diff --git a/.bumpversion.cfg b/.bumpversion.cfg deleted file mode 100644 index 681a9f46..00000000 --- a/.bumpversion.cfg +++ /dev/null @@ -1,6 +0,0 @@ -[bumpversion] -current_version = 7.0.2 -commit = True -tag = True - -[bumpversion:file:caveclient/__init__.py] diff --git a/.github/workflows/dev.yml b/.github/workflows/dev.yml index 3167f954..6614da91 100644 --- a/.github/workflows/dev.yml +++ b/.github/workflows/dev.yml @@ -7,9 +7,9 @@ on: push: branches: - master - paths-ignore: - - "README.rst" pull_request: + branches: + - master # Allows you to run this workflow manually from the Actions tab workflow_dispatch: # Allows other workflows to trigger this workflow @@ -27,32 +27,15 @@ jobs: steps: - uses: actions/checkout@v4 - - name: Set up Python - uses: actions/setup-python@v5 - with: - python-version: ${{ matrix.python-version }} - - - uses: actions/cache@v4 + - name: Install the latest version of uv + id: setup-uv + uses: astral-sh/setup-uv@v2 with: - path: ~/.cache/pip - key: ${{ runner.os }}-${{ matrix.python-version }}-pip-${{ hashFiles('**/test_requirements.txt') }} - restore-keys: | - ${{ runner.os }}-${{ matrix.python-version }}-pip- + version: "0.5.2" - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install flake8 pytest - pip install -r requirements.txt - pip install -r test_requirements.txt - - - 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=10 --max-line-length=127 --statistics + - name: Set up venv + run: uv sync --python ${{ matrix.python-version }} - name: Test with pytest run: | - pytest + uvx --from poethepoet poe test \ No newline at end of file diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 4eae4dce..ffbc5bd8 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -28,33 +28,19 @@ jobs: - name: Get gh-pages branch run: git fetch origin gh-pages --depth=1 - - name: Setup Python - uses: actions/setup-python@v5 - with: - python-version: ${{ matrix.python-version }} - - - name: Update pip - run: python -m pip install --upgrade pip - - - name: Cache for virtual environment - uses: actions/cache@v3 - with: - path: ./.venv - key: venv-${{ matrix.os }}-${{ matrix.python-version }}-${{ hashFiles('doc_requirements.txt') }} - - - name: Install dependencies - run: pip install -r doc_requirements.txt - - name: Configure git for github-actions[bot] run: | git config --global user.name "github-actions[bot]" git config --global user.email "github-actions[bot]@users.noreply.github.com" - # - name: Build and push versioned docs with mike - # run: | - # poetry run mike deploy --push --update-aliases dev - # poetry run mike set-default stable --push + - name: Install the latest version of uv + id: setup-uv + uses: astral-sh/setup-uv@v2 + with: + version: "0.5.2" - - name: Build and push docs - run: | - mkdocs gh-deploy --force --remote-branch gh-pages --remote-name origin + - name: Set up Python + run: uv sync --python ${{ matrix.python-version }} + + - name: Install dependencies + run: uvx --from poethepoet poe doc-push diff --git a/.github/workflows/format.yml b/.github/workflows/format.yml index bb927427..db6d0fb3 100644 --- a/.github/workflows/format.yml +++ b/.github/workflows/format.yml @@ -14,9 +14,12 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v4 - - uses: chartboost/ruff-action@v1 - with: # the --extend-select flag adds import sorting - args: check . --extend-select I - - uses: chartboost/ruff-action@v1 + - name: Install uv + id: setup-uv + uses: astral-sh/setup-uv@v2 with: - args: format . --check + version: "0.5.2" + - name: Set up environment + run: uv sync --python 3.11 + - name: Run format checks + run: uvx --from poethepoet poe lint diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 44acd577..81e6fdb2 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -16,11 +16,6 @@ on: type: boolean required: true default: true - skip-tests: - description: "Skip tests" - type: boolean - required: true - default: false jobs: bump: @@ -37,23 +32,20 @@ jobs: steps: - name: Checkout uses: actions/checkout@v4 + - name: Install uv + id: setup-uv + uses: astral-sh/setup-uv@v2 + with: + version: "0.5.2" - name: Get tags run: git fetch --tags origin - name: Configure git for github-actions[bot] run: | git config --global user.name "github-actions[bot]" git config --global user.email "github-actions[bot]@users.noreply.github.com" - - name: Install Python - uses: actions/setup-python@v5 - with: - python-version: "3.11" - - name: Install Twine - run: pip install twine - - name: Install bumpversion - run: pip install bumpversion - name: Bump version with bumpversion run: | - bumpversion ${{ github.event.inputs.part }} + uvx --from bump-my-version bump-my-version bump ${{ github.event.inputs.part }} - name: Commit and push with tags if: ${{ github.event.inputs.dry-run == 'false' }} run: git push --follow-tags @@ -86,12 +78,13 @@ jobs: with: # want this to be the version that was just bumped ref: master - - name: Set up Python - uses: actions/setup-python@v5 + - name: Install uv + id: setup-uv + uses: astral-sh/setup-uv@v2 with: - python-version: "3.11" - - name: build sdist - run: python setup.py sdist + version: "0.5.2" + - name: Build + run: uv build - name: Store the distribution packages uses: actions/upload-artifact@v4 with: diff --git a/MANIFEST.in b/MANIFEST.in deleted file mode 100644 index 540b7204..00000000 --- a/MANIFEST.in +++ /dev/null @@ -1 +0,0 @@ -include requirements.txt \ No newline at end of file diff --git a/README.md b/README.md index 077853df..325f3f52 100644 --- a/README.md +++ b/README.md @@ -17,8 +17,17 @@ A full description of the Connectome Annotation Versioning Engine can be found [ ```bash pip install caveclient ``` + +To add optional dependencies (currently for interfacing with the segmentation, imagery, +and some skeleton formats via cloud-volume), you can install with the following: + +```bash +pip install caveclient[cv] +``` + ## Python version support -Currently we are officially supporting and testing against python 3.8, 3.9, 3.10, 3.11 and 3.12. + +Currently we are officially supporting and testing against Python 3.8, 3.9, 3.10, 3.11 and 3.12. ## Documentation diff --git a/caveclient/__init__.py b/caveclient/__init__.py index 950a1908..2101974d 100644 --- a/caveclient/__init__.py +++ b/caveclient/__init__.py @@ -1,4 +1,6 @@ -__version__ = "7.0.2" +import importlib.metadata + +__version__ = importlib.metadata.version("CAVEclient") from .frameworkclient import CAVEclient from .session_config import get_session_defaults, set_session_defaults diff --git a/doc_requirements.txt b/doc_requirements.txt deleted file mode 100644 index 02586e5b..00000000 --- a/doc_requirements.txt +++ /dev/null @@ -1,14 +0,0 @@ -mkdocs -mkdocs-autorefs -mkdocs-git-authors-plugin -mkdocs-git-committers-plugin-2 -mkdocs-git-revision-date-localized-plugin -mkdocs-include-markdown-plugin -mkdocs-jupyter -mkdocs-macros-plugin -mkdocs-material -mkdocs-material-extensions -mkdocs-section-index -mkdocstrings[crystal,python] -mknotebooks -pymdown-extensions \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 00000000..49287c48 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,94 @@ +[project] +authors = [{ name = "CAVE Developers" }] +classifiers = [] +dependencies = [ + "attrs>=21.3.0", + "cachetools>=4.2.1", + "ipython>6", + "jsonschema", + "networkx", + "oldest-supported-numpy", + "packaging>=24.1", + "pandas<3.0.0", + "pyarrow>=3", + "requests", + "urllib3", +] +description = "A client for interacting with the Connectome Annotation Versioning Engine" +license = "MIT" +maintainers = [{ name = "CAVE Developers" }] +name = "caveclient" +readme = "README.md" +requires-python = ">=3.8" +version = "7.0.2" + +[project.urls] +Documentation = "https://caveconnectome.github.io/CAVEclient/" +Homepage = "https://caveconnectome.github.io/CAVEclient/" +Issues = "https://github.com/CAVEconnectome/CAVEclient/issues" +Repository = "https://github.com/CAVEconnectome/CAVEclient/" + +[project.optional-dependencies] +cv = ["cloud-volume"] + +[dependency-groups] +bump = ['bump-my-version'] +dev = [ + { include-group = 'bump' }, + { include-group = 'docs' }, + { include-group = 'lint' }, + { include-group = 'test' }, +] +docs = [ + "mkdocs", + "mkdocs-autorefs", + "mkdocs-git-authors-plugin", + "mkdocs-git-committers-plugin-2", + "mkdocs-git-revision-date-localized-plugin", + "mkdocs-include-markdown-plugin", + "mkdocs-jupyter", + "mkdocs-macros-plugin", + "mkdocs-material", + "mkdocs-material-extensions", + "mkdocs-section-index", + "mkdocstrings[crystal,python]", + "mknotebooks", + "pymdown-extensions", +] +lint = ["ruff"] +test = ["pytest", "pytest-cov", "pytest-env", "pytest-mock", "responses"] + +[tool.bumpversion] +allow_dirty = false +commit = true +commit_args = "" +current_version = "7.0.2" +ignore_missing_version = false +message = "Bump version: {current_version} → {new_version}" +parse = "(?P\\d+)\\.(?P\\d+)\\.(?P\\d+)" +regex = false +replace = "{new_version}" +search = "{current_version}" +serialize = ["{major}.{minor}.{patch}"] +sign_tags = false +tag = true +tag_message = "Bump version: {current_version} → {new_version}" +tag_name = "v{new_version}" + +[[tool.bumpversion.files]] +filename = "pyproject.toml" + +[tool.poe.tasks] +checks = ['doc-build', 'lint', 'test'] +doc-build = "mkdocs build" +doc-push = "mkdocs gh-deploy --force --remote-branch gh-pages --remote-name origin" +doc-serve = "mkdocs serve" +dry-bump = "uv run bump-my-version bump --dry-run --verbose" +lint = ['lint-check', 'lint-format'] +lint-check = "uv run ruff check . --extend-select I" +lint-format = "uv run ruff format . --check" +test = "uv run pytest tests" + +[build-system] +build-backend = "hatchling.build" +requires = ["hatchling"] diff --git a/setup.py b/setup.py deleted file mode 100644 index 22a7fa44..00000000 --- a/setup.py +++ /dev/null @@ -1,45 +0,0 @@ -import codecs -import os -import re -from pathlib import Path - -from setuptools import find_packages, setup - -here = os.path.abspath(os.path.dirname(__file__)) - - -def read(*parts): - with codecs.open(os.path.join(here, *parts), "r") as fp: - return fp.read() - - -def find_version(*file_paths): - version_file = read(*file_paths) - version_match = re.search(r"^__version__ = ['\"]([^'\"]*)['\"]", version_file, re.M) - if version_match: - return version_match.group(1) - raise RuntimeError("Unable to find version string.") - - -with open("requirements.txt", "r") as f: - required = f.read().splitlines() - -# read the contents of README file -this_directory = Path(__file__).parent -long_description = (this_directory / "README.md").read_text() - -setup( - version=find_version("caveclient", "__init__.py"), - name="caveclient", - description="A client for interacting with the Connectome Annotation Versioning Engine", - long_description=long_description, - long_description_content_type="text/markdown", - author="Forrest Collman, Casey Schneider-Mizell, Sven Dorkenwald", - author_email="forrestc@alleninstute.org,caseys@alleninstitute.org,svenmd@princeton.edu,", - url="https://github.com/CAVEconnectome/CAVEclient", - packages=find_packages(where="."), - include_package_data=True, - install_requires=required, - setup_requires=["pytest-runner"], - python_requires=">=3.7", -) diff --git a/test_requirements.txt b/test_requirements.txt deleted file mode 100644 index fefdccd9..00000000 --- a/test_requirements.txt +++ /dev/null @@ -1,5 +0,0 @@ -pytest -pytest-cov -pytest-env -responses -pytest-mock diff --git a/uv.lock b/uv.lock new file mode 100644 index 00000000..d88b2818 --- /dev/null +++ b/uv.lock @@ -0,0 +1,4820 @@ +version = 1 +requires-python = ">=3.8" +resolution-markers = [ + "(python_full_version < '3.9' and platform_machine != 'aarch64' and platform_machine != 'arm64' and platform_machine != 'loongarch64' and platform_machine != 's390x' and platform_python_implementation != 'PyPy' and sys_platform != 'win32' and platform_machine in 'arm64|aarch64|s390x|loongarch64') or (python_full_version < '3.9' and platform_machine == 'arm64' and platform_python_implementation != 'PyPy' and platform_system 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