update pyproject.toml to work for uv

.github/workflows/python-package.yml

@@ -11,36 +11,23 @@ on:
 
 jobs:
   build:
-
+    name: python
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
         python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
-
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install Hatch
-      run: |
-        python -m pip install --upgrade pip
-        pip install pipx flake8
-        pipx install hatch
-    - name: Set up pip cache
-      if: runner.os == 'Linux'
-      uses: actions/cache@v3
-      with:
-        path: ~/.cache/pip
-        key: ${{ runner.os }}-pip-${{ hashFiles('pyproject.toml') }}-py#{{ matrix.python-version }}
-        restore-keys: ${{ runner.os }}-pip-
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Run tests
-      run: hatch test -i python=${{ matrix.python-version }}
+      - uses: actions/checkout@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v2
+        with:
+          version: "0.5.2"
+      - name: Set up Python ${{ matrix.python-version }}
+        run : uv python install ${{ matrix.python-version }}
+      - name: Install project and dependencies
+        run: uv sync
+      - name: Run tests
+        run: uv run pytest tests
+      - name: Lint with ruff
+        run: uv run ruff check src/*

.pre-commit-config.yaml

@@ -0,0 +1,12 @@
+files: src|tests
+
+repos:
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.7.4
+  hooks:
+    # Run the linter.
+    - id: ruff 
+      types_or: [ python, pyi]
+    - id: ruff-format
+      types_or: [ python, pyi]

pyproject.toml

@@ -4,29 +4,26 @@ build-backend = "hatchling.build"
 
 [project]
 name = "nglui"
-dynamic = ["version"]
+version = "3.6.1"
 description = "Framework for data-driven generation of neuroglancer states."
 readme = "README.md"
-license = "MIT"
-requires-python = ">= 3.9"
+requires-python = ">=3.9"
+dependencies = [
+    "attrs>=24.2.0",
+    "caveclient>=7.0.0",
+    "ipython>=8.18.1",
+    "neuroglancer>=2.40.1",
+    "numpy>=1.26.4",
+    "pandas>=2.2.3",
+    "python-box>=7.2.0",
+    "requests>=2.32.3",
+    "six>=1.16.0",
+    "webcolors>=24.11.1",
+]
 authors = [
     { name = "Casey Schneider-Mizell", email = "[email protected]" },
-    { name = "Derrick Brittain"},
     { name = "Forrest Collman" },
 ]
-
-dependencies = [
-    "python-box",
-    "caveclient>=6.4.1",
-    "ipython",
-    "neuroglancer >= 2.40.1",
-    "numpy>=1.11.0",
-    "pandas>=1.0.0",
-    "requests",
-    "six",
-    "webcolors",
-    "attrs>=23.2.0",
-]
 classifiers = [
     "License :: OSI Approved :: MIT License",
     "Development Status :: 4 - Beta",
@@ -43,44 +40,53 @@ Repository = "https://github.com/CAVEconnectome/nglui.git"
 Changelog = "https://caveconnectome.github.io/nglui/changelog/"
 Issues = "https://github.com/CAVEconnectome/nglui/issues"
 
-[tool.hatch.version]
-path = "src/nglui/__init__.py"
-
-[tool.hatch.build.targets.sdist]
-include = [
-    "/src",
-]
-
-[tool.hatch.envs.default]
-python = "3.12"
-installer = "uv"
-
-[tool.hatch.envs.nglui-nb]
-python = "3.12"
-installer = "uv"
-extra-dependencies = [
-    "ipykernel",
-]
-
-[tool.hatch.envs.hatch-test]
-extra-dependencies = [
+[dependency-groups]
+dev = [
     "pytest",
-    "pytest-mock",
     "pytest-cov",
+    "pytest-mock",
     "responses",
+    "ipykernel",
+    "bump-my-version",
 ]
+docs = [
+    "mkdocs",
+    "mkdocs-material",
+    "mkdocstrings[python]",
+]
+lint = [
+    "ruff"
+]
+[tool.uv]
+default-groups = ["dev", "docs", "lint"]
 
+[tool.bumpversion]
+current_version = "3.6.1"
+parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
+serialize = ["{major}.{minor}.{patch}"]
+search = "{current_version}"
+replace = "{new_version}"
+regex = false
+ignore_missing_version = false
+tag = true
+sign_tags = false
+tag_name = "v{new_version}"
+tag_message = "Bump version: {current_version} → {new_version}"
+allow_dirty = false
+commit = false
+message = "v{new_version}"
+commit_args = ""
 
-[[tool.hatch.envs.hatch-test.matrix]]
-python = ["3.9", "3.10", "3.11", "3.12"]
+[[tool.bumpversion.files]]
+filename = "src/nglui/__init__.py"
 
+[tool.ruff.lint]
+select=["E9","F63","F7","F82"]
 
-[tool.hatch.envs.docs]
-dependencies = [
-  "mkdocs",
-  "mkdocs-material",
-  "mkdocstrings[python]",
-]
-[tool.hatch.envs.docs.scripts]
-build = "mkdocs build --clean --strict"
-serve = "mkdocs serve --dev-addr localhost:8000"
+[tool.poe.tasks.drybump]
+cmd = "uv run bump-my-version bump --dry-run --verbose"
+help = "Dry run of version bump for the project. Use with 'patch', 'minor', or 'major' to specify the version change."
+
+[tool.poe.tasks.bump]
+cmd = "uv run bump-my-version bump"
+help = "Bump the version number in the project. Use with 'patch', 'minor', or 'major' to specify the version change."

src/nglui/easyviewer/ev_base/nglite/json_wrappers.py

@@ -13,7 +13,6 @@
 # limitations under the License.
 """Facilities for converting JSON <-> Python objects"""
 
-
 import collections
 import copy
 import inspect

src/nglui/easyviewer/ev_base/nglite/skeleton.py

@@ -37,7 +37,6 @@ def encode(self, source):
         result.write(edges.tobytes())
         if len(source.vertex_attributes) > 0:
             for name, info in six.iteritems(source.vertex_attributes):
-
                 attribute = np.array(
                     vertex_attributes[name], np.dtype(info.data_type).newbyteorder("<")
                 )

src/nglui/easyviewer/ev_base/nglite_compatibility/base.py

@@ -1,2 +1 @@
 
-

src/nglui/segmentprops/base.py

@@ -388,8 +388,9 @@ def to_dataframe(self):
         "Converts the segment properties to a pandas dataframe"
         df_dict = {"ids": self.ids}
         for prop in self._property_list():
-            if (
-                isinstance(prop, (DescriptionProperty, LabelProperty, NumberProperty, StringProperty))
+            if isinstance(
+                prop,
+                (DescriptionProperty, LabelProperty, NumberProperty, StringProperty),
             ):
                 df_dict[prop.id] = prop.values
             elif isinstance(prop, TagProperty):