Update template & add task metadata

.copier-answers.yml

@@ -1,5 +1,5 @@
 # Do not edit - changes here will be overwritten by Copier
-_commit: v0.3.0
+_commit: v0.4.2
 _src_path: gh:fractal-analytics-platform/fractal-tasks-template
 author_email: [email protected]
 author_name: Joel Luethi

.github/workflows/build_and_test.yml

@@ -0,0 +1,108 @@
+name: CI (build and test)
+
+on:
+  push:
+    branches: ["main"]
+    tags:
+      - "*"
+  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: 30
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 1
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: "pip"
+
+      - name: Install package
+        run: python -m pip install -e .[dev]
+
+      - name: Install some testing dependencies (hard-coded)
+        run: python -m pip install pytest pytest-cov devtools jsonschema requests wget pooch
+
+      - name: Regenerate the manifest
+        run: python src/fractal_helper_tasks/dev/create_manifest.py
+
+      - name: Cache Pooch folder
+        id: cache-pooch-folder
+        uses: actions/cache@v3
+        with:
+          path: ~/.cache/pooch
+          key: pooch-cache
+
+      - name: Check if manifest has changed
+        run: |
+          if [ -n "$(git diff --exit-code ./src/fractal_helper_tasks/__FRACTAL_MANIFEST__.json)" ]; then
+          echo "__FRACTAL_MANIFEST__.json has changed. Please run 'python src/fractal_helper_tasks/dev/create_manifest.py' and commit the changes."
+            exit 1
+          else
+            echo "__FRACTAL_MANIFEST__.json has not changed."
+          fi
+
+      - name: Test tasks with pytest
+        run: pytest --color=yes --cov --cov-report=xml --cov-report=term-missing -s --log-cli-level debug
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/[email protected]
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          slug: jluethi/fractal-helper-tasks
+
+  deploy:
+    name: Deploy
+    needs: tests
+    if: success() && startsWith(github.ref, 'refs/tags/') && github.event_name != 'schedule'
+    runs-on: ubuntu-latest
+
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing on PyPi
+      # see https://docs.pypi.org/trusted-publishers/
+      id-token: write
+      # This permission allows writing releases
+      contents: write
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: 🐍 Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: 👷 Build
+        run: |
+          python -m pip install build
+          python -m build
+
+      - name: 🚢 Publish to PyPI
+        # TODO remove the "if: false" line when the package is ready for pypi release
+        if: false
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+      - uses: softprops/action-gh-release@v2
+        with:
+          generate_release_notes: true
+          files: './dist/*'

.gitignore

@@ -1,3 +1,4 @@
+# Git ignored is sourced from https://github.com/pydev-guide/pyrepo-copier/blob/main/LICENSE
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -108,4 +109,4 @@ ENV/
 
 # IDE settings
 .vscode/
-.idea/
+.idea/

pyproject.toml

@@ -5,18 +5,12 @@ 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"]
+packages = ["src/fractal_helper_tasks"]
 
 
 # Project metadata (see https://peps.python.org/pep-0621)
@@ -33,7 +27,7 @@ authors = [
 # Required Python version and dependencies
 requires-python = ">=3.9"
 dependencies = [
-    "fractal-tasks-core==1.2.0"
+    "fractal-tasks-core==1.3.3"
 ]
 
 # Optional dependencies (e.g. for `pip install -e ".[dev]"`, see

src/fractal_helper_tasks/__FRACTAL_MANIFEST__.json

@@ -6,6 +6,9 @@
       "output_types": {
         "has_t": false
       },
+      "tags": [
+        "Singelton time dimension"
+      ],
       "executable_non_parallel": "drop_t_dimension.py",
       "meta_non_parallel": {
         "cpus_per_task": 2,
@@ -45,6 +48,10 @@
       "input_types": {
         "is_3D": false
       },
+      "tags": [
+        "Mixed modality",
+        "2D to 3D workflows"
+      ],
       "executable_parallel": "convert_2D_segmentation_to_3D.py",
       "meta_parallel": {
         "cpus_per_task": 2,
@@ -122,5 +129,6 @@
     }
   ],
   "has_args_schemas": true,
-  "args_schema_version": "pydantic_v2"
+  "args_schema_version": "pydantic_v2",
+  "authors": "Joel Luethi"
 }

src/fractal_helper_tasks/dev/create_manifest.py

@@ -7,4 +7,5 @@
     to the package manifest.
     """
     PACKAGE = "fractal_helper_tasks"
-    create_manifest(package=PACKAGE)
+    AUTHORS = "Joel Luethi"
+    create_manifest(package=PACKAGE, authors=AUTHORS)

src/fractal_helper_tasks/dev/task_list.py

@@ -8,11 +8,16 @@
         executable="drop_t_dimension.py",
         meta={"cpus_per_task": 2, "mem": 8000},
         output_types=dict(has_t=False),
+        tags=["Singelton time dimension"],
     ),
     ParallelTask(
         input_types=dict(is_3D=False),
         name="Convert 2D segmentation to 3D",
         executable="convert_2D_segmentation_to_3D.py",
         meta={"cpus_per_task": 2, "mem": 8000},
+        tags=[
+            "Mixed modality",
+            "2D to 3D workflows",
+        ],
     ),
 ]

tests/__init__.py

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

tests/test_valid_task_interface.py

@@ -1,7 +1,6 @@
 import json
 import subprocess
 from shlex import split as shlex_split
-from subprocess import PIPE
 
 import pytest
 from devtools import debug
@@ -16,22 +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",
-    # # because we are including some invalid arguments
-    # assert "unexpected keyword arguments" in stderr
+    # Valid stderr must include a mention of "Unexpected keyword argument",
+    # because we are including some invalid arguments
+    assert "Unexpected keyword argument" in stderr
 
     # # Invalid stderr includes ValueError
     # assert "ValueError" not in stderr
@@ -46,7 +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"]: