Merge pull request #13 from jluethi/update_template

Update template & switch to Pydantic V2

Author: jluethi

.copier-answers.yml

@@ -1,10 +1,10 @@
 # Do not edit - changes here will be overwritten by Copier
-_commit: v0.1.3
+_commit: v0.3.0
 _src_path: gh:fractal-analytics-platform/fractal-tasks-template
 author_email: [email protected]
 author_name: Joel Luethi
 package_name: fractal_helper_tasks
 project_name: fractal-helper-tasks
 project_short_description: Collection of Fractal helper tasks
-project_url: ''
+project_url: https://github.com/jluethi/fractal-helper-tasks
 

.pre-commit-config.yaml

@@ -1,11 +1,4 @@
 # enable pre-commit.ci at https://pre-commit.ci/
-# it adds:
-# 1. auto fixing pull requests
-# 2. auto updating the pre-commit configuration
-ci:
-  autoupdate_schedule: monthly
-  autofix_commit_msg: "style(pre-commit.ci): auto fixes [...]"
-  autoupdate_commit_msg: "ci(pre-commit.ci): autoupdate"
 
 repos:
   - repo: https://github.com/abravalheri/validate-pyproject
@@ -14,12 +7,8 @@ repos:
       - id: validate-pyproject
 
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.1.3
+    rev: v0.5.0
     hooks:
       - id: ruff
         args: [--fix]
-
-  - repo: https://github.com/psf/black
-    rev: 23.10.1
-    hooks:
-      - id: black
+      - id: ruff-format

README.md

@@ -2,7 +2,7 @@
 
 [![License](https://img.shields.io/badge/License-BSD_3--Clause-blue.svg)](LICENSE)
 ![Python version](https://img.shields.io/badge/python-%3E%3D3.9-blue)
-![GitHub Workflow Status](https://img.shields.io/github/actions/workflow/status/jluethi/fractal-helper-tasks/your-workflow-file.yml?branch=main)
+![GitHub Workflow Status](https://img.shields.io/github/actions/workflow/status/jluethi/fractal-helper-tasks/ci_pip.yml?branch=main)
 [![codecov](https://codecov.io/gh/jluethi/fractal-helper-tasks/graph/badge.svg?token=ednmg2GzOw)](https://codecov.io/gh/jluethi/fractal-helper-tasks)
 
 Collection of Fractal helper tasks

pyproject.toml

@@ -1,7 +1,28 @@
+# 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/fractal_helper_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 = "fractal-helper-tasks"
-version = "0.1.0"
+dynamic = ["version"]
 description = "Collection of Fractal helper tasks"
 readme = "README.md"
 license = { text = "BSD-3-Clause" }
@@ -12,39 +33,30 @@ authors = [
 # Required Python version and dependencies
 requires-python = ">=3.9"
 dependencies = [
-    "fractal-tasks-core==1.0.0"
+    "fractal-tasks-core==1.2.0"
 ]
 
 # Optional dependencies (e.g. for `pip install -e ".[dev]"`, see
 # https://peps.python.org/pep-0621/#dependencies-optional-dependencies)
 [project.optional-dependencies]
-dev = ["devtools", "pytest", "requests", "build", "jsonschema", "pooch"]
+dev = ["devtools", "hatch", "pytest", "requests", "jsonschema", "ruff", "pre-commit", "pooch"]
 test = ["pytest", "pytest-cov"]
 
-# Build options (see https://peps.python.org/pep-0517)
-[build-system]
-requires = ["setuptools"]
-build-backend = "setuptools.build_meta"
-
-[tool.setuptools.packages.find]
-where = ["src"]
-include = ["fractal_helper_tasks"]
-
-# Always include the __FRACTAL_MANIFEST__.json file in the package
-[tool.setuptools.package-data]
-"*" = ["__FRACTAL_MANIFEST__.json"]
-
 # https://docs.astral.sh/ruff
 [tool.ruff]
 line-length = 88
-target-version = "py38"
+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
@@ -54,20 +66,24 @@ select = [
     "TCH",  # flake8-type-checking
     "TID",  # flake8-tidy-imports
 ]
-
-[tool.ruff.lint]
-pydocstyle = { convention = "numpy" }
 extend-select = [
     "D417", # Missing argument descriptions in Docstrings
 ]
-extend-ignore = [
+ignore = [
     "D401", # First line should be in imperative mood (remove to opt in)
     "C408", # Unnecessary `dict` call
+    "D415", # First line should end with a period (remove to opt in)
+    "UP022" # Used in validate_command test, waiting for template fix
 ]
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 "tests/*.py" = ["D", "S"]
-"setup.py" = ["D"]
+
+# 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
 
 [tool.coverage.run]
 # Include only the specific package directories for coverage, exclude tests
@@ -78,4 +94,4 @@ omit = [
     "*/tests/*",
     "*_test.py",
     "setup.py"
-]
+]

src/fractal_helper_tasks/__FRACTAL_MANIFEST__.json

@@ -12,31 +12,31 @@
         "mem": 8000
       },
       "args_schema_non_parallel": {
-        "title": "DropTDimension",
-        "type": "object",
+        "additionalProperties": false,
         "properties": {
           "zarr_url": {
             "title": "Zarr Url",
             "type": "string",
             "description": "Path or url to the individual OME-Zarr image to be processed. (standard argument for Fractal tasks, managed by Fractal server)."
           },
           "suffix": {
-            "title": "Suffix",
             "default": "no_T",
+            "title": "Suffix",
             "type": "string",
             "description": "Suffix to be used for the new Zarr image. If overwrite_input is True, this file is only temporary."
           },
           "overwrite_input": {
-            "title": "Overwrite Input",
             "default": false,
+            "title": "Overwrite Input",
             "type": "boolean",
             "description": "Whether"
           }
         },
         "required": [
           "zarr_url"
         ],
-        "additionalProperties": false
+        "type": "object",
+        "title": "DropTDimension"
       },
       "docs_info": "## drop_t_dimension\nDrops singleton t dimension.\n"
     },
@@ -51,8 +51,7 @@
         "mem": 8000
       },
       "args_schema_parallel": {
-        "title": "Convert2dSegmentationTo3d",
-        "type": "object",
+        "additionalProperties": false,
         "properties": {
           "zarr_url": {
             "title": "Zarr Url",
@@ -65,17 +64,17 @@
             "description": "Name of the label to copy from 2D OME-Zarr to 3D OME-Zarr"
           },
           "level": {
-            "title": "Level",
             "default": 0,
+            "title": "Level",
             "type": "integer",
             "description": "Level of the 2D OME-Zarr label to copy from"
           },
           "ROI_tables_to_copy": {
-            "title": "Roi Tables To Copy",
-            "type": "array",
             "items": {
               "type": "string"
             },
+            "title": "Roi Tables To Copy",
+            "type": "array",
             "description": "List of ROI table names to copy from 2D OME-Zarr to 3D OME-Zarr"
           },
           "new_label_name": {
@@ -84,14 +83,14 @@
             "description": "Optionally overwriting the name of the label in the 3D OME-Zarr"
           },
           "new_table_names": {
+            "items": {},
             "title": "New Table Names",
             "type": "array",
-            "items": {},
             "description": "Optionally overwriting the names of the ROI tables in the 3D OME-Zarr"
           },
           "plate_suffix": {
-            "title": "Plate Suffix",
             "default": "_mip",
+            "title": "Plate Suffix",
             "type": "string",
             "description": "Suffix of the 2D OME-Zarr that needs to be removed to generate the path to the 3D OME-Zarr. If the 2D OME-Zarr is \"/path/to/my_plate_mip.zarr/B/03/0\" and the 3D OME-Zarr is located in \"/path/to/my_plate.zarr/B/03/0\", the correct suffix is \"_mip\"."
           },
@@ -106,8 +105,8 @@
             "description": "If the image name between 2D & 3D don't match, this is the suffix that should be added to the 3D image. If the 2D image is in \"/path/to/my_plate_mip.zarr/B/03/0\" and the 3D image is in \"/path/to/my_plate.zarr/B/03/0_illum_corr\", the value should be \"_illum_corr\"."
           },
           "overwrite": {
-            "title": "Overwrite",
             "default": false,
+            "title": "Overwrite",
             "type": "boolean",
             "description": "If `True`, overwrite existing label and ROI tables in the 3D OME-Zarr"
           }
@@ -116,11 +115,12 @@
           "zarr_url",
           "label_name"
         ],
-        "additionalProperties": false
+        "type": "object",
+        "title": "Convert2dSegmentationTo3d"
       },
       "docs_info": "## convert_2D_segmentation_to_3D\nConvert 2D segmentation to 3D segmentation.\n\nThis task loads the 2D segmentation, replicates it along the Z slice and\nstores it back into the 3D OME-Zarr image.\n\nThis is a temporary workaround task, as long as we store 2D data in\na separate OME-Zarr file from the 3D data. If the 2D & 3D OME-Zarr images\nhave different suffixes in their name, use `image_suffix_2D_to_remove` &\n`image_suffix_3D_to_add`. If their base names are different, this task\ndoes not support processing them at the moment.\n\nIt makes the assumption that the 3D OME-Zarrs are stored in the same place\nas the 2D OME-Zarrs (same based folder).\n"
     }
   ],
   "has_args_schemas": true,
-  "args_schema_version": "pydantic_v1"
+  "args_schema_version": "pydantic_v2"
 }

src/fractal_helper_tasks/__init__.py

@@ -1,3 +1,8 @@
-"""
-Collection of Fractal helper tasks
-"""
+"""Collection of Fractal helper tasks"""
+
+from importlib.metadata import PackageNotFoundError, version
+
+try:
+    __version__ = version("fractal-helper-tasks")
+except PackageNotFoundError:
+    __version__ = "uninstalled"

src/fractal_helper_tasks/convert_2D_segmentation_to_3D.py

@@ -1,4 +1,5 @@
 """Fractal task to convert 2D segmentations into 3D segmentations."""
+
 import logging
 from typing import Optional
 
@@ -10,7 +11,7 @@
 from fractal_tasks_core.ngff.zarr_utils import load_NgffImageMeta
 from fractal_tasks_core.pyramids import build_pyramid
 from fractal_tasks_core.tables import write_table
-from pydantic.decorator import validate_arguments
+from pydantic import validate_call
 
 logger = logging.getLogger(__name__)
 
@@ -38,8 +39,7 @@ def get_zattrs(zarr_url):
 
 
 def make_zattrs_3D(attrs, z_pixel_size, new_label_name):
-    """
-    Creates 3D zattrs based on 2D attrs.
+    """Creates 3D zattrs based on 2D attrs.
 
     Performs the following checks:
     1) If the label image has 2 axes, add a Z axis and updadte the
@@ -88,7 +88,7 @@ def check_table_validity(new_table_names, old_table_names):
             )
 
 
-@validate_arguments
+@validate_call
 def convert_2D_segmentation_to_3D(
     zarr_url: str,
     label_name: str,
@@ -101,8 +101,7 @@ def convert_2D_segmentation_to_3D(
     image_suffix_3D_to_add: Optional[str] = None,
     overwrite: bool = False,
 ) -> None:
-    """
-    Convert 2D segmentation to 3D segmentation.
+    """Convert 2D segmentation to 3D segmentation.
 
     This task loads the 2D segmentation, replicates it along the Z slice and
     stores it back into the 3D OME-Zarr image.

src/fractal_helper_tasks/dev/create_manifest.py

@@ -1,7 +1,10 @@
-"""Generate JSON schemas for tasks and write them to the Fractal manifest."""
+"""Manifest generation"""
 
 from fractal_tasks_core.dev.create_manifest import create_manifest
 
 if __name__ == "__main__":
+    """Generate JSON schemas for task arguments afresh, and write them
+    to the package manifest.
+    """
     PACKAGE = "fractal_helper_tasks"
     create_manifest(package=PACKAGE)

src/fractal_helper_tasks/drop_t_dimension.py

@@ -6,21 +6,21 @@
 # This file is derived from a Fractal task core task developed by
 # Tommaso Comparin & Marco Franzon
 """Task to remove singelton T dimension from an OME-Zarr."""
+
 import logging
 from typing import Any
 
 import dask.array as da
 import zarr
 from fractal_tasks_core.ngff import load_NgffImageMeta
 from fractal_tasks_core.pyramids import build_pyramid
-from pydantic.decorator import validate_arguments
+from pydantic import validate_call
 
 logger = logging.getLogger(__name__)
 
 
 def get_attrs_without_t(zarr_url: str):
-    """
-    Generate zattrs without the t dimension.
+    """Generate zattrs without the t dimension.
 
     Args:
         zarr_url: Path to the zarr image
@@ -39,15 +39,14 @@ def get_attrs_without_t(zarr_url: str):
     return zattrs
 
 
-@validate_arguments
+@validate_call
 def drop_t_dimension(
     *,
     zarr_url: str,
     suffix: str = "no_T",
     overwrite_input: bool = False,
 ) -> dict[str, Any]:
-    """
-    Drops singleton t dimension.
+    """Drops singleton t dimension.
 
     Args:
         zarr_url: Path or url to the individual OME-Zarr image to be processed.