Merge pull request #14 from lorenzocerrone/update_to_fractal_task_cor…

…e_1_2

Update to fractal task core 1.3

.github/workflows/copy-install-test-build.yml

@@ -4,7 +4,7 @@ on:
   push:
     branches: ["main"]
   pull_request:
-    branches: ["main"]
+    branches: ["main", "update_to_fractal_task_core_1_2"]
 
 jobs:
   copy_install_test_build:

project/.github/workflows/build_and_test.yml.jinja

@@ -0,0 +1,52 @@
+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: ${{ '{{' }} matrix.python-version {{ '}}' }}
+          cache: "pip"
+
+      - name: Install package
+        run: python -m pip install -e .[dev]
+
+      - name: Regenerate the manifest
+        run: python src/{{package_name}}/dev/create_manifest.py
+
+      - name: Check if manifest has changed
+        run: |
+          if [ -n "$(git diff --exit-code ./src/{{package_name}}/__FRACTAL_MANIFEST__.json)" ]; then
+          echo "__FRACTAL_MANIFEST__.json has changed. Please run 'python src/{{package_name}}/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

project/.gitignore

@@ -0,0 +1,112 @@
+# 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/

project/pyproject.toml.jinja

@@ -32,7 +32,7 @@ authors = [
 
 # Required Python version and dependencies
 requires-python = ">=3.9"
-dependencies = ["fractal-tasks-core == 1.1.0", "scikit-image"]
+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/src/{{package_name}}/__FRACTAL_MANIFEST__.json

@@ -0,0 +1,79 @@
+{
+  "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"
+}

project/src/{{package_name}}/thresholding_label_task.py

@@ -17,14 +17,14 @@
 from fractal_tasks_core.ngff.specs import NgffImageMeta
 from fractal_tasks_core.pyramids import build_pyramid
 from fractal_tasks_core.utils import rescale_datasets
-from pydantic.v1.decorator import validate_arguments
+from pydantic import validate_call
 from skimage.measure import label
 from skimage.morphology import ball, dilation, opening, remove_small_objects
 
 __OME_NGFF_VERSION__ = fractal_tasks_core.__OME_NGFF_VERSION__
 
 
-@validate_arguments
+@validate_call
 def thresholding_label_task(
     *,
     zarr_url: str,

project/tests/__init__.py.jinja

@@ -1,7 +1,7 @@
-import {{package_name}}
 import json
 from pathlib import Path
 
+import {{package_name}}
 
 PACKAGE = "{{package_name}}"
 PACKAGE_DIR = Path({{package_name}}.__file__).parent

project/tests/test_thresholding_label_task.py.jinja

@@ -3,8 +3,8 @@ from pathlib import Path
 
 import pytest
 from devtools import debug
-
 from fractal_tasks_core.channels import ChannelInputModel
+
 from {{package_name}}.thresholding_label_task import thresholding_label_task
 
 

project/tests/test_valid_args_schemas.py.jinja

@@ -2,22 +2,22 @@ import json
 from pathlib import Path
 
 import pytest
-from jsonschema.validators import Draft201909Validator
-from jsonschema.validators import Draft202012Validator
-from jsonschema.validators import Draft7Validator
-
 from fractal_tasks_core.dev.lib_args_schemas import (
     create_schema_for_single_task,
 )
-from fractal_tasks_core.dev.lib_signature_constraints import _extract_function
 from fractal_tasks_core.dev.lib_signature_constraints import (
+    _extract_function,
     _validate_function_signature,
 )
+from jsonschema.validators import (
+    Draft7Validator,
+    Draft201909Validator,
+    Draft202012Validator,
+)
 
 from . import TASK_LIST
 
 
-
 def test_task_functions_have_valid_signatures():
     """
     Test that task functions have valid signatures.

project/tests/test_valid_manifest.py

@@ -1,4 +1,5 @@
 import json
+
 import requests
 from jsonschema import validate
 

project/tests/test_valid_task_interface.py

@@ -1,13 +1,11 @@
 import json
 import subprocess
 from shlex import split as shlex_split
-from subprocess import PIPE
 
 import pytest
 from devtools import debug
 
-from . import MANIFEST
-from . import PACKAGE_DIR
+from . import MANIFEST, PACKAGE_DIR
 
 
 def validate_command(cmd: str):
@@ -17,22 +15,21 @@ def validate_command(cmd: str):
     debug(cmd)
     result = subprocess.run(  # nosec
         shlex_split(cmd),
-        stdout=PIPE,
-        stderr=PIPE,
+        capture_output=True,
     )
     # The command must always fail, since tmp_file_args includes invalid
     # arguments
     assert result.returncode == 1
     stderr = result.stderr.decode()
     debug(stderr)
 
-    # Valid stderr includes pydantic.error_wrappers.ValidationError (type
+    # Valid stderr includes pydantic.v1.error_wrappers.ValidationError (type
     # match between model and function, but tmp_file_args has wrong arguments)
-    assert "pydantic.v1.error_wrappers.ValidationError" in stderr
+    assert "ValidationError" in stderr
 
-    # Valid stderr must include a mention of "unexpected keyword arguments",
+    # Valid stderr must include a mention of "Unexpected keyword argument",
     # because we are including some invalid arguments
-    assert "unexpected keyword arguments" in stderr
+    assert "Unexpected keyword argument" in stderr
 
     # Invalid stderr includes ValueError
     assert "ValueError" not in stderr
@@ -47,7 +44,7 @@ def test_task_interface(task, tmp_path):
     tmp_file_args = str(tmp_path / "args.json")
     tmp_file_metadiff = str(tmp_path / "metadiff.json")
     with open(tmp_file_args, "w") as fout:
-        args = dict(wrong_arg_1=123, wrong_arg_2=[1, 2, 3])
+        args = {"wrong_arg_1": 123, "wrong_arg_2": [1, 2, 3]}
         json.dump(args, fout, indent=4)
 
     for key in ["executable_non_parallel", "executable_parallel"]: