linkinpy 0.0.1__tar.gz

linkinpy-0.0.1/.gitignore

@@ -0,0 +1,12 @@
+*.DS_Store
+*uv.lock
+*/__pycache__/*
+*.pyc
+*.tif
+*/target/
+*/build/
+*/.gradle/
+*/dist/
+*/.pytest_cache/
+*/.ruff_cache/
+.vscode/settings.json

linkinpy-0.0.1/CHANGELOG.md

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+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+## [v0.0.1] - Date
+
+### Fixed
+
+
+### Added
+
+
+### Changed
+

linkinpy-0.0.1/CONTRIBUTING.md

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+# Contributing to linkinpy
+
+Thanks for contributing. This guide keeps the local workflow simple and consistent.
+
+## Development Setup
+
+Clone the repository, then enter the Python package folder:
+
+```bash
+git clone https://github.com/YOUR_USERNAME/LinkinPy.git
+cd LinkinPy
+cd LinkinPy/
+```
+
+Create the development environment:
+
+```bash
+uv sync
+uv run pre-commit install
+```
+
+## Daily Workflow
+
+Create a branch for your work:
+
+```bash
+git checkout -b feature/short-description
+```
+
+Run the main local checks before opening a pull request:
+
+```bash
+uv run pytest
+uv run ruff check .
+uv run ruff format .
+uv run python -m build
+```
+
+Or use the shorter `make` targets:
+
+```bash
+make test
+make lint
+make format
+make build
+```
+
+## Command Reference
+
+- `uv sync`: create or update the local environment from `pyproject.toml`
+- `uv run pytest`: run the test suite
+- `uv run ruff check .`: run lint checks
+- `uv run ruff format .`: format the codebase
+- `uv run python -m build`: verify the package builds correctly
+
+The repository also includes a `.python-version` file so local development and CI agree on the interpreter target.
+
+This guide applies to the Python package in `LinkinPy/`.
+Other top-level folders in the repository should keep their own contributing and setup instructions.
+
+## Pull Requests
+
+Before opening a pull request, please make sure:
+
+- tests pass locally
+- linting and formatting are clean
+- the package builds successfully
+- docs are updated if the workflow or public API changed
+- notable changes are reflected in `CHANGELOG.md`
+
+## Code Style
+
+This project keeps the toolchain intentionally small:
+
+- Ruff for linting and formatting
+- Pytest for tests
+- pre-commit for git hook integration
+
+Prefer small, focused changes with clear commit messages and matching tests when behavior changes.
+
+## Getting Help
+
+Open an issue for bugs or feature requests, or contact the maintainers at bruno.msaraiva2@gmail.com if you need help.

linkinpy-0.0.1/GETTING_STARTED.md

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+# Getting Started
+
+This project uses `uv` to manage the local development environment.
+Run every command below from the `LinkinPy/` folder.
+
+The `.python-version` file pins the interpreter version expected for local development and CI.
+
+## 1. Create the environment
+
+```bash
+uv sync
+```
+
+What it does:
+
+- creates a virtual environment if needed
+- installs the project in editable mode
+- installs the default development and test dependency groups
+
+## 2. Install git hooks
+
+```bash
+uv run pre-commit install
+```
+
+What it does:
+
+- enables local checks before each commit
+- runs formatting and lightweight validation automatically
+
+## 3. Run the tests
+
+```bash
+uv run pytest
+```
+
+What it does:
+
+- runs the test suite from `tests/`
+- confirms the package imports correctly from the `src/` layout
+
+## 4. Run linting and formatting
+
+```bash
+uv run ruff check .
+uv run ruff format .
+```
+
+What they do:
+
+- `ruff check .` finds lint issues
+- `ruff format .` applies consistent formatting
+
+## 5. Build the package
+
+```bash
+uv run python -m build
+```
+
+What it does:
+
+- creates distribution artifacts in `dist/`
+- verifies the package metadata and build configuration are valid
+
+## Optional Make Targets
+
+If you like `make`, these commands wrap the same workflow:
+
+```bash
+make sync
+make test
+make lint
+make format
+make build
+```
+
+For repository-level navigation, go back to the [root README](../README.md).

linkinpy-0.0.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: linkinpy
+Version: 0.0.1
+Summary: A python package to bring uv managed workflows to all common image analysis tools
+Project-URL: Homepage, https://github.com/your-username/MyPackageFolder
+Project-URL: Repository, https://github.com/your-username/MyPackageFolder
+Project-URL: Issues, https://github.com/your-username/MyPackageFolder/issues
+Project-URL: Changelog, https://github.com/your-username/MyPackageFolder/blob/main/CHANGELOG.md
+Author-email: "Bruno M. Saraiva" <bruno.msaraiva2@gmail.com>
+License-Expression: MIT
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Requires-Python: >=3.9
+Requires-Dist: ipyfilechooser>=0.6.0
+Requires-Dist: ipywidgets>=8.0
+Requires-Dist: magicgui>=0.10.0
+Requires-Dist: numpy>=1.26
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: stackview>=0.14.0
+Requires-Dist: tifffile>=2024.8.10
+Provides-Extra: gui
+Requires-Dist: pyqt6>=6.7.0; extra == 'gui'
+Provides-Extra: napari
+Requires-Dist: napari>=0.5.0; extra == 'napari'
+Description-Content-Type: text/markdown
+
+# linkinpy
+
+A Python package to bring `uv`-managed workflows to common image analysis tools.
+
+## Quick Start
+
+```bash
+uv sync
+uv run pytest
+```
+
+Run these commands from the `LinkinPy/` folder.
+
+This package pins its local development interpreter in `.python-version` and keeps package metadata in `pyproject.toml`.
+
+## Common Commands
+
+```bash
+uv sync                  # create/update the local environment
+uv run pytest            # run the test suite
+uv run ruff check .      # lint the codebase
+uv run ruff format .     # format the codebase
+uv run python -m build   # build the source and wheel distributions
+uv run pre-commit install
+```
+
+If you prefer shorter aliases, the same workflow is available through `make`:
+
+```bash
+make sync
+make test
+make lint
+make format
+make build
+```
+
+## LinkinPy Spec Workflow
+
+LinkinPy reads YAML spec files such as `../Library/nanopyx.yaml`. Each spec file owns exactly one isolated `uv` virtual environment at `~/.linkinpy/<spec-file-name>/`, and all runs for that spec execute inside that environment. LinkinPy checks whether `uv` is installed, bootstraps it when missing, and installs the core package into every spec-owned environment automatically.
+
+```bash
+uv run linkinpy list ../Library/nanopyx.yaml
+uv run linkinpy install ../Library/nanopyx.yaml --interface cli
+uv run linkinpy run ../Library/nanopyx.yaml eSRRF image=input.tif --output result.tif
+```
+
+The `run` command accepts callable arguments as `name=value`. Image arguments declared as `np.ndarray` can be passed as image file paths for the CLI path. The core also exposes Python APIs for spec parsing, environment management, image transport, direct callable execution, and magicgui widget construction.
+
+## Project Layout
+
+```text
+src/linkinpy/
+tests/
+pyproject.toml
+.python-version
+GETTING_STARTED.md
+CONTRIBUTING.md
+```
+
+## Documentation
+
+- Start with [GETTING_STARTED.md](GETTING_STARTED.md) for first-time setup
+- See [CONTRIBUTING.md](CONTRIBUTING.md) for the contributor workflow
+- Track user-facing changes in [CHANGELOG.md](CHANGELOG.md)
+
+For the multi-project repository overview, see the [repository root README](../README.md).

linkinpy-0.0.1/README.md

@@ -0,0 +1,66 @@
+# linkinpy
+
+A Python package to bring `uv`-managed workflows to common image analysis tools.
+
+## Quick Start
+
+```bash
+uv sync
+uv run pytest
+```
+
+Run these commands from the `LinkinPy/` folder.
+
+This package pins its local development interpreter in `.python-version` and keeps package metadata in `pyproject.toml`.
+
+## Common Commands
+
+```bash
+uv sync                  # create/update the local environment
+uv run pytest            # run the test suite
+uv run ruff check .      # lint the codebase
+uv run ruff format .     # format the codebase
+uv run python -m build   # build the source and wheel distributions
+uv run pre-commit install
+```
+
+If you prefer shorter aliases, the same workflow is available through `make`:
+
+```bash
+make sync
+make test
+make lint
+make format
+make build
+```
+
+## LinkinPy Spec Workflow
+
+LinkinPy reads YAML spec files such as `../Library/nanopyx.yaml`. Each spec file owns exactly one isolated `uv` virtual environment at `~/.linkinpy/<spec-file-name>/`, and all runs for that spec execute inside that environment. LinkinPy checks whether `uv` is installed, bootstraps it when missing, and installs the core package into every spec-owned environment automatically.
+
+```bash
+uv run linkinpy list ../Library/nanopyx.yaml
+uv run linkinpy install ../Library/nanopyx.yaml --interface cli
+uv run linkinpy run ../Library/nanopyx.yaml eSRRF image=input.tif --output result.tif
+```
+
+The `run` command accepts callable arguments as `name=value`. Image arguments declared as `np.ndarray` can be passed as image file paths for the CLI path. The core also exposes Python APIs for spec parsing, environment management, image transport, direct callable execution, and magicgui widget construction.
+
+## Project Layout
+
+```text
+src/linkinpy/
+tests/
+pyproject.toml
+.python-version
+GETTING_STARTED.md
+CONTRIBUTING.md
+```
+
+## Documentation
+
+- Start with [GETTING_STARTED.md](GETTING_STARTED.md) for first-time setup
+- See [CONTRIBUTING.md](CONTRIBUTING.md) for the contributor workflow
+- Track user-facing changes in [CHANGELOG.md](CHANGELOG.md)
+
+For the multi-project repository overview, see the [repository root README](../README.md).

linkinpy-0.0.1/makefile

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+.PHONY: help sync sync-dev test lint format check build docs
+
+help:
+	@echo "Available commands:"
+	@echo "  sync      Create/update the local environment with uv"
+	@echo "  sync-dev  Alias for sync"
+	@echo "  test      Run the test suite"
+	@echo "  lint      Run Ruff lint checks"
+	@echo "  format    Format the codebase with Ruff"
+	@echo "  check     Run lint, tests, and build"
+	@echo "  build     Build source and wheel distributions"
+	@echo "  docs      Generate API docs with pdoc"
+
+sync:
+	uv sync
+
+sync-dev:
+	uv sync
+
+test:
+	uv run pytest
+
+lint:
+	uv run ruff check .
+
+format:
+	uv run ruff format .
+
+check:
+	uv run ruff check .
+	uv run pytest
+	uv run python -m build
+
+build:
+	uv run python -m build
+
+docs:
+	rm -rf docs
+	uv run pdoc src/linkinpy -o docs
+
+.DEFAULT_GOAL := help

linkinpy-0.0.1/pyproject.toml

@@ -0,0 +1,80 @@
+[build-system]
+requires = ["hatchling>=1.26.0"]
+build-backend = "hatchling.build"
+
+[project]
+name = "linkinpy"
+version = "0.0.1"
+description = "A python package to bring uv managed workflows to all common image analysis tools"
+readme = "README.md"
+requires-python = ">=3.9"
+license = "MIT"
+license-files = ["LICENSE*"]
+authors = [
+    { name = "Bruno M. Saraiva", email = "bruno.msaraiva2@gmail.com" }
+]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Developers",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Operating System :: OS Independent",
+]
+dependencies = [
+    "magicgui>=0.10.0",
+    "numpy>=1.26",
+    "pyyaml>=6.0",
+    "tifffile>=2024.8.10",
+    "ipywidgets>=8.0",
+    "ipyfilechooser>=0.6.0",
+    "stackview>=0.14.0",
+]
+
+[project.optional-dependencies]
+gui = [
+    "pyqt6>=6.7.0",
+]
+napari = [
+    "napari>=0.5.0",
+]
+
+[project.urls]
+Homepage = "https://github.com/your-username/MyPackageFolder"
+Repository = "https://github.com/your-username/MyPackageFolder"
+Issues = "https://github.com/your-username/MyPackageFolder/issues"
+Changelog = "https://github.com/your-username/MyPackageFolder/blob/main/CHANGELOG.md"
+
+[project.scripts]
+linkinpy = "linkinpy.cli:main"
+
+[dependency-groups]
+dev = [
+    "build>=1.2.2",
+    "pdoc>=15.0.0",
+    "pre-commit>=4.2.0",
+    "pyqt6>=6.7.0",
+    "ruff>=0.11.0",
+]
+test = [
+    "pytest>=8.3.0",
+    "pytest-cov>=6.0.0",
+    "pytest-xdist>=3.6.1",
+]
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/linkinpy"]
+
+[tool.pytest.ini_options]
+addopts = "-ra"
+testpaths = ["tests"]
+
+[tool.coverage.run]
+source = ["linkinpy"]
+branch = true
+
+[tool.coverage.report]
+show_missing = true
+skip_covered = true
+
+[tool.uv]
+default-groups = ["dev", "test"]

linkinpy-0.0.1/ruff.toml

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+exclude = [
+    ".bzr",
+    ".direnv",
+    ".eggs",
+    ".git",
+    ".git-rewrite",
+    ".hg",
+    ".ipynb_checkpoints",
+    ".mypy_cache",
+    ".nox",
+    ".pants.d",
+    ".pyenv",
+    ".pytest_cache",
+    ".pytype",
+    ".ruff_cache",
+    ".svn",
+    ".tox",
+    ".venv",
+    ".vscode",
+    "__pypackages__",
+    "_build",
+    "buck-out",
+    "build",
+    "dist",
+    "node_modules",
+    "site-packages",
+    "venv",
+]
+line-length = 88
+indent-width = 4
+target-version = "py39"
+
+[lint]
+fixable = ["ALL"]
+unfixable = []
+dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
+ignore = [
+    "UP007", # Keep Python 3.9-compatible Union annotations.
+    "UP045", # Keep Python 3.9-compatible Optional annotations.
+]
+
+[format]
+quote-style = "double"
+indent-style = "space"
+skip-magic-trailing-comma = false
+line-ending = "auto"
+docstring-code-format = true
+docstring-code-line-length = "dynamic"
+
+[lint.pydocstyle]
+convention = "google"

linkinpy-0.0.1/src/linkinpy/__init__.py

@@ -0,0 +1,63 @@
+from .colab import (
+    choose_colab_spec,
+    install_colab_spec,
+    installed_colab_specs,
+    launch_colab,
+    mount_google_drive,
+    run_installed_colab_method,
+)
+from .environment import EnvironmentManager, ensure_uv, find_uv
+from .images import (
+    SharedArray,
+    attach_shared_array,
+    create_shared_array,
+    read_image,
+    write_image,
+)
+from .linkinpy import LinkinPy
+from .runner import (
+    get_callable,
+    resolve_callable,
+    run_callable_in_process,
+    run_spec_callable,
+    run_spec_callable_in_environment,
+)
+from .spec import (
+    CallableSpec,
+    InputSpec,
+    LinkinPySpec,
+    PackageSpec,
+    SpecError,
+    load_spec,
+    parse_spec,
+)
+
+__all__ = [
+    "CallableSpec",
+    "EnvironmentManager",
+    "InputSpec",
+    "LinkinPy",
+    "LinkinPySpec",
+    "PackageSpec",
+    "SharedArray",
+    "SpecError",
+    "attach_shared_array",
+    "choose_colab_spec",
+    "create_shared_array",
+    "ensure_uv",
+    "find_uv",
+    "get_callable",
+    "install_colab_spec",
+    "installed_colab_specs",
+    "launch_colab",
+    "load_spec",
+    "mount_google_drive",
+    "parse_spec",
+    "read_image",
+    "resolve_callable",
+    "run_callable_in_process",
+    "run_installed_colab_method",
+    "run_spec_callable",
+    "run_spec_callable_in_environment",
+    "write_image",
+]

linkinpy-0.0.1/src/linkinpy/_shm.py

@@ -0,0 +1,30 @@
+from __future__ import annotations
+
+import argparse
+import json
+from typing import Optional
+
+from .images import create_empty_untracked_shared_array
+
+
+def main(argv: Optional[list[str]] = None) -> int:
+    parser = argparse.ArgumentParser(description="Internal LinkinPy shared-memory helper.")
+    subparsers = parser.add_subparsers(dest="command", required=True)
+
+    allocate = subparsers.add_parser("allocate", help="Allocate an untracked shared-memory array.")
+    allocate.add_argument("--shape", required=True, help="JSON list of dimensions.")
+    allocate.add_argument("--dtype", required=True)
+    allocate.add_argument("--axes")
+
+    args = parser.parse_args(argv)
+    if args.command == "allocate":
+        shape = json.loads(args.shape)
+        descriptor, block = create_empty_untracked_shared_array(shape, args.dtype, axes=args.axes)
+        block.close()
+        print(json.dumps(descriptor.to_descriptor()), flush=True)
+        return 0
+    return 1
+
+
+if __name__ == "__main__":
+    raise SystemExit(main())

linkinpy-0.0.1/src/linkinpy/_testing.py

@@ -0,0 +1,15 @@
+from __future__ import annotations
+
+import numpy as np
+
+
+def add_one(x: float) -> float:
+    return x + 1
+
+
+def image_plus_one(image: np.ndarray) -> np.ndarray:
+    return image + 1
+
+
+def make_image() -> np.ndarray:
+    return np.arange(4, dtype=np.float32).reshape(2, 2)