[MAINT] switch to tox (#84)

* set up tox

* rm package workflow

.github/workflows/check_md_links.yml

@@ -7,7 +7,6 @@ on:
     push:
         branches:
         -   main
-        -   dev
     pull_request:
         branches: ['*']
 

.github/workflows/test.yml

@@ -0,0 +1,66 @@
+---
+name: Python tests
+
+on:
+    push:
+        branches:
+        -   main
+    pull_request: {}
+    schedule:
+    # 8am EST / 9am EDT Mondays
+    -   cron: 0 13 * * 1
+  # Allow job to be triggered manually from GitHub interface
+    workflow_dispatch:
+
+defaults:
+    run:
+        shell: bash
+
+# Force tox and pytest to use color
+env:
+    FORCE_COLOR: true
+
+concurrency:
+    group: ${{ github.workflow }}-${{ github.ref }}
+    cancel-in-progress: true
+
+permissions:
+    contents: read
+
+jobs:
+    test:
+    # Check each OS, all supported Python, minimum versions and latest releases
+        runs-on: ${{ matrix.os }}
+        strategy:
+            matrix:
+                os: [macos-latest, ubuntu-latest, windows-latest]
+                python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+            fail-fast: false
+
+        steps:
+        -   uses: actions/checkout@v4
+            with:
+                submodules: recursive
+                fetch-depth: 0
+        -   name: Set up Python ${{ matrix.python-version }}
+            uses: actions/setup-python@v5
+            with:
+                python-version: ${{ matrix.python-version }}
+                allow-prereleases: true
+        -   name: Display Python version
+            run: python -c "import sys; print(sys.version)"
+        -   name: Install tox
+            run: |
+                python -m pip install --upgrade pip
+                python -m pip install tox tox-gh-actions
+        -   name: Show tox config
+            run: tox c
+        -   name: Run tox
+            run: tox run -v --exit-and-dump-after 1200 -e test
+        -   name: Upload coverage to Codecov
+            uses: codecov/codecov-action@v4
+            with:
+                file: ./coverage.xml
+                flags: tests
+                name: codecov-umbrella
+                fail_ci_if_error: false

.pre-commit-config.yaml

@@ -55,7 +55,7 @@ repos:
     rev: v1.10.0
     hooks:
     -   id: mypy
-        additional_dependencies: [types-all, pandas-stubs]
+        additional_dependencies: [types-all, pandas-stubs, types-requests]
         args: [--config-file=pyproject.toml]
 
 

.vscode/settings.json

@@ -1,3 +1,4 @@
 {
-  "esbonio.sphinx.confDir": ""
+  "esbonio.sphinx.confDir": "",
+  "circleci.persistedProjectSelection": []
 }

Makefile

@@ -1,4 +1,4 @@
-.PHONY: clean clean-build clean-pyc clean-test coverage dist  help install
+.PHONY: clean clean-build clean-pyc clean-test coverage help
 .DEFAULT_GOAL := help
 
 define BROWSER_PYSCRIPT
@@ -43,7 +43,6 @@ clean-pyc: ## remove Python file artifacts
 	find . -name '__pycache__' -exec rm -fr {} +
 
 clean-test: ## remove test and coverage artifacts
-	rm -fr .tox/
 	rm -f .coverage
 	rm -fr htmlcov/
 	rm -fr .pytest_cache
@@ -53,58 +52,18 @@ clean-test: ## remove test and coverage artifacts
 	rm -f tests/bids/CITATION.cff
 	rm -rf tests/bids/derivatives
 
-## INSTALL
-
-install: clean  ## install the package to the active Python's site-packages
-	pip install .
-
-release: dist ## package and upload a release
-	twine upload dist/*
-
-dist: clean ## builds source and wheel package
-	python setup.py sdist
-	python setup.py bdist_wheel
-	ls -l dist
-
-## STYLE
-
-lint/flake8: ## check style with flake8
-	flake8 bids2cite tests
-lint/black: ## check style with black
-	black bids2cite tests
-lint/mypy: ## check style with mypy
-	mypy bids2cite
-
-lint: lint/black lint/mypy lint/flake8  ## check style
-
-validate_cff: ## Validate the citation file
-	cffconvert --validate
-
-
 ## DOC
 .PHONY: docs
 
 docs: ## generate Sphinx HTML documentation, including API docs
-	rm -f docs/source/bids2cite.rst
-	rm -f docs/source/modules.rst
-	sphinx-apidoc -o docs/source bids2cite
-	$(MAKE) -C docs clean
-	$(MAKE) -C docs html
 	$(BROWSER) docs/_build/html/index.html
 
-servedocs: docs ## compile the docs watching for changes
-	watchmedo shell-command -p '*.rst' -c '$(MAKE) -C docs html' -R -D .
-
-
 ## TESTS
 
 coverage: ## use coverage
 	coverage erase
 	coverage run --source bids2cite -m pytest
 
-test: ## run tests with pytest
-	pytest
-
 test-cli:
 	bids2cite tests/bids \
 		--skip-prompt \

pyproject.toml

@@ -18,7 +18,8 @@ classifiers = [
     "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
-    "Programming Language :: Python :: 3.11"
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12"
 ]
 dependencies = [
     "cffconvert",
@@ -40,18 +41,7 @@ requires-python = ">=3.8"
 [project.optional-dependencies]
 dev = [
     "bids2cite[doc,test]",
-    "codespell",
-    "black",
-    "flake8",
-    "flake8-docstrings",
-    "flake8-use-fstring",
-    "flake8-functions",
-    "mypy",
-    "pandas-stubs",
-    "pre-commit",
-    "sourcery",
-    "types-requests",
-    'tomli'
+    "sourcery"
 ]
 doc = [
     "myst-parser",

tox.ini

@@ -0,0 +1,90 @@
+[tox]
+requires =
+  tox>=4
+skip_missing_interpreters = true
+
+; run lint by default when just calling "tox"
+env_list = lint
+
+; ENVIRONMENTS
+; ------------
+[style]
+description = common environment for style checkers (rely on pre-commit hooks)
+skip_install = true
+deps =
+    pre-commit
+
+# Configuration that allows us to split tests across GitHub runners effectively
+[gh-actions]
+python =
+  3.8: py38
+  3.9: py39
+  3.10: py310
+  3.11: py311
+  3.12: py312
+
+; COMMANDS
+; --------
+[testenv:lint]
+description = run all linters and formatters
+skip_install = true
+deps =
+    {[style]deps}
+commands =
+	pre-commit run --all-files --show-diff-on-failure {posargs:}
+
+[testenv:test]
+description = Pytest with coverage
+labels = test
+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
+extras = test
+
+commands =
+  coverage erase
+  coverage run --source bids2cite -m pytest
+  coverage xml
+
+[testenv:docs]
+description = Build documentation site
+labels = docs
+allowlist_externals = make
+extras = doc
+commands =
+  make -C docs clean
+  make -C docs html
+
+[testenv:build{,-strict}]
+labels =
+  check
+  pre-release
+allowlist_externals = make
+deps =
+  build
+  twine
+skip_install = true
+set_env =
+  build-strict: PYTHONWARNINGS=error
+commands =
+  make clean-build
+  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/*