Use pyproject.toml and new build system (#232)

* draft pyproject.toml

* refactor versioning logic

* try redo dev workflow

* add lockfile

* try sync

* specify test dev

* lock

* remove 3.7

* add ipython

* try no ipython again

* add ipython back in

* add new lock

* test on 3.8 again

* skip locking

* fix venv command

* try uv run

* try oldest supported numpy

* docs

* rename

* fix up actions

* wip actions

* action fixes

* add pyproject.toml to bumpversion

* fix action

* change message name

.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

.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

.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

.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:

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
 

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

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<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\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"]