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Merge pull request #14 from fractal-analytics-platform/add_task_metadata
Update template & add task metadata
2 parents d81a335 + a776fb7 commit f60bf03

10 files changed

+137
-74
lines changed

‎.copier-answers.yml

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# Do not edit - changes here will be overwritten by Copier
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_commit: v0.3.0
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_commit: v0.4.2
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_src_path: gh:fractal-analytics-platform/fractal-tasks-template
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author_email: [email protected]
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author_name: Joel Luethi

‎.github/workflows/build_and_test.yml

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name: CI (build and test)
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on:
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push:
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branches: ["main"]
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tags:
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- "*"
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pull_request:
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branches: ["main"]
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jobs:
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tests:
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strategy:
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matrix:
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os: [ubuntu-22.04, macos-latest]
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python-version: ["3.9", "3.10", "3.11"]
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exclude:
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- os: macos-latest
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python-version: '3.9'
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- os: macos-latest
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python-version: '3.10'
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name: "Core, Python ${{ matrix.python-version }}, ${{ matrix.os }}"
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runs-on: ${{ matrix.os }}
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timeout-minutes: 30
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: 1
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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cache: "pip"
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- name: Install package
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run: python -m pip install -e .[dev]
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- name: Install some testing dependencies (hard-coded)
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run: python -m pip install pytest pytest-cov devtools jsonschema requests wget pooch
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- name: Regenerate the manifest
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run: python src/fractal_helper_tasks/dev/create_manifest.py
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- name: Cache Pooch folder
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id: cache-pooch-folder
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uses: actions/cache@v3
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with:
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path: ~/.cache/pooch
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key: pooch-cache
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- name: Check if manifest has changed
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run: |
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if [ -n "$(git diff --exit-code ./src/fractal_helper_tasks/__FRACTAL_MANIFEST__.json)" ]; then
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echo "__FRACTAL_MANIFEST__.json has changed. Please run 'python src/fractal_helper_tasks/dev/create_manifest.py' and commit the changes."
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exit 1
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else
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echo "__FRACTAL_MANIFEST__.json has not changed."
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fi
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- name: Test tasks with pytest
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run: pytest --color=yes --cov --cov-report=xml --cov-report=term-missing -s --log-cli-level debug
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- name: Upload coverage reports to Codecov
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uses: codecov/[email protected]
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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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slug: jluethi/fractal-helper-tasks
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deploy:
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name: Deploy
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needs: tests
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if: success() && startsWith(github.ref, 'refs/tags/') && github.event_name != 'schedule'
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runs-on: ubuntu-latest
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permissions:
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# IMPORTANT: this permission is mandatory for trusted publishing on PyPi
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# see https://docs.pypi.org/trusted-publishers/
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id-token: write
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# This permission allows writing releases
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contents: write
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: 🐍 Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: "3.x"
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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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- 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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with:
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generate_release_notes: true
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files: './dist/*'

‎.github/workflows/ci_pip.yml

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This file was deleted.

‎.gitignore

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# Git ignored is sourced from https://github.com/pydev-guide/pyrepo-copier/blob/main/LICENSE
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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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# IDE settings
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.vscode/
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.idea/
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.idea/

‎pyproject.toml

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@@ -5,18 +5,12 @@ build-backend = "hatchling.build"
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# https://hatch.pypa.io/latest/config/metadata/
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[tool.hatch.version]
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#path = "src/fractal_helper_tasks/__init__.py"
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source = "vcs"
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# read more about configuring hatch at:
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# https://hatch.pypa.io/latest/config/build/
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[tool.hatch.build.targets.wheel]
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only-include = ["src"]
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sources = ["src"]
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# Always include the __FRACTAL_MANIFEST__.json file in the package
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[tool.hatch.build]
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include = ["__FRACTAL_MANIFEST__.json"]
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packages = ["src/fractal_helper_tasks"]
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# Project metadata (see https://peps.python.org/pep-0621)
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# Required Python version and dependencies
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requires-python = ">=3.9"
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dependencies = [
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"fractal-tasks-core==1.2.0"
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"fractal-tasks-core==1.3.3"
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]
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# Optional dependencies (e.g. for `pip install -e ".[dev]"`, see

‎src/fractal_helper_tasks/__FRACTAL_MANIFEST__.json

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"output_types": {
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"has_t": false
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},
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"tags": [
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"Singelton time dimension"
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],
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"executable_non_parallel": "drop_t_dimension.py",
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"meta_non_parallel": {
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"cpus_per_task": 2,
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"input_types": {
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"is_3D": false
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},
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"tags": [
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"Mixed modality",
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"2D to 3D workflows"
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],
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"executable_parallel": "convert_2D_segmentation_to_3D.py",
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"meta_parallel": {
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"cpus_per_task": 2,
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}
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],
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"has_args_schemas": true,
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"args_schema_version": "pydantic_v2"
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"args_schema_version": "pydantic_v2",
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"authors": "Joel Luethi"
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}

‎src/fractal_helper_tasks/dev/create_manifest.py

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to the package manifest.
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"""
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PACKAGE = "fractal_helper_tasks"
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create_manifest(package=PACKAGE)
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AUTHORS = "Joel Luethi"
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create_manifest(package=PACKAGE, authors=AUTHORS)

‎src/fractal_helper_tasks/dev/task_list.py

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executable="drop_t_dimension.py",
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meta={"cpus_per_task": 2, "mem": 8000},
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output_types=dict(has_t=False),
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tags=["Singelton time dimension"],
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),
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ParallelTask(
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input_types=dict(is_3D=False),
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name="Convert 2D segmentation to 3D",
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executable="convert_2D_segmentation_to_3D.py",
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meta={"cpus_per_task": 2, "mem": 8000},
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tags=[
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"Mixed modality",
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"2D to 3D workflows",
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],
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),
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]

‎tests/__init__.py

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import fractal_helper_tasks
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import json
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from pathlib import Path
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import fractal_helper_tasks
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PACKAGE = "fractal_helper_tasks"
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PACKAGE_DIR = Path(fractal_helper_tasks.__file__).parent

‎tests/test_valid_task_interface.py

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import json
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import subprocess
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from shlex import split as shlex_split
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from subprocess import PIPE
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import pytest
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from devtools import debug
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debug(cmd)
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result = subprocess.run( # nosec
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shlex_split(cmd),
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stdout=PIPE,
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stderr=PIPE,
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capture_output=True,
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)
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# The command must always fail, since tmp_file_args includes invalid
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# arguments
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assert result.returncode == 1
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stderr = result.stderr.decode()
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debug(stderr)
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# Valid stderr includes pydantic.error_wrappers.ValidationError (type
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# Valid stderr includes pydantic.v1.error_wrappers.ValidationError (type
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# match between model and function, but tmp_file_args has wrong arguments)
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# assert "pydantic.v1.error_wrappers.ValidationError" in stderr
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assert "ValidationError" in stderr
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# # Valid stderr must include a mention of "unexpected keyword arguments",
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# # because we are including some invalid arguments
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# assert "unexpected keyword arguments" in stderr
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# Valid stderr must include a mention of "Unexpected keyword argument",
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# because we are including some invalid arguments
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assert "Unexpected keyword argument" in stderr
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# # Invalid stderr includes ValueError
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# assert "ValueError" not in stderr
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tmp_file_args = str(tmp_path / "args.json")
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tmp_file_metadiff = str(tmp_path / "metadiff.json")
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with open(tmp_file_args, "w") as fout:
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args = dict(wrong_arg_1=123, wrong_arg_2=[1, 2, 3])
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args = {"wrong_arg_1": 123, "wrong_arg_2": [1, 2, 3]}
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json.dump(args, fout, indent=4)
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for key in ["executable_non_parallel", "executable_parallel"]:

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