Replace versioneer with hatch (ME-ICA#35)

* Update gitignore.

* Delete _version.py

* Adopt new packaging.

* Ignore the _version.py file.

.git_archival.txt

@@ -0,0 +1,4 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
+ref-names: $Format:%D$

.gitattributes

@@ -1,4 +1,5 @@
-tedana/_version.py export-subst
+.git_archival.txt  export-subst
+
 # Set the default behavior, in case people don't have core.autocrlf set.
 * text=auto
 

.gitignore

@@ -1,3 +1,6 @@
+# setuptools-scm
+tedana/_version.py
+
 .DS_Store
 docs/generated/
 .pytest_cache/

.readthedocs.yml

@@ -1,16 +1,17 @@
-# .readthedocs.yml
-# Read the Docs configuration file
-# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
-
-# Required
 version: 2
 
-# Build documentation in the docs/ directory with Sphinx
 sphinx:
-  configuration: docs/conf.py
+   configuration: docs/conf.py
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.8"
+  jobs:
+    post_checkout:
+      - git fetch --unshallow
 
 python:
-  version: 3.7
   install:
     - method: pip
       path: .

pyproject.toml

@@ -1,14 +1,98 @@
+[build-system]
+requires = ["hatchling", "hatch-vcs"]
+build-backend = "hatchling.build"
+
 [project]
 name = "tedana"
-version = "0.0.12"
+description = "TE-Dependent Analysis (tedana) of multi-echo functional magnetic resonance imaging (fMRI) data."
+readme = "README.md"
+authors = [{name = "tedana developers"}]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Information Analysis",
+    "License :: OSI Approved :: GNU Library or Lesser General Public License (LGPL)",
+    "Programming Language :: Python :: 3.7",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+]
+license = {file = "LICENSE"}
+requires-python = ">=3.7"
+dependencies = [
+    "bokeh<2.3.0",
+    "mapca>=0.0.3",
+    "matplotlib",
+    "nibabel>=2.5.1",
+    "nilearn>=0.7",
+    "numpy>=1.16",
+    "pandas>=0.24",
+    "scikit-learn>=0.21",
+    "scipy>=1.2.0",
+    "threadpoolctl",
+    "jinja2==3.0.1",
+]
+dynamic = ["version"]
+
+[project.urls]
+Homepage = "https://github.com/ME-ICA/tedana"
+Documentation = "https://www.tedana.readthedocs.io"
+Paper = "https://joss.theoj.org/papers/10.21105/joss.03669"
+
+[project.optional-dependencies]
+doc = [
+    "sphinx>=1.5.3",
+    "sphinx_copybutton",
+    "sphinx_rtd_theme",
+    "sphinx-argparse",
+    "sphinxcontrib-bibtex",
+]
+tests = [
+    "codecov",
+    "coverage<5.0",
+    "flake8>=3.7",
+    "flake8-black",
+    "flake8-isort",
+    "pytest",
+    "pytest-cov",
+    "requests",
+]
+
+# Aliases
+all = ["tedana[doc,tests]"]
 
 [project.scripts]
-tedana = "tedana.workflows.tedana:_main"
 ica_reclassify = "tedana.workflows.ica_reclassify:_main"
 t2smap = "tedana.workflows.t2smap:_main"
+tedana = "tedana.workflows.tedana:_main"
 
-[build-system]
-requires = ["setuptools>=64", "wheel"]
+#
+# Hatch configurations
+#
+
+[tool.hatch.metadata]
+allow-direct-references = true
+
+[tool.hatch.build.targets.sdist]
+exclude = [".git_archival.txt"]  # No longer needed in sdist
+
+[tool.hatch.build.targets.wheel]
+packages = ["tedana"]
+exclude = [
+    "tedana/tests/data",  # Large test data directory
+]
+
+##  The following two sections configure setuptools_scm in the hatch way
+
+[tool.hatch.version]
+source = "vcs"
+
+[tool.hatch.build.hooks.vcs]
+version-file = "tedana/_version.py"
+
+#
+# Developer tool configurations
+#
 
 [tool.black]
 line-length = 99
@@ -28,13 +112,41 @@ exclude = '''
     | build
     | dist
   )/
-  | get_version.py
-  | versioneer.py
+  | tedana/_version.py
 )
 '''
 
 [tool.isort]
 profile = "black"
 multi_line_output = 3
 
+[tool.flake8]
+max-line-length = 99
+exclude = [
+    "*build/",
+    "tedana/_version.py",
+]
+ignore = ["E203", "E402", "W503"]
+per-file-ignores = [
+    "*/__init__.py: F401",
+]
+docstring-convention = "numpy"
+
+[tool.coverage.run]
+branch = true
+omit = [
+    "*/tests/*",
+    "*/__init__.py",
+    "*/conftest.py",
+    "tedana/_version.py",
+]
+
+[tool.coverage.report]
+# Regexes for lines to exclude from consideration
+exclude_lines = [
+    'raise NotImplementedError',
+    'warnings\.warn',
+]
 
+[tool.pytest]
+log_cli = true

tedana/__about__.py

@@ -0,0 +1,18 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+"""Base module variables."""
+
+try:
+    from tedana._version import __version__
+except ImportError:
+    __version__ = "0+unknown"
+
+__packagename__ = "tedana"
+__copyright__ = "Copyright 2023, The ME-ICA Developers"
+__credits__ = (
+    "Contributors: please check the ``.zenodo.json`` file at the top-level folder"
+    "of the repository"
+)
+__url__ = "https://github.com/ME-ICA/tedana"
+
+DOWNLOAD_URL = f"https://github.com/ME-ICA/{__packagename__}/archive/{__version__}.tar.gz"

tedana/__init__.py

@@ -1,17 +1,17 @@
 # -*- coding: utf-8 -*-
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-"""
-tedana: A Python package for TE-dependent analysis of multi-echo data.
-"""
-
+"""tedana: A Python package for TE-dependent analysis of multi-echo data."""
 import warnings
 
-from ._version import get_versions
-
-__version__ = get_versions()["version"]
+from tedana.__about__ import __copyright__, __credits__, __packagename__, __version__
 
 # cmp is not used, so ignore nipype-generated warnings
 warnings.filterwarnings("ignore", r"cmp not installed")
 
-del get_versions
+__all__ = [
+    "__copyright__",
+    "__credits__",
+    "__packagename__",
+    "__version__",
+]