Swap to pyproject.toml setup (#507)

CodyCBakerPhD · CodyCBakerPhD · stephprince · web-flow · commit 42667563419d · 2024-09-17T13:42:24.000-04:00
* swap to pyproject.toml

* changelog

* remove

* center README logo and badges; fix logo link in README so will show up in PyPI

* remove 3.8 from testing

* add changelog mention

* fix import

* fix import

* fix import; remove ros3 install; use hatchling instead of setuptools

* Update pyproject.toml

Co-authored-by: Steph Prince &lt;40640337+stephprince@users.noreply.github.com&gt;

* Update pyproject.toml

Co-authored-by: Steph Prince &lt;40640337+stephprince@users.noreply.github.com&gt;

* Update pyproject.toml

---------

Co-authored-by: CodyCBakerPhD &lt;codycbakerphd@gmail.com&gt;
Co-authored-by: Steph Prince &lt;40640337+stephprince@users.noreply.github.com&gt;
diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
@@ -31,8 +31,6 @@ jobs:
           pip install pytest
           pip install pytest-cov
 
-      - name: Install ROS3
-        run: conda install -c conda-forge h5py
       - name: Install package
         run: pip install ".[dandi]"
       - name: Download testing data and set config path
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,6 +10,8 @@
 * Removed the `robust_ros3_read` utility helper. [#506](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/506)
 * Simplified the `nwbinspector.testing` configuration framework. [#509](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/509)
 * Cleaned old references to non-recent PyNWB and HDMF versions. Current policy is that latest NWB Inspector releases should only support compatibility with latest PyNWB and HDMF. [#510](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/510)
+* Swapped setup approach to the modern `pyproject.toml` standard. [#507](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/507)
+
 
 
 
diff --git a/README.md b/README.md
@@ -1,18 +1,40 @@
-<img src="docs/logo/logo.png" width="300">
+<p align="center">
+  <img src="https://raw.githubusercontent.com/neurodatawithoutborders/nwbinspector/dev/docs/logo/logo.png" width="250" alt="NWB Inspector logo"/>
+
+  <p align="center">
+    <a href="https://pypi.org/project/dandi_s3_log_parser/"><img alt="Supported Python versions" src="https://img.shields.io/pypi/pyversions/nwbinspector.svg"></a>
+    <a href="https://codecov.io/github/CatalystNeuro/dandi_s3_log_parser?branch=main"><img alt="codecov" src="https://codecov.io/github/NeurodataWithoutBorders/nwbinspector/coverage.svg?branch=main"></a>
+  </p>
+  <p align="center">
+    <a href="https://pypi.org/project/nwbinpsector/"><img alt="PyPI latest release version" src="https://badge.fury.io/py/nwbinspector.svg?id=py&kill_cache=1"></a>
+    <a href="https://github.com/NeurodataWithoutBorders/nwbinspector/blob/dev/license.txt"><img alt="License: BSD-3" src="https://img.shields.io/pypi/l/nwbinspector.svg"></a>
+  </p>
+  <p align="center">
+    <a href="https://github.com/psf/black"><img alt="Python code style: Black" src="https://img.shields.io/badge/python_code_style-black-000000.svg"></a>
+    <a href="https://github.com/astral-sh/ruff"><img alt="Python code style: Ruff" src="https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json"></a>
+  </p>
+  <p align="center">
+    <a href="https://nwbinspector.readthedocs.io/"><img alt="Documentation build status" src="https://readthedocs.org/projects/nwbinspector/badge/?version=dev"></a>
+    <a href="https://github.com/NeurodataWithoutBorders/nwbinspector/actions/workflows/dailies.yml/badge.svg"><img alt="Daily tests" src="https://github.com/NeurodataWithoutBorders/nwbinspector/actions/workflows/dailies.yml/badge.svg"></a>
+  </p>
+</p>
+
+Inspect NWB files for compliance with [NWB Best Practices](https://nwbinspector.readthedocs.io/en/dev/best_practices/best_practices_index.html).
+
+This inspector is meant as a companion to the PyNWB validator, which checks for strict schema compliance. This tool attempts to apply some common sense to find components of the file that are technically compliant, but possibly incorrect, suboptimal in their representation, or deviate from best practices.
+
+This tool is meant simply as a data review aid. It does not catch all possible violations of best practices and any warnings it does produce should be checked by a knowledgeable reviewer.
 
-[![PyPI version](https://badge.fury.io/py/nwbinspector.svg)](https://badge.fury.io/py/nwbinspector)
-[![ReadTheDocs](https://readthedocs.org/projects/nwbinspector/badge/?version=dev)](https://nwbinspector.readthedocs.io/)
-![Tests](https://github.com/NeurodataWithoutBorders/nwbinspector/actions/workflows/dailies.yml/badge.svg)
-[![codecov](https://codecov.io/gh/NeurodataWithoutBorders/nwbinspector/branch/dev/graphs/badge.svg?branch=dev)](https://codecov.io/github/NeurodataWithoutBorders/nwbinspector?branch=dev)
-[![License](https://img.shields.io/pypi/l/nwbinspector.svg)](https://github.com/NeurodataWithoutBorders/nwbinspector/blob/dev/license.txt)
 
-Inspect NWB files for compliance with [NWB Best Practices](https://nwbinspector.readthedocs.io/en/dev/best_practices/best_practices_index.html). This inspector is meant as a companion to the PyNWB validator, which checks for strict schema compliance. In contrast, this tool attempts to apply some common sense to find components of the file that are technically compliant, but possibly incorrect, suboptimal in their representation, or deviate from best practices. This tool is meant simply as a data review aid. It does not catch all best practice violations, and any warnings it does produce should be checked by a knowledgeable reviewer.
 
 ## Installation
+
 ```bash
 pip install nwbinspector
 ```
 
+
+
 ## Usage
 
 ```bash
@@ -22,3 +44,5 @@ nwbinspector path/to/my/data.nwb
 # supply a path to a directory containing NWB files
 nwbinspector path/to/my/data/folder/
 ```
+
+Read about more detailed usage in the main [documentation](https://nwbinspector.readthedocs.io/en/dev/user_guide/user_guide_index.html).
diff --git a/docs/.readthedocs.yaml b/docs/.readthedocs.yaml
@@ -0,0 +1,23 @@
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.9"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+  fail_on_warning: true
+
+# Python requirements required to build your docs
+python:
+  install:
+    - requirements: requirements-rtd.txt
+    - method: pip
+      path: .
diff --git a/docs/requirements-rtd.txt b/docs/requirements-rtd.txt
@@ -0,0 +1,7 @@
+numpy
+jsonschema==3.2.0
+Jinja2>=3.1.3
+sphinx==5.1.1
+sphinx_rtd_theme==0.5.1
+readthedocs-sphinx-search==0.3.2
+sphinx-copybutton==0.5.0
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,3 +1,67 @@
+[build-system]
+requires = ["hatchling", "hatch-vcs"]
+build-backend = "hatchling.build"
+
+[project]
+name = "nwbinspector"
+version = "0.6.0"
+description = "Tool to inspect NWB files for best practices compliance."
+readme = "README.md"
+authors = [
+    {name = "Cody Baker"},
+    {name = "Steph Prince"},
+    {name = "Szonja Weigl"},
+    {name = "Heberto Mayorquin"},
+    {name = "Paul Adkisson"},
+    {name = "Luiz Tauffer"},
+    {name = "Ben Dichter",  email = "ben.dichter@catalystneuro.com"}
+]
+urls = { "Homepage" = "https://github.com/NeurodataWithoutBorders/nwbinspector" }
+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 :: OSI Approved :: BSD License",
+]
+requires-python = ">=3.9"
+dependencies = [
+    "pynwb>=2.8",   # NWB Inspector should always be used with most recent minor versions of PyNWB
+    "hdmf-zarr",
+    "fsspec",
+    "s3fs",
+    "requests",
+    "aiohttp",
+    "PyYAML",
+    "jsonschema",
+    "packaging",
+    "natsort",
+    "click",
+    "tqdm",
+    "isodate",
+    "numpy>=1.22.0,<2.0.0" # TODO: add compatibility for 2.0
+]
+
+[project.optional-dependencies]
+dandi = [
+    "dandi",
+    "remfile",
+]
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[project.scripts]
+nwbinspector = "nwbinspector._nwbinspector_cli:_nwbinspector_cli"
+
+
+
 [tool.black]
 line-length = 120
 target-version = ['py37']
diff --git a/requirements.txt b/requirements.txt
diff --git a/setup.cfg b/setup.cfg
diff --git a/setup.py b/setup.py
diff --git a/src/nwbinspector/__init__.py b/src/nwbinspector/__init__.py
@@ -1,4 +1,5 @@
-from ._version import __version__
+import importlib.metadata
+
 from ._registration import available_checks, register_check
 from ._types import Importance, Severity, InspectorMessage
 from ._configuration import load_config, validate_config, configure_checks
@@ -22,6 +23,9 @@
 
 default_check_registry = {check.__name__: check for check in available_checks}
 
+# Still keeping the legacy magic version attribute requested by some users
+__version__ = importlib.metadata.version(distribution_name="nwbinspector")
+
 __all__ = [
     "available_checks",
     "default_check_registry",
diff --git a/src/nwbinspector/_nwbinspector_cli.py b/src/nwbinspector/_nwbinspector_cli.py
@@ -1,6 +1,7 @@
 """Primary functions for inspecting NWBFiles."""
 
 import importlib
+import importlib.metadata
 import json
 import os
 from pathlib import Path
@@ -18,7 +19,6 @@
 )
 from ._nwb_inspection import inspect_all
 from ._types import Importance
-from ._version import __version__
 from .utils import strtobool
 
 
@@ -83,7 +83,7 @@
     required=False,
     default=None,
 )
-@click.version_option(__version__)
+@click.version_option(version=importlib.metadata.version(distribution_name="nwbinspector"))
 def _nwbinspector_cli(
     *,
     path: str,
diff --git a/src/nwbinspector/_version.py b/src/nwbinspector/_version.py
diff --git a/src/nwbinspector/version/__init__.py b/src/nwbinspector/version/__init__.py
@@ -1,3 +1,5 @@
+import importlib.metadata
+
 import warnings
 
 message = (
@@ -9,4 +11,4 @@
 
 # Still keep imports functional with warning for soft deprecation cycle
 # TODO: remove after 9/15/2024
-from .._version import __version__
+__version__ = importlib.metadata.version(distribution_name="nwbinspector")
