initial commit

.copier-answers.yml

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+# Do not edit - changes here will be overwritten by Copier
+_commit: 0.4.0
+_src_path: gh:fractal-analytics-platform/fractal-tasks-template
+author_email: [email protected]
+author_name: Lorenzo Cerrone
+package_name: ilastik_tasks
+project_name: ilastik-tasks
+project_short_description: Package description.
+project_url: ''
+

.github/workflows/build_and_test.yml

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+name: CI (build and test)
+
+on:
+  push:
+    branches: ["main"]
+  pull_request:
+    branches: ["main"]
+
+
+jobs:
+  tests:
+    strategy:
+      matrix:
+        os: [ubuntu-22.04, macos-latest]
+        python-version: ["3.9", "3.10", "3.11"]
+        exclude:
+          - os: macos-latest
+            python-version: '3.9'
+          - os: macos-latest
+            python-version: '3.10'
+    name: "Core, Python ${{ matrix.python-version }}, ${{ matrix.os }}"
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 10
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 1
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: "pip"
+
+      - name: Install package
+        run: python -m pip install -e .[dev]
+
+      - name: Regenerate the manifest
+        run: python src/ilastik_tasks/dev/create_manifest.py
+
+      - name: Check if manifest has changed
+        run: |
+          if [ -n "$(git diff --exit-code ./src/ilastik_tasks/__FRACTAL_MANIFEST__.json)" ]; then
+          echo "__FRACTAL_MANIFEST__.json has changed. Please run 'python src/ilastik_tasks/dev/create_manifest.py' and commit the changes."
+            exit 1
+          else
+            echo "__FRACTAL_MANIFEST__.json has not changed."
+          fi
+
+      - name: Test core library with pytest
+        run: python -m pytest tests

.gitignore

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+# Git ignored is sourced from https://github.com/pydev-guide/pyrepo-copier/blob/main/LICENSE
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+.DS_Store
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# ruff
+.ruff_cache/
+
+# IDE settings
+.vscode/
+.idea/

.pre-commit-config.yaml

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+# enable pre-commit.ci at https://pre-commit.ci/
+
+repos:
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: v0.15
+    hooks:
+      - id: validate-pyproject
+
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: v0.5.0
+    hooks:
+      - id: ruff
+        args: [--fix]
+      - id: ruff-format

LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2023, Lorenzo Cerrone
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

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+# ilastik-tasks
+
+Package description.
+
+## Development instructions
+
+Specific instructions on how to install your package, managing your environment, versioning and more can be found in the [DEVELOPERS_GUIDE](https://github.com/fractal-analytics-platform/fractal-tasks-template/blob/main/DEVELOPERS_GUIDE.md).

pyproject.toml

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+# https://peps.python.org/pep-0517/
+[build-system]
+requires = ["hatchling", "hatch-vcs"]
+build-backend = "hatchling.build"
+
+# https://hatch.pypa.io/latest/config/metadata/
+[tool.hatch.version]
+#path = "src/ilastik_tasks/__init__.py"
+source = "vcs"
+
+# read more about configuring hatch at:
+# https://hatch.pypa.io/latest/config/build/
+[tool.hatch.build.targets.wheel]
+only-include = ["src"]
+sources = ["src"]
+
+# Always include the __FRACTAL_MANIFEST__.json file in the package
+[tool.hatch.build]
+include = ["__FRACTAL_MANIFEST__.json"]
+
+
+# Project metadata (see https://peps.python.org/pep-0621)
+[project]
+name = "ilastik-tasks"
+dynamic = ["version"]
+description = "Package description."
+readme = "README.md"
+license = { text = "BSD-3-Clause" }
+authors = [
+    { name = "Lorenzo Cerrone", email = "[email protected]" },
+]
+
+# Required Python version and dependencies
+requires-python = ">=3.9"
+dependencies = ["fractal-tasks-core == 1.3.0", "scikit-image"]
+
+# Optional dependencies (e.g. for `pip install -e ".[dev]"`, see
+# https://peps.python.org/pep-0621/#dependencies-optional-dependencies)
+[project.optional-dependencies]
+dev = ["devtools", "hatch", "pytest", "requests", "jsonschema", "ruff", "pre-commit"]
+
+# https://docs.astral.sh/ruff
+[tool.ruff]
+line-length = 88
+target-version = "py39"
+src = ["src"]
+
+# https://docs.astral.sh/ruff/rules
+[tool.ruff.lint]
+pydocstyle = { convention = "google" }
+select = [
+    "E",    # style errors
+    "W",    # style warnings
+    "F",    # flakes
+    "D",    # pydocstyle
+    "D417", # Missing argument descriptions in Docstrings
+    "I",    # isort
+    "UP",   # pyupgrade
+    "C4",   # flake8-comprehensions
+    "B",    # flake8-bugbear
+    "A001", # flake8-builtins
+    "RUF",  # ruff-specific rules
+    "TCH",  # flake8-type-checking
+    "TID",  # flake8-tidy-imports
+]
+ignore = [
+    "D401", # First line should be in imperative mood (remove to opt in)
+    "D415", # First line should end with a period (remove to opt in)
+]
+
+[tool.ruff.lint.per-file-ignores]
+"tests/*.py" = ["D", "S"]
+
+# https://docs.astral.sh/ruff/formatter/
+[tool.ruff.format]
+docstring-code-format = true
+docstring-code-line-length = 89
+skip-magic-trailing-comma = false  # default is false

src/ilastik_tasks/__FRACTAL_MANIFEST__.json

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+{
+  "manifest_version": "2",
+  "task_list": [
+    {
+      "name": "Thresholding Label Task",
+      "executable_parallel": "thresholding_label_task.py",
+      "meta_parallel": {
+        "cpus_per_task": 1,
+        "mem": 4000
+      },
+      "args_schema_parallel": {
+        "$defs": {
+          "ChannelInputModel": {
+            "description": "A channel which is specified by either `wavelength_id` or `label`.",
+            "properties": {
+              "wavelength_id": {
+                "title": "Wavelength Id",
+                "type": "string",
+                "description": "Unique ID for the channel wavelength, e.g. `A01_C01`. Can only be specified if label is not set."
+              },
+              "label": {
+                "title": "Label",
+                "type": "string",
+                "description": "Name of the channel. Can only be specified if wavelength_id is not set."
+              }
+            },
+            "title": "ChannelInputModel",
+            "type": "object"
+          }
+        },
+        "additionalProperties": false,
+        "properties": {
+          "zarr_url": {
+            "title": "Zarr Url",
+            "type": "string",
+            "description": "Absolute path to the OME-Zarr image."
+          },
+          "threshold": {
+            "title": "Threshold",
+            "type": "integer",
+            "description": "Threshold value to be applied."
+          },
+          "channel": {
+            "$ref": "#/$defs/ChannelInputModel",
+            "title": "Channel",
+            "description": "Channel to be thresholded."
+          },
+          "label_name": {
+            "title": "Label Name",
+            "type": "string",
+            "description": "Name of the resulting label image"
+          },
+          "min_size": {
+            "default": 50,
+            "title": "Min Size",
+            "type": "integer",
+            "description": "Minimum size of objects. Smaller objects are filtered out."
+          },
+          "overwrite": {
+            "default": true,
+            "title": "Overwrite",
+            "type": "boolean",
+            "description": "Whether to overwrite an existing label image"
+          }
+        },
+        "required": [
+          "zarr_url",
+          "threshold",
+          "channel"
+        ],
+        "type": "object",
+        "title": "ThresholdingLabelTask"
+      },
+      "docs_info": "## thresholding_label_task\nThreshold an image and find connected components.\n"
+    }
+  ],
+  "has_args_schemas": true,
+  "args_schema_version": "pydantic_v2"
+}