Merge pull request #793 from fractal-analytics-platform/pydantic-v2-second-attempt

Fully move to Pydantic v2

Author: tcompa

.github/workflows/manifest_external_packages.yml

@@ -23,36 +23,46 @@ jobs:
 
         package: [skip]
         github_repo: [skip]
+        github_branch: [skip]
         manifest_path: [skip]
         cmd_install: [skip]
         cmd_create_manifest: [skip]
+        custom_dependencies: [skip]
 
         include:
 
           - package: scMultipleX
             github_repo: fmi-basel/gliberal-scMultipleX
+            github_branch: main
             manifest_path: src/scmultiplex/__FRACTAL_MANIFEST__.json
             cmd_install: 'python -m pip install -e .[fractal-tasks]'
             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: pydantic_v2
             manifest_path: src/apx_fractal_task_collection/__FRACTAL_MANIFEST__.json
             cmd_install: 'python -m pip install -e .'
             cmd_create_manifest: 'python src/apx_fractal_task_collection/dev/update_manifest.py'
+            custom_dependencies: ''
 
         exclude:
           - package: skip
             github_repo: skip
+            github_branch: skip
             manifest_path: skip
             cmd_install: skip
             cmd_create_manifest: skip
+            custom_dependencies: skip
 
     steps:
 
@@ -63,6 +73,7 @@ jobs:
         uses: actions/checkout@v4
         with:
           repository: ${{ matrix.github_repo }}
+          ref: ${{ matrix.github_branch }}
 
       - uses: actions/setup-python@v5
         with:
@@ -75,11 +86,29 @@ jobs:
       - name: Install package
         run:  ${{ matrix.cmd_install }}
 
+      - name: Get current branch of `fractal-tasks-core`
+        uses: actions/checkout@v4
+        with:
+          path: fractal-tasks-core
+
+      - name: Install current fractal-tasks-core (this may fail)
+        run: python -m pip install -e ./fractal-tasks-core
+
+      - name: Install custom additional dependencies (see issue 803)
+        if: ${{ matrix.custom_dependencies != '' }}
+        run: python -m pip install ${{ matrix.custom_dependencies }}
+
       - name: Create manifest
         run: ${{ matrix.cmd_create_manifest }}
 
+      - name: Setup friendly diff style
+        run: echo "*.json diff=json" >> .gitattributes && git config diff.json.textconv "jq --sort-keys '.' \$1"
+
       - name: Run git diff for manifest
         run: git diff ${{ matrix.manifest_path }}
 
+      - name: Clean up before checking repo status
+        run: rm -rf fractal-tasks-core .gitattributes
+
       - name: Check repo status
         run: if [[ -z $(git status -s) ]]; then echo "Clean status"; else echo "Dirty status"; git status; exit 1; fi

CHANGELOG.md

@@ -1,10 +1,20 @@
 **Note**: Numbers like (\#123) point to closed Pull Requests on the fractal-tasks-core repository.
 
+# 1.2.0 (unreleased)
+
+* Core-library and tasks:
+    * Switch all core models to Pydantic V2 (\#793).
+* JSON Schema generation tools:
+    * Move JSON-Schema tools to Pydantic V2 (\#793).
+* Testing:
+    * Remove dependency on `pytest-pretty` (\#793).
+    * Update `manifest_external_packages.yml` GitHub Action so that it installs the current `fractal-tasks-core` (\#793).
+
 # 1.1.1
 
 * Tasks:
-    * Fix issue with masked ROI & relabeling in Cellpose task (\#785).
-    * Fix issue with masking ROI label types in `masked_loading_wrapper` for Cellpose task (\#785).
+    * Fix issue with masked ROI & relabeling in Cellpose task (\#786).
+    * Fix issue with masking ROI label types in `masked_loading_wrapper` for Cellpose task (\#786).
     * Enable workaround to support yx images in Cellpose task (\#789).
     * Fix error handling in `calculate_registration_image_based` (\#799).
     * Fix minor issues with call-signature and type hints in `calculate_registration_image_based` (\#799).
@@ -22,8 +32,8 @@
     * Refactor Cellpose Task inputs: Support independent normalization of 2 input channels in the Cellpose task (\#738).
     * Rename `task.cellpose_transforms` into `tasks.cellpose_utils` (\#738).
     * Fix wrong repeated overlap checks for bounding-boxes in Cellpose task (\#778).
-    * Fix minor MIP issues related to plate metadata and expecting acquisition metadata in all NGFF plates(\#781).
-    * Add `chi2_shift` option to Calculate Registration (image-based) task(\#741).
+    * Fix minor MIP issues related to plate metadata and expecting acquisition metadata in all NGFF plates (\#781).
+    * Add `chi2_shift` option to Calculate Registration (image-based) task (\#741).
 * Development:
     * Switch to transitional pydantic.v1 imports, changes pydantic requirement to `==1.10.16` or `>=2.6.3` (\#760).
     * Support JSON-Schema generation for `Enum` task arguments (\#749).
@@ -35,6 +45,8 @@
     * Test manifest creation for three other tasks packages (\#763).
 * NGFF subpackage
     * Fix Plate model to correspond better to 0.4.0 NGFF spec: Now makes acquisition metadata optional (\#781).
+* Dependencies:
+    * Add `image_registration` within `fractal-tasks` extra (\#741).
 
 # 1.0.2