Merge pull request #7 from funkelab/array-overhaul

Array overhaul

.github/workflows/black.yaml

@@ -0,0 +1,19 @@
+name: Python Black
+
+on: [push, pull_request]
+
+jobs:
+  lint:
+    name: Python Lint
+    runs-on: ubuntu-latest
+    steps:
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10' 
+      - name: Setup checkout
+        uses: actions/checkout@master
+      - name: Lint with Black
+        run: |
+          pip install black
+          black funlib/show/neuroglancer --diff --check

.github/workflows/publish.yaml

@@ -0,0 +1,34 @@
+name: Publish
+
+on:
+  push:
+    tags: ["*"]
+
+jobs:
+  build-n-publish:
+    name: Build and publish Python 🐍 distributions 📦 to PyPI and TestPyPI
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@master
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v3
+        with:
+          python-version: "3.10"
+      - name: Install pypa/build
+        run: >-
+          python -m
+          pip install
+          build
+          --user
+      - name: Build a binary wheel and a source tarball
+        run: >-
+          python -m
+          build
+          --sdist
+          --wheel
+          --outdir dist/
+      - name: Publish distribution 📦 to PyPI
+        if: startsWith(github.ref, 'refs/tags')
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}

README.rst

@@ -11,3 +11,32 @@ Currently contains:
 - a modified ``video_tool.py`` to work with ``LocalVolume``
 
 - a convenience method to add daisy-like arrays to a neuroglancer context
+
+Usage
+-----
+
+You can use terminal glob syntax to select multiple volumes for visualization:
+
+`neuroglancer path/to/your/data.zarr/and/volumes/*`
+
+Extra optional arguments are:
+
+- `--no-browser`
+- `--bind-address`
+- `--port`
+
+
+We also have slicing support (This command will select only the first channel of raw from every crop):
+
+`neuroglancer data.zarr/crop_*/raw[0]`
+
+This can lead to a conflict if you want to use glob expansion to select multiple arrays.
+Here it is unclear if you want to visualize the arrays `raw_1`, `raw_3`, `raw_4` and `raw_5`,
+or if you want to visualize channel `1345` of the array `raw_`.
+
+`neuroglancer data.zarr/raw_[1345]`
+
+To make this less ambiguous, we allow the use of the `:` character to separate the array glob from the
+slicing patter. So the following command will select the arrays `raw_1`, `raw_3`, `raw_4` and `raw_5`:
+
+`neuroglancer data.zarr/raw_[1345]:`

funlib/show/neuroglancer/__init__.py

@@ -1,3 +1,7 @@
-from .video_tool import RenderArgs, run_edit, run_render
-from .scale_pyramid import ScalePyramid
-from .add_layer import add_layer
+from .video_tool import (
+    RenderArgs as RenderArgs,
+    run_edit as run_edit,
+    run_render as run_render,
+)
+from .scale_pyramid import ScalePyramid as ScalePyramid
+from .add_layer import add_layer as add_layer