
-                   facecolor=spike_color, edgecolor=spike_color,
-                   s=markersize)
+        ax.scatter(
+            x[:-1][is_spikes_in_bin],
+            y[:-1][is_spikes_in_bin],
+            facecolor=spike_color,
+            edgecolor=spike_color,
+            s=markersize,
+        )
 
     ax.grid(False)
-    if origin == 'upper':
+    if origin == "upper":
         ax.invert_yaxis()
     return ax
 
 
-def animate_path(x, y, t, box_size, spike_times=None,
-              color='grey', alpha=0.5, origin='upper',
-              spike_color='r', rate_markersize=False, markersize=10.,
-              animate=False, ax=None, title=''):
+def animate_path(
+    x,
+    y,
+    t,
+    box_size,
+    spike_times=None,
+    color="grey",
+    alpha=0.5,
+    origin="upper",
+    spike_color="r",
+    rate_markersize=False,
+    markersize=10.0,
+    animate=False,
+    ax=None,
+    title="",
+):
     """
     Plot path visited
 
@@ -93,35 +119,35 @@ def animate_path(x, y, t, box_size, spike_times=None,
     """
     if ax is None:
         fig = plt.figure()
-        ax = fig.add_subplot(
-            111, xlim=[0, box_size], ylim=[0, box_size], aspect=1)
+        ax = fig.add_subplot(111, xlim=[0, box_size], ylim=[0, box_size], aspect=1)
     if spike_times is not None:
         spikes_in_bin, _ = np.histogram(spike_times, t)
         is_spikes_in_bin = np.array(spikes_in_bin, dtype=bool)
 
         if rate_markersize:
-            markersizes = spikes_in_bin[is_spikes_in_bin]*markersize
+            markersizes = spikes_in_bin[is_spikes_in_bin] * markersize
         else:
-            markersizes = markersize*np.ones(is_spikes_in_bin.size)
+            markersizes = markersize * np.ones(is_spikes_in_bin.size)
     ax.set_title(title)
     ax.grid(False)
-    if origin == 'upper':
+    if origin == "upper":
         ax.invert_yaxis()
     import time
+
     plt.show()
     for idx, x, y, active, msize in zip(range(len(x)), x, y):
         ax.plot(x, y, c=color, alpha=alpha)
         if spike_times is not None:
             if is_spikes_in_bin[idx]:
-                ax.scatter(x, y, facecolor=spike_color, edgecolor=spike_color,
-                           s=markersizes[idx])
+                ax.scatter(x, y, facecolor=spike_color, edgecolor=spike_color, s=markersizes[idx])
         time.sleep(0.1)  # plt.pause(0.0001)
         plt.draw()
     return ax
 
 
-def plot_head_direction_rate(spike_times, ang_bins, rate_in_ang, projection='polar',
-                             normalization=False, ax=None, color='k'):
+def plot_head_direction_rate(
+    spike_times, ang_bins, rate_in_ang, projection="polar", normalization=False, ax=None, color="k"
+):
     """
 
 
@@ -142,26 +168,38 @@ def plot_head_direction_rate(spike_times, ang_bins, rate_in_ang, projection='pol
     out : ax
     """
     import math
+
     if normalization:
-        rate_in_ang = normalize(rate_in_ang, mode='minmax')
+        rate_in_ang = normalize(rate_in_ang, mode="minmax")
     if ax is None:
         fig = plt.figure()
         ax = fig.add_subplot(111, projection=projection)
     bin_size = ang_bins[1] - ang_bins[0]
     if projection is None:
         ax.set_xticks(range(0, 360 + 60, 60))
         ax.set_xlim(0, 360)
-    elif projection == 'polar':
+    elif projection == "polar":
         ang_bins = [math.radians(deg) for deg in ang_bins]
         bin_size = math.radians(bin_size)
         ax.set_xticks([0, np.pi])
     ax.bar(ang_bins, rate_in_ang, width=bin_size, color=color)
     return ax
 
 
-def plot_ratemap(x, y, t, spike_times, bin_size=0.05, box_size=1,
-                 box_size=1, vmin=0, ax=None, smoothing=.05,
-                 origin='upper', cmap='viridis'):
+def plot_ratemap(
+    x,
+    y,
+    t,
+    spike_times,
+    bin_size=0.05,
+    box_size=1,
+    box_size=1,
+    vmin=0,
+    ax=None,
+    smoothing=0.05,
+    origin="upper",
+    cmap="viridis",
+):
     """
 
 
@@ -184,19 +222,17 @@ def plot_ratemap(x, y, t, spike_times, bin_size=0.05, box_size=1,
         fig = plt.figure()
         ax = fig.add_subplot(111, xlim=[0, 1], ylim=[0, 1], aspect=1)
 
-    map = SpatialMap(
-        x, y, t, spike_times, bin_size=bin_size, box_size=box_size)
+    map = SpatialMap(x, y, t, spike_times, bin_size=bin_size, box_size=box_size)
     rate_map = map.rate_map(smoothing)
-    ax.imshow(rate_map, interpolation='none', origin=origin,
-              extent=(0, 1, 0, 1), vmin=vmin, cmap=cmap)
-    ax.set_title('%.2f Hz' % np.nanmax(rate_map))
+    ax.imshow(rate_map, interpolation="none", origin=origin, extent=(0, 1, 0, 1), vmin=vmin, cmap=cmap)
+    ax.set_title("%.2f Hz" % np.nanmax(rate_map))
     ax.grid(False)
     return ax
 
 
-def plot_occupancy(x, y, t, bin_size=0.05, box_size=1, box_size=1,
-                  vmin=0, ax=None, convolve=True,
-                  origin='upper', cmap='jet'):
+def plot_occupancy(
+    x, y, t, bin_size=0.05, box_size=1, box_size=1, vmin=0, ax=None, convolve=True, origin="upper", cmap="jet"
+):
     """
 
 
@@ -219,10 +255,10 @@ def plot_occupancy(x, y, t, bin_size=0.05, box_size=1, box_size=1,
         fig = plt.figure()
         ax = fig.add_subplot(111, xlim=[0, 1], ylim=[0, 1], aspect=1)
 
-    occ_map = occupancy_map(x, y, t, bin_size=bin_size, box_size=box_size,
-                             box_size=box_size, convolve=convolve)
-    cax = ax.imshow(occ_map, interpolation='none', origin=origin,
-                   extent=(0, 1, 0, 1), vmin=vmin, cmap=cmap, aspect='auto')
+    occ_map = occupancy_map(x, y, t, bin_size=bin_size, box_size=box_size, box_size=box_size, convolve=convolve)
+    cax = ax.imshow(
+        occ_map, interpolation="none", origin=origin, extent=(0, 1, 0, 1), vmin=vmin, cmap=cmap, aspect="auto"
+    )
     # ax.set_title('%.2f s' % np.nanmax(occ_map))
     ax.grid(False)
     return cax, np.nanmax(occ_map)

pyproject.toml

@@ -0,0 +1,58 @@
+[project]
+name = "spatial_maps"
+version = "0.2.0"
+authors = [
+    { name = "Mikkel Lepperod", email = "[email protected]" },
+    { name = "Alessio Buccino", email = "[email protected]" },
+]
+
+description = "Compute spatial maps for neural data."
+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",
+    "scikit-image",
+    "astropy",
+    "pandas",
+    "elephant",
+    "matplotlib"
+]
+
+[project.urls]
+homepage = "https://github.com/CINPLA/spatial-maps"
+repository = "https://github.com/CINPLA/spatial-maps"
+
+[build-system]
+requires = ["setuptools>=62.0"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.packages.find]
+where = ["src"]
+include = ["spatial_maps*"]
+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 = [
+    "spatial_maps[dev]",
+    "spatial_maps[test]",
+    "spatial_maps[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="spatial_maps",
-    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()