Modularize biahub

.github/workflows/pull-request-ci.yml

@@ -11,37 +11,39 @@ jobs:
     name: Check Style
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v6
       - uses: actions/setup-python@v5
         with:
           python-version: "3.11"
       - uses: psf/black@stable
         with:
           src: "biahub"
           options: "--check --verbose"
-          use_pyproject: true # Requires python >3.11
+          use_pyproject: true
       - uses: py-actions/flake8@v2
         with:
           path: "biahub"
-          flake8-version: "7.2.0" # Duplicates the version in pyproject.toml
+          flake8-version: "7.2.0"
       - uses: isort/isort-action@v1
         with:
-          isort-version: "6.0.1" # Duplicates the version in pyproject.toml
+          isort-version: "6.0.1"
 
   test:
     name: Run Tests
     needs: [style]
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
+    - uses: astral-sh/setup-uv@v6
     - uses: actions/setup-python@v5
       with:
         python-version: "3.11"
 
     - name: Install the biahub package
-      run: |
-        python -m pip install --upgrade pip
-        pip install torch torchvision ".[dev]" --extra-index-url https://download.pytorch.org/whl/cpu
+      run: uv sync --extra dev
+      env:
+        UV_EXTRA_INDEX_URL: https://download.pytorch.org/whl/cpu
 
     - name: Test with pytest
-      run: pytest -v
+      run: uv run pytest -v

CLAUDE.md

@@ -0,0 +1,55 @@
+# Claude Code Instructions for biahub
+
+## Environment
+
+- **Conda envs**: `/hpc/mydata/$USER/envs/`
+- **biautils** (iohub, biahub CLI): `module load anaconda; module load comp_micro; conda activate biautils`
+- **neuroglancer**: `conda activate /hpc/mydata/$USER/envs/neuroglancer_iohub`
+
+## Repository Structure
+
+Single package, managed with uv (migration in progress from setuptools).
+
+```
+biahub/
+├── pyproject.toml       # uv-managed project
+├── biahub/              # Main package
+│   ├── cli/             # Click CLI + Hydra pipeline CLI
+│   ├── *.py             # Processing modules
+│   └── vendor/          # Vendored dependencies
+├── settings/            # Example YAML configs
+├── tests/
+└── plans/               # Migration plans
+```
+
+## Reference Data
+
+- **Widefield (Hummingbird)**: `/hpc/projects/intracellular_dashboard/virtual_stain_ft_infected/2026_01_29_A549_H2B_CAAX_DAPI_DENV_ZIKV/`
+- **Light-sheet (Mantis)**: `/hpc/projects/intracellular_dashboard/organelle_dynamics/2025_08_26_A549_SEC61_TOMM20_ZIKV/`
+- **Test data**: `/hpc/projects/intracellular_dashboard/refactor_biahub/`
+
+## Plans
+
+- `plans/biahub-uv.md` — Migrate packaging from setuptools to uv
+- `plans/biahub-cli-refactor.md` — Add Hydra pipeline CLI and config templates
+
+## Code Conventions
+
+- Click for CLI, Pydantic v2 for settings (`extra="forbid"`)
+- Absolute imports: `from biahub.X import Y`
+- OME-Zarr format via iohub library
+- Use absolute HPC paths
+
+## Viewing Data
+
+```bash
+# Neuroglancer (preferred)
+neuroglancer_view.py /path/to/data.zarr --position A/1/0
+
+# Browser dashboard (nd-embedding-atlas)
+python /hpc/mydata/$USER/code/nd-embedding-atlas/scripts/ndimg_view.py /path/to/data.zarr --position A/1/0
+```
+
+## Related PRs
+
+- PR #200 (feature/merge-mantis-analysis-template): Do NOT merge

plans/biahub-cli-refactor.md

@@ -0,0 +1,90 @@
+# Plan: Add Hydra pipeline CLI and config templates to biahub
+
+## Goal
+
+Add a Hydra-based pipeline CLI (`biahub-pipeline`) that orchestrates multi-step processing workflows. Config templates define microscope-specific parameters and step sequences. Everything lives inside the existing `biahub` package.
+
+## Key Decisions
+
+- **Single package**: Hydra CLI and configs live inside `biahub/`, not a separate package
+- **Microscope naming**: Configs will be named after the microscope and first objective to specify the type of experiment, which specifies good defaults (e.g., `mantis_63x_1.35`, `hummingbird_20x_0.55`, `dragonfly_20x_0.55`, `dragonfly_63x_1.47`, `hummingbird_63x_1.47`). Each microscope config template will contain a comment section that specifies NA, wavelength, channels.
+- **First pipeline**: 4-stage widefield+label-free (convert → reconstruct → register → virtual stain)
+- **Logging**: Save resolved YAML configs alongside output data
+
+## Directory Structure (additions)
+
+```
+biahub/
+├── cli/
+│   ├── main.py              # Existing Click CLI
+│   └── pipeline.py          # New Hydra entry point
+├── conf/                    # Hydra config templates
+│   ├── config.yaml          # Main defaults
+│   ├── microscope/
+│   │   ├── mantis_63x_1.35.yaml
+│   │   └── hummingbird_63x_1.47.yaml
+│   ├── step/
+│   │   ├── reconstruct.yaml
+│   │   ├── register.yaml
+│   │   └── virtual_stain.yaml
+│   └── slurm/
+│       ├── default.yaml
+│       └── gpu.yaml
+└── pipeline/                # Step orchestration
+    ├── __init__.py
+    ├── runner.py            # Pipeline executor
+    └── steps.py             # Step wrappers (convert, reconstruct, register, etc.)
+```
+
+## Entry Point
+
+Add to `pyproject.toml`:
+```toml
+[project.scripts]
+biahub-pipeline = "biahub.cli.pipeline:main"
+```
+
+## Usage
+
+```bash
+# Run full pipeline
+biahub-pipeline microscope=hummingbird_63x_1.47 \
+  input_path=/data/raw output_path=/data/processed
+
+# Dry run
+biahub-pipeline ... dry_run=true
+
+# Skip a step
+biahub-pipeline ... steps.virtual_stain=false
+
+# Submit to SLURM with GPU
+biahub-pipeline ... slurm=gpu
+```
+
+## Pipeline Steps
+
+| Step | Wraps |
+|------|-------|
+| convert | `iohub convert` |
+| reconstruct | `biahub reconstruct` |
+| register | `biahub estimate-registration` + `biahub register` |
+| virtual_stain | `viscy preprocess` + `viscy predict` |
+
+## Dependencies to Add
+
+```
+hydra-core>=1.3
+hydra-submitit-launcher>=1.2
+omegaconf>=2.3
+```
+
+## Reference Data
+
+- **Ground truth**: `/hpc/projects/intracellular_dashboard/virtual_stain_ft_infected/2026_01_29_A549_H2B_CAAX_DAPI_DENV_ZIKV/`
+- **Test data**: `/hpc/projects/intracellular_dashboard/refactor_biahub/test_widefield.zarr`
+  - 2 FOVs from the widefield dataset (channels: DAPI, TXR, BF)
+
+## Validation
+
+1. Run pipeline on test data, compare output structure to ground truth
+2. Ensure existing Click CLI (`biahub --help`) still works unchanged

plans/biahub-uv.md

@@ -0,0 +1,39 @@
+# Plan: Migrate biahub packaging from setuptools to uv
+
+## Goal
+
+Convert biahub from setuptools to uv as the package manager. Single package — no workspaces.
+
+## Changes
+
+### 1. Replace build system in pyproject.toml
+
+- Replace `[build-system]` from setuptools to hatchling (uv's default)
+- Remove `[tool.setuptools]` and `[tool.setuptools.dynamic]` sections
+- Set a static version or use hatch-vcs for versioning
+- Keep all existing dependencies, scripts, optional-dependencies unchanged
+
+### 2. Add uv-specific configuration
+
+- Add `[tool.uv]` section if needed (e.g., for git dependency overrides)
+- Handle git dependencies (`stitch`, `waveorder`) — may need `[tool.uv.sources]` for these
+
+### 3. Generate lockfile
+
+- Run `uv lock` to generate `uv.lock`
+- Add `uv.lock` to version control
+
+### 4. Verify
+
+```bash
+uv sync --all-extras
+biahub --help
+pytest tests/
+```
+
+## Notes
+
+- No directory moves — `biahub/` package stays where it is
+- All imports unchanged
+- Click CLI entry point unchanged
+- Existing `settings/` YAML configs unchanged

pyproject.toml

@@ -1,30 +1,27 @@
 [build-system]
-requires = ["setuptools >= 61", "setuptools_scm[toml]>=3.4", "wheel"]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
 
 [project]
 name = "biahub"
+version = "0.1.0"
 description = "Bioimage analysis hub."
 readme = "README.md"
 license = { file = "LICENSE" }
 requires-python = ">=3.11, <4.0"
 
-# the dynamically determined project metadata attributes
-dynamic = ["version"]
-
 classifiers = [
   "Development Status :: 3 - Alpha",
   "Intended Audience :: Science/Research",
   "Programming Language :: Python :: 3 :: Only",
   "Programming Language :: Python :: 3.11",
 ]
 
-# list package dependencies here
 dependencies = [
   "iohub[tensorstore]>=0.3.0a5,<0.4",
-  "stitch @ git+https://github.com/ahillsley/stitching@jen",
+  "stitch",
   "matplotlib",
-  "napari",
-  "PyQt6",
+  "napari[all]",
   "natsort",
   "numpy",
   "markdown",
@@ -35,7 +32,7 @@ dependencies = [
   "submitit",
   "torch",
   "tqdm",
-  "waveorder @ git+https://github.com/mehta-lab/waveorder.git",
+  "waveorder",
   "largestinteriorrectangle",
   "antspyx",
   "pystackreg",
@@ -76,16 +73,9 @@ doc = [
 [project.scripts]
 biahub = "biahub.cli.main:cli"
 
-[tool.setuptools]
-# explicitly specify the package name
-# TODO: is there a better way to do this?
-packages = ["biahub"]
-
-# allow use of __file__ to load data files included in the package
-zip-safe = false
-
-[tool.setuptools.dynamic]
-version = { attr = "biahub.__version__" }
+[tool.uv.sources]
+stitch = { git = "https://github.com/ahillsley/stitching", branch = "jen" }
+waveorder = { git = "https://github.com/mehta-lab/waveorder.git" }
 
 [tool.black]
 line-length = 95