Move towards pyproject.toml standard (#955)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Cody Baker <[email protected]>

.readthedocs.yaml

@@ -17,7 +17,6 @@ sphinx:
 # Python requirements required to build your docs
 python:
   install:
-    - requirements: requirements-minimal.txt
     - method: pip
       path: .
       extra_requirements:

CHANGELOG.md

@@ -3,6 +3,7 @@
 ### Improvements
 
 * The `OpenEphysBinaryRecordingInterface` now uses `lxml` for extracting the session start time from the settings.xml file and does not depend on `pyopenephys` anymore. [PR #971](https://github.com/catalystneuro/neuroconv/pull/971)
+* Swap the majority of package setup and build steps to `pyproject.toml` instead of `setup.py`. [PR #955](https://github.com/catalystneuro/neuroconv/pull/955)
 * The `DeeplabcutInterface` now skips inferring timestamps from movie when timestamps are specified, running faster. [PR #967](https://github.com/catalystneuro/neuroconv/pull/967)
 
 

pyproject.toml

@@ -1,3 +1,90 @@
+[build-system]
+requires = ["setuptools>=52", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "neuroconv"
+version = "0.5.1"
+description = "Convert data from proprietary formats to NWB format."
+readme = "README.md"
+authors = [
+    {name = "Cody Baker"},
+    {name = "Szonja Weigl"},
+    {name = "Heberto Mayorquin"},
+    {name = "Luiz Tauffer"},
+    {name = "Ben Dichter",  email = "[email protected]"}
+]
+urls = { "Homepage" = "https://github.com/catalystneuro/neuroconv" }
+license = {file = "license.txt"}
+keywords = ["nwb"]
+classifiers = [
+    "Intended Audience :: Science/Research",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Operating System :: POSIX :: Linux",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: MacOS",
+    "License ::  BSD-3-Clause ",
+]
+requires-python = ">=3.9"
+dependencies = [
+    "numpy>=1.22.0; python_version <= '3.11'",
+    "numpy>=1.26.0; python_version >= '3.12'",
+    "jsonschema>=3.2.0",
+    "PyYAML>=5.4",
+    "scipy>=1.4.1",
+    "h5py>=3.9.0",
+    "hdmf>=3.13.0",
+    "hdmf_zarr>=0.7.0",
+    "pynwb>=2.7.0",
+    "pydantic>=2.0.0",
+    "typing_extensions>=4.1.0",
+    "psutil>=5.8.0",
+    "tqdm>=4.60.0",
+    "pandas",
+    "parse>=1.20.0",
+    "click",
+    "docstring-parser",
+    "packaging"  # Issue 903
+]
+
+
+[project.optional-dependencies]
+test = [
+    "pytest",
+    "pytest-cov",
+    "ndx-events>=0.2.0",  # for special tests to ensure load_namespaces is set to allow NWBFile load at all times
+    "parameterized>=0.8.1",
+    "ndx-miniscope",
+    "spikeinterface[qualitymetrics]>=0.100.0",
+    "zarr<2.18.0",  # Error with Blosc (read-only during decode) in numcodecs on May 7; check later if resolved
+    "pytest-xdist"
+]
+
+docs = [
+    "Jinja2<3.1",
+    "Sphinx==5.1.1",
+    "sphinx_rtd_theme==1.0.0",
+    "readthedocs-sphinx-search==0.1.2",
+    "sphinx-toggleprompt==0.2.0",
+    "sphinx-copybutton==0.5.0",
+    "roiextractors",  # Needed for the API documentation
+    "spikeinterface",  # Needed for the API documentation
+    "pydata_sphinx_theme==0.12.0"
+]
+dandi = ["dandi>=0.58.1"]
+compressors = ["hdf5plugin"]
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+
+[project.scripts]
+neuroconv = "neuroconv.tools.yaml_conversion_specification._yaml_conversion_specification:run_conversion_from_yaml_cli"
+
+
 [tool.pytest.ini_options]
 minversion = "6.0"
 addopts = "-ra --doctest-glob='*.rst'"

setup.py

@@ -4,93 +4,52 @@
 from pathlib import Path
 from shutil import copy
 
-from setuptools import find_packages, setup
+from setuptools import setup
 
 root = Path(__file__).parent
 
-with open(root / "README.md") as f:
-    long_description = f.read()
-with open(root / "requirements-minimal.txt") as f:
-    install_requires = f.readlines()
-with open(root / "requirements-rtd.txt") as f:
-    documentation_dependencies = f.readlines()
-with open(root / "requirements-testing.txt") as f:
-    testing_suite_dependencies = f.readlines()
 
-extras_require = defaultdict(list)
+def read_requirements(file):
+    with open(root / file) as f:
+        return f.readlines()
+
 
-extras_require["dandi"].append("dandi>=0.58.1")
-extras_require["full"].extend(extras_require["dandi"])
+extras_require = defaultdict(list)
+extras_require["full"] = ["dandi>=0.58.1", "hdf5plugin"]
 
-extras_require.update(compressors=["hdf5plugin"])
-extras_require["full"].extend(["hdf5plugin"])
 
-extras_require.update(test=testing_suite_dependencies, docs=documentation_dependencies)
 for modality in ["ophys", "ecephys", "icephys", "behavior", "text"]:
     modality_path = root / "src" / "neuroconv" / "datainterfaces" / modality
     modality_requirement_file = modality_path / "requirements.txt"
     if modality_requirement_file.exists():
-        with open(modality_requirement_file) as f:
-            modality_requirements = f.readlines()
-            extras_require["full"].extend(modality_requirements)
-            extras_require[modality].extend(modality_requirements)
+        modality_requirements = read_requirements(modality_requirement_file)
+        extras_require["full"].extend(modality_requirements)
+        extras_require[modality] = modality_requirements
     else:
-        modality_requirements = list()
+        modality_requirements = []
 
     format_subpaths = [path for path in modality_path.iterdir() if path.is_dir() and path.name != "__pycache__"]
     for format_subpath in format_subpaths:
         format_requirement_file = format_subpath / "requirements.txt"
-        extras_require[format_subpath.name].extend(modality_requirements)
+        extras_require[format_subpath.name] = modality_requirements.copy()
         if format_requirement_file.exists():
-            with open(format_requirement_file) as f:
-                format_requirements = f.readlines()
-                extras_require["full"].extend(format_requirements)
-                extras_require[modality].extend(format_requirements)
-                extras_require[format_subpath.name].extend(format_requirements)
+            format_requirements = read_requirements(format_requirement_file)
+            extras_require["full"].extend(format_requirements)
+            extras_require[modality].extend(format_requirements)
+            extras_require[format_subpath.name].extend(format_requirements)
 
 # Create a local copy for the gin test configuration file based on the master file `base_gin_test_config.json`
-gin_config_file_base = Path("./base_gin_test_config.json")
-gin_config_file_local = Path("./tests/test_on_data/gin_test_config.json")
+gin_config_file_base = root / "base_gin_test_config.json"
+gin_config_file_local = root / "tests/test_on_data/gin_test_config.json"
 if not gin_config_file_local.exists():
     copy(src=gin_config_file_base, dst=gin_config_file_local)
 
 # Bug related to sonpy on M1 Mac being installed but not running properly
 if sys.platform == "darwin" and platform.processor() == "arm":
-    extras_require.pop("spike2")
-
-    extras_require["ecephys"].remove(
-        next(requirement for requirement in extras_require["ecephys"] if "sonpy" in requirement)
-    )
-    extras_require["full"].remove(next(requirement for requirement in extras_require["full"] if "sonpy" in requirement))
+    extras_require.pop("spike2", None)
+    extras_require["ecephys"] = [req for req in extras_require["ecephys"] if "sonpy" not in req]
+    extras_require["full"] = [req for req in extras_require["full"] if "sonpy" not in req]
 
 setup(
-    name="neuroconv",
-    version="0.5.1",
-    description="Convert data from proprietary formats to NWB format.",
-    long_description=long_description,
-    long_description_content_type="text/markdown",
-    author="Cody Baker, Szonja Weigl, Heberto Mayorquin, Luiz Tauffer, and Ben Dichter.",
-    author_email="[email protected]",
-    url="https://github.com/catalystneuro/neuroconv",
-    keywords="nwb",
-    license_files=("license.txt",),
-    packages=find_packages(where="src"),
-    package_dir={"": "src"},
-    include_package_data=True,  # Includes files described in MANIFEST.in in the installation.
-    python_requires=">=3.9",
-    install_requires=install_requires,
     extras_require=extras_require,
-    entry_points={
-        "console_scripts": [
-            "neuroconv = neuroconv.tools.yaml_conversion_specification._yaml_conversion_specification:run_conversion_from_yaml_cli",
-        ],
-    },
-    license="BSD-3-Clause",
-    classifiers=[
-        "Intended Audience :: Science/Research",
-        "Programming Language :: Python :: 3.9",
-        "Programming Language :: Python :: 3.10",
-        "Programming Language :: Python :: 3.11",
-        "Programming Language :: Python :: 3.12",
-    ],
 )

tests/test_on_data/test_metadata/test_maxwell_metadata.py

@@ -4,10 +4,10 @@
 from platform import system
 from shutil import rmtree
 from tempfile import mkdtemp
+from zoneinfo import ZoneInfo
 
 import pytest
 from hdmf.testing import TestCase
-from zoneinfo import ZoneInfo
 
 from neuroconv.datainterfaces import MaxOneRecordingInterface