Move from setup.py to pyproject.toml

.github/workflows/core-test.yml

@@ -20,13 +20,9 @@ jobs:
       matrix:
         os: ["ubuntu-latest", "windows-latest"]
         # "macos-latest",
-        python-version: ['3.7', '3.8', '3.9', '3.10']
-        numpy-version: ['1.18.5', '1.19.5', '1.20.3', '1.21.6', '1.22.4', '1.23.0']
+        python-version: ['3.8', '3.9', '3.10']
+        numpy-version: [ '1.20.3', '1.21.6', '1.22.4', '1.23.4']
         exclude:
-           - python-version: '3.7'
-             numpy-version: '1.22.4'
-           - python-version: '3.7'
-             numpy-version: '1.23.0'
            - python-version: '3.10'
              numpy-version: '1.18.5'
            - python-version: '3.10'

.github/workflows/io-test.yml

@@ -19,7 +19,7 @@ jobs:
       matrix:
         # "macos-latest", "windows-latest"
         os: ["ubuntu-latest", ]
-        python-version: ['3.8', ]
+        python-version: ['3.9', ]
     defaults:
       # by default run in bash mode (required for conda usage)
       run:
@@ -59,7 +59,7 @@ jobs:
         id: cache-conda-env
         with:
           path: /usr/share/miniconda/envs/neo-test-env
-          key: ${{ runner.os }}-conda-env-${{ hashFiles('**/requirements.txt') }}-${{ hashFiles('**/requirements_testing.txt') }}-${{ hashFiles('**/environment_testing.txt') }}-${{ steps.date.outputs.date }}
+          key: ${{ runner.os }}-conda-env-${{ hashFiles('**/pyproject.toml') }}-${{ steps.date.outputs.date }}
 
       - name: Install testing dependencies
         # testing environment is only installed if no cache was found
@@ -75,6 +75,7 @@ jobs:
       - name: Install neo
         run: |
           pip install --upgrade -e .
+          pip install .[test]
 
       - name: Test with pytest
         run: |

.readthedocs.yaml

@@ -12,4 +12,6 @@ python:
   install:
     - method: pip
       path: .
-    - requirements: doc/requirements_docs.txt
+      extra_requirements:
+        - docs
+

doc/source/conf.py

@@ -13,17 +13,16 @@
 
 import os
 import sys
+import re
 
 from packaging.version import Version
 
-with open("../../neo/version.py") as fp:
-    d = {}
-    exec(fp.read(), d)
-    neo_release = d['version']
+with open('../../pyproject.toml', mode='r') as f:
+    txt = f.read()
+    neo_release = re.findall('version = "(\S+)"', txt)[0]
 
 neo_version = '.'.join((str(e) for e in Version(neo_release).release[:2]))
 
-
 AUTHORS = 'Neo authors and contributors <[email protected]>'
 
 # If extensions (or modules to document with autodoc) are in another directory,

environment_testing.yml

@@ -4,5 +4,3 @@ channels:
 dependencies:
   - datalad
   - pip
-  - pip:
-    - -r requirements_testing.txt

neo/__init__.py

@@ -2,6 +2,9 @@
 Neo is a package for representing electrophysiology data in Python,
 together with support for reading a wide range of neurophysiology file formats
 '''
+import importlib.metadata
+# this need to be at the begining because some sub module will need the version
+__version__ = importlib.metadata.version("neo")
 
 import logging
 
@@ -10,4 +13,3 @@
 from neo.core import *
 from neo.io import *
 
-from neo.version import version as __version__

neo/io/nixio.py

@@ -37,7 +37,7 @@
                     IrregularlySampledSignal, Epoch, Event, SpikeTrain,
                     ImageSequence, ChannelView, Group)
 from ..io.proxyobjects import BaseProxy
-from ..version import version as neover
+from .. import __version__ as neover
 
 
 datetime_types = (date, time, datetime)

pyproject.toml

@@ -0,0 +1,80 @@
+[project]
+name = "neo"
+version = "0.12.0.dev0"
+
+authors = [{name = "Neo authors and contributors"}]
+
+description = "Neo is a package for representing electrophysiology data in Python, together with support for reading a wide range of neurophysiology file formats"
+
+readme = "README.rst"
+requires-python = ">=3.7"
+license = {text = "BSD 3-Clause License"}
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Operating System :: OS Independent",
+    "Intended Audience :: Science/Research",
+    "Natural Language :: English",
+    "Topic :: Scientific/Engineering",
+]
+
+dependencies = [
+    "packaging",
+    "numpy>=1.18.5",
+    "quantities>=0.12.1",
+]
+
+[project.urls]
+"Homepage" = "https://neuralensemble.org/neo"
+
+[build-system]
+requires = ["setuptools>=62.0"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools]
+packages = ["neo"]
+package-dir = {"neo" = "neo"}
+
+[project.optional-dependencies]
+
+test = [
+    "pytest",
+    "pytest-cov",
+
+    # datalad   # this dependency is covered by conda (environment_testing.yml)
+    "scipy>=1.0.0",
+    "pyedflib",
+    "h5py",
+    "igor",
+    "klusta",
+    "tqdm",
+    "nixio",
+    "matplotlib",
+    "ipython",
+    "coverage",
+    "coveralls",
+    "pillow",
+    "sonpy",
+    "pynwb",
+    "probeinterface",
+]
+
+docs = [
+    "docutils<0.18",
+]
+
+igorproio = ['igor']
+kwikio = ['klusta']
+neomatlabio = ['scipy>=1.0.0']
+nixio = ['nixio>=1.5.0']
+stimfitio = ['stfio']
+tiffio = ['pillow']
+edf = ['pyedflib']
+ced = ['sonpy']
+nwb = ['pynwb']
+maxwell = ['h5py']
+biocam = ['h5py']
+
+# TODO [all]
+
+
+

setup.py

@@ -1,58 +1,4 @@
-#!/usr/bin/env python
+import setuptools
 
-from setuptools import setup, find_packages
-import os
-
-long_description = open("README.rst").read()
-install_requires = ['packaging',
-                    'numpy>=1.18.5',
-                    'quantities>=0.12.1']
-extras_require = {
-    'igorproio': ['igor'],
-    'kwikio': ['klusta'],
-    'neomatlabio': ['scipy>=1.0.0'],
-    'nixio': ['nixio>=1.5.0'],
-    'stimfitio': ['stfio'],
-    'tiffio': ['pillow'],
-    'edf': ['pyedflib'],
-    'ced': ['sonpy'],
-    'nwb': ['pynwb'],
-    'maxwell': ['h5py'],
-    'biocam': ['h5py'],
-}
-extras_require["all"] = sum(extras_require.values(), [])
-
-with open("neo/version.py") as fp:
-    d = {}
-    exec(fp.read(), d)
-    neo_version = d['version']
-
-setup(
-    name="neo",
-    version=neo_version,
-    packages=find_packages(),
-    install_requires=install_requires,
-    extras_require=extras_require,
-    author="Neo authors and contributors",
-    author_email="[email protected]",
-    description="Neo is a package for representing electrophysiology data in "
-                "Python, together with support for reading a wide range of "
-                "neurophysiology file formats",
-    long_description=long_description,
-    license="BSD-3-Clause",
-    url='https://neuralensemble.org/neo',
-    python_requires=">=3.7",
-    classifiers=[
-        'Development Status :: 4 - Beta',
-        'Intended Audience :: Science/Research',
-        'License :: OSI Approved :: BSD License',
-        'Natural Language :: English',
-        'Operating System :: OS Independent',
-        'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.7',
-        'Programming Language :: Python :: 3.8',
-        'Programming Language :: Python :: 3.9',
-        'Programming Language :: Python :: 3.10',
-        'Programming Language :: Python :: 3 :: Only',
-        'Topic :: Scientific/Engineering']
-)
+if __name__ == "__main__":
+    setuptools.setup()