Ngio projection task (#937)

* upgrade to ngio>=0.2
* refactor projection task to use ngio 0.2
* new testing suite ngio based

Author: lorenzocerrone

.github/workflows/ci_pip.yml

@@ -40,7 +40,7 @@ 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' }}
@@ -78,4 +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

@@ -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
@@ -102,7 +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

.github/workflows/manifest_external_packages.yml

@@ -39,13 +39,13 @@ 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: 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

.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

@@ -1,5 +1,14 @@
 **Note**: Numbers like (\#123) point to closed Pull Requests on the fractal-tasks-core repository.
 
+# 1.5.0 (a2 prerelease)
+* Dependencies:
+    * Bump `ngio` to `>=0.2.2,<0.3.0`.
+* Tasks:
+    * Refactor `projection` task to use the new `ngio` API.
+    * Refactor `copy_ome_zarr_plate` init task to support the upcoming flexibility.
+* Testing:
+    * Add new (redundand) `ngio` based testing
+
 # 1.5.0 (a1 prerelease)
 
 * Dependencies:

fractal_tasks_core/__FRACTAL_MANIFEST__.json

@@ -676,11 +676,17 @@
             "title": "Method",
             "description": "Choose which method to use for intensity projection along the Z axis. mip is the default and performs a maximum intensity projection. minip performs a minimum intensity projection, meanip a mean intensity projection and sumip a sum intensity projection."
           },
-          "overwrite": {
+          "overwrite_images": {
             "default": false,
-            "title": "Overwrite",
+            "title": "Overwrite Images",
             "type": "boolean",
-            "description": "If `True`, overwrite the task output."
+            "description": "If `True`, overwrite the MIP images if they are already present in the new OME-Zarr Plate."
+          },
+          "re_initialize_plate": {
+            "default": false,
+            "title": "Re Initialize Plate",
+            "type": "boolean",
+            "description": "If `True`, re-initialize the plate, deleting all existing wells and images. If `False`, the task will only incrementally add new wells and images to the plate."
           }
         },
         "required": [