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lorenzocerronelorenzocerrone
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Merge pull request #8 from fractal-analytics-platform/pixi
use pixi for managing the task env
2 parents 32c4da5 + bcbb49e commit d20daf0

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‎.gitattributes‎

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# SCM syntax highlighting & preventing 3-way merges
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pixi.lock merge=binary linguist-language=YAML linguist-generated=true

‎.github/workflows/build_and_test.yml‎

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with:
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fetch-depth: 1
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- uses: mamba-org/setup-micromamba@v1
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- uses: prefix-dev/setup-[email protected]
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with:
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# Using the newest version of micromamba
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# causes a weird bug in the manifest generation
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micromamba-version: '1.5.6-0' # any version from https://github.com/mamba-org/micromamba-releases
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environment-name: 'ilastik-tasks'
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create-args: >-
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--override-channels
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-c pytorch
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-c ilastik-forge
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-c conda-forge python=${{ matrix.python-version }} ilastik-core
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--no-channel-priority
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pixi-version: v0.44.0
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post-cleanup: 'all'
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- name: Install package
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run: micromamba run -n ilastik-tasks python -m pip install -e .[dev]
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- name: Regenerate the manifest
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run: micromamba run -n ilastik-tasks python src/ilastik_tasks/dev/create_manifest.py
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- name: re-create manifest
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run: pixi run -e dev python src/ilastik_tasks/dev/create_manifest.py
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- name: Check if manifest has changed
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run: |
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echo "__FRACTAL_MANIFEST__.json has not changed."
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fi
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- name: Test core library with pytest
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run: micromamba run -n ilastik-tasks python -m pytest tests
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- name: Run tests
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run: pixi run -e dev pytest
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deploy:
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name: Deploy
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with:
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python-version: "3.x"
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- name: 👷 Build
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- name: Build
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run: |
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python -m pip install build
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python -m build
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python -m pip install hatch hatch-vcs
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hatch build
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- name: 🚢 Publish to PyPI
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# TODO remove the "if: false" line when the package is ready for pypi release
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if: false
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uses: pypa/gh-action-pypi-publish@release/v1
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# This depends on conda packages not available on PyPI
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#- name: 🚢 Publish to PyPI
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# TODO remove the "if: false" line when the package is ready for pypi release
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# if: false
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# uses: pypa/gh-action-pypi-publish@release/v1
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- uses: softprops/action-gh-release@v2
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- name: Release
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uses: softprops/action-gh-release@v2
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with:
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generate_release_notes: true
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files: './dist/*'

‎.gitignore‎

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*.zarr
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# Test data loaded via pooch
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/tests/data/10_5281_zenodo_14883998
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/tests/data/10_5281_zenodo_14883998
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# pixi environments
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.pixi
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*.egg-info
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pixi.lock

‎README.md‎

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@@ -9,31 +9,15 @@ Collection of Fractal task to run Headless ilastik workflows.
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## Installation and Deployment
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* Install the `mamba` package manager
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* Download the installation script from this repository
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* Install `pixi` package manager [instructions](https://pixi.sh/latest/installation/)
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* run the task:
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```bash
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curl -O https://raw.githubusercontent.com/fractal-analytics-platform/fractal-ilastik-tasks/main/create_env_script.sh
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pixi run python some_script.py
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```
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* The scrip might require some small modifications.
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```bash
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VERSION="v0.2.0" # Version of the package to install (by default the latest version)
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COMMMAND="mamba" # Command to use to create the environment (mamba or conda)
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# Location of the environment
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# If ENVPREFIX is not NULL, the environment will be created with the prefix $ENVPREFIX/$ENVNAME
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# If ENVPREFIX is NULL, the environment will be created in the default location
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ENVPREFIX="NULL"
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```
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if you need to use the `dev` version of the package, you can run:
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* Install the package using the installation script
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```bash
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bash create_env_script.sh
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pixi run -e dev python some_script.py
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```
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The installation script will create a conda environment with the name `fractal-ilastik-tasks` and install the package in the environment. It will also download the correct `__FRACTAL_MANIFEST__.json` file.
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* In the fractal web interface add the task to the workflow as a "local env" task.

‎legacy_instructions.md‎

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# Installation and Deployment
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* Install the `mamba` package manager
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* Download the installation script from this repository
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```bash
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curl -O https://raw.githubusercontent.com/fractal-analytics-platform/fractal-ilastik-tasks/main/create_env_script.sh
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```
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* The scrip might require some small modifications.
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```bash
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VERSION="v0.2.0" # Version of the package to install (by default the latest version)
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COMMMAND="mamba" # Command to use to create the environment (mamba or conda)
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# Location of the environment
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# If ENVPREFIX is not NULL, the environment will be created with the prefix $ENVPREFIX/$ENVNAME
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# If ENVPREFIX is NULL, the environment will be created in the default location
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ENVPREFIX="NULL"
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```
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* Install the package using the installation script
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```bash
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bash create_env_script.sh
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```
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The installation script will create a conda environment with the name `fractal-ilastik-tasks` and install the package in the environment. It will also download the correct `__FRACTAL_MANIFEST__.json` file.
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* In the fractal web interface add the task to the workflow as a "local env" task.

‎pyproject.toml‎

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[tool.hatch.build.targets.wheel]
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packages = ["src/ilastik_tasks"]
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# Clean up the source distribution to avoid big tag.gz files
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[tool.hatch.build.targets.sdist]
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exclude = [
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# Pixi lock excluded by default see https://github.com/fractal-analytics-platform/fractal-server/issues/2624
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"pixi.lock",
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# Exclude tests from the source distribution
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"tests",
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# Exclude typically large files and directories that are not needed
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# This might not exists or be named differently in your project
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# TBD if we want to include these or not
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"docs",
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"data",
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"examples",
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"notebooks",
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".github",
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# Remove all jupyter notebook and checkpoints
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"**/*.ipynb_checkpoints",
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"**/*.ipynb",
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# NB all things in .gitignore are excluded by default of hatchling
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]
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# Project metadata (see https://peps.python.org/pep-0621)
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[project]
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docstring-code-format = true
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docstring-code-line-length = 89
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skip-magic-trailing-comma = false # default is false
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[tool.pixi.workspace]
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channels = ["conda-forge", "ilastik-forge"]
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platforms = ["osx-arm64", "linux-64"]
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[tool.pixi.pypi-dependencies]
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ilastik-tasks = { path = ".", editable = true }
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[tool.pixi.environments]
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default = { solve-group = "default" }
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dev = { features = ["dev"], solve-group = "default" }
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[tool.pixi.tasks]
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[tool.pixi.dependencies]
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pydantic = "==2.8.2"
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docstring_parser = "==0.15"
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ilastik-core = ">=1.4.2a1,<2"
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vigra = ">=1.12.1,<2"

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