Merge pull request #117 from templateflow/maint/pep517-update

MAINT: Finalize migration of package build to PEP517/8

Author: oesteban

.circleci/config.yml

@@ -13,6 +13,11 @@ jobs:
       - checkout:
           path: /tmp/src/templateflow
 
+      - run:
+          name: Generate requirements.txt
+          command: |
+            python /tmp/src/templateflow/.maint/update_requirements.py
+
       - restore_cache:
           keys:
             - deps-v10-{{ checksum "/tmp/src/templateflow/requirements.txt"}}-{{ epoch }}
@@ -168,7 +173,8 @@ jobs:
           name: Build only this commit
           command: |
             export PATH="$HOME/.conda/bin:$PATH"
-            python setup.py --version
+            python -m pip install "setuptools_scm>=8"
+            python -m setuptools_scm
             make -C docs SPHINXOPTS="-W" BUILDDIR="$HOME/html" CURBRANCH="${CIRCLE_TAG}" html
       - store_artifacts:
           path: ~/html

.github/workflows/pythonpackage.yml

@@ -131,3 +131,11 @@ jobs:
         find ${TEMPLATEFLOW_HOME} >> /tmp/.install-2.txt
         diff /tmp/.install.txt /tmp/.install-2.txt
         exit $?
+
+  flake8:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v4
+    - run: pipx run flake8-pyproject templateflow/

.gitignore

@@ -1,6 +1,10 @@
 # setuptools_scm
 templateflow/_version.py
 
+# circleci hash checking
+requirements.txt
+min-requirements.txt
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

update_changes.sh renamed to .maint/update_changes.sh

@@ -0,0 +1,45 @@
+#!/usr/bin/env python3
+from copy import copy
+from pathlib import Path
+
+from packaging.requirements import Requirement, SpecifierSet
+
+try:
+    from tomllib import loads  # Python +3.11
+except ImportError:
+    from pip._vendor.tomli import loads
+
+repo_root = Path(__file__).parent.parent
+pyproject = repo_root / 'pyproject.toml'
+reqs = repo_root / 'requirements.txt'
+min_reqs = repo_root / 'min-requirements.txt'
+
+requirements = [
+    Requirement(req)
+    for req in loads(pyproject.read_text())['project']['dependencies']
+]
+
+script_name = Path(__file__).relative_to(repo_root)
+
+
+def to_min(req):
+    if req.specifier:
+        req = copy(req)
+        try:
+            min_spec = [spec for spec in req.specifier if spec.operator in ('>=', '~=')][0]
+        except IndexError:
+            return req
+        min_spec._spec = ('==',) + min_spec._spec[1:]
+        req.specifier = SpecifierSet(str(min_spec))
+    return req
+
+
+lines = [f'# Auto-generated by {script_name}', '']
+
+# Write requirements
+lines[1:-1] = [str(req) for req in requirements]
+reqs.write_text('\n'.join(lines))
+
+# Write minimum requirements
+lines[1:-1] = [str(to_min(req)) for req in requirements]
+min_reqs.write_text('\n'.join(lines))

.maint/update_requirements.py

@@ -4,5 +4,6 @@ recursive-exclude docs/ *
 
 recursive-exclude .circleci/ *
 recursive-exclude .github/ *
+recursive-exclude .maint/ *
 
-exclude .gitignore .gitattributes .git_archival.txt .travis.yml .zenodo.json codecov.yml update_changes.sh
+exclude .gitignore .gitattributes .git_archival.txt .travis.yml .zenodo.json codecov.yml

MANIFEST.in

@@ -1,16 +1,164 @@
 [build-system]
 requires = [
-    "setuptools >= 45",
-    "setuptools_scm >= 6.2",
-    "nipreps-versions",
+    "setuptools>=64",
+    "setuptools_scm>=8",
 ]
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools_scm]
-write_to = "templateflow/_version.py"
-write_to_template = """\
+version_file = "templateflow/_version.py"
+version_file_template = """\
 \"\"\"Version file, automatically generated by setuptools_scm.\"\"\"
 __version__ = "{version}"
 """
 fallback_version = "0.0"
-version_scheme = "nipreps-calver"
+# version_scheme = "nipreps-calver"
+
+[project]
+name = "templateflow"
+description = "TemplateFlow Python Client - TemplateFlow is the Zone of neuroimaging templates."
+readme = "README.rst"
+authors = [{name = "The NiPreps Developers", email = "[email protected]"}]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Image Recognition",
+    "License :: OSI Approved :: Apache Software License",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+]
+license = {file = "LICENSE"}
+requires-python = ">=3.8"
+dependencies = [
+    "pybids >= 0.15.2",
+    "importlib_resources >= 5.7; python_version < '3.11'",
+    "requests",
+    "tqdm",
+]
+dynamic = ["version"]
+
+[project.urls]
+Archive = "https://github.com/templateflow/templateflow"
+"Bug Tracker" = "https://github.com/templateflow/python-client/issues"
+Home = "https://www.templateflow.org"
+Documentation = "https://www.templateflow.org/python-client/"
+"Source Code" = "https://github.com/templateflow/python-client"
+
+[project.optional-dependencies]
+test = [
+    "pytest",
+    "pytest-xdist",
+    "pytest-cov == 2.5.1",
+    "coverage",
+]
+datalad = [
+    "datalad ~= 0.12.0"
+]
+doc = [
+    "nbsphinx",
+    "packaging",
+    "pydot>=1.2.3",
+    "pydotplus",
+    "sphinx-argparse",
+    "sphinx ~= 4.0",
+    "sphinx_rtd_theme >= 0.4.3",
+    "sphinxcontrib-apidoc",
+    "sphinx_multiversion",
+]
+# Aliases
+tests = ["templateflow[test]"]
+docs = ["templateflow[doc]"]
+all = ["templateflow[datalad,doc,test]"]
+
+#
+# Developer tool configurations
+#
+
+[tool.black]
+line-length = 99
+skip-string-normalization = true
+
+[tool.isort]
+profile = 'black'
+
+[tool.flake8]
+max-line-length = "99"
+doctests = "False"
+exclude = "*build/"
+ignore = ["W503", "E203"]
+per-file-ignores = [
+    "**/__init__.py : F401",
+    "docs/conf.py : E265",
+]
+
+[tool.pytest.ini_options]
+norecursedirs = [".git"]
+addopts = "-svx --doctest-modules"
+doctest_optionflags = "ALLOW_UNICODE NORMALIZE_WHITESPACE ELLIPSIS"
+env = "PYTHONHASHSEED=0"
+filterwarnings = ["ignore::DeprecationWarning"]
+junit_family = "xunit2"
+
+[tool.coverage.run]
+branch = true
+concurrency = 'multiprocessing'
+omit = [
+    '*/tests/*',
+    '*/conftest.py',
+    'templateflow/_version.py'
+]
+
+[tool.coverage.report]
+# Regexes for lines to exclude from consideration
+exclude_lines = [
+    'raise NotImplementedError',
+    'warnings\.warn',
+]
+
+[tool.ruff]
+line-length = 99
+
+[tool.ruff.lint]
+extend-select = [
+  "F",
+  "E",
+  "W",
+  "I",
+  "UP",
+  "YTT",
+  "S",
+  "BLE",
+  "B",
+  "A",
+  # "CPY",
+  "C4",
+  "DTZ",
+  "T10",
+  # "EM",
+  "EXE",
+  "FA",
+  "ISC",
+  "ICN",
+  "PT",
+  "Q",
+]
+extend-ignore = [
+  "S311",  # We are not using random for cryptographic purposes
+  "ISC001",
+  "S603",
+]
+
+[tool.ruff.lint.flake8-quotes]
+inline-quotes = "single"
+
+[tool.ruff.lint.extend-per-file-ignores]
+"*/test_*.py" = ["S101"]
+"fmriprep/utils/debug.py" = ["A002", "T100"]
+"docs/conf.py" = ["A001"]
+"docs/sphinxext/github_link.py" = ["BLE001"]
+
+[tool.ruff.format]
+quote-style = "single"