Version 1.5.0

.github/workflows/ci_pip.yml

@@ -15,10 +15,8 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-22.04, macos-latest]
-        python-version: ["3.10", "3.11", "3.12"]
-        exclude:
-          - os: macos-latest
-            python-version: '3.10'
+        python-version: ["3.11", "3.12"]
+
     name: "Core, Python ${{ matrix.python-version }}, ${{ matrix.os }}"
     runs-on: ${{ matrix.os }}
     timeout-minutes: 10
@@ -42,17 +40,14 @@ jobs:
         run: python -m pip install pytest devtools jsonschema requests wget pooch
 
       - name: Test core library with pytest
-        run: python -m pytest tests --ignore tests/tasks --ignore tests/dev
+        run: python -m pytest tests --ignore tests/tasks --ignore tests/dev --ignore tests/tasks_v2
 
   tests_tasks:
     if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: ["3.10", "3.11", "3.12"]
-        exclude:
-          - os: macos-latest
-            python-version: '3.10'
+        python-version: ["3.11", "3.12"]
     name: "Tasks, Python ${{ matrix.python-version }}, ${{ matrix.os }}"
     runs-on: ${{ matrix.os }}
     timeout-minutes: 30
@@ -83,4 +78,4 @@ jobs:
           key: pooch-cache
 
       - name: Test tasks with pytest
-        run: python -m pytest tests/dev tests/tasks -s --log-cli-level info
+        run: python -m pytest tests/dev tests/tasks tests/tasks_v2 -s --log-cli-level info

.github/workflows/ci_poetry.yml

@@ -15,7 +15,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.11", "3.12"]
 
     steps:
       - uses: actions/checkout@v4
@@ -46,7 +46,7 @@ jobs:
       - name: Test core library with pytest
         env:
           COVERAGE_FILE: coverage-data-core-${{ matrix.python-version }}
-        run: poetry run coverage run -m pytest tests --ignore tests/tasks  --ignore tests/dev
+        run: poetry run coverage run -m pytest tests --ignore tests/tasks  --ignore tests/dev --ignore tests/tasks_v2
 
       - name: Upload coverage data
         uses: actions/upload-artifact@v4
@@ -61,7 +61,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.11", "3.12"]
 
     steps:
       - uses: actions/checkout@v4
@@ -90,16 +90,7 @@ jobs:
         run: poetry install --with dev --without docs --no-interaction -E fractal-tasks
 
       - name: Check if manifest has changed
-        run: |
-          poetry run python fractal_tasks_core/dev/create_manifest.py
-          echo "*.json diff=json" >> .gitattributes && git config diff.json.textconv "jq --sort-keys '.' \$1"
-          git diff ./fractal_tasks_core/__FRACTAL_MANIFEST__.json
-          if [ -n "$(git diff --exit-code ./fractal_tasks_core/__FRACTAL_MANIFEST__.json)" ]; then
-          echo "__FRACTAL_MANIFEST__.json has changed. Please run 'poetry run python fractal_tasks_core/dev/create_manifest.py' and commit the changes."
-            exit 1
-          else
-            echo "__FRACTAL_MANIFEST__.json has not changed."
-          fi
+        run: poetry run fractal-manifest check --package fractal-tasks-core
 
       - name: Cache Pooch folder
         id: cache-pooch-folder
@@ -111,7 +102,7 @@ jobs:
       - name: Test tasks with pytest
         env:
           COVERAGE_FILE: coverage-data-tasks-${{ matrix.python-version }}
-        run: poetry run coverage run -m pytest tests/dev tests/tasks
+        run: poetry run coverage run -m pytest tests/dev tests/tasks tests/tasks_v2
 
       - name: Upload coverage data
         uses: actions/upload-artifact@v4
@@ -130,7 +121,7 @@ jobs:
       - run: poetry config virtualenvs.in-project true
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Install dependencies
         run: poetry install --with dev

.github/workflows/documentation.yaml

@@ -36,7 +36,7 @@ jobs:
 
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
+          python-version: '3.11'
           cache: pip
 
       - name: Install dependencies

.github/workflows/manifest_external_packages.yml

@@ -39,14 +39,6 @@ jobs:
             cmd_create_manifest: 'python src/scmultiplex/dev/create_manifest.py'
             custom_dependencies: 'image_registration'
 
-          - package: fractal-helper-tasks
-            github_repo: jluethi/fractal-helper-tasks
-            github_branch: main
-            manifest_path: src/fractal_helper_tasks/__FRACTAL_MANIFEST__.json
-            cmd_install: 'python -m pip install -e .'
-            cmd_create_manifest: 'python src/fractal_helper_tasks/dev/create_manifest.py'
-            custom_dependencies: ''
-
           - package: APx_fractal_task_collection
             github_repo: Apricot-Therapeutics/APx_fractal_task_collection
             github_branch: main

.github/workflows/package.yml

@@ -19,10 +19,10 @@ jobs:
           fetch-depth: 1
           persist-credentials: false
 
-      - name: Set up Python 3.10
+      - name: Set up Python 3.11
         uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
           cache: pip
 
       - name: Run pre-commit (fail upon errors)

.github/workflows/poetry_build.yml

@@ -15,10 +15,10 @@ jobs:
         with:
           persist-credentials: false
 
-      - name: "Set up Python 3.10"
+      - name: "Set up Python 3.11"
         uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: "Install poetry 1.8.2"
         run: curl -sSL https://install.python-poetry.org | python3 - --version 1.8.2

.github/workflows/poetry_update.yml

@@ -23,7 +23,7 @@ jobs:
         run: pipx install poetry==1.8.2
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - uses: fredrikaverpil/[email protected]
 

.github/workflows/publish_pypi.yml

@@ -27,7 +27,7 @@ jobs:
 
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: "Install poetry 1.8.2"
         run: curl -sSL https://install.python-poetry.org | python3 - --version 1.8.2

.pre-commit-config.yaml

@@ -23,3 +23,10 @@ repos:
     hooks:
     - id: bandit
       args: ["-x", "tests/*"]
+-   repo: local
+    hooks:
+    - id: grep-for-devtools
+      name: Check for devtools in fractal_tasks_core
+      entry: bash -c 'for file in "$@"; do if grep -n "devtools" "$file"; then echo "$file" && exit 1; fi; done' --
+      language: system
+      files: fractal_tasks_core/

CHANGELOG.md

@@ -1,14 +1,30 @@
 **Note**: Numbers like (\#123) point to closed Pull Requests on the fractal-tasks-core repository.
 
-# Unreleased
+# 1.5.0
 
+* Tasks:
+    * Refactor `projection` task to use the new `ngio` API (\#937, \#943).
+    * Refactor `copy_ome_zarr_plate` init task to support the upcoming flexibility.
+    * Rely on `fractal-task-tools` for `run_fractal_task` wrapper (\#923).
+    * Mark some existing tasks as _converter_ tasks(\#923).
+    * Mark existing `run_fractal_task` wrapper as deprecated (\#923).
+* Manifest generation:
+    * Rely on `fractal-task-tools` for manifest building (\#923).
+    * Mark existing tools as deprecated (\#923).
 * Testing:
+    * Add new (redundand) `ngio`-based testing.
     * Fix links to ome/ngff specs (\#930).
+* Dependencies:
+    * Add `fractal-task-tools==0.0.10` dependency (\#923).
+    * Bump `ngio` to `>=0.2.4,<0.3.0` (\#943).
+    * Drop support for Python 3.10 (\#932).
+    * Bump `fractal-task-tools` to `0.0.12` (\#933).
+    * Pin `numcodecs` to `<0.16` (\#932).
 
 # 1.4.3
 
 * Tasks:
-    * Update apply_registration_to_image to handle race conditions better (\#919).
+    * Update `apply_registration_to_image` to handle race conditions better (\#919).
 * Testing
     * Add `spherical-harmonics` extra to scmultiplex, for testing manifest build (\#899).
     * Move manifest-creation CI to Python 3.11 (\#915).

docs/custom_tasks_old.md

@@ -70,7 +70,7 @@ endpoints (see [Task package](#task-package)).
 Some examples of task commands may look like
 
 * `python3 /some/path/my_task.py`,
-* `/some/absolute/path/python3.10 /some/other/absolute/path/my_task.py`,
+* `/some/absolute/path/python3.11 /some/other/absolute/path/my_task.py`,
 * `/some/path/my_executable_task.py`,
 * any other executable command (not necessarily based on Python).
 

docs/development.md

@@ -36,7 +36,7 @@ poetry run pytest --ignore tests/tasks
 
 The tests files are in the `tests` folder of the repository. Its structure reflects the `fractal_tasks_core` structure, with tests for the core library in the main folder and tests for `tasks` and `dev` subpckages in their own subfolders.
 
-Tests are also run through GitHub Actions, with Python 3.10, 3.11 and 3.12. Note that within GitHub actions we run tests for both the `poetry`-installed and `pip`-installed versions of the code, which may e.g. have different versions of some dependencies (since `pip install` does not rely on the `poetry.lock` lockfile).
+Tests are also run through GitHub Actions, with Python 3.11 and 3.12. Note that within GitHub actions we run tests for both the `poetry`-installed and `pip`-installed versions of the code, which may e.g. have different versions of some dependencies (since `pip install` does not rely on the `poetry.lock` lockfile).
 
 ## Documentation
 

examples/01_cardio_tiny_dataset/run_workflow.py

@@ -62,7 +62,6 @@
 
 # Create zarr structure
 parallelization_list = cellvoyager_to_ome_zarr_init(
-    zarr_urls=[],
     zarr_dir=zarr_dir,
     image_dirs=[img_path],
     allowed_channels=allowed_channels,

examples/02_cardio_tiny_mip/run_workflow.py

@@ -67,7 +67,6 @@
 
 # Create zarr structure
 parallelization_list = cellvoyager_to_ome_zarr_init(
-    zarr_urls=[],
     zarr_dir=zarr_dir,
     image_dirs=[img_path],
     allowed_channels=allowed_channels,