Annotation removal

.github/dependabot.yml

@@ -0,0 +1,17 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://help.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  # Maintain dependencies for GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "daily"
+
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "daily"

.github/workflows/publish.yml

@@ -0,0 +1,141 @@
+name: publish
+
+on:
+  push:
+    branches:
+      - main
+      - master
+    tags:
+      - '*'
+
+jobs:
+
+  build:
+    name: Build
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v5
+      with:
+        python-version: 3.12
+
+    - name: Install requirements
+      run: |
+        pip install --upgrade build
+        pip install --upgrade setuptools wheel setuptools-scm[toml] importlib-metadata
+        pip install git+https://github.com/jic-dtool/dtool-annotation.git@main
+        pip list
+
+    - name: Package distribution
+      run: |
+        python -m build
+
+    - name: Upload artifact
+      uses: actions/upload-artifact@v3
+      with:
+        name: python-package-distributions
+        path: dist/
+
+
+  publish-to-testpypi:
+    name: Publish to TestPyPI
+    needs:
+    - build
+    runs-on: ubuntu-latest
+
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/dtool-annotation
+
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v3
+      with:
+        name: python-package-distributions
+        path: dist/
+
+    - name: Publish distribution 📦 to TestPyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        repository-url: https://test.pypi.org/legacy/
+        verbose: true
+        skip-existing: true
+
+
+  publish-to-pypi:
+    name: Publish to PyPI
+    if: startsWith(github.ref, 'refs/tags/')  # only publish to PyPI on tag pushes
+    needs:
+    - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/dtool-annotation  # Replace <package-name> with your PyPI project name
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+    - name: Download artifact
+      uses: actions/download-artifact@v3
+      with:
+        name: python-package-distributions
+        path: dist/
+
+    - name: Publish distribution to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        verbose: true
+
+
+  github-release:
+    name: >-
+      Make github release
+    needs:
+    - publish-to-pypi
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: write  # IMPORTANT: mandatory for making GitHub Releases
+      id-token: write  # IMPORTANT: mandatory for sigstore
+
+    steps:
+    - name: Download artifact
+      uses: actions/download-artifact@v3
+      with:
+        name: python-package-distributions
+        path: dist/
+
+    - name: Sign with Sigstore
+      uses: sigstore/gh-action-sigstore-python@v2.1.1
+      with:
+        inputs: >-
+          ./dist/*.tar.gz
+          ./dist/*.whl
+
+    - name: Create GitHub Release
+      env:
+        GITHUB_TOKEN: ${{ github.token }}
+      run: >-
+        gh release create
+        '${{ github.ref_name }}'
+        --repo '${{ github.repository }}'
+        --notes ""
+
+    - name: Upload artifact signatures to GitHub Release
+      env:
+        GITHUB_TOKEN: ${{ github.token }}
+      # Upload to GitHub Release using the `gh` CLI.
+      # `dist/` contains the built packages, and the
+      # sigstore-produced signatures and certificates.
+      run: >-
+        gh release upload
+        '${{ github.ref_name }}' dist/**
+        --repo '${{ github.repository }}'

.github/workflows/test.yml

@@ -0,0 +1,45 @@
+name: test
+
+on:
+  push:
+    branches:
+      - main
+      - master
+    tags:
+      - '*'
+  pull_request:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11', '3.12', '3.13']
+
+    steps:
+    - name: Git checkout
+      uses: actions/checkout@v4
+
+    - name: Set up python3 ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install requirements
+      run: |
+        python -m pip install --upgrade pip
+        pip install .[test]
+        pip install flake8
+        pip list
+
+    - name: Test with pytest
+      run: |
+        pytest -sv
+
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=12 --max-line-length=127 --statistics

CHANGELOG.rst

@@ -10,10 +10,16 @@ This change log uses principles from `keep a changelog <http://keepachangelog.co
 Added
 ^^^^^
 
+- The CLI command 'dtool annotation delete'
+- github CI test workflow
+- github CI publication workflow
+- Activated dependabot
 
 Changed
 ^^^^^^^
 
+- Moved from ``setup.py`` to ``pyproject.toml``
+- Dynamic versioning
 
 Deprecated
 ^^^^^^^^^^

dtool_annotation/__init__.py

@@ -1,3 +1,12 @@
 """dtool_annotation package."""
 
-__version__ = "0.1.1"
+try:
+    from importlib.metadata import version, PackageNotFoundError
+except ModuleNotFoundError:
+    from importlib_metadata import version, PackageNotFoundError
+
+try:
+    __version__ = version(__name__)
+except PackageNotFoundError:
+    # package is not installed
+    pass

dtool_annotation/cli.py

@@ -126,3 +126,21 @@ def list_annotations(dataset_uri):
     for name in sorted(dataset.list_annotation_names()):
         value = str(dataset.get_annotation(name))
         click.secho("{}\t{}".format(name, value))
+
+
+@annotation.command(name="delete")
+@base_dataset_uri_argument
+@click.argument("key")
+def delete_annotation(dataset_uri, key):
+    """Delete dataset annotation."""
+    try:
+        dataset = dtoolcore.ProtoDataSet.from_uri(
+            uri=dataset_uri,
+            config_path=dtoolcore.utils.DEFAULT_CONFIG_PATH
+        )
+    except dtoolcore.DtoolCoreTypeError:
+        dataset = dtoolcore.DataSet.from_uri(
+            uri=dataset_uri,
+            config_path=dtoolcore.utils.DEFAULT_CONFIG_PATH
+        )
+    dataset.delete_annotation(key)

pyproject.toml

@@ -0,0 +1,47 @@
+[build-system]
+requires = ["setuptools>=42", "setuptools_scm[toml]>=6.3"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "dtool-annotation"
+description = "Add ability to annotate datasets using the dtool CLI"
+authors = [
+    {name = "Tjelvar Olsson", email = "tjelvar.olsson@gmail.com"},
+    {name = "Johannes L. Hörmann", email = "johannes.laurin@gmail.com"},
+]
+readme = "README.rst"
+requires-python = ">=3.7"
+license = {file = "LICENSE"}
+dynamic = ["version"]
+dependencies = [
+    "click",
+    "dtoolcore>=3.19.0",
+    "dtool-cli",
+]
+
+[project.optional-dependencies]
+test = [
+    "pytest",
+    "pytest-cov"
+]
+docs = [
+    "sphinx",
+    "sphinx_rtd_theme",
+    "sphinxcontrib-spelling"
+]
+
+[project.urls]
+Repository = "https://github.com/jic-dtool/dtool-annotation"
+Documentation = "https://github.com/jic-dtool/dtool-annotation/blob/master/README.rst"
+Changelog = "https://github.com/jic-dtool/dtool-annotation/blob/master/CHANGELOG.rst"
+
+[tool.setuptools_scm]
+version_scheme = "guess-next-dev"
+local_scheme = "no-local-version"
+write_to = "dtool_annotation/version.py"
+
+[tool.setuptools]
+packages = ["dtool_annotation"]
+
+[project.entry-points."dtool.cli"]
+annotation = "dtool_annotation.cli:annotation"

tests/test_annotation_functional.py

@@ -30,6 +30,23 @@ def test_annotation_basic(tmp_dataset_fixture):  # NOQA
     actual = result.output.strip()
     assert actual == expected
 
+    result = runner.invoke(annotation, [
+        "delete",
+        tmp_dataset_fixture.uri,
+        "project"
+    ])
+    assert result.exit_code == 0
+
+    result = runner.invoke(annotation, [
+        "get",
+        tmp_dataset_fixture.uri,
+        "project"
+    ])
+    assert result.exit_code != 0
+    expected = "No annotation named: 'project'"
+    actual = result.output.strip()
+    assert actual == expected
+
 
 def test_annotation_invalid_name(tmp_dataset_fixture):  # NOQA
 
@@ -72,6 +89,20 @@ def test_get_non_existing_annotation(tmp_dataset_fixture):  # NOQA
     assert result.output.strip() == expected
 
 
+def test_delete_non_existing_annotation(tmp_dataset_fixture):  # NOQA
+
+    from dtool_annotation.cli import annotation
+
+    runner = CliRunner()
+
+    result = runner.invoke(annotation, [
+        "delete",
+        tmp_dataset_fixture.uri,
+        "project",
+    ])
+    assert result.exit_code == 0
+
+
 def test_annotation_types(tmp_dataset_fixture):  # NOQA
 
     from dtool_annotation.cli import annotation