switching to hatchling build process

.github/workflows/ci-cd.yml

@@ -0,0 +1,157 @@
+name: CI/CD
+
+on:
+  push:
+    branches: [ main, develop ]
+  pull_request:
+    branches: [ main, develop ]
+  release:
+    types: [published]
+
+defaults:
+  run:
+    shell: bash
+
+jobs:
+  test:
+    strategy:
+      matrix:
+        os: [macos-latest, ubuntu-latest, windows-latest]
+        python-version: ["3.8", "3.9", "3.12"]
+      fail-fast: false
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v2
+    - name: Unset header
+      # checkout@v2 adds a header that makes branch protection report errors
+      # because the Github action bot is not a collaborator on the repo
+      run: git config --local --unset http.https://github.com/.extraheader
+    - name: Fetch tags
+      run: git fetch --prune --unshallow
+    - name: Disable etelemetry
+      run:  echo "NO_ET=TRUE" >> $GITHUB_ENV
+    - name: Set up Python ${{ matrix.python-version }} on ${{ matrix.os }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Update build tools
+      run: python3 -m pip install --break-system-packages --upgrade pip
+    - name: Install Package
+      run: python3 -m pip install --break-system-packages -e .[test]
+    # - name: Change out of root directory
+    #   run: cd docs
+    # - name: Pytest
+    #   run: pytest -vvs --cov xnatutils --cov-config .coveragerc --cov-report xml .
+    # - name: Upload coverage to Codecov
+    #   uses: codecov/codecov-action@v2
+    #   with:
+    #     fail_ci_if_error: true
+    #     token: ${{ secrets.CODECOV_TOKEN }}
+
+  build:
+    needs: [test]
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        submodules: recursive
+        fetch-depth: 0
+    - name: Unset header
+      # checkout@v2 adds a header that makes branch protection report errors
+      # because the Github action bot is not a collaborator on the repo
+      run: git config --local --unset http.https://github.com/.extraheader
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.12'
+    - name: Install build tools
+      run: python3 -m pip install --break-system-packages build twine
+    - name: Build source and wheel distributions
+      run: python3 -m build .
+    - name: Check distributions
+      run: twine check dist/*
+    - uses: actions/upload-artifact@v3
+      with:
+        name: build
+        path: dist
+
+  # build-docs:
+  #   runs-on: ubuntu-latest
+  #   needs: [build]
+  #   steps:
+  #   - name: Checkout repository
+  #     uses: actions/checkout@v2
+  #   - name: Unset header
+  #     # checkout@v2 adds a header that makes branch protection report errors
+  #     # because the Github action bot is not a collaborator on the repo
+  #     run: git config --local --unset http.https://github.com/.extraheader
+  #   - name: Setup Python
+  #     uses: actions/setup-python@v2
+  #     with:
+  #       python-version: 3.x
+  #   - name: Install dependencies
+  #     run: |
+  #       python3 -m pip install --break-system-packages --upgrade pip
+  #       pip install .[docs]
+  #   - name: Build documentation
+  #     run: |
+  #       cd docs
+  #       make html
+  #       cd ..
+  #   - uses: actions/upload-artifact@v3
+  #     with:
+  #       name: built-docs
+  #       path: docs/build/html
+
+  deploy:
+    needs: [build]  # , build-docs]
+    runs-on: ubuntu-latest
+    steps:
+    - name: Download build
+      uses: actions/download-artifact@v3
+      with:
+        name: built-main
+        path: dist
+    - name: Check for PyPI token on tag
+      id: deployable
+      if: github.event_name == 'release'
+      env:
+        PYPI_API_TOKEN: "${{ secrets.PYPI_API_TOKEN }}"
+      run: if [ -n "$PYPI_API_TOKEN" ]; then echo "DEPLOY=true" >> $GITHUB_OUTPUT; fi
+    - name: Upload to PyPI
+      if: steps.deployable.outputs.DEPLOY
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}
+
+  # deploy-docs:
+  #   needs: [build-docs, deploy]
+  #   runs-on: ubuntu-latest
+  #   steps:
+  #   - name: Download built docs
+  #     uses: actions/download-artifact@v3
+  #     with:
+  #       name: built-docs
+  #       path: docs-build
+  #   - name: Check for GHPAGES_DEPLOY_KEY token
+  #     id: deployable
+  #     if: github.event_name == 'release'
+  #     env:
+  #       GHPAGES_DEPLOY_KEY: "${{ secrets.GHPAGES_DEPLOY_KEY }}"
+  #     run: if [ -n "$GHPAGES_DEPLOY_KEY" ]; then echo "DEPLOY=true" >> $GITHUB_OUTPUT; fi
+  #   - name: Deploy Docs to GitHub Pages
+  #     if: steps.deployable.outputs.DEPLOY
+  #     uses: peaceiris/actions-gh-pages@v3
+  #     with:
+  #       github_token: ${{ secrets.GHPAGES_DEPLOY_KEY }}
+  #       publish_dir: docs-build
+
+# Deploy on tags if PYPI_API_TOKEN is defined in the repository secrets.
+# Secrets are not accessible in the if: condition [0], so set an output variable [1]
+# [0] https://github.community/t/16928
+# [1] https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-output-parameter

.gitignore

@@ -13,3 +13,4 @@
 test/*.xml
 .vscode
 *.venv
+_version.py

pyproject.toml

@@ -0,0 +1,96 @@
+[build-system]
+requires = ["hatchling", "hatch-vcs"]
+build-backend = "hatchling.build"
+
+[project]
+name = "xnatutils"
+description = "A collection of scripts for downloading/uploading and listing data from XNAT repositories."
+readme = "README.rst"
+requires-python = ">=3.8"
+dependencies = ["xnat>=0.6", "progressbar2>=3.16.0", "future>=0.16"]
+license = { file = "LICENSE" }
+authors = [{ name = "Thomas G. Close", email = "[email protected]" }]
+maintainers = [{ name = "Thomas G. Close", email = "[email protected]" }]
+keywords = ["XNAT", "REST API", "DICOM", "uploader"]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Healthcare Industry",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: Apache Software License",
+    "Natural Language :: English",
+    "Programming Language :: Python :: 3.4",
+    "Programming Language :: Python :: 3.5",
+    "Programming Language :: Python :: 3.6",
+    "Programming Language :: Python :: 3.7",
+    "Programming Language :: Python :: 3.8",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Topic :: Scientific/Engineering :: Medical Science Apps.",
+]
+dynamic = ["version"]
+
+# [project.optional-dependencies]
+# dev = [
+#     "black",
+#     "pre-commit",
+#     "codespell",
+#     "flake8",
+#     "flake8-pyproject",
+#     "xnatutils[test]",
+#     "pydata-sphinx-theme >=0.13",
+# ]
+# test = [
+#     "pytest >=6.2.5",
+#     "pytest-env>=0.6.2",
+#     "pytest-cov>=2.12.1",
+#     "pydra >=0.23.0a0",
+# ]
+# docs = [
+# ]
+
+[project.urls]
+repository = "https://github.com/Australian-Imaging-Service/xnatutils"
+
+
+[tool.hatch.version]
+source = "vcs"
+
+[tool.hatch.build.hooks.vcs]
+version-file = "xnatutils/_version.py"
+
+[tool.hatch.metadata]
+allow-direct-references = true
+
+[tool.hatch.build]
+packages = ["xnatutils"]
+exclude = ["tests"]
+include = ["./xnatutils"]
+
+[project.scripts]
+xnat-get = "xnatutils.get_:cmd"
+xnat-put = "xnatutils.put_:cmd"
+xnat-ls = "xnatutils.ls_:cmd"
+xnat-varget = "xnatutils.varget_:cmd"
+xnat-varput = "xnatutils.varput_:cmd"
+xnat-rename = "xnatutils.rename_:cmd"
+
+[tool.black]
+target-version = ['py38']
+exclude = "xnatutils/core/_version.py"
+# [tool.mypy]
+# python_version = "3.8"
+# ignore_missing_imports = true
+# strict = true
+# namespace_packages = true
+# explicit_package_bases = true
+# exclude = ["tests", "scripts", "docs", "build", "dist", "xnatutils/_version.py"]
+
+
+[tool.codespell]
+ignore-words = ".codespell-ignorewords"
+
+[tool.flake8]
+doctests = true
+per-file-ignores = ["__init__.py:F401"]
+max-line-length = 88
+select = "C,E,F,W,B,B950"
+extend-ignore = ['E203', 'E501', 'E129', 'W503', 'E704']