Migration from microDL

.codecov.yml

@@ -0,0 +1,14 @@
+coverage:
+  precision: 2
+  round: down
+  range: "70...100"
+
+  status:
+    project: yes
+    patch: no
+    changes: no
+
+comment:
+  layout: "header, reach, diff, flags, files, footer"
+  behavior: default
+  require_changes: no

.github/workflows/pr.yml

@@ -0,0 +1,35 @@
+name: Lint and Test
+
+on: pull_request
+
+jobs:
+  lint:
+    name: Lint
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: psf/black@stable
+        with:
+          src: "viscy"
+          options: "--check --verbose"
+      - uses: chartboost/ruff-action@v1
+        with:
+          src: "viscy"
+
+  test:
+    needs: [lint]
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10"]
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install ".[metrics,dev]"
+      - name: Test with pytest
+        run: pytest -v

.gitignore

@@ -0,0 +1,40 @@
+.idea
+.DS_Store
+__pycache__/
+.ipynb_checkpoints/
+.vscode
+
+# written by setuptools_scm
+*/_version.py
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/

CONTRIBUTING.md

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+# Contributing to viscy
+
+## Development installation
+
+Clone or fork the repository,
+then make an editable installation with optional dependencies:
+
+```sh
+# in project root directory
+pip install ".[dev,metrics]"
+```
+
+## Testing
+
+Run tests with `pytest`:
+
+```sh
+pytest
+```

LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2023, Computational Microscopy Platform (Mehta Lab), CZ Biohub
+Copyright (c) 2023, CZ Biohub SF
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:

README.md

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+# viscy
+
+viscy is a machine learning toolkit to solve computer vision problems
+in high-throughput imaging of cells.
+
+## Installation
+
+(Optional) create a new virtual/Conda environment.
+
+Clone this repository and install viscy:
+
+```sh
+git clone https://github.com/mehta-lab/viscy.git
+pip install viscy
+```
+
+Verify installation by accessing the CLI help message:
+
+```sh
+viscy --help
+```
+
+For development installation, see [the contributing guide](CONTRIBUTING.md).
+
+Full functionality is only tested on Linux `x86_64` with NVIDIA Ampere GPUs (CUDA 12.0).
+Some features (e.g. mixed precision and distributed training) may not work with other setups,
+see [PyTorch documentation](https://pytorch.org) for details.
+
+## Predicting sub-cellular structure
+
+Training a model for the segmentation of sub-cellular landmarks
+such as nuclei and membrane
+directly can require laborious manual annotation.
+We use fluorescent markers as a proxy of human-annotated masks
+and turn this instance segmentation problem into
+an image-to-image translation (I2I) problem.
+
+viscy features an end-to-end pipeline to design, train and evaluate
+I2I models in a declarative manner.
+It supports 2D, 2.5D (3D encoder, 2D decoder) and 3D U-Nets,
+as well as 3D networks with anisotropic filters.

pyproject.toml

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+[build-system]
+requires = ["setuptools", "setuptools-scm[toml]"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "viscy"
+description = "Learning vision for cells"
+readme = "README.md"
+# cannot build on 3.11 due to https://github.com/cheind/py-lapsolver/pull/18
+requires-python = ">=3.9,!=3.11"
+license = { file = "LICENSE" }
+authors = [{ name = "CZ Biohub SF", email = "[email protected]" }]
+dependencies = [
+    "iohub==0.1.0.dev3",
+    "torch>=2.0.0",
+    "torchvision>=0.15.1",
+    "tensorboard>=2.13.0",
+    "lightning>=2.0.1",
+    "monai>=1.2.0",
+    "jsonargparse[signatures]>=4.20.1",
+    "scikit-image>=0.19.2",
+    "matplotlib",
+]
+dynamic = ["version"]
+
+[project.optional-dependencies]
+metrics = [
+    "cellpose==2.1.0",
+    "lapsolver==1.1.0",
+    "scikit-learn>=1.1.3",
+    "scipy>=1.8.0",
+    "torchmetrics[detection]>=1.0.0",
+]
+dev = ["pytest", "pytest-cov", "hypothesis", "profilehooks", "onnxruntime"]
+
+[project.scripts]
+viscy = "viscy.cli.cli:main"
+
+[tool.setuptools_scm]
+write_to = "viscy/_version.py"
+
+[tool.black]
+src = ["viscy"]
+line-length = 88
+
+[tool.ruff]
+src = ["viscy", "tests"]
+extend-select = ["I001"]
+
+[tool.ruff.isort]
+known-first-party = ["viscy"]

tests/__init__.py

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+"""Tests for viscy"""