Merge pull request #1180 from samuelgarcia/pyproject

Move from setup.py to pyproject.toml

Author: apdavison

.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/requirements_docs.txt

@@ -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,

doc/source/conf.py

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

environment_testing.yml

@@ -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/__init__.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)

neo/io/nixio.py

@@ -0,0 +1,99 @@
+[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 = ">=3.8"
+license = {text = "BSD 3-Clause License"}
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Programming Language :: Python :: 3",
+    "Operating System :: OS Independent",
+    "Intended Audience :: Science/Research",
+    "Natural Language :: English",
+    "Topic :: Scientific/Engineering",
+    "License :: OSI Approved :: BSD License",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3 :: Only",
+]
+
+dependencies = [
+    "packaging",
+    "numpy>=1.19.5",
+    "quantities>=0.14.0",
+]
+
+[project.urls]
+homepage = "https://neuralensemble.org/neo"
+documentation = "http://neo.readthedocs.io/"
+repository = "https://github.com/NeuralEnsemble/python-neo"
+download = "http://pypi.python.org/pypi/neo"
+
+
+[build-system]
+requires = ["setuptools>=62.0"]
+build-backend = "setuptools.build_meta"
+
+[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"]
+
+all = [
+    "coverage",
+    "coveralls",
+    "h5py",
+    "igor",
+    "ipython",
+    "klusta",
+    "matplotlib",
+    "nixio>=1.5.0",
+    "pillow",
+    "probeinterface",
+    "pyedflib",
+    "pynwb",
+    "pytest",
+    "pytest-cov",
+    "scipy>=1.0.0",
+    "sonpy",
+    "tqdm",
+]
+# we do not include 'stfio' in 'all' as it is not pip installable