Configure CI

.github/workflows/ci.yaml

@@ -0,0 +1,95 @@
+name: CI
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+
+# Automatically stop old builds on the same branch/PR
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  setup:
+    name: Setup workflow
+    runs-on: ubuntu-latest
+    permissions:
+      pull-requests: read
+    outputs:
+      code_change: ${{ steps.filter.outputs.code }}
+      matrix: ${{ env.MATRIX }}
+    steps:
+      - uses: actions/checkout@v4
+        if: github.event_name != 'pull_request'
+
+      - name: Check for code changes
+        uses: dorny/paths-filter@v3
+        id: filter
+        with:
+          filters: |
+            code:
+              - 'src/**'
+              - 'pyproject.toml'
+              - '.github/workflows/ci.yaml'
+
+      - name: Set matrix option
+        run: |
+          if [[ '${{ github.event_name }}' == 'workflow_dispatch' ]]; then
+            OPTION=${{ github.event.inputs.target }}
+          elif [[ '${{ github.event_name }}' == 'schedule' ]]; then
+            OPTION="full"
+          elif [[ '${{ github.event_name }}' == 'push' && '${{ github.ref_type }}' == 'tag' ]]; then
+            OPTION="full"
+          else
+            OPTION="default"
+          fi
+          echo "MATRIX_OPTION=$OPTION" >> $GITHUB_ENV
+
+      - name: Set test matrix with 'default' option
+        if: env.MATRIX_OPTION == 'default'
+        run: |
+          MATRIX=$(jq -nsc '{
+              "os": ["ubuntu-latest", "macos-latest", "windows-latest"],
+              "environment": ["test-310", "test-312"],
+          }')
+          echo "MATRIX=$MATRIX" >> $GITHUB_ENV
+
+      - name: Set test matrix with 'full' option
+        if: env.MATRIX_OPTION == 'full'
+        run: |
+          MATRIX=$(jq -nsc '{
+              "os": ["ubuntu-latest", "macos-latest", "windows-latest"],
+              "environment": ["test-310", "test-311", "test-312"]
+          }')
+          echo "MATRIX=$MATRIX" >> $GITHUB_ENV
+
+      - name: Set test matrix with 'downstream' option
+        if: env.MATRIX_OPTION == 'downstream'
+        run: |
+          MATRIX=$(jq -nsc '{
+              "os": ["ubuntu-latest"],
+              "environment": ["test-311"]
+          }')
+          echo "MATRIX=$MATRIX" >> $GITHUB_ENV
+
+  pixi_lock:
+    name: Pixi lock
+    runs-on: ubuntu-latest
+    steps:
+      - uses: holoviz-dev/holoviz_tasks/pixi_lock@v0
+        with:
+          cache: ${{ github.event.inputs.cache == 'true' || github.event.inputs.cache == '' }}
+
+  pre-commit:
+    timeout-minutes: 30
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout branch
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+      - name: Set up pixi
+        uses: prefix-dev/setup-pixi@ba3bb36eb2066252b2363392b7739741bb777659 # v0.8.1
+        with:
+          environments: default lint
+      - name: pre-commit
+        run: pixi run pre-commit-run --color=always --show-diff-on-failure

.gitignore

@@ -1,3 +1,3 @@
 .venv
 .pyc
-.env
+.env

.pre-commit-config.yaml

@@ -0,0 +1,31 @@
+default_stages: [pre-commit]
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: check-builtin-literals
+      - id: check-case-conflict
+      - id: check-docstring-first
+      - id: check-executables-have-shebangs
+      - id: check-toml
+      - id: check-json
+      - id: detect-private-key
+      - id: end-of-file-fixer
+        exclude: \.min\.js$
+      - id: trailing-whitespace
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.7.0
+    hooks:
+      - id: ruff
+        files: src/panel_neuroglancer
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
+    hooks:
+      - id: codespell
+        additional_dependencies:
+          - tomli
+  - repo: https://github.com/shssoichiro/oxipng
+    rev: v8.0.0
+    hooks:
+      - id: oxipng
+        stages: [manual]

pixi.toml

@@ -0,0 +1,63 @@
+[project]
+name = "panel-neuroglancer"
+channels = ["conda-forge"]
+platforms = ["osx-arm64", "osx-64", "linux-64", "win-64"]
+
+[tasks]
+postinstall = "pip install --no-build-isolation --no-deps --disable-pip-version-check -e ."
+
+[dependencies]
+python = ">=3.10"
+panel = ">=1.5.4"
+packaging = "*"
+
+[pypi-dependencies]
+neuroglancer = ">=2.40.1"
+
+[host-dependencies]
+pip = "*"
+setuptools = ">=61"
+setuptools-scm = "*"
+hatchling = "*"
+hatch-vcs = "*"
+
+[feature.test.dependencies]
+pytest = ">=6"
+pytest-cov = "*"
+pytest-rerunfailures = "*"
+pytest-xdist = "*"
+mypy = "*"
+[feature.test.tasks]
+test = "pytest"
+test-coverage = "pytest --cov=panel_neuroglancer--cov-report=xml --cov-report=term-missing"
+
+[feature.build.dependencies]
+python-build = "*"
+twine = "*"
+wheel = "*"
+
+[feature.build.tasks]
+build-wheel = "python -m build --no-isolation ."
+check-wheel = "twine check dist/*"
+
+[feature.lint.dependencies]
+pre-commit = "*"
+
+[feature.lint.tasks]
+pre-commit-install = "pre-commit install"
+pre-commit-run = "pre-commit run -a"
+
+[feature.py310.dependencies]
+python = "3.10.*"
+[feature.py311.dependencies]
+python = "3.11.*"
+[feature.py312.dependencies]
+python = "3.12.*"
+
+[environments]
+default = ["test"]
+py310 = ["py310", "test"]
+py311 = ["py311", "test"]
+py312 = ["py312", "test"]
+build = ["build"]
+lint = { features = ["lint"], no-default-feature = true }

pyproject.toml

@@ -1,10 +1,91 @@
+[build-system]
+requires = ["hatchling", "hatch-vcs", "panel>=1.5.4", "packaging"]
+build-backend = "hatchling.build"
+
 [project]
 name = "panel-neuroglancer"
-version = "0.1.0"
-description = "Add your description here"
+dynamic = ["version"]
+description = "Volumetric data viewer built on HoloViz Panel and Neuroglancer"
 readme = "README.md"
 requires-python = ">=3.10"
 dependencies = [
     "neuroglancer>=2.40.1",
     "panel>=1.5.4",
 ]
+classifiers = [
+  "License :: OSI Approved :: BSD License",
+  "Development Status :: 5 - Production/Stable",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
+  "Operating System :: OS Independent",
+  "Intended Audience :: Developers",
+  "Intended Audience :: Science/Research",
+  "Natural Language :: English",
+  "Topic :: Scientific/Engineering",
+  "Topic :: Software Development :: Libraries",
+]
+
+[project.urls]
+Homepage = "https://github.com/panel-extensions/panel-neuroglancer"
+Source = "https://github.com/panel-extensions/panel-neuroglancer"
+
+[tool.ruff]
+exclude = [
+  ".git",
+  "__pycache__",
+  ".tox",
+  ".eggs",
+  "*.egg",
+  "doc",
+  "dist",
+  "build",
+  "_build",
+  "examples",
+  ".ipynb_checkpoints",
+  "node_modules",
+]
+line-length = 165
+fix = true
+
+
+[tool.ruff.lint]
+ignore = [
+  "E402", # Module level import not at top of file
+  "E712", # Avoid equality comparisons to True
+  "E731", # Do not assign a lambda expression, use a def
+  "N803", # Argument name should be lowercase
+  "N806", # Variable name should be lowercase
+]
+select = [
+  "B",      # flake8-bugbear
+  "E",      # pycodestyle errors
+  "F",      # pyflakes
+  "W",      # pycodestyle warnings
+  "I",      # isort
+  "PIE",
+  "T20",
+  "RUF006",
+  "UP004",
+  "UP006",
+  "UP020",
+  "UP028",
+  "UP030",
+  "UP031",
+  "UP032",
+  "UP034",
+  "UP036",
+]
+
+[tool.hatch.version]
+source = "vcs"
+raw-options = { version_scheme = "no-guess-dev" }
+
+[tool.isort]
+force_grid_wrap = 4
+multi_line_output = 5
+combine_as_imports = true
+lines_between_types = 1
+include_trailing_comma = true

src/panel_neuroglancer/neuroglancer.py

@@ -3,11 +3,9 @@
 import neuroglancer
 import panel as pn
 import param
-
 from neuroglancer.viewer import Viewer
 from panel.custom import PyComponent
 
-
 DEMO_URL = "https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22%3A%7B%22x%22%3A%5B6.000000000000001e-9%2C%22m%22%5D%2C%22y%22%3A%5B6.000000000000001e-9%2C%22m%22%5D%2C%22z%22%3A%5B3.0000000000000004e-8%2C%22m%22%5D%7D%2C%22position%22%3A%5B5029.42333984375%2C6217.5849609375%2C1182.5%5D%2C%22crossSectionScale%22%3A3.7621853549999242%2C%22projectionOrientation%22%3A%5B-0.05179581791162491%2C-0.8017329573631287%2C0.0831851214170456%2C-0.5895944833755493%5D%2C%22projectionScale%22%3A4699.372698097029%2C%22layers%22%3A%5B%7B%22type%22%3A%22image%22%2C%22source%22%3A%22precomputed%3A%2F%2Fgs%3A%2F%2Fneuroglancer-public-data%2Fkasthuri2011%2Fimage%22%2C%22tab%22%3A%22source%22%2C%22name%22%3A%22original-image%22%7D%2C%7B%22type%22%3A%22image%22%2C%22source%22%3A%22precomputed%3A%2F%2Fgs%3A%2F%2Fneuroglancer-public-data%2Fkasthuri2011%2Fimage_color_corrected%22%2C%22tab%22%3A%22source%22%2C%22name%22%3A%22corrected-image%22%7D%2C%7B%22type%22%3A%22segmentation%22%2C%22source%22%3A%22precomputed%3A%2F%2Fgs%3A%2F%2Fneuroglancer-public-data%2Fkasthuri2011%2Fground_truth%22%2C%22tab%22%3A%22source%22%2C%22selectedAlpha%22%3A0.63%2C%22notSelectedAlpha%22%3A0.14%2C%22segments%22%3A%5B%223208%22%2C%224901%22%2C%2213%22%2C%224965%22%2C%224651%22%2C%222282%22%2C%223189%22%2C%223758%22%2C%2215%22%2C%224027%22%2C%223228%22%2C%22444%22%2C%223207%22%2C%223224%22%2C%223710%22%5D%2C%22name%22%3A%22ground_truth%22%7D%5D%2C%22layout%22%3A%224panel%22%7D"
 
 
@@ -104,7 +102,7 @@ def _load_state_from_url(self, url):
             new_state = self._parse_state_from_url(url)
             self.viewer.set_state(new_state)
         except Exception as e:
-            print(f"Error loading Neuroglancer state: {e}")
+            print(f"Error loading Neuroglancer state: {e}")  # noqa
 
     def _parse_state_from_url(self, url):
         return neuroglancer.parse_url(url)