From 08c0539651981bf54cb99f39ed3e491df0148d62 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Tue, 16 Jul 2024 13:52:36 -0400
Subject: [PATCH] TOX: Add tox config

---
 pyproject.toml |  28 +++++++++++--
 tox.ini        | 110 +++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 135 insertions(+), 3 deletions(-)
 create mode 100644 tox.ini

diff --git a/pyproject.toml b/pyproject.toml
index 80412448..8efb7041 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -75,7 +75,7 @@ telemetry = [
     "sentry-sdk >= 1.3",
 ]
 test = [
-    "coverage",
+    "coverage[toml]",
     "pytest",
     "pytest-cov",
     "pytest-env",
@@ -127,11 +127,21 @@ exclude = ".*"
 
 [tool.pytest.ini_options]
 minversion = "6"
-testpaths = ["fmriprep/tests"]
+testpaths = ["fmriprep"]
 log_cli_level = "INFO"
 xfail_strict = true
 norecursedirs = [".git"]
-addopts = ["-svx", "-ra", "--strict-config", "--strict-markers", "--doctest-modules"]
+addopts = [
+  "-svx",
+  "-ra",
+  "--strict-config",
+  "--strict-markers",
+  "--doctest-modules",
+  # Config pytest-cov
+  "--cov=fmriprep",
+  "--cov-report=xml",
+  "--cov-config=pyproject.toml",
+]
 doctest_optionflags = "ALLOW_UNICODE NORMALIZE_WHITESPACE ELLIPSIS"
 env = "PYTHONHASHSEED=0"
 filterwarnings = ["ignore::DeprecationWarning"]
@@ -181,3 +191,15 @@ inline-quotes = "single"
 
 [tool.ruff.format]
 quote-style = "single"
+
+[tool.coverage.run]
+branch = true
+omit = [
+    "*/_version.py"
+]
+
+[tool.coverage.paths]
+source = [
+  "fmriprep",
+  "**/site-packages/fmriprep"
+]
diff --git a/tox.ini b/tox.ini
new file mode 100644
index 00000000..a09cd588
--- /dev/null
+++ b/tox.ini
@@ -0,0 +1,110 @@
+[tox]
+requires =
+  tox>=4
+envlist =
+  py3{10,11,12}
+  py310-min
+  py3{10,11,12}-pre
+skip_missing_interpreters = true
+
+# Configuration that allows us to split tests across GitHub runners effectively
+[gh-actions]
+python =
+  3.10: py310
+  3.11: py311
+  3.12: py312
+
+[gh-actions:env]
+DEPENDS =
+  min: min
+  pre: pre
+
+[testenv]
+description = Pytest with coverage
+labels = test
+pip_pre =
+  pre: true
+pass_env =
+  # getpass.getuser() sources for Windows:
+  LOGNAME
+  USER
+  LNAME
+  USERNAME
+  # Pass user color preferences through
+  PY_COLORS
+  FORCE_COLOR
+  NO_COLOR
+  CLICOLOR
+  CLICOLOR_FORCE
+  PYTHON_GIL
+extras = test
+setenv =
+  pre: PIP_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
+deps =
+  min: nibabel == 4.0.1
+  min: nipype == 1.8.5
+  min: nitransforms == 21.0.0
+  min: numpy == 1.22
+  min: psutil == 5.4
+  min: pybids == 0.15.2
+  min: tedana == 23.0.2
+  min: templateflow == 24.1.0
+
+commands =
+  pytest --cov-report term-missing --durations=20 --durations-min=1.0 {posargs}
+
+[testenv:style]
+description = Check our style guide
+labels = check
+deps =
+  ruff
+skip_install = true
+commands =
+  ruff check --diff
+  ruff format --diff
+
+[testenv:style-fix]
+description = Auto-apply style guide to the extent possible
+labels = pre-release
+deps =
+  ruff
+skip_install = true
+commands =
+  ruff check --fix
+  ruff format
+  ruff check --select ISC001
+
+[testenv:spellcheck]
+description = Check spelling
+labels = check
+deps =
+  codespell[toml]
+skip_install = true
+commands =
+  codespell . {posargs}
+
+[testenv:build{,-strict}]
+labels =
+  check
+  pre-release
+deps =
+  build
+  twine
+skip_install = true
+set_env =
+  # Ignore specific known warnings:
+  # https://github.com/pypa/pip/issues/11684
+  # https://github.com/pypa/pip/issues/12243
+  strict: PYTHONWARNINGS=error,once:pkg_resources is deprecated as an API.:DeprecationWarning:pip._internal.metadata.importlib._envs,once:Unimplemented abstract methods {'locate_file'}:DeprecationWarning:pip._internal.metadata.importlib._dists
+commands =
+  python -m build
+  python -m twine check dist/*
+
+[testenv:publish]
+depends = build
+labels = release
+deps =
+  twine
+skip_install = true
+commands =
+  python -m twine upload dist/*